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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/mdrun/mdmodules.h"
63 #include "gromacs/mdtypes/awh_params.h"
64 #include "gromacs/mdtypes/inputrec.h"
65 #include "gromacs/mdtypes/md_enums.h"
66 #include "gromacs/mdtypes/multipletimestepping.h"
67 #include "gromacs/mdtypes/pull_params.h"
68 #include "gromacs/options/options.h"
69 #include "gromacs/options/treesupport.h"
70 #include "gromacs/pbcutil/pbc.h"
71 #include "gromacs/selection/indexutil.h"
72 #include "gromacs/topology/block.h"
73 #include "gromacs/topology/ifunc.h"
74 #include "gromacs/topology/index.h"
75 #include "gromacs/topology/mtop_util.h"
76 #include "gromacs/topology/symtab.h"
77 #include "gromacs/topology/topology.h"
78 #include "gromacs/utility/arrayref.h"
79 #include "gromacs/utility/cstringutil.h"
80 #include "gromacs/utility/exceptions.h"
81 #include "gromacs/utility/fatalerror.h"
82 #include "gromacs/utility/filestream.h"
83 #include "gromacs/utility/gmxassert.h"
84 #include "gromacs/utility/ikeyvaluetreeerror.h"
85 #include "gromacs/utility/keyvaluetree.h"
86 #include "gromacs/utility/keyvaluetreebuilder.h"
87 #include "gromacs/utility/keyvaluetreemdpwriter.h"
88 #include "gromacs/utility/keyvaluetreetransform.h"
89 #include "gromacs/utility/mdmodulesnotifiers.h"
90 #include "gromacs/utility/smalloc.h"
91 #include "gromacs/utility/strconvert.h"
92 #include "gromacs/utility/stringcompare.h"
93 #include "gromacs/utility/stringutil.h"
94 #include "gromacs/utility/textwriter.h"
99 /* Resource parameters
100 * Do not change any of these until you read the instruction
101 * in readinp.h. Some cpp's do not take spaces after the backslash
102 * (like the c-shell), which will give you a very weird compiler
106 struct gmx_inputrec_strings
108 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN], freeze[STRLEN], frdim[STRLEN],
109 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
110 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
111 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
112 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::string> fep_lambda;
113 char lambda_weights[STRLEN];
114 std::vector<std::string> pullGroupNames;
115 std::vector<std::string> rotateGroupNames;
116 char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
119 // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
120 static gmx_inputrec_strings* inputrecStrings = nullptr;
122 void init_inputrec_strings()
127 "Attempted to call init_inputrec_strings before calling done_inputrec_strings. "
128 "Only one inputrec (i.e. .mdp file) can be parsed at a time.");
130 inputrecStrings = new gmx_inputrec_strings();
133 void done_inputrec_strings()
135 delete inputrecStrings;
136 inputrecStrings = nullptr;
142 egrptpALL, /* All particles have to be a member of a group. */
143 egrptpALL_GENREST, /* A rest group with name is generated for particles *
144 * that are not part of any group. */
145 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
146 * for the rest group. */
147 egrptpONE /* Merge all selected groups into one group, *
148 * make a rest group for the remaining particles. */
151 // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
152 static const char* constraints[eshNR + 1] = { "none", "h-bonds", "all-bonds",
153 "h-angles", "all-angles", nullptr };
155 // NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
156 static const char* couple_lam[ecouplamNR + 1] = { "vdw-q", "vdw", "q", "none", nullptr };
158 static void getSimTemps(int ntemps, t_simtemp* simtemp, gmx::ArrayRef<double> temperature_lambdas)
163 for (i = 0; i < ntemps; i++)
165 /* simple linear scaling -- allows more control */
166 if (simtemp->eSimTempScale == SimulatedTempering::Linear)
168 simtemp->temperatures[i] =
170 + (simtemp->simtemp_high - simtemp->simtemp_low) * temperature_lambdas[i];
172 else if (simtemp->eSimTempScale
173 == SimulatedTempering::Geometric) /* should give roughly equal acceptance for constant heat capacity . . . */
175 simtemp->temperatures[i] = simtemp->simtemp_low
176 * std::pow(simtemp->simtemp_high / simtemp->simtemp_low,
177 static_cast<real>((1.0 * i) / (ntemps - 1)));
179 else if (simtemp->eSimTempScale == SimulatedTempering::Exponential)
181 simtemp->temperatures[i] = simtemp->simtemp_low
182 + (simtemp->simtemp_high - simtemp->simtemp_low)
183 * (std::expm1(temperature_lambdas[i]) / std::expm1(1.0));
188 sprintf(errorstr, "eSimTempScale=%s not defined", enumValueToString(simtemp->eSimTempScale));
189 gmx_fatal(FARGS, "%s", errorstr);
195 static void _low_check(bool b, const char* s, warninp_t wi)
199 warning_error(wi, s);
203 static void check_nst(const char* desc_nst, int nst, const char* desc_p, int* p, warninp_t wi)
207 if (*p > 0 && *p % nst != 0)
209 /* Round up to the next multiple of nst */
210 *p = ((*p) / nst + 1) * nst;
211 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n", desc_p, desc_nst, desc_p, *p);
216 //! Convert legacy mdp entries to modern ones.
217 static void process_interaction_modifier(InteractionModifiers* eintmod)
219 if (*eintmod == InteractionModifiers::PotShiftVerletUnsupported)
221 *eintmod = InteractionModifiers::PotShift;
225 void check_ir(const char* mdparin,
226 const gmx::MDModulesNotifiers& mdModulesNotifiers,
230 /* Check internal consistency.
231 * NOTE: index groups are not set here yet, don't check things
232 * like temperature coupling group options here, but in triple_check
235 /* Strange macro: first one fills the err_buf, and then one can check
236 * the condition, which will print the message and increase the error
239 #define CHECK(b) _low_check(b, err_buf, wi)
240 char err_buf[256], warn_buf[STRLEN];
243 t_lambda* fep = ir->fepvals.get();
244 t_expanded* expand = ir->expandedvals.get();
246 set_warning_line(wi, mdparin, -1);
248 /* We cannot check MTS requirements with an invalid MTS setup
249 * and we will already have generated errors with an invalid MTS setup.
251 if (gmx::haveValidMtsSetup(*ir))
253 std::vector<std::string> errorMessages = gmx::checkMtsRequirements(*ir);
255 for (const auto& errorMessage : errorMessages)
257 warning_error(wi, errorMessage.c_str());
261 if (ir->coulombtype == CoulombInteractionType::RFNecUnsupported)
263 std::string message =
264 gmx::formatString("%s electrostatics is no longer supported",
265 enumValueToString(CoulombInteractionType::RFNecUnsupported));
266 warning_error(wi, message);
269 /* BASIC CUT-OFF STUFF */
270 if (ir->rcoulomb < 0)
272 warning_error(wi, "rcoulomb should be >= 0");
276 warning_error(wi, "rvdw should be >= 0");
278 if (ir->rlist < 0 && !(ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0))
280 warning_error(wi, "rlist should be >= 0");
283 "nstlist can not be smaller than 0. (If you were trying to use the heuristic "
284 "neighbour-list update scheme for efficient buffering for improved energy "
285 "conservation, please use the Verlet cut-off scheme instead.)");
286 CHECK(ir->nstlist < 0);
288 process_interaction_modifier(&ir->coulomb_modifier);
289 process_interaction_modifier(&ir->vdw_modifier);
291 if (ir->cutoff_scheme == CutoffScheme::Group)
294 "The group cutoff scheme has been removed since GROMACS 2020. "
295 "Please use the Verlet cutoff scheme.");
297 if (ir->cutoff_scheme == CutoffScheme::Verlet)
301 /* Normal Verlet type neighbor-list, currently only limited feature support */
302 if (inputrec2nboundeddim(ir) < 3)
304 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
307 // We don't (yet) have general Verlet kernels for rcoulomb!=rvdw
308 if (ir->rcoulomb != ir->rvdw)
310 // Since we have PME coulomb + LJ cut-off kernels with rcoulomb>rvdw
311 // for PME load balancing, we can support this exception.
312 bool bUsesPmeTwinRangeKernel =
313 (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == VanDerWaalsType::Cut
314 && ir->rcoulomb > ir->rvdw);
315 if (!bUsesPmeTwinRangeKernel)
318 "With Verlet lists rcoulomb!=rvdw is not supported (except for "
319 "rcoulomb>rvdw with PME electrostatics)");
323 if (ir->vdwtype == VanDerWaalsType::Shift || ir->vdwtype == VanDerWaalsType::Switch)
325 if (ir->vdw_modifier == InteractionModifiers::None
326 || ir->vdw_modifier == InteractionModifiers::PotShift)
329 (ir->vdwtype == VanDerWaalsType::Shift ? InteractionModifiers::ForceSwitch
330 : InteractionModifiers::PotSwitch);
333 "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and "
335 enumValueToString(ir->vdwtype),
336 enumValueToString(VanDerWaalsType::Cut),
337 enumValueToString(ir->vdw_modifier));
338 warning_note(wi, warn_buf);
340 ir->vdwtype = VanDerWaalsType::Cut;
345 "Unsupported combination of vdwtype=%s and vdw_modifier=%s",
346 enumValueToString(ir->vdwtype),
347 enumValueToString(ir->vdw_modifier));
348 warning_error(wi, warn_buf);
352 if (!(ir->vdwtype == VanDerWaalsType::Cut || ir->vdwtype == VanDerWaalsType::Pme))
355 "With Verlet lists only cut-off and PME LJ interactions are supported");
357 if (!(ir->coulombtype == CoulombInteractionType::Cut || EEL_RF(ir->coulombtype)
358 || EEL_PME(ir->coulombtype) || ir->coulombtype == CoulombInteractionType::Ewald))
361 "With Verlet lists only cut-off, reaction-field, PME and Ewald "
362 "electrostatics are supported");
364 if (!(ir->coulomb_modifier == InteractionModifiers::None
365 || ir->coulomb_modifier == InteractionModifiers::PotShift))
367 sprintf(warn_buf, "coulomb_modifier=%s is not supported", enumValueToString(ir->coulomb_modifier));
368 warning_error(wi, warn_buf);
371 if (EEL_USER(ir->coulombtype))
374 "Coulomb type %s is not supported with the verlet scheme",
375 enumValueToString(ir->coulombtype));
376 warning_error(wi, warn_buf);
379 if (ir->nstlist <= 0)
381 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
384 if (ir->nstlist < 10)
387 "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note "
388 "that with the Verlet scheme, nstlist has no effect on the accuracy of "
392 rc_max = std::max(ir->rvdw, ir->rcoulomb);
396 /* With TPI we set the pairlist cut-off later using the radius of the insterted molecule */
397 ir->verletbuf_tol = 0;
400 else if (ir->verletbuf_tol <= 0)
402 if (ir->verletbuf_tol == 0)
404 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
407 if (ir->rlist < rc_max)
410 "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
413 if (ir->rlist == rc_max && ir->nstlist > 1)
417 "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet "
418 "buffer. The cluster pair list does have a buffering effect, but choosing "
419 "a larger rlist might be necessary for good energy conservation.");
424 if (ir->rlist > rc_max)
427 "You have set rlist larger than the interaction cut-off, but you also "
428 "have verlet-buffer-tolerance > 0. Will set rlist using "
429 "verlet-buffer-tolerance.");
432 if (ir->nstlist == 1)
434 /* No buffer required */
439 if (EI_DYNAMICS(ir->eI))
441 if (inputrec2nboundeddim(ir) < 3)
444 "The box volume is required for calculating rlist from the "
445 "energy drift with verlet-buffer-tolerance > 0. You are "
446 "using at least one unbounded dimension, so no volume can be "
447 "computed. Either use a finite box, or set rlist yourself "
448 "together with verlet-buffer-tolerance = -1.");
450 /* Set rlist temporarily so we can continue processing */
455 /* Set the buffer to 5% of the cut-off */
456 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics) * rc_max;
462 /* GENERAL INTEGRATOR STUFF */
465 if (ir->etc != TemperatureCoupling::No)
467 if (EI_RANDOM(ir->eI))
470 "Setting tcoupl from '%s' to 'no'. %s handles temperature coupling "
471 "implicitly. See the documentation for more information on which "
472 "parameters affect temperature for %s.",
473 enumValueToString(ir->etc),
474 enumValueToString(ir->eI),
475 enumValueToString(ir->eI));
480 "Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to "
482 enumValueToString(ir->etc),
483 enumValueToString(ir->eI));
485 warning_note(wi, warn_buf);
487 ir->etc = TemperatureCoupling::No;
489 if (ir->eI == IntegrationAlgorithm::VVAK)
492 "Integrator method %s is implemented primarily for validation purposes; for "
493 "molecular dynamics, you should probably be using %s or %s",
494 enumValueToString(IntegrationAlgorithm::VVAK),
495 enumValueToString(IntegrationAlgorithm::MD),
496 enumValueToString(IntegrationAlgorithm::VV));
497 warning_note(wi, warn_buf);
499 if (!EI_DYNAMICS(ir->eI))
501 if (ir->epc != PressureCoupling::No)
504 "Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.",
505 enumValueToString(ir->epc),
506 enumValueToString(ir->eI));
507 warning_note(wi, warn_buf);
509 ir->epc = PressureCoupling::No;
511 if (EI_DYNAMICS(ir->eI))
513 if (ir->nstcalcenergy < 0)
515 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
516 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
518 /* nstcalcenergy larger than nstener does not make sense.
519 * We ideally want nstcalcenergy=nstener.
523 ir->nstcalcenergy = std::gcd(ir->nstenergy, ir->nstlist);
527 ir->nstcalcenergy = ir->nstenergy;
531 else if ((ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy)
532 || (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl > 0
533 && (ir->nstcalcenergy > ir->fepvals->nstdhdl)))
536 const char* nsten = "nstenergy";
537 const char* nstdh = "nstdhdl";
538 const char* min_name = nsten;
539 int min_nst = ir->nstenergy;
541 /* find the smallest of ( nstenergy, nstdhdl ) */
542 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl > 0
543 && (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
545 min_nst = ir->fepvals->nstdhdl;
548 /* If the user sets nstenergy small, we should respect that */
549 sprintf(warn_buf, "Setting nstcalcenergy (%d) equal to %s (%d)", ir->nstcalcenergy, min_name, min_nst);
550 warning_note(wi, warn_buf);
551 ir->nstcalcenergy = min_nst;
554 if (ir->epc != PressureCoupling::No)
556 if (ir->nstpcouple < 0)
558 ir->nstpcouple = ir_optimal_nstpcouple(ir);
560 if (ir->useMts && ir->nstpcouple % ir->mtsLevels.back().stepFactor != 0)
563 "With multiple time stepping, nstpcouple should be a mutiple of "
568 if (ir->nstcalcenergy > 0)
570 if (ir->efep != FreeEnergyPerturbationType::No)
572 /* nstdhdl should be a multiple of nstcalcenergy */
573 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstdhdl", &ir->fepvals->nstdhdl, wi);
577 /* nstexpanded should be a multiple of nstcalcenergy */
578 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstexpanded", &ir->expandedvals->nstexpanded, wi);
580 /* for storing exact averages nstenergy should be
581 * a multiple of nstcalcenergy
583 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstenergy", &ir->nstenergy, wi);
586 // Inquire all MDModules, if their parameters match with the energy
587 // calculation frequency
588 gmx::EnergyCalculationFrequencyErrors energyCalculationFrequencyErrors(ir->nstcalcenergy);
589 mdModulesNotifiers.preProcessingNotifier_.notify(&energyCalculationFrequencyErrors);
591 // Emit all errors from the energy calculation frequency checks
592 for (const std::string& energyFrequencyErrorMessage :
593 energyCalculationFrequencyErrors.errorMessages())
595 warning_error(wi, energyFrequencyErrorMessage);
599 if (ir->nsteps == 0 && !ir->bContinuation)
602 "For a correct single-point energy evaluation with nsteps = 0, use "
603 "continuation = yes to avoid constraining the input coordinates.");
607 if ((EI_SD(ir->eI) || ir->eI == IntegrationAlgorithm::BD) && ir->bContinuation && ir->ld_seed != -1)
610 "You are doing a continuation with SD or BD, make sure that ld_seed is "
611 "different from the previous run (using ld_seed=-1 will ensure this)");
617 sprintf(err_buf, "TPI only works with pbc = %s", c_pbcTypeNames[PbcType::Xyz].c_str());
618 CHECK(ir->pbcType != PbcType::Xyz);
619 sprintf(err_buf, "with TPI nstlist should be larger than zero");
620 CHECK(ir->nstlist <= 0);
621 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
622 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
626 if ((opts->nshake > 0) && (opts->bMorse))
628 sprintf(warn_buf, "Using morse bond-potentials while constraining bonds is useless");
629 warning(wi, warn_buf);
632 if ((EI_SD(ir->eI) || ir->eI == IntegrationAlgorithm::BD) && ir->bContinuation && ir->ld_seed != -1)
635 "You are doing a continuation with SD or BD, make sure that ld_seed is "
636 "different from the previous run (using ld_seed=-1 will ensure this)");
638 /* verify simulated tempering options */
642 bool bAllTempZero = TRUE;
643 for (i = 0; i < fep->n_lambda; i++)
646 "Entry %d for %s must be between 0 and 1, instead is %g",
648 enumValueToString(FreeEnergyPerturbationCouplingType::Temperature),
649 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i]);
650 CHECK((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i] < 0)
651 || (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i]
653 if (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i] > 0)
655 bAllTempZero = FALSE;
658 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
659 CHECK(bAllTempZero == TRUE);
661 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
662 CHECK(ir->eI != IntegrationAlgorithm::VV);
664 /* check compatability of the temperature coupling with simulated tempering */
666 if (ir->etc == TemperatureCoupling::NoseHoover)
669 "Nose-Hoover based temperature control such as [%s] my not be "
670 "entirelyconsistent with simulated tempering",
671 enumValueToString(ir->etc));
672 warning_note(wi, warn_buf);
675 /* check that the temperatures make sense */
678 "Higher simulated tempering temperature (%g) must be >= than the simulated "
679 "tempering lower temperature (%g)",
680 ir->simtempvals->simtemp_high,
681 ir->simtempvals->simtemp_low);
682 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
685 "Higher simulated tempering temperature (%g) must be >= zero",
686 ir->simtempvals->simtemp_high);
687 CHECK(ir->simtempvals->simtemp_high <= 0);
690 "Lower simulated tempering temperature (%g) must be >= zero",
691 ir->simtempvals->simtemp_low);
692 CHECK(ir->simtempvals->simtemp_low <= 0);
695 /* verify free energy options */
697 if (ir->efep != FreeEnergyPerturbationType::No)
699 fep = ir->fepvals.get();
700 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2", fep->sc_power);
701 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
704 "The soft-core sc-r-power is %d and can only be 6. (sc-r-power 48 is no longer "
706 static_cast<int>(fep->sc_r_power));
707 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0);
710 "Can't use positive delta-lambda (%g) if initial state/lambda does not start at "
713 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
716 "Can't use positive delta-lambda (%g) with expanded ensemble simulations",
718 CHECK(fep->delta_lambda > 0 && (ir->efep == FreeEnergyPerturbationType::Expanded));
720 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
721 CHECK(!(EI_VV(ir->eI)) && (ir->efep == FreeEnergyPerturbationType::Expanded));
723 sprintf(err_buf, "Free-energy not implemented for Ewald");
724 CHECK(ir->coulombtype == CoulombInteractionType::Ewald);
726 /* check validty of lambda inputs */
727 if (fep->n_lambda == 0)
729 /* Clear output in case of no states:*/
730 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
731 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
736 "initial thermodynamic state %d does not exist, only goes to %d",
739 CHECK((fep->init_fep_state >= fep->n_lambda));
743 "Lambda state must be set, either with init-lambda-state or with init-lambda");
744 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
747 "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with "
748 "init-lambda-state or with init-lambda, but not both",
750 fep->init_fep_state);
751 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
754 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
758 for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
760 if (fep->separate_dvdl[i])
765 if (n_lambda_terms > 1)
768 "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't "
769 "use init-lambda to set lambda state (except for slow growth). Use "
770 "init-lambda-state instead.");
771 warning(wi, warn_buf);
774 if (n_lambda_terms < 2 && fep->n_lambda > 0)
777 "init-lambda is deprecated for setting lambda state (except for slow "
778 "growth). Use init-lambda-state instead.");
782 for (j = 0; j < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); j++)
784 for (i = 0; i < fep->n_lambda; i++)
786 auto enumValue = static_cast<FreeEnergyPerturbationCouplingType>(j);
788 "Entry %d for %s must be between 0 and 1, instead is %g",
790 enumValueToString(enumValue),
791 fep->all_lambda[j][i]);
792 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
796 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
798 for (i = 0; i < fep->n_lambda; i++)
801 "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while "
802 "coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to "
803 "crashes, and is not supported.",
805 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i],
806 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i]);
807 CHECK((fep->sc_alpha > 0)
808 && (((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i] > 0.0)
809 && (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i] < 1.0))
810 && ((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i] > 0.0)
811 && (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i]
816 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
818 real sigma, lambda, r_sc;
821 /* Maximum estimate for A and B charges equal with lambda power 1 */
823 r_sc = std::pow(lambda * fep->sc_alpha * std::pow(sigma / ir->rcoulomb, fep->sc_r_power) + 1.0,
824 1.0 / fep->sc_r_power);
826 "With PME there is a minor soft core effect present at the cut-off, "
827 "proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on "
828 "energy conservation, but usually other effects dominate. With a common sigma "
829 "value of %g nm the fraction of the particle-particle potential at the cut-off "
830 "at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
836 warning_note(wi, warn_buf);
839 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
840 be treated differently, but that's the next step */
842 for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
844 auto enumValue = static_cast<FreeEnergyPerturbationCouplingType>(i);
845 for (j = 0; j < fep->n_lambda; j++)
847 sprintf(err_buf, "%s[%d] must be between 0 and 1", enumValueToString(enumValue), j);
848 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
853 if ((ir->bSimTemp) || (ir->efep == FreeEnergyPerturbationType::Expanded))
855 fep = ir->fepvals.get();
857 /* checking equilibration of weights inputs for validity */
860 "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal "
862 expand->equil_n_at_lam,
863 enumValueToString(LambdaWeightWillReachEquilibrium::NumAtLambda));
864 CHECK((expand->equil_n_at_lam > 0)
865 && (expand->elmceq != LambdaWeightWillReachEquilibrium::NumAtLambda));
868 "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to "
870 expand->equil_samples,
871 enumValueToString(LambdaWeightWillReachEquilibrium::Samples));
872 CHECK((expand->equil_samples > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Samples));
875 "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
877 enumValueToString(LambdaWeightWillReachEquilibrium::Steps));
878 CHECK((expand->equil_steps > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Steps));
881 "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
882 expand->equil_samples,
883 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta));
884 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::WLDelta));
887 "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
889 enumValueToString(LambdaWeightWillReachEquilibrium::Ratio));
890 CHECK((expand->equil_ratio > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Ratio));
893 "weight-equil-number-all-lambda (%d) must be a positive integer if "
894 "lmc-weights-equil=%s",
895 expand->equil_n_at_lam,
896 enumValueToString(LambdaWeightWillReachEquilibrium::NumAtLambda));
897 CHECK((expand->equil_n_at_lam <= 0)
898 && (expand->elmceq == LambdaWeightWillReachEquilibrium::NumAtLambda));
901 "weight-equil-number-samples (%d) must be a positive integer if "
902 "lmc-weights-equil=%s",
903 expand->equil_samples,
904 enumValueToString(LambdaWeightWillReachEquilibrium::Samples));
905 CHECK((expand->equil_samples <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Samples));
908 "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
910 enumValueToString(LambdaWeightWillReachEquilibrium::Steps));
911 CHECK((expand->equil_steps <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Steps));
914 "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
915 expand->equil_wl_delta,
916 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta));
917 CHECK((expand->equil_wl_delta <= 0)
918 && (expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta));
921 "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
923 enumValueToString(LambdaWeightWillReachEquilibrium::Ratio));
924 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Ratio));
927 "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
928 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta),
929 enumValueToString(LambdaWeightCalculation::WL),
930 enumValueToString(LambdaWeightCalculation::WWL));
931 CHECK((expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta) && (!EWL(expand->elamstats)));
933 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
934 CHECK((expand->lmc_repeats <= 0));
935 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
936 CHECK((expand->minvarmin <= 0));
937 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
938 CHECK((expand->c_range < 0));
940 "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != "
943 expand->lmc_forced_nstart);
944 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0)
945 && (expand->elmcmove != LambdaMoveCalculation::No));
946 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
947 CHECK((expand->lmc_forced_nstart < 0));
949 "init-lambda-state (%d) must be in the interval [0,number of lambdas)",
950 fep->init_fep_state);
951 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
953 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
954 CHECK((expand->init_wl_delta < 0));
955 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
956 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
957 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
958 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
960 /* if there is no temperature control, we need to specify an MC temperature */
961 if (!integratorHasReferenceTemperature(ir)
962 && (expand->elmcmove != LambdaMoveCalculation::No) && (expand->mc_temp <= 0.0))
965 "If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set "
966 "to a positive number");
967 warning_error(wi, err_buf);
969 if (expand->nstTij > 0)
971 sprintf(err_buf, "nstlog must be non-zero");
972 CHECK(ir->nstlog == 0);
973 // Avoid modulus by zero in the case that already triggered an error exit.
977 "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
980 CHECK((expand->nstTij % ir->nstlog) != 0);
986 sprintf(err_buf, "walls only work with pbc=%s", c_pbcTypeNames[PbcType::XY].c_str());
987 CHECK(ir->nwall && ir->pbcType != PbcType::XY);
990 if (ir->pbcType != PbcType::Xyz && ir->nwall != 2)
992 if (ir->pbcType == PbcType::No)
994 if (ir->epc != PressureCoupling::No)
996 warning(wi, "Turning off pressure coupling for vacuum system");
997 ir->epc = PressureCoupling::No;
1003 "Can not have pressure coupling with pbc=%s",
1004 c_pbcTypeNames[ir->pbcType].c_str());
1005 CHECK(ir->epc != PressureCoupling::No);
1007 sprintf(err_buf, "Can not have Ewald with pbc=%s", c_pbcTypeNames[ir->pbcType].c_str());
1008 CHECK(EEL_FULL(ir->coulombtype));
1011 "Can not have dispersion correction with pbc=%s",
1012 c_pbcTypeNames[ir->pbcType].c_str());
1013 CHECK(ir->eDispCorr != DispersionCorrectionType::No);
1016 if (ir->rlist == 0.0)
1019 "can only have neighborlist cut-off zero (=infinite)\n"
1020 "with coulombtype = %s or coulombtype = %s\n"
1021 "without periodic boundary conditions (pbc = %s) and\n"
1022 "rcoulomb and rvdw set to zero",
1023 enumValueToString(CoulombInteractionType::Cut),
1024 enumValueToString(CoulombInteractionType::User),
1025 c_pbcTypeNames[PbcType::No].c_str());
1026 CHECK(((ir->coulombtype != CoulombInteractionType::Cut)
1027 && (ir->coulombtype != CoulombInteractionType::User))
1028 || (ir->pbcType != PbcType::No) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
1030 if (ir->nstlist > 0)
1033 "Simulating without cut-offs can be (slightly) faster with nstlist=0, "
1034 "nstype=simple and only one MPI rank");
1039 if (ir->nstcomm == 0)
1041 // TODO Change this behaviour. There should be exactly one way
1042 // to turn off an algorithm.
1043 ir->comm_mode = ComRemovalAlgorithm::No;
1045 if (ir->comm_mode != ComRemovalAlgorithm::No)
1047 if (ir->nstcomm < 0)
1049 // TODO Such input was once valid. Now that we've been
1050 // helpful for a few years, we should reject such input,
1051 // lest we have to support every historical decision
1054 "If you want to remove the rotation around the center of mass, you should set "
1055 "comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to "
1056 "its absolute value");
1057 ir->nstcomm = abs(ir->nstcomm);
1060 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
1063 "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting "
1064 "nstcomm to nstcalcenergy");
1065 ir->nstcomm = ir->nstcalcenergy;
1068 if (ir->comm_mode == ComRemovalAlgorithm::Angular)
1071 "Can not remove the rotation around the center of mass with periodic "
1073 CHECK(ir->bPeriodicMols);
1074 if (ir->pbcType != PbcType::No)
1077 "Removing the rotation around the center of mass in a periodic system, "
1078 "this can lead to artifacts. Only use this on a single (cluster of) "
1079 "molecules. This cluster should not cross periodic boundaries.");
1084 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->pbcType == PbcType::No
1085 && ir->comm_mode != ComRemovalAlgorithm::Angular)
1088 "Tumbling and flying ice-cubes: We are not removing rotation around center of mass "
1089 "in a non-periodic system. You should probably set comm_mode = ANGULAR or use "
1091 enumValueToString(IntegrationAlgorithm::SD1));
1092 warning_note(wi, warn_buf);
1095 /* TEMPERATURE COUPLING */
1096 if (ir->etc == TemperatureCoupling::Yes)
1098 ir->etc = TemperatureCoupling::Berendsen;
1100 "Old option for temperature coupling given: "
1101 "changing \"yes\" to \"Berendsen\"\n");
1104 if ((ir->etc == TemperatureCoupling::NoseHoover) || (ir->epc == PressureCoupling::Mttk))
1106 if (ir->opts.nhchainlength < 1)
1109 "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to "
1111 ir->opts.nhchainlength);
1112 ir->opts.nhchainlength = 1;
1113 warning(wi, warn_buf);
1116 if (ir->etc == TemperatureCoupling::NoseHoover && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
1120 "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
1121 ir->opts.nhchainlength = 1;
1126 ir->opts.nhchainlength = 0;
1129 if (ir->eI == IntegrationAlgorithm::VVAK)
1132 "%s implemented primarily for validation, and requires nsttcouple = 1 and "
1134 enumValueToString(IntegrationAlgorithm::VVAK));
1135 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
1138 if (ETC_ANDERSEN(ir->etc))
1141 "%s temperature control not supported for integrator %s.",
1142 enumValueToString(ir->etc),
1143 enumValueToString(ir->eI));
1144 CHECK(!(EI_VV(ir->eI)));
1146 if (ir->nstcomm > 0 && (ir->etc == TemperatureCoupling::Andersen))
1149 "Center of mass removal not necessary for %s. All velocities of coupled "
1150 "groups are rerandomized periodically, so flying ice cube errors will not "
1152 enumValueToString(ir->etc));
1153 warning_note(wi, warn_buf);
1157 "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are "
1158 "randomized every time step",
1160 enumValueToString(ir->etc));
1161 CHECK(ir->nstcomm > 1 && (ir->etc == TemperatureCoupling::Andersen));
1164 if (ir->etc == TemperatureCoupling::Berendsen)
1167 "The %s thermostat does not generate the correct kinetic energy distribution. You "
1168 "might want to consider using the %s thermostat.",
1169 enumValueToString(ir->etc),
1170 enumValueToString(TemperatureCoupling::VRescale));
1171 warning_note(wi, warn_buf);
1174 if ((ir->etc == TemperatureCoupling::NoseHoover || ETC_ANDERSEN(ir->etc))
1175 && ir->epc == PressureCoupling::Berendsen)
1178 "Using Berendsen pressure coupling invalidates the "
1179 "true ensemble for the thermostat");
1180 warning(wi, warn_buf);
1183 /* PRESSURE COUPLING */
1184 if (ir->epc == PressureCoupling::Isotropic)
1186 ir->epc = PressureCoupling::Berendsen;
1188 "Old option for pressure coupling given: "
1189 "changing \"Isotropic\" to \"Berendsen\"\n");
1192 if (ir->epc != PressureCoupling::No)
1194 dt_pcoupl = ir->nstpcouple * ir->delta_t;
1196 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1197 CHECK(ir->tau_p <= 0);
1199 if (ir->tau_p / dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10 * GMX_REAL_EPS)
1202 "For proper integration of the %s barostat, tau-p (%g) should be at least %d "
1203 "times larger than nstpcouple*dt (%g)",
1204 enumValueToString(ir->epc),
1206 pcouple_min_integration_steps(ir->epc),
1208 warning(wi, warn_buf);
1212 "compressibility must be > 0 when using pressure"
1214 enumValueToString(ir->epc));
1215 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 || ir->compress[ZZ][ZZ] < 0
1216 || (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 && ir->compress[ZZ][XX] <= 0
1217 && ir->compress[ZZ][YY] <= 0));
1219 if (PressureCoupling::ParrinelloRahman == ir->epc && opts->bGenVel)
1222 "You are generating velocities so I am assuming you "
1223 "are equilibrating a system. You are using "
1224 "%s pressure coupling, but this can be "
1225 "unstable for equilibration. If your system crashes, try "
1226 "equilibrating first with Berendsen pressure coupling. If "
1227 "you are not equilibrating the system, you can probably "
1228 "ignore this warning.",
1229 enumValueToString(ir->epc));
1230 warning(wi, warn_buf);
1236 if (ir->epc == PressureCoupling::Mttk)
1238 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1242 /* ELECTROSTATICS */
1243 /* More checks are in triple check (grompp.c) */
1245 if (ir->coulombtype == CoulombInteractionType::Switch)
1248 "coulombtype = %s is only for testing purposes and can lead to serious "
1249 "artifacts, advice: use coulombtype = %s",
1250 enumValueToString(ir->coulombtype),
1251 enumValueToString(CoulombInteractionType::RFZero));
1252 warning(wi, warn_buf);
1255 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1258 "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old "
1259 "format and exchanging epsilon-r and epsilon-rf",
1261 warning(wi, warn_buf);
1262 ir->epsilon_rf = ir->epsilon_r;
1263 ir->epsilon_r = 1.0;
1266 if (ir->epsilon_r == 0)
1269 "It is pointless to use long-range electrostatics with infinite relative "
1271 "Since you are effectively turning of electrostatics, a plain cutoff will be much "
1273 CHECK(EEL_FULL(ir->coulombtype));
1276 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1278 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1279 CHECK(ir->epsilon_r < 0);
1282 if (EEL_RF(ir->coulombtype))
1284 /* reaction field (at the cut-off) */
1286 if (ir->coulombtype == CoulombInteractionType::RFZero && ir->epsilon_rf != 0)
1289 "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1290 enumValueToString(ir->coulombtype));
1291 warning(wi, warn_buf);
1292 ir->epsilon_rf = 0.0;
1295 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1296 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) || (ir->epsilon_r == 0));
1297 if (ir->epsilon_rf == ir->epsilon_r)
1300 "Using epsilon-rf = epsilon-r with %s does not make sense",
1301 enumValueToString(ir->coulombtype));
1302 warning(wi, warn_buf);
1305 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1306 * means the interaction is zero outside rcoulomb, but it helps to
1307 * provide accurate energy conservation.
1309 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1311 if (ir_coulomb_switched(ir))
1314 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the "
1315 "potential modifier options!",
1316 enumValueToString(ir->coulombtype));
1317 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1321 if (ir->coulombtype == CoulombInteractionType::Switch || ir->coulombtype == CoulombInteractionType::Shift)
1324 "Explicit switch/shift coulomb interactions cannot be used in combination with a "
1325 "secondary coulomb-modifier.");
1326 CHECK(ir->coulomb_modifier != InteractionModifiers::None);
1328 if (ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift)
1331 "Explicit switch/shift vdw interactions cannot be used in combination with a "
1332 "secondary vdw-modifier.");
1333 CHECK(ir->vdw_modifier != InteractionModifiers::None);
1336 if (ir->coulombtype == CoulombInteractionType::Switch || ir->coulombtype == CoulombInteractionType::Shift
1337 || ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift)
1340 "The switch/shift interaction settings are just for compatibility; you will get "
1342 "performance from applying potential modifiers to your interactions!\n");
1343 warning_note(wi, warn_buf);
1346 if (ir->coulombtype == CoulombInteractionType::PmeSwitch
1347 || ir->coulomb_modifier == InteractionModifiers::PotSwitch)
1349 if (ir->rcoulomb_switch / ir->rcoulomb < 0.9499)
1351 real percentage = 100 * (ir->rcoulomb - ir->rcoulomb_switch) / ir->rcoulomb;
1353 "The switching range should be 5%% or less (currently %.2f%% using a switching "
1354 "range of %4f-%4f) for accurate electrostatic energies, energy conservation "
1355 "will be good regardless, since ewald_rtol = %g.",
1357 ir->rcoulomb_switch,
1360 warning(wi, warn_buf);
1364 if (ir->vdwtype == VanDerWaalsType::Switch || ir->vdw_modifier == InteractionModifiers::PotSwitch)
1366 if (ir->rvdw_switch == 0)
1369 "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones "
1370 "potential. This suggests it was not set in the mdp, which can lead to large "
1371 "energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw "
1372 "switching range.");
1373 warning(wi, warn_buf);
1377 if (EEL_FULL(ir->coulombtype))
1379 if (ir->coulombtype == CoulombInteractionType::PmeSwitch
1380 || ir->coulombtype == CoulombInteractionType::PmeUser
1381 || ir->coulombtype == CoulombInteractionType::PmeUserSwitch)
1384 "With coulombtype = %s, rcoulomb must be <= rlist",
1385 enumValueToString(ir->coulombtype));
1386 CHECK(ir->rcoulomb > ir->rlist);
1390 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1392 // TODO: Move these checks into the ewald module with the options class
1394 int orderMax = (ir->coulombtype == CoulombInteractionType::P3mAD ? 8 : 12);
1396 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1399 "With coulombtype = %s, you should have %d <= pme-order <= %d",
1400 enumValueToString(ir->coulombtype),
1403 warning_error(wi, warn_buf);
1407 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1409 if (ir->ewald_geometry == EwaldGeometry::ThreeD)
1412 "With pbc=%s you should use ewald-geometry=%s",
1413 c_pbcTypeNames[ir->pbcType].c_str(),
1414 enumValueToString(EwaldGeometry::ThreeDC));
1415 warning(wi, warn_buf);
1417 /* This check avoids extra pbc coding for exclusion corrections */
1418 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1419 CHECK(ir->wall_ewald_zfac < 2);
1421 if ((ir->ewald_geometry == EwaldGeometry::ThreeDC) && (ir->pbcType != PbcType::XY)
1422 && EEL_FULL(ir->coulombtype))
1425 "With %s and ewald_geometry = %s you should use pbc = %s",
1426 enumValueToString(ir->coulombtype),
1427 enumValueToString(EwaldGeometry::ThreeDC),
1428 c_pbcTypeNames[PbcType::XY].c_str());
1429 warning(wi, warn_buf);
1431 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1433 sprintf(err_buf, "Cannot have periodic molecules with epsilon_surface > 0");
1434 CHECK(ir->bPeriodicMols);
1435 sprintf(warn_buf, "With epsilon_surface > 0 all molecules should be neutral.");
1436 warning_note(wi, warn_buf);
1438 "With epsilon_surface > 0 you can only use domain decomposition "
1439 "when there are only small molecules with all bonds constrained (mdrun will check "
1441 warning_note(wi, warn_buf);
1444 if (ir_vdw_switched(ir))
1446 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1447 CHECK(ir->rvdw_switch >= ir->rvdw);
1449 if (ir->rvdw_switch < 0.5 * ir->rvdw)
1452 "You are applying a switch function to vdw forces or potentials from %g to %g "
1453 "nm, which is more than half the interaction range, whereas switch functions "
1454 "are intended to act only close to the cut-off.",
1457 warning_note(wi, warn_buf);
1461 if (ir->vdwtype == VanDerWaalsType::Pme)
1463 if (!(ir->vdw_modifier == InteractionModifiers::None
1464 || ir->vdw_modifier == InteractionModifiers::PotShift))
1467 "With vdwtype = %s, the only supported modifiers are %s and %s",
1468 enumValueToString(ir->vdwtype),
1469 enumValueToString(InteractionModifiers::PotShift),
1470 enumValueToString(InteractionModifiers::None));
1471 warning_error(wi, err_buf);
1475 if (ir->vdwtype == VanDerWaalsType::User && ir->eDispCorr != DispersionCorrectionType::No)
1478 "You have selected user tables with dispersion correction, the dispersion "
1479 "will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction "
1480 "between rvdw_switch and rvdw will not be double counted). Make sure that you "
1481 "really want dispersion correction to -C6/r^6.");
1484 if (ir->eI == IntegrationAlgorithm::LBFGS
1485 && (ir->coulombtype == CoulombInteractionType::Cut || ir->vdwtype == VanDerWaalsType::Cut)
1488 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1491 if (ir->eI == IntegrationAlgorithm::LBFGS && ir->nbfgscorr <= 0)
1493 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1496 /* IMPLICIT SOLVENT */
1497 if (ir->coulombtype == CoulombInteractionType::GBNotused)
1499 sprintf(warn_buf, "Invalid option %s for coulombtype", enumValueToString(ir->coulombtype));
1500 warning_error(wi, warn_buf);
1505 warning_error(wi, "The QMMM integration you are trying to use is no longer supported");
1510 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1513 // cosine acceleration is only supported in leap-frog
1514 if (ir->cos_accel != 0.0 && ir->eI != IntegrationAlgorithm::MD)
1516 warning_error(wi, "cos-acceleration is only supported by integrator = md");
1520 /* interpret a number of doubles from a string and put them in an array,
1521 after allocating space for them.
1522 str = the input string
1523 n = the (pre-allocated) number of doubles read
1524 r = the output array of doubles. */
1525 static std::vector<real> parse_n_real(const std::string& str, int* n, warninp_t wi)
1527 auto values = gmx::splitString(str);
1530 std::vector<real> r;
1531 for (int i = 0; i < *n; i++)
1535 r.emplace_back(gmx::fromString<real>(values[i]));
1537 catch (gmx::GromacsException&)
1540 "Invalid value " + values[i]
1541 + " in string in mdp file. Expected a real number.");
1548 static void do_fep_params(t_inputrec* ir, gmx::ArrayRef<std::string> fep_lambda, char weights[STRLEN], warninp_t wi)
1551 int i, j, max_n_lambda, nweights;
1552 t_lambda* fep = ir->fepvals.get();
1553 t_expanded* expand = ir->expandedvals.get();
1554 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::vector<real>> count_fep_lambdas;
1555 bool bOneLambda = TRUE;
1556 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, int> nfep;
1558 /* FEP input processing */
1559 /* first, identify the number of lambda values for each type.
1560 All that are nonzero must have the same number */
1562 for (auto i : keysOf(nfep))
1564 count_fep_lambdas[i] = parse_n_real(fep_lambda[static_cast<int>(i)], &(nfep[i]), wi);
1567 /* now, determine the number of components. All must be either zero, or equal. */
1570 for (auto i : keysOf(nfep))
1572 if (nfep[i] > max_n_lambda)
1574 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1575 must have the same number if its not zero.*/
1580 for (auto i : keysOf(nfep))
1584 ir->fepvals->separate_dvdl[i] = FALSE;
1586 else if (nfep[i] == max_n_lambda)
1588 if (i != FreeEnergyPerturbationCouplingType::Temperature) /* we treat this differently -- not really a reason to compute
1589 the derivative with respect to the temperature currently */
1591 ir->fepvals->separate_dvdl[i] = TRUE;
1597 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1600 enumValueToString(i),
1604 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1605 ir->fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Temperature] = FALSE;
1607 /* the number of lambdas is the number we've read in, which is either zero
1608 or the same for all */
1609 fep->n_lambda = max_n_lambda;
1611 /* if init_lambda is defined, we need to set lambda */
1612 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1614 ir->fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
1616 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1617 for (auto i : keysOf(nfep))
1619 fep->all_lambda[i].resize(fep->n_lambda);
1620 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1623 for (j = 0; j < fep->n_lambda; j++)
1625 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1630 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1631 internal bookkeeping -- for now, init_lambda */
1633 if ((nfep[FreeEnergyPerturbationCouplingType::Fep] == 0) && (fep->init_lambda >= 0))
1635 for (i = 0; i < fep->n_lambda; i++)
1637 fep->all_lambda[FreeEnergyPerturbationCouplingType::Fep][i] = fep->init_lambda;
1641 /* check to see if only a single component lambda is defined, and soft core is defined.
1642 In this case, turn on coulomb soft core */
1644 if (max_n_lambda == 0)
1650 for (auto i : keysOf(nfep))
1652 if ((nfep[i] != 0) && (i != FreeEnergyPerturbationCouplingType::Fep))
1658 if ((bOneLambda) && (fep->sc_alpha > 0))
1660 fep->bScCoul = TRUE;
1663 /* Fill in the others with the efptFEP if they are not explicitly
1664 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1665 they are all zero. */
1667 for (auto i : keysOf(nfep))
1669 if ((nfep[i] == 0) && (i != FreeEnergyPerturbationCouplingType::Fep))
1671 for (j = 0; j < fep->n_lambda; j++)
1673 fep->all_lambda[i][j] = fep->all_lambda[FreeEnergyPerturbationCouplingType::Fep][j];
1679 /* now read in the weights */
1680 expand->init_lambda_weights = parse_n_real(weights, &nweights, wi);
1683 expand->init_lambda_weights.resize(fep->n_lambda); /* initialize to zero */
1685 else if (nweights != fep->n_lambda)
1688 "Number of weights (%d) is not equal to number of lambda values (%d)",
1692 if ((expand->nstexpanded < 0) && (ir->efep != FreeEnergyPerturbationType::No))
1694 expand->nstexpanded = fep->nstdhdl;
1695 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1700 static void do_simtemp_params(t_inputrec* ir)
1702 ir->simtempvals->temperatures.resize(ir->fepvals->n_lambda);
1703 getSimTemps(ir->fepvals->n_lambda,
1704 ir->simtempvals.get(),
1705 ir->fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Temperature]);
1708 template<typename T>
1709 void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
1712 for (const auto& input : inputs)
1716 outputs[i] = gmx::fromStdString<T>(input);
1718 catch (gmx::GromacsException&)
1720 auto message = gmx::formatString(
1721 "Invalid value for mdp option %s. %s should only consist of integers separated "
1725 warning_error(wi, message);
1731 static void convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, real* outputs)
1734 for (const auto& input : inputs)
1738 outputs[i] = gmx::fromString<real>(input);
1740 catch (gmx::GromacsException&)
1742 auto message = gmx::formatString(
1743 "Invalid value for mdp option %s. %s should only consist of real numbers "
1744 "separated by spaces.",
1747 warning_error(wi, message);
1753 static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
1755 opts->wall_atomtype[0] = nullptr;
1756 opts->wall_atomtype[1] = nullptr;
1758 ir->wall_atomtype[0] = -1;
1759 ir->wall_atomtype[1] = -1;
1760 ir->wall_density[0] = 0;
1761 ir->wall_density[1] = 0;
1765 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1766 if (wallAtomTypes.size() != size_t(ir->nwall))
1769 "Expected %d elements for wall_atomtype, found %zu",
1771 wallAtomTypes.size());
1773 GMX_RELEASE_ASSERT(ir->nwall < 3, "Invalid number of walls");
1774 for (int i = 0; i < ir->nwall; i++)
1776 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1779 if (ir->wall_type == WallType::NineThree || ir->wall_type == WallType::TenFour)
1781 auto wallDensity = gmx::splitString(wall_density);
1782 if (wallDensity.size() != size_t(ir->nwall))
1785 "Expected %d elements for wall-density, found %zu",
1787 wallDensity.size());
1789 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1790 for (int i = 0; i < ir->nwall; i++)
1792 if (ir->wall_density[i] <= 0)
1794 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1801 static void add_wall_energrps(SimulationGroups* groups, int nwall, t_symtab* symtab)
1805 AtomGroupIndices* grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1806 for (int i = 0; i < nwall; i++)
1808 groups->groupNames.emplace_back(put_symtab(symtab, gmx::formatString("wall%d", i).c_str()));
1809 grps->emplace_back(groups->groupNames.size() - 1);
1814 static void read_expandedparams(std::vector<t_inpfile>* inp, t_expanded* expand, warninp_t wi)
1816 /* read expanded ensemble parameters */
1817 printStringNewline(inp, "expanded ensemble variables");
1818 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1819 expand->elamstats = getEnum<LambdaWeightCalculation>(inp, "lmc-stats", wi);
1820 expand->elmcmove = getEnum<LambdaMoveCalculation>(inp, "lmc-move", wi);
1821 expand->elmceq = getEnum<LambdaWeightWillReachEquilibrium>(inp, "lmc-weights-equil", wi);
1822 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1823 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1824 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1825 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1826 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1827 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1828 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1829 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1830 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1831 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1832 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1833 expand->bSymmetrizedTMatrix =
1834 (getEnum<Boolean>(inp, "symmetrized-transition-matrix", wi) != Boolean::No);
1835 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1836 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1837 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1838 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1839 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1840 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1841 expand->bWLoneovert = (getEnum<Boolean>(inp, "wl-oneovert", wi) != Boolean::No);
1844 /*! \brief Return whether an end state with the given coupling-lambda
1845 * value describes fully-interacting VDW.
1847 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1848 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1850 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1852 return (couple_lambda_value == ecouplamVDW || couple_lambda_value == ecouplamVDWQ);
1858 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1861 explicit MdpErrorHandler(warninp_t wi) : wi_(wi), mapping_(nullptr) {}
1863 void setBackMapping(const gmx::IKeyValueTreeBackMapping& mapping) { mapping_ = &mapping; }
1865 bool onError(gmx::UserInputError* ex, const gmx::KeyValueTreePath& context) override
1868 gmx::formatString("Error in mdp option \"%s\":", getOptionName(context).c_str()));
1869 std::string message = gmx::formatExceptionMessageToString(*ex);
1870 warning_error(wi_, message.c_str());
1875 std::string getOptionName(const gmx::KeyValueTreePath& context)
1877 if (mapping_ != nullptr)
1879 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1880 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1883 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1888 const gmx::IKeyValueTreeBackMapping* mapping_;
1893 void get_ir(const char* mdparin,
1894 const char* mdparout,
1895 gmx::MDModules* mdModules,
1898 WriteMdpHeader writeMdpHeader,
1902 double dumdub[2][6];
1904 char warn_buf[STRLEN];
1905 t_lambda* fep = ir->fepvals.get();
1906 t_expanded* expand = ir->expandedvals.get();
1908 const char* no_names[] = { "no", nullptr };
1910 init_inputrec_strings();
1911 gmx::TextInputFile stream(mdparin);
1912 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1914 snew(dumstr[0], STRLEN);
1915 snew(dumstr[1], STRLEN);
1917 /* ignore the following deprecated commands */
1918 replace_inp_entry(inp, "title", nullptr);
1919 replace_inp_entry(inp, "cpp", nullptr);
1920 replace_inp_entry(inp, "domain-decomposition", nullptr);
1921 replace_inp_entry(inp, "andersen-seed", nullptr);
1922 replace_inp_entry(inp, "dihre", nullptr);
1923 replace_inp_entry(inp, "dihre-fc", nullptr);
1924 replace_inp_entry(inp, "dihre-tau", nullptr);
1925 replace_inp_entry(inp, "nstdihreout", nullptr);
1926 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1927 replace_inp_entry(inp, "optimize-fft", nullptr);
1928 replace_inp_entry(inp, "adress_type", nullptr);
1929 replace_inp_entry(inp, "adress_const_wf", nullptr);
1930 replace_inp_entry(inp, "adress_ex_width", nullptr);
1931 replace_inp_entry(inp, "adress_hy_width", nullptr);
1932 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1933 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1934 replace_inp_entry(inp, "adress_site", nullptr);
1935 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1936 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1937 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1938 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1939 replace_inp_entry(inp, "rlistlong", nullptr);
1940 replace_inp_entry(inp, "nstcalclr", nullptr);
1941 replace_inp_entry(inp, "pull-print-com2", nullptr);
1942 replace_inp_entry(inp, "gb-algorithm", nullptr);
1943 replace_inp_entry(inp, "nstgbradii", nullptr);
1944 replace_inp_entry(inp, "rgbradii", nullptr);
1945 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1946 replace_inp_entry(inp, "gb-saltconc", nullptr);
1947 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1948 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1949 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1950 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1951 replace_inp_entry(inp, "sa-algorithm", nullptr);
1952 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1953 replace_inp_entry(inp, "ns-type", nullptr);
1955 /* replace the following commands with the clearer new versions*/
1956 replace_inp_entry(inp, "unconstrained-start", "continuation");
1957 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1958 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1959 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1960 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1961 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1962 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1964 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1965 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1966 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1967 setStringEntry(&inp, "include", opts->include, nullptr);
1968 printStringNoNewline(
1969 &inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1970 setStringEntry(&inp, "define", opts->define, nullptr);
1972 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1973 ir->eI = getEnum<IntegrationAlgorithm>(&inp, "integrator", wi);
1974 printStringNoNewline(&inp, "Start time and timestep in ps");
1975 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1976 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1977 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1978 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1979 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1980 printStringNoNewline(
1981 &inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1982 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1983 printStringNoNewline(&inp, "Multiple time-stepping");
1984 ir->useMts = (getEnum<Boolean>(&inp, "mts", wi) != Boolean::No);
1987 gmx::GromppMtsOpts& mtsOpts = opts->mtsOpts;
1988 mtsOpts.numLevels = get_eint(&inp, "mts-levels", 2, wi);
1989 mtsOpts.level2Forces = setStringEntry(&inp, "mts-level2-forces", "longrange-nonbonded");
1990 mtsOpts.level2Factor = get_eint(&inp, "mts-level2-factor", 2, wi);
1992 // We clear after reading without dynamics to not force the user to remove MTS mdp options
1993 if (!EI_DYNAMICS(ir->eI))
1998 printStringNoNewline(&inp, "mode for center of mass motion removal");
1999 ir->comm_mode = getEnum<ComRemovalAlgorithm>(&inp, "comm-mode", wi);
2000 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
2001 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
2002 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
2003 setStringEntry(&inp, "comm-grps", inputrecStrings->vcm, nullptr);
2005 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
2006 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
2007 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
2008 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
2011 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
2012 printStringNoNewline(&inp, "Force tolerance and initial step-size");
2013 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
2014 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
2015 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
2016 ir->niter = get_eint(&inp, "niter", 20, wi);
2017 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
2018 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
2019 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
2020 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
2021 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
2023 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
2024 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
2026 /* Output options */
2027 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
2028 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
2029 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
2030 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
2031 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
2032 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
2033 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
2034 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
2035 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
2036 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
2037 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
2038 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
2039 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
2040 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
2041 printStringNoNewline(&inp, "default, all atoms will be written.");
2042 setStringEntry(&inp, "compressed-x-grps", inputrecStrings->x_compressed_groups, nullptr);
2043 printStringNoNewline(&inp, "Selection of energy groups");
2044 setStringEntry(&inp, "energygrps", inputrecStrings->energy, nullptr);
2046 /* Neighbor searching */
2047 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
2048 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
2049 ir->cutoff_scheme = getEnum<CutoffScheme>(&inp, "cutoff-scheme", wi);
2050 printStringNoNewline(&inp, "nblist update frequency");
2051 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
2052 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
2053 // TODO This conversion should be removed when proper std:string handling will be added to get_eeenum(...), etc.
2054 std::vector<const char*> pbcTypesNamesChar;
2055 for (const auto& pbcTypeName : c_pbcTypeNames)
2057 pbcTypesNamesChar.push_back(pbcTypeName.c_str());
2059 ir->pbcType = static_cast<PbcType>(get_eeenum(&inp, "pbc", pbcTypesNamesChar.data(), wi));
2060 ir->bPeriodicMols = getEnum<Boolean>(&inp, "periodic-molecules", wi) != Boolean::No;
2061 printStringNoNewline(&inp,
2062 "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
2063 printStringNoNewline(&inp, "a value of -1 means: use rlist");
2064 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
2065 printStringNoNewline(&inp, "nblist cut-off");
2066 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
2067 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
2069 /* Electrostatics */
2070 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
2071 printStringNoNewline(&inp, "Method for doing electrostatics");
2072 ir->coulombtype = getEnum<CoulombInteractionType>(&inp, "coulombtype", wi);
2073 ir->coulomb_modifier = getEnum<InteractionModifiers>(&inp, "coulomb-modifier", wi);
2074 printStringNoNewline(&inp, "cut-off lengths");
2075 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
2076 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
2077 printStringNoNewline(&inp, "Relative dielectric constant for the medium and the reaction field");
2078 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
2079 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
2080 printStringNoNewline(&inp, "Method for doing Van der Waals");
2081 ir->vdwtype = getEnum<VanDerWaalsType>(&inp, "vdw-type", wi);
2082 ir->vdw_modifier = getEnum<InteractionModifiers>(&inp, "vdw-modifier", wi);
2083 printStringNoNewline(&inp, "cut-off lengths");
2084 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
2085 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
2086 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
2087 ir->eDispCorr = getEnum<DispersionCorrectionType>(&inp, "DispCorr", wi);
2088 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
2089 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
2090 printStringNoNewline(&inp, "Separate tables between energy group pairs");
2091 setStringEntry(&inp, "energygrp-table", inputrecStrings->egptable, nullptr);
2092 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
2093 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
2094 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
2095 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
2096 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
2097 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
2098 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
2099 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
2100 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
2101 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
2102 ir->ljpme_combination_rule = getEnum<LongRangeVdW>(&inp, "lj-pme-comb-rule", wi);
2103 ir->ewald_geometry = getEnum<EwaldGeometry>(&inp, "ewald-geometry", wi);
2104 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
2106 /* Implicit solvation is no longer supported, but we need grompp
2107 to be able to refuse old .mdp files that would have built a tpr
2108 to run it. Thus, only "no" is accepted. */
2109 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
2111 /* Coupling stuff */
2112 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
2113 printStringNoNewline(&inp, "Temperature coupling");
2114 ir->etc = getEnum<TemperatureCoupling>(&inp, "tcoupl", wi);
2115 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
2116 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
2117 ir->bPrintNHChains = (getEnum<Boolean>(&inp, "print-nose-hoover-chain-variables", wi) != Boolean::No);
2118 printStringNoNewline(&inp, "Groups to couple separately");
2119 setStringEntry(&inp, "tc-grps", inputrecStrings->tcgrps, nullptr);
2120 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
2121 setStringEntry(&inp, "tau-t", inputrecStrings->tau_t, nullptr);
2122 setStringEntry(&inp, "ref-t", inputrecStrings->ref_t, nullptr);
2123 printStringNoNewline(&inp, "pressure coupling");
2124 ir->epc = getEnum<PressureCoupling>(&inp, "pcoupl", wi);
2125 ir->epct = getEnum<PressureCouplingType>(&inp, "pcoupltype", wi);
2126 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
2127 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
2128 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
2129 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
2130 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
2131 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
2132 ir->refcoord_scaling = getEnum<RefCoordScaling>(&inp, "refcoord-scaling", wi);
2135 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2136 ir->bQMMM = (getEnum<Boolean>(&inp, "QMMM", wi) != Boolean::No);
2137 printStringNoNewline(&inp, "Groups treated with MiMiC");
2138 setStringEntry(&inp, "QMMM-grps", inputrecStrings->QMMM, nullptr);
2140 /* Simulated annealing */
2141 printStringNewline(&inp, "SIMULATED ANNEALING");
2142 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2143 setStringEntry(&inp, "annealing", inputrecStrings->anneal, nullptr);
2144 printStringNoNewline(&inp,
2145 "Number of time points to use for specifying annealing in each group");
2146 setStringEntry(&inp, "annealing-npoints", inputrecStrings->anneal_npoints, nullptr);
2147 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2148 setStringEntry(&inp, "annealing-time", inputrecStrings->anneal_time, nullptr);
2149 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2150 setStringEntry(&inp, "annealing-temp", inputrecStrings->anneal_temp, nullptr);
2153 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2154 opts->bGenVel = (getEnum<Boolean>(&inp, "gen-vel", wi) != Boolean::No);
2155 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2156 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2159 printStringNewline(&inp, "OPTIONS FOR BONDS");
2160 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2161 printStringNoNewline(&inp, "Type of constraint algorithm");
2162 ir->eConstrAlg = getEnum<ConstraintAlgorithm>(&inp, "constraint-algorithm", wi);
2163 printStringNoNewline(&inp, "Do not constrain the start configuration");
2164 ir->bContinuation = (getEnum<Boolean>(&inp, "continuation", wi) != Boolean::No);
2165 printStringNoNewline(&inp,
2166 "Use successive overrelaxation to reduce the number of shake iterations");
2167 ir->bShakeSOR = (getEnum<Boolean>(&inp, "Shake-SOR", wi) != Boolean::No);
2168 printStringNoNewline(&inp, "Relative tolerance of shake");
2169 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2170 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2171 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2172 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2173 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2174 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2175 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2176 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2177 printStringNoNewline(&inp, "rotates over more degrees than");
2178 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2179 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2180 opts->bMorse = (getEnum<Boolean>(&inp, "morse", wi) != Boolean::No);
2182 /* Energy group exclusions */
2183 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2184 printStringNoNewline(
2185 &inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2186 setStringEntry(&inp, "energygrp-excl", inputrecStrings->egpexcl, nullptr);
2189 printStringNewline(&inp, "WALLS");
2190 printStringNoNewline(
2191 &inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2192 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2193 ir->wall_type = getEnum<WallType>(&inp, "wall-type", wi);
2194 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2195 setStringEntry(&inp, "wall-atomtype", inputrecStrings->wall_atomtype, nullptr);
2196 setStringEntry(&inp, "wall-density", inputrecStrings->wall_density, nullptr);
2197 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2200 printStringNewline(&inp, "COM PULLING");
2201 ir->bPull = (getEnum<Boolean>(&inp, "pull", wi) != Boolean::No);
2204 ir->pull = std::make_unique<pull_params_t>();
2205 inputrecStrings->pullGroupNames = read_pullparams(&inp, ir->pull.get(), wi);
2209 for (int c = 0; c < ir->pull->ncoord; c++)
2211 if (ir->pull->coord[c].eType == PullingAlgorithm::Constraint)
2214 "Constraint COM pulling is not supported in combination with "
2215 "multiple time stepping");
2223 NOTE: needs COM pulling or free energy input */
2224 printStringNewline(&inp, "AWH biasing");
2225 ir->bDoAwh = (getEnum<Boolean>(&inp, "awh", wi) != Boolean::No);
2228 ir->awhParams = std::make_unique<gmx::AwhParams>(&inp, wi);
2231 /* Enforced rotation */
2232 printStringNewline(&inp, "ENFORCED ROTATION");
2233 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2234 ir->bRot = (getEnum<Boolean>(&inp, "rotation", wi) != Boolean::No);
2238 inputrecStrings->rotateGroupNames = read_rotparams(&inp, ir->rot, wi);
2241 /* Interactive MD */
2243 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2244 setStringEntry(&inp, "IMD-group", inputrecStrings->imd_grp, nullptr);
2245 if (inputrecStrings->imd_grp[0] != '\0')
2252 printStringNewline(&inp, "NMR refinement stuff");
2253 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2254 ir->eDisre = getEnum<DistanceRestraintRefinement>(&inp, "disre", wi);
2255 printStringNoNewline(
2256 &inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2257 ir->eDisreWeighting = getEnum<DistanceRestraintWeighting>(&inp, "disre-weighting", wi);
2258 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2259 ir->bDisreMixed = (getEnum<Boolean>(&inp, "disre-mixed", wi) != Boolean::No);
2260 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2261 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2262 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2263 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2264 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2265 opts->bOrire = (getEnum<Boolean>(&inp, "orire", wi) != Boolean::No);
2266 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2267 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2268 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2269 setStringEntry(&inp, "orire-fitgrp", inputrecStrings->orirefitgrp, nullptr);
2270 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2271 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2273 /* free energy variables */
2274 printStringNewline(&inp, "Free energy variables");
2275 ir->efep = getEnum<FreeEnergyPerturbationType>(&inp, "free-energy", wi);
2276 setStringEntry(&inp, "couple-moltype", inputrecStrings->couple_moltype, nullptr);
2277 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2278 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2279 opts->bCoupleIntra = (getEnum<Boolean>(&inp, "couple-intramol", wi) != Boolean::No);
2281 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2283 it was not entered */
2284 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2285 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2286 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2287 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Fep] =
2288 setStringEntry(&inp, "fep-lambdas", "");
2289 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Mass] =
2290 setStringEntry(&inp, "mass-lambdas", "");
2291 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Coul] =
2292 setStringEntry(&inp, "coul-lambdas", "");
2293 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Vdw] =
2294 setStringEntry(&inp, "vdw-lambdas", "");
2295 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Bonded] =
2296 setStringEntry(&inp, "bonded-lambdas", "");
2297 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Restraint] =
2298 setStringEntry(&inp, "restraint-lambdas", "");
2299 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Temperature] =
2300 setStringEntry(&inp, "temperature-lambdas", "");
2301 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2302 setStringEntry(&inp, "init-lambda-weights", inputrecStrings->lambda_weights, nullptr);
2303 fep->edHdLPrintEnergy = getEnum<FreeEnergyPrintEnergy>(&inp, "dhdl-print-energy", wi);
2304 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2305 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2306 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2307 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2308 fep->bScCoul = (getEnum<Boolean>(&inp, "sc-coul", wi) != Boolean::No);
2309 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2310 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2311 fep->separate_dhdl_file = getEnum<SeparateDhdlFile>(&inp, "separate-dhdl-file", wi);
2312 fep->dhdl_derivatives = getEnum<DhDlDerivativeCalculation>(&inp, "dhdl-derivatives", wi);
2313 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2314 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2316 /* Non-equilibrium MD stuff */
2317 printStringNewline(&inp, "Non-equilibrium MD stuff");
2318 setStringEntry(&inp, "freezegrps", inputrecStrings->freeze, nullptr);
2319 setStringEntry(&inp, "freezedim", inputrecStrings->frdim, nullptr);
2320 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2321 setStringEntry(&inp, "deform", inputrecStrings->deform, nullptr);
2323 /* simulated tempering variables */
2324 printStringNewline(&inp, "simulated tempering variables");
2325 ir->bSimTemp = (getEnum<Boolean>(&inp, "simulated-tempering", wi) != Boolean::No);
2326 ir->simtempvals->eSimTempScale = getEnum<SimulatedTempering>(&inp, "simulated-tempering-scaling", wi);
2327 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2328 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2330 /* expanded ensemble variables */
2331 if (ir->efep == FreeEnergyPerturbationType::Expanded || ir->bSimTemp)
2333 read_expandedparams(&inp, expand, wi);
2336 /* Electric fields */
2338 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2339 gmx::KeyValueTreeTransformer transform;
2340 transform.rules()->addRule().keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2341 mdModules->initMdpTransform(transform.rules());
2342 for (const auto& path : transform.mappedPaths())
2344 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2345 mark_einp_set(inp, path[0].c_str());
2347 MdpErrorHandler errorHandler(wi);
2348 auto result = transform.transform(convertedValues, &errorHandler);
2349 ir->params = new gmx::KeyValueTreeObject(result.object());
2350 mdModules->adjustInputrecBasedOnModules(ir);
2351 errorHandler.setBackMapping(result.backMapping());
2352 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2355 /* Ion/water position swapping ("computational electrophysiology") */
2356 printStringNewline(&inp,
2357 "Ion/water position swapping for computational electrophysiology setups");
2358 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2359 ir->eSwapCoords = getEnum<SwapType>(&inp, "swapcoords", wi);
2360 if (ir->eSwapCoords != SwapType::No)
2367 printStringNoNewline(&inp, "Swap attempt frequency");
2368 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2369 printStringNoNewline(&inp, "Number of ion types to be controlled");
2370 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2373 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2375 ir->swap->ngrp = nIonTypes + static_cast<int>(SwapGroupSplittingType::Count);
2376 snew(ir->swap->grp, ir->swap->ngrp);
2377 for (i = 0; i < ir->swap->ngrp; i++)
2379 snew(ir->swap->grp[i].molname, STRLEN);
2381 printStringNoNewline(&inp,
2382 "Two index groups that contain the compartment-partitioning atoms");
2383 setStringEntry(&inp,
2385 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname,
2387 setStringEntry(&inp,
2389 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname,
2391 printStringNoNewline(&inp,
2392 "Use center of mass of split groups (yes/no), otherwise center of "
2393 "geometry is used");
2394 ir->swap->massw_split[0] = (getEnum<Boolean>(&inp, "massw-split0", wi) != Boolean::No);
2395 ir->swap->massw_split[1] = (getEnum<Boolean>(&inp, "massw-split1", wi) != Boolean::No);
2397 printStringNoNewline(&inp, "Name of solvent molecules");
2398 setStringEntry(&inp,
2400 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].molname,
2403 printStringNoNewline(&inp,
2404 "Split cylinder: radius, upper and lower extension (nm) (this will "
2405 "define the channels)");
2406 printStringNoNewline(&inp,
2407 "Note that the split cylinder settings do not have an influence on "
2408 "the swapping protocol,");
2409 printStringNoNewline(
2411 "however, if correctly defined, the permeation events are recorded per channel");
2412 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2413 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2414 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2415 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2416 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2417 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2419 printStringNoNewline(
2421 "Average the number of ions per compartment over these many swap attempt steps");
2422 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2424 printStringNoNewline(
2425 &inp, "Names of the ion types that can be exchanged with solvent molecules,");
2426 printStringNoNewline(
2427 &inp, "and the requested number of ions of this type in compartments A and B");
2428 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2429 for (i = 0; i < nIonTypes; i++)
2431 int ig = static_cast<int>(SwapGroupSplittingType::Count) + i;
2433 sprintf(buf, "iontype%d-name", i);
2434 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2435 sprintf(buf, "iontype%d-in-A", i);
2436 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2437 sprintf(buf, "iontype%d-in-B", i);
2438 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2441 printStringNoNewline(
2443 "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2444 printStringNoNewline(
2446 "at maximum distance (= bulk concentration) to the split group layers. However,");
2447 printStringNoNewline(&inp,
2448 "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk "
2449 "layer from the middle at 0.0");
2450 printStringNoNewline(&inp,
2451 "towards one of the compartment-partitioning layers (at +/- 1.0).");
2452 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2453 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2454 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2455 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0))
2457 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2460 printStringNoNewline(
2461 &inp, "Start to swap ions if threshold difference to requested count is reached");
2462 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2465 /* AdResS is no longer supported, but we need grompp to be able to
2466 refuse to process old .mdp files that used it. */
2467 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2469 /* User defined thingies */
2470 printStringNewline(&inp, "User defined thingies");
2471 setStringEntry(&inp, "user1-grps", inputrecStrings->user1, nullptr);
2472 setStringEntry(&inp, "user2-grps", inputrecStrings->user2, nullptr);
2473 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2474 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2475 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2476 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2477 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2478 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2479 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2480 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2484 gmx::TextOutputFile stream(mdparout);
2485 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2487 // Transform module data into a flat key-value tree for output.
2488 gmx::KeyValueTreeBuilder builder;
2489 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2490 mdModules->buildMdpOutput(&builderObject);
2492 gmx::TextWriter writer(&stream);
2493 writeKeyValueTreeAsMdp(&writer, builder.build());
2498 /* Process options if necessary */
2499 for (m = 0; m < 2; m++)
2501 for (i = 0; i < 2 * DIM; i++)
2505 if (ir->epc != PressureCoupling::No)
2509 case PressureCouplingType::Isotropic:
2510 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2514 "Pressure coupling incorrect number of values (I need exactly 1)");
2516 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2518 case PressureCouplingType::SemiIsotropic:
2519 case PressureCouplingType::SurfaceTension:
2520 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2524 "Pressure coupling incorrect number of values (I need exactly 2)");
2526 dumdub[m][YY] = dumdub[m][XX];
2528 case PressureCouplingType::Anisotropic:
2529 if (sscanf(dumstr[m],
2530 "%lf%lf%lf%lf%lf%lf",
2541 "Pressure coupling incorrect number of values (I need exactly 6)");
2546 "Pressure coupling type %s not implemented yet",
2547 enumValueToString(ir->epct));
2551 clear_mat(ir->ref_p);
2552 clear_mat(ir->compress);
2553 for (i = 0; i < DIM; i++)
2555 ir->ref_p[i][i] = dumdub[1][i];
2556 ir->compress[i][i] = dumdub[0][i];
2558 if (ir->epct == PressureCouplingType::Anisotropic)
2560 ir->ref_p[XX][YY] = dumdub[1][3];
2561 ir->ref_p[XX][ZZ] = dumdub[1][4];
2562 ir->ref_p[YY][ZZ] = dumdub[1][5];
2563 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2566 "All off-diagonal reference pressures are non-zero. Are you sure you want to "
2567 "apply a threefold shear stress?\n");
2569 ir->compress[XX][YY] = dumdub[0][3];
2570 ir->compress[XX][ZZ] = dumdub[0][4];
2571 ir->compress[YY][ZZ] = dumdub[0][5];
2572 for (i = 0; i < DIM; i++)
2574 for (m = 0; m < i; m++)
2576 ir->ref_p[i][m] = ir->ref_p[m][i];
2577 ir->compress[i][m] = ir->compress[m][i];
2582 if (ir->comm_mode == ComRemovalAlgorithm::No)
2587 opts->couple_moltype = nullptr;
2588 if (strlen(inputrecStrings->couple_moltype) > 0)
2590 if (ir->efep != FreeEnergyPerturbationType::No)
2592 opts->couple_moltype = gmx_strdup(inputrecStrings->couple_moltype);
2593 if (opts->couple_lam0 == opts->couple_lam1)
2595 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2597 if (ir->eI == IntegrationAlgorithm::MD
2598 && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
2602 "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
2609 "Free energy is turned off, so we will not decouple the molecule listed "
2613 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2614 if (ir->efep != FreeEnergyPerturbationType::No)
2616 if (fep->delta_lambda != 0)
2618 ir->efep = FreeEnergyPerturbationType::SlowGrowth;
2622 if (fep->edHdLPrintEnergy == FreeEnergyPrintEnergy::Yes)
2624 fep->edHdLPrintEnergy = FreeEnergyPrintEnergy::Total;
2626 "Old option for dhdl-print-energy given: "
2627 "changing \"yes\" to \"total\"\n");
2630 if (ir->bSimTemp && (fep->edHdLPrintEnergy == FreeEnergyPrintEnergy::No))
2632 /* always print out the energy to dhdl if we are doing
2633 expanded ensemble, since we need the total energy for
2634 analysis if the temperature is changing. In some
2635 conditions one may only want the potential energy, so
2636 we will allow that if the appropriate mdp setting has
2637 been enabled. Otherwise, total it is:
2639 fep->edHdLPrintEnergy = FreeEnergyPrintEnergy::Total;
2642 if ((ir->efep != FreeEnergyPerturbationType::No) || ir->bSimTemp)
2644 ir->bExpanded = FALSE;
2645 if ((ir->efep == FreeEnergyPerturbationType::Expanded) || ir->bSimTemp)
2647 ir->bExpanded = TRUE;
2649 do_fep_params(ir, inputrecStrings->fep_lambda, inputrecStrings->lambda_weights, wi);
2650 if (ir->bSimTemp) /* done after fep params */
2652 do_simtemp_params(ir);
2655 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2656 * setup and not on the old way of specifying the free-energy setup,
2657 * we should check for using soft-core when not needed, since that
2658 * can complicate the sampling significantly.
2659 * Note that we only check for the automated coupling setup.
2660 * If the (advanced) user does FEP through manual topology changes,
2661 * this check will not be triggered.
2663 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->n_lambda == 0
2664 && ir->fepvals->sc_alpha != 0
2665 && (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
2668 "You are using soft-core interactions while the Van der Waals interactions are "
2669 "not decoupled (note that the sc-coul option is only active when using lambda "
2670 "states). Although this will not lead to errors, you will need much more "
2671 "sampling than without soft-core interactions. Consider using sc-alpha=0.");
2676 ir->fepvals->n_lambda = 0;
2679 /* WALL PARAMETERS */
2681 do_wall_params(ir, inputrecStrings->wall_atomtype, inputrecStrings->wall_density, opts, wi);
2683 /* ORIENTATION RESTRAINT PARAMETERS */
2685 if (opts->bOrire && gmx::splitString(inputrecStrings->orirefitgrp).size() != 1)
2687 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2690 /* DEFORMATION PARAMETERS */
2692 clear_mat(ir->deform);
2693 for (i = 0; i < 6; i++)
2698 double gmx_unused canary;
2699 int ndeform = sscanf(inputrecStrings->deform,
2700 "%lf %lf %lf %lf %lf %lf %lf",
2709 if (strlen(inputrecStrings->deform) > 0 && ndeform != 6)
2713 "Cannot parse exactly 6 box deformation velocities from string '%s'",
2714 inputrecStrings->deform)
2717 for (i = 0; i < 3; i++)
2719 ir->deform[i][i] = dumdub[0][i];
2721 ir->deform[YY][XX] = dumdub[0][3];
2722 ir->deform[ZZ][XX] = dumdub[0][4];
2723 ir->deform[ZZ][YY] = dumdub[0][5];
2724 if (ir->epc != PressureCoupling::No)
2726 for (i = 0; i < 3; i++)
2728 for (j = 0; j <= i; j++)
2730 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2732 warning_error(wi, "A box element has deform set and compressibility > 0");
2736 for (i = 0; i < 3; i++)
2738 for (j = 0; j < i; j++)
2740 if (ir->deform[i][j] != 0)
2742 for (m = j; m < DIM; m++)
2744 if (ir->compress[m][j] != 0)
2747 "An off-diagonal box element has deform set while "
2748 "compressibility > 0 for the same component of another box "
2749 "vector, this might lead to spurious periodicity effects.");
2750 warning(wi, warn_buf);
2758 /* Ion/water position swapping checks */
2759 if (ir->eSwapCoords != SwapType::No)
2761 if (ir->swap->nstswap < 1)
2763 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2765 if (ir->swap->nAverage < 1)
2767 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2769 if (ir->swap->threshold < 1.0)
2771 warning_error(wi, "Ion count threshold must be at least 1.\n");
2775 /* Set up MTS levels, this needs to happen before checking AWH parameters */
2778 std::vector<std::string> errorMessages;
2779 ir->mtsLevels = gmx::setupMtsLevels(opts->mtsOpts, &errorMessages);
2781 for (const auto& errorMessage : errorMessages)
2783 warning_error(wi, errorMessage.c_str());
2789 gmx::checkAwhParams(*ir->awhParams, *ir, wi);
2796 /* We would like gn to be const as well, but C doesn't allow this */
2797 /* TODO this is utility functionality (search for the index of a
2798 string in a collection), so should be refactored and located more
2800 int search_string(const char* s, int ng, char* gn[])
2804 for (i = 0; (i < ng); i++)
2806 if (gmx_strcasecmp(s, gn[i]) == 0)
2813 "Group %s referenced in the .mdp file was not found in the index file.\n"
2814 "Group names must match either [moleculetype] names or custom index group\n"
2815 "names, in which case you must supply an index file to the '-n' option\n"
2820 static void atomGroupRangeValidation(int natoms, int groupIndex, const t_blocka& block)
2822 /* Now go over the atoms in the group */
2823 for (int j = block.index[groupIndex]; (j < block.index[groupIndex + 1]); j++)
2825 int aj = block.a[j];
2827 /* Range checking */
2828 if ((aj < 0) || (aj >= natoms))
2830 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2835 static void do_numbering(int natoms,
2836 SimulationGroups* groups,
2837 gmx::ArrayRef<std::string> groupsFromMdpFile,
2840 SimulationAtomGroupType gtype,
2846 unsigned short* cbuf;
2847 AtomGroupIndices* grps = &(groups->groups[gtype]);
2850 char warn_buf[STRLEN];
2852 title = shortName(gtype);
2855 /* Mark all id's as not set */
2856 for (int i = 0; (i < natoms); i++)
2861 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2863 /* Lookup the group name in the block structure */
2864 const int gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2865 if ((grptp != egrptpONE) || (i == 0))
2867 grps->emplace_back(gid);
2869 GMX_ASSERT(block, "Can't have a nullptr block");
2870 atomGroupRangeValidation(natoms, gid, *block);
2871 /* Now go over the atoms in the group */
2872 for (int j = block->index[gid]; (j < block->index[gid + 1]); j++)
2874 const int aj = block->a[j];
2875 /* Lookup up the old group number */
2876 const int ognr = cbuf[aj];
2879 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title, ognr + 1, i + 1);
2883 /* Store the group number in buffer */
2884 if (grptp == egrptpONE)
2897 /* Now check whether we have done all atoms */
2900 if (grptp == egrptpALL)
2902 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2904 else if (grptp == egrptpPART)
2906 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2907 warning_note(wi, warn_buf);
2909 /* Assign all atoms currently unassigned to a rest group */
2910 for (int j = 0; (j < natoms); j++)
2912 if (cbuf[j] == NOGID)
2914 cbuf[j] = grps->size();
2917 if (grptp != egrptpPART)
2921 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title, natoms - ntot);
2923 /* Add group name "rest" */
2924 grps->emplace_back(restnm);
2926 /* Assign the rest name to all atoms not currently assigned to a group */
2927 for (int j = 0; (j < natoms); j++)
2929 if (cbuf[j] == NOGID)
2931 // group size was not updated before this here, so need to use -1.
2932 cbuf[j] = grps->size() - 1;
2938 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2940 /* All atoms are part of one (or no) group, no index required */
2941 groups->groupNumbers[gtype].clear();
2945 for (int j = 0; (j < natoms); j++)
2947 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2954 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
2957 pull_params_t* pull;
2958 int natoms, imin, jmin;
2959 int * nrdf2, *na_vcm, na_tot;
2960 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2965 * First calc 3xnr-atoms for each group
2966 * then subtract half a degree of freedom for each constraint
2968 * Only atoms and nuclei contribute to the degrees of freedom...
2973 const SimulationGroups& groups = mtop->groups;
2974 natoms = mtop->natoms;
2976 /* Allocate one more for a possible rest group */
2977 /* We need to sum degrees of freedom into doubles,
2978 * since floats give too low nrdf's above 3 million atoms.
2980 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
2981 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2982 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2983 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2984 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2986 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
2990 for (gmx::index i = 0;
2991 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
2995 clear_ivec(dof_vcm[i]);
2997 nrdf_vcm_sub[i] = 0;
2999 snew(nrdf2, natoms);
3000 for (const AtomProxy atomP : AtomRange(*mtop))
3002 const t_atom& local = atomP.atom();
3003 int i = atomP.globalAtomNumber();
3005 if (local.ptype == ParticleType::Atom || local.ptype == ParticleType::Nucleus)
3007 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
3008 for (int d = 0; d < DIM; d++)
3010 if (opts->nFreeze[g][d] == 0)
3012 /* Add one DOF for particle i (counted as 2*1) */
3014 /* VCM group i has dim d as a DOF */
3015 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
3019 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
3021 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
3027 for (const gmx_molblock_t& molb : mtop->molblock)
3029 const gmx_moltype_t& molt = mtop->moltype[molb.type];
3030 const t_atom* atom = molt.atoms.atom;
3031 for (int mol = 0; mol < molb.nmol; mol++)
3033 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
3035 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
3036 for (int i = 0; i < molt.ilist[ftype].size();)
3038 /* Subtract degrees of freedom for the constraints,
3039 * if the particles still have degrees of freedom left.
3040 * If one of the particles is a vsite or a shell, then all
3041 * constraint motion will go there, but since they do not
3042 * contribute to the constraints the degrees of freedom do not
3045 int ai = as + ia[i + 1];
3046 int aj = as + ia[i + 2];
3047 if (((atom[ia[i + 1]].ptype == ParticleType::Nucleus)
3048 || (atom[ia[i + 1]].ptype == ParticleType::Atom))
3049 && ((atom[ia[i + 2]].ptype == ParticleType::Nucleus)
3050 || (atom[ia[i + 2]].ptype == ParticleType::Atom)))
3068 imin = std::min(imin, nrdf2[ai]);
3069 jmin = std::min(jmin, nrdf2[aj]);
3072 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3074 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
3076 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3078 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
3081 i += interaction_function[ftype].nratoms + 1;
3084 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
3085 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
3087 /* Subtract 1 dof from every atom in the SETTLE */
3088 for (int j = 0; j < 3; j++)
3090 int ai = as + ia[i + 1 + j];
3091 imin = std::min(2, nrdf2[ai]);
3093 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3095 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3100 as += molt.atoms.nr;
3106 /* Correct nrdf for the COM constraints.
3107 * We correct using the TC and VCM group of the first atom
3108 * in the reference and pull group. If atoms in one pull group
3109 * belong to different TC or VCM groups it is anyhow difficult
3110 * to determine the optimal nrdf assignment.
3112 pull = ir->pull.get();
3114 for (int i = 0; i < pull->ncoord; i++)
3116 if (pull->coord[i].eType != PullingAlgorithm::Constraint)
3123 for (int j = 0; j < 2; j++)
3125 const t_pull_group* pgrp;
3127 pgrp = &pull->group[pull->coord[i].group[j]];
3129 if (!pgrp->ind.empty())
3131 /* Subtract 1/2 dof from each group */
3132 int ai = pgrp->ind[0];
3133 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3135 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3137 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
3140 "Center of mass pulling constraints caused the number of degrees "
3141 "of freedom for temperature coupling group %s to be negative",
3142 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
3143 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
3148 /* We need to subtract the whole DOF from group j=1 */
3155 if (ir->nstcomm != 0)
3157 GMX_RELEASE_ASSERT(!groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty(),
3158 "Expect at least one group when removing COM motion");
3160 /* We remove COM motion up to dim ndof_com() */
3161 const int ndim_rm_vcm = ndof_com(ir);
3163 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3164 * the number of degrees of freedom in each vcm group when COM
3165 * translation is removed and 6 when rotation is removed as well.
3166 * Note that we do not and should not include the rest group here.
3168 for (gmx::index j = 0;
3169 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]);
3172 switch (ir->comm_mode)
3174 case ComRemovalAlgorithm::Linear:
3175 case ComRemovalAlgorithm::LinearAccelerationCorrection:
3176 nrdf_vcm_sub[j] = 0;
3177 for (int d = 0; d < ndim_rm_vcm; d++)
3185 case ComRemovalAlgorithm::Angular: nrdf_vcm_sub[j] = 6; break;
3186 default: gmx_incons("Checking comm_mode");
3190 for (gmx::index i = 0;
3191 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]);
3194 /* Count the number of atoms of TC group i for every VCM group */
3195 for (gmx::index j = 0;
3196 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3202 for (int ai = 0; ai < natoms; ai++)
3204 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3206 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3210 /* Correct for VCM removal according to the fraction of each VCM
3211 * group present in this TC group.
3213 nrdf_uc = nrdf_tc[i];
3215 for (gmx::index j = 0;
3216 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3219 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3221 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3222 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3227 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3229 opts->nrdf[i] = nrdf_tc[i];
3230 if (opts->nrdf[i] < 0)
3235 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3236 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]],
3245 sfree(nrdf_vcm_sub);
3248 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3250 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3251 * But since this is much larger than STRLEN, such a line can not be parsed.
3252 * The real maximum is the number of names that fit in a string: STRLEN/2.
3254 #define EGP_MAX (STRLEN / 2)
3258 auto names = gmx::splitString(val);
3259 if (names.size() % 2 != 0)
3261 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3263 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3265 for (size_t i = 0; i < names.size() / 2; i++)
3267 // TODO this needs to be replaced by a solution using std::find_if
3271 names[2 * i].c_str(),
3272 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3278 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3283 names[2 * i + 1].c_str(),
3284 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3290 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3292 if ((j < nr) && (k < nr))
3294 ir->opts.egp_flags[nr * j + k] |= flag;
3295 ir->opts.egp_flags[nr * k + j] |= flag;
3304 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3306 int ig = -1, i = 0, gind;
3310 /* Just a quick check here, more thorough checks are in mdrun */
3311 if (strcmp(swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname,
3312 swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname)
3316 "The split groups can not both be '%s'.",
3317 swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname);
3320 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3321 for (ig = 0; ig < swap->ngrp; ig++)
3323 swapg = &swap->grp[ig];
3324 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3325 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3330 "%s group '%s' contains %d atoms.\n",
3331 ig < 3 ? enumValueToString(static_cast<SwapGroupSplittingType>(ig)) : "Swap",
3332 swap->grp[ig].molname,
3334 snew(swapg->ind, swapg->nat);
3335 for (i = 0; i < swapg->nat; i++)
3337 swapg->ind[i] = grps->a[grps->index[gind] + i];
3342 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3348 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3353 ig = search_string(IMDgname, grps->nr, gnames);
3354 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3356 if (IMDgroup->nat > 0)
3359 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3363 snew(IMDgroup->ind, IMDgroup->nat);
3364 for (i = 0; i < IMDgroup->nat; i++)
3366 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3371 /* Checks whether atoms are both part of a COM removal group and frozen.
3372 * If a fully frozen atom is part of a COM removal group, it is removed
3373 * from the COM removal group. A note is issued if such atoms are present.
3374 * A warning is issued for atom with one or two dimensions frozen that
3375 * are part of a COM removal group (mdrun would need to compute COM mass
3376 * per dimension to handle this correctly).
3377 * Also issues a warning when non-frozen atoms are not part of a COM
3378 * removal group while COM removal is active.
3380 static void checkAndUpdateVcmFreezeGroupConsistency(SimulationGroups* groups,
3382 const t_grpopts& opts,
3385 const int vcmRestGroup =
3386 std::max(int(groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()), 1);
3388 int numFullyFrozenVcmAtoms = 0;
3389 int numPartiallyFrozenVcmAtoms = 0;
3390 int numNonVcmAtoms = 0;
3391 for (int a = 0; a < numAtoms; a++)
3393 const int freezeGroup = getGroupType(*groups, SimulationAtomGroupType::Freeze, a);
3394 int numFrozenDims = 0;
3395 for (int d = 0; d < DIM; d++)
3397 numFrozenDims += opts.nFreeze[freezeGroup][d];
3400 const int vcmGroup = getGroupType(*groups, SimulationAtomGroupType::MassCenterVelocityRemoval, a);
3401 if (vcmGroup < vcmRestGroup)
3403 if (numFrozenDims == DIM)
3405 /* Do not remove COM motion for this fully frozen atom */
3406 if (groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
3408 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(
3411 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
3412 numFullyFrozenVcmAtoms++;
3414 else if (numFrozenDims > 0)
3416 numPartiallyFrozenVcmAtoms++;
3419 else if (numFrozenDims < DIM)
3425 if (numFullyFrozenVcmAtoms > 0)
3427 std::string warningText = gmx::formatString(
3428 "There are %d atoms that are fully frozen and part of COMM removal group(s), "
3429 "removing these atoms from the COMM removal group(s)",
3430 numFullyFrozenVcmAtoms);
3431 warning_note(wi, warningText.c_str());
3433 if (numPartiallyFrozenVcmAtoms > 0 && numPartiallyFrozenVcmAtoms < numAtoms)
3435 std::string warningText = gmx::formatString(
3436 "There are %d atoms that are frozen along less then %d dimensions and part of COMM "
3437 "removal group(s), due to limitations in the code these still contribute to the "
3438 "mass of the COM along frozen dimensions and therefore the COMM correction will be "
3440 numPartiallyFrozenVcmAtoms,
3442 warning(wi, warningText.c_str());
3444 if (numNonVcmAtoms > 0)
3446 std::string warningText = gmx::formatString(
3447 "%d atoms are not part of any center of mass motion removal group.\n"
3448 "This may lead to artifacts.\n"
3449 "In most cases one should use one group for the whole system.",
3451 warning(wi, warningText.c_str());
3455 void do_index(const char* mdparin,
3459 const gmx::MDModulesNotifiers& mdModulesNotifiers,
3463 t_blocka* defaultIndexGroups;
3471 int i, j, k, restnm;
3472 bool bExcl, bTable, bAnneal;
3473 char warn_buf[STRLEN];
3477 fprintf(stderr, "processing index file...\n");
3481 snew(defaultIndexGroups, 1);
3482 snew(defaultIndexGroups->index, 1);
3484 atoms_all = gmx_mtop_global_atoms(*mtop);
3485 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3486 done_atom(&atoms_all);
3490 defaultIndexGroups = init_index(ndx, &gnames);
3493 SimulationGroups* groups = &mtop->groups;
3494 natoms = mtop->natoms;
3495 symtab = &mtop->symtab;
3497 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3499 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3501 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3502 restnm = groups->groupNames.size() - 1;
3503 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3504 srenew(gnames, defaultIndexGroups->nr + 1);
3505 gnames[restnm] = *(groups->groupNames.back());
3507 set_warning_line(wi, mdparin, -1);
3509 auto temperatureCouplingTauValues = gmx::splitString(inputrecStrings->tau_t);
3510 auto temperatureCouplingReferenceValues = gmx::splitString(inputrecStrings->ref_t);
3511 auto temperatureCouplingGroupNames = gmx::splitString(inputrecStrings->tcgrps);
3512 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3513 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3516 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3518 temperatureCouplingGroupNames.size(),
3519 temperatureCouplingReferenceValues.size(),
3520 temperatureCouplingTauValues.size());
3523 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3524 do_numbering(natoms,
3526 temperatureCouplingGroupNames,
3529 SimulationAtomGroupType::TemperatureCoupling,
3531 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST,
3534 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3536 snew(ir->opts.nrdf, nr);
3537 snew(ir->opts.tau_t, nr);
3538 snew(ir->opts.ref_t, nr);
3539 if (ir->eI == IntegrationAlgorithm::BD && ir->bd_fric == 0)
3541 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3544 if (useReferenceTemperature)
3546 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3548 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3552 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3553 for (i = 0; (i < nr); i++)
3555 if ((ir->eI == IntegrationAlgorithm::BD) && ir->opts.tau_t[i] <= 0)
3558 "With integrator %s tau-t should be larger than 0",
3559 enumValueToString(ir->eI));
3560 warning_error(wi, warn_buf);
3563 if (ir->etc != TemperatureCoupling::VRescale && ir->opts.tau_t[i] == 0)
3567 "tau-t = -1 is the value to signal that a group should not have "
3568 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3571 if (ir->opts.tau_t[i] >= 0)
3573 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3576 if (ir->etc != TemperatureCoupling::No && ir->nsttcouple == -1)
3578 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3583 if ((ir->etc == TemperatureCoupling::NoseHoover) && (ir->epc == PressureCoupling::Berendsen))
3586 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3587 "md-vv; use either vrescale temperature with berendsen pressure or "
3588 "Nose-Hoover temperature with MTTK pressure");
3590 if (ir->epc == PressureCoupling::Mttk)
3592 if (ir->etc != TemperatureCoupling::NoseHoover)
3595 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3600 if (ir->nstpcouple != ir->nsttcouple)
3602 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3603 ir->nstpcouple = ir->nsttcouple = mincouple;
3605 "for current Trotter decomposition methods with vv, nsttcouple and "
3606 "nstpcouple must be equal. Both have been reset to "
3607 "min(nsttcouple,nstpcouple) = %d",
3609 warning_note(wi, warn_buf);
3614 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3615 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3617 if (ETC_ANDERSEN(ir->etc))
3619 if (ir->nsttcouple != 1)
3623 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3624 "need for larger nsttcouple > 1, since no global parameters are computed. "
3625 "nsttcouple has been reset to 1");
3626 warning_note(wi, warn_buf);
3629 nstcmin = tcouple_min_integration_steps(ir->etc);
3632 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3635 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3636 "least %d times larger than nsttcouple*dt (%g)",
3637 enumValueToString(ir->etc),
3640 ir->nsttcouple * ir->delta_t);
3641 warning(wi, warn_buf);
3644 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3645 for (i = 0; (i < nr); i++)
3647 if (ir->opts.ref_t[i] < 0)
3649 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3652 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3653 if we are in this conditional) if mc_temp is negative */
3654 if (ir->expandedvals->mc_temp < 0)
3656 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3660 /* Simulated annealing for each group. There are nr groups */
3661 auto simulatedAnnealingGroupNames = gmx::splitString(inputrecStrings->anneal);
3662 if (simulatedAnnealingGroupNames.size() == 1
3663 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3665 simulatedAnnealingGroupNames.resize(0);
3667 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3670 "Wrong number of annealing values: %zu (for %d groups)\n",
3671 simulatedAnnealingGroupNames.size(),
3676 snew(ir->opts.annealing, nr);
3677 snew(ir->opts.anneal_npoints, nr);
3678 snew(ir->opts.anneal_time, nr);
3679 snew(ir->opts.anneal_temp, nr);
3680 for (i = 0; i < nr; i++)
3682 ir->opts.annealing[i] = SimulatedAnnealing::No;
3683 ir->opts.anneal_npoints[i] = 0;
3684 ir->opts.anneal_time[i] = nullptr;
3685 ir->opts.anneal_temp[i] = nullptr;
3687 if (!simulatedAnnealingGroupNames.empty())
3690 for (i = 0; i < nr; i++)
3692 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3694 ir->opts.annealing[i] = SimulatedAnnealing::No;
3696 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3698 ir->opts.annealing[i] = SimulatedAnnealing::Single;
3701 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3703 ir->opts.annealing[i] = SimulatedAnnealing::Periodic;
3709 /* Read the other fields too */
3710 auto simulatedAnnealingPoints = gmx::splitString(inputrecStrings->anneal_npoints);
3711 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3714 "Found %zu annealing-npoints values for %zu groups\n",
3715 simulatedAnnealingPoints.size(),
3716 simulatedAnnealingGroupNames.size());
3718 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3719 size_t numSimulatedAnnealingFields = 0;
3720 for (i = 0; i < nr; i++)
3722 if (ir->opts.anneal_npoints[i] == 1)
3726 "Please specify at least a start and an end point for annealing\n");
3728 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3729 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3730 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3733 auto simulatedAnnealingTimes = gmx::splitString(inputrecStrings->anneal_time);
3735 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3738 "Found %zu annealing-time values, wanted %zu\n",
3739 simulatedAnnealingTimes.size(),
3740 numSimulatedAnnealingFields);
3742 auto simulatedAnnealingTemperatures = gmx::splitString(inputrecStrings->anneal_temp);
3743 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3746 "Found %zu annealing-temp values, wanted %zu\n",
3747 simulatedAnnealingTemperatures.size(),
3748 numSimulatedAnnealingFields);
3751 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3752 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3753 convertReals(wi, simulatedAnnealingTimes, "anneal-time", allSimulatedAnnealingTimes.data());
3755 simulatedAnnealingTemperatures,
3757 allSimulatedAnnealingTemperatures.data());
3758 for (i = 0, k = 0; i < nr; i++)
3760 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3762 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3763 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3766 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3768 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3774 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3777 "Annealing timepoints out of order: t=%f comes after "
3779 ir->opts.anneal_time[i][j],
3780 ir->opts.anneal_time[i][j - 1]);
3783 if (ir->opts.anneal_temp[i][j] < 0)
3786 "Found negative temperature in annealing: %f\n",
3787 ir->opts.anneal_temp[i][j]);
3792 /* Print out some summary information, to make sure we got it right */
3793 for (i = 0; i < nr; i++)
3795 if (ir->opts.annealing[i] != SimulatedAnnealing::No)
3797 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3799 "Simulated annealing for group %s: %s, %d timepoints\n",
3800 *(groups->groupNames[j]),
3801 enumValueToString(ir->opts.annealing[i]),
3802 ir->opts.anneal_npoints[i]);
3803 fprintf(stderr, "Time (ps) Temperature (K)\n");
3804 /* All terms except the last one */
3805 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3809 ir->opts.anneal_time[i][j],
3810 ir->opts.anneal_temp[i][j]);
3813 /* Finally the last one */
3814 j = ir->opts.anneal_npoints[i] - 1;
3815 if (ir->opts.annealing[i] == SimulatedAnnealing::Single)
3819 ir->opts.anneal_time[i][j],
3820 ir->opts.anneal_temp[i][j]);
3826 ir->opts.anneal_time[i][j],
3827 ir->opts.anneal_temp[i][j]);
3828 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3831 "There is a temperature jump when your annealing "
3843 for (int i = 1; i < ir->pull->ngroup; i++)
3845 const int gid = search_string(
3846 inputrecStrings->pullGroupNames[i].c_str(), defaultIndexGroups->nr, gnames);
3847 GMX_ASSERT(defaultIndexGroups, "Must have initialized default index groups");
3848 atomGroupRangeValidation(natoms, gid, *defaultIndexGroups);
3851 process_pull_groups(ir->pull->group, inputrecStrings->pullGroupNames, defaultIndexGroups, gnames);
3853 checkPullCoords(ir->pull->group, ir->pull->coord);
3858 make_rotation_groups(ir->rot, inputrecStrings->rotateGroupNames, defaultIndexGroups, gnames);
3861 if (ir->eSwapCoords != SwapType::No)
3863 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3866 /* Make indices for IMD session */
3869 make_IMD_group(ir->imd, inputrecStrings->imd_grp, defaultIndexGroups, gnames);
3872 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3873 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3874 mdModulesNotifiers.preProcessingNotifier_.notify(defaultIndexGroupsAndNames);
3876 auto freezeDims = gmx::splitString(inputrecStrings->frdim);
3877 auto freezeGroupNames = gmx::splitString(inputrecStrings->freeze);
3878 if (freezeDims.size() != DIM * freezeGroupNames.size())
3881 "Invalid Freezing input: %zu groups and %zu freeze values",
3882 freezeGroupNames.size(),
3885 do_numbering(natoms,
3890 SimulationAtomGroupType::Freeze,
3895 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3896 ir->opts.ngfrz = nr;
3897 snew(ir->opts.nFreeze, nr);
3898 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3900 for (j = 0; (j < DIM); j++, k++)
3902 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3903 if (!ir->opts.nFreeze[i][j])
3905 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3908 "Please use Y(ES) or N(O) for freezedim only "
3910 freezeDims[k].c_str());
3911 warning(wi, warn_buf);
3916 for (; (i < nr); i++)
3918 for (j = 0; (j < DIM); j++)
3920 ir->opts.nFreeze[i][j] = 0;
3924 auto energyGroupNames = gmx::splitString(inputrecStrings->energy);
3925 do_numbering(natoms,
3930 SimulationAtomGroupType::EnergyOutput,
3935 add_wall_energrps(groups, ir->nwall, symtab);
3936 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3937 auto vcmGroupNames = gmx::splitString(inputrecStrings->vcm);
3938 do_numbering(natoms,
3943 SimulationAtomGroupType::MassCenterVelocityRemoval,
3945 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART,
3949 if (ir->comm_mode != ComRemovalAlgorithm::No)
3951 checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
3954 /* Now we have filled the freeze struct, so we can calculate NRDF */
3955 calc_nrdf(mtop, ir, gnames);
3957 auto user1GroupNames = gmx::splitString(inputrecStrings->user1);
3958 do_numbering(natoms,
3963 SimulationAtomGroupType::User1,
3968 auto user2GroupNames = gmx::splitString(inputrecStrings->user2);
3969 do_numbering(natoms,
3974 SimulationAtomGroupType::User2,
3979 auto compressedXGroupNames = gmx::splitString(inputrecStrings->x_compressed_groups);
3980 do_numbering(natoms,
3982 compressedXGroupNames,
3985 SimulationAtomGroupType::CompressedPositionOutput,
3990 auto orirefFitGroupNames = gmx::splitString(inputrecStrings->orirefitgrp);
3991 do_numbering(natoms,
3993 orirefFitGroupNames,
3996 SimulationAtomGroupType::OrientationRestraintsFit,
4002 /* MiMiC QMMM input processing */
4003 auto qmGroupNames = gmx::splitString(inputrecStrings->QMMM);
4004 if (qmGroupNames.size() > 1)
4006 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
4008 /* group rest, if any, is always MM! */
4009 do_numbering(natoms,
4014 SimulationAtomGroupType::QuantumMechanics,
4019 ir->opts.ngQM = qmGroupNames.size();
4021 /* end of MiMiC QMMM input */
4025 for (auto group : gmx::keysOf(groups->groups))
4027 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
4028 for (const auto& entry : groups->groups[group])
4030 fprintf(stderr, " %s", *(groups->groupNames[entry]));
4032 fprintf(stderr, "\n");
4036 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
4037 snew(ir->opts.egp_flags, nr * nr);
4039 bExcl = do_egp_flag(ir, groups, "energygrp-excl", inputrecStrings->egpexcl, EGP_EXCL);
4040 if (bExcl && ir->cutoff_scheme == CutoffScheme::Verlet)
4042 warning_error(wi, "Energy group exclusions are currently not supported");
4044 if (bExcl && EEL_FULL(ir->coulombtype))
4046 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
4049 bTable = do_egp_flag(ir, groups, "energygrp-table", inputrecStrings->egptable, EGP_TABLE);
4050 if (bTable && !(ir->vdwtype == VanDerWaalsType::User)
4051 && !(ir->coulombtype == CoulombInteractionType::User)
4052 && !(ir->coulombtype == CoulombInteractionType::PmeUser)
4053 && !(ir->coulombtype == CoulombInteractionType::PmeUserSwitch))
4056 "Can only have energy group pair tables in combination with user tables for VdW "
4060 /* final check before going out of scope if simulated tempering variables
4061 * need to be set to default values.
4063 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
4065 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
4068 "the value for nstexpanded was not specified for "
4069 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
4070 "by default, but it is recommended to set it to an explicit value!",
4071 ir->expandedvals->nstexpanded));
4073 for (i = 0; (i < defaultIndexGroups->nr); i++)
4078 done_blocka(defaultIndexGroups);
4079 sfree(defaultIndexGroups);
4083 static void check_disre(const gmx_mtop_t& mtop)
4085 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
4087 const gmx_ffparams_t& ffparams = mtop.ffparams;
4090 for (int i = 0; i < ffparams.numTypes(); i++)
4092 int ftype = ffparams.functype[i];
4093 if (ftype == F_DISRES)
4095 int label = ffparams.iparams[i].disres.label;
4096 if (label == old_label)
4098 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
4107 "Found %d double distance restraint indices,\n"
4108 "probably the parameters for multiple pairs in one restraint "
4109 "are not identical\n",
4115 static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t& sys, const bool posres_only, ivec AbsRef)
4118 const t_iparams* pr;
4125 for (d = 0; d < DIM; d++)
4127 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
4129 /* Check for freeze groups */
4130 for (g = 0; g < ir->opts.ngfrz; g++)
4132 for (d = 0; d < DIM; d++)
4134 if (ir->opts.nFreeze[g][d] != 0)
4142 /* Check for position restraints */
4143 for (const auto ilist : IListRange(sys))
4145 if (ilist.nmol() > 0 && (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
4147 for (int i = 0; i < ilist.list()[F_POSRES].size(); i += 2)
4149 pr = &sys.ffparams.iparams[ilist.list()[F_POSRES].iatoms[i]];
4150 for (d = 0; d < DIM; d++)
4152 if (pr->posres.fcA[d] != 0)
4158 for (i = 0; i < ilist.list()[F_FBPOSRES].size(); i += 2)
4160 /* Check for flat-bottom posres */
4161 pr = &sys.ffparams.iparams[ilist.list()[F_FBPOSRES].iatoms[i]];
4162 if (pr->fbposres.k != 0)
4164 switch (pr->fbposres.geom)
4166 case efbposresSPHERE: AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1; break;
4167 case efbposresCYLINDERX: AbsRef[YY] = AbsRef[ZZ] = 1; break;
4168 case efbposresCYLINDERY: AbsRef[XX] = AbsRef[ZZ] = 1; break;
4169 case efbposresCYLINDER:
4170 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
4171 case efbposresCYLINDERZ: AbsRef[XX] = AbsRef[YY] = 1; break;
4172 case efbposresX: /* d=XX */
4173 case efbposresY: /* d=YY */
4174 case efbposresZ: /* d=ZZ */
4175 d = pr->fbposres.geom - efbposresX;
4180 " Invalid geometry for flat-bottom position restraint.\n"
4181 "Expected nr between 1 and %d. Found %d\n",
4190 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
4193 static void check_combination_rule_differences(const gmx_mtop_t& mtop,
4195 bool* bC6ParametersWorkWithGeometricRules,
4196 bool* bC6ParametersWorkWithLBRules,
4197 bool* bLBRulesPossible)
4199 int ntypes, tpi, tpj;
4202 double c6i, c6j, c12i, c12j;
4203 double c6, c6_geometric, c6_LB;
4204 double sigmai, sigmaj, epsi, epsj;
4205 bool bCanDoLBRules, bCanDoGeometricRules;
4208 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
4209 * force-field floating point parameters.
4212 ptr = getenv("GMX_LJCOMB_TOL");
4216 double gmx_unused canary;
4218 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
4221 FARGS, "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
4226 *bC6ParametersWorkWithLBRules = TRUE;
4227 *bC6ParametersWorkWithGeometricRules = TRUE;
4228 bCanDoLBRules = TRUE;
4229 ntypes = mtop.ffparams.atnr;
4230 snew(typecount, ntypes);
4231 gmx_mtop_count_atomtypes(mtop, state, typecount);
4232 *bLBRulesPossible = TRUE;
4233 for (tpi = 0; tpi < ntypes; ++tpi)
4235 c6i = mtop.ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
4236 c12i = mtop.ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
4237 for (tpj = tpi; tpj < ntypes; ++tpj)
4239 c6j = mtop.ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
4240 c12j = mtop.ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
4241 c6 = mtop.ffparams.iparams[ntypes * tpi + tpj].lj.c6;
4242 c6_geometric = std::sqrt(c6i * c6j);
4243 if (!gmx_numzero(c6_geometric))
4245 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4247 sigmai = gmx::sixthroot(c12i / c6i);
4248 sigmaj = gmx::sixthroot(c12j / c6j);
4249 epsi = c6i * c6i / (4.0 * c12i);
4250 epsj = c6j * c6j / (4.0 * c12j);
4251 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4255 *bLBRulesPossible = FALSE;
4256 c6_LB = c6_geometric;
4258 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4263 *bC6ParametersWorkWithLBRules = FALSE;
4266 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4268 if (!bCanDoGeometricRules)
4270 *bC6ParametersWorkWithGeometricRules = FALSE;
4277 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t& mtop, warninp_t wi)
4279 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4281 check_combination_rule_differences(
4282 mtop, 0, &bC6ParametersWorkWithGeometricRules, &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4283 if (ir->ljpme_combination_rule == LongRangeVdW::LB)
4285 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4288 "You are using arithmetic-geometric combination rules "
4289 "in LJ-PME, but your non-bonded C6 parameters do not "
4290 "follow these rules.");
4295 if (!bC6ParametersWorkWithGeometricRules)
4297 if (ir->eDispCorr != DispersionCorrectionType::No)
4300 "You are using geometric combination rules in "
4301 "LJ-PME, but your non-bonded C6 parameters do "
4302 "not follow these rules. "
4303 "This will introduce very small errors in the forces and energies in "
4304 "your simulations. Dispersion correction will correct total energy "
4305 "and/or pressure for isotropic systems, but not forces or surface "
4311 "You are using geometric combination rules in "
4312 "LJ-PME, but your non-bonded C6 parameters do "
4313 "not follow these rules. "
4314 "This will introduce very small errors in the forces and energies in "
4315 "your simulations. If your system is homogeneous, consider using "
4316 "dispersion correction "
4317 "for the total energy and pressure.");
4323 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4325 // Not meeting MTS requirements should have resulted in a fatal error, so we can assert here
4326 GMX_ASSERT(gmx::checkMtsRequirements(*ir).empty(), "All MTS requirements should be met here");
4328 char err_buf[STRLEN];
4331 gmx_mtop_atomloop_block_t aloopb;
4333 char warn_buf[STRLEN];
4335 set_warning_line(wi, mdparin, -1);
4337 if (absolute_reference(ir, *sys, false, AbsRef))
4340 "Removing center of mass motion in the presence of position restraints might "
4341 "cause artifacts. When you are using position restraints to equilibrate a "
4342 "macro-molecule, the artifacts are usually negligible.");
4345 if (ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0 && ir->nstlist > 1
4346 && ((EI_MD(ir->eI) || EI_SD(ir->eI))
4347 && (ir->etc == TemperatureCoupling::VRescale || ir->etc == TemperatureCoupling::Berendsen)))
4349 /* Check if a too small Verlet buffer might potentially
4350 * cause more drift than the thermostat can couple off.
4352 /* Temperature error fraction for warning and suggestion */
4353 const real T_error_warn = 0.002;
4354 const real T_error_suggest = 0.001;
4355 /* For safety: 2 DOF per atom (typical with constraints) */
4356 const real nrdf_at = 2;
4357 real T, tau, max_T_error;
4362 for (i = 0; i < ir->opts.ngtc; i++)
4364 T = std::max(T, ir->opts.ref_t[i]);
4365 tau = std::max(tau, ir->opts.tau_t[i]);
4369 /* This is a worst case estimate of the temperature error,
4370 * assuming perfect buffer estimation and no cancelation
4371 * of errors. The factor 0.5 is because energy distributes
4372 * equally over Ekin and Epot.
4374 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * gmx::c_boltz * T);
4375 if (max_T_error > T_error_warn)
4378 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4379 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4380 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4381 "%.0e or decrease tau_t.",
4386 100 * T_error_suggest,
4387 ir->verletbuf_tol * T_error_suggest / max_T_error);
4388 warning(wi, warn_buf);
4393 if (ETC_ANDERSEN(ir->etc))
4397 for (i = 0; i < ir->opts.ngtc; i++)
4400 "all tau_t must currently be equal using Andersen temperature control, "
4401 "violated for group %d",
4403 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4405 "all tau_t must be positive using Andersen temperature control, "
4409 CHECK(ir->opts.tau_t[i] < 0);
4412 if (ir->etc == TemperatureCoupling::AndersenMassive && ir->comm_mode != ComRemovalAlgorithm::No)
4414 for (i = 0; i < ir->opts.ngtc; i++)
4416 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4418 "tau_t/delta_t for group %d for temperature control method %s must be a "
4419 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4420 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4423 enumValueToString(ir->etc),
4427 CHECK(nsteps % ir->nstcomm != 0);
4432 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != IntegrationAlgorithm::BD
4433 && ir->comm_mode == ComRemovalAlgorithm::No
4434 && !(absolute_reference(ir, *sys, FALSE, AbsRef) || ir->nsteps <= 10) && !ETC_ANDERSEN(ir->etc))
4437 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4438 "rounding errors can lead to build up of kinetic energy of the center of mass");
4441 if (ir->epc == PressureCoupling::ParrinelloRahman && ir->etc == TemperatureCoupling::NoseHoover)
4444 for (int g = 0; g < ir->opts.ngtc; g++)
4446 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4448 if (ir->tau_p < 1.9 * tau_t_max)
4450 std::string message = gmx::formatString(
4451 "With %s T-coupling and %s p-coupling, "
4452 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4453 enumValueToString(ir->etc),
4454 enumValueToString(ir->epc),
4459 warning(wi, message.c_str());
4463 /* Check for pressure coupling with absolute position restraints */
4464 if (ir->epc != PressureCoupling::No && ir->refcoord_scaling == RefCoordScaling::No)
4466 absolute_reference(ir, *sys, TRUE, AbsRef);
4468 for (m = 0; m < DIM; m++)
4470 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4473 "You are using pressure coupling with absolute position restraints, "
4474 "this will give artifacts. Use the refcoord_scaling option.");
4482 aloopb = gmx_mtop_atomloop_block_init(*sys);
4484 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4486 if (atom->q != 0 || atom->qB != 0)
4494 if (EEL_FULL(ir->coulombtype))
4497 "You are using full electrostatics treatment %s for a system without charges.\n"
4498 "This costs a lot of performance for just processing zeros, consider using %s "
4500 enumValueToString(ir->coulombtype),
4501 enumValueToString(CoulombInteractionType::Cut));
4502 warning(wi, err_buf);
4507 if (ir->coulombtype == CoulombInteractionType::Cut && ir->rcoulomb > 0)
4510 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4511 "You might want to consider using %s electrostatics.\n",
4512 enumValueToString(CoulombInteractionType::Pme));
4513 warning_note(wi, err_buf);
4517 /* Check if combination rules used in LJ-PME are the same as in the force field */
4518 if (EVDW_PME(ir->vdwtype))
4520 check_combination_rules(ir, *sys, wi);
4523 /* Generalized reaction field */
4524 if (ir->coulombtype == CoulombInteractionType::GRFNotused)
4527 "Generalized reaction-field electrostatics is no longer supported. "
4528 "You can use normal reaction-field instead and compute the reaction-field "
4529 "constant by hand.");
4532 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->sc_alpha != 0
4533 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4535 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4543 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4545 if (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0)
4547 absolute_reference(ir, *sys, FALSE, AbsRef);
4548 for (m = 0; m < DIM; m++)
4550 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4553 "You are using an absolute reference for pulling, but the rest of "
4554 "the system does not have an absolute reference. This will lead to "
4563 for (i = 0; i < 3; i++)
4565 for (m = 0; m <= i; m++)
4567 if ((ir->epc != PressureCoupling::No && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4569 for (c = 0; c < ir->pull->ncoord; c++)
4571 if (ir->pull->coord[c].eGeom == PullGroupGeometry::DirectionPBC
4572 && ir->pull->coord[c].vec[m] != 0)
4575 "Can not have dynamic box while using pull geometry '%s' "
4577 enumValueToString(ir->pull->coord[c].eGeom),
4589 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4591 char warn_buf[STRLEN];
4594 ptr = check_box(ir->pbcType, box);
4597 warning_error(wi, ptr);
4600 if (bHasNormalConstraints && ir->eConstrAlg == ConstraintAlgorithm::Shake)
4602 if (ir->shake_tol <= 0.0)
4604 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4605 warning_error(wi, warn_buf);
4609 if ((ir->eConstrAlg == ConstraintAlgorithm::Lincs) && bHasNormalConstraints)
4611 /* If we have Lincs constraints: */
4612 if (ir->eI == IntegrationAlgorithm::MD && ir->etc == TemperatureCoupling::No
4613 && ir->eConstrAlg == ConstraintAlgorithm::Lincs && ir->nLincsIter == 1)
4616 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4617 warning_note(wi, warn_buf);
4620 if ((ir->eI == IntegrationAlgorithm::CG || ir->eI == IntegrationAlgorithm::LBFGS)
4621 && (ir->nProjOrder < 8))
4624 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4625 enumValueToString(ir->eI));
4626 warning_note(wi, warn_buf);
4628 if (ir->epc == PressureCoupling::Mttk)
4630 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4634 if (bHasAnyConstraints && ir->epc == PressureCoupling::Mttk)
4636 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4639 if (ir->LincsWarnAngle > 90.0)
4641 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4642 warning(wi, warn_buf);
4643 ir->LincsWarnAngle = 90.0;
4646 if (ir->pbcType != PbcType::No)
4648 if (ir->nstlist == 0)
4651 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4652 "atoms might cause the simulation to crash.");
4654 if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
4657 "ERROR: The cut-off length is longer than half the shortest box vector or "
4658 "longer than the smallest box diagonal element. Increase the box size or "
4659 "decrease rlist.\n");
4660 warning_error(wi, warn_buf);