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51 #include "gromacs/applied_forces/awh/read_params.h"
52 #include "gromacs/fileio/readinp.h"
53 #include "gromacs/fileio/warninp.h"
54 #include "gromacs/gmxlib/network.h"
55 #include "gromacs/gmxpreprocess/toputil.h"
56 #include "gromacs/math/functions.h"
57 #include "gromacs/math/units.h"
58 #include "gromacs/math/vec.h"
59 #include "gromacs/mdlib/calc_verletbuf.h"
60 #include "gromacs/mdrun/mdmodules.h"
61 #include "gromacs/mdtypes/inputrec.h"
62 #include "gromacs/mdtypes/md_enums.h"
63 #include "gromacs/mdtypes/multipletimestepping.h"
64 #include "gromacs/mdtypes/pull_params.h"
65 #include "gromacs/options/options.h"
66 #include "gromacs/options/treesupport.h"
67 #include "gromacs/pbcutil/pbc.h"
68 #include "gromacs/selection/indexutil.h"
69 #include "gromacs/topology/block.h"
70 #include "gromacs/topology/ifunc.h"
71 #include "gromacs/topology/index.h"
72 #include "gromacs/topology/mtop_util.h"
73 #include "gromacs/topology/symtab.h"
74 #include "gromacs/topology/topology.h"
75 #include "gromacs/utility/cstringutil.h"
76 #include "gromacs/utility/exceptions.h"
77 #include "gromacs/utility/fatalerror.h"
78 #include "gromacs/utility/filestream.h"
79 #include "gromacs/utility/gmxassert.h"
80 #include "gromacs/utility/ikeyvaluetreeerror.h"
81 #include "gromacs/utility/keyvaluetree.h"
82 #include "gromacs/utility/keyvaluetreebuilder.h"
83 #include "gromacs/utility/keyvaluetreemdpwriter.h"
84 #include "gromacs/utility/keyvaluetreetransform.h"
85 #include "gromacs/utility/mdmodulenotification.h"
86 #include "gromacs/utility/smalloc.h"
87 #include "gromacs/utility/strconvert.h"
88 #include "gromacs/utility/stringcompare.h"
89 #include "gromacs/utility/stringutil.h"
90 #include "gromacs/utility/textwriter.h"
95 /* Resource parameters
96 * Do not change any of these until you read the instruction
97 * in readinp.h. Some cpp's do not take spaces after the backslash
98 * (like the c-shell), which will give you a very weird compiler
102 struct gmx_inputrec_strings
104 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN], acc[STRLEN], accgrps[STRLEN], freeze[STRLEN],
105 frdim[STRLEN], energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN],
106 x_compressed_groups[STRLEN], couple_moltype[STRLEN], orirefitgrp[STRLEN],
107 egptable[STRLEN], egpexcl[STRLEN], wall_atomtype[STRLEN], wall_density[STRLEN],
108 deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
109 char fep_lambda[efptNR][STRLEN];
110 char lambda_weights[STRLEN];
111 std::vector<std::string> pullGroupNames;
112 std::vector<std::string> rotateGroupNames;
113 char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
116 static gmx_inputrec_strings* inputrecStrings = nullptr;
118 void init_inputrec_strings()
123 "Attempted to call init_inputrec_strings before calling done_inputrec_strings. "
124 "Only one inputrec (i.e. .mdp file) can be parsed at a time.");
126 inputrecStrings = new gmx_inputrec_strings();
129 void done_inputrec_strings()
131 delete inputrecStrings;
132 inputrecStrings = nullptr;
138 egrptpALL, /* All particles have to be a member of a group. */
139 egrptpALL_GENREST, /* A rest group with name is generated for particles *
140 * that are not part of any group. */
141 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
142 * for the rest group. */
143 egrptpONE /* Merge all selected groups into one group, *
144 * make a rest group for the remaining particles. */
147 static const char* constraints[eshNR + 1] = { "none", "h-bonds", "all-bonds",
148 "h-angles", "all-angles", nullptr };
150 static const char* couple_lam[ecouplamNR + 1] = { "vdw-q", "vdw", "q", "none", nullptr };
152 static void GetSimTemps(int ntemps, t_simtemp* simtemp, double* temperature_lambdas)
157 for (i = 0; i < ntemps; i++)
159 /* simple linear scaling -- allows more control */
160 if (simtemp->eSimTempScale == esimtempLINEAR)
162 simtemp->temperatures[i] =
164 + (simtemp->simtemp_high - simtemp->simtemp_low) * temperature_lambdas[i];
166 else if (simtemp->eSimTempScale
167 == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
169 simtemp->temperatures[i] = simtemp->simtemp_low
170 * std::pow(simtemp->simtemp_high / simtemp->simtemp_low,
171 static_cast<real>((1.0 * i) / (ntemps - 1)));
173 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
175 simtemp->temperatures[i] = simtemp->simtemp_low
176 + (simtemp->simtemp_high - simtemp->simtemp_low)
177 * (std::expm1(temperature_lambdas[i]) / std::expm1(1.0));
182 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
183 gmx_fatal(FARGS, "%s", errorstr);
189 static void _low_check(bool b, const char* s, warninp_t wi)
193 warning_error(wi, s);
197 static void check_nst(const char* desc_nst, int nst, const char* desc_p, int* p, warninp_t wi)
201 if (*p > 0 && *p % nst != 0)
203 /* Round up to the next multiple of nst */
204 *p = ((*p) / nst + 1) * nst;
205 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n", desc_p, desc_nst, desc_p, *p);
210 static int lcd(int n1, int n2)
215 for (i = 2; (i <= n1 && i <= n2); i++)
217 if (n1 % i == 0 && n2 % i == 0)
226 //! Convert legacy mdp entries to modern ones.
227 static void process_interaction_modifier(int* eintmod)
229 if (*eintmod == eintmodPOTSHIFT_VERLET_UNSUPPORTED)
231 *eintmod = eintmodPOTSHIFT;
235 void check_ir(const char* mdparin,
236 const gmx::MdModulesNotifier& mdModulesNotifier,
240 /* Check internal consistency.
241 * NOTE: index groups are not set here yet, don't check things
242 * like temperature coupling group options here, but in triple_check
245 /* Strange macro: first one fills the err_buf, and then one can check
246 * the condition, which will print the message and increase the error
249 #define CHECK(b) _low_check(b, err_buf, wi)
250 char err_buf[256], warn_buf[STRLEN];
253 t_lambda* fep = ir->fepvals;
254 t_expanded* expand = ir->expandedvals;
256 set_warning_line(wi, mdparin, -1);
258 /* We cannot check MTS requirements with an invalid MTS setup
259 * and we will already have generated errors with an invalid MTS setup.
261 if (gmx::haveValidMtsSetup(*ir))
263 std::vector<std::string> errorMessages = gmx::checkMtsRequirements(*ir);
265 for (const auto& errorMessage : errorMessages)
267 warning_error(wi, errorMessage.c_str());
271 if (ir->coulombtype == eelRF_NEC_UNSUPPORTED)
273 sprintf(warn_buf, "%s electrostatics is no longer supported", eel_names[eelRF_NEC_UNSUPPORTED]);
274 warning_error(wi, warn_buf);
277 /* BASIC CUT-OFF STUFF */
278 if (ir->rcoulomb < 0)
280 warning_error(wi, "rcoulomb should be >= 0");
284 warning_error(wi, "rvdw should be >= 0");
286 if (ir->rlist < 0 && !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
288 warning_error(wi, "rlist should be >= 0");
291 "nstlist can not be smaller than 0. (If you were trying to use the heuristic "
292 "neighbour-list update scheme for efficient buffering for improved energy "
293 "conservation, please use the Verlet cut-off scheme instead.)");
294 CHECK(ir->nstlist < 0);
296 process_interaction_modifier(&ir->coulomb_modifier);
297 process_interaction_modifier(&ir->vdw_modifier);
299 if (ir->cutoff_scheme == ecutsGROUP)
302 "The group cutoff scheme has been removed since GROMACS 2020. "
303 "Please use the Verlet cutoff scheme.");
305 if (ir->cutoff_scheme == ecutsVERLET)
309 /* Normal Verlet type neighbor-list, currently only limited feature support */
310 if (inputrec2nboundeddim(ir) < 3)
312 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
315 // We don't (yet) have general Verlet kernels for rcoulomb!=rvdw
316 if (ir->rcoulomb != ir->rvdw)
318 // Since we have PME coulomb + LJ cut-off kernels with rcoulomb>rvdw
319 // for PME load balancing, we can support this exception.
320 bool bUsesPmeTwinRangeKernel = (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == evdwCUT
321 && ir->rcoulomb > ir->rvdw);
322 if (!bUsesPmeTwinRangeKernel)
325 "With Verlet lists rcoulomb!=rvdw is not supported (except for "
326 "rcoulomb>rvdw with PME electrostatics)");
330 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
332 if (ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT)
334 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
337 "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and "
339 evdw_names[ir->vdwtype],
341 eintmod_names[ir->vdw_modifier]);
342 warning_note(wi, warn_buf);
344 ir->vdwtype = evdwCUT;
349 "Unsupported combination of vdwtype=%s and vdw_modifier=%s",
350 evdw_names[ir->vdwtype],
351 eintmod_names[ir->vdw_modifier]);
352 warning_error(wi, warn_buf);
356 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
359 "With Verlet lists only cut-off and PME LJ interactions are supported");
361 if (!(ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype) || EEL_PME(ir->coulombtype)
362 || ir->coulombtype == eelEWALD))
365 "With Verlet lists only cut-off, reaction-field, PME and Ewald "
366 "electrostatics are supported");
368 if (!(ir->coulomb_modifier == eintmodNONE || ir->coulomb_modifier == eintmodPOTSHIFT))
370 sprintf(warn_buf, "coulomb_modifier=%s is not supported", eintmod_names[ir->coulomb_modifier]);
371 warning_error(wi, warn_buf);
374 if (EEL_USER(ir->coulombtype))
377 "Coulomb type %s is not supported with the verlet scheme",
378 eel_names[ir->coulombtype]);
379 warning_error(wi, warn_buf);
382 if (ir->nstlist <= 0)
384 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
387 if (ir->nstlist < 10)
390 "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note "
391 "that with the Verlet scheme, nstlist has no effect on the accuracy of "
395 rc_max = std::max(ir->rvdw, ir->rcoulomb);
399 /* With TPI we set the pairlist cut-off later using the radius of the insterted molecule */
400 ir->verletbuf_tol = 0;
403 else if (ir->verletbuf_tol <= 0)
405 if (ir->verletbuf_tol == 0)
407 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
410 if (ir->rlist < rc_max)
413 "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
416 if (ir->rlist == rc_max && ir->nstlist > 1)
420 "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet "
421 "buffer. The cluster pair list does have a buffering effect, but choosing "
422 "a larger rlist might be necessary for good energy conservation.");
427 if (ir->rlist > rc_max)
430 "You have set rlist larger than the interaction cut-off, but you also "
431 "have verlet-buffer-tolerance > 0. Will set rlist using "
432 "verlet-buffer-tolerance.");
435 if (ir->nstlist == 1)
437 /* No buffer required */
442 if (EI_DYNAMICS(ir->eI))
444 if (inputrec2nboundeddim(ir) < 3)
447 "The box volume is required for calculating rlist from the "
448 "energy drift with verlet-buffer-tolerance > 0. You are "
449 "using at least one unbounded dimension, so no volume can be "
450 "computed. Either use a finite box, or set rlist yourself "
451 "together with verlet-buffer-tolerance = -1.");
453 /* Set rlist temporarily so we can continue processing */
458 /* Set the buffer to 5% of the cut-off */
459 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics) * rc_max;
465 /* GENERAL INTEGRATOR STUFF */
468 if (ir->etc != etcNO)
470 if (EI_RANDOM(ir->eI))
473 "Setting tcoupl from '%s' to 'no'. %s handles temperature coupling "
474 "implicitly. See the documentation for more information on which "
475 "parameters affect temperature for %s.",
476 etcoupl_names[ir->etc],
483 "Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to "
485 etcoupl_names[ir->etc],
488 warning_note(wi, warn_buf);
492 if (ir->eI == eiVVAK)
495 "Integrator method %s is implemented primarily for validation purposes; for "
496 "molecular dynamics, you should probably be using %s or %s",
500 warning_note(wi, warn_buf);
502 if (!EI_DYNAMICS(ir->eI))
504 if (ir->epc != epcNO)
507 "Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.",
508 epcoupl_names[ir->epc],
510 warning_note(wi, warn_buf);
514 if (EI_DYNAMICS(ir->eI))
516 if (ir->nstcalcenergy < 0)
518 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
519 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
521 /* nstcalcenergy larger than nstener does not make sense.
522 * We ideally want nstcalcenergy=nstener.
526 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
530 ir->nstcalcenergy = ir->nstenergy;
534 else if ((ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy)
535 || (ir->efep != efepNO && ir->fepvals->nstdhdl > 0
536 && (ir->nstcalcenergy > ir->fepvals->nstdhdl)))
539 const char* nsten = "nstenergy";
540 const char* nstdh = "nstdhdl";
541 const char* min_name = nsten;
542 int min_nst = ir->nstenergy;
544 /* find the smallest of ( nstenergy, nstdhdl ) */
545 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0
546 && (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
548 min_nst = ir->fepvals->nstdhdl;
551 /* If the user sets nstenergy small, we should respect that */
552 sprintf(warn_buf, "Setting nstcalcenergy (%d) equal to %s (%d)", ir->nstcalcenergy, min_name, min_nst);
553 warning_note(wi, warn_buf);
554 ir->nstcalcenergy = min_nst;
557 if (ir->epc != epcNO)
559 if (ir->nstpcouple < 0)
561 ir->nstpcouple = ir_optimal_nstpcouple(ir);
563 if (ir->useMts && ir->nstpcouple % ir->mtsLevels.back().stepFactor != 0)
566 "With multiple time stepping, nstpcouple should be a mutiple of "
571 if (ir->nstcalcenergy > 0)
573 if (ir->efep != efepNO)
575 /* nstdhdl should be a multiple of nstcalcenergy */
576 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstdhdl", &ir->fepvals->nstdhdl, wi);
580 /* nstexpanded should be a multiple of nstcalcenergy */
581 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstexpanded", &ir->expandedvals->nstexpanded, wi);
583 /* for storing exact averages nstenergy should be
584 * a multiple of nstcalcenergy
586 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstenergy", &ir->nstenergy, wi);
589 // Inquire all MdModules, if their parameters match with the energy
590 // calculation frequency
591 gmx::EnergyCalculationFrequencyErrors energyCalculationFrequencyErrors(ir->nstcalcenergy);
592 mdModulesNotifier.preProcessingNotifications_.notify(&energyCalculationFrequencyErrors);
594 // Emit all errors from the energy calculation frequency checks
595 for (const std::string& energyFrequencyErrorMessage :
596 energyCalculationFrequencyErrors.errorMessages())
598 warning_error(wi, energyFrequencyErrorMessage);
602 if (ir->nsteps == 0 && !ir->bContinuation)
605 "For a correct single-point energy evaluation with nsteps = 0, use "
606 "continuation = yes to avoid constraining the input coordinates.");
610 if ((EI_SD(ir->eI) || ir->eI == eiBD) && ir->bContinuation && ir->ld_seed != -1)
613 "You are doing a continuation with SD or BD, make sure that ld_seed is "
614 "different from the previous run (using ld_seed=-1 will ensure this)");
620 sprintf(err_buf, "TPI only works with pbc = %s", c_pbcTypeNames[PbcType::Xyz].c_str());
621 CHECK(ir->pbcType != PbcType::Xyz);
622 sprintf(err_buf, "with TPI nstlist should be larger than zero");
623 CHECK(ir->nstlist <= 0);
624 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
625 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
629 if ((opts->nshake > 0) && (opts->bMorse))
631 sprintf(warn_buf, "Using morse bond-potentials while constraining bonds is useless");
632 warning(wi, warn_buf);
635 if ((EI_SD(ir->eI) || ir->eI == eiBD) && ir->bContinuation && ir->ld_seed != -1)
638 "You are doing a continuation with SD or BD, make sure that ld_seed is "
639 "different from the previous run (using ld_seed=-1 will ensure this)");
641 /* verify simulated tempering options */
645 bool bAllTempZero = TRUE;
646 for (i = 0; i < fep->n_lambda; i++)
649 "Entry %d for %s must be between 0 and 1, instead is %g",
651 efpt_names[efptTEMPERATURE],
652 fep->all_lambda[efptTEMPERATURE][i]);
653 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
654 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
656 bAllTempZero = FALSE;
659 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
660 CHECK(bAllTempZero == TRUE);
662 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
663 CHECK(ir->eI != eiVV);
665 /* check compatability of the temperature coupling with simulated tempering */
667 if (ir->etc == etcNOSEHOOVER)
670 "Nose-Hoover based temperature control such as [%s] my not be "
671 "entirelyconsistent with simulated tempering",
672 etcoupl_names[ir->etc]);
673 warning_note(wi, warn_buf);
676 /* check that the temperatures make sense */
679 "Higher simulated tempering temperature (%g) must be >= than the simulated "
680 "tempering lower temperature (%g)",
681 ir->simtempvals->simtemp_high,
682 ir->simtempvals->simtemp_low);
683 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
686 "Higher simulated tempering temperature (%g) must be >= zero",
687 ir->simtempvals->simtemp_high);
688 CHECK(ir->simtempvals->simtemp_high <= 0);
691 "Lower simulated tempering temperature (%g) must be >= zero",
692 ir->simtempvals->simtemp_low);
693 CHECK(ir->simtempvals->simtemp_low <= 0);
696 /* verify free energy options */
698 if (ir->efep != efepNO)
701 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2", fep->sc_power);
702 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
705 "The soft-core sc-r-power is %d and can only be 6. (sc-r-power 48 is no longer "
707 static_cast<int>(fep->sc_r_power));
708 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0);
711 "Can't use positive delta-lambda (%g) if initial state/lambda does not start at "
714 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
717 "Can't use positive delta-lambda (%g) with expanded ensemble simulations",
719 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
721 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
722 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
724 sprintf(err_buf, "Free-energy not implemented for Ewald");
725 CHECK(ir->coulombtype == eelEWALD);
727 /* check validty of lambda inputs */
728 if (fep->n_lambda == 0)
730 /* Clear output in case of no states:*/
731 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
732 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
737 "initial thermodynamic state %d does not exist, only goes to %d",
740 CHECK((fep->init_fep_state >= fep->n_lambda));
744 "Lambda state must be set, either with init-lambda-state or with init-lambda");
745 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
748 "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with "
749 "init-lambda-state or with init-lambda, but not both",
751 fep->init_fep_state);
752 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
755 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
759 for (i = 0; i < efptNR; i++)
761 if (fep->separate_dvdl[i])
766 if (n_lambda_terms > 1)
769 "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't "
770 "use init-lambda to set lambda state (except for slow growth). Use "
771 "init-lambda-state instead.");
772 warning(wi, warn_buf);
775 if (n_lambda_terms < 2 && fep->n_lambda > 0)
778 "init-lambda is deprecated for setting lambda state (except for slow "
779 "growth). Use init-lambda-state instead.");
783 for (j = 0; j < efptNR; j++)
785 for (i = 0; i < fep->n_lambda; i++)
788 "Entry %d for %s must be between 0 and 1, instead is %g",
791 fep->all_lambda[j][i]);
792 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
796 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
798 for (i = 0; i < fep->n_lambda; i++)
801 "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while "
802 "coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to "
803 "crashes, and is not supported.",
805 fep->all_lambda[efptVDW][i],
806 fep->all_lambda[efptCOUL][i]);
807 CHECK((fep->sc_alpha > 0)
808 && (((fep->all_lambda[efptCOUL][i] > 0.0) && (fep->all_lambda[efptCOUL][i] < 1.0))
809 && ((fep->all_lambda[efptVDW][i] > 0.0) && (fep->all_lambda[efptVDW][i] < 1.0))));
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 < efptNR; i++)
841 for (j = 0; j < fep->n_lambda; j++)
843 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
844 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
849 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
853 /* checking equilibration of weights inputs for validity */
856 "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal "
858 expand->equil_n_at_lam,
859 elmceq_names[elmceqNUMATLAM]);
860 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
863 "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to "
865 expand->equil_samples,
866 elmceq_names[elmceqSAMPLES]);
867 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
870 "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
872 elmceq_names[elmceqSTEPS]);
873 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
876 "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
877 expand->equil_samples,
878 elmceq_names[elmceqWLDELTA]);
879 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
882 "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
884 elmceq_names[elmceqRATIO]);
885 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
888 "weight-equil-number-all-lambda (%d) must be a positive integer if "
889 "lmc-weights-equil=%s",
890 expand->equil_n_at_lam,
891 elmceq_names[elmceqNUMATLAM]);
892 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
895 "weight-equil-number-samples (%d) must be a positive integer if "
896 "lmc-weights-equil=%s",
897 expand->equil_samples,
898 elmceq_names[elmceqSAMPLES]);
899 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
902 "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
904 elmceq_names[elmceqSTEPS]);
905 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
908 "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
909 expand->equil_wl_delta,
910 elmceq_names[elmceqWLDELTA]);
911 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
914 "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
916 elmceq_names[elmceqRATIO]);
917 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
920 "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
921 elmceq_names[elmceqWLDELTA],
922 elamstats_names[elamstatsWL],
923 elamstats_names[elamstatsWWL]);
924 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
926 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
927 CHECK((expand->lmc_repeats <= 0));
928 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
929 CHECK((expand->minvarmin <= 0));
930 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
931 CHECK((expand->c_range < 0));
933 "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != "
936 expand->lmc_forced_nstart);
937 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0)
938 && (expand->elmcmove != elmcmoveNO));
939 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
940 CHECK((expand->lmc_forced_nstart < 0));
942 "init-lambda-state (%d) must be in the interval [0,number of lambdas)",
943 fep->init_fep_state);
944 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
946 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
947 CHECK((expand->init_wl_delta < 0));
948 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
949 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
950 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
951 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
953 /* if there is no temperature control, we need to specify an MC temperature */
954 if (!integratorHasReferenceTemperature(ir) && (expand->elmcmove != elmcmoveNO)
955 && (expand->mc_temp <= 0.0))
958 "If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set "
959 "to a positive number");
960 warning_error(wi, err_buf);
962 if (expand->nstTij > 0)
964 sprintf(err_buf, "nstlog must be non-zero");
965 CHECK(ir->nstlog == 0);
966 // Avoid modulus by zero in the case that already triggered an error exit.
970 "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
973 CHECK((expand->nstTij % ir->nstlog) != 0);
979 sprintf(err_buf, "walls only work with pbc=%s", c_pbcTypeNames[PbcType::XY].c_str());
980 CHECK(ir->nwall && ir->pbcType != PbcType::XY);
983 if (ir->pbcType != PbcType::Xyz && ir->nwall != 2)
985 if (ir->pbcType == PbcType::No)
987 if (ir->epc != epcNO)
989 warning(wi, "Turning off pressure coupling for vacuum system");
996 "Can not have pressure coupling with pbc=%s",
997 c_pbcTypeNames[ir->pbcType].c_str());
998 CHECK(ir->epc != epcNO);
1000 sprintf(err_buf, "Can not have Ewald with pbc=%s", c_pbcTypeNames[ir->pbcType].c_str());
1001 CHECK(EEL_FULL(ir->coulombtype));
1004 "Can not have dispersion correction with pbc=%s",
1005 c_pbcTypeNames[ir->pbcType].c_str());
1006 CHECK(ir->eDispCorr != edispcNO);
1009 if (ir->rlist == 0.0)
1012 "can only have neighborlist cut-off zero (=infinite)\n"
1013 "with coulombtype = %s or coulombtype = %s\n"
1014 "without periodic boundary conditions (pbc = %s) and\n"
1015 "rcoulomb and rvdw set to zero",
1018 c_pbcTypeNames[PbcType::No].c_str());
1019 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER))
1020 || (ir->pbcType != PbcType::No) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
1022 if (ir->nstlist > 0)
1025 "Simulating without cut-offs can be (slightly) faster with nstlist=0, "
1026 "nstype=simple and only one MPI rank");
1031 if (ir->nstcomm == 0)
1033 // TODO Change this behaviour. There should be exactly one way
1034 // to turn off an algorithm.
1035 ir->comm_mode = ecmNO;
1037 if (ir->comm_mode != ecmNO)
1039 if (ir->nstcomm < 0)
1041 // TODO Such input was once valid. Now that we've been
1042 // helpful for a few years, we should reject such input,
1043 // lest we have to support every historical decision
1046 "If you want to remove the rotation around the center of mass, you should set "
1047 "comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to "
1048 "its absolute value");
1049 ir->nstcomm = abs(ir->nstcomm);
1052 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
1055 "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting "
1056 "nstcomm to nstcalcenergy");
1057 ir->nstcomm = ir->nstcalcenergy;
1060 if (ir->comm_mode == ecmANGULAR)
1063 "Can not remove the rotation around the center of mass with periodic "
1065 CHECK(ir->bPeriodicMols);
1066 if (ir->pbcType != PbcType::No)
1069 "Removing the rotation around the center of mass in a periodic system, "
1070 "this can lead to artifacts. Only use this on a single (cluster of) "
1071 "molecules. This cluster should not cross periodic boundaries.");
1076 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->pbcType == PbcType::No && ir->comm_mode != ecmANGULAR)
1079 "Tumbling and flying ice-cubes: We are not removing rotation around center of mass "
1080 "in a non-periodic system. You should probably set comm_mode = ANGULAR or use "
1083 warning_note(wi, warn_buf);
1086 /* TEMPERATURE COUPLING */
1087 if (ir->etc == etcYES)
1089 ir->etc = etcBERENDSEN;
1091 "Old option for temperature coupling given: "
1092 "changing \"yes\" to \"Berendsen\"\n");
1095 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
1097 if (ir->opts.nhchainlength < 1)
1100 "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to "
1102 ir->opts.nhchainlength);
1103 ir->opts.nhchainlength = 1;
1104 warning(wi, warn_buf);
1107 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
1111 "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
1112 ir->opts.nhchainlength = 1;
1117 ir->opts.nhchainlength = 0;
1120 if (ir->eI == eiVVAK)
1123 "%s implemented primarily for validation, and requires nsttcouple = 1 and "
1126 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
1129 if (ETC_ANDERSEN(ir->etc))
1132 "%s temperature control not supported for integrator %s.",
1133 etcoupl_names[ir->etc],
1135 CHECK(!(EI_VV(ir->eI)));
1137 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
1140 "Center of mass removal not necessary for %s. All velocities of coupled "
1141 "groups are rerandomized periodically, so flying ice cube errors will not "
1143 etcoupl_names[ir->etc]);
1144 warning_note(wi, warn_buf);
1148 "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are "
1149 "randomized every time step",
1151 etcoupl_names[ir->etc]);
1152 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
1155 if (ir->etc == etcBERENDSEN)
1158 "The %s thermostat does not generate the correct kinetic energy distribution. You "
1159 "might want to consider using the %s thermostat.",
1160 ETCOUPLTYPE(ir->etc),
1161 ETCOUPLTYPE(etcVRESCALE));
1162 warning_note(wi, warn_buf);
1165 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc)) && ir->epc == epcBERENDSEN)
1168 "Using Berendsen pressure coupling invalidates the "
1169 "true ensemble for the thermostat");
1170 warning(wi, warn_buf);
1173 /* PRESSURE COUPLING */
1174 if (ir->epc == epcISOTROPIC)
1176 ir->epc = epcBERENDSEN;
1178 "Old option for pressure coupling given: "
1179 "changing \"Isotropic\" to \"Berendsen\"\n");
1182 if (ir->epc != epcNO)
1184 dt_pcoupl = ir->nstpcouple * ir->delta_t;
1186 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1187 CHECK(ir->tau_p <= 0);
1189 if (ir->tau_p / dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10 * GMX_REAL_EPS)
1192 "For proper integration of the %s barostat, tau-p (%g) should be at least %d "
1193 "times larger than nstpcouple*dt (%g)",
1194 EPCOUPLTYPE(ir->epc),
1196 pcouple_min_integration_steps(ir->epc),
1198 warning(wi, warn_buf);
1202 "compressibility must be > 0 when using pressure"
1204 EPCOUPLTYPE(ir->epc));
1205 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 || ir->compress[ZZ][ZZ] < 0
1206 || (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 && ir->compress[ZZ][XX] <= 0
1207 && ir->compress[ZZ][YY] <= 0));
1209 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1212 "You are generating velocities so I am assuming you "
1213 "are equilibrating a system. You are using "
1214 "%s pressure coupling, but this can be "
1215 "unstable for equilibration. If your system crashes, try "
1216 "equilibrating first with Berendsen pressure coupling. If "
1217 "you are not equilibrating the system, you can probably "
1218 "ignore this warning.",
1219 epcoupl_names[ir->epc]);
1220 warning(wi, warn_buf);
1226 if (ir->epc == epcMTTK)
1228 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1232 /* ELECTROSTATICS */
1233 /* More checks are in triple check (grompp.c) */
1235 if (ir->coulombtype == eelSWITCH)
1238 "coulombtype = %s is only for testing purposes and can lead to serious "
1239 "artifacts, advice: use coulombtype = %s",
1240 eel_names[ir->coulombtype],
1241 eel_names[eelRF_ZERO]);
1242 warning(wi, warn_buf);
1245 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1248 "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old "
1249 "format and exchanging epsilon-r and epsilon-rf",
1251 warning(wi, warn_buf);
1252 ir->epsilon_rf = ir->epsilon_r;
1253 ir->epsilon_r = 1.0;
1256 if (ir->epsilon_r == 0)
1259 "It is pointless to use long-range electrostatics with infinite relative "
1261 "Since you are effectively turning of electrostatics, a plain cutoff will be much "
1263 CHECK(EEL_FULL(ir->coulombtype));
1266 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1268 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1269 CHECK(ir->epsilon_r < 0);
1272 if (EEL_RF(ir->coulombtype))
1274 /* reaction field (at the cut-off) */
1276 if (ir->coulombtype == eelRF_ZERO && ir->epsilon_rf != 0)
1279 "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1280 eel_names[ir->coulombtype]);
1281 warning(wi, warn_buf);
1282 ir->epsilon_rf = 0.0;
1285 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1286 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) || (ir->epsilon_r == 0));
1287 if (ir->epsilon_rf == ir->epsilon_r)
1290 "Using epsilon-rf = epsilon-r with %s does not make sense",
1291 eel_names[ir->coulombtype]);
1292 warning(wi, warn_buf);
1295 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1296 * means the interaction is zero outside rcoulomb, but it helps to
1297 * provide accurate energy conservation.
1299 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1301 if (ir_coulomb_switched(ir))
1304 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the "
1305 "potential modifier options!",
1306 eel_names[ir->coulombtype]);
1307 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1311 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1314 "Explicit switch/shift coulomb interactions cannot be used in combination with a "
1315 "secondary coulomb-modifier.");
1316 CHECK(ir->coulomb_modifier != eintmodNONE);
1318 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1321 "Explicit switch/shift vdw interactions cannot be used in combination with a "
1322 "secondary vdw-modifier.");
1323 CHECK(ir->vdw_modifier != eintmodNONE);
1326 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT || ir->vdwtype == evdwSWITCH
1327 || ir->vdwtype == evdwSHIFT)
1330 "The switch/shift interaction settings are just for compatibility; you will get "
1332 "performance from applying potential modifiers to your interactions!\n");
1333 warning_note(wi, warn_buf);
1336 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1338 if (ir->rcoulomb_switch / ir->rcoulomb < 0.9499)
1340 real percentage = 100 * (ir->rcoulomb - ir->rcoulomb_switch) / ir->rcoulomb;
1342 "The switching range should be 5%% or less (currently %.2f%% using a switching "
1343 "range of %4f-%4f) for accurate electrostatic energies, energy conservation "
1344 "will be good regardless, since ewald_rtol = %g.",
1346 ir->rcoulomb_switch,
1349 warning(wi, warn_buf);
1353 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1355 if (ir->rvdw_switch == 0)
1358 "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones "
1359 "potential. This suggests it was not set in the mdp, which can lead to large "
1360 "energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw "
1361 "switching range.");
1362 warning(wi, warn_buf);
1366 if (EEL_FULL(ir->coulombtype))
1368 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER
1369 || ir->coulombtype == eelPMEUSERSWITCH)
1371 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist", eel_names[ir->coulombtype]);
1372 CHECK(ir->rcoulomb > ir->rlist);
1376 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1378 // TODO: Move these checks into the ewald module with the options class
1380 int orderMax = (ir->coulombtype == eelP3M_AD ? 8 : 12);
1382 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1385 "With coulombtype = %s, you should have %d <= pme-order <= %d",
1386 eel_names[ir->coulombtype],
1389 warning_error(wi, warn_buf);
1393 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1395 if (ir->ewald_geometry == eewg3D)
1398 "With pbc=%s you should use ewald-geometry=%s",
1399 c_pbcTypeNames[ir->pbcType].c_str(),
1400 eewg_names[eewg3DC]);
1401 warning(wi, warn_buf);
1403 /* This check avoids extra pbc coding for exclusion corrections */
1404 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1405 CHECK(ir->wall_ewald_zfac < 2);
1407 if ((ir->ewald_geometry == eewg3DC) && (ir->pbcType != PbcType::XY) && EEL_FULL(ir->coulombtype))
1410 "With %s and ewald_geometry = %s you should use pbc = %s",
1411 eel_names[ir->coulombtype],
1412 eewg_names[eewg3DC],
1413 c_pbcTypeNames[PbcType::XY].c_str());
1414 warning(wi, warn_buf);
1416 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1418 sprintf(err_buf, "Cannot have periodic molecules with epsilon_surface > 0");
1419 CHECK(ir->bPeriodicMols);
1420 sprintf(warn_buf, "With epsilon_surface > 0 all molecules should be neutral.");
1421 warning_note(wi, warn_buf);
1423 "With epsilon_surface > 0 you can only use domain decomposition "
1424 "when there are only small molecules with all bonds constrained (mdrun will check "
1426 warning_note(wi, warn_buf);
1429 if (ir_vdw_switched(ir))
1431 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1432 CHECK(ir->rvdw_switch >= ir->rvdw);
1434 if (ir->rvdw_switch < 0.5 * ir->rvdw)
1437 "You are applying a switch function to vdw forces or potentials from %g to %g "
1438 "nm, which is more than half the interaction range, whereas switch functions "
1439 "are intended to act only close to the cut-off.",
1442 warning_note(wi, warn_buf);
1446 if (ir->vdwtype == evdwPME)
1448 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1451 "With vdwtype = %s, the only supported modifiers are %s and %s",
1452 evdw_names[ir->vdwtype],
1453 eintmod_names[eintmodPOTSHIFT],
1454 eintmod_names[eintmodNONE]);
1455 warning_error(wi, err_buf);
1459 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1462 "You have selected user tables with dispersion correction, the dispersion "
1463 "will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction "
1464 "between rvdw_switch and rvdw will not be double counted). Make sure that you "
1465 "really want dispersion correction to -C6/r^6.");
1468 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT) && ir->rvdw != 0)
1470 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1473 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1475 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1478 /* IMPLICIT SOLVENT */
1479 if (ir->coulombtype == eelGB_NOTUSED)
1481 sprintf(warn_buf, "Invalid option %s for coulombtype", eel_names[ir->coulombtype]);
1482 warning_error(wi, warn_buf);
1487 warning_error(wi, "The QMMM integration you are trying to use is no longer supported");
1492 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1496 /* interpret a number of doubles from a string and put them in an array,
1497 after allocating space for them.
1498 str = the input string
1499 n = the (pre-allocated) number of doubles read
1500 r = the output array of doubles. */
1501 static void parse_n_real(char* str, int* n, real** r, warninp_t wi)
1503 auto values = gmx::splitString(str);
1507 for (int i = 0; i < *n; i++)
1511 (*r)[i] = gmx::fromString<real>(values[i]);
1513 catch (gmx::GromacsException&)
1516 "Invalid value " + values[i]
1517 + " in string in mdp file. Expected a real number.");
1523 static void do_fep_params(t_inputrec* ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
1526 int i, j, max_n_lambda, nweights, nfep[efptNR];
1527 t_lambda* fep = ir->fepvals;
1528 t_expanded* expand = ir->expandedvals;
1529 real** count_fep_lambdas;
1530 bool bOneLambda = TRUE;
1532 snew(count_fep_lambdas, efptNR);
1534 /* FEP input processing */
1535 /* first, identify the number of lambda values for each type.
1536 All that are nonzero must have the same number */
1538 for (i = 0; i < efptNR; i++)
1540 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
1543 /* now, determine the number of components. All must be either zero, or equal. */
1546 for (i = 0; i < efptNR; i++)
1548 if (nfep[i] > max_n_lambda)
1550 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1551 must have the same number if its not zero.*/
1556 for (i = 0; i < efptNR; i++)
1560 ir->fepvals->separate_dvdl[i] = FALSE;
1562 else if (nfep[i] == max_n_lambda)
1564 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute
1565 the derivative with respect to the temperature currently */
1567 ir->fepvals->separate_dvdl[i] = TRUE;
1573 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1580 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1581 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1583 /* the number of lambdas is the number we've read in, which is either zero
1584 or the same for all */
1585 fep->n_lambda = max_n_lambda;
1587 /* allocate space for the array of lambda values */
1588 snew(fep->all_lambda, efptNR);
1589 /* if init_lambda is defined, we need to set lambda */
1590 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1592 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1594 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1595 for (i = 0; i < efptNR; i++)
1597 snew(fep->all_lambda[i], fep->n_lambda);
1598 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1601 for (j = 0; j < fep->n_lambda; j++)
1603 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1605 sfree(count_fep_lambdas[i]);
1608 sfree(count_fep_lambdas);
1610 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1611 internal bookkeeping -- for now, init_lambda */
1613 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1615 for (i = 0; i < fep->n_lambda; i++)
1617 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1621 /* check to see if only a single component lambda is defined, and soft core is defined.
1622 In this case, turn on coulomb soft core */
1624 if (max_n_lambda == 0)
1630 for (i = 0; i < efptNR; i++)
1632 if ((nfep[i] != 0) && (i != efptFEP))
1638 if ((bOneLambda) && (fep->sc_alpha > 0))
1640 fep->bScCoul = TRUE;
1643 /* Fill in the others with the efptFEP if they are not explicitly
1644 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1645 they are all zero. */
1647 for (i = 0; i < efptNR; i++)
1649 if ((nfep[i] == 0) && (i != efptFEP))
1651 for (j = 0; j < fep->n_lambda; j++)
1653 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1659 /* now read in the weights */
1660 parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
1663 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1665 else if (nweights != fep->n_lambda)
1668 "Number of weights (%d) is not equal to number of lambda values (%d)",
1672 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1674 expand->nstexpanded = fep->nstdhdl;
1675 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1680 static void do_simtemp_params(t_inputrec* ir)
1683 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1684 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1687 template<typename T>
1688 void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
1691 for (const auto& input : inputs)
1695 outputs[i] = gmx::fromStdString<T>(input);
1697 catch (gmx::GromacsException&)
1699 auto message = gmx::formatString(
1700 "Invalid value for mdp option %s. %s should only consist of integers separated "
1704 warning_error(wi, message);
1710 static void convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, real* outputs)
1713 for (const auto& input : inputs)
1717 outputs[i] = gmx::fromString<real>(input);
1719 catch (gmx::GromacsException&)
1721 auto message = gmx::formatString(
1722 "Invalid value for mdp option %s. %s should only consist of real numbers "
1723 "separated by spaces.",
1726 warning_error(wi, message);
1732 static void convertRvecs(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, rvec* outputs)
1735 for (const auto& input : inputs)
1739 outputs[i][d] = gmx::fromString<real>(input);
1741 catch (gmx::GromacsException&)
1743 auto message = gmx::formatString(
1744 "Invalid value for mdp option %s. %s should only consist of real numbers "
1745 "separated by spaces.",
1748 warning_error(wi, message);
1759 static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
1761 opts->wall_atomtype[0] = nullptr;
1762 opts->wall_atomtype[1] = nullptr;
1764 ir->wall_atomtype[0] = -1;
1765 ir->wall_atomtype[1] = -1;
1766 ir->wall_density[0] = 0;
1767 ir->wall_density[1] = 0;
1771 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1772 if (wallAtomTypes.size() != size_t(ir->nwall))
1775 "Expected %d elements for wall_atomtype, found %zu",
1777 wallAtomTypes.size());
1779 GMX_RELEASE_ASSERT(ir->nwall < 3, "Invalid number of walls");
1780 for (int i = 0; i < ir->nwall; i++)
1782 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1785 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1787 auto wallDensity = gmx::splitString(wall_density);
1788 if (wallDensity.size() != size_t(ir->nwall))
1791 "Expected %d elements for wall-density, found %zu",
1793 wallDensity.size());
1795 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1796 for (int i = 0; i < ir->nwall; i++)
1798 if (ir->wall_density[i] <= 0)
1800 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1807 static void add_wall_energrps(SimulationGroups* groups, int nwall, t_symtab* symtab)
1811 AtomGroupIndices* grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1812 for (int i = 0; i < nwall; i++)
1814 groups->groupNames.emplace_back(put_symtab(symtab, gmx::formatString("wall%d", i).c_str()));
1815 grps->emplace_back(groups->groupNames.size() - 1);
1820 static void read_expandedparams(std::vector<t_inpfile>* inp, t_expanded* expand, warninp_t wi)
1822 /* read expanded ensemble parameters */
1823 printStringNewline(inp, "expanded ensemble variables");
1824 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1825 expand->elamstats = get_eeenum(inp, "lmc-stats", elamstats_names, wi);
1826 expand->elmcmove = get_eeenum(inp, "lmc-move", elmcmove_names, wi);
1827 expand->elmceq = get_eeenum(inp, "lmc-weights-equil", elmceq_names, wi);
1828 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1829 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1830 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1831 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1832 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1833 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1834 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1835 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1836 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1837 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1838 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1839 expand->bSymmetrizedTMatrix =
1840 (get_eeenum(inp, "symmetrized-transition-matrix", yesno_names, wi) != 0);
1841 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1842 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1843 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1844 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1845 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1846 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1847 expand->bWLoneovert = (get_eeenum(inp, "wl-oneovert", yesno_names, wi) != 0);
1850 /*! \brief Return whether an end state with the given coupling-lambda
1851 * value describes fully-interacting VDW.
1853 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1854 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1856 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1858 return (couple_lambda_value == ecouplamVDW || couple_lambda_value == ecouplamVDWQ);
1864 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1867 explicit MdpErrorHandler(warninp_t wi) : wi_(wi), mapping_(nullptr) {}
1869 void setBackMapping(const gmx::IKeyValueTreeBackMapping& mapping) { mapping_ = &mapping; }
1871 bool onError(gmx::UserInputError* ex, const gmx::KeyValueTreePath& context) override
1874 gmx::formatString("Error in mdp option \"%s\":", getOptionName(context).c_str()));
1875 std::string message = gmx::formatExceptionMessageToString(*ex);
1876 warning_error(wi_, message.c_str());
1881 std::string getOptionName(const gmx::KeyValueTreePath& context)
1883 if (mapping_ != nullptr)
1885 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1886 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1889 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1894 const gmx::IKeyValueTreeBackMapping* mapping_;
1899 void get_ir(const char* mdparin,
1900 const char* mdparout,
1901 gmx::MDModules* mdModules,
1904 WriteMdpHeader writeMdpHeader,
1908 double dumdub[2][6];
1910 char warn_buf[STRLEN];
1911 t_lambda* fep = ir->fepvals;
1912 t_expanded* expand = ir->expandedvals;
1914 const char* no_names[] = { "no", nullptr };
1916 init_inputrec_strings();
1917 gmx::TextInputFile stream(mdparin);
1918 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1920 snew(dumstr[0], STRLEN);
1921 snew(dumstr[1], STRLEN);
1923 /* ignore the following deprecated commands */
1924 replace_inp_entry(inp, "title", nullptr);
1925 replace_inp_entry(inp, "cpp", nullptr);
1926 replace_inp_entry(inp, "domain-decomposition", nullptr);
1927 replace_inp_entry(inp, "andersen-seed", nullptr);
1928 replace_inp_entry(inp, "dihre", nullptr);
1929 replace_inp_entry(inp, "dihre-fc", nullptr);
1930 replace_inp_entry(inp, "dihre-tau", nullptr);
1931 replace_inp_entry(inp, "nstdihreout", nullptr);
1932 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1933 replace_inp_entry(inp, "optimize-fft", nullptr);
1934 replace_inp_entry(inp, "adress_type", nullptr);
1935 replace_inp_entry(inp, "adress_const_wf", nullptr);
1936 replace_inp_entry(inp, "adress_ex_width", nullptr);
1937 replace_inp_entry(inp, "adress_hy_width", nullptr);
1938 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1939 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1940 replace_inp_entry(inp, "adress_site", nullptr);
1941 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1942 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1943 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1944 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1945 replace_inp_entry(inp, "rlistlong", nullptr);
1946 replace_inp_entry(inp, "nstcalclr", nullptr);
1947 replace_inp_entry(inp, "pull-print-com2", nullptr);
1948 replace_inp_entry(inp, "gb-algorithm", nullptr);
1949 replace_inp_entry(inp, "nstgbradii", nullptr);
1950 replace_inp_entry(inp, "rgbradii", nullptr);
1951 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1952 replace_inp_entry(inp, "gb-saltconc", nullptr);
1953 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1954 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1955 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1956 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1957 replace_inp_entry(inp, "sa-algorithm", nullptr);
1958 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1959 replace_inp_entry(inp, "ns-type", nullptr);
1961 /* replace the following commands with the clearer new versions*/
1962 replace_inp_entry(inp, "unconstrained-start", "continuation");
1963 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1964 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1965 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1966 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1967 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1968 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1970 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1971 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1972 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1973 setStringEntry(&inp, "include", opts->include, nullptr);
1974 printStringNoNewline(
1975 &inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1976 setStringEntry(&inp, "define", opts->define, nullptr);
1978 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1979 ir->eI = get_eeenum(&inp, "integrator", ei_names, wi);
1980 printStringNoNewline(&inp, "Start time and timestep in ps");
1981 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1982 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1983 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1984 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1985 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1986 printStringNoNewline(
1987 &inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1988 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1989 printStringNoNewline(&inp, "Multiple time-stepping");
1990 ir->useMts = (get_eeenum(&inp, "mts", yesno_names, wi) != 0);
1993 gmx::GromppMtsOpts& mtsOpts = opts->mtsOpts;
1994 mtsOpts.numLevels = get_eint(&inp, "mts-levels", 2, wi);
1995 ir->mtsLevels.resize(2);
1996 mtsOpts.level2Forces = setStringEntry(
1997 &inp, "mts-level2-forces", "longrange-nonbonded nonbonded pair dihedral");
1998 mtsOpts.level2Factor = get_eint(&inp, "mts-level2-factor", 2, wi);
2000 // We clear after reading without dynamics to not force the user to remove MTS mdp options
2001 if (!EI_DYNAMICS(ir->eI))
2006 printStringNoNewline(&inp, "mode for center of mass motion removal");
2007 ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
2008 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
2009 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
2010 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
2011 setStringEntry(&inp, "comm-grps", inputrecStrings->vcm, nullptr);
2013 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
2014 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
2015 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
2016 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
2019 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
2020 printStringNoNewline(&inp, "Force tolerance and initial step-size");
2021 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
2022 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
2023 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
2024 ir->niter = get_eint(&inp, "niter", 20, wi);
2025 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
2026 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
2027 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
2028 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
2029 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
2031 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
2032 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
2034 /* Output options */
2035 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
2036 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
2037 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
2038 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
2039 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
2040 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
2041 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
2042 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
2043 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
2044 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
2045 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
2046 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
2047 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
2048 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
2049 printStringNoNewline(&inp, "default, all atoms will be written.");
2050 setStringEntry(&inp, "compressed-x-grps", inputrecStrings->x_compressed_groups, nullptr);
2051 printStringNoNewline(&inp, "Selection of energy groups");
2052 setStringEntry(&inp, "energygrps", inputrecStrings->energy, nullptr);
2054 /* Neighbor searching */
2055 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
2056 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
2057 ir->cutoff_scheme = get_eeenum(&inp, "cutoff-scheme", ecutscheme_names, wi);
2058 printStringNoNewline(&inp, "nblist update frequency");
2059 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
2060 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
2061 // TODO This conversion should be removed when proper std:string handling will be added to get_eeenum(...), etc.
2062 std::vector<const char*> pbcTypesNamesChar;
2063 for (const auto& pbcTypeName : c_pbcTypeNames)
2065 pbcTypesNamesChar.push_back(pbcTypeName.c_str());
2067 ir->pbcType = static_cast<PbcType>(get_eeenum(&inp, "pbc", pbcTypesNamesChar.data(), wi));
2068 ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi) != 0;
2069 printStringNoNewline(&inp,
2070 "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
2071 printStringNoNewline(&inp, "a value of -1 means: use rlist");
2072 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
2073 printStringNoNewline(&inp, "nblist cut-off");
2074 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
2075 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
2077 /* Electrostatics */
2078 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
2079 printStringNoNewline(&inp, "Method for doing electrostatics");
2080 ir->coulombtype = get_eeenum(&inp, "coulombtype", eel_names, wi);
2081 ir->coulomb_modifier = get_eeenum(&inp, "coulomb-modifier", eintmod_names, wi);
2082 printStringNoNewline(&inp, "cut-off lengths");
2083 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
2084 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
2085 printStringNoNewline(&inp, "Relative dielectric constant for the medium and the reaction field");
2086 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
2087 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
2088 printStringNoNewline(&inp, "Method for doing Van der Waals");
2089 ir->vdwtype = get_eeenum(&inp, "vdw-type", evdw_names, wi);
2090 ir->vdw_modifier = get_eeenum(&inp, "vdw-modifier", eintmod_names, wi);
2091 printStringNoNewline(&inp, "cut-off lengths");
2092 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
2093 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
2094 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
2095 ir->eDispCorr = get_eeenum(&inp, "DispCorr", edispc_names, wi);
2096 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
2097 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
2098 printStringNoNewline(&inp, "Separate tables between energy group pairs");
2099 setStringEntry(&inp, "energygrp-table", inputrecStrings->egptable, nullptr);
2100 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
2101 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
2102 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
2103 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
2104 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
2105 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
2106 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
2107 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
2108 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
2109 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
2110 ir->ljpme_combination_rule = get_eeenum(&inp, "lj-pme-comb-rule", eljpme_names, wi);
2111 ir->ewald_geometry = get_eeenum(&inp, "ewald-geometry", eewg_names, wi);
2112 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
2114 /* Implicit solvation is no longer supported, but we need grompp
2115 to be able to refuse old .mdp files that would have built a tpr
2116 to run it. Thus, only "no" is accepted. */
2117 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
2119 /* Coupling stuff */
2120 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
2121 printStringNoNewline(&inp, "Temperature coupling");
2122 ir->etc = get_eeenum(&inp, "tcoupl", etcoupl_names, wi);
2123 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
2124 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
2125 ir->bPrintNHChains = (get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi) != 0);
2126 printStringNoNewline(&inp, "Groups to couple separately");
2127 setStringEntry(&inp, "tc-grps", inputrecStrings->tcgrps, nullptr);
2128 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
2129 setStringEntry(&inp, "tau-t", inputrecStrings->tau_t, nullptr);
2130 setStringEntry(&inp, "ref-t", inputrecStrings->ref_t, nullptr);
2131 printStringNoNewline(&inp, "pressure coupling");
2132 ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
2133 ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
2134 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
2135 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
2136 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
2137 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
2138 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
2139 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
2140 ir->refcoord_scaling = get_eeenum(&inp, "refcoord-scaling", erefscaling_names, wi);
2143 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2144 ir->bQMMM = (get_eeenum(&inp, "QMMM", yesno_names, wi) != 0);
2145 printStringNoNewline(&inp, "Groups treated with MiMiC");
2146 setStringEntry(&inp, "QMMM-grps", inputrecStrings->QMMM, nullptr);
2148 /* Simulated annealing */
2149 printStringNewline(&inp, "SIMULATED ANNEALING");
2150 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2151 setStringEntry(&inp, "annealing", inputrecStrings->anneal, nullptr);
2152 printStringNoNewline(&inp,
2153 "Number of time points to use for specifying annealing in each group");
2154 setStringEntry(&inp, "annealing-npoints", inputrecStrings->anneal_npoints, nullptr);
2155 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2156 setStringEntry(&inp, "annealing-time", inputrecStrings->anneal_time, nullptr);
2157 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2158 setStringEntry(&inp, "annealing-temp", inputrecStrings->anneal_temp, nullptr);
2161 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2162 opts->bGenVel = (get_eeenum(&inp, "gen-vel", yesno_names, wi) != 0);
2163 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2164 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2167 printStringNewline(&inp, "OPTIONS FOR BONDS");
2168 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2169 printStringNoNewline(&inp, "Type of constraint algorithm");
2170 ir->eConstrAlg = get_eeenum(&inp, "constraint-algorithm", econstr_names, wi);
2171 printStringNoNewline(&inp, "Do not constrain the start configuration");
2172 ir->bContinuation = (get_eeenum(&inp, "continuation", yesno_names, wi) != 0);
2173 printStringNoNewline(&inp,
2174 "Use successive overrelaxation to reduce the number of shake iterations");
2175 ir->bShakeSOR = (get_eeenum(&inp, "Shake-SOR", yesno_names, wi) != 0);
2176 printStringNoNewline(&inp, "Relative tolerance of shake");
2177 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2178 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2179 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2180 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2181 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2182 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2183 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2184 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2185 printStringNoNewline(&inp, "rotates over more degrees than");
2186 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2187 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2188 opts->bMorse = (get_eeenum(&inp, "morse", yesno_names, wi) != 0);
2190 /* Energy group exclusions */
2191 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2192 printStringNoNewline(
2193 &inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2194 setStringEntry(&inp, "energygrp-excl", inputrecStrings->egpexcl, nullptr);
2197 printStringNewline(&inp, "WALLS");
2198 printStringNoNewline(
2199 &inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2200 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2201 ir->wall_type = get_eeenum(&inp, "wall-type", ewt_names, wi);
2202 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2203 setStringEntry(&inp, "wall-atomtype", inputrecStrings->wall_atomtype, nullptr);
2204 setStringEntry(&inp, "wall-density", inputrecStrings->wall_density, nullptr);
2205 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2208 printStringNewline(&inp, "COM PULLING");
2209 ir->bPull = (get_eeenum(&inp, "pull", yesno_names, wi) != 0);
2212 ir->pull = std::make_unique<pull_params_t>();
2213 inputrecStrings->pullGroupNames = read_pullparams(&inp, ir->pull.get(), wi);
2217 for (int c = 0; c < ir->pull->ncoord; c++)
2219 if (ir->pull->coord[c].eType == epullCONSTRAINT)
2222 "Constraint COM pulling is not supported in combination with "
2223 "multiple time stepping");
2231 NOTE: needs COM pulling or free energy input */
2232 printStringNewline(&inp, "AWH biasing");
2233 ir->bDoAwh = (get_eeenum(&inp, "awh", yesno_names, wi) != 0);
2236 ir->awhParams = gmx::readAwhParams(&inp, wi);
2239 /* Enforced rotation */
2240 printStringNewline(&inp, "ENFORCED ROTATION");
2241 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2242 ir->bRot = (get_eeenum(&inp, "rotation", yesno_names, wi) != 0);
2246 inputrecStrings->rotateGroupNames = read_rotparams(&inp, ir->rot, wi);
2249 /* Interactive MD */
2251 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2252 setStringEntry(&inp, "IMD-group", inputrecStrings->imd_grp, nullptr);
2253 if (inputrecStrings->imd_grp[0] != '\0')
2260 printStringNewline(&inp, "NMR refinement stuff");
2261 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2262 ir->eDisre = get_eeenum(&inp, "disre", edisre_names, wi);
2263 printStringNoNewline(
2264 &inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2265 ir->eDisreWeighting = get_eeenum(&inp, "disre-weighting", edisreweighting_names, wi);
2266 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2267 ir->bDisreMixed = (get_eeenum(&inp, "disre-mixed", yesno_names, wi) != 0);
2268 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2269 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2270 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2271 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2272 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2273 opts->bOrire = (get_eeenum(&inp, "orire", yesno_names, wi) != 0);
2274 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2275 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2276 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2277 setStringEntry(&inp, "orire-fitgrp", inputrecStrings->orirefitgrp, nullptr);
2278 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2279 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2281 /* free energy variables */
2282 printStringNewline(&inp, "Free energy variables");
2283 ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
2284 setStringEntry(&inp, "couple-moltype", inputrecStrings->couple_moltype, nullptr);
2285 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2286 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2287 opts->bCoupleIntra = (get_eeenum(&inp, "couple-intramol", yesno_names, wi) != 0);
2289 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2291 it was not entered */
2292 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2293 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2294 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2295 setStringEntry(&inp, "fep-lambdas", inputrecStrings->fep_lambda[efptFEP], nullptr);
2296 setStringEntry(&inp, "mass-lambdas", inputrecStrings->fep_lambda[efptMASS], nullptr);
2297 setStringEntry(&inp, "coul-lambdas", inputrecStrings->fep_lambda[efptCOUL], nullptr);
2298 setStringEntry(&inp, "vdw-lambdas", inputrecStrings->fep_lambda[efptVDW], nullptr);
2299 setStringEntry(&inp, "bonded-lambdas", inputrecStrings->fep_lambda[efptBONDED], nullptr);
2300 setStringEntry(&inp, "restraint-lambdas", inputrecStrings->fep_lambda[efptRESTRAINT], nullptr);
2301 setStringEntry(&inp, "temperature-lambdas", inputrecStrings->fep_lambda[efptTEMPERATURE], nullptr);
2302 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2303 setStringEntry(&inp, "init-lambda-weights", inputrecStrings->lambda_weights, nullptr);
2304 fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
2305 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2306 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2307 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2308 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2309 fep->bScCoul = (get_eeenum(&inp, "sc-coul", yesno_names, wi) != 0);
2310 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2311 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2312 fep->separate_dhdl_file = get_eeenum(&inp, "separate-dhdl-file", separate_dhdl_file_names, wi);
2313 fep->dhdl_derivatives = get_eeenum(&inp, "dhdl-derivatives", dhdl_derivatives_names, wi);
2314 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2315 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2317 /* Non-equilibrium MD stuff */
2318 printStringNewline(&inp, "Non-equilibrium MD stuff");
2319 setStringEntry(&inp, "acc-grps", inputrecStrings->accgrps, nullptr);
2320 setStringEntry(&inp, "accelerate", inputrecStrings->acc, nullptr);
2321 setStringEntry(&inp, "freezegrps", inputrecStrings->freeze, nullptr);
2322 setStringEntry(&inp, "freezedim", inputrecStrings->frdim, nullptr);
2323 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2324 setStringEntry(&inp, "deform", inputrecStrings->deform, nullptr);
2326 /* simulated tempering variables */
2327 printStringNewline(&inp, "simulated tempering variables");
2328 ir->bSimTemp = (get_eeenum(&inp, "simulated-tempering", yesno_names, wi) != 0);
2329 ir->simtempvals->eSimTempScale = get_eeenum(&inp, "simulated-tempering-scaling", esimtemp_names, wi);
2330 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2331 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2333 /* expanded ensemble variables */
2334 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2336 read_expandedparams(&inp, expand, wi);
2339 /* Electric fields */
2341 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2342 gmx::KeyValueTreeTransformer transform;
2343 transform.rules()->addRule().keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2344 mdModules->initMdpTransform(transform.rules());
2345 for (const auto& path : transform.mappedPaths())
2347 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2348 mark_einp_set(inp, path[0].c_str());
2350 MdpErrorHandler errorHandler(wi);
2351 auto result = transform.transform(convertedValues, &errorHandler);
2352 ir->params = new gmx::KeyValueTreeObject(result.object());
2353 mdModules->adjustInputrecBasedOnModules(ir);
2354 errorHandler.setBackMapping(result.backMapping());
2355 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2358 /* Ion/water position swapping ("computational electrophysiology") */
2359 printStringNewline(&inp,
2360 "Ion/water position swapping for computational electrophysiology setups");
2361 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2362 ir->eSwapCoords = get_eeenum(&inp, "swapcoords", eSwapTypes_names, wi);
2363 if (ir->eSwapCoords != eswapNO)
2370 printStringNoNewline(&inp, "Swap attempt frequency");
2371 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2372 printStringNoNewline(&inp, "Number of ion types to be controlled");
2373 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2376 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2378 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2379 snew(ir->swap->grp, ir->swap->ngrp);
2380 for (i = 0; i < ir->swap->ngrp; i++)
2382 snew(ir->swap->grp[i].molname, STRLEN);
2384 printStringNoNewline(&inp,
2385 "Two index groups that contain the compartment-partitioning atoms");
2386 setStringEntry(&inp, "split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2387 setStringEntry(&inp, "split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2388 printStringNoNewline(&inp,
2389 "Use center of mass of split groups (yes/no), otherwise center of "
2390 "geometry is used");
2391 ir->swap->massw_split[0] = (get_eeenum(&inp, "massw-split0", yesno_names, wi) != 0);
2392 ir->swap->massw_split[1] = (get_eeenum(&inp, "massw-split1", yesno_names, wi) != 0);
2394 printStringNoNewline(&inp, "Name of solvent molecules");
2395 setStringEntry(&inp, "solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2397 printStringNoNewline(&inp,
2398 "Split cylinder: radius, upper and lower extension (nm) (this will "
2399 "define the channels)");
2400 printStringNoNewline(&inp,
2401 "Note that the split cylinder settings do not have an influence on "
2402 "the swapping protocol,");
2403 printStringNoNewline(
2405 "however, if correctly defined, the permeation events are recorded per channel");
2406 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2407 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2408 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2409 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2410 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2411 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2413 printStringNoNewline(
2415 "Average the number of ions per compartment over these many swap attempt steps");
2416 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2418 printStringNoNewline(
2419 &inp, "Names of the ion types that can be exchanged with solvent molecules,");
2420 printStringNoNewline(
2421 &inp, "and the requested number of ions of this type in compartments A and B");
2422 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2423 for (i = 0; i < nIonTypes; i++)
2425 int ig = eSwapFixedGrpNR + i;
2427 sprintf(buf, "iontype%d-name", i);
2428 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2429 sprintf(buf, "iontype%d-in-A", i);
2430 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2431 sprintf(buf, "iontype%d-in-B", i);
2432 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2435 printStringNoNewline(
2437 "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2438 printStringNoNewline(
2440 "at maximum distance (= bulk concentration) to the split group layers. However,");
2441 printStringNoNewline(&inp,
2442 "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk "
2443 "layer from the middle at 0.0");
2444 printStringNoNewline(&inp,
2445 "towards one of the compartment-partitioning layers (at +/- 1.0).");
2446 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2447 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2448 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2449 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0))
2451 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2454 printStringNoNewline(
2455 &inp, "Start to swap ions if threshold difference to requested count is reached");
2456 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2459 /* AdResS is no longer supported, but we need grompp to be able to
2460 refuse to process old .mdp files that used it. */
2461 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2463 /* User defined thingies */
2464 printStringNewline(&inp, "User defined thingies");
2465 setStringEntry(&inp, "user1-grps", inputrecStrings->user1, nullptr);
2466 setStringEntry(&inp, "user2-grps", inputrecStrings->user2, nullptr);
2467 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2468 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2469 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2470 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2471 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2472 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2473 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2474 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2478 gmx::TextOutputFile stream(mdparout);
2479 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2481 // Transform module data into a flat key-value tree for output.
2482 gmx::KeyValueTreeBuilder builder;
2483 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2484 mdModules->buildMdpOutput(&builderObject);
2486 gmx::TextWriter writer(&stream);
2487 writeKeyValueTreeAsMdp(&writer, builder.build());
2492 /* Process options if necessary */
2493 for (m = 0; m < 2; m++)
2495 for (i = 0; i < 2 * DIM; i++)
2504 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2508 "Pressure coupling incorrect number of values (I need exactly 1)");
2510 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2512 case epctSEMIISOTROPIC:
2513 case epctSURFACETENSION:
2514 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2518 "Pressure coupling incorrect number of values (I need exactly 2)");
2520 dumdub[m][YY] = dumdub[m][XX];
2522 case epctANISOTROPIC:
2523 if (sscanf(dumstr[m],
2524 "%lf%lf%lf%lf%lf%lf",
2535 "Pressure coupling incorrect number of values (I need exactly 6)");
2540 "Pressure coupling type %s not implemented yet",
2541 epcoupltype_names[ir->epct]);
2545 clear_mat(ir->ref_p);
2546 clear_mat(ir->compress);
2547 for (i = 0; i < DIM; i++)
2549 ir->ref_p[i][i] = dumdub[1][i];
2550 ir->compress[i][i] = dumdub[0][i];
2552 if (ir->epct == epctANISOTROPIC)
2554 ir->ref_p[XX][YY] = dumdub[1][3];
2555 ir->ref_p[XX][ZZ] = dumdub[1][4];
2556 ir->ref_p[YY][ZZ] = dumdub[1][5];
2557 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2560 "All off-diagonal reference pressures are non-zero. Are you sure you want to "
2561 "apply a threefold shear stress?\n");
2563 ir->compress[XX][YY] = dumdub[0][3];
2564 ir->compress[XX][ZZ] = dumdub[0][4];
2565 ir->compress[YY][ZZ] = dumdub[0][5];
2566 for (i = 0; i < DIM; i++)
2568 for (m = 0; m < i; m++)
2570 ir->ref_p[i][m] = ir->ref_p[m][i];
2571 ir->compress[i][m] = ir->compress[m][i];
2576 if (ir->comm_mode == ecmNO)
2581 opts->couple_moltype = nullptr;
2582 if (strlen(inputrecStrings->couple_moltype) > 0)
2584 if (ir->efep != efepNO)
2586 opts->couple_moltype = gmx_strdup(inputrecStrings->couple_moltype);
2587 if (opts->couple_lam0 == opts->couple_lam1)
2589 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2591 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
2595 "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
2602 "Free energy is turned off, so we will not decouple the molecule listed "
2606 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2607 if (ir->efep != efepNO)
2609 if (fep->delta_lambda != 0)
2611 ir->efep = efepSLOWGROWTH;
2615 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2617 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2619 "Old option for dhdl-print-energy given: "
2620 "changing \"yes\" to \"total\"\n");
2623 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2625 /* always print out the energy to dhdl if we are doing
2626 expanded ensemble, since we need the total energy for
2627 analysis if the temperature is changing. In some
2628 conditions one may only want the potential energy, so
2629 we will allow that if the appropriate mdp setting has
2630 been enabled. Otherwise, total it is:
2632 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2635 if ((ir->efep != efepNO) || ir->bSimTemp)
2637 ir->bExpanded = FALSE;
2638 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2640 ir->bExpanded = TRUE;
2642 do_fep_params(ir, inputrecStrings->fep_lambda, inputrecStrings->lambda_weights, wi);
2643 if (ir->bSimTemp) /* done after fep params */
2645 do_simtemp_params(ir);
2648 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2649 * setup and not on the old way of specifying the free-energy setup,
2650 * we should check for using soft-core when not needed, since that
2651 * can complicate the sampling significantly.
2652 * Note that we only check for the automated coupling setup.
2653 * If the (advanced) user does FEP through manual topology changes,
2654 * this check will not be triggered.
2656 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 && ir->fepvals->sc_alpha != 0
2657 && (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
2660 "You are using soft-core interactions while the Van der Waals interactions are "
2661 "not decoupled (note that the sc-coul option is only active when using lambda "
2662 "states). Although this will not lead to errors, you will need much more "
2663 "sampling than without soft-core interactions. Consider using sc-alpha=0.");
2668 ir->fepvals->n_lambda = 0;
2671 /* WALL PARAMETERS */
2673 do_wall_params(ir, inputrecStrings->wall_atomtype, inputrecStrings->wall_density, opts, wi);
2675 /* ORIENTATION RESTRAINT PARAMETERS */
2677 if (opts->bOrire && gmx::splitString(inputrecStrings->orirefitgrp).size() != 1)
2679 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2682 /* DEFORMATION PARAMETERS */
2684 clear_mat(ir->deform);
2685 for (i = 0; i < 6; i++)
2690 double gmx_unused canary;
2691 int ndeform = sscanf(inputrecStrings->deform,
2692 "%lf %lf %lf %lf %lf %lf %lf",
2701 if (strlen(inputrecStrings->deform) > 0 && ndeform != 6)
2705 "Cannot parse exactly 6 box deformation velocities from string '%s'",
2706 inputrecStrings->deform)
2709 for (i = 0; i < 3; i++)
2711 ir->deform[i][i] = dumdub[0][i];
2713 ir->deform[YY][XX] = dumdub[0][3];
2714 ir->deform[ZZ][XX] = dumdub[0][4];
2715 ir->deform[ZZ][YY] = dumdub[0][5];
2716 if (ir->epc != epcNO)
2718 for (i = 0; i < 3; i++)
2720 for (j = 0; j <= i; j++)
2722 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2724 warning_error(wi, "A box element has deform set and compressibility > 0");
2728 for (i = 0; i < 3; i++)
2730 for (j = 0; j < i; j++)
2732 if (ir->deform[i][j] != 0)
2734 for (m = j; m < DIM; m++)
2736 if (ir->compress[m][j] != 0)
2739 "An off-diagonal box element has deform set while "
2740 "compressibility > 0 for the same component of another box "
2741 "vector, this might lead to spurious periodicity effects.");
2742 warning(wi, warn_buf);
2750 /* Ion/water position swapping checks */
2751 if (ir->eSwapCoords != eswapNO)
2753 if (ir->swap->nstswap < 1)
2755 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2757 if (ir->swap->nAverage < 1)
2759 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2761 if (ir->swap->threshold < 1.0)
2763 warning_error(wi, "Ion count threshold must be at least 1.\n");
2767 /* Set up MTS levels, this needs to happen before checking AWH parameters */
2770 std::vector<std::string> errorMessages;
2771 ir->mtsLevels = gmx::setupMtsLevels(opts->mtsOpts, &errorMessages);
2773 for (const auto& errorMessage : errorMessages)
2775 warning_error(wi, errorMessage.c_str());
2781 gmx::checkAwhParams(ir->awhParams, ir, wi);
2788 /* We would like gn to be const as well, but C doesn't allow this */
2789 /* TODO this is utility functionality (search for the index of a
2790 string in a collection), so should be refactored and located more
2792 int search_string(const char* s, int ng, char* gn[])
2796 for (i = 0; (i < ng); i++)
2798 if (gmx_strcasecmp(s, gn[i]) == 0)
2805 "Group %s referenced in the .mdp file was not found in the index file.\n"
2806 "Group names must match either [moleculetype] names or custom index group\n"
2807 "names, in which case you must supply an index file to the '-n' option\n"
2812 static void do_numbering(int natoms,
2813 SimulationGroups* groups,
2814 gmx::ArrayRef<std::string> groupsFromMdpFile,
2817 SimulationAtomGroupType gtype,
2823 unsigned short* cbuf;
2824 AtomGroupIndices* grps = &(groups->groups[gtype]);
2825 int j, gid, aj, ognr, ntot = 0;
2827 char warn_buf[STRLEN];
2829 title = shortName(gtype);
2832 /* Mark all id's as not set */
2833 for (int i = 0; (i < natoms); i++)
2838 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2840 /* Lookup the group name in the block structure */
2841 gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2842 if ((grptp != egrptpONE) || (i == 0))
2844 grps->emplace_back(gid);
2847 /* Now go over the atoms in the group */
2848 for (j = block->index[gid]; (j < block->index[gid + 1]); j++)
2853 /* Range checking */
2854 if ((aj < 0) || (aj >= natoms))
2856 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2858 /* Lookup up the old group number */
2862 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title, ognr + 1, i + 1);
2866 /* Store the group number in buffer */
2867 if (grptp == egrptpONE)
2880 /* Now check whether we have done all atoms */
2883 if (grptp == egrptpALL)
2885 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2887 else if (grptp == egrptpPART)
2889 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2890 warning_note(wi, warn_buf);
2892 /* Assign all atoms currently unassigned to a rest group */
2893 for (j = 0; (j < natoms); j++)
2895 if (cbuf[j] == NOGID)
2897 cbuf[j] = grps->size();
2900 if (grptp != egrptpPART)
2904 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title, natoms - ntot);
2906 /* Add group name "rest" */
2907 grps->emplace_back(restnm);
2909 /* Assign the rest name to all atoms not currently assigned to a group */
2910 for (j = 0; (j < natoms); j++)
2912 if (cbuf[j] == NOGID)
2914 // group size was not updated before this here, so need to use -1.
2915 cbuf[j] = grps->size() - 1;
2921 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2923 /* All atoms are part of one (or no) group, no index required */
2924 groups->groupNumbers[gtype].clear();
2928 for (int j = 0; (j < natoms); j++)
2930 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2937 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
2940 pull_params_t* pull;
2941 int natoms, imin, jmin;
2942 int * nrdf2, *na_vcm, na_tot;
2943 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2948 * First calc 3xnr-atoms for each group
2949 * then subtract half a degree of freedom for each constraint
2951 * Only atoms and nuclei contribute to the degrees of freedom...
2956 const SimulationGroups& groups = mtop->groups;
2957 natoms = mtop->natoms;
2959 /* Allocate one more for a possible rest group */
2960 /* We need to sum degrees of freedom into doubles,
2961 * since floats give too low nrdf's above 3 million atoms.
2963 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
2964 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2965 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2966 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2967 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2969 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
2973 for (gmx::index i = 0;
2974 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
2978 clear_ivec(dof_vcm[i]);
2980 nrdf_vcm_sub[i] = 0;
2982 snew(nrdf2, natoms);
2983 for (const AtomProxy atomP : AtomRange(*mtop))
2985 const t_atom& local = atomP.atom();
2986 int i = atomP.globalAtomNumber();
2988 if (local.ptype == eptAtom || local.ptype == eptNucleus)
2990 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
2991 for (int d = 0; d < DIM; d++)
2993 if (opts->nFreeze[g][d] == 0)
2995 /* Add one DOF for particle i (counted as 2*1) */
2997 /* VCM group i has dim d as a DOF */
2998 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
3002 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
3004 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
3010 for (const gmx_molblock_t& molb : mtop->molblock)
3012 const gmx_moltype_t& molt = mtop->moltype[molb.type];
3013 const t_atom* atom = molt.atoms.atom;
3014 for (int mol = 0; mol < molb.nmol; mol++)
3016 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
3018 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
3019 for (int i = 0; i < molt.ilist[ftype].size();)
3021 /* Subtract degrees of freedom for the constraints,
3022 * if the particles still have degrees of freedom left.
3023 * If one of the particles is a vsite or a shell, then all
3024 * constraint motion will go there, but since they do not
3025 * contribute to the constraints the degrees of freedom do not
3028 int ai = as + ia[i + 1];
3029 int aj = as + ia[i + 2];
3030 if (((atom[ia[i + 1]].ptype == eptNucleus) || (atom[ia[i + 1]].ptype == eptAtom))
3031 && ((atom[ia[i + 2]].ptype == eptNucleus) || (atom[ia[i + 2]].ptype == eptAtom)))
3049 imin = std::min(imin, nrdf2[ai]);
3050 jmin = std::min(jmin, nrdf2[aj]);
3053 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3055 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
3057 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3059 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
3062 i += interaction_function[ftype].nratoms + 1;
3065 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
3066 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
3068 /* Subtract 1 dof from every atom in the SETTLE */
3069 for (int j = 0; j < 3; j++)
3071 int ai = as + ia[i + 1 + j];
3072 imin = std::min(2, nrdf2[ai]);
3074 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3076 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3081 as += molt.atoms.nr;
3087 /* Correct nrdf for the COM constraints.
3088 * We correct using the TC and VCM group of the first atom
3089 * in the reference and pull group. If atoms in one pull group
3090 * belong to different TC or VCM groups it is anyhow difficult
3091 * to determine the optimal nrdf assignment.
3093 pull = ir->pull.get();
3095 for (int i = 0; i < pull->ncoord; i++)
3097 if (pull->coord[i].eType != epullCONSTRAINT)
3104 for (int j = 0; j < 2; j++)
3106 const t_pull_group* pgrp;
3108 pgrp = &pull->group[pull->coord[i].group[j]];
3110 if (!pgrp->ind.empty())
3112 /* Subtract 1/2 dof from each group */
3113 int ai = pgrp->ind[0];
3114 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3116 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3118 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
3121 "Center of mass pulling constraints caused the number of degrees "
3122 "of freedom for temperature coupling group %s to be negative",
3123 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
3124 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
3129 /* We need to subtract the whole DOF from group j=1 */
3136 if (ir->nstcomm != 0)
3138 GMX_RELEASE_ASSERT(!groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty(),
3139 "Expect at least one group when removing COM motion");
3141 /* We remove COM motion up to dim ndof_com() */
3142 const int ndim_rm_vcm = ndof_com(ir);
3144 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3145 * the number of degrees of freedom in each vcm group when COM
3146 * translation is removed and 6 when rotation is removed as well.
3147 * Note that we do not and should not include the rest group here.
3149 for (gmx::index j = 0;
3150 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]);
3153 switch (ir->comm_mode)
3156 case ecmLINEAR_ACCELERATION_CORRECTION:
3157 nrdf_vcm_sub[j] = 0;
3158 for (int d = 0; d < ndim_rm_vcm; d++)
3166 case ecmANGULAR: nrdf_vcm_sub[j] = 6; break;
3167 default: gmx_incons("Checking comm_mode");
3171 for (gmx::index i = 0;
3172 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]);
3175 /* Count the number of atoms of TC group i for every VCM group */
3176 for (gmx::index j = 0;
3177 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3183 for (int ai = 0; ai < natoms; ai++)
3185 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3187 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3191 /* Correct for VCM removal according to the fraction of each VCM
3192 * group present in this TC group.
3194 nrdf_uc = nrdf_tc[i];
3196 for (gmx::index j = 0;
3197 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1;
3200 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3202 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3203 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3208 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3210 opts->nrdf[i] = nrdf_tc[i];
3211 if (opts->nrdf[i] < 0)
3216 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3217 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]],
3226 sfree(nrdf_vcm_sub);
3229 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3231 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3232 * But since this is much larger than STRLEN, such a line can not be parsed.
3233 * The real maximum is the number of names that fit in a string: STRLEN/2.
3235 #define EGP_MAX (STRLEN / 2)
3239 auto names = gmx::splitString(val);
3240 if (names.size() % 2 != 0)
3242 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3244 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3246 for (size_t i = 0; i < names.size() / 2; i++)
3248 // TODO this needs to be replaced by a solution using std::find_if
3252 names[2 * i].c_str(),
3253 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3259 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3264 names[2 * i + 1].c_str(),
3265 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3271 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3273 if ((j < nr) && (k < nr))
3275 ir->opts.egp_flags[nr * j + k] |= flag;
3276 ir->opts.egp_flags[nr * k + j] |= flag;
3285 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3287 int ig = -1, i = 0, gind;
3291 /* Just a quick check here, more thorough checks are in mdrun */
3292 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3294 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3297 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3298 for (ig = 0; ig < swap->ngrp; ig++)
3300 swapg = &swap->grp[ig];
3301 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3302 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3307 "%s group '%s' contains %d atoms.\n",
3308 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap",
3309 swap->grp[ig].molname,
3311 snew(swapg->ind, swapg->nat);
3312 for (i = 0; i < swapg->nat; i++)
3314 swapg->ind[i] = grps->a[grps->index[gind] + i];
3319 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3325 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3330 ig = search_string(IMDgname, grps->nr, gnames);
3331 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3333 if (IMDgroup->nat > 0)
3336 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3340 snew(IMDgroup->ind, IMDgroup->nat);
3341 for (i = 0; i < IMDgroup->nat; i++)
3343 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3348 /* Checks whether atoms are both part of a COM removal group and frozen.
3349 * If a fully frozen atom is part of a COM removal group, it is removed
3350 * from the COM removal group. A note is issued if such atoms are present.
3351 * A warning is issued for atom with one or two dimensions frozen that
3352 * are part of a COM removal group (mdrun would need to compute COM mass
3353 * per dimension to handle this correctly).
3354 * Also issues a warning when non-frozen atoms are not part of a COM
3355 * removal group while COM removal is active.
3357 static void checkAndUpdateVcmFreezeGroupConsistency(SimulationGroups* groups,
3359 const t_grpopts& opts,
3362 const int vcmRestGroup =
3363 std::max(int(groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()), 1);
3365 int numFullyFrozenVcmAtoms = 0;
3366 int numPartiallyFrozenVcmAtoms = 0;
3367 int numNonVcmAtoms = 0;
3368 for (int a = 0; a < numAtoms; a++)
3370 const int freezeGroup = getGroupType(*groups, SimulationAtomGroupType::Freeze, a);
3371 int numFrozenDims = 0;
3372 for (int d = 0; d < DIM; d++)
3374 numFrozenDims += opts.nFreeze[freezeGroup][d];
3377 const int vcmGroup = getGroupType(*groups, SimulationAtomGroupType::MassCenterVelocityRemoval, a);
3378 if (vcmGroup < vcmRestGroup)
3380 if (numFrozenDims == DIM)
3382 /* Do not remove COM motion for this fully frozen atom */
3383 if (groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
3385 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(
3388 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
3389 numFullyFrozenVcmAtoms++;
3391 else if (numFrozenDims > 0)
3393 numPartiallyFrozenVcmAtoms++;
3396 else if (numFrozenDims < DIM)
3402 if (numFullyFrozenVcmAtoms > 0)
3404 std::string warningText = gmx::formatString(
3405 "There are %d atoms that are fully frozen and part of COMM removal group(s), "
3406 "removing these atoms from the COMM removal group(s)",
3407 numFullyFrozenVcmAtoms);
3408 warning_note(wi, warningText.c_str());
3410 if (numPartiallyFrozenVcmAtoms > 0 && numPartiallyFrozenVcmAtoms < numAtoms)
3412 std::string warningText = gmx::formatString(
3413 "There are %d atoms that are frozen along less then %d dimensions and part of COMM "
3414 "removal group(s), due to limitations in the code these still contribute to the "
3415 "mass of the COM along frozen dimensions and therefore the COMM correction will be "
3417 numPartiallyFrozenVcmAtoms,
3419 warning(wi, warningText.c_str());
3421 if (numNonVcmAtoms > 0)
3423 std::string warningText = gmx::formatString(
3424 "%d atoms are not part of any center of mass motion removal group.\n"
3425 "This may lead to artifacts.\n"
3426 "In most cases one should use one group for the whole system.",
3428 warning(wi, warningText.c_str());
3432 void do_index(const char* mdparin,
3436 const gmx::MdModulesNotifier& notifier,
3440 t_blocka* defaultIndexGroups;
3448 int i, j, k, restnm;
3449 bool bExcl, bTable, bAnneal;
3450 char warn_buf[STRLEN];
3454 fprintf(stderr, "processing index file...\n");
3458 snew(defaultIndexGroups, 1);
3459 snew(defaultIndexGroups->index, 1);
3461 atoms_all = gmx_mtop_global_atoms(mtop);
3462 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3463 done_atom(&atoms_all);
3467 defaultIndexGroups = init_index(ndx, &gnames);
3470 SimulationGroups* groups = &mtop->groups;
3471 natoms = mtop->natoms;
3472 symtab = &mtop->symtab;
3474 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3476 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3478 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3479 restnm = groups->groupNames.size() - 1;
3480 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3481 srenew(gnames, defaultIndexGroups->nr + 1);
3482 gnames[restnm] = *(groups->groupNames.back());
3484 set_warning_line(wi, mdparin, -1);
3486 auto temperatureCouplingTauValues = gmx::splitString(inputrecStrings->tau_t);
3487 auto temperatureCouplingReferenceValues = gmx::splitString(inputrecStrings->ref_t);
3488 auto temperatureCouplingGroupNames = gmx::splitString(inputrecStrings->tcgrps);
3489 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3490 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3493 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3495 temperatureCouplingGroupNames.size(),
3496 temperatureCouplingReferenceValues.size(),
3497 temperatureCouplingTauValues.size());
3500 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3501 do_numbering(natoms,
3503 temperatureCouplingGroupNames,
3506 SimulationAtomGroupType::TemperatureCoupling,
3508 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST,
3511 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3513 snew(ir->opts.nrdf, nr);
3514 snew(ir->opts.tau_t, nr);
3515 snew(ir->opts.ref_t, nr);
3516 if (ir->eI == eiBD && ir->bd_fric == 0)
3518 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3521 if (useReferenceTemperature)
3523 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3525 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3529 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3530 for (i = 0; (i < nr); i++)
3532 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3534 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3535 warning_error(wi, warn_buf);
3538 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3542 "tau-t = -1 is the value to signal that a group should not have "
3543 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3546 if (ir->opts.tau_t[i] >= 0)
3548 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3551 if (ir->etc != etcNO && ir->nsttcouple == -1)
3553 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3558 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3561 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3562 "md-vv; use either vrescale temperature with berendsen pressure or "
3563 "Nose-Hoover temperature with MTTK pressure");
3565 if (ir->epc == epcMTTK)
3567 if (ir->etc != etcNOSEHOOVER)
3570 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3575 if (ir->nstpcouple != ir->nsttcouple)
3577 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3578 ir->nstpcouple = ir->nsttcouple = mincouple;
3580 "for current Trotter decomposition methods with vv, nsttcouple and "
3581 "nstpcouple must be equal. Both have been reset to "
3582 "min(nsttcouple,nstpcouple) = %d",
3584 warning_note(wi, warn_buf);
3589 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3590 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3592 if (ETC_ANDERSEN(ir->etc))
3594 if (ir->nsttcouple != 1)
3598 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3599 "need for larger nsttcouple > 1, since no global parameters are computed. "
3600 "nsttcouple has been reset to 1");
3601 warning_note(wi, warn_buf);
3604 nstcmin = tcouple_min_integration_steps(ir->etc);
3607 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3610 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3611 "least %d times larger than nsttcouple*dt (%g)",
3612 ETCOUPLTYPE(ir->etc),
3615 ir->nsttcouple * ir->delta_t);
3616 warning(wi, warn_buf);
3619 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3620 for (i = 0; (i < nr); i++)
3622 if (ir->opts.ref_t[i] < 0)
3624 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3627 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3628 if we are in this conditional) if mc_temp is negative */
3629 if (ir->expandedvals->mc_temp < 0)
3631 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3635 /* Simulated annealing for each group. There are nr groups */
3636 auto simulatedAnnealingGroupNames = gmx::splitString(inputrecStrings->anneal);
3637 if (simulatedAnnealingGroupNames.size() == 1
3638 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3640 simulatedAnnealingGroupNames.resize(0);
3642 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3645 "Wrong number of annealing values: %zu (for %d groups)\n",
3646 simulatedAnnealingGroupNames.size(),
3651 snew(ir->opts.annealing, nr);
3652 snew(ir->opts.anneal_npoints, nr);
3653 snew(ir->opts.anneal_time, nr);
3654 snew(ir->opts.anneal_temp, nr);
3655 for (i = 0; i < nr; i++)
3657 ir->opts.annealing[i] = eannNO;
3658 ir->opts.anneal_npoints[i] = 0;
3659 ir->opts.anneal_time[i] = nullptr;
3660 ir->opts.anneal_temp[i] = nullptr;
3662 if (!simulatedAnnealingGroupNames.empty())
3665 for (i = 0; i < nr; i++)
3667 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3669 ir->opts.annealing[i] = eannNO;
3671 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3673 ir->opts.annealing[i] = eannSINGLE;
3676 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3678 ir->opts.annealing[i] = eannPERIODIC;
3684 /* Read the other fields too */
3685 auto simulatedAnnealingPoints = gmx::splitString(inputrecStrings->anneal_npoints);
3686 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3689 "Found %zu annealing-npoints values for %zu groups\n",
3690 simulatedAnnealingPoints.size(),
3691 simulatedAnnealingGroupNames.size());
3693 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3694 size_t numSimulatedAnnealingFields = 0;
3695 for (i = 0; i < nr; i++)
3697 if (ir->opts.anneal_npoints[i] == 1)
3701 "Please specify at least a start and an end point for annealing\n");
3703 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3704 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3705 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3708 auto simulatedAnnealingTimes = gmx::splitString(inputrecStrings->anneal_time);
3710 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3713 "Found %zu annealing-time values, wanted %zu\n",
3714 simulatedAnnealingTimes.size(),
3715 numSimulatedAnnealingFields);
3717 auto simulatedAnnealingTemperatures = gmx::splitString(inputrecStrings->anneal_temp);
3718 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3721 "Found %zu annealing-temp values, wanted %zu\n",
3722 simulatedAnnealingTemperatures.size(),
3723 numSimulatedAnnealingFields);
3726 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3727 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3728 convertReals(wi, simulatedAnnealingTimes, "anneal-time", allSimulatedAnnealingTimes.data());
3730 simulatedAnnealingTemperatures,
3732 allSimulatedAnnealingTemperatures.data());
3733 for (i = 0, k = 0; i < nr; i++)
3735 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3737 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3738 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3741 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3743 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3749 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3752 "Annealing timepoints out of order: t=%f comes after "
3754 ir->opts.anneal_time[i][j],
3755 ir->opts.anneal_time[i][j - 1]);
3758 if (ir->opts.anneal_temp[i][j] < 0)
3761 "Found negative temperature in annealing: %f\n",
3762 ir->opts.anneal_temp[i][j]);
3767 /* Print out some summary information, to make sure we got it right */
3768 for (i = 0; i < nr; i++)
3770 if (ir->opts.annealing[i] != eannNO)
3772 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3774 "Simulated annealing for group %s: %s, %d timepoints\n",
3775 *(groups->groupNames[j]),
3776 eann_names[ir->opts.annealing[i]],
3777 ir->opts.anneal_npoints[i]);
3778 fprintf(stderr, "Time (ps) Temperature (K)\n");
3779 /* All terms except the last one */
3780 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3784 ir->opts.anneal_time[i][j],
3785 ir->opts.anneal_temp[i][j]);
3788 /* Finally the last one */
3789 j = ir->opts.anneal_npoints[i] - 1;
3790 if (ir->opts.annealing[i] == eannSINGLE)
3794 ir->opts.anneal_time[i][j],
3795 ir->opts.anneal_temp[i][j]);
3801 ir->opts.anneal_time[i][j],
3802 ir->opts.anneal_temp[i][j]);
3803 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3806 "There is a temperature jump when your annealing "
3818 process_pull_groups(ir->pull->group, inputrecStrings->pullGroupNames, defaultIndexGroups, gnames);
3820 checkPullCoords(ir->pull->group, ir->pull->coord);
3825 make_rotation_groups(ir->rot, inputrecStrings->rotateGroupNames, defaultIndexGroups, gnames);
3828 if (ir->eSwapCoords != eswapNO)
3830 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3833 /* Make indices for IMD session */
3836 make_IMD_group(ir->imd, inputrecStrings->imd_grp, defaultIndexGroups, gnames);
3839 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3840 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3841 notifier.preProcessingNotifications_.notify(defaultIndexGroupsAndNames);
3843 auto accelerations = gmx::splitString(inputrecStrings->acc);
3844 auto accelerationGroupNames = gmx::splitString(inputrecStrings->accgrps);
3845 if (accelerationGroupNames.size() * DIM != accelerations.size())
3848 "Invalid Acceleration input: %zu groups and %zu acc. values",
3849 accelerationGroupNames.size(),
3850 accelerations.size());
3852 do_numbering(natoms,
3854 accelerationGroupNames,
3857 SimulationAtomGroupType::Acceleration,
3862 nr = groups->groups[SimulationAtomGroupType::Acceleration].size();
3863 snew(ir->opts.acc, nr);
3864 ir->opts.ngacc = nr;
3866 convertRvecs(wi, accelerations, "anneal-time", ir->opts.acc);
3868 auto freezeDims = gmx::splitString(inputrecStrings->frdim);
3869 auto freezeGroupNames = gmx::splitString(inputrecStrings->freeze);
3870 if (freezeDims.size() != DIM * freezeGroupNames.size())
3873 "Invalid Freezing input: %zu groups and %zu freeze values",
3874 freezeGroupNames.size(),
3877 do_numbering(natoms,
3882 SimulationAtomGroupType::Freeze,
3887 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3888 ir->opts.ngfrz = nr;
3889 snew(ir->opts.nFreeze, nr);
3890 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3892 for (j = 0; (j < DIM); j++, k++)
3894 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3895 if (!ir->opts.nFreeze[i][j])
3897 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3900 "Please use Y(ES) or N(O) for freezedim only "
3902 freezeDims[k].c_str());
3903 warning(wi, warn_buf);
3908 for (; (i < nr); i++)
3910 for (j = 0; (j < DIM); j++)
3912 ir->opts.nFreeze[i][j] = 0;
3916 auto energyGroupNames = gmx::splitString(inputrecStrings->energy);
3917 do_numbering(natoms,
3922 SimulationAtomGroupType::EnergyOutput,
3927 add_wall_energrps(groups, ir->nwall, symtab);
3928 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3929 auto vcmGroupNames = gmx::splitString(inputrecStrings->vcm);
3930 do_numbering(natoms,
3935 SimulationAtomGroupType::MassCenterVelocityRemoval,
3937 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART,
3941 if (ir->comm_mode != ecmNO)
3943 checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
3946 /* Now we have filled the freeze struct, so we can calculate NRDF */
3947 calc_nrdf(mtop, ir, gnames);
3949 auto user1GroupNames = gmx::splitString(inputrecStrings->user1);
3950 do_numbering(natoms,
3955 SimulationAtomGroupType::User1,
3960 auto user2GroupNames = gmx::splitString(inputrecStrings->user2);
3961 do_numbering(natoms,
3966 SimulationAtomGroupType::User2,
3971 auto compressedXGroupNames = gmx::splitString(inputrecStrings->x_compressed_groups);
3972 do_numbering(natoms,
3974 compressedXGroupNames,
3977 SimulationAtomGroupType::CompressedPositionOutput,
3982 auto orirefFitGroupNames = gmx::splitString(inputrecStrings->orirefitgrp);
3983 do_numbering(natoms,
3985 orirefFitGroupNames,
3988 SimulationAtomGroupType::OrientationRestraintsFit,
3994 /* MiMiC QMMM input processing */
3995 auto qmGroupNames = gmx::splitString(inputrecStrings->QMMM);
3996 if (qmGroupNames.size() > 1)
3998 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
4000 /* group rest, if any, is always MM! */
4001 do_numbering(natoms,
4006 SimulationAtomGroupType::QuantumMechanics,
4011 ir->opts.ngQM = qmGroupNames.size();
4013 /* end of MiMiC QMMM input */
4017 for (auto group : gmx::keysOf(groups->groups))
4019 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
4020 for (const auto& entry : groups->groups[group])
4022 fprintf(stderr, " %s", *(groups->groupNames[entry]));
4024 fprintf(stderr, "\n");
4028 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
4029 snew(ir->opts.egp_flags, nr * nr);
4031 bExcl = do_egp_flag(ir, groups, "energygrp-excl", inputrecStrings->egpexcl, EGP_EXCL);
4032 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
4034 warning_error(wi, "Energy group exclusions are currently not supported");
4036 if (bExcl && EEL_FULL(ir->coulombtype))
4038 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
4041 bTable = do_egp_flag(ir, groups, "energygrp-table", inputrecStrings->egptable, EGP_TABLE);
4042 if (bTable && !(ir->vdwtype == evdwUSER) && !(ir->coulombtype == eelUSER)
4043 && !(ir->coulombtype == eelPMEUSER) && !(ir->coulombtype == eelPMEUSERSWITCH))
4046 "Can only have energy group pair tables in combination with user tables for VdW "
4050 /* final check before going out of scope if simulated tempering variables
4051 * need to be set to default values.
4053 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
4055 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
4058 "the value for nstexpanded was not specified for "
4059 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
4060 "by default, but it is recommended to set it to an explicit value!",
4061 ir->expandedvals->nstexpanded));
4063 for (i = 0; (i < defaultIndexGroups->nr); i++)
4068 done_blocka(defaultIndexGroups);
4069 sfree(defaultIndexGroups);
4073 static void check_disre(const gmx_mtop_t* mtop)
4075 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
4077 const gmx_ffparams_t& ffparams = mtop->ffparams;
4080 for (int i = 0; i < ffparams.numTypes(); i++)
4082 int ftype = ffparams.functype[i];
4083 if (ftype == F_DISRES)
4085 int label = ffparams.iparams[i].disres.label;
4086 if (label == old_label)
4088 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
4097 "Found %d double distance restraint indices,\n"
4098 "probably the parameters for multiple pairs in one restraint "
4099 "are not identical\n",
4105 static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t* sys, const bool posres_only, ivec AbsRef)
4108 gmx_mtop_ilistloop_t iloop;
4110 const t_iparams* pr;
4117 for (d = 0; d < DIM; d++)
4119 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
4121 /* Check for freeze groups */
4122 for (g = 0; g < ir->opts.ngfrz; g++)
4124 for (d = 0; d < DIM; d++)
4126 if (ir->opts.nFreeze[g][d] != 0)
4134 /* Check for position restraints */
4135 iloop = gmx_mtop_ilistloop_init(sys);
4136 while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
4138 if (nmol > 0 && (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
4140 for (i = 0; i < (*ilist)[F_POSRES].size(); i += 2)
4142 pr = &sys->ffparams.iparams[(*ilist)[F_POSRES].iatoms[i]];
4143 for (d = 0; d < DIM; d++)
4145 if (pr->posres.fcA[d] != 0)
4151 for (i = 0; i < (*ilist)[F_FBPOSRES].size(); i += 2)
4153 /* Check for flat-bottom posres */
4154 pr = &sys->ffparams.iparams[(*ilist)[F_FBPOSRES].iatoms[i]];
4155 if (pr->fbposres.k != 0)
4157 switch (pr->fbposres.geom)
4159 case efbposresSPHERE: AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1; break;
4160 case efbposresCYLINDERX: AbsRef[YY] = AbsRef[ZZ] = 1; break;
4161 case efbposresCYLINDERY: AbsRef[XX] = AbsRef[ZZ] = 1; break;
4162 case efbposresCYLINDER:
4163 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
4164 case efbposresCYLINDERZ: AbsRef[XX] = AbsRef[YY] = 1; break;
4165 case efbposresX: /* d=XX */
4166 case efbposresY: /* d=YY */
4167 case efbposresZ: /* d=ZZ */
4168 d = pr->fbposres.geom - efbposresX;
4173 " Invalid geometry for flat-bottom position restraint.\n"
4174 "Expected nr between 1 and %d. Found %d\n",
4183 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
4186 static void check_combination_rule_differences(const gmx_mtop_t* mtop,
4188 bool* bC6ParametersWorkWithGeometricRules,
4189 bool* bC6ParametersWorkWithLBRules,
4190 bool* bLBRulesPossible)
4192 int ntypes, tpi, tpj;
4195 double c6i, c6j, c12i, c12j;
4196 double c6, c6_geometric, c6_LB;
4197 double sigmai, sigmaj, epsi, epsj;
4198 bool bCanDoLBRules, bCanDoGeometricRules;
4201 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
4202 * force-field floating point parameters.
4205 ptr = getenv("GMX_LJCOMB_TOL");
4209 double gmx_unused canary;
4211 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
4214 FARGS, "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
4219 *bC6ParametersWorkWithLBRules = TRUE;
4220 *bC6ParametersWorkWithGeometricRules = TRUE;
4221 bCanDoLBRules = TRUE;
4222 ntypes = mtop->ffparams.atnr;
4223 snew(typecount, ntypes);
4224 gmx_mtop_count_atomtypes(mtop, state, typecount);
4225 *bLBRulesPossible = TRUE;
4226 for (tpi = 0; tpi < ntypes; ++tpi)
4228 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
4229 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
4230 for (tpj = tpi; tpj < ntypes; ++tpj)
4232 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
4233 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
4234 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
4235 c6_geometric = std::sqrt(c6i * c6j);
4236 if (!gmx_numzero(c6_geometric))
4238 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4240 sigmai = gmx::sixthroot(c12i / c6i);
4241 sigmaj = gmx::sixthroot(c12j / c6j);
4242 epsi = c6i * c6i / (4.0 * c12i);
4243 epsj = c6j * c6j / (4.0 * c12j);
4244 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4248 *bLBRulesPossible = FALSE;
4249 c6_LB = c6_geometric;
4251 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4256 *bC6ParametersWorkWithLBRules = FALSE;
4259 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4261 if (!bCanDoGeometricRules)
4263 *bC6ParametersWorkWithGeometricRules = FALSE;
4270 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t* mtop, warninp_t wi)
4272 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4274 check_combination_rule_differences(
4275 mtop, 0, &bC6ParametersWorkWithGeometricRules, &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4276 if (ir->ljpme_combination_rule == eljpmeLB)
4278 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4281 "You are using arithmetic-geometric combination rules "
4282 "in LJ-PME, but your non-bonded C6 parameters do not "
4283 "follow these rules.");
4288 if (!bC6ParametersWorkWithGeometricRules)
4290 if (ir->eDispCorr != edispcNO)
4293 "You are using geometric combination rules in "
4294 "LJ-PME, but your non-bonded C6 parameters do "
4295 "not follow these rules. "
4296 "This will introduce very small errors in the forces and energies in "
4297 "your simulations. Dispersion correction will correct total energy "
4298 "and/or pressure for isotropic systems, but not forces or surface "
4304 "You are using geometric combination rules in "
4305 "LJ-PME, but your non-bonded C6 parameters do "
4306 "not follow these rules. "
4307 "This will introduce very small errors in the forces and energies in "
4308 "your simulations. If your system is homogeneous, consider using "
4309 "dispersion correction "
4310 "for the total energy and pressure.");
4316 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4318 // Not meeting MTS requirements should have resulted in a fatal error, so we can assert here
4319 GMX_ASSERT(gmx::checkMtsRequirements(*ir).empty(), "All MTS requirements should be met here");
4321 char err_buf[STRLEN];
4326 gmx_mtop_atomloop_block_t aloopb;
4328 char warn_buf[STRLEN];
4330 set_warning_line(wi, mdparin, -1);
4332 if (absolute_reference(ir, sys, false, AbsRef))
4335 "Removing center of mass motion in the presence of position restraints might "
4336 "cause artifacts. When you are using position restraints to equilibrate a "
4337 "macro-molecule, the artifacts are usually negligible.");
4340 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 && ir->nstlist > 1
4341 && ((EI_MD(ir->eI) || EI_SD(ir->eI)) && (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4343 /* Check if a too small Verlet buffer might potentially
4344 * cause more drift than the thermostat can couple off.
4346 /* Temperature error fraction for warning and suggestion */
4347 const real T_error_warn = 0.002;
4348 const real T_error_suggest = 0.001;
4349 /* For safety: 2 DOF per atom (typical with constraints) */
4350 const real nrdf_at = 2;
4351 real T, tau, max_T_error;
4356 for (i = 0; i < ir->opts.ngtc; i++)
4358 T = std::max(T, ir->opts.ref_t[i]);
4359 tau = std::max(tau, ir->opts.tau_t[i]);
4363 /* This is a worst case estimate of the temperature error,
4364 * assuming perfect buffer estimation and no cancelation
4365 * of errors. The factor 0.5 is because energy distributes
4366 * equally over Ekin and Epot.
4368 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * BOLTZ * T);
4369 if (max_T_error > T_error_warn)
4372 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4373 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4374 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4375 "%.0e or decrease tau_t.",
4380 100 * T_error_suggest,
4381 ir->verletbuf_tol * T_error_suggest / max_T_error);
4382 warning(wi, warn_buf);
4387 if (ETC_ANDERSEN(ir->etc))
4391 for (i = 0; i < ir->opts.ngtc; i++)
4394 "all tau_t must currently be equal using Andersen temperature control, "
4395 "violated for group %d",
4397 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4399 "all tau_t must be positive using Andersen temperature control, "
4403 CHECK(ir->opts.tau_t[i] < 0);
4406 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4408 for (i = 0; i < ir->opts.ngtc; i++)
4410 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4412 "tau_t/delta_t for group %d for temperature control method %s must be a "
4413 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4414 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4417 etcoupl_names[ir->etc],
4421 CHECK(nsteps % ir->nstcomm != 0);
4426 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD && ir->comm_mode == ecmNO
4427 && !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) && !ETC_ANDERSEN(ir->etc))
4430 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4431 "rounding errors can lead to build up of kinetic energy of the center of mass");
4434 if (ir->epc == epcPARRINELLORAHMAN && ir->etc == etcNOSEHOOVER)
4437 for (int g = 0; g < ir->opts.ngtc; g++)
4439 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4441 if (ir->tau_p < 1.9 * tau_t_max)
4443 std::string message = gmx::formatString(
4444 "With %s T-coupling and %s p-coupling, "
4445 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4446 etcoupl_names[ir->etc],
4447 epcoupl_names[ir->epc],
4452 warning(wi, message.c_str());
4456 /* Check for pressure coupling with absolute position restraints */
4457 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4459 absolute_reference(ir, sys, TRUE, AbsRef);
4461 for (m = 0; m < DIM; m++)
4463 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4466 "You are using pressure coupling with absolute position restraints, "
4467 "this will give artifacts. Use the refcoord_scaling option.");
4475 aloopb = gmx_mtop_atomloop_block_init(sys);
4477 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4479 if (atom->q != 0 || atom->qB != 0)
4487 if (EEL_FULL(ir->coulombtype))
4490 "You are using full electrostatics treatment %s for a system without charges.\n"
4491 "This costs a lot of performance for just processing zeros, consider using %s "
4493 EELTYPE(ir->coulombtype),
4495 warning(wi, err_buf);
4500 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
4503 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4504 "You might want to consider using %s electrostatics.\n",
4506 warning_note(wi, err_buf);
4510 /* Check if combination rules used in LJ-PME are the same as in the force field */
4511 if (EVDW_PME(ir->vdwtype))
4513 check_combination_rules(ir, sys, wi);
4516 /* Generalized reaction field */
4517 if (ir->coulombtype == eelGRF_NOTUSED)
4520 "Generalized reaction-field electrostatics is no longer supported. "
4521 "You can use normal reaction-field instead and compute the reaction-field "
4522 "constant by hand.");
4526 for (int i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4528 for (m = 0; (m < DIM); m++)
4530 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4539 snew(mgrp, sys->groups.groups[SimulationAtomGroupType::Acceleration].size());
4540 for (const AtomProxy atomP : AtomRange(*sys))
4542 const t_atom& local = atomP.atom();
4543 int i = atomP.globalAtomNumber();
4544 mgrp[getGroupType(sys->groups, SimulationAtomGroupType::Acceleration, i)] += local.m;
4547 for (i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4549 for (m = 0; (m < DIM); m++)
4551 acc[m] += ir->opts.acc[i][m] * mgrp[i];
4555 for (m = 0; (m < DIM); m++)
4557 if (fabs(acc[m]) > 1e-6)
4559 const char* dim[DIM] = { "X", "Y", "Z" };
4561 "Net Acceleration in %s direction, will %s be corrected\n",
4563 ir->nstcomm != 0 ? "" : "not");
4564 if (ir->nstcomm != 0 && m < ndof_com(ir))
4568 (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration]));
4571 ir->opts.acc[i][m] -= acc[m];
4579 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0
4580 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4582 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4590 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4592 if (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0)
4594 absolute_reference(ir, sys, FALSE, AbsRef);
4595 for (m = 0; m < DIM; m++)
4597 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4600 "You are using an absolute reference for pulling, but the rest of "
4601 "the system does not have an absolute reference. This will lead to "
4610 for (i = 0; i < 3; i++)
4612 for (m = 0; m <= i; m++)
4614 if ((ir->epc != epcNO && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4616 for (c = 0; c < ir->pull->ncoord; c++)
4618 if (ir->pull->coord[c].eGeom == epullgDIRPBC && ir->pull->coord[c].vec[m] != 0)
4621 "Can not have dynamic box while using pull geometry '%s' "
4623 EPULLGEOM(ir->pull->coord[c].eGeom),
4635 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4637 char warn_buf[STRLEN];
4640 ptr = check_box(ir->pbcType, box);
4643 warning_error(wi, ptr);
4646 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4648 if (ir->shake_tol <= 0.0)
4650 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4651 warning_error(wi, warn_buf);
4655 if ((ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4657 /* If we have Lincs constraints: */
4658 if (ir->eI == eiMD && ir->etc == etcNO && ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4661 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4662 warning_note(wi, warn_buf);
4665 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4668 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4670 warning_note(wi, warn_buf);
4672 if (ir->epc == epcMTTK)
4674 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4678 if (bHasAnyConstraints && ir->epc == epcMTTK)
4680 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4683 if (ir->LincsWarnAngle > 90.0)
4685 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4686 warning(wi, warn_buf);
4687 ir->LincsWarnAngle = 90.0;
4690 if (ir->pbcType != PbcType::No)
4692 if (ir->nstlist == 0)
4695 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4696 "atoms might cause the simulation to crash.");
4698 if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
4701 "ERROR: The cut-off length is longer than half the shortest box vector or "
4702 "longer than the smallest box diagonal element. Increase the box size or "
4703 "decrease rlist.\n");
4704 warning_error(wi, warn_buf);