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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/mdmodulenotification.h"
90 #include "gromacs/utility/smalloc.h"
91 #include "gromacs/utility/strconvert.h"
92 #include "gromacs/utility/stringcompare.h"
93 #include "gromacs/utility/stringutil.h"
94 #include "gromacs/utility/textwriter.h"
99 /* Resource parameters
100 * Do not change any of these until you read the instruction
101 * in readinp.h. Some cpp's do not take spaces after the backslash
102 * (like the c-shell), which will give you a very weird compiler
106 struct gmx_inputrec_strings
108 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN], freeze[STRLEN], frdim[STRLEN],
109 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
110 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
111 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
112 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::string> fep_lambda;
113 char lambda_weights[STRLEN];
114 std::vector<std::string> pullGroupNames;
115 std::vector<std::string> rotateGroupNames;
116 char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
119 static gmx_inputrec_strings* inputrecStrings = nullptr;
121 void init_inputrec_strings()
126 "Attempted to call init_inputrec_strings before calling done_inputrec_strings. "
127 "Only one inputrec (i.e. .mdp file) can be parsed at a time.");
129 inputrecStrings = new gmx_inputrec_strings();
132 void done_inputrec_strings()
134 delete inputrecStrings;
135 inputrecStrings = nullptr;
141 egrptpALL, /* All particles have to be a member of a group. */
142 egrptpALL_GENREST, /* A rest group with name is generated for particles *
143 * that are not part of any group. */
144 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
145 * for the rest group. */
146 egrptpONE /* Merge all selected groups into one group, *
147 * make a rest group for the remaining particles. */
150 static const char* constraints[eshNR + 1] = { "none", "h-bonds", "all-bonds",
151 "h-angles", "all-angles", nullptr };
153 static const char* couple_lam[ecouplamNR + 1] = { "vdw-q", "vdw", "q", "none", nullptr };
155 static void getSimTemps(int ntemps, t_simtemp* simtemp, gmx::ArrayRef<double> temperature_lambdas)
160 for (i = 0; i < ntemps; i++)
162 /* simple linear scaling -- allows more control */
163 if (simtemp->eSimTempScale == SimulatedTempering::Linear)
165 simtemp->temperatures[i] =
167 + (simtemp->simtemp_high - simtemp->simtemp_low) * temperature_lambdas[i];
169 else if (simtemp->eSimTempScale
170 == SimulatedTempering::Geometric) /* should give roughly equal acceptance for constant heat capacity . . . */
172 simtemp->temperatures[i] = simtemp->simtemp_low
173 * std::pow(simtemp->simtemp_high / simtemp->simtemp_low,
174 static_cast<real>((1.0 * i) / (ntemps - 1)));
176 else if (simtemp->eSimTempScale == SimulatedTempering::Exponential)
178 simtemp->temperatures[i] = simtemp->simtemp_low
179 + (simtemp->simtemp_high - simtemp->simtemp_low)
180 * (std::expm1(temperature_lambdas[i]) / std::expm1(1.0));
185 sprintf(errorstr, "eSimTempScale=%s not defined", enumValueToString(simtemp->eSimTempScale));
186 gmx_fatal(FARGS, "%s", errorstr);
192 static void _low_check(bool b, const char* s, warninp_t wi)
196 warning_error(wi, s);
200 static void check_nst(const char* desc_nst, int nst, const char* desc_p, int* p, warninp_t wi)
204 if (*p > 0 && *p % nst != 0)
206 /* Round up to the next multiple of nst */
207 *p = ((*p) / nst + 1) * nst;
208 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n", desc_p, desc_nst, desc_p, *p);
213 //! Convert legacy mdp entries to modern ones.
214 static void process_interaction_modifier(InteractionModifiers* eintmod)
216 if (*eintmod == InteractionModifiers::PotShiftVerletUnsupported)
218 *eintmod = InteractionModifiers::PotShift;
222 void check_ir(const char* mdparin,
223 const gmx::MdModulesNotifier& mdModulesNotifier,
227 /* Check internal consistency.
228 * NOTE: index groups are not set here yet, don't check things
229 * like temperature coupling group options here, but in triple_check
232 /* Strange macro: first one fills the err_buf, and then one can check
233 * the condition, which will print the message and increase the error
236 #define CHECK(b) _low_check(b, err_buf, wi)
237 char err_buf[256], warn_buf[STRLEN];
240 t_lambda* fep = ir->fepvals.get();
241 t_expanded* expand = ir->expandedvals.get();
243 set_warning_line(wi, mdparin, -1);
245 /* We cannot check MTS requirements with an invalid MTS setup
246 * and we will already have generated errors with an invalid MTS setup.
248 if (gmx::haveValidMtsSetup(*ir))
250 std::vector<std::string> errorMessages = gmx::checkMtsRequirements(*ir);
252 for (const auto& errorMessage : errorMessages)
254 warning_error(wi, errorMessage.c_str());
258 if (ir->coulombtype == CoulombInteractionType::RFNecUnsupported)
260 std::string message =
261 gmx::formatString("%s electrostatics is no longer supported",
262 enumValueToString(CoulombInteractionType::RFNecUnsupported));
263 warning_error(wi, message);
266 /* BASIC CUT-OFF STUFF */
267 if (ir->rcoulomb < 0)
269 warning_error(wi, "rcoulomb should be >= 0");
273 warning_error(wi, "rvdw should be >= 0");
275 if (ir->rlist < 0 && !(ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0))
277 warning_error(wi, "rlist should be >= 0");
280 "nstlist can not be smaller than 0. (If you were trying to use the heuristic "
281 "neighbour-list update scheme for efficient buffering for improved energy "
282 "conservation, please use the Verlet cut-off scheme instead.)");
283 CHECK(ir->nstlist < 0);
285 process_interaction_modifier(&ir->coulomb_modifier);
286 process_interaction_modifier(&ir->vdw_modifier);
288 if (ir->cutoff_scheme == CutoffScheme::Group)
291 "The group cutoff scheme has been removed since GROMACS 2020. "
292 "Please use the Verlet cutoff scheme.");
294 if (ir->cutoff_scheme == CutoffScheme::Verlet)
298 /* Normal Verlet type neighbor-list, currently only limited feature support */
299 if (inputrec2nboundeddim(ir) < 3)
301 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
304 // We don't (yet) have general Verlet kernels for rcoulomb!=rvdw
305 if (ir->rcoulomb != ir->rvdw)
307 // Since we have PME coulomb + LJ cut-off kernels with rcoulomb>rvdw
308 // for PME load balancing, we can support this exception.
309 bool bUsesPmeTwinRangeKernel =
310 (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == VanDerWaalsType::Cut
311 && ir->rcoulomb > ir->rvdw);
312 if (!bUsesPmeTwinRangeKernel)
315 "With Verlet lists rcoulomb!=rvdw is not supported (except for "
316 "rcoulomb>rvdw with PME electrostatics)");
320 if (ir->vdwtype == VanDerWaalsType::Shift || ir->vdwtype == VanDerWaalsType::Switch)
322 if (ir->vdw_modifier == InteractionModifiers::None
323 || ir->vdw_modifier == InteractionModifiers::PotShift)
326 (ir->vdwtype == VanDerWaalsType::Shift ? InteractionModifiers::ForceSwitch
327 : InteractionModifiers::PotSwitch);
330 "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and "
332 enumValueToString(ir->vdwtype),
333 enumValueToString(VanDerWaalsType::Cut),
334 enumValueToString(ir->vdw_modifier));
335 warning_note(wi, warn_buf);
337 ir->vdwtype = VanDerWaalsType::Cut;
342 "Unsupported combination of vdwtype=%s and vdw_modifier=%s",
343 enumValueToString(ir->vdwtype),
344 enumValueToString(ir->vdw_modifier));
345 warning_error(wi, warn_buf);
349 if (!(ir->vdwtype == VanDerWaalsType::Cut || ir->vdwtype == VanDerWaalsType::Pme))
352 "With Verlet lists only cut-off and PME LJ interactions are supported");
354 if (!(ir->coulombtype == CoulombInteractionType::Cut || EEL_RF(ir->coulombtype)
355 || EEL_PME(ir->coulombtype) || ir->coulombtype == CoulombInteractionType::Ewald))
358 "With Verlet lists only cut-off, reaction-field, PME and Ewald "
359 "electrostatics are supported");
361 if (!(ir->coulomb_modifier == InteractionModifiers::None
362 || ir->coulomb_modifier == InteractionModifiers::PotShift))
364 sprintf(warn_buf, "coulomb_modifier=%s is not supported", enumValueToString(ir->coulomb_modifier));
365 warning_error(wi, warn_buf);
368 if (EEL_USER(ir->coulombtype))
371 "Coulomb type %s is not supported with the verlet scheme",
372 enumValueToString(ir->coulombtype));
373 warning_error(wi, warn_buf);
376 if (ir->nstlist <= 0)
378 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
381 if (ir->nstlist < 10)
384 "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note "
385 "that with the Verlet scheme, nstlist has no effect on the accuracy of "
389 rc_max = std::max(ir->rvdw, ir->rcoulomb);
393 /* With TPI we set the pairlist cut-off later using the radius of the insterted molecule */
394 ir->verletbuf_tol = 0;
397 else if (ir->verletbuf_tol <= 0)
399 if (ir->verletbuf_tol == 0)
401 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
404 if (ir->rlist < rc_max)
407 "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
410 if (ir->rlist == rc_max && ir->nstlist > 1)
414 "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet "
415 "buffer. The cluster pair list does have a buffering effect, but choosing "
416 "a larger rlist might be necessary for good energy conservation.");
421 if (ir->rlist > rc_max)
424 "You have set rlist larger than the interaction cut-off, but you also "
425 "have verlet-buffer-tolerance > 0. Will set rlist using "
426 "verlet-buffer-tolerance.");
429 if (ir->nstlist == 1)
431 /* No buffer required */
436 if (EI_DYNAMICS(ir->eI))
438 if (inputrec2nboundeddim(ir) < 3)
441 "The box volume is required for calculating rlist from the "
442 "energy drift with verlet-buffer-tolerance > 0. You are "
443 "using at least one unbounded dimension, so no volume can be "
444 "computed. Either use a finite box, or set rlist yourself "
445 "together with verlet-buffer-tolerance = -1.");
447 /* Set rlist temporarily so we can continue processing */
452 /* Set the buffer to 5% of the cut-off */
453 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics) * rc_max;
459 /* GENERAL INTEGRATOR STUFF */
462 if (ir->etc != TemperatureCoupling::No)
464 if (EI_RANDOM(ir->eI))
467 "Setting tcoupl from '%s' to 'no'. %s handles temperature coupling "
468 "implicitly. See the documentation for more information on which "
469 "parameters affect temperature for %s.",
470 enumValueToString(ir->etc),
471 enumValueToString(ir->eI),
472 enumValueToString(ir->eI));
477 "Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to "
479 enumValueToString(ir->etc),
480 enumValueToString(ir->eI));
482 warning_note(wi, warn_buf);
484 ir->etc = TemperatureCoupling::No;
486 if (ir->eI == IntegrationAlgorithm::VVAK)
489 "Integrator method %s is implemented primarily for validation purposes; for "
490 "molecular dynamics, you should probably be using %s or %s",
491 enumValueToString(IntegrationAlgorithm::VVAK),
492 enumValueToString(IntegrationAlgorithm::MD),
493 enumValueToString(IntegrationAlgorithm::VV));
494 warning_note(wi, warn_buf);
496 if (!EI_DYNAMICS(ir->eI))
498 if (ir->epc != PressureCoupling::No)
501 "Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.",
502 enumValueToString(ir->epc),
503 enumValueToString(ir->eI));
504 warning_note(wi, warn_buf);
506 ir->epc = PressureCoupling::No;
508 if (EI_DYNAMICS(ir->eI))
510 if (ir->nstcalcenergy < 0)
512 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
513 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
515 /* nstcalcenergy larger than nstener does not make sense.
516 * We ideally want nstcalcenergy=nstener.
520 ir->nstcalcenergy = std::gcd(ir->nstenergy, ir->nstlist);
524 ir->nstcalcenergy = ir->nstenergy;
528 else if ((ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy)
529 || (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl > 0
530 && (ir->nstcalcenergy > ir->fepvals->nstdhdl)))
533 const char* nsten = "nstenergy";
534 const char* nstdh = "nstdhdl";
535 const char* min_name = nsten;
536 int min_nst = ir->nstenergy;
538 /* find the smallest of ( nstenergy, nstdhdl ) */
539 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl > 0
540 && (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
542 min_nst = ir->fepvals->nstdhdl;
545 /* If the user sets nstenergy small, we should respect that */
546 sprintf(warn_buf, "Setting nstcalcenergy (%d) equal to %s (%d)", ir->nstcalcenergy, min_name, min_nst);
547 warning_note(wi, warn_buf);
548 ir->nstcalcenergy = min_nst;
551 if (ir->epc != PressureCoupling::No)
553 if (ir->nstpcouple < 0)
555 ir->nstpcouple = ir_optimal_nstpcouple(ir);
557 if (ir->useMts && ir->nstpcouple % ir->mtsLevels.back().stepFactor != 0)
560 "With multiple time stepping, nstpcouple should be a mutiple of "
565 if (ir->nstcalcenergy > 0)
567 if (ir->efep != FreeEnergyPerturbationType::No)
569 /* nstdhdl should be a multiple of nstcalcenergy */
570 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstdhdl", &ir->fepvals->nstdhdl, wi);
574 /* nstexpanded should be a multiple of nstcalcenergy */
575 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstexpanded", &ir->expandedvals->nstexpanded, wi);
577 /* for storing exact averages nstenergy should be
578 * a multiple of nstcalcenergy
580 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstenergy", &ir->nstenergy, wi);
583 // Inquire all MdModules, if their parameters match with the energy
584 // calculation frequency
585 gmx::EnergyCalculationFrequencyErrors energyCalculationFrequencyErrors(ir->nstcalcenergy);
586 mdModulesNotifier.preProcessingNotifications_.notify(&energyCalculationFrequencyErrors);
588 // Emit all errors from the energy calculation frequency checks
589 for (const std::string& energyFrequencyErrorMessage :
590 energyCalculationFrequencyErrors.errorMessages())
592 warning_error(wi, energyFrequencyErrorMessage);
596 if (ir->nsteps == 0 && !ir->bContinuation)
599 "For a correct single-point energy evaluation with nsteps = 0, use "
600 "continuation = yes to avoid constraining the input coordinates.");
604 if ((EI_SD(ir->eI) || ir->eI == IntegrationAlgorithm::BD) && ir->bContinuation && ir->ld_seed != -1)
607 "You are doing a continuation with SD or BD, make sure that ld_seed is "
608 "different from the previous run (using ld_seed=-1 will ensure this)");
614 sprintf(err_buf, "TPI only works with pbc = %s", c_pbcTypeNames[PbcType::Xyz].c_str());
615 CHECK(ir->pbcType != PbcType::Xyz);
616 sprintf(err_buf, "with TPI nstlist should be larger than zero");
617 CHECK(ir->nstlist <= 0);
618 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
619 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
623 if ((opts->nshake > 0) && (opts->bMorse))
625 sprintf(warn_buf, "Using morse bond-potentials while constraining bonds is useless");
626 warning(wi, warn_buf);
629 if ((EI_SD(ir->eI) || ir->eI == IntegrationAlgorithm::BD) && ir->bContinuation && ir->ld_seed != -1)
632 "You are doing a continuation with SD or BD, make sure that ld_seed is "
633 "different from the previous run (using ld_seed=-1 will ensure this)");
635 /* verify simulated tempering options */
639 bool bAllTempZero = TRUE;
640 for (i = 0; i < fep->n_lambda; i++)
643 "Entry %d for %s must be between 0 and 1, instead is %g",
645 enumValueToString(FreeEnergyPerturbationCouplingType::Temperature),
646 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i]);
647 CHECK((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i] < 0)
648 || (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i]
650 if (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Temperature)][i] > 0)
652 bAllTempZero = FALSE;
655 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
656 CHECK(bAllTempZero == TRUE);
658 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
659 CHECK(ir->eI != IntegrationAlgorithm::VV);
661 /* check compatability of the temperature coupling with simulated tempering */
663 if (ir->etc == TemperatureCoupling::NoseHoover)
666 "Nose-Hoover based temperature control such as [%s] my not be "
667 "entirelyconsistent with simulated tempering",
668 enumValueToString(ir->etc));
669 warning_note(wi, warn_buf);
672 /* check that the temperatures make sense */
675 "Higher simulated tempering temperature (%g) must be >= than the simulated "
676 "tempering lower temperature (%g)",
677 ir->simtempvals->simtemp_high,
678 ir->simtempvals->simtemp_low);
679 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
682 "Higher simulated tempering temperature (%g) must be >= zero",
683 ir->simtempvals->simtemp_high);
684 CHECK(ir->simtempvals->simtemp_high <= 0);
687 "Lower simulated tempering temperature (%g) must be >= zero",
688 ir->simtempvals->simtemp_low);
689 CHECK(ir->simtempvals->simtemp_low <= 0);
692 /* verify free energy options */
694 if (ir->efep != FreeEnergyPerturbationType::No)
696 fep = ir->fepvals.get();
697 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2", fep->sc_power);
698 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
701 "The soft-core sc-r-power is %d and can only be 6. (sc-r-power 48 is no longer "
703 static_cast<int>(fep->sc_r_power));
704 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0);
707 "Can't use positive delta-lambda (%g) if initial state/lambda does not start at "
710 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
713 "Can't use positive delta-lambda (%g) with expanded ensemble simulations",
715 CHECK(fep->delta_lambda > 0 && (ir->efep == FreeEnergyPerturbationType::Expanded));
717 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
718 CHECK(!(EI_VV(ir->eI)) && (ir->efep == FreeEnergyPerturbationType::Expanded));
720 sprintf(err_buf, "Free-energy not implemented for Ewald");
721 CHECK(ir->coulombtype == CoulombInteractionType::Ewald);
723 /* check validty of lambda inputs */
724 if (fep->n_lambda == 0)
726 /* Clear output in case of no states:*/
727 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
728 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
733 "initial thermodynamic state %d does not exist, only goes to %d",
736 CHECK((fep->init_fep_state >= fep->n_lambda));
740 "Lambda state must be set, either with init-lambda-state or with init-lambda");
741 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
744 "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with "
745 "init-lambda-state or with init-lambda, but not both",
747 fep->init_fep_state);
748 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
751 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
755 for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
757 if (fep->separate_dvdl[i])
762 if (n_lambda_terms > 1)
765 "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't "
766 "use init-lambda to set lambda state (except for slow growth). Use "
767 "init-lambda-state instead.");
768 warning(wi, warn_buf);
771 if (n_lambda_terms < 2 && fep->n_lambda > 0)
774 "init-lambda is deprecated for setting lambda state (except for slow "
775 "growth). Use init-lambda-state instead.");
779 for (j = 0; j < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); j++)
781 for (i = 0; i < fep->n_lambda; i++)
783 auto enumValue = static_cast<FreeEnergyPerturbationCouplingType>(j);
785 "Entry %d for %s must be between 0 and 1, instead is %g",
787 enumValueToString(enumValue),
788 fep->all_lambda[j][i]);
789 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
793 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
795 for (i = 0; i < fep->n_lambda; i++)
798 "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while "
799 "coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to "
800 "crashes, and is not supported.",
802 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i],
803 fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i]);
804 CHECK((fep->sc_alpha > 0)
805 && (((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i] > 0.0)
806 && (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)][i] < 1.0))
807 && ((fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i] > 0.0)
808 && (fep->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)][i]
813 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
815 real sigma, lambda, r_sc;
818 /* Maximum estimate for A and B charges equal with lambda power 1 */
820 r_sc = std::pow(lambda * fep->sc_alpha * std::pow(sigma / ir->rcoulomb, fep->sc_r_power) + 1.0,
821 1.0 / fep->sc_r_power);
823 "With PME there is a minor soft core effect present at the cut-off, "
824 "proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on "
825 "energy conservation, but usually other effects dominate. With a common sigma "
826 "value of %g nm the fraction of the particle-particle potential at the cut-off "
827 "at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
833 warning_note(wi, warn_buf);
836 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
837 be treated differently, but that's the next step */
839 for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
841 auto enumValue = static_cast<FreeEnergyPerturbationCouplingType>(i);
842 for (j = 0; j < fep->n_lambda; j++)
844 sprintf(err_buf, "%s[%d] must be between 0 and 1", enumValueToString(enumValue), j);
845 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
850 if ((ir->bSimTemp) || (ir->efep == FreeEnergyPerturbationType::Expanded))
852 fep = ir->fepvals.get();
854 /* checking equilibration of weights inputs for validity */
857 "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal "
859 expand->equil_n_at_lam,
860 enumValueToString(LambdaWeightWillReachEquilibrium::NumAtLambda));
861 CHECK((expand->equil_n_at_lam > 0)
862 && (expand->elmceq != LambdaWeightWillReachEquilibrium::NumAtLambda));
865 "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to "
867 expand->equil_samples,
868 enumValueToString(LambdaWeightWillReachEquilibrium::Samples));
869 CHECK((expand->equil_samples > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Samples));
872 "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
874 enumValueToString(LambdaWeightWillReachEquilibrium::Steps));
875 CHECK((expand->equil_steps > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Steps));
878 "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
879 expand->equil_samples,
880 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta));
881 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::WLDelta));
884 "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
886 enumValueToString(LambdaWeightWillReachEquilibrium::Ratio));
887 CHECK((expand->equil_ratio > 0) && (expand->elmceq != LambdaWeightWillReachEquilibrium::Ratio));
890 "weight-equil-number-all-lambda (%d) must be a positive integer if "
891 "lmc-weights-equil=%s",
892 expand->equil_n_at_lam,
893 enumValueToString(LambdaWeightWillReachEquilibrium::NumAtLambda));
894 CHECK((expand->equil_n_at_lam <= 0)
895 && (expand->elmceq == LambdaWeightWillReachEquilibrium::NumAtLambda));
898 "weight-equil-number-samples (%d) must be a positive integer if "
899 "lmc-weights-equil=%s",
900 expand->equil_samples,
901 enumValueToString(LambdaWeightWillReachEquilibrium::Samples));
902 CHECK((expand->equil_samples <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Samples));
905 "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
907 enumValueToString(LambdaWeightWillReachEquilibrium::Steps));
908 CHECK((expand->equil_steps <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Steps));
911 "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
912 expand->equil_wl_delta,
913 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta));
914 CHECK((expand->equil_wl_delta <= 0)
915 && (expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta));
918 "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
920 enumValueToString(LambdaWeightWillReachEquilibrium::Ratio));
921 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == LambdaWeightWillReachEquilibrium::Ratio));
924 "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
925 enumValueToString(LambdaWeightWillReachEquilibrium::WLDelta),
926 enumValueToString(LambdaWeightCalculation::WL),
927 enumValueToString(LambdaWeightCalculation::WWL));
928 CHECK((expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta) && (!EWL(expand->elamstats)));
930 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
931 CHECK((expand->lmc_repeats <= 0));
932 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
933 CHECK((expand->minvarmin <= 0));
934 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
935 CHECK((expand->c_range < 0));
937 "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != "
940 expand->lmc_forced_nstart);
941 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0)
942 && (expand->elmcmove != LambdaMoveCalculation::No));
943 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
944 CHECK((expand->lmc_forced_nstart < 0));
946 "init-lambda-state (%d) must be in the interval [0,number of lambdas)",
947 fep->init_fep_state);
948 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
950 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
951 CHECK((expand->init_wl_delta < 0));
952 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
953 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
954 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
955 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
957 /* if there is no temperature control, we need to specify an MC temperature */
958 if (!integratorHasReferenceTemperature(ir)
959 && (expand->elmcmove != LambdaMoveCalculation::No) && (expand->mc_temp <= 0.0))
962 "If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set "
963 "to a positive number");
964 warning_error(wi, err_buf);
966 if (expand->nstTij > 0)
968 sprintf(err_buf, "nstlog must be non-zero");
969 CHECK(ir->nstlog == 0);
970 // Avoid modulus by zero in the case that already triggered an error exit.
974 "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
977 CHECK((expand->nstTij % ir->nstlog) != 0);
983 sprintf(err_buf, "walls only work with pbc=%s", c_pbcTypeNames[PbcType::XY].c_str());
984 CHECK(ir->nwall && ir->pbcType != PbcType::XY);
987 if (ir->pbcType != PbcType::Xyz && ir->nwall != 2)
989 if (ir->pbcType == PbcType::No)
991 if (ir->epc != PressureCoupling::No)
993 warning(wi, "Turning off pressure coupling for vacuum system");
994 ir->epc = PressureCoupling::No;
1000 "Can not have pressure coupling with pbc=%s",
1001 c_pbcTypeNames[ir->pbcType].c_str());
1002 CHECK(ir->epc != PressureCoupling::No);
1004 sprintf(err_buf, "Can not have Ewald with pbc=%s", c_pbcTypeNames[ir->pbcType].c_str());
1005 CHECK(EEL_FULL(ir->coulombtype));
1008 "Can not have dispersion correction with pbc=%s",
1009 c_pbcTypeNames[ir->pbcType].c_str());
1010 CHECK(ir->eDispCorr != DispersionCorrectionType::No);
1013 if (ir->rlist == 0.0)
1016 "can only have neighborlist cut-off zero (=infinite)\n"
1017 "with coulombtype = %s or coulombtype = %s\n"
1018 "without periodic boundary conditions (pbc = %s) and\n"
1019 "rcoulomb and rvdw set to zero",
1020 enumValueToString(CoulombInteractionType::Cut),
1021 enumValueToString(CoulombInteractionType::User),
1022 c_pbcTypeNames[PbcType::No].c_str());
1023 CHECK(((ir->coulombtype != CoulombInteractionType::Cut)
1024 && (ir->coulombtype != CoulombInteractionType::User))
1025 || (ir->pbcType != PbcType::No) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
1027 if (ir->nstlist > 0)
1030 "Simulating without cut-offs can be (slightly) faster with nstlist=0, "
1031 "nstype=simple and only one MPI rank");
1036 if (ir->nstcomm == 0)
1038 // TODO Change this behaviour. There should be exactly one way
1039 // to turn off an algorithm.
1040 ir->comm_mode = ComRemovalAlgorithm::No;
1042 if (ir->comm_mode != ComRemovalAlgorithm::No)
1044 if (ir->nstcomm < 0)
1046 // TODO Such input was once valid. Now that we've been
1047 // helpful for a few years, we should reject such input,
1048 // lest we have to support every historical decision
1051 "If you want to remove the rotation around the center of mass, you should set "
1052 "comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to "
1053 "its absolute value");
1054 ir->nstcomm = abs(ir->nstcomm);
1057 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
1060 "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting "
1061 "nstcomm to nstcalcenergy");
1062 ir->nstcomm = ir->nstcalcenergy;
1065 if (ir->comm_mode == ComRemovalAlgorithm::Angular)
1068 "Can not remove the rotation around the center of mass with periodic "
1070 CHECK(ir->bPeriodicMols);
1071 if (ir->pbcType != PbcType::No)
1074 "Removing the rotation around the center of mass in a periodic system, "
1075 "this can lead to artifacts. Only use this on a single (cluster of) "
1076 "molecules. This cluster should not cross periodic boundaries.");
1081 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->pbcType == PbcType::No
1082 && ir->comm_mode != ComRemovalAlgorithm::Angular)
1085 "Tumbling and flying ice-cubes: We are not removing rotation around center of mass "
1086 "in a non-periodic system. You should probably set comm_mode = ANGULAR or use "
1088 enumValueToString(IntegrationAlgorithm::SD1));
1089 warning_note(wi, warn_buf);
1092 /* TEMPERATURE COUPLING */
1093 if (ir->etc == TemperatureCoupling::Yes)
1095 ir->etc = TemperatureCoupling::Berendsen;
1097 "Old option for temperature coupling given: "
1098 "changing \"yes\" to \"Berendsen\"\n");
1101 if ((ir->etc == TemperatureCoupling::NoseHoover) || (ir->epc == PressureCoupling::Mttk))
1103 if (ir->opts.nhchainlength < 1)
1106 "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to "
1108 ir->opts.nhchainlength);
1109 ir->opts.nhchainlength = 1;
1110 warning(wi, warn_buf);
1113 if (ir->etc == TemperatureCoupling::NoseHoover && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
1117 "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
1118 ir->opts.nhchainlength = 1;
1123 ir->opts.nhchainlength = 0;
1126 if (ir->eI == IntegrationAlgorithm::VVAK)
1129 "%s implemented primarily for validation, and requires nsttcouple = 1 and "
1131 enumValueToString(IntegrationAlgorithm::VVAK));
1132 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
1135 if (ETC_ANDERSEN(ir->etc))
1138 "%s temperature control not supported for integrator %s.",
1139 enumValueToString(ir->etc),
1140 enumValueToString(ir->eI));
1141 CHECK(!(EI_VV(ir->eI)));
1143 if (ir->nstcomm > 0 && (ir->etc == TemperatureCoupling::Andersen))
1146 "Center of mass removal not necessary for %s. All velocities of coupled "
1147 "groups are rerandomized periodically, so flying ice cube errors will not "
1149 enumValueToString(ir->etc));
1150 warning_note(wi, warn_buf);
1154 "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are "
1155 "randomized every time step",
1157 enumValueToString(ir->etc));
1158 CHECK(ir->nstcomm > 1 && (ir->etc == TemperatureCoupling::Andersen));
1161 if (ir->etc == TemperatureCoupling::Berendsen)
1164 "The %s thermostat does not generate the correct kinetic energy distribution. You "
1165 "might want to consider using the %s thermostat.",
1166 enumValueToString(ir->etc),
1167 enumValueToString(TemperatureCoupling::VRescale));
1168 warning_note(wi, warn_buf);
1171 if ((ir->etc == TemperatureCoupling::NoseHoover || ETC_ANDERSEN(ir->etc))
1172 && ir->epc == PressureCoupling::Berendsen)
1175 "Using Berendsen pressure coupling invalidates the "
1176 "true ensemble for the thermostat");
1177 warning(wi, warn_buf);
1180 /* PRESSURE COUPLING */
1181 if (ir->epc == PressureCoupling::Isotropic)
1183 ir->epc = PressureCoupling::Berendsen;
1185 "Old option for pressure coupling given: "
1186 "changing \"Isotropic\" to \"Berendsen\"\n");
1189 if (ir->epc != PressureCoupling::No)
1191 dt_pcoupl = ir->nstpcouple * ir->delta_t;
1193 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1194 CHECK(ir->tau_p <= 0);
1196 if (ir->tau_p / dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10 * GMX_REAL_EPS)
1199 "For proper integration of the %s barostat, tau-p (%g) should be at least %d "
1200 "times larger than nstpcouple*dt (%g)",
1201 enumValueToString(ir->epc),
1203 pcouple_min_integration_steps(ir->epc),
1205 warning(wi, warn_buf);
1209 "compressibility must be > 0 when using pressure"
1211 enumValueToString(ir->epc));
1212 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 || ir->compress[ZZ][ZZ] < 0
1213 || (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 && ir->compress[ZZ][XX] <= 0
1214 && ir->compress[ZZ][YY] <= 0));
1216 if (PressureCoupling::ParrinelloRahman == ir->epc && opts->bGenVel)
1219 "You are generating velocities so I am assuming you "
1220 "are equilibrating a system. You are using "
1221 "%s pressure coupling, but this can be "
1222 "unstable for equilibration. If your system crashes, try "
1223 "equilibrating first with Berendsen pressure coupling. If "
1224 "you are not equilibrating the system, you can probably "
1225 "ignore this warning.",
1226 enumValueToString(ir->epc));
1227 warning(wi, warn_buf);
1233 if (ir->epc == PressureCoupling::Mttk)
1235 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1239 /* ELECTROSTATICS */
1240 /* More checks are in triple check (grompp.c) */
1242 if (ir->coulombtype == CoulombInteractionType::Switch)
1245 "coulombtype = %s is only for testing purposes and can lead to serious "
1246 "artifacts, advice: use coulombtype = %s",
1247 enumValueToString(ir->coulombtype),
1248 enumValueToString(CoulombInteractionType::RFZero));
1249 warning(wi, warn_buf);
1252 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1255 "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old "
1256 "format and exchanging epsilon-r and epsilon-rf",
1258 warning(wi, warn_buf);
1259 ir->epsilon_rf = ir->epsilon_r;
1260 ir->epsilon_r = 1.0;
1263 if (ir->epsilon_r == 0)
1266 "It is pointless to use long-range electrostatics with infinite relative "
1268 "Since you are effectively turning of electrostatics, a plain cutoff will be much "
1270 CHECK(EEL_FULL(ir->coulombtype));
1273 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1275 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1276 CHECK(ir->epsilon_r < 0);
1279 if (EEL_RF(ir->coulombtype))
1281 /* reaction field (at the cut-off) */
1283 if (ir->coulombtype == CoulombInteractionType::RFZero && ir->epsilon_rf != 0)
1286 "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1287 enumValueToString(ir->coulombtype));
1288 warning(wi, warn_buf);
1289 ir->epsilon_rf = 0.0;
1292 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1293 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) || (ir->epsilon_r == 0));
1294 if (ir->epsilon_rf == ir->epsilon_r)
1297 "Using epsilon-rf = epsilon-r with %s does not make sense",
1298 enumValueToString(ir->coulombtype));
1299 warning(wi, warn_buf);
1302 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1303 * means the interaction is zero outside rcoulomb, but it helps to
1304 * provide accurate energy conservation.
1306 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1308 if (ir_coulomb_switched(ir))
1311 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the "
1312 "potential modifier options!",
1313 enumValueToString(ir->coulombtype));
1314 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1318 if (ir->coulombtype == CoulombInteractionType::Switch || ir->coulombtype == CoulombInteractionType::Shift)
1321 "Explicit switch/shift coulomb interactions cannot be used in combination with a "
1322 "secondary coulomb-modifier.");
1323 CHECK(ir->coulomb_modifier != InteractionModifiers::None);
1325 if (ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift)
1328 "Explicit switch/shift vdw interactions cannot be used in combination with a "
1329 "secondary vdw-modifier.");
1330 CHECK(ir->vdw_modifier != InteractionModifiers::None);
1333 if (ir->coulombtype == CoulombInteractionType::Switch || ir->coulombtype == CoulombInteractionType::Shift
1334 || ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift)
1337 "The switch/shift interaction settings are just for compatibility; you will get "
1339 "performance from applying potential modifiers to your interactions!\n");
1340 warning_note(wi, warn_buf);
1343 if (ir->coulombtype == CoulombInteractionType::PmeSwitch
1344 || ir->coulomb_modifier == InteractionModifiers::PotSwitch)
1346 if (ir->rcoulomb_switch / ir->rcoulomb < 0.9499)
1348 real percentage = 100 * (ir->rcoulomb - ir->rcoulomb_switch) / ir->rcoulomb;
1350 "The switching range should be 5%% or less (currently %.2f%% using a switching "
1351 "range of %4f-%4f) for accurate electrostatic energies, energy conservation "
1352 "will be good regardless, since ewald_rtol = %g.",
1354 ir->rcoulomb_switch,
1357 warning(wi, warn_buf);
1361 if (ir->vdwtype == VanDerWaalsType::Switch || ir->vdw_modifier == InteractionModifiers::PotSwitch)
1363 if (ir->rvdw_switch == 0)
1366 "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones "
1367 "potential. This suggests it was not set in the mdp, which can lead to large "
1368 "energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw "
1369 "switching range.");
1370 warning(wi, warn_buf);
1374 if (EEL_FULL(ir->coulombtype))
1376 if (ir->coulombtype == CoulombInteractionType::PmeSwitch
1377 || ir->coulombtype == CoulombInteractionType::PmeUser
1378 || ir->coulombtype == CoulombInteractionType::PmeUserSwitch)
1381 "With coulombtype = %s, rcoulomb must be <= rlist",
1382 enumValueToString(ir->coulombtype));
1383 CHECK(ir->rcoulomb > ir->rlist);
1387 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1389 // TODO: Move these checks into the ewald module with the options class
1391 int orderMax = (ir->coulombtype == CoulombInteractionType::P3mAD ? 8 : 12);
1393 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1396 "With coulombtype = %s, you should have %d <= pme-order <= %d",
1397 enumValueToString(ir->coulombtype),
1400 warning_error(wi, warn_buf);
1404 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1406 if (ir->ewald_geometry == EwaldGeometry::ThreeD)
1409 "With pbc=%s you should use ewald-geometry=%s",
1410 c_pbcTypeNames[ir->pbcType].c_str(),
1411 enumValueToString(EwaldGeometry::ThreeDC));
1412 warning(wi, warn_buf);
1414 /* This check avoids extra pbc coding for exclusion corrections */
1415 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1416 CHECK(ir->wall_ewald_zfac < 2);
1418 if ((ir->ewald_geometry == EwaldGeometry::ThreeDC) && (ir->pbcType != PbcType::XY)
1419 && EEL_FULL(ir->coulombtype))
1422 "With %s and ewald_geometry = %s you should use pbc = %s",
1423 enumValueToString(ir->coulombtype),
1424 enumValueToString(EwaldGeometry::ThreeDC),
1425 c_pbcTypeNames[PbcType::XY].c_str());
1426 warning(wi, warn_buf);
1428 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1430 sprintf(err_buf, "Cannot have periodic molecules with epsilon_surface > 0");
1431 CHECK(ir->bPeriodicMols);
1432 sprintf(warn_buf, "With epsilon_surface > 0 all molecules should be neutral.");
1433 warning_note(wi, warn_buf);
1435 "With epsilon_surface > 0 you can only use domain decomposition "
1436 "when there are only small molecules with all bonds constrained (mdrun will check "
1438 warning_note(wi, warn_buf);
1441 if (ir_vdw_switched(ir))
1443 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1444 CHECK(ir->rvdw_switch >= ir->rvdw);
1446 if (ir->rvdw_switch < 0.5 * ir->rvdw)
1449 "You are applying a switch function to vdw forces or potentials from %g to %g "
1450 "nm, which is more than half the interaction range, whereas switch functions "
1451 "are intended to act only close to the cut-off.",
1454 warning_note(wi, warn_buf);
1458 if (ir->vdwtype == VanDerWaalsType::Pme)
1460 if (!(ir->vdw_modifier == InteractionModifiers::None
1461 || ir->vdw_modifier == InteractionModifiers::PotShift))
1464 "With vdwtype = %s, the only supported modifiers are %s and %s",
1465 enumValueToString(ir->vdwtype),
1466 enumValueToString(InteractionModifiers::PotShift),
1467 enumValueToString(InteractionModifiers::None));
1468 warning_error(wi, err_buf);
1472 if (ir->vdwtype == VanDerWaalsType::User && ir->eDispCorr != DispersionCorrectionType::No)
1475 "You have selected user tables with dispersion correction, the dispersion "
1476 "will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction "
1477 "between rvdw_switch and rvdw will not be double counted). Make sure that you "
1478 "really want dispersion correction to -C6/r^6.");
1481 if (ir->eI == IntegrationAlgorithm::LBFGS
1482 && (ir->coulombtype == CoulombInteractionType::Cut || ir->vdwtype == VanDerWaalsType::Cut)
1485 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1488 if (ir->eI == IntegrationAlgorithm::LBFGS && ir->nbfgscorr <= 0)
1490 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1493 /* IMPLICIT SOLVENT */
1494 if (ir->coulombtype == CoulombInteractionType::GBNotused)
1496 sprintf(warn_buf, "Invalid option %s for coulombtype", enumValueToString(ir->coulombtype));
1497 warning_error(wi, warn_buf);
1502 warning_error(wi, "The QMMM integration you are trying to use is no longer supported");
1507 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1510 // cosine acceleration is only supported in leap-frog
1511 if (ir->cos_accel != 0.0 && ir->eI != IntegrationAlgorithm::MD)
1513 warning_error(wi, "cos-acceleration is only supported by integrator = md");
1517 /* interpret a number of doubles from a string and put them in an array,
1518 after allocating space for them.
1519 str = the input string
1520 n = the (pre-allocated) number of doubles read
1521 r = the output array of doubles. */
1522 static std::vector<real> parse_n_real(const std::string& str, int* n, warninp_t wi)
1524 auto values = gmx::splitString(str);
1527 std::vector<real> r;
1528 for (int i = 0; i < *n; i++)
1532 r.emplace_back(gmx::fromString<real>(values[i]));
1534 catch (gmx::GromacsException&)
1537 "Invalid value " + values[i]
1538 + " in string in mdp file. Expected a real number.");
1545 static void do_fep_params(t_inputrec* ir, gmx::ArrayRef<std::string> fep_lambda, char weights[STRLEN], warninp_t wi)
1548 int i, j, max_n_lambda, nweights;
1549 t_lambda* fep = ir->fepvals.get();
1550 t_expanded* expand = ir->expandedvals.get();
1551 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, std::vector<real>> count_fep_lambdas;
1552 bool bOneLambda = TRUE;
1553 gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, int> nfep;
1555 /* FEP input processing */
1556 /* first, identify the number of lambda values for each type.
1557 All that are nonzero must have the same number */
1559 for (auto i : keysOf(nfep))
1561 count_fep_lambdas[i] = parse_n_real(fep_lambda[static_cast<int>(i)], &(nfep[i]), wi);
1564 /* now, determine the number of components. All must be either zero, or equal. */
1567 for (auto i : keysOf(nfep))
1569 if (nfep[i] > max_n_lambda)
1571 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1572 must have the same number if its not zero.*/
1577 for (auto i : keysOf(nfep))
1581 ir->fepvals->separate_dvdl[i] = FALSE;
1583 else if (nfep[i] == max_n_lambda)
1585 if (i != FreeEnergyPerturbationCouplingType::Temperature) /* we treat this differently -- not really a reason to compute
1586 the derivative with respect to the temperature currently */
1588 ir->fepvals->separate_dvdl[i] = TRUE;
1594 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1597 enumValueToString(i),
1601 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1602 ir->fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Temperature] = FALSE;
1604 /* the number of lambdas is the number we've read in, which is either zero
1605 or the same for all */
1606 fep->n_lambda = max_n_lambda;
1608 /* if init_lambda is defined, we need to set lambda */
1609 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1611 ir->fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
1613 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1614 for (auto i : keysOf(nfep))
1616 fep->all_lambda[i].resize(fep->n_lambda);
1617 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1620 for (j = 0; j < fep->n_lambda; j++)
1622 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1627 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1628 internal bookkeeping -- for now, init_lambda */
1630 if ((nfep[FreeEnergyPerturbationCouplingType::Fep] == 0) && (fep->init_lambda >= 0))
1632 for (i = 0; i < fep->n_lambda; i++)
1634 fep->all_lambda[FreeEnergyPerturbationCouplingType::Fep][i] = fep->init_lambda;
1638 /* check to see if only a single component lambda is defined, and soft core is defined.
1639 In this case, turn on coulomb soft core */
1641 if (max_n_lambda == 0)
1647 for (auto i : keysOf(nfep))
1649 if ((nfep[i] != 0) && (i != FreeEnergyPerturbationCouplingType::Fep))
1655 if ((bOneLambda) && (fep->sc_alpha > 0))
1657 fep->bScCoul = TRUE;
1660 /* Fill in the others with the efptFEP if they are not explicitly
1661 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1662 they are all zero. */
1664 for (auto i : keysOf(nfep))
1666 if ((nfep[i] == 0) && (i != FreeEnergyPerturbationCouplingType::Fep))
1668 for (j = 0; j < fep->n_lambda; j++)
1670 fep->all_lambda[i][j] = fep->all_lambda[FreeEnergyPerturbationCouplingType::Fep][j];
1676 /* now read in the weights */
1677 expand->init_lambda_weights = parse_n_real(weights, &nweights, wi);
1680 expand->init_lambda_weights.resize(fep->n_lambda); /* initialize to zero */
1682 else if (nweights != fep->n_lambda)
1685 "Number of weights (%d) is not equal to number of lambda values (%d)",
1689 if ((expand->nstexpanded < 0) && (ir->efep != FreeEnergyPerturbationType::No))
1691 expand->nstexpanded = fep->nstdhdl;
1692 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1697 static void do_simtemp_params(t_inputrec* ir)
1700 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1701 getSimTemps(ir->fepvals->n_lambda,
1702 ir->simtempvals.get(),
1703 ir->fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Temperature]);
1706 template<typename T>
1707 void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
1710 for (const auto& input : inputs)
1714 outputs[i] = gmx::fromStdString<T>(input);
1716 catch (gmx::GromacsException&)
1718 auto message = gmx::formatString(
1719 "Invalid value for mdp option %s. %s should only consist of integers separated "
1723 warning_error(wi, message);
1729 static void convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, real* outputs)
1732 for (const auto& input : inputs)
1736 outputs[i] = gmx::fromString<real>(input);
1738 catch (gmx::GromacsException&)
1740 auto message = gmx::formatString(
1741 "Invalid value for mdp option %s. %s should only consist of real numbers "
1742 "separated by spaces.",
1745 warning_error(wi, message);
1751 static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
1753 opts->wall_atomtype[0] = nullptr;
1754 opts->wall_atomtype[1] = nullptr;
1756 ir->wall_atomtype[0] = -1;
1757 ir->wall_atomtype[1] = -1;
1758 ir->wall_density[0] = 0;
1759 ir->wall_density[1] = 0;
1763 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1764 if (wallAtomTypes.size() != size_t(ir->nwall))
1767 "Expected %d elements for wall_atomtype, found %zu",
1769 wallAtomTypes.size());
1771 GMX_RELEASE_ASSERT(ir->nwall < 3, "Invalid number of walls");
1772 for (int i = 0; i < ir->nwall; i++)
1774 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1777 if (ir->wall_type == WallType::NineThree || ir->wall_type == WallType::TenFour)
1779 auto wallDensity = gmx::splitString(wall_density);
1780 if (wallDensity.size() != size_t(ir->nwall))
1783 "Expected %d elements for wall-density, found %zu",
1785 wallDensity.size());
1787 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1788 for (int i = 0; i < ir->nwall; i++)
1790 if (ir->wall_density[i] <= 0)
1792 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1799 static void add_wall_energrps(SimulationGroups* groups, int nwall, t_symtab* symtab)
1803 AtomGroupIndices* grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1804 for (int i = 0; i < nwall; i++)
1806 groups->groupNames.emplace_back(put_symtab(symtab, gmx::formatString("wall%d", i).c_str()));
1807 grps->emplace_back(groups->groupNames.size() - 1);
1812 static void read_expandedparams(std::vector<t_inpfile>* inp, t_expanded* expand, warninp_t wi)
1814 /* read expanded ensemble parameters */
1815 printStringNewline(inp, "expanded ensemble variables");
1816 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1817 expand->elamstats = getEnum<LambdaWeightCalculation>(inp, "lmc-stats", wi);
1818 expand->elmcmove = getEnum<LambdaMoveCalculation>(inp, "lmc-move", wi);
1819 expand->elmceq = getEnum<LambdaWeightWillReachEquilibrium>(inp, "lmc-weights-equil", wi);
1820 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1821 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1822 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1823 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1824 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1825 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1826 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1827 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1828 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1829 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1830 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1831 expand->bSymmetrizedTMatrix =
1832 (getEnum<Boolean>(inp, "symmetrized-transition-matrix", wi) != Boolean::No);
1833 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1834 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1835 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1836 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1837 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1838 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1839 expand->bWLoneovert = (getEnum<Boolean>(inp, "wl-oneovert", wi) != Boolean::No);
1842 /*! \brief Return whether an end state with the given coupling-lambda
1843 * value describes fully-interacting VDW.
1845 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1846 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1848 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1850 return (couple_lambda_value == ecouplamVDW || couple_lambda_value == ecouplamVDWQ);
1856 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1859 explicit MdpErrorHandler(warninp_t wi) : wi_(wi), mapping_(nullptr) {}
1861 void setBackMapping(const gmx::IKeyValueTreeBackMapping& mapping) { mapping_ = &mapping; }
1863 bool onError(gmx::UserInputError* ex, const gmx::KeyValueTreePath& context) override
1866 gmx::formatString("Error in mdp option \"%s\":", getOptionName(context).c_str()));
1867 std::string message = gmx::formatExceptionMessageToString(*ex);
1868 warning_error(wi_, message.c_str());
1873 std::string getOptionName(const gmx::KeyValueTreePath& context)
1875 if (mapping_ != nullptr)
1877 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1878 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1881 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1886 const gmx::IKeyValueTreeBackMapping* mapping_;
1891 void get_ir(const char* mdparin,
1892 const char* mdparout,
1893 gmx::MDModules* mdModules,
1896 WriteMdpHeader writeMdpHeader,
1900 double dumdub[2][6];
1902 char warn_buf[STRLEN];
1903 t_lambda* fep = ir->fepvals.get();
1904 t_expanded* expand = ir->expandedvals.get();
1906 const char* no_names[] = { "no", nullptr };
1908 init_inputrec_strings();
1909 gmx::TextInputFile stream(mdparin);
1910 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1912 snew(dumstr[0], STRLEN);
1913 snew(dumstr[1], STRLEN);
1915 /* ignore the following deprecated commands */
1916 replace_inp_entry(inp, "title", nullptr);
1917 replace_inp_entry(inp, "cpp", nullptr);
1918 replace_inp_entry(inp, "domain-decomposition", nullptr);
1919 replace_inp_entry(inp, "andersen-seed", nullptr);
1920 replace_inp_entry(inp, "dihre", nullptr);
1921 replace_inp_entry(inp, "dihre-fc", nullptr);
1922 replace_inp_entry(inp, "dihre-tau", nullptr);
1923 replace_inp_entry(inp, "nstdihreout", nullptr);
1924 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1925 replace_inp_entry(inp, "optimize-fft", nullptr);
1926 replace_inp_entry(inp, "adress_type", nullptr);
1927 replace_inp_entry(inp, "adress_const_wf", nullptr);
1928 replace_inp_entry(inp, "adress_ex_width", nullptr);
1929 replace_inp_entry(inp, "adress_hy_width", nullptr);
1930 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1931 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1932 replace_inp_entry(inp, "adress_site", nullptr);
1933 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1934 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1935 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1936 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1937 replace_inp_entry(inp, "rlistlong", nullptr);
1938 replace_inp_entry(inp, "nstcalclr", nullptr);
1939 replace_inp_entry(inp, "pull-print-com2", nullptr);
1940 replace_inp_entry(inp, "gb-algorithm", nullptr);
1941 replace_inp_entry(inp, "nstgbradii", nullptr);
1942 replace_inp_entry(inp, "rgbradii", nullptr);
1943 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1944 replace_inp_entry(inp, "gb-saltconc", nullptr);
1945 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1946 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1947 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1948 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1949 replace_inp_entry(inp, "sa-algorithm", nullptr);
1950 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1951 replace_inp_entry(inp, "ns-type", nullptr);
1953 /* replace the following commands with the clearer new versions*/
1954 replace_inp_entry(inp, "unconstrained-start", "continuation");
1955 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1956 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1957 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1958 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1959 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1960 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1962 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1963 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1964 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1965 setStringEntry(&inp, "include", opts->include, nullptr);
1966 printStringNoNewline(
1967 &inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1968 setStringEntry(&inp, "define", opts->define, nullptr);
1970 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1971 ir->eI = getEnum<IntegrationAlgorithm>(&inp, "integrator", wi);
1972 printStringNoNewline(&inp, "Start time and timestep in ps");
1973 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1974 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1975 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1976 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1977 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1978 printStringNoNewline(
1979 &inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1980 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1981 printStringNoNewline(&inp, "Multiple time-stepping");
1982 ir->useMts = (getEnum<Boolean>(&inp, "mts", wi) != Boolean::No);
1985 gmx::GromppMtsOpts& mtsOpts = opts->mtsOpts;
1986 mtsOpts.numLevels = get_eint(&inp, "mts-levels", 2, wi);
1987 mtsOpts.level2Forces = setStringEntry(&inp, "mts-level2-forces", "longrange-nonbonded");
1988 mtsOpts.level2Factor = get_eint(&inp, "mts-level2-factor", 2, wi);
1990 // We clear after reading without dynamics to not force the user to remove MTS mdp options
1991 if (!EI_DYNAMICS(ir->eI))
1996 printStringNoNewline(&inp, "mode for center of mass motion removal");
1997 ir->comm_mode = getEnum<ComRemovalAlgorithm>(&inp, "comm-mode", wi);
1998 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
1999 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
2000 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
2001 setStringEntry(&inp, "comm-grps", inputrecStrings->vcm, nullptr);
2003 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
2004 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
2005 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
2006 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
2009 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
2010 printStringNoNewline(&inp, "Force tolerance and initial step-size");
2011 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
2012 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
2013 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
2014 ir->niter = get_eint(&inp, "niter", 20, wi);
2015 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
2016 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
2017 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
2018 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
2019 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
2021 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
2022 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
2024 /* Output options */
2025 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
2026 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
2027 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
2028 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
2029 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
2030 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
2031 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
2032 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
2033 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
2034 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
2035 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
2036 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
2037 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
2038 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
2039 printStringNoNewline(&inp, "default, all atoms will be written.");
2040 setStringEntry(&inp, "compressed-x-grps", inputrecStrings->x_compressed_groups, nullptr);
2041 printStringNoNewline(&inp, "Selection of energy groups");
2042 setStringEntry(&inp, "energygrps", inputrecStrings->energy, nullptr);
2044 /* Neighbor searching */
2045 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
2046 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
2047 ir->cutoff_scheme = getEnum<CutoffScheme>(&inp, "cutoff-scheme", wi);
2048 printStringNoNewline(&inp, "nblist update frequency");
2049 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
2050 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
2051 // TODO This conversion should be removed when proper std:string handling will be added to get_eeenum(...), etc.
2052 std::vector<const char*> pbcTypesNamesChar;
2053 for (const auto& pbcTypeName : c_pbcTypeNames)
2055 pbcTypesNamesChar.push_back(pbcTypeName.c_str());
2057 ir->pbcType = static_cast<PbcType>(get_eeenum(&inp, "pbc", pbcTypesNamesChar.data(), wi));
2058 ir->bPeriodicMols = getEnum<Boolean>(&inp, "periodic-molecules", wi) != Boolean::No;
2059 printStringNoNewline(&inp,
2060 "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
2061 printStringNoNewline(&inp, "a value of -1 means: use rlist");
2062 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
2063 printStringNoNewline(&inp, "nblist cut-off");
2064 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
2065 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
2067 /* Electrostatics */
2068 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
2069 printStringNoNewline(&inp, "Method for doing electrostatics");
2070 ir->coulombtype = getEnum<CoulombInteractionType>(&inp, "coulombtype", wi);
2071 ir->coulomb_modifier = getEnum<InteractionModifiers>(&inp, "coulomb-modifier", wi);
2072 printStringNoNewline(&inp, "cut-off lengths");
2073 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
2074 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
2075 printStringNoNewline(&inp, "Relative dielectric constant for the medium and the reaction field");
2076 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
2077 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
2078 printStringNoNewline(&inp, "Method for doing Van der Waals");
2079 ir->vdwtype = getEnum<VanDerWaalsType>(&inp, "vdw-type", wi);
2080 ir->vdw_modifier = getEnum<InteractionModifiers>(&inp, "vdw-modifier", wi);
2081 printStringNoNewline(&inp, "cut-off lengths");
2082 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
2083 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
2084 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
2085 ir->eDispCorr = getEnum<DispersionCorrectionType>(&inp, "DispCorr", wi);
2086 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
2087 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
2088 printStringNoNewline(&inp, "Separate tables between energy group pairs");
2089 setStringEntry(&inp, "energygrp-table", inputrecStrings->egptable, nullptr);
2090 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
2091 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
2092 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
2093 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
2094 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
2095 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
2096 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
2097 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
2098 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
2099 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
2100 ir->ljpme_combination_rule = getEnum<LongRangeVdW>(&inp, "lj-pme-comb-rule", wi);
2101 ir->ewald_geometry = getEnum<EwaldGeometry>(&inp, "ewald-geometry", wi);
2102 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
2104 /* Implicit solvation is no longer supported, but we need grompp
2105 to be able to refuse old .mdp files that would have built a tpr
2106 to run it. Thus, only "no" is accepted. */
2107 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
2109 /* Coupling stuff */
2110 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
2111 printStringNoNewline(&inp, "Temperature coupling");
2112 ir->etc = getEnum<TemperatureCoupling>(&inp, "tcoupl", wi);
2113 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
2114 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
2115 ir->bPrintNHChains = (getEnum<Boolean>(&inp, "print-nose-hoover-chain-variables", wi) != Boolean::No);
2116 printStringNoNewline(&inp, "Groups to couple separately");
2117 setStringEntry(&inp, "tc-grps", inputrecStrings->tcgrps, nullptr);
2118 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
2119 setStringEntry(&inp, "tau-t", inputrecStrings->tau_t, nullptr);
2120 setStringEntry(&inp, "ref-t", inputrecStrings->ref_t, nullptr);
2121 printStringNoNewline(&inp, "pressure coupling");
2122 ir->epc = getEnum<PressureCoupling>(&inp, "pcoupl", wi);
2123 ir->epct = getEnum<PressureCouplingType>(&inp, "pcoupltype", wi);
2124 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
2125 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
2126 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
2127 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
2128 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
2129 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
2130 ir->refcoord_scaling = getEnum<RefCoordScaling>(&inp, "refcoord-scaling", wi);
2133 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2134 ir->bQMMM = (getEnum<Boolean>(&inp, "QMMM", wi) != Boolean::No);
2135 printStringNoNewline(&inp, "Groups treated with MiMiC");
2136 setStringEntry(&inp, "QMMM-grps", inputrecStrings->QMMM, nullptr);
2138 /* Simulated annealing */
2139 printStringNewline(&inp, "SIMULATED ANNEALING");
2140 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2141 setStringEntry(&inp, "annealing", inputrecStrings->anneal, nullptr);
2142 printStringNoNewline(&inp,
2143 "Number of time points to use for specifying annealing in each group");
2144 setStringEntry(&inp, "annealing-npoints", inputrecStrings->anneal_npoints, nullptr);
2145 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2146 setStringEntry(&inp, "annealing-time", inputrecStrings->anneal_time, nullptr);
2147 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2148 setStringEntry(&inp, "annealing-temp", inputrecStrings->anneal_temp, nullptr);
2151 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2152 opts->bGenVel = (getEnum<Boolean>(&inp, "gen-vel", wi) != Boolean::No);
2153 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2154 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2157 printStringNewline(&inp, "OPTIONS FOR BONDS");
2158 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2159 printStringNoNewline(&inp, "Type of constraint algorithm");
2160 ir->eConstrAlg = getEnum<ConstraintAlgorithm>(&inp, "constraint-algorithm", wi);
2161 printStringNoNewline(&inp, "Do not constrain the start configuration");
2162 ir->bContinuation = (getEnum<Boolean>(&inp, "continuation", wi) != Boolean::No);
2163 printStringNoNewline(&inp,
2164 "Use successive overrelaxation to reduce the number of shake iterations");
2165 ir->bShakeSOR = (getEnum<Boolean>(&inp, "Shake-SOR", wi) != Boolean::No);
2166 printStringNoNewline(&inp, "Relative tolerance of shake");
2167 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2168 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2169 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2170 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2171 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2172 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2173 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2174 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2175 printStringNoNewline(&inp, "rotates over more degrees than");
2176 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2177 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2178 opts->bMorse = (getEnum<Boolean>(&inp, "morse", wi) != Boolean::No);
2180 /* Energy group exclusions */
2181 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2182 printStringNoNewline(
2183 &inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2184 setStringEntry(&inp, "energygrp-excl", inputrecStrings->egpexcl, nullptr);
2187 printStringNewline(&inp, "WALLS");
2188 printStringNoNewline(
2189 &inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2190 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2191 ir->wall_type = getEnum<WallType>(&inp, "wall-type", wi);
2192 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2193 setStringEntry(&inp, "wall-atomtype", inputrecStrings->wall_atomtype, nullptr);
2194 setStringEntry(&inp, "wall-density", inputrecStrings->wall_density, nullptr);
2195 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2198 printStringNewline(&inp, "COM PULLING");
2199 ir->bPull = (getEnum<Boolean>(&inp, "pull", wi) != Boolean::No);
2202 ir->pull = std::make_unique<pull_params_t>();
2203 inputrecStrings->pullGroupNames = read_pullparams(&inp, ir->pull.get(), wi);
2207 for (int c = 0; c < ir->pull->ncoord; c++)
2209 if (ir->pull->coord[c].eType == PullingAlgorithm::Constraint)
2212 "Constraint COM pulling is not supported in combination with "
2213 "multiple time stepping");
2221 NOTE: needs COM pulling or free energy input */
2222 printStringNewline(&inp, "AWH biasing");
2223 ir->bDoAwh = (getEnum<Boolean>(&inp, "awh", wi) != Boolean::No);
2226 ir->awhParams = std::make_unique<gmx::AwhParams>(&inp, *ir, wi);
2229 /* Enforced rotation */
2230 printStringNewline(&inp, "ENFORCED ROTATION");
2231 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2232 ir->bRot = (getEnum<Boolean>(&inp, "rotation", wi) != Boolean::No);
2236 inputrecStrings->rotateGroupNames = read_rotparams(&inp, ir->rot, wi);
2239 /* Interactive MD */
2241 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2242 setStringEntry(&inp, "IMD-group", inputrecStrings->imd_grp, nullptr);
2243 if (inputrecStrings->imd_grp[0] != '\0')
2250 printStringNewline(&inp, "NMR refinement stuff");
2251 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2252 ir->eDisre = getEnum<DistanceRestraintRefinement>(&inp, "disre", wi);
2253 printStringNoNewline(
2254 &inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2255 ir->eDisreWeighting = getEnum<DistanceRestraintWeighting>(&inp, "disre-weighting", wi);
2256 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2257 ir->bDisreMixed = (getEnum<Boolean>(&inp, "disre-mixed", wi) != Boolean::No);
2258 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2259 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2260 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2261 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2262 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2263 opts->bOrire = (getEnum<Boolean>(&inp, "orire", wi) != Boolean::No);
2264 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2265 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2266 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2267 setStringEntry(&inp, "orire-fitgrp", inputrecStrings->orirefitgrp, nullptr);
2268 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2269 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2271 /* free energy variables */
2272 printStringNewline(&inp, "Free energy variables");
2273 ir->efep = getEnum<FreeEnergyPerturbationType>(&inp, "free-energy", wi);
2274 setStringEntry(&inp, "couple-moltype", inputrecStrings->couple_moltype, nullptr);
2275 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2276 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2277 opts->bCoupleIntra = (getEnum<Boolean>(&inp, "couple-intramol", wi) != Boolean::No);
2279 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2281 it was not entered */
2282 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2283 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2284 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2285 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Fep] =
2286 setStringEntry(&inp, "fep-lambdas", "");
2287 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Mass] =
2288 setStringEntry(&inp, "mass-lambdas", "");
2289 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Coul] =
2290 setStringEntry(&inp, "coul-lambdas", "");
2291 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Vdw] =
2292 setStringEntry(&inp, "vdw-lambdas", "");
2293 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Bonded] =
2294 setStringEntry(&inp, "bonded-lambdas", "");
2295 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Restraint] =
2296 setStringEntry(&inp, "restraint-lambdas", "");
2297 inputrecStrings->fep_lambda[FreeEnergyPerturbationCouplingType::Temperature] =
2298 setStringEntry(&inp, "temperature-lambdas", "");
2299 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2300 setStringEntry(&inp, "init-lambda-weights", inputrecStrings->lambda_weights, nullptr);
2301 fep->edHdLPrintEnergy = getEnum<FreeEnergyPrintEnergy>(&inp, "dhdl-print-energy", wi);
2302 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2303 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2304 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2305 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2306 fep->bScCoul = (getEnum<Boolean>(&inp, "sc-coul", wi) != Boolean::No);
2307 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2308 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2309 fep->separate_dhdl_file = getEnum<SeparateDhdlFile>(&inp, "separate-dhdl-file", wi);
2310 fep->dhdl_derivatives = getEnum<DhDlDerivativeCalculation>(&inp, "dhdl-derivatives", wi);
2311 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2312 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2314 /* Non-equilibrium MD stuff */
2315 printStringNewline(&inp, "Non-equilibrium MD stuff");
2316 setStringEntry(&inp, "freezegrps", inputrecStrings->freeze, nullptr);
2317 setStringEntry(&inp, "freezedim", inputrecStrings->frdim, nullptr);
2318 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2319 setStringEntry(&inp, "deform", inputrecStrings->deform, nullptr);
2321 /* simulated tempering variables */
2322 printStringNewline(&inp, "simulated tempering variables");
2323 ir->bSimTemp = (getEnum<Boolean>(&inp, "simulated-tempering", wi) != Boolean::No);
2324 ir->simtempvals->eSimTempScale = getEnum<SimulatedTempering>(&inp, "simulated-tempering-scaling", wi);
2325 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2326 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2328 /* expanded ensemble variables */
2329 if (ir->efep == FreeEnergyPerturbationType::Expanded || ir->bSimTemp)
2331 read_expandedparams(&inp, expand, wi);
2334 /* Electric fields */
2336 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2337 gmx::KeyValueTreeTransformer transform;
2338 transform.rules()->addRule().keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2339 mdModules->initMdpTransform(transform.rules());
2340 for (const auto& path : transform.mappedPaths())
2342 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2343 mark_einp_set(inp, path[0].c_str());
2345 MdpErrorHandler errorHandler(wi);
2346 auto result = transform.transform(convertedValues, &errorHandler);
2347 ir->params = new gmx::KeyValueTreeObject(result.object());
2348 mdModules->adjustInputrecBasedOnModules(ir);
2349 errorHandler.setBackMapping(result.backMapping());
2350 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2353 /* Ion/water position swapping ("computational electrophysiology") */
2354 printStringNewline(&inp,
2355 "Ion/water position swapping for computational electrophysiology setups");
2356 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2357 ir->eSwapCoords = getEnum<SwapType>(&inp, "swapcoords", wi);
2358 if (ir->eSwapCoords != SwapType::No)
2365 printStringNoNewline(&inp, "Swap attempt frequency");
2366 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2367 printStringNoNewline(&inp, "Number of ion types to be controlled");
2368 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2371 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2373 ir->swap->ngrp = nIonTypes + static_cast<int>(SwapGroupSplittingType::Count);
2374 snew(ir->swap->grp, ir->swap->ngrp);
2375 for (i = 0; i < ir->swap->ngrp; i++)
2377 snew(ir->swap->grp[i].molname, STRLEN);
2379 printStringNoNewline(&inp,
2380 "Two index groups that contain the compartment-partitioning atoms");
2381 setStringEntry(&inp,
2383 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname,
2385 setStringEntry(&inp,
2387 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname,
2389 printStringNoNewline(&inp,
2390 "Use center of mass of split groups (yes/no), otherwise center of "
2391 "geometry is used");
2392 ir->swap->massw_split[0] = (getEnum<Boolean>(&inp, "massw-split0", wi) != Boolean::No);
2393 ir->swap->massw_split[1] = (getEnum<Boolean>(&inp, "massw-split1", wi) != Boolean::No);
2395 printStringNoNewline(&inp, "Name of solvent molecules");
2396 setStringEntry(&inp,
2398 ir->swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].molname,
2401 printStringNoNewline(&inp,
2402 "Split cylinder: radius, upper and lower extension (nm) (this will "
2403 "define the channels)");
2404 printStringNoNewline(&inp,
2405 "Note that the split cylinder settings do not have an influence on "
2406 "the swapping protocol,");
2407 printStringNoNewline(
2409 "however, if correctly defined, the permeation events are recorded per channel");
2410 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2411 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2412 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2413 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2414 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2415 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2417 printStringNoNewline(
2419 "Average the number of ions per compartment over these many swap attempt steps");
2420 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2422 printStringNoNewline(
2423 &inp, "Names of the ion types that can be exchanged with solvent molecules,");
2424 printStringNoNewline(
2425 &inp, "and the requested number of ions of this type in compartments A and B");
2426 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2427 for (i = 0; i < nIonTypes; i++)
2429 int ig = static_cast<int>(SwapGroupSplittingType::Count) + i;
2431 sprintf(buf, "iontype%d-name", i);
2432 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2433 sprintf(buf, "iontype%d-in-A", i);
2434 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2435 sprintf(buf, "iontype%d-in-B", i);
2436 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2439 printStringNoNewline(
2441 "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2442 printStringNoNewline(
2444 "at maximum distance (= bulk concentration) to the split group layers. However,");
2445 printStringNoNewline(&inp,
2446 "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk "
2447 "layer from the middle at 0.0");
2448 printStringNoNewline(&inp,
2449 "towards one of the compartment-partitioning layers (at +/- 1.0).");
2450 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2451 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2452 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2453 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0))
2455 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2458 printStringNoNewline(
2459 &inp, "Start to swap ions if threshold difference to requested count is reached");
2460 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2463 /* AdResS is no longer supported, but we need grompp to be able to
2464 refuse to process old .mdp files that used it. */
2465 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2467 /* User defined thingies */
2468 printStringNewline(&inp, "User defined thingies");
2469 setStringEntry(&inp, "user1-grps", inputrecStrings->user1, nullptr);
2470 setStringEntry(&inp, "user2-grps", inputrecStrings->user2, nullptr);
2471 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2472 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2473 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2474 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2475 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2476 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2477 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2478 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2482 gmx::TextOutputFile stream(mdparout);
2483 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2485 // Transform module data into a flat key-value tree for output.
2486 gmx::KeyValueTreeBuilder builder;
2487 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2488 mdModules->buildMdpOutput(&builderObject);
2490 gmx::TextWriter writer(&stream);
2491 writeKeyValueTreeAsMdp(&writer, builder.build());
2496 /* Process options if necessary */
2497 for (m = 0; m < 2; m++)
2499 for (i = 0; i < 2 * DIM; i++)
2503 if (ir->epc != PressureCoupling::No)
2507 case PressureCouplingType::Isotropic:
2508 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2512 "Pressure coupling incorrect number of values (I need exactly 1)");
2514 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2516 case PressureCouplingType::SemiIsotropic:
2517 case PressureCouplingType::SurfaceTension:
2518 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2522 "Pressure coupling incorrect number of values (I need exactly 2)");
2524 dumdub[m][YY] = dumdub[m][XX];
2526 case PressureCouplingType::Anisotropic:
2527 if (sscanf(dumstr[m],
2528 "%lf%lf%lf%lf%lf%lf",
2539 "Pressure coupling incorrect number of values (I need exactly 6)");
2544 "Pressure coupling type %s not implemented yet",
2545 enumValueToString(ir->epct));
2549 clear_mat(ir->ref_p);
2550 clear_mat(ir->compress);
2551 for (i = 0; i < DIM; i++)
2553 ir->ref_p[i][i] = dumdub[1][i];
2554 ir->compress[i][i] = dumdub[0][i];
2556 if (ir->epct == PressureCouplingType::Anisotropic)
2558 ir->ref_p[XX][YY] = dumdub[1][3];
2559 ir->ref_p[XX][ZZ] = dumdub[1][4];
2560 ir->ref_p[YY][ZZ] = dumdub[1][5];
2561 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2564 "All off-diagonal reference pressures are non-zero. Are you sure you want to "
2565 "apply a threefold shear stress?\n");
2567 ir->compress[XX][YY] = dumdub[0][3];
2568 ir->compress[XX][ZZ] = dumdub[0][4];
2569 ir->compress[YY][ZZ] = dumdub[0][5];
2570 for (i = 0; i < DIM; i++)
2572 for (m = 0; m < i; m++)
2574 ir->ref_p[i][m] = ir->ref_p[m][i];
2575 ir->compress[i][m] = ir->compress[m][i];
2580 if (ir->comm_mode == ComRemovalAlgorithm::No)
2585 opts->couple_moltype = nullptr;
2586 if (strlen(inputrecStrings->couple_moltype) > 0)
2588 if (ir->efep != FreeEnergyPerturbationType::No)
2590 opts->couple_moltype = gmx_strdup(inputrecStrings->couple_moltype);
2591 if (opts->couple_lam0 == opts->couple_lam1)
2593 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2595 if (ir->eI == IntegrationAlgorithm::MD
2596 && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
2600 "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
2607 "Free energy is turned off, so we will not decouple the molecule listed "
2611 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2612 if (ir->efep != FreeEnergyPerturbationType::No)
2614 if (fep->delta_lambda != 0)
2616 ir->efep = FreeEnergyPerturbationType::SlowGrowth;
2620 if (fep->edHdLPrintEnergy == FreeEnergyPrintEnergy::Yes)
2622 fep->edHdLPrintEnergy = FreeEnergyPrintEnergy::Total;
2624 "Old option for dhdl-print-energy given: "
2625 "changing \"yes\" to \"total\"\n");
2628 if (ir->bSimTemp && (fep->edHdLPrintEnergy == FreeEnergyPrintEnergy::No))
2630 /* always print out the energy to dhdl if we are doing
2631 expanded ensemble, since we need the total energy for
2632 analysis if the temperature is changing. In some
2633 conditions one may only want the potential energy, so
2634 we will allow that if the appropriate mdp setting has
2635 been enabled. Otherwise, total it is:
2637 fep->edHdLPrintEnergy = FreeEnergyPrintEnergy::Total;
2640 if ((ir->efep != FreeEnergyPerturbationType::No) || ir->bSimTemp)
2642 ir->bExpanded = FALSE;
2643 if ((ir->efep == FreeEnergyPerturbationType::Expanded) || ir->bSimTemp)
2645 ir->bExpanded = TRUE;
2647 do_fep_params(ir, inputrecStrings->fep_lambda, inputrecStrings->lambda_weights, wi);
2648 if (ir->bSimTemp) /* done after fep params */
2650 do_simtemp_params(ir);
2653 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2654 * setup and not on the old way of specifying the free-energy setup,
2655 * we should check for using soft-core when not needed, since that
2656 * can complicate the sampling significantly.
2657 * Note that we only check for the automated coupling setup.
2658 * If the (advanced) user does FEP through manual topology changes,
2659 * this check will not be triggered.
2661 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->n_lambda == 0
2662 && ir->fepvals->sc_alpha != 0
2663 && (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
2666 "You are using soft-core interactions while the Van der Waals interactions are "
2667 "not decoupled (note that the sc-coul option is only active when using lambda "
2668 "states). Although this will not lead to errors, you will need much more "
2669 "sampling than without soft-core interactions. Consider using sc-alpha=0.");
2674 ir->fepvals->n_lambda = 0;
2677 /* WALL PARAMETERS */
2679 do_wall_params(ir, inputrecStrings->wall_atomtype, inputrecStrings->wall_density, opts, wi);
2681 /* ORIENTATION RESTRAINT PARAMETERS */
2683 if (opts->bOrire && gmx::splitString(inputrecStrings->orirefitgrp).size() != 1)
2685 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2688 /* DEFORMATION PARAMETERS */
2690 clear_mat(ir->deform);
2691 for (i = 0; i < 6; i++)
2696 double gmx_unused canary;
2697 int ndeform = sscanf(inputrecStrings->deform,
2698 "%lf %lf %lf %lf %lf %lf %lf",
2707 if (strlen(inputrecStrings->deform) > 0 && ndeform != 6)
2711 "Cannot parse exactly 6 box deformation velocities from string '%s'",
2712 inputrecStrings->deform)
2715 for (i = 0; i < 3; i++)
2717 ir->deform[i][i] = dumdub[0][i];
2719 ir->deform[YY][XX] = dumdub[0][3];
2720 ir->deform[ZZ][XX] = dumdub[0][4];
2721 ir->deform[ZZ][YY] = dumdub[0][5];
2722 if (ir->epc != PressureCoupling::No)
2724 for (i = 0; i < 3; i++)
2726 for (j = 0; j <= i; j++)
2728 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2730 warning_error(wi, "A box element has deform set and compressibility > 0");
2734 for (i = 0; i < 3; i++)
2736 for (j = 0; j < i; j++)
2738 if (ir->deform[i][j] != 0)
2740 for (m = j; m < DIM; m++)
2742 if (ir->compress[m][j] != 0)
2745 "An off-diagonal box element has deform set while "
2746 "compressibility > 0 for the same component of another box "
2747 "vector, this might lead to spurious periodicity effects.");
2748 warning(wi, warn_buf);
2756 /* Ion/water position swapping checks */
2757 if (ir->eSwapCoords != SwapType::No)
2759 if (ir->swap->nstswap < 1)
2761 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2763 if (ir->swap->nAverage < 1)
2765 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2767 if (ir->swap->threshold < 1.0)
2769 warning_error(wi, "Ion count threshold must be at least 1.\n");
2773 /* Set up MTS levels, this needs to happen before checking AWH parameters */
2776 std::vector<std::string> errorMessages;
2777 ir->mtsLevels = gmx::setupMtsLevels(opts->mtsOpts, &errorMessages);
2779 for (const auto& errorMessage : errorMessages)
2781 warning_error(wi, errorMessage.c_str());
2787 gmx::checkAwhParams(*ir->awhParams, *ir, wi);
2794 /* We would like gn to be const as well, but C doesn't allow this */
2795 /* TODO this is utility functionality (search for the index of a
2796 string in a collection), so should be refactored and located more
2798 int search_string(const char* s, int ng, char* gn[])
2802 for (i = 0; (i < ng); i++)
2804 if (gmx_strcasecmp(s, gn[i]) == 0)
2811 "Group %s referenced in the .mdp file was not found in the index file.\n"
2812 "Group names must match either [moleculetype] names or custom index group\n"
2813 "names, in which case you must supply an index file to the '-n' option\n"
2818 static void atomGroupRangeValidation(int natoms, int groupIndex, const t_blocka& block)
2820 /* Now go over the atoms in the group */
2821 for (int j = block.index[groupIndex]; (j < block.index[groupIndex + 1]); j++)
2823 int aj = block.a[j];
2825 /* Range checking */
2826 if ((aj < 0) || (aj >= natoms))
2828 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2833 static void do_numbering(int natoms,
2834 SimulationGroups* groups,
2835 gmx::ArrayRef<std::string> groupsFromMdpFile,
2838 SimulationAtomGroupType gtype,
2844 unsigned short* cbuf;
2845 AtomGroupIndices* grps = &(groups->groups[gtype]);
2848 char warn_buf[STRLEN];
2850 title = shortName(gtype);
2853 /* Mark all id's as not set */
2854 for (int i = 0; (i < natoms); i++)
2859 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2861 /* Lookup the group name in the block structure */
2862 const int gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2863 if ((grptp != egrptpONE) || (i == 0))
2865 grps->emplace_back(gid);
2867 GMX_ASSERT(block, "Can't have a nullptr block");
2868 atomGroupRangeValidation(natoms, gid, *block);
2869 /* Now go over the atoms in the group */
2870 for (int j = block->index[gid]; (j < block->index[gid + 1]); j++)
2872 const int aj = block->a[j];
2873 /* Lookup up the old group number */
2874 const int ognr = cbuf[aj];
2877 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title, ognr + 1, i + 1);
2881 /* Store the group number in buffer */
2882 if (grptp == egrptpONE)
2895 /* Now check whether we have done all atoms */
2898 if (grptp == egrptpALL)
2900 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2902 else if (grptp == egrptpPART)
2904 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2905 warning_note(wi, warn_buf);
2907 /* Assign all atoms currently unassigned to a rest group */
2908 for (int j = 0; (j < natoms); j++)
2910 if (cbuf[j] == NOGID)
2912 cbuf[j] = grps->size();
2915 if (grptp != egrptpPART)
2919 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title, natoms - ntot);
2921 /* Add group name "rest" */
2922 grps->emplace_back(restnm);
2924 /* Assign the rest name to all atoms not currently assigned to a group */
2925 for (int j = 0; (j < natoms); j++)
2927 if (cbuf[j] == NOGID)
2929 // group size was not updated before this here, so need to use -1.
2930 cbuf[j] = grps->size() - 1;
2936 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2938 /* All atoms are part of one (or no) group, no index required */
2939 groups->groupNumbers[gtype].clear();
2943 for (int j = 0; (j < natoms); j++)
2945 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2952 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
2955 pull_params_t* pull;
2956 int natoms, imin, jmin;
2957 int * nrdf2, *na_vcm, na_tot;
2958 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2963 * First calc 3xnr-atoms for each group
2964 * then subtract half a degree of freedom for each constraint
2966 * Only atoms and nuclei contribute to the degrees of freedom...
2971 const SimulationGroups& groups = mtop->groups;
2972 natoms = mtop->natoms;
2974 /* Allocate one more for a possible rest group */
2975 /* We need to sum degrees of freedom into doubles,
2976 * since floats give too low nrdf's above 3 million atoms.
2978 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
2979 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2980 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2981 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2982 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2984 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
2988 for (gmx::index i = 0;
2989 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
2993 clear_ivec(dof_vcm[i]);
2995 nrdf_vcm_sub[i] = 0;
2997 snew(nrdf2, natoms);
2998 for (const AtomProxy atomP : AtomRange(*mtop))
3000 const t_atom& local = atomP.atom();
3001 int i = atomP.globalAtomNumber();
3003 if (local.ptype == ParticleType::Atom || local.ptype == ParticleType::Nucleus)
3005 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
3006 for (int d = 0; d < DIM; d++)
3008 if (opts->nFreeze[g][d] == 0)
3010 /* Add one DOF for particle i (counted as 2*1) */
3012 /* VCM group i has dim d as a DOF */
3013 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
3017 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
3019 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
3025 for (const gmx_molblock_t& molb : mtop->molblock)
3027 const gmx_moltype_t& molt = mtop->moltype[molb.type];
3028 const t_atom* atom = molt.atoms.atom;
3029 for (int mol = 0; mol < molb.nmol; mol++)
3031 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
3033 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
3034 for (int i = 0; i < molt.ilist[ftype].size();)
3036 /* Subtract degrees of freedom for the constraints,
3037 * if the particles still have degrees of freedom left.
3038 * If one of the particles is a vsite or a shell, then all
3039 * constraint motion will go there, but since they do not
3040 * contribute to the constraints the degrees of freedom do not
3043 int ai = as + ia[i + 1];
3044 int aj = as + ia[i + 2];
3045 if (((atom[ia[i + 1]].ptype == ParticleType::Nucleus)
3046 || (atom[ia[i + 1]].ptype == ParticleType::Atom))
3047 && ((atom[ia[i + 2]].ptype == ParticleType::Nucleus)
3048 || (atom[ia[i + 2]].ptype == ParticleType::Atom)))
3066 imin = std::min(imin, nrdf2[ai]);
3067 jmin = std::min(jmin, nrdf2[aj]);
3070 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3072 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
3074 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3076 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
3079 i += interaction_function[ftype].nratoms + 1;
3082 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
3083 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
3085 /* Subtract 1 dof from every atom in the SETTLE */
3086 for (int j = 0; j < 3; j++)
3088 int ai = as + ia[i + 1 + j];
3089 imin = std::min(2, nrdf2[ai]);
3091 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3093 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3098 as += molt.atoms.nr;
3104 /* Correct nrdf for the COM constraints.
3105 * We correct using the TC and VCM group of the first atom
3106 * in the reference and pull group. If atoms in one pull group
3107 * belong to different TC or VCM groups it is anyhow difficult
3108 * to determine the optimal nrdf assignment.
3110 pull = ir->pull.get();
3112 for (int i = 0; i < pull->ncoord; i++)
3114 if (pull->coord[i].eType != PullingAlgorithm::Constraint)
3121 for (int j = 0; j < 2; j++)
3123 const t_pull_group* pgrp;
3125 pgrp = &pull->group[pull->coord[i].group[j]];
3127 if (!pgrp->ind.empty())
3129 /* Subtract 1/2 dof from each group */
3130 int ai = pgrp->ind[0];
3131 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3133 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3135 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
3138 "Center of mass pulling constraints caused the number of degrees "
3139 "of freedom for temperature coupling group %s to be negative",
3140 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
3141 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
3146 /* We need to subtract the whole DOF from group j=1 */
3153 if (ir->nstcomm != 0)
3155 GMX_RELEASE_ASSERT(!groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty(),
3156 "Expect at least one group when removing COM motion");
3158 /* We remove COM motion up to dim ndof_com() */
3159 const int ndim_rm_vcm = ndof_com(ir);
3161 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3162 * the number of degrees of freedom in each vcm group when COM
3163 * translation is removed and 6 when rotation is removed as well.
3164 * Note that we do not and should not include the rest group here.
3166 for (gmx::index j = 0;
3167 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]);
3170 switch (ir->comm_mode)
3172 case ComRemovalAlgorithm::Linear:
3173 case ComRemovalAlgorithm::LinearAccelerationCorrection:
3174 nrdf_vcm_sub[j] = 0;
3175 for (int d = 0; d < ndim_rm_vcm; d++)
3183 case ComRemovalAlgorithm::Angular: nrdf_vcm_sub[j] = 6; break;
3184 default: gmx_incons("Checking comm_mode");
3188 for (gmx::index i = 0;
3189 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]);
3192 /* Count the number of atoms of TC group i for every VCM group */
3193 for (gmx::index j = 0;
3194 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3200 for (int ai = 0; ai < natoms; ai++)
3202 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3204 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3208 /* Correct for VCM removal according to the fraction of each VCM
3209 * group present in this TC group.
3211 nrdf_uc = nrdf_tc[i];
3213 for (gmx::index j = 0;
3214 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3217 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3219 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3220 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3225 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3227 opts->nrdf[i] = nrdf_tc[i];
3228 if (opts->nrdf[i] < 0)
3233 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3234 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]],
3243 sfree(nrdf_vcm_sub);
3246 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3248 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3249 * But since this is much larger than STRLEN, such a line can not be parsed.
3250 * The real maximum is the number of names that fit in a string: STRLEN/2.
3252 #define EGP_MAX (STRLEN / 2)
3256 auto names = gmx::splitString(val);
3257 if (names.size() % 2 != 0)
3259 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3261 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3263 for (size_t i = 0; i < names.size() / 2; i++)
3265 // TODO this needs to be replaced by a solution using std::find_if
3269 names[2 * i].c_str(),
3270 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3276 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3281 names[2 * i + 1].c_str(),
3282 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3288 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3290 if ((j < nr) && (k < nr))
3292 ir->opts.egp_flags[nr * j + k] |= flag;
3293 ir->opts.egp_flags[nr * k + j] |= flag;
3302 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3304 int ig = -1, i = 0, gind;
3308 /* Just a quick check here, more thorough checks are in mdrun */
3309 if (strcmp(swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname,
3310 swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname)
3314 "The split groups can not both be '%s'.",
3315 swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname);
3318 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3319 for (ig = 0; ig < swap->ngrp; ig++)
3321 swapg = &swap->grp[ig];
3322 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3323 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3328 "%s group '%s' contains %d atoms.\n",
3329 ig < 3 ? enumValueToString(static_cast<SwapGroupSplittingType>(ig)) : "Swap",
3330 swap->grp[ig].molname,
3332 snew(swapg->ind, swapg->nat);
3333 for (i = 0; i < swapg->nat; i++)
3335 swapg->ind[i] = grps->a[grps->index[gind] + i];
3340 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3346 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3351 ig = search_string(IMDgname, grps->nr, gnames);
3352 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3354 if (IMDgroup->nat > 0)
3357 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3361 snew(IMDgroup->ind, IMDgroup->nat);
3362 for (i = 0; i < IMDgroup->nat; i++)
3364 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3369 /* Checks whether atoms are both part of a COM removal group and frozen.
3370 * If a fully frozen atom is part of a COM removal group, it is removed
3371 * from the COM removal group. A note is issued if such atoms are present.
3372 * A warning is issued for atom with one or two dimensions frozen that
3373 * are part of a COM removal group (mdrun would need to compute COM mass
3374 * per dimension to handle this correctly).
3375 * Also issues a warning when non-frozen atoms are not part of a COM
3376 * removal group while COM removal is active.
3378 static void checkAndUpdateVcmFreezeGroupConsistency(SimulationGroups* groups,
3380 const t_grpopts& opts,
3383 const int vcmRestGroup =
3384 std::max(int(groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()), 1);
3386 int numFullyFrozenVcmAtoms = 0;
3387 int numPartiallyFrozenVcmAtoms = 0;
3388 int numNonVcmAtoms = 0;
3389 for (int a = 0; a < numAtoms; a++)
3391 const int freezeGroup = getGroupType(*groups, SimulationAtomGroupType::Freeze, a);
3392 int numFrozenDims = 0;
3393 for (int d = 0; d < DIM; d++)
3395 numFrozenDims += opts.nFreeze[freezeGroup][d];
3398 const int vcmGroup = getGroupType(*groups, SimulationAtomGroupType::MassCenterVelocityRemoval, a);
3399 if (vcmGroup < vcmRestGroup)
3401 if (numFrozenDims == DIM)
3403 /* Do not remove COM motion for this fully frozen atom */
3404 if (groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
3406 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(
3409 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
3410 numFullyFrozenVcmAtoms++;
3412 else if (numFrozenDims > 0)
3414 numPartiallyFrozenVcmAtoms++;
3417 else if (numFrozenDims < DIM)
3423 if (numFullyFrozenVcmAtoms > 0)
3425 std::string warningText = gmx::formatString(
3426 "There are %d atoms that are fully frozen and part of COMM removal group(s), "
3427 "removing these atoms from the COMM removal group(s)",
3428 numFullyFrozenVcmAtoms);
3429 warning_note(wi, warningText.c_str());
3431 if (numPartiallyFrozenVcmAtoms > 0 && numPartiallyFrozenVcmAtoms < numAtoms)
3433 std::string warningText = gmx::formatString(
3434 "There are %d atoms that are frozen along less then %d dimensions and part of COMM "
3435 "removal group(s), due to limitations in the code these still contribute to the "
3436 "mass of the COM along frozen dimensions and therefore the COMM correction will be "
3438 numPartiallyFrozenVcmAtoms,
3440 warning(wi, warningText.c_str());
3442 if (numNonVcmAtoms > 0)
3444 std::string warningText = gmx::formatString(
3445 "%d atoms are not part of any center of mass motion removal group.\n"
3446 "This may lead to artifacts.\n"
3447 "In most cases one should use one group for the whole system.",
3449 warning(wi, warningText.c_str());
3453 void do_index(const char* mdparin,
3457 const gmx::MdModulesNotifier& notifier,
3461 t_blocka* defaultIndexGroups;
3469 int i, j, k, restnm;
3470 bool bExcl, bTable, bAnneal;
3471 char warn_buf[STRLEN];
3475 fprintf(stderr, "processing index file...\n");
3479 snew(defaultIndexGroups, 1);
3480 snew(defaultIndexGroups->index, 1);
3482 atoms_all = gmx_mtop_global_atoms(*mtop);
3483 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3484 done_atom(&atoms_all);
3488 defaultIndexGroups = init_index(ndx, &gnames);
3491 SimulationGroups* groups = &mtop->groups;
3492 natoms = mtop->natoms;
3493 symtab = &mtop->symtab;
3495 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3497 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3499 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3500 restnm = groups->groupNames.size() - 1;
3501 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3502 srenew(gnames, defaultIndexGroups->nr + 1);
3503 gnames[restnm] = *(groups->groupNames.back());
3505 set_warning_line(wi, mdparin, -1);
3507 auto temperatureCouplingTauValues = gmx::splitString(inputrecStrings->tau_t);
3508 auto temperatureCouplingReferenceValues = gmx::splitString(inputrecStrings->ref_t);
3509 auto temperatureCouplingGroupNames = gmx::splitString(inputrecStrings->tcgrps);
3510 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3511 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3514 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3516 temperatureCouplingGroupNames.size(),
3517 temperatureCouplingReferenceValues.size(),
3518 temperatureCouplingTauValues.size());
3521 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3522 do_numbering(natoms,
3524 temperatureCouplingGroupNames,
3527 SimulationAtomGroupType::TemperatureCoupling,
3529 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST,
3532 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3534 snew(ir->opts.nrdf, nr);
3535 snew(ir->opts.tau_t, nr);
3536 snew(ir->opts.ref_t, nr);
3537 if (ir->eI == IntegrationAlgorithm::BD && ir->bd_fric == 0)
3539 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3542 if (useReferenceTemperature)
3544 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3546 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3550 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3551 for (i = 0; (i < nr); i++)
3553 if ((ir->eI == IntegrationAlgorithm::BD) && ir->opts.tau_t[i] <= 0)
3556 "With integrator %s tau-t should be larger than 0",
3557 enumValueToString(ir->eI));
3558 warning_error(wi, warn_buf);
3561 if (ir->etc != TemperatureCoupling::VRescale && ir->opts.tau_t[i] == 0)
3565 "tau-t = -1 is the value to signal that a group should not have "
3566 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3569 if (ir->opts.tau_t[i] >= 0)
3571 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3574 if (ir->etc != TemperatureCoupling::No && ir->nsttcouple == -1)
3576 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3581 if ((ir->etc == TemperatureCoupling::NoseHoover) && (ir->epc == PressureCoupling::Berendsen))
3584 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3585 "md-vv; use either vrescale temperature with berendsen pressure or "
3586 "Nose-Hoover temperature with MTTK pressure");
3588 if (ir->epc == PressureCoupling::Mttk)
3590 if (ir->etc != TemperatureCoupling::NoseHoover)
3593 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3598 if (ir->nstpcouple != ir->nsttcouple)
3600 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3601 ir->nstpcouple = ir->nsttcouple = mincouple;
3603 "for current Trotter decomposition methods with vv, nsttcouple and "
3604 "nstpcouple must be equal. Both have been reset to "
3605 "min(nsttcouple,nstpcouple) = %d",
3607 warning_note(wi, warn_buf);
3612 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3613 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3615 if (ETC_ANDERSEN(ir->etc))
3617 if (ir->nsttcouple != 1)
3621 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3622 "need for larger nsttcouple > 1, since no global parameters are computed. "
3623 "nsttcouple has been reset to 1");
3624 warning_note(wi, warn_buf);
3627 nstcmin = tcouple_min_integration_steps(ir->etc);
3630 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3633 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3634 "least %d times larger than nsttcouple*dt (%g)",
3635 enumValueToString(ir->etc),
3638 ir->nsttcouple * ir->delta_t);
3639 warning(wi, warn_buf);
3642 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3643 for (i = 0; (i < nr); i++)
3645 if (ir->opts.ref_t[i] < 0)
3647 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3650 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3651 if we are in this conditional) if mc_temp is negative */
3652 if (ir->expandedvals->mc_temp < 0)
3654 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3658 /* Simulated annealing for each group. There are nr groups */
3659 auto simulatedAnnealingGroupNames = gmx::splitString(inputrecStrings->anneal);
3660 if (simulatedAnnealingGroupNames.size() == 1
3661 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3663 simulatedAnnealingGroupNames.resize(0);
3665 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3668 "Wrong number of annealing values: %zu (for %d groups)\n",
3669 simulatedAnnealingGroupNames.size(),
3674 snew(ir->opts.annealing, nr);
3675 snew(ir->opts.anneal_npoints, nr);
3676 snew(ir->opts.anneal_time, nr);
3677 snew(ir->opts.anneal_temp, nr);
3678 for (i = 0; i < nr; i++)
3680 ir->opts.annealing[i] = SimulatedAnnealing::No;
3681 ir->opts.anneal_npoints[i] = 0;
3682 ir->opts.anneal_time[i] = nullptr;
3683 ir->opts.anneal_temp[i] = nullptr;
3685 if (!simulatedAnnealingGroupNames.empty())
3688 for (i = 0; i < nr; i++)
3690 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3692 ir->opts.annealing[i] = SimulatedAnnealing::No;
3694 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3696 ir->opts.annealing[i] = SimulatedAnnealing::Single;
3699 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3701 ir->opts.annealing[i] = SimulatedAnnealing::Periodic;
3707 /* Read the other fields too */
3708 auto simulatedAnnealingPoints = gmx::splitString(inputrecStrings->anneal_npoints);
3709 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3712 "Found %zu annealing-npoints values for %zu groups\n",
3713 simulatedAnnealingPoints.size(),
3714 simulatedAnnealingGroupNames.size());
3716 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3717 size_t numSimulatedAnnealingFields = 0;
3718 for (i = 0; i < nr; i++)
3720 if (ir->opts.anneal_npoints[i] == 1)
3724 "Please specify at least a start and an end point for annealing\n");
3726 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3727 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3728 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3731 auto simulatedAnnealingTimes = gmx::splitString(inputrecStrings->anneal_time);
3733 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3736 "Found %zu annealing-time values, wanted %zu\n",
3737 simulatedAnnealingTimes.size(),
3738 numSimulatedAnnealingFields);
3740 auto simulatedAnnealingTemperatures = gmx::splitString(inputrecStrings->anneal_temp);
3741 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3744 "Found %zu annealing-temp values, wanted %zu\n",
3745 simulatedAnnealingTemperatures.size(),
3746 numSimulatedAnnealingFields);
3749 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3750 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3751 convertReals(wi, simulatedAnnealingTimes, "anneal-time", allSimulatedAnnealingTimes.data());
3753 simulatedAnnealingTemperatures,
3755 allSimulatedAnnealingTemperatures.data());
3756 for (i = 0, k = 0; i < nr; i++)
3758 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3760 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3761 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3764 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3766 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3772 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3775 "Annealing timepoints out of order: t=%f comes after "
3777 ir->opts.anneal_time[i][j],
3778 ir->opts.anneal_time[i][j - 1]);
3781 if (ir->opts.anneal_temp[i][j] < 0)
3784 "Found negative temperature in annealing: %f\n",
3785 ir->opts.anneal_temp[i][j]);
3790 /* Print out some summary information, to make sure we got it right */
3791 for (i = 0; i < nr; i++)
3793 if (ir->opts.annealing[i] != SimulatedAnnealing::No)
3795 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3797 "Simulated annealing for group %s: %s, %d timepoints\n",
3798 *(groups->groupNames[j]),
3799 enumValueToString(ir->opts.annealing[i]),
3800 ir->opts.anneal_npoints[i]);
3801 fprintf(stderr, "Time (ps) Temperature (K)\n");
3802 /* All terms except the last one */
3803 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3807 ir->opts.anneal_time[i][j],
3808 ir->opts.anneal_temp[i][j]);
3811 /* Finally the last one */
3812 j = ir->opts.anneal_npoints[i] - 1;
3813 if (ir->opts.annealing[i] == SimulatedAnnealing::Single)
3817 ir->opts.anneal_time[i][j],
3818 ir->opts.anneal_temp[i][j]);
3824 ir->opts.anneal_time[i][j],
3825 ir->opts.anneal_temp[i][j]);
3826 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3829 "There is a temperature jump when your annealing "
3841 for (int i = 1; i < ir->pull->ngroup; i++)
3843 const int gid = search_string(
3844 inputrecStrings->pullGroupNames[i].c_str(), defaultIndexGroups->nr, gnames);
3845 GMX_ASSERT(defaultIndexGroups, "Must have initialized default index groups");
3846 atomGroupRangeValidation(natoms, gid, *defaultIndexGroups);
3849 process_pull_groups(ir->pull->group, inputrecStrings->pullGroupNames, defaultIndexGroups, gnames);
3851 checkPullCoords(ir->pull->group, ir->pull->coord);
3856 make_rotation_groups(ir->rot, inputrecStrings->rotateGroupNames, defaultIndexGroups, gnames);
3859 if (ir->eSwapCoords != SwapType::No)
3861 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3864 /* Make indices for IMD session */
3867 make_IMD_group(ir->imd, inputrecStrings->imd_grp, defaultIndexGroups, gnames);
3870 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3871 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3872 notifier.preProcessingNotifications_.notify(defaultIndexGroupsAndNames);
3874 auto freezeDims = gmx::splitString(inputrecStrings->frdim);
3875 auto freezeGroupNames = gmx::splitString(inputrecStrings->freeze);
3876 if (freezeDims.size() != DIM * freezeGroupNames.size())
3879 "Invalid Freezing input: %zu groups and %zu freeze values",
3880 freezeGroupNames.size(),
3883 do_numbering(natoms,
3888 SimulationAtomGroupType::Freeze,
3893 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3894 ir->opts.ngfrz = nr;
3895 snew(ir->opts.nFreeze, nr);
3896 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3898 for (j = 0; (j < DIM); j++, k++)
3900 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3901 if (!ir->opts.nFreeze[i][j])
3903 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3906 "Please use Y(ES) or N(O) for freezedim only "
3908 freezeDims[k].c_str());
3909 warning(wi, warn_buf);
3914 for (; (i < nr); i++)
3916 for (j = 0; (j < DIM); j++)
3918 ir->opts.nFreeze[i][j] = 0;
3922 auto energyGroupNames = gmx::splitString(inputrecStrings->energy);
3923 do_numbering(natoms,
3928 SimulationAtomGroupType::EnergyOutput,
3933 add_wall_energrps(groups, ir->nwall, symtab);
3934 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3935 auto vcmGroupNames = gmx::splitString(inputrecStrings->vcm);
3936 do_numbering(natoms,
3941 SimulationAtomGroupType::MassCenterVelocityRemoval,
3943 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART,
3947 if (ir->comm_mode != ComRemovalAlgorithm::No)
3949 checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
3952 /* Now we have filled the freeze struct, so we can calculate NRDF */
3953 calc_nrdf(mtop, ir, gnames);
3955 auto user1GroupNames = gmx::splitString(inputrecStrings->user1);
3956 do_numbering(natoms,
3961 SimulationAtomGroupType::User1,
3966 auto user2GroupNames = gmx::splitString(inputrecStrings->user2);
3967 do_numbering(natoms,
3972 SimulationAtomGroupType::User2,
3977 auto compressedXGroupNames = gmx::splitString(inputrecStrings->x_compressed_groups);
3978 do_numbering(natoms,
3980 compressedXGroupNames,
3983 SimulationAtomGroupType::CompressedPositionOutput,
3988 auto orirefFitGroupNames = gmx::splitString(inputrecStrings->orirefitgrp);
3989 do_numbering(natoms,
3991 orirefFitGroupNames,
3994 SimulationAtomGroupType::OrientationRestraintsFit,
4000 /* MiMiC QMMM input processing */
4001 auto qmGroupNames = gmx::splitString(inputrecStrings->QMMM);
4002 if (qmGroupNames.size() > 1)
4004 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
4006 /* group rest, if any, is always MM! */
4007 do_numbering(natoms,
4012 SimulationAtomGroupType::QuantumMechanics,
4017 ir->opts.ngQM = qmGroupNames.size();
4019 /* end of MiMiC QMMM input */
4023 for (auto group : gmx::keysOf(groups->groups))
4025 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
4026 for (const auto& entry : groups->groups[group])
4028 fprintf(stderr, " %s", *(groups->groupNames[entry]));
4030 fprintf(stderr, "\n");
4034 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
4035 snew(ir->opts.egp_flags, nr * nr);
4037 bExcl = do_egp_flag(ir, groups, "energygrp-excl", inputrecStrings->egpexcl, EGP_EXCL);
4038 if (bExcl && ir->cutoff_scheme == CutoffScheme::Verlet)
4040 warning_error(wi, "Energy group exclusions are currently not supported");
4042 if (bExcl && EEL_FULL(ir->coulombtype))
4044 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
4047 bTable = do_egp_flag(ir, groups, "energygrp-table", inputrecStrings->egptable, EGP_TABLE);
4048 if (bTable && !(ir->vdwtype == VanDerWaalsType::User)
4049 && !(ir->coulombtype == CoulombInteractionType::User)
4050 && !(ir->coulombtype == CoulombInteractionType::PmeUser)
4051 && !(ir->coulombtype == CoulombInteractionType::PmeUserSwitch))
4054 "Can only have energy group pair tables in combination with user tables for VdW "
4058 /* final check before going out of scope if simulated tempering variables
4059 * need to be set to default values.
4061 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
4063 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
4066 "the value for nstexpanded was not specified for "
4067 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
4068 "by default, but it is recommended to set it to an explicit value!",
4069 ir->expandedvals->nstexpanded));
4071 for (i = 0; (i < defaultIndexGroups->nr); i++)
4076 done_blocka(defaultIndexGroups);
4077 sfree(defaultIndexGroups);
4081 static void check_disre(const gmx_mtop_t& mtop)
4083 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
4085 const gmx_ffparams_t& ffparams = mtop.ffparams;
4088 for (int i = 0; i < ffparams.numTypes(); i++)
4090 int ftype = ffparams.functype[i];
4091 if (ftype == F_DISRES)
4093 int label = ffparams.iparams[i].disres.label;
4094 if (label == old_label)
4096 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
4105 "Found %d double distance restraint indices,\n"
4106 "probably the parameters for multiple pairs in one restraint "
4107 "are not identical\n",
4113 static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t& sys, const bool posres_only, ivec AbsRef)
4116 gmx_mtop_ilistloop_t iloop;
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 iloop = gmx_mtop_ilistloop_init(sys);
4144 while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
4146 if (nmol > 0 && (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
4148 for (i = 0; i < (*ilist)[F_POSRES].size(); i += 2)
4150 pr = &sys.ffparams.iparams[(*ilist)[F_POSRES].iatoms[i]];
4151 for (d = 0; d < DIM; d++)
4153 if (pr->posres.fcA[d] != 0)
4159 for (i = 0; i < (*ilist)[F_FBPOSRES].size(); i += 2)
4161 /* Check for flat-bottom posres */
4162 pr = &sys.ffparams.iparams[(*ilist)[F_FBPOSRES].iatoms[i]];
4163 if (pr->fbposres.k != 0)
4165 switch (pr->fbposres.geom)
4167 case efbposresSPHERE: AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1; break;
4168 case efbposresCYLINDERX: AbsRef[YY] = AbsRef[ZZ] = 1; break;
4169 case efbposresCYLINDERY: AbsRef[XX] = AbsRef[ZZ] = 1; break;
4170 case efbposresCYLINDER:
4171 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
4172 case efbposresCYLINDERZ: AbsRef[XX] = AbsRef[YY] = 1; break;
4173 case efbposresX: /* d=XX */
4174 case efbposresY: /* d=YY */
4175 case efbposresZ: /* d=ZZ */
4176 d = pr->fbposres.geom - efbposresX;
4181 " Invalid geometry for flat-bottom position restraint.\n"
4182 "Expected nr between 1 and %d. Found %d\n",
4191 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
4194 static void check_combination_rule_differences(const gmx_mtop_t& mtop,
4196 bool* bC6ParametersWorkWithGeometricRules,
4197 bool* bC6ParametersWorkWithLBRules,
4198 bool* bLBRulesPossible)
4200 int ntypes, tpi, tpj;
4203 double c6i, c6j, c12i, c12j;
4204 double c6, c6_geometric, c6_LB;
4205 double sigmai, sigmaj, epsi, epsj;
4206 bool bCanDoLBRules, bCanDoGeometricRules;
4209 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
4210 * force-field floating point parameters.
4213 ptr = getenv("GMX_LJCOMB_TOL");
4217 double gmx_unused canary;
4219 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
4222 FARGS, "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
4227 *bC6ParametersWorkWithLBRules = TRUE;
4228 *bC6ParametersWorkWithGeometricRules = TRUE;
4229 bCanDoLBRules = TRUE;
4230 ntypes = mtop.ffparams.atnr;
4231 snew(typecount, ntypes);
4232 gmx_mtop_count_atomtypes(mtop, state, typecount);
4233 *bLBRulesPossible = TRUE;
4234 for (tpi = 0; tpi < ntypes; ++tpi)
4236 c6i = mtop.ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
4237 c12i = mtop.ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
4238 for (tpj = tpi; tpj < ntypes; ++tpj)
4240 c6j = mtop.ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
4241 c12j = mtop.ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
4242 c6 = mtop.ffparams.iparams[ntypes * tpi + tpj].lj.c6;
4243 c6_geometric = std::sqrt(c6i * c6j);
4244 if (!gmx_numzero(c6_geometric))
4246 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4248 sigmai = gmx::sixthroot(c12i / c6i);
4249 sigmaj = gmx::sixthroot(c12j / c6j);
4250 epsi = c6i * c6i / (4.0 * c12i);
4251 epsj = c6j * c6j / (4.0 * c12j);
4252 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4256 *bLBRulesPossible = FALSE;
4257 c6_LB = c6_geometric;
4259 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4264 *bC6ParametersWorkWithLBRules = FALSE;
4267 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4269 if (!bCanDoGeometricRules)
4271 *bC6ParametersWorkWithGeometricRules = FALSE;
4278 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t& mtop, warninp_t wi)
4280 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4282 check_combination_rule_differences(
4283 mtop, 0, &bC6ParametersWorkWithGeometricRules, &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4284 if (ir->ljpme_combination_rule == LongRangeVdW::LB)
4286 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4289 "You are using arithmetic-geometric combination rules "
4290 "in LJ-PME, but your non-bonded C6 parameters do not "
4291 "follow these rules.");
4296 if (!bC6ParametersWorkWithGeometricRules)
4298 if (ir->eDispCorr != DispersionCorrectionType::No)
4301 "You are using geometric combination rules in "
4302 "LJ-PME, but your non-bonded C6 parameters do "
4303 "not follow these rules. "
4304 "This will introduce very small errors in the forces and energies in "
4305 "your simulations. Dispersion correction will correct total energy "
4306 "and/or pressure for isotropic systems, but not forces or surface "
4312 "You are using geometric combination rules in "
4313 "LJ-PME, but your non-bonded C6 parameters do "
4314 "not follow these rules. "
4315 "This will introduce very small errors in the forces and energies in "
4316 "your simulations. If your system is homogeneous, consider using "
4317 "dispersion correction "
4318 "for the total energy and pressure.");
4324 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4326 // Not meeting MTS requirements should have resulted in a fatal error, so we can assert here
4327 GMX_ASSERT(gmx::checkMtsRequirements(*ir).empty(), "All MTS requirements should be met here");
4329 char err_buf[STRLEN];
4332 gmx_mtop_atomloop_block_t aloopb;
4334 char warn_buf[STRLEN];
4336 set_warning_line(wi, mdparin, -1);
4338 if (absolute_reference(ir, *sys, false, AbsRef))
4341 "Removing center of mass motion in the presence of position restraints might "
4342 "cause artifacts. When you are using position restraints to equilibrate a "
4343 "macro-molecule, the artifacts are usually negligible.");
4346 if (ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0 && ir->nstlist > 1
4347 && ((EI_MD(ir->eI) || EI_SD(ir->eI))
4348 && (ir->etc == TemperatureCoupling::VRescale || ir->etc == TemperatureCoupling::Berendsen)))
4350 /* Check if a too small Verlet buffer might potentially
4351 * cause more drift than the thermostat can couple off.
4353 /* Temperature error fraction for warning and suggestion */
4354 const real T_error_warn = 0.002;
4355 const real T_error_suggest = 0.001;
4356 /* For safety: 2 DOF per atom (typical with constraints) */
4357 const real nrdf_at = 2;
4358 real T, tau, max_T_error;
4363 for (i = 0; i < ir->opts.ngtc; i++)
4365 T = std::max(T, ir->opts.ref_t[i]);
4366 tau = std::max(tau, ir->opts.tau_t[i]);
4370 /* This is a worst case estimate of the temperature error,
4371 * assuming perfect buffer estimation and no cancelation
4372 * of errors. The factor 0.5 is because energy distributes
4373 * equally over Ekin and Epot.
4375 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * gmx::c_boltz * T);
4376 if (max_T_error > T_error_warn)
4379 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4380 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4381 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4382 "%.0e or decrease tau_t.",
4387 100 * T_error_suggest,
4388 ir->verletbuf_tol * T_error_suggest / max_T_error);
4389 warning(wi, warn_buf);
4394 if (ETC_ANDERSEN(ir->etc))
4398 for (i = 0; i < ir->opts.ngtc; i++)
4401 "all tau_t must currently be equal using Andersen temperature control, "
4402 "violated for group %d",
4404 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4406 "all tau_t must be positive using Andersen temperature control, "
4410 CHECK(ir->opts.tau_t[i] < 0);
4413 if (ir->etc == TemperatureCoupling::AndersenMassive && ir->comm_mode != ComRemovalAlgorithm::No)
4415 for (i = 0; i < ir->opts.ngtc; i++)
4417 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4419 "tau_t/delta_t for group %d for temperature control method %s must be a "
4420 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4421 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4424 enumValueToString(ir->etc),
4428 CHECK(nsteps % ir->nstcomm != 0);
4433 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != IntegrationAlgorithm::BD
4434 && ir->comm_mode == ComRemovalAlgorithm::No
4435 && !(absolute_reference(ir, *sys, FALSE, AbsRef) || ir->nsteps <= 10) && !ETC_ANDERSEN(ir->etc))
4438 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4439 "rounding errors can lead to build up of kinetic energy of the center of mass");
4442 if (ir->epc == PressureCoupling::ParrinelloRahman && ir->etc == TemperatureCoupling::NoseHoover)
4445 for (int g = 0; g < ir->opts.ngtc; g++)
4447 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4449 if (ir->tau_p < 1.9 * tau_t_max)
4451 std::string message = gmx::formatString(
4452 "With %s T-coupling and %s p-coupling, "
4453 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4454 enumValueToString(ir->etc),
4455 enumValueToString(ir->epc),
4460 warning(wi, message.c_str());
4464 /* Check for pressure coupling with absolute position restraints */
4465 if (ir->epc != PressureCoupling::No && ir->refcoord_scaling == RefCoordScaling::No)
4467 absolute_reference(ir, *sys, TRUE, AbsRef);
4469 for (m = 0; m < DIM; m++)
4471 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4474 "You are using pressure coupling with absolute position restraints, "
4475 "this will give artifacts. Use the refcoord_scaling option.");
4483 aloopb = gmx_mtop_atomloop_block_init(*sys);
4485 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4487 if (atom->q != 0 || atom->qB != 0)
4495 if (EEL_FULL(ir->coulombtype))
4498 "You are using full electrostatics treatment %s for a system without charges.\n"
4499 "This costs a lot of performance for just processing zeros, consider using %s "
4501 enumValueToString(ir->coulombtype),
4502 enumValueToString(CoulombInteractionType::Cut));
4503 warning(wi, err_buf);
4508 if (ir->coulombtype == CoulombInteractionType::Cut && ir->rcoulomb > 0)
4511 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4512 "You might want to consider using %s electrostatics.\n",
4513 enumValueToString(CoulombInteractionType::Pme));
4514 warning_note(wi, err_buf);
4518 /* Check if combination rules used in LJ-PME are the same as in the force field */
4519 if (EVDW_PME(ir->vdwtype))
4521 check_combination_rules(ir, *sys, wi);
4524 /* Generalized reaction field */
4525 if (ir->coulombtype == CoulombInteractionType::GRFNotused)
4528 "Generalized reaction-field electrostatics is no longer supported. "
4529 "You can use normal reaction-field instead and compute the reaction-field "
4530 "constant by hand.");
4533 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->sc_alpha != 0
4534 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4536 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4544 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4546 if (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0)
4548 absolute_reference(ir, *sys, FALSE, AbsRef);
4549 for (m = 0; m < DIM; m++)
4551 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4554 "You are using an absolute reference for pulling, but the rest of "
4555 "the system does not have an absolute reference. This will lead to "
4564 for (i = 0; i < 3; i++)
4566 for (m = 0; m <= i; m++)
4568 if ((ir->epc != PressureCoupling::No && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4570 for (c = 0; c < ir->pull->ncoord; c++)
4572 if (ir->pull->coord[c].eGeom == PullGroupGeometry::DirectionPBC
4573 && ir->pull->coord[c].vec[m] != 0)
4576 "Can not have dynamic box while using pull geometry '%s' "
4578 enumValueToString(ir->pull->coord[c].eGeom),
4590 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4592 char warn_buf[STRLEN];
4595 ptr = check_box(ir->pbcType, box);
4598 warning_error(wi, ptr);
4601 if (bHasNormalConstraints && ir->eConstrAlg == ConstraintAlgorithm::Shake)
4603 if (ir->shake_tol <= 0.0)
4605 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4606 warning_error(wi, warn_buf);
4610 if ((ir->eConstrAlg == ConstraintAlgorithm::Lincs) && bHasNormalConstraints)
4612 /* If we have Lincs constraints: */
4613 if (ir->eI == IntegrationAlgorithm::MD && ir->etc == TemperatureCoupling::No
4614 && ir->eConstrAlg == ConstraintAlgorithm::Lincs && ir->nLincsIter == 1)
4617 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4618 warning_note(wi, warn_buf);
4621 if ((ir->eI == IntegrationAlgorithm::CG || ir->eI == IntegrationAlgorithm::LBFGS)
4622 && (ir->nProjOrder < 8))
4625 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4626 enumValueToString(ir->eI));
4627 warning_note(wi, warn_buf);
4629 if (ir->epc == PressureCoupling::Mttk)
4631 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4635 if (bHasAnyConstraints && ir->epc == PressureCoupling::Mttk)
4637 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4640 if (ir->LincsWarnAngle > 90.0)
4642 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4643 warning(wi, warn_buf);
4644 ir->LincsWarnAngle = 90.0;
4647 if (ir->pbcType != PbcType::No)
4649 if (ir->nstlist == 0)
4652 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4653 "atoms might cause the simulation to crash.");
4655 if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
4658 "ERROR: The cut-off length is longer than half the shortest box vector or "
4659 "longer than the smallest box diagonal element. Increase the box size or "
4660 "decrease rlist.\n");
4661 warning_error(wi, warn_buf);