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50 #include "gromacs/awh/read_params.h"
51 #include "gromacs/fileio/readinp.h"
52 #include "gromacs/fileio/warninp.h"
53 #include "gromacs/gmxlib/network.h"
54 #include "gromacs/gmxpreprocess/toputil.h"
55 #include "gromacs/math/functions.h"
56 #include "gromacs/math/units.h"
57 #include "gromacs/math/vec.h"
58 #include "gromacs/mdlib/calc_verletbuf.h"
59 #include "gromacs/mdrun/mdmodules.h"
60 #include "gromacs/mdtypes/inputrec.h"
61 #include "gromacs/mdtypes/md_enums.h"
62 #include "gromacs/mdtypes/pull_params.h"
63 #include "gromacs/options/options.h"
64 #include "gromacs/options/treesupport.h"
65 #include "gromacs/pbcutil/pbc.h"
66 #include "gromacs/selection/indexutil.h"
67 #include "gromacs/topology/block.h"
68 #include "gromacs/topology/ifunc.h"
69 #include "gromacs/topology/index.h"
70 #include "gromacs/topology/mtop_util.h"
71 #include "gromacs/topology/symtab.h"
72 #include "gromacs/topology/topology.h"
73 #include "gromacs/utility/cstringutil.h"
74 #include "gromacs/utility/exceptions.h"
75 #include "gromacs/utility/fatalerror.h"
76 #include "gromacs/utility/filestream.h"
77 #include "gromacs/utility/gmxassert.h"
78 #include "gromacs/utility/ikeyvaluetreeerror.h"
79 #include "gromacs/utility/keyvaluetree.h"
80 #include "gromacs/utility/keyvaluetreebuilder.h"
81 #include "gromacs/utility/keyvaluetreemdpwriter.h"
82 #include "gromacs/utility/keyvaluetreetransform.h"
83 #include "gromacs/utility/mdmodulenotification.h"
84 #include "gromacs/utility/smalloc.h"
85 #include "gromacs/utility/strconvert.h"
86 #include "gromacs/utility/stringcompare.h"
87 #include "gromacs/utility/stringutil.h"
88 #include "gromacs/utility/textwriter.h"
93 /* Resource parameters
94 * Do not change any of these until you read the instruction
95 * in readinp.h. Some cpp's do not take spaces after the backslash
96 * (like the c-shell), which will give you a very weird compiler
100 struct gmx_inputrec_strings
102 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN], acc[STRLEN], accgrps[STRLEN], freeze[STRLEN],
103 frdim[STRLEN], energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN],
104 x_compressed_groups[STRLEN], couple_moltype[STRLEN], orirefitgrp[STRLEN],
105 egptable[STRLEN], egpexcl[STRLEN], wall_atomtype[STRLEN], wall_density[STRLEN],
106 deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
107 char fep_lambda[efptNR][STRLEN];
108 char lambda_weights[STRLEN];
109 std::vector<std::string> pullGroupNames;
110 std::vector<std::string> rotateGroupNames;
111 char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
112 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN], bSH[STRLEN],
113 CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN], SAoff[STRLEN], SAsteps[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 if (ir->coulombtype == eelRF_NEC_UNSUPPORTED)
260 sprintf(warn_buf, "%s electrostatics is no longer supported", eel_names[eelRF_NEC_UNSUPPORTED]);
261 warning_error(wi, warn_buf);
264 /* BASIC CUT-OFF STUFF */
265 if (ir->rcoulomb < 0)
267 warning_error(wi, "rcoulomb should be >= 0");
271 warning_error(wi, "rvdw should be >= 0");
273 if (ir->rlist < 0 && !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
275 warning_error(wi, "rlist should be >= 0");
278 "nstlist can not be smaller than 0. (If you were trying to use the heuristic "
279 "neighbour-list update scheme for efficient buffering for improved energy "
280 "conservation, please use the Verlet cut-off scheme instead.)");
281 CHECK(ir->nstlist < 0);
283 process_interaction_modifier(&ir->coulomb_modifier);
284 process_interaction_modifier(&ir->vdw_modifier);
286 if (ir->cutoff_scheme == ecutsGROUP)
289 "The group cutoff scheme has been removed since GROMACS 2020. "
290 "Please use the Verlet cutoff scheme.");
292 if (ir->cutoff_scheme == ecutsVERLET)
296 /* Normal Verlet type neighbor-list, currently only limited feature support */
297 if (inputrec2nboundeddim(ir) < 3)
299 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
302 // We don't (yet) have general Verlet kernels for rcoulomb!=rvdw
303 if (ir->rcoulomb != ir->rvdw)
305 // Since we have PME coulomb + LJ cut-off kernels with rcoulomb>rvdw
306 // for PME load balancing, we can support this exception.
307 bool bUsesPmeTwinRangeKernel = (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == evdwCUT
308 && ir->rcoulomb > ir->rvdw);
309 if (!bUsesPmeTwinRangeKernel)
312 "With Verlet lists rcoulomb!=rvdw is not supported (except for "
313 "rcoulomb>rvdw with PME electrostatics)");
317 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
319 if (ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT)
321 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
324 "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and "
326 evdw_names[ir->vdwtype], evdw_names[evdwCUT], eintmod_names[ir->vdw_modifier]);
327 warning_note(wi, warn_buf);
329 ir->vdwtype = evdwCUT;
333 sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s",
334 evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
335 warning_error(wi, warn_buf);
339 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
342 "With Verlet lists only cut-off and PME LJ interactions are supported");
344 if (!(ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype) || EEL_PME(ir->coulombtype)
345 || ir->coulombtype == eelEWALD))
348 "With Verlet lists only cut-off, reaction-field, PME and Ewald "
349 "electrostatics are supported");
351 if (!(ir->coulomb_modifier == eintmodNONE || ir->coulomb_modifier == eintmodPOTSHIFT))
353 sprintf(warn_buf, "coulomb_modifier=%s is not supported", eintmod_names[ir->coulomb_modifier]);
354 warning_error(wi, warn_buf);
357 if (EEL_USER(ir->coulombtype))
359 sprintf(warn_buf, "Coulomb type %s is not supported with the verlet scheme",
360 eel_names[ir->coulombtype]);
361 warning_error(wi, warn_buf);
364 if (ir->nstlist <= 0)
366 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
369 if (ir->nstlist < 10)
372 "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note "
373 "that with the Verlet scheme, nstlist has no effect on the accuracy of "
377 rc_max = std::max(ir->rvdw, ir->rcoulomb);
381 /* With TPI we set the pairlist cut-off later using the radius of the insterted molecule */
382 ir->verletbuf_tol = 0;
385 else if (ir->verletbuf_tol <= 0)
387 if (ir->verletbuf_tol == 0)
389 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
392 if (ir->rlist < rc_max)
395 "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
398 if (ir->rlist == rc_max && ir->nstlist > 1)
402 "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet "
403 "buffer. The cluster pair list does have a buffering effect, but choosing "
404 "a larger rlist might be necessary for good energy conservation.");
409 if (ir->rlist > rc_max)
412 "You have set rlist larger than the interaction cut-off, but you also "
413 "have verlet-buffer-tolerance > 0. Will set rlist using "
414 "verlet-buffer-tolerance.");
417 if (ir->nstlist == 1)
419 /* No buffer required */
424 if (EI_DYNAMICS(ir->eI))
426 if (inputrec2nboundeddim(ir) < 3)
429 "The box volume is required for calculating rlist from the "
430 "energy drift with verlet-buffer-tolerance > 0. You are "
431 "using at least one unbounded dimension, so no volume can be "
432 "computed. Either use a finite box, or set rlist yourself "
433 "together with verlet-buffer-tolerance = -1.");
435 /* Set rlist temporarily so we can continue processing */
440 /* Set the buffer to 5% of the cut-off */
441 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics) * rc_max;
447 /* GENERAL INTEGRATOR STUFF */
450 if (ir->etc != etcNO)
452 if (EI_RANDOM(ir->eI))
455 "Setting tcoupl from '%s' to 'no'. %s handles temperature coupling "
456 "implicitly. See the documentation for more information on which "
457 "parameters affect temperature for %s.",
458 etcoupl_names[ir->etc], ei_names[ir->eI], ei_names[ir->eI]);
463 "Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to "
465 etcoupl_names[ir->etc], ei_names[ir->eI]);
467 warning_note(wi, warn_buf);
471 if (ir->eI == eiVVAK)
474 "Integrator method %s is implemented primarily for validation purposes; for "
475 "molecular dynamics, you should probably be using %s or %s",
476 ei_names[eiVVAK], ei_names[eiMD], ei_names[eiVV]);
477 warning_note(wi, warn_buf);
479 if (!EI_DYNAMICS(ir->eI))
481 if (ir->epc != epcNO)
484 "Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.",
485 epcoupl_names[ir->epc], ei_names[ir->eI]);
486 warning_note(wi, warn_buf);
490 if (EI_DYNAMICS(ir->eI))
492 if (ir->nstcalcenergy < 0)
494 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
495 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
497 /* nstcalcenergy larger than nstener does not make sense.
498 * We ideally want nstcalcenergy=nstener.
502 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
506 ir->nstcalcenergy = ir->nstenergy;
510 else if ((ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy)
511 || (ir->efep != efepNO && ir->fepvals->nstdhdl > 0
512 && (ir->nstcalcenergy > ir->fepvals->nstdhdl)))
515 const char* nsten = "nstenergy";
516 const char* nstdh = "nstdhdl";
517 const char* min_name = nsten;
518 int min_nst = ir->nstenergy;
520 /* find the smallest of ( nstenergy, nstdhdl ) */
521 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0
522 && (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
524 min_nst = ir->fepvals->nstdhdl;
527 /* If the user sets nstenergy small, we should respect that */
528 sprintf(warn_buf, "Setting nstcalcenergy (%d) equal to %s (%d)", ir->nstcalcenergy,
530 warning_note(wi, warn_buf);
531 ir->nstcalcenergy = min_nst;
534 if (ir->epc != epcNO)
536 if (ir->nstpcouple < 0)
538 ir->nstpcouple = ir_optimal_nstpcouple(ir);
542 if (ir->nstcalcenergy > 0)
544 if (ir->efep != efepNO)
546 /* nstdhdl should be a multiple of nstcalcenergy */
547 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstdhdl", &ir->fepvals->nstdhdl, wi);
551 /* nstexpanded should be a multiple of nstcalcenergy */
552 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstexpanded",
553 &ir->expandedvals->nstexpanded, wi);
555 /* for storing exact averages nstenergy should be
556 * a multiple of nstcalcenergy
558 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstenergy", &ir->nstenergy, wi);
561 // Inquire all MdModules, if their parameters match with the energy
562 // calculation frequency
563 gmx::EnergyCalculationFrequencyErrors energyCalculationFrequencyErrors(ir->nstcalcenergy);
564 mdModulesNotifier.preProcessingNotifications_.notify(&energyCalculationFrequencyErrors);
566 // Emit all errors from the energy calculation frequency checks
567 for (const std::string& energyFrequencyErrorMessage :
568 energyCalculationFrequencyErrors.errorMessages())
570 warning_error(wi, energyFrequencyErrorMessage);
574 if (ir->nsteps == 0 && !ir->bContinuation)
577 "For a correct single-point energy evaluation with nsteps = 0, use "
578 "continuation = yes to avoid constraining the input coordinates.");
582 if ((EI_SD(ir->eI) || ir->eI == eiBD) && ir->bContinuation && ir->ld_seed != -1)
585 "You are doing a continuation with SD or BD, make sure that ld_seed is "
586 "different from the previous run (using ld_seed=-1 will ensure this)");
592 sprintf(err_buf, "TPI only works with pbc = %s", c_pbcTypeNames[PbcType::Xyz].c_str());
593 CHECK(ir->pbcType != PbcType::Xyz);
594 sprintf(err_buf, "with TPI nstlist should be larger than zero");
595 CHECK(ir->nstlist <= 0);
596 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
597 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
601 if ((opts->nshake > 0) && (opts->bMorse))
603 sprintf(warn_buf, "Using morse bond-potentials while constraining bonds is useless");
604 warning(wi, warn_buf);
607 if ((EI_SD(ir->eI) || ir->eI == eiBD) && ir->bContinuation && ir->ld_seed != -1)
610 "You are doing a continuation with SD or BD, make sure that ld_seed is "
611 "different from the previous run (using ld_seed=-1 will ensure this)");
613 /* verify simulated tempering options */
617 bool bAllTempZero = TRUE;
618 for (i = 0; i < fep->n_lambda; i++)
620 sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i,
621 efpt_names[efptTEMPERATURE], fep->all_lambda[efptTEMPERATURE][i]);
622 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
623 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
625 bAllTempZero = FALSE;
628 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
629 CHECK(bAllTempZero == TRUE);
631 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
632 CHECK(ir->eI != eiVV);
634 /* check compatability of the temperature coupling with simulated tempering */
636 if (ir->etc == etcNOSEHOOVER)
639 "Nose-Hoover based temperature control such as [%s] my not be "
640 "entirelyconsistent with simulated tempering",
641 etcoupl_names[ir->etc]);
642 warning_note(wi, warn_buf);
645 /* check that the temperatures make sense */
648 "Higher simulated tempering temperature (%g) must be >= than the simulated "
649 "tempering lower temperature (%g)",
650 ir->simtempvals->simtemp_high, ir->simtempvals->simtemp_low);
651 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
653 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero",
654 ir->simtempvals->simtemp_high);
655 CHECK(ir->simtempvals->simtemp_high <= 0);
657 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero",
658 ir->simtempvals->simtemp_low);
659 CHECK(ir->simtempvals->simtemp_low <= 0);
662 /* verify free energy options */
664 if (ir->efep != efepNO)
667 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2", fep->sc_power);
668 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
671 "The soft-core sc-r-power is %d and can only be 6. (sc-r-power 48 is no longer "
673 static_cast<int>(fep->sc_r_power));
674 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0);
677 "Can't use positive delta-lambda (%g) if initial state/lambda does not start at "
680 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
682 sprintf(err_buf, "Can't use positive delta-lambda (%g) with expanded ensemble simulations",
684 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
686 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
687 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
689 sprintf(err_buf, "Free-energy not implemented for Ewald");
690 CHECK(ir->coulombtype == eelEWALD);
692 /* check validty of lambda inputs */
693 if (fep->n_lambda == 0)
695 /* Clear output in case of no states:*/
696 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.",
697 fep->init_fep_state);
698 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
702 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d",
703 fep->init_fep_state, fep->n_lambda - 1);
704 CHECK((fep->init_fep_state >= fep->n_lambda));
708 "Lambda state must be set, either with init-lambda-state or with init-lambda");
709 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
712 "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with "
713 "init-lambda-state or with init-lambda, but not both",
714 fep->init_lambda, fep->init_fep_state);
715 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
718 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
722 for (i = 0; i < efptNR; i++)
724 if (fep->separate_dvdl[i])
729 if (n_lambda_terms > 1)
732 "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't "
733 "use init-lambda to set lambda state (except for slow growth). Use "
734 "init-lambda-state instead.");
735 warning(wi, warn_buf);
738 if (n_lambda_terms < 2 && fep->n_lambda > 0)
741 "init-lambda is deprecated for setting lambda state (except for slow "
742 "growth). Use init-lambda-state instead.");
746 for (j = 0; j < efptNR; j++)
748 for (i = 0; i < fep->n_lambda; i++)
750 sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i,
751 efpt_names[j], fep->all_lambda[j][i]);
752 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
756 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
758 for (i = 0; i < fep->n_lambda; i++)
761 "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while "
762 "coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to "
763 "crashes, and is not supported.",
764 i, fep->all_lambda[efptVDW][i], fep->all_lambda[efptCOUL][i]);
765 CHECK((fep->sc_alpha > 0)
766 && (((fep->all_lambda[efptCOUL][i] > 0.0) && (fep->all_lambda[efptCOUL][i] < 1.0))
767 && ((fep->all_lambda[efptVDW][i] > 0.0) && (fep->all_lambda[efptVDW][i] < 1.0))));
771 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
773 real sigma, lambda, r_sc;
776 /* Maximum estimate for A and B charges equal with lambda power 1 */
778 r_sc = std::pow(lambda * fep->sc_alpha * std::pow(sigma / ir->rcoulomb, fep->sc_r_power) + 1.0,
779 1.0 / fep->sc_r_power);
781 "With PME there is a minor soft core effect present at the cut-off, "
782 "proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on "
783 "energy conservation, but usually other effects dominate. With a common sigma "
784 "value of %g nm the fraction of the particle-particle potential at the cut-off "
785 "at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
786 fep->sc_r_power, sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
787 warning_note(wi, warn_buf);
790 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
791 be treated differently, but that's the next step */
793 for (i = 0; i < efptNR; i++)
795 for (j = 0; j < fep->n_lambda; j++)
797 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
798 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
803 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
807 /* checking equilibration of weights inputs for validity */
810 "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal "
812 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
813 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
816 "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to "
818 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
819 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
822 "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
823 expand->equil_steps, elmceq_names[elmceqSTEPS]);
824 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
827 "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
828 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
829 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
832 "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
833 expand->equil_ratio, elmceq_names[elmceqRATIO]);
834 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
837 "weight-equil-number-all-lambda (%d) must be a positive integer if "
838 "lmc-weights-equil=%s",
839 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
840 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
843 "weight-equil-number-samples (%d) must be a positive integer if "
844 "lmc-weights-equil=%s",
845 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
846 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
849 "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
850 expand->equil_steps, elmceq_names[elmceqSTEPS]);
851 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
853 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
854 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
855 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
857 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
858 expand->equil_ratio, elmceq_names[elmceqRATIO]);
859 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
861 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
862 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
863 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
865 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
866 CHECK((expand->lmc_repeats <= 0));
867 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
868 CHECK((expand->minvarmin <= 0));
869 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
870 CHECK((expand->c_range < 0));
872 "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != "
874 fep->init_fep_state, expand->lmc_forced_nstart);
875 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0)
876 && (expand->elmcmove != elmcmoveNO));
877 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
878 CHECK((expand->lmc_forced_nstart < 0));
879 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)",
880 fep->init_fep_state);
881 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
883 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
884 CHECK((expand->init_wl_delta < 0));
885 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
886 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
887 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
888 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
890 /* if there is no temperature control, we need to specify an MC temperature */
891 if (!integratorHasReferenceTemperature(ir) && (expand->elmcmove != elmcmoveNO)
892 && (expand->mc_temp <= 0.0))
895 "If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set "
896 "to a positive number");
897 warning_error(wi, err_buf);
899 if (expand->nstTij > 0)
901 sprintf(err_buf, "nstlog must be non-zero");
902 CHECK(ir->nstlog == 0);
903 // Avoid modulus by zero in the case that already triggered an error exit.
907 "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
908 expand->nstTij, ir->nstlog);
909 CHECK((expand->nstTij % ir->nstlog) != 0);
915 sprintf(err_buf, "walls only work with pbc=%s", c_pbcTypeNames[PbcType::XY].c_str());
916 CHECK(ir->nwall && ir->pbcType != PbcType::XY);
919 if (ir->pbcType != PbcType::Xyz && ir->nwall != 2)
921 if (ir->pbcType == PbcType::No)
923 if (ir->epc != epcNO)
925 warning(wi, "Turning off pressure coupling for vacuum system");
931 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
932 c_pbcTypeNames[ir->pbcType].c_str());
933 CHECK(ir->epc != epcNO);
935 sprintf(err_buf, "Can not have Ewald with pbc=%s", c_pbcTypeNames[ir->pbcType].c_str());
936 CHECK(EEL_FULL(ir->coulombtype));
938 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
939 c_pbcTypeNames[ir->pbcType].c_str());
940 CHECK(ir->eDispCorr != edispcNO);
943 if (ir->rlist == 0.0)
946 "can only have neighborlist cut-off zero (=infinite)\n"
947 "with coulombtype = %s or coulombtype = %s\n"
948 "without periodic boundary conditions (pbc = %s) and\n"
949 "rcoulomb and rvdw set to zero",
950 eel_names[eelCUT], eel_names[eelUSER], c_pbcTypeNames[PbcType::No].c_str());
951 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER))
952 || (ir->pbcType != PbcType::No) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
957 "Simulating without cut-offs can be (slightly) faster with nstlist=0, "
958 "nstype=simple and only one MPI rank");
963 if (ir->nstcomm == 0)
965 // TODO Change this behaviour. There should be exactly one way
966 // to turn off an algorithm.
967 ir->comm_mode = ecmNO;
969 if (ir->comm_mode != ecmNO)
973 // TODO Such input was once valid. Now that we've been
974 // helpful for a few years, we should reject such input,
975 // lest we have to support every historical decision
978 "If you want to remove the rotation around the center of mass, you should set "
979 "comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to "
980 "its absolute value");
981 ir->nstcomm = abs(ir->nstcomm);
984 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
987 "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting "
988 "nstcomm to nstcalcenergy");
989 ir->nstcomm = ir->nstcalcenergy;
992 if (ir->comm_mode == ecmANGULAR)
995 "Can not remove the rotation around the center of mass with periodic "
997 CHECK(ir->bPeriodicMols);
998 if (ir->pbcType != PbcType::No)
1001 "Removing the rotation around the center of mass in a periodic system, "
1002 "this can lead to artifacts. Only use this on a single (cluster of) "
1003 "molecules. This cluster should not cross periodic boundaries.");
1008 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->pbcType == PbcType::No && ir->comm_mode != ecmANGULAR)
1011 "Tumbling and flying ice-cubes: We are not removing rotation around center of mass "
1012 "in a non-periodic system. You should probably set comm_mode = ANGULAR or use "
1015 warning_note(wi, warn_buf);
1018 /* TEMPERATURE COUPLING */
1019 if (ir->etc == etcYES)
1021 ir->etc = etcBERENDSEN;
1023 "Old option for temperature coupling given: "
1024 "changing \"yes\" to \"Berendsen\"\n");
1027 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
1029 if (ir->opts.nhchainlength < 1)
1032 "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to "
1034 ir->opts.nhchainlength);
1035 ir->opts.nhchainlength = 1;
1036 warning(wi, warn_buf);
1039 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
1043 "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
1044 ir->opts.nhchainlength = 1;
1049 ir->opts.nhchainlength = 0;
1052 if (ir->eI == eiVVAK)
1055 "%s implemented primarily for validation, and requires nsttcouple = 1 and "
1058 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
1061 if (ETC_ANDERSEN(ir->etc))
1063 sprintf(err_buf, "%s temperature control not supported for integrator %s.",
1064 etcoupl_names[ir->etc], ei_names[ir->eI]);
1065 CHECK(!(EI_VV(ir->eI)));
1067 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
1070 "Center of mass removal not necessary for %s. All velocities of coupled "
1071 "groups are rerandomized periodically, so flying ice cube errors will not "
1073 etcoupl_names[ir->etc]);
1074 warning_note(wi, warn_buf);
1078 "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are "
1079 "randomized every time step",
1080 ir->nstcomm, etcoupl_names[ir->etc]);
1081 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
1084 if (ir->etc == etcBERENDSEN)
1087 "The %s thermostat does not generate the correct kinetic energy distribution. You "
1088 "might want to consider using the %s thermostat.",
1089 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
1090 warning_note(wi, warn_buf);
1093 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc)) && ir->epc == epcBERENDSEN)
1096 "Using Berendsen pressure coupling invalidates the "
1097 "true ensemble for the thermostat");
1098 warning(wi, warn_buf);
1101 /* PRESSURE COUPLING */
1102 if (ir->epc == epcISOTROPIC)
1104 ir->epc = epcBERENDSEN;
1106 "Old option for pressure coupling given: "
1107 "changing \"Isotropic\" to \"Berendsen\"\n");
1110 if (ir->epc != epcNO)
1112 dt_pcoupl = ir->nstpcouple * ir->delta_t;
1114 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1115 CHECK(ir->tau_p <= 0);
1117 if (ir->tau_p / dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10 * GMX_REAL_EPS)
1120 "For proper integration of the %s barostat, tau-p (%g) should be at least %d "
1121 "times larger than nstpcouple*dt (%g)",
1122 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1123 warning(wi, warn_buf);
1127 "compressibility must be > 0 when using pressure"
1129 EPCOUPLTYPE(ir->epc));
1130 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 || ir->compress[ZZ][ZZ] < 0
1131 || (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 && ir->compress[ZZ][XX] <= 0
1132 && ir->compress[ZZ][YY] <= 0));
1134 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1137 "You are generating velocities so I am assuming you "
1138 "are equilibrating a system. You are using "
1139 "%s pressure coupling, but this can be "
1140 "unstable for equilibration. If your system crashes, try "
1141 "equilibrating first with Berendsen pressure coupling. If "
1142 "you are not equilibrating the system, you can probably "
1143 "ignore this warning.",
1144 epcoupl_names[ir->epc]);
1145 warning(wi, warn_buf);
1151 if (ir->epc == epcMTTK)
1153 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1157 /* ELECTROSTATICS */
1158 /* More checks are in triple check (grompp.c) */
1160 if (ir->coulombtype == eelSWITCH)
1163 "coulombtype = %s is only for testing purposes and can lead to serious "
1164 "artifacts, advice: use coulombtype = %s",
1165 eel_names[ir->coulombtype], eel_names[eelRF_ZERO]);
1166 warning(wi, warn_buf);
1169 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1172 "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old "
1173 "format and exchanging epsilon-r and epsilon-rf",
1175 warning(wi, warn_buf);
1176 ir->epsilon_rf = ir->epsilon_r;
1177 ir->epsilon_r = 1.0;
1180 if (ir->epsilon_r == 0)
1183 "It is pointless to use long-range electrostatics with infinite relative "
1185 "Since you are effectively turning of electrostatics, a plain cutoff will be much "
1187 CHECK(EEL_FULL(ir->coulombtype));
1190 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1192 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1193 CHECK(ir->epsilon_r < 0);
1196 if (EEL_RF(ir->coulombtype))
1198 /* reaction field (at the cut-off) */
1200 if (ir->coulombtype == eelRF_ZERO && ir->epsilon_rf != 0)
1203 "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1204 eel_names[ir->coulombtype]);
1205 warning(wi, warn_buf);
1206 ir->epsilon_rf = 0.0;
1209 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1210 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) || (ir->epsilon_r == 0));
1211 if (ir->epsilon_rf == ir->epsilon_r)
1213 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1214 eel_names[ir->coulombtype]);
1215 warning(wi, warn_buf);
1218 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1219 * means the interaction is zero outside rcoulomb, but it helps to
1220 * provide accurate energy conservation.
1222 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1224 if (ir_coulomb_switched(ir))
1227 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the "
1228 "potential modifier options!",
1229 eel_names[ir->coulombtype]);
1230 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1234 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1237 "Explicit switch/shift coulomb interactions cannot be used in combination with a "
1238 "secondary coulomb-modifier.");
1239 CHECK(ir->coulomb_modifier != eintmodNONE);
1241 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1244 "Explicit switch/shift vdw interactions cannot be used in combination with a "
1245 "secondary vdw-modifier.");
1246 CHECK(ir->vdw_modifier != eintmodNONE);
1249 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT || ir->vdwtype == evdwSWITCH
1250 || ir->vdwtype == evdwSHIFT)
1253 "The switch/shift interaction settings are just for compatibility; you will get "
1255 "performance from applying potential modifiers to your interactions!\n");
1256 warning_note(wi, warn_buf);
1259 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1261 if (ir->rcoulomb_switch / ir->rcoulomb < 0.9499)
1263 real percentage = 100 * (ir->rcoulomb - ir->rcoulomb_switch) / ir->rcoulomb;
1265 "The switching range should be 5%% or less (currently %.2f%% using a switching "
1266 "range of %4f-%4f) for accurate electrostatic energies, energy conservation "
1267 "will be good regardless, since ewald_rtol = %g.",
1268 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1269 warning(wi, warn_buf);
1273 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1275 if (ir->rvdw_switch == 0)
1278 "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones "
1279 "potential. This suggests it was not set in the mdp, which can lead to large "
1280 "energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw "
1281 "switching range.");
1282 warning(wi, warn_buf);
1286 if (EEL_FULL(ir->coulombtype))
1288 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER
1289 || ir->coulombtype == eelPMEUSERSWITCH)
1291 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1292 eel_names[ir->coulombtype]);
1293 CHECK(ir->rcoulomb > ir->rlist);
1297 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1299 // TODO: Move these checks into the ewald module with the options class
1301 int orderMax = (ir->coulombtype == eelP3M_AD ? 8 : 12);
1303 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1305 sprintf(warn_buf, "With coulombtype = %s, you should have %d <= pme-order <= %d",
1306 eel_names[ir->coulombtype], orderMin, orderMax);
1307 warning_error(wi, warn_buf);
1311 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1313 if (ir->ewald_geometry == eewg3D)
1315 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1316 c_pbcTypeNames[ir->pbcType].c_str(), eewg_names[eewg3DC]);
1317 warning(wi, warn_buf);
1319 /* This check avoids extra pbc coding for exclusion corrections */
1320 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1321 CHECK(ir->wall_ewald_zfac < 2);
1323 if ((ir->ewald_geometry == eewg3DC) && (ir->pbcType != PbcType::XY) && EEL_FULL(ir->coulombtype))
1325 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1326 eel_names[ir->coulombtype], eewg_names[eewg3DC], c_pbcTypeNames[PbcType::XY].c_str());
1327 warning(wi, warn_buf);
1329 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1331 sprintf(err_buf, "Cannot have periodic molecules with epsilon_surface > 0");
1332 CHECK(ir->bPeriodicMols);
1333 sprintf(warn_buf, "With epsilon_surface > 0 all molecules should be neutral.");
1334 warning_note(wi, warn_buf);
1336 "With epsilon_surface > 0 you can only use domain decomposition "
1337 "when there are only small molecules with all bonds constrained (mdrun will check "
1339 warning_note(wi, warn_buf);
1342 if (ir_vdw_switched(ir))
1344 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1345 CHECK(ir->rvdw_switch >= ir->rvdw);
1347 if (ir->rvdw_switch < 0.5 * ir->rvdw)
1350 "You are applying a switch function to vdw forces or potentials from %g to %g "
1351 "nm, which is more than half the interaction range, whereas switch functions "
1352 "are intended to act only close to the cut-off.",
1353 ir->rvdw_switch, ir->rvdw);
1354 warning_note(wi, warn_buf);
1358 if (ir->vdwtype == evdwPME)
1360 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1362 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s and %s",
1363 evdw_names[ir->vdwtype], eintmod_names[eintmodPOTSHIFT], eintmod_names[eintmodNONE]);
1364 warning_error(wi, err_buf);
1368 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1371 "You have selected user tables with dispersion correction, the dispersion "
1372 "will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction "
1373 "between rvdw_switch and rvdw will not be double counted). Make sure that you "
1374 "really want dispersion correction to -C6/r^6.");
1377 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT) && ir->rvdw != 0)
1379 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1382 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1384 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1387 /* IMPLICIT SOLVENT */
1388 if (ir->coulombtype == eelGB_NOTUSED)
1390 sprintf(warn_buf, "Invalid option %s for coulombtype", eel_names[ir->coulombtype]);
1391 warning_error(wi, warn_buf);
1396 warning_error(wi, "The QMMM integration you are trying to use is no longer supported");
1401 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1405 /* interpret a number of doubles from a string and put them in an array,
1406 after allocating space for them.
1407 str = the input string
1408 n = the (pre-allocated) number of doubles read
1409 r = the output array of doubles. */
1410 static void parse_n_real(char* str, int* n, real** r, warninp_t wi)
1412 auto values = gmx::splitString(str);
1416 for (int i = 0; i < *n; i++)
1420 (*r)[i] = gmx::fromString<real>(values[i]);
1422 catch (gmx::GromacsException&)
1424 warning_error(wi, "Invalid value " + values[i]
1425 + " in string in mdp file. Expected a real number.");
1431 static void do_fep_params(t_inputrec* ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
1434 int i, j, max_n_lambda, nweights, nfep[efptNR];
1435 t_lambda* fep = ir->fepvals;
1436 t_expanded* expand = ir->expandedvals;
1437 real** count_fep_lambdas;
1438 bool bOneLambda = TRUE;
1440 snew(count_fep_lambdas, efptNR);
1442 /* FEP input processing */
1443 /* first, identify the number of lambda values for each type.
1444 All that are nonzero must have the same number */
1446 for (i = 0; i < efptNR; i++)
1448 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
1451 /* now, determine the number of components. All must be either zero, or equal. */
1454 for (i = 0; i < efptNR; i++)
1456 if (nfep[i] > max_n_lambda)
1458 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1459 must have the same number if its not zero.*/
1464 for (i = 0; i < efptNR; i++)
1468 ir->fepvals->separate_dvdl[i] = FALSE;
1470 else if (nfep[i] == max_n_lambda)
1472 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute
1473 the derivative with respect to the temperature currently */
1475 ir->fepvals->separate_dvdl[i] = TRUE;
1481 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1483 nfep[i], efpt_names[i], max_n_lambda);
1486 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1487 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1489 /* the number of lambdas is the number we've read in, which is either zero
1490 or the same for all */
1491 fep->n_lambda = max_n_lambda;
1493 /* allocate space for the array of lambda values */
1494 snew(fep->all_lambda, efptNR);
1495 /* if init_lambda is defined, we need to set lambda */
1496 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1498 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1500 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1501 for (i = 0; i < efptNR; i++)
1503 snew(fep->all_lambda[i], fep->n_lambda);
1504 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1507 for (j = 0; j < fep->n_lambda; j++)
1509 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1511 sfree(count_fep_lambdas[i]);
1514 sfree(count_fep_lambdas);
1516 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1517 internal bookkeeping -- for now, init_lambda */
1519 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1521 for (i = 0; i < fep->n_lambda; i++)
1523 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1527 /* check to see if only a single component lambda is defined, and soft core is defined.
1528 In this case, turn on coulomb soft core */
1530 if (max_n_lambda == 0)
1536 for (i = 0; i < efptNR; i++)
1538 if ((nfep[i] != 0) && (i != efptFEP))
1544 if ((bOneLambda) && (fep->sc_alpha > 0))
1546 fep->bScCoul = TRUE;
1549 /* Fill in the others with the efptFEP if they are not explicitly
1550 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1551 they are all zero. */
1553 for (i = 0; i < efptNR; i++)
1555 if ((nfep[i] == 0) && (i != efptFEP))
1557 for (j = 0; j < fep->n_lambda; j++)
1559 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1565 /* now read in the weights */
1566 parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
1569 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1571 else if (nweights != fep->n_lambda)
1573 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1574 nweights, fep->n_lambda);
1576 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1578 expand->nstexpanded = fep->nstdhdl;
1579 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1584 static void do_simtemp_params(t_inputrec* ir)
1587 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1588 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1591 template<typename T>
1592 void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
1595 for (const auto& input : inputs)
1599 outputs[i] = gmx::fromStdString<T>(input);
1601 catch (gmx::GromacsException&)
1603 auto message = gmx::formatString(
1604 "Invalid value for mdp option %s. %s should only consist of integers separated "
1607 warning_error(wi, message);
1613 static void convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, real* outputs)
1616 for (const auto& input : inputs)
1620 outputs[i] = gmx::fromString<real>(input);
1622 catch (gmx::GromacsException&)
1624 auto message = gmx::formatString(
1625 "Invalid value for mdp option %s. %s should only consist of real numbers "
1626 "separated by spaces.",
1628 warning_error(wi, message);
1634 static void convertRvecs(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, rvec* outputs)
1637 for (const auto& input : inputs)
1641 outputs[i][d] = gmx::fromString<real>(input);
1643 catch (gmx::GromacsException&)
1645 auto message = gmx::formatString(
1646 "Invalid value for mdp option %s. %s should only consist of real numbers "
1647 "separated by spaces.",
1649 warning_error(wi, message);
1660 static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
1662 opts->wall_atomtype[0] = nullptr;
1663 opts->wall_atomtype[1] = nullptr;
1665 ir->wall_atomtype[0] = -1;
1666 ir->wall_atomtype[1] = -1;
1667 ir->wall_density[0] = 0;
1668 ir->wall_density[1] = 0;
1672 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1673 if (wallAtomTypes.size() != size_t(ir->nwall))
1675 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %zu", ir->nwall,
1676 wallAtomTypes.size());
1678 GMX_RELEASE_ASSERT(ir->nwall < 3, "Invalid number of walls");
1679 for (int i = 0; i < ir->nwall; i++)
1681 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1684 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1686 auto wallDensity = gmx::splitString(wall_density);
1687 if (wallDensity.size() != size_t(ir->nwall))
1689 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %zu", ir->nwall,
1690 wallDensity.size());
1692 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1693 for (int i = 0; i < ir->nwall; i++)
1695 if (ir->wall_density[i] <= 0)
1697 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1704 static void add_wall_energrps(SimulationGroups* groups, int nwall, t_symtab* symtab)
1708 AtomGroupIndices* grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1709 for (int i = 0; i < nwall; i++)
1711 groups->groupNames.emplace_back(put_symtab(symtab, gmx::formatString("wall%d", i).c_str()));
1712 grps->emplace_back(groups->groupNames.size() - 1);
1717 static void read_expandedparams(std::vector<t_inpfile>* inp, t_expanded* expand, warninp_t wi)
1719 /* read expanded ensemble parameters */
1720 printStringNewline(inp, "expanded ensemble variables");
1721 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1722 expand->elamstats = get_eeenum(inp, "lmc-stats", elamstats_names, wi);
1723 expand->elmcmove = get_eeenum(inp, "lmc-move", elmcmove_names, wi);
1724 expand->elmceq = get_eeenum(inp, "lmc-weights-equil", elmceq_names, wi);
1725 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1726 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1727 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1728 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1729 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1730 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1731 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1732 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1733 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1734 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1735 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1736 expand->bSymmetrizedTMatrix =
1737 (get_eeenum(inp, "symmetrized-transition-matrix", yesno_names, wi) != 0);
1738 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1739 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1740 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1741 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1742 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1743 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1744 expand->bWLoneovert = (get_eeenum(inp, "wl-oneovert", yesno_names, wi) != 0);
1747 /*! \brief Return whether an end state with the given coupling-lambda
1748 * value describes fully-interacting VDW.
1750 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1751 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1753 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1755 return (couple_lambda_value == ecouplamVDW || couple_lambda_value == ecouplamVDWQ);
1761 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1764 explicit MdpErrorHandler(warninp_t wi) : wi_(wi), mapping_(nullptr) {}
1766 void setBackMapping(const gmx::IKeyValueTreeBackMapping& mapping) { mapping_ = &mapping; }
1768 bool onError(gmx::UserInputError* ex, const gmx::KeyValueTreePath& context) override
1771 gmx::formatString("Error in mdp option \"%s\":", getOptionName(context).c_str()));
1772 std::string message = gmx::formatExceptionMessageToString(*ex);
1773 warning_error(wi_, message.c_str());
1778 std::string getOptionName(const gmx::KeyValueTreePath& context)
1780 if (mapping_ != nullptr)
1782 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1783 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1786 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1791 const gmx::IKeyValueTreeBackMapping* mapping_;
1796 void get_ir(const char* mdparin,
1797 const char* mdparout,
1798 gmx::MDModules* mdModules,
1801 WriteMdpHeader writeMdpHeader,
1805 double dumdub[2][6];
1807 char warn_buf[STRLEN];
1808 t_lambda* fep = ir->fepvals;
1809 t_expanded* expand = ir->expandedvals;
1811 const char* no_names[] = { "no", nullptr };
1813 init_inputrec_strings();
1814 gmx::TextInputFile stream(mdparin);
1815 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1817 snew(dumstr[0], STRLEN);
1818 snew(dumstr[1], STRLEN);
1820 /* ignore the following deprecated commands */
1821 replace_inp_entry(inp, "title", nullptr);
1822 replace_inp_entry(inp, "cpp", nullptr);
1823 replace_inp_entry(inp, "domain-decomposition", nullptr);
1824 replace_inp_entry(inp, "andersen-seed", nullptr);
1825 replace_inp_entry(inp, "dihre", nullptr);
1826 replace_inp_entry(inp, "dihre-fc", nullptr);
1827 replace_inp_entry(inp, "dihre-tau", nullptr);
1828 replace_inp_entry(inp, "nstdihreout", nullptr);
1829 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1830 replace_inp_entry(inp, "optimize-fft", nullptr);
1831 replace_inp_entry(inp, "adress_type", nullptr);
1832 replace_inp_entry(inp, "adress_const_wf", nullptr);
1833 replace_inp_entry(inp, "adress_ex_width", nullptr);
1834 replace_inp_entry(inp, "adress_hy_width", nullptr);
1835 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1836 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1837 replace_inp_entry(inp, "adress_site", nullptr);
1838 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1839 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1840 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1841 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1842 replace_inp_entry(inp, "rlistlong", nullptr);
1843 replace_inp_entry(inp, "nstcalclr", nullptr);
1844 replace_inp_entry(inp, "pull-print-com2", nullptr);
1845 replace_inp_entry(inp, "gb-algorithm", nullptr);
1846 replace_inp_entry(inp, "nstgbradii", nullptr);
1847 replace_inp_entry(inp, "rgbradii", nullptr);
1848 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1849 replace_inp_entry(inp, "gb-saltconc", nullptr);
1850 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1851 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1852 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1853 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1854 replace_inp_entry(inp, "sa-algorithm", nullptr);
1855 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1856 replace_inp_entry(inp, "ns-type", nullptr);
1858 /* replace the following commands with the clearer new versions*/
1859 replace_inp_entry(inp, "unconstrained-start", "continuation");
1860 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1861 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1862 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1863 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1864 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1865 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1867 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1868 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1869 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1870 setStringEntry(&inp, "include", opts->include, nullptr);
1871 printStringNoNewline(
1872 &inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1873 setStringEntry(&inp, "define", opts->define, nullptr);
1875 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1876 ir->eI = get_eeenum(&inp, "integrator", ei_names, wi);
1877 printStringNoNewline(&inp, "Start time and timestep in ps");
1878 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1879 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1880 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1881 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1882 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1883 printStringNoNewline(
1884 &inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1885 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1886 printStringNoNewline(&inp, "mode for center of mass motion removal");
1887 ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
1888 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
1889 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
1890 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
1891 setStringEntry(&inp, "comm-grps", inputrecStrings->vcm, nullptr);
1893 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
1894 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
1895 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
1896 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
1899 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
1900 printStringNoNewline(&inp, "Force tolerance and initial step-size");
1901 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
1902 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
1903 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
1904 ir->niter = get_eint(&inp, "niter", 20, wi);
1905 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
1906 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
1907 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
1908 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
1909 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
1911 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
1912 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
1914 /* Output options */
1915 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
1916 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
1917 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
1918 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
1919 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
1920 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
1921 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
1922 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
1923 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
1924 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
1925 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
1926 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
1927 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
1928 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
1929 printStringNoNewline(&inp, "default, all atoms will be written.");
1930 setStringEntry(&inp, "compressed-x-grps", inputrecStrings->x_compressed_groups, nullptr);
1931 printStringNoNewline(&inp, "Selection of energy groups");
1932 setStringEntry(&inp, "energygrps", inputrecStrings->energy, nullptr);
1934 /* Neighbor searching */
1935 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
1936 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
1937 ir->cutoff_scheme = get_eeenum(&inp, "cutoff-scheme", ecutscheme_names, wi);
1938 printStringNoNewline(&inp, "nblist update frequency");
1939 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
1940 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
1941 // TODO This conversion should be removed when proper std:string handling will be added to get_eeenum(...), etc.
1942 std::vector<const char*> pbcTypesNamesChar;
1943 for (const auto& pbcTypeName : c_pbcTypeNames)
1945 pbcTypesNamesChar.push_back(pbcTypeName.c_str());
1947 ir->pbcType = static_cast<PbcType>(get_eeenum(&inp, "pbc", pbcTypesNamesChar.data(), wi));
1948 ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi) != 0;
1949 printStringNoNewline(&inp,
1950 "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1951 printStringNoNewline(&inp, "a value of -1 means: use rlist");
1952 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
1953 printStringNoNewline(&inp, "nblist cut-off");
1954 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
1955 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
1957 /* Electrostatics */
1958 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
1959 printStringNoNewline(&inp, "Method for doing electrostatics");
1960 ir->coulombtype = get_eeenum(&inp, "coulombtype", eel_names, wi);
1961 ir->coulomb_modifier = get_eeenum(&inp, "coulomb-modifier", eintmod_names, wi);
1962 printStringNoNewline(&inp, "cut-off lengths");
1963 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
1964 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
1965 printStringNoNewline(&inp,
1966 "Relative dielectric constant for the medium and the reaction field");
1967 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
1968 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
1969 printStringNoNewline(&inp, "Method for doing Van der Waals");
1970 ir->vdwtype = get_eeenum(&inp, "vdw-type", evdw_names, wi);
1971 ir->vdw_modifier = get_eeenum(&inp, "vdw-modifier", eintmod_names, wi);
1972 printStringNoNewline(&inp, "cut-off lengths");
1973 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
1974 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
1975 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
1976 ir->eDispCorr = get_eeenum(&inp, "DispCorr", edispc_names, wi);
1977 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
1978 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
1979 printStringNoNewline(&inp, "Separate tables between energy group pairs");
1980 setStringEntry(&inp, "energygrp-table", inputrecStrings->egptable, nullptr);
1981 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
1982 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
1983 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
1984 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
1985 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
1986 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
1987 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
1988 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
1989 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
1990 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
1991 ir->ljpme_combination_rule = get_eeenum(&inp, "lj-pme-comb-rule", eljpme_names, wi);
1992 ir->ewald_geometry = get_eeenum(&inp, "ewald-geometry", eewg_names, wi);
1993 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
1995 /* Implicit solvation is no longer supported, but we need grompp
1996 to be able to refuse old .mdp files that would have built a tpr
1997 to run it. Thus, only "no" is accepted. */
1998 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
2000 /* Coupling stuff */
2001 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
2002 printStringNoNewline(&inp, "Temperature coupling");
2003 ir->etc = get_eeenum(&inp, "tcoupl", etcoupl_names, wi);
2004 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
2005 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
2006 ir->bPrintNHChains = (get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi) != 0);
2007 printStringNoNewline(&inp, "Groups to couple separately");
2008 setStringEntry(&inp, "tc-grps", inputrecStrings->tcgrps, nullptr);
2009 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
2010 setStringEntry(&inp, "tau-t", inputrecStrings->tau_t, nullptr);
2011 setStringEntry(&inp, "ref-t", inputrecStrings->ref_t, nullptr);
2012 printStringNoNewline(&inp, "pressure coupling");
2013 ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
2014 ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
2015 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
2016 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
2017 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
2018 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
2019 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
2020 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
2021 ir->refcoord_scaling = get_eeenum(&inp, "refcoord-scaling", erefscaling_names, wi);
2024 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2025 ir->bQMMM = (get_eeenum(&inp, "QMMM", yesno_names, wi) != 0);
2026 printStringNoNewline(&inp, "Groups treated Quantum Mechanically");
2027 setStringEntry(&inp, "QMMM-grps", inputrecStrings->QMMM, nullptr);
2028 printStringNoNewline(&inp, "QM method");
2029 setStringEntry(&inp, "QMmethod", inputrecStrings->QMmethod, nullptr);
2030 printStringNoNewline(&inp, "QMMM scheme");
2031 const char* noQMMMSchemeName = "normal";
2032 get_eeenum(&inp, "QMMMscheme", &noQMMMSchemeName, wi);
2033 printStringNoNewline(&inp, "QM basisset");
2034 setStringEntry(&inp, "QMbasis", inputrecStrings->QMbasis, nullptr);
2035 printStringNoNewline(&inp, "QM charge");
2036 setStringEntry(&inp, "QMcharge", inputrecStrings->QMcharge, nullptr);
2037 printStringNoNewline(&inp, "QM multiplicity");
2038 setStringEntry(&inp, "QMmult", inputrecStrings->QMmult, nullptr);
2039 printStringNoNewline(&inp, "Surface Hopping");
2040 setStringEntry(&inp, "SH", inputrecStrings->bSH, nullptr);
2041 printStringNoNewline(&inp, "CAS space options");
2042 setStringEntry(&inp, "CASorbitals", inputrecStrings->CASorbitals, nullptr);
2043 setStringEntry(&inp, "CASelectrons", inputrecStrings->CASelectrons, nullptr);
2044 setStringEntry(&inp, "SAon", inputrecStrings->SAon, nullptr);
2045 setStringEntry(&inp, "SAoff", inputrecStrings->SAoff, nullptr);
2046 setStringEntry(&inp, "SAsteps", inputrecStrings->SAsteps, nullptr);
2047 printStringNoNewline(&inp, "Scale factor for MM charges");
2048 get_ereal(&inp, "MMChargeScaleFactor", 1.0, wi);
2050 /* Simulated annealing */
2051 printStringNewline(&inp, "SIMULATED ANNEALING");
2052 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2053 setStringEntry(&inp, "annealing", inputrecStrings->anneal, nullptr);
2054 printStringNoNewline(&inp,
2055 "Number of time points to use for specifying annealing in each group");
2056 setStringEntry(&inp, "annealing-npoints", inputrecStrings->anneal_npoints, nullptr);
2057 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2058 setStringEntry(&inp, "annealing-time", inputrecStrings->anneal_time, nullptr);
2059 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2060 setStringEntry(&inp, "annealing-temp", inputrecStrings->anneal_temp, nullptr);
2063 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2064 opts->bGenVel = (get_eeenum(&inp, "gen-vel", yesno_names, wi) != 0);
2065 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2066 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2069 printStringNewline(&inp, "OPTIONS FOR BONDS");
2070 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2071 printStringNoNewline(&inp, "Type of constraint algorithm");
2072 ir->eConstrAlg = get_eeenum(&inp, "constraint-algorithm", econstr_names, wi);
2073 printStringNoNewline(&inp, "Do not constrain the start configuration");
2074 ir->bContinuation = (get_eeenum(&inp, "continuation", yesno_names, wi) != 0);
2075 printStringNoNewline(&inp,
2076 "Use successive overrelaxation to reduce the number of shake iterations");
2077 ir->bShakeSOR = (get_eeenum(&inp, "Shake-SOR", yesno_names, wi) != 0);
2078 printStringNoNewline(&inp, "Relative tolerance of shake");
2079 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2080 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2081 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2082 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2083 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2084 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2085 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2086 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2087 printStringNoNewline(&inp, "rotates over more degrees than");
2088 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2089 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2090 opts->bMorse = (get_eeenum(&inp, "morse", yesno_names, wi) != 0);
2092 /* Energy group exclusions */
2093 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2094 printStringNoNewline(
2095 &inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2096 setStringEntry(&inp, "energygrp-excl", inputrecStrings->egpexcl, nullptr);
2099 printStringNewline(&inp, "WALLS");
2100 printStringNoNewline(
2101 &inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2102 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2103 ir->wall_type = get_eeenum(&inp, "wall-type", ewt_names, wi);
2104 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2105 setStringEntry(&inp, "wall-atomtype", inputrecStrings->wall_atomtype, nullptr);
2106 setStringEntry(&inp, "wall-density", inputrecStrings->wall_density, nullptr);
2107 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2110 printStringNewline(&inp, "COM PULLING");
2111 ir->bPull = (get_eeenum(&inp, "pull", yesno_names, wi) != 0);
2115 inputrecStrings->pullGroupNames = read_pullparams(&inp, ir->pull, wi);
2119 NOTE: needs COM pulling input */
2120 printStringNewline(&inp, "AWH biasing");
2121 ir->bDoAwh = (get_eeenum(&inp, "awh", yesno_names, wi) != 0);
2124 ir->awhParams = gmx::readAwhParams(&inp, wi);
2127 /* Enforced rotation */
2128 printStringNewline(&inp, "ENFORCED ROTATION");
2129 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2130 ir->bRot = (get_eeenum(&inp, "rotation", yesno_names, wi) != 0);
2134 inputrecStrings->rotateGroupNames = read_rotparams(&inp, ir->rot, wi);
2137 /* Interactive MD */
2139 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2140 setStringEntry(&inp, "IMD-group", inputrecStrings->imd_grp, nullptr);
2141 if (inputrecStrings->imd_grp[0] != '\0')
2148 printStringNewline(&inp, "NMR refinement stuff");
2149 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2150 ir->eDisre = get_eeenum(&inp, "disre", edisre_names, wi);
2151 printStringNoNewline(
2152 &inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2153 ir->eDisreWeighting = get_eeenum(&inp, "disre-weighting", edisreweighting_names, wi);
2154 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2155 ir->bDisreMixed = (get_eeenum(&inp, "disre-mixed", yesno_names, wi) != 0);
2156 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2157 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2158 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2159 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2160 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2161 opts->bOrire = (get_eeenum(&inp, "orire", yesno_names, wi) != 0);
2162 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2163 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2164 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2165 setStringEntry(&inp, "orire-fitgrp", inputrecStrings->orirefitgrp, nullptr);
2166 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2167 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2169 /* free energy variables */
2170 printStringNewline(&inp, "Free energy variables");
2171 ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
2172 setStringEntry(&inp, "couple-moltype", inputrecStrings->couple_moltype, nullptr);
2173 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2174 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2175 opts->bCoupleIntra = (get_eeenum(&inp, "couple-intramol", yesno_names, wi) != 0);
2177 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2179 it was not entered */
2180 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2181 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2182 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2183 setStringEntry(&inp, "fep-lambdas", inputrecStrings->fep_lambda[efptFEP], nullptr);
2184 setStringEntry(&inp, "mass-lambdas", inputrecStrings->fep_lambda[efptMASS], nullptr);
2185 setStringEntry(&inp, "coul-lambdas", inputrecStrings->fep_lambda[efptCOUL], nullptr);
2186 setStringEntry(&inp, "vdw-lambdas", inputrecStrings->fep_lambda[efptVDW], nullptr);
2187 setStringEntry(&inp, "bonded-lambdas", inputrecStrings->fep_lambda[efptBONDED], nullptr);
2188 setStringEntry(&inp, "restraint-lambdas", inputrecStrings->fep_lambda[efptRESTRAINT], nullptr);
2189 setStringEntry(&inp, "temperature-lambdas", inputrecStrings->fep_lambda[efptTEMPERATURE], nullptr);
2190 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2191 setStringEntry(&inp, "init-lambda-weights", inputrecStrings->lambda_weights, nullptr);
2192 fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
2193 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2194 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2195 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2196 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2197 fep->bScCoul = (get_eeenum(&inp, "sc-coul", yesno_names, wi) != 0);
2198 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2199 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2200 fep->separate_dhdl_file = get_eeenum(&inp, "separate-dhdl-file", separate_dhdl_file_names, wi);
2201 fep->dhdl_derivatives = get_eeenum(&inp, "dhdl-derivatives", dhdl_derivatives_names, wi);
2202 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2203 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2205 /* Non-equilibrium MD stuff */
2206 printStringNewline(&inp, "Non-equilibrium MD stuff");
2207 setStringEntry(&inp, "acc-grps", inputrecStrings->accgrps, nullptr);
2208 setStringEntry(&inp, "accelerate", inputrecStrings->acc, nullptr);
2209 setStringEntry(&inp, "freezegrps", inputrecStrings->freeze, nullptr);
2210 setStringEntry(&inp, "freezedim", inputrecStrings->frdim, nullptr);
2211 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2212 setStringEntry(&inp, "deform", inputrecStrings->deform, nullptr);
2214 /* simulated tempering variables */
2215 printStringNewline(&inp, "simulated tempering variables");
2216 ir->bSimTemp = (get_eeenum(&inp, "simulated-tempering", yesno_names, wi) != 0);
2217 ir->simtempvals->eSimTempScale = get_eeenum(&inp, "simulated-tempering-scaling", esimtemp_names, wi);
2218 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2219 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2221 /* expanded ensemble variables */
2222 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2224 read_expandedparams(&inp, expand, wi);
2227 /* Electric fields */
2229 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2230 gmx::KeyValueTreeTransformer transform;
2231 transform.rules()->addRule().keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2232 mdModules->initMdpTransform(transform.rules());
2233 for (const auto& path : transform.mappedPaths())
2235 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2236 mark_einp_set(inp, path[0].c_str());
2238 MdpErrorHandler errorHandler(wi);
2239 auto result = transform.transform(convertedValues, &errorHandler);
2240 ir->params = new gmx::KeyValueTreeObject(result.object());
2241 mdModules->adjustInputrecBasedOnModules(ir);
2242 errorHandler.setBackMapping(result.backMapping());
2243 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2246 /* Ion/water position swapping ("computational electrophysiology") */
2247 printStringNewline(&inp,
2248 "Ion/water position swapping for computational electrophysiology setups");
2249 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2250 ir->eSwapCoords = get_eeenum(&inp, "swapcoords", eSwapTypes_names, wi);
2251 if (ir->eSwapCoords != eswapNO)
2258 printStringNoNewline(&inp, "Swap attempt frequency");
2259 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2260 printStringNoNewline(&inp, "Number of ion types to be controlled");
2261 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2264 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2266 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2267 snew(ir->swap->grp, ir->swap->ngrp);
2268 for (i = 0; i < ir->swap->ngrp; i++)
2270 snew(ir->swap->grp[i].molname, STRLEN);
2272 printStringNoNewline(&inp,
2273 "Two index groups that contain the compartment-partitioning atoms");
2274 setStringEntry(&inp, "split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2275 setStringEntry(&inp, "split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2276 printStringNoNewline(&inp,
2277 "Use center of mass of split groups (yes/no), otherwise center of "
2278 "geometry is used");
2279 ir->swap->massw_split[0] = (get_eeenum(&inp, "massw-split0", yesno_names, wi) != 0);
2280 ir->swap->massw_split[1] = (get_eeenum(&inp, "massw-split1", yesno_names, wi) != 0);
2282 printStringNoNewline(&inp, "Name of solvent molecules");
2283 setStringEntry(&inp, "solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2285 printStringNoNewline(&inp,
2286 "Split cylinder: radius, upper and lower extension (nm) (this will "
2287 "define the channels)");
2288 printStringNoNewline(&inp,
2289 "Note that the split cylinder settings do not have an influence on "
2290 "the swapping protocol,");
2291 printStringNoNewline(
2293 "however, if correctly defined, the permeation events are recorded per channel");
2294 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2295 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2296 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2297 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2298 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2299 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2301 printStringNoNewline(
2303 "Average the number of ions per compartment over these many swap attempt steps");
2304 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2306 printStringNoNewline(
2307 &inp, "Names of the ion types that can be exchanged with solvent molecules,");
2308 printStringNoNewline(
2309 &inp, "and the requested number of ions of this type in compartments A and B");
2310 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2311 for (i = 0; i < nIonTypes; i++)
2313 int ig = eSwapFixedGrpNR + i;
2315 sprintf(buf, "iontype%d-name", i);
2316 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2317 sprintf(buf, "iontype%d-in-A", i);
2318 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2319 sprintf(buf, "iontype%d-in-B", i);
2320 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2323 printStringNoNewline(
2325 "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2326 printStringNoNewline(
2328 "at maximum distance (= bulk concentration) to the split group layers. However,");
2329 printStringNoNewline(&inp,
2330 "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk "
2331 "layer from the middle at 0.0");
2332 printStringNoNewline(&inp,
2333 "towards one of the compartment-partitioning layers (at +/- 1.0).");
2334 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2335 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2336 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2337 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0))
2339 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2342 printStringNoNewline(
2343 &inp, "Start to swap ions if threshold difference to requested count is reached");
2344 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2347 /* AdResS is no longer supported, but we need grompp to be able to
2348 refuse to process old .mdp files that used it. */
2349 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2351 /* User defined thingies */
2352 printStringNewline(&inp, "User defined thingies");
2353 setStringEntry(&inp, "user1-grps", inputrecStrings->user1, nullptr);
2354 setStringEntry(&inp, "user2-grps", inputrecStrings->user2, nullptr);
2355 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2356 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2357 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2358 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2359 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2360 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2361 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2362 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2366 gmx::TextOutputFile stream(mdparout);
2367 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2369 // Transform module data into a flat key-value tree for output.
2370 gmx::KeyValueTreeBuilder builder;
2371 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2372 mdModules->buildMdpOutput(&builderObject);
2374 gmx::TextWriter writer(&stream);
2375 writeKeyValueTreeAsMdp(&writer, builder.build());
2380 /* Process options if necessary */
2381 for (m = 0; m < 2; m++)
2383 for (i = 0; i < 2 * DIM; i++)
2392 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2396 "Pressure coupling incorrect number of values (I need exactly 1)");
2398 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2400 case epctSEMIISOTROPIC:
2401 case epctSURFACETENSION:
2402 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2406 "Pressure coupling incorrect number of values (I need exactly 2)");
2408 dumdub[m][YY] = dumdub[m][XX];
2410 case epctANISOTROPIC:
2411 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf", &(dumdub[m][XX]), &(dumdub[m][YY]),
2412 &(dumdub[m][ZZ]), &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5]))
2417 "Pressure coupling incorrect number of values (I need exactly 6)");
2421 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2422 epcoupltype_names[ir->epct]);
2426 clear_mat(ir->ref_p);
2427 clear_mat(ir->compress);
2428 for (i = 0; i < DIM; i++)
2430 ir->ref_p[i][i] = dumdub[1][i];
2431 ir->compress[i][i] = dumdub[0][i];
2433 if (ir->epct == epctANISOTROPIC)
2435 ir->ref_p[XX][YY] = dumdub[1][3];
2436 ir->ref_p[XX][ZZ] = dumdub[1][4];
2437 ir->ref_p[YY][ZZ] = dumdub[1][5];
2438 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2441 "All off-diagonal reference pressures are non-zero. Are you sure you want to "
2442 "apply a threefold shear stress?\n");
2444 ir->compress[XX][YY] = dumdub[0][3];
2445 ir->compress[XX][ZZ] = dumdub[0][4];
2446 ir->compress[YY][ZZ] = dumdub[0][5];
2447 for (i = 0; i < DIM; i++)
2449 for (m = 0; m < i; m++)
2451 ir->ref_p[i][m] = ir->ref_p[m][i];
2452 ir->compress[i][m] = ir->compress[m][i];
2457 if (ir->comm_mode == ecmNO)
2462 opts->couple_moltype = nullptr;
2463 if (strlen(inputrecStrings->couple_moltype) > 0)
2465 if (ir->efep != efepNO)
2467 opts->couple_moltype = gmx_strdup(inputrecStrings->couple_moltype);
2468 if (opts->couple_lam0 == opts->couple_lam1)
2470 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2472 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
2476 "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
2483 "Free energy is turned off, so we will not decouple the molecule listed "
2487 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2488 if (ir->efep != efepNO)
2490 if (fep->delta_lambda > 0)
2492 ir->efep = efepSLOWGROWTH;
2496 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2498 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2500 "Old option for dhdl-print-energy given: "
2501 "changing \"yes\" to \"total\"\n");
2504 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2506 /* always print out the energy to dhdl if we are doing
2507 expanded ensemble, since we need the total energy for
2508 analysis if the temperature is changing. In some
2509 conditions one may only want the potential energy, so
2510 we will allow that if the appropriate mdp setting has
2511 been enabled. Otherwise, total it is:
2513 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2516 if ((ir->efep != efepNO) || ir->bSimTemp)
2518 ir->bExpanded = FALSE;
2519 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2521 ir->bExpanded = TRUE;
2523 do_fep_params(ir, inputrecStrings->fep_lambda, inputrecStrings->lambda_weights, wi);
2524 if (ir->bSimTemp) /* done after fep params */
2526 do_simtemp_params(ir);
2529 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2530 * setup and not on the old way of specifying the free-energy setup,
2531 * we should check for using soft-core when not needed, since that
2532 * can complicate the sampling significantly.
2533 * Note that we only check for the automated coupling setup.
2534 * If the (advanced) user does FEP through manual topology changes,
2535 * this check will not be triggered.
2537 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 && ir->fepvals->sc_alpha != 0
2538 && (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
2541 "You are using soft-core interactions while the Van der Waals interactions are "
2542 "not decoupled (note that the sc-coul option is only active when using lambda "
2543 "states). Although this will not lead to errors, you will need much more "
2544 "sampling than without soft-core interactions. Consider using sc-alpha=0.");
2549 ir->fepvals->n_lambda = 0;
2552 /* WALL PARAMETERS */
2554 do_wall_params(ir, inputrecStrings->wall_atomtype, inputrecStrings->wall_density, opts, wi);
2556 /* ORIENTATION RESTRAINT PARAMETERS */
2558 if (opts->bOrire && gmx::splitString(inputrecStrings->orirefitgrp).size() != 1)
2560 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2563 /* DEFORMATION PARAMETERS */
2565 clear_mat(ir->deform);
2566 for (i = 0; i < 6; i++)
2571 double gmx_unused canary;
2572 int ndeform = sscanf(inputrecStrings->deform, "%lf %lf %lf %lf %lf %lf %lf", &(dumdub[0][0]),
2573 &(dumdub[0][1]), &(dumdub[0][2]), &(dumdub[0][3]), &(dumdub[0][4]),
2574 &(dumdub[0][5]), &canary);
2576 if (strlen(inputrecStrings->deform) > 0 && ndeform != 6)
2580 "Cannot parse exactly 6 box deformation velocities from string '%s'",
2581 inputrecStrings->deform)
2584 for (i = 0; i < 3; i++)
2586 ir->deform[i][i] = dumdub[0][i];
2588 ir->deform[YY][XX] = dumdub[0][3];
2589 ir->deform[ZZ][XX] = dumdub[0][4];
2590 ir->deform[ZZ][YY] = dumdub[0][5];
2591 if (ir->epc != epcNO)
2593 for (i = 0; i < 3; i++)
2595 for (j = 0; j <= i; j++)
2597 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2599 warning_error(wi, "A box element has deform set and compressibility > 0");
2603 for (i = 0; i < 3; i++)
2605 for (j = 0; j < i; j++)
2607 if (ir->deform[i][j] != 0)
2609 for (m = j; m < DIM; m++)
2611 if (ir->compress[m][j] != 0)
2614 "An off-diagonal box element has deform set while "
2615 "compressibility > 0 for the same component of another box "
2616 "vector, this might lead to spurious periodicity effects.");
2617 warning(wi, warn_buf);
2625 /* Ion/water position swapping checks */
2626 if (ir->eSwapCoords != eswapNO)
2628 if (ir->swap->nstswap < 1)
2630 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2632 if (ir->swap->nAverage < 1)
2634 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2636 if (ir->swap->threshold < 1.0)
2638 warning_error(wi, "Ion count threshold must be at least 1.\n");
2644 gmx::checkAwhParams(ir->awhParams, ir, wi);
2651 /* We would like gn to be const as well, but C doesn't allow this */
2652 /* TODO this is utility functionality (search for the index of a
2653 string in a collection), so should be refactored and located more
2655 int search_string(const char* s, int ng, char* gn[])
2659 for (i = 0; (i < ng); i++)
2661 if (gmx_strcasecmp(s, gn[i]) == 0)
2668 "Group %s referenced in the .mdp file was not found in the index file.\n"
2669 "Group names must match either [moleculetype] names or custom index group\n"
2670 "names, in which case you must supply an index file to the '-n' option\n"
2675 static void do_numbering(int natoms,
2676 SimulationGroups* groups,
2677 gmx::ArrayRef<std::string> groupsFromMdpFile,
2680 SimulationAtomGroupType gtype,
2686 unsigned short* cbuf;
2687 AtomGroupIndices* grps = &(groups->groups[gtype]);
2688 int j, gid, aj, ognr, ntot = 0;
2690 char warn_buf[STRLEN];
2692 title = shortName(gtype);
2695 /* Mark all id's as not set */
2696 for (int i = 0; (i < natoms); i++)
2701 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2703 /* Lookup the group name in the block structure */
2704 gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2705 if ((grptp != egrptpONE) || (i == 0))
2707 grps->emplace_back(gid);
2710 /* Now go over the atoms in the group */
2711 for (j = block->index[gid]; (j < block->index[gid + 1]); j++)
2716 /* Range checking */
2717 if ((aj < 0) || (aj >= natoms))
2719 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2721 /* Lookup up the old group number */
2725 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title,
2730 /* Store the group number in buffer */
2731 if (grptp == egrptpONE)
2744 /* Now check whether we have done all atoms */
2747 if (grptp == egrptpALL)
2749 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2751 else if (grptp == egrptpPART)
2753 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2754 warning_note(wi, warn_buf);
2756 /* Assign all atoms currently unassigned to a rest group */
2757 for (j = 0; (j < natoms); j++)
2759 if (cbuf[j] == NOGID)
2761 cbuf[j] = grps->size();
2764 if (grptp != egrptpPART)
2768 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title,
2771 /* Add group name "rest" */
2772 grps->emplace_back(restnm);
2774 /* Assign the rest name to all atoms not currently assigned to a group */
2775 for (j = 0; (j < natoms); j++)
2777 if (cbuf[j] == NOGID)
2779 // group size was not updated before this here, so need to use -1.
2780 cbuf[j] = grps->size() - 1;
2786 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2788 /* All atoms are part of one (or no) group, no index required */
2789 groups->groupNumbers[gtype].clear();
2793 for (int j = 0; (j < natoms); j++)
2795 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2802 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
2805 pull_params_t* pull;
2806 int natoms, imin, jmin;
2807 int * nrdf2, *na_vcm, na_tot;
2808 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2813 * First calc 3xnr-atoms for each group
2814 * then subtract half a degree of freedom for each constraint
2816 * Only atoms and nuclei contribute to the degrees of freedom...
2821 const SimulationGroups& groups = mtop->groups;
2822 natoms = mtop->natoms;
2824 /* Allocate one more for a possible rest group */
2825 /* We need to sum degrees of freedom into doubles,
2826 * since floats give too low nrdf's above 3 million atoms.
2828 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
2829 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2830 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2831 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2832 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2834 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
2838 for (gmx::index i = 0;
2839 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; i++)
2842 clear_ivec(dof_vcm[i]);
2844 nrdf_vcm_sub[i] = 0;
2846 snew(nrdf2, natoms);
2847 for (const AtomProxy atomP : AtomRange(*mtop))
2849 const t_atom& local = atomP.atom();
2850 int i = atomP.globalAtomNumber();
2852 if (local.ptype == eptAtom || local.ptype == eptNucleus)
2854 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
2855 for (int d = 0; d < DIM; d++)
2857 if (opts->nFreeze[g][d] == 0)
2859 /* Add one DOF for particle i (counted as 2*1) */
2861 /* VCM group i has dim d as a DOF */
2862 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
2866 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
2868 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
2874 for (const gmx_molblock_t& molb : mtop->molblock)
2876 const gmx_moltype_t& molt = mtop->moltype[molb.type];
2877 const t_atom* atom = molt.atoms.atom;
2878 for (int mol = 0; mol < molb.nmol; mol++)
2880 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2882 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
2883 for (int i = 0; i < molt.ilist[ftype].size();)
2885 /* Subtract degrees of freedom for the constraints,
2886 * if the particles still have degrees of freedom left.
2887 * If one of the particles is a vsite or a shell, then all
2888 * constraint motion will go there, but since they do not
2889 * contribute to the constraints the degrees of freedom do not
2892 int ai = as + ia[i + 1];
2893 int aj = as + ia[i + 2];
2894 if (((atom[ia[i + 1]].ptype == eptNucleus) || (atom[ia[i + 1]].ptype == eptAtom))
2895 && ((atom[ia[i + 2]].ptype == eptNucleus) || (atom[ia[i + 2]].ptype == eptAtom)))
2913 imin = std::min(imin, nrdf2[ai]);
2914 jmin = std::min(jmin, nrdf2[aj]);
2917 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2919 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
2921 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2923 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
2926 i += interaction_function[ftype].nratoms + 1;
2929 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
2930 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
2932 /* Subtract 1 dof from every atom in the SETTLE */
2933 for (int j = 0; j < 3; j++)
2935 int ai = as + ia[i + 1 + j];
2936 imin = std::min(2, nrdf2[ai]);
2938 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2940 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2945 as += molt.atoms.nr;
2951 /* Correct nrdf for the COM constraints.
2952 * We correct using the TC and VCM group of the first atom
2953 * in the reference and pull group. If atoms in one pull group
2954 * belong to different TC or VCM groups it is anyhow difficult
2955 * to determine the optimal nrdf assignment.
2959 for (int i = 0; i < pull->ncoord; i++)
2961 if (pull->coord[i].eType != epullCONSTRAINT)
2968 for (int j = 0; j < 2; j++)
2970 const t_pull_group* pgrp;
2972 pgrp = &pull->group[pull->coord[i].group[j]];
2976 /* Subtract 1/2 dof from each group */
2977 int ai = pgrp->ind[0];
2978 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2980 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2982 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
2985 "Center of mass pulling constraints caused the number of degrees "
2986 "of freedom for temperature coupling group %s to be negative",
2987 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
2988 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
2993 /* We need to subtract the whole DOF from group j=1 */
3000 if (ir->nstcomm != 0)
3002 GMX_RELEASE_ASSERT(!groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty(),
3003 "Expect at least one group when removing COM motion");
3005 /* We remove COM motion up to dim ndof_com() */
3006 const int ndim_rm_vcm = ndof_com(ir);
3008 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3009 * the number of degrees of freedom in each vcm group when COM
3010 * translation is removed and 6 when rotation is removed as well.
3011 * Note that we do not and should not include the rest group here.
3013 for (gmx::index j = 0;
3014 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]); j++)
3016 switch (ir->comm_mode)
3019 case ecmLINEAR_ACCELERATION_CORRECTION:
3020 nrdf_vcm_sub[j] = 0;
3021 for (int d = 0; d < ndim_rm_vcm; d++)
3029 case ecmANGULAR: nrdf_vcm_sub[j] = 6; break;
3030 default: gmx_incons("Checking comm_mode");
3034 for (gmx::index i = 0;
3035 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
3037 /* Count the number of atoms of TC group i for every VCM group */
3038 for (gmx::index j = 0;
3039 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3044 for (int ai = 0; ai < natoms; ai++)
3046 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3048 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3052 /* Correct for VCM removal according to the fraction of each VCM
3053 * group present in this TC group.
3055 nrdf_uc = nrdf_tc[i];
3057 for (gmx::index j = 0;
3058 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3060 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3062 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3063 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3068 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3070 opts->nrdf[i] = nrdf_tc[i];
3071 if (opts->nrdf[i] < 0)
3075 fprintf(stderr, "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3076 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]], opts->nrdf[i]);
3084 sfree(nrdf_vcm_sub);
3087 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3089 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3090 * But since this is much larger than STRLEN, such a line can not be parsed.
3091 * The real maximum is the number of names that fit in a string: STRLEN/2.
3093 #define EGP_MAX (STRLEN / 2)
3097 auto names = gmx::splitString(val);
3098 if (names.size() % 2 != 0)
3100 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3102 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3104 for (size_t i = 0; i < names.size() / 2; i++)
3106 // TODO this needs to be replaced by a solution using std::find_if
3110 names[2 * i].c_str(),
3111 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3117 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3122 names[2 * i + 1].c_str(),
3123 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3129 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3131 if ((j < nr) && (k < nr))
3133 ir->opts.egp_flags[nr * j + k] |= flag;
3134 ir->opts.egp_flags[nr * k + j] |= flag;
3143 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3145 int ig = -1, i = 0, gind;
3149 /* Just a quick check here, more thorough checks are in mdrun */
3150 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3152 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3155 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3156 for (ig = 0; ig < swap->ngrp; ig++)
3158 swapg = &swap->grp[ig];
3159 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3160 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3164 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3165 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap", swap->grp[ig].molname, swapg->nat);
3166 snew(swapg->ind, swapg->nat);
3167 for (i = 0; i < swapg->nat; i++)
3169 swapg->ind[i] = grps->a[grps->index[gind] + i];
3174 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3180 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3185 ig = search_string(IMDgname, grps->nr, gnames);
3186 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3188 if (IMDgroup->nat > 0)
3191 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3193 IMDgname, IMDgroup->nat);
3194 snew(IMDgroup->ind, IMDgroup->nat);
3195 for (i = 0; i < IMDgroup->nat; i++)
3197 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3202 /* Checks whether atoms are both part of a COM removal group and frozen.
3203 * If a fully frozen atom is part of a COM removal group, it is removed
3204 * from the COM removal group. A note is issued if such atoms are present.
3205 * A warning is issued for atom with one or two dimensions frozen that
3206 * are part of a COM removal group (mdrun would need to compute COM mass
3207 * per dimension to handle this correctly).
3208 * Also issues a warning when non-frozen atoms are not part of a COM
3209 * removal group while COM removal is active.
3211 static void checkAndUpdateVcmFreezeGroupConsistency(SimulationGroups* groups,
3213 const t_grpopts& opts,
3216 const int vcmRestGroup =
3217 std::max(int(groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()), 1);
3219 int numFullyFrozenVcmAtoms = 0;
3220 int numPartiallyFrozenVcmAtoms = 0;
3221 int numNonVcmAtoms = 0;
3222 for (int a = 0; a < numAtoms; a++)
3224 const int freezeGroup = getGroupType(*groups, SimulationAtomGroupType::Freeze, a);
3225 int numFrozenDims = 0;
3226 for (int d = 0; d < DIM; d++)
3228 numFrozenDims += opts.nFreeze[freezeGroup][d];
3231 const int vcmGroup = getGroupType(*groups, SimulationAtomGroupType::MassCenterVelocityRemoval, a);
3232 if (vcmGroup < vcmRestGroup)
3234 if (numFrozenDims == DIM)
3236 /* Do not remove COM motion for this fully frozen atom */
3237 if (groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
3239 groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(numAtoms, 0);
3241 groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
3242 numFullyFrozenVcmAtoms++;
3244 else if (numFrozenDims > 0)
3246 numPartiallyFrozenVcmAtoms++;
3249 else if (numFrozenDims < DIM)
3255 if (numFullyFrozenVcmAtoms > 0)
3257 std::string warningText = gmx::formatString(
3258 "There are %d atoms that are fully frozen and part of COMM removal group(s), "
3259 "removing these atoms from the COMM removal group(s)",
3260 numFullyFrozenVcmAtoms);
3261 warning_note(wi, warningText.c_str());
3263 if (numPartiallyFrozenVcmAtoms > 0 && numPartiallyFrozenVcmAtoms < numAtoms)
3265 std::string warningText = gmx::formatString(
3266 "There are %d atoms that are frozen along less then %d dimensions and part of COMM "
3267 "removal group(s), due to limitations in the code these still contribute to the "
3268 "mass of the COM along frozen dimensions and therefore the COMM correction will be "
3270 numPartiallyFrozenVcmAtoms, DIM);
3271 warning(wi, warningText.c_str());
3273 if (numNonVcmAtoms > 0)
3275 std::string warningText = gmx::formatString(
3276 "%d atoms are not part of any center of mass motion removal group.\n"
3277 "This may lead to artifacts.\n"
3278 "In most cases one should use one group for the whole system.",
3280 warning(wi, warningText.c_str());
3284 void do_index(const char* mdparin,
3288 const gmx::MdModulesNotifier& notifier,
3292 t_blocka* defaultIndexGroups;
3300 int i, j, k, restnm;
3301 bool bExcl, bTable, bAnneal;
3302 char warn_buf[STRLEN];
3306 fprintf(stderr, "processing index file...\n");
3310 snew(defaultIndexGroups, 1);
3311 snew(defaultIndexGroups->index, 1);
3313 atoms_all = gmx_mtop_global_atoms(mtop);
3314 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3315 done_atom(&atoms_all);
3319 defaultIndexGroups = init_index(ndx, &gnames);
3322 SimulationGroups* groups = &mtop->groups;
3323 natoms = mtop->natoms;
3324 symtab = &mtop->symtab;
3326 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3328 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3330 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3331 restnm = groups->groupNames.size() - 1;
3332 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3333 srenew(gnames, defaultIndexGroups->nr + 1);
3334 gnames[restnm] = *(groups->groupNames.back());
3336 set_warning_line(wi, mdparin, -1);
3338 auto temperatureCouplingTauValues = gmx::splitString(inputrecStrings->tau_t);
3339 auto temperatureCouplingReferenceValues = gmx::splitString(inputrecStrings->ref_t);
3340 auto temperatureCouplingGroupNames = gmx::splitString(inputrecStrings->tcgrps);
3341 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3342 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3345 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3347 temperatureCouplingGroupNames.size(), temperatureCouplingReferenceValues.size(),
3348 temperatureCouplingTauValues.size());
3351 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3352 do_numbering(natoms, groups, temperatureCouplingGroupNames, defaultIndexGroups, gnames,
3353 SimulationAtomGroupType::TemperatureCoupling, restnm,
3354 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3355 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3357 snew(ir->opts.nrdf, nr);
3358 snew(ir->opts.tau_t, nr);
3359 snew(ir->opts.ref_t, nr);
3360 if (ir->eI == eiBD && ir->bd_fric == 0)
3362 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3365 if (useReferenceTemperature)
3367 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3369 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3373 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3374 for (i = 0; (i < nr); i++)
3376 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3378 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3379 warning_error(wi, warn_buf);
3382 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3386 "tau-t = -1 is the value to signal that a group should not have "
3387 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3390 if (ir->opts.tau_t[i] >= 0)
3392 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3395 if (ir->etc != etcNO && ir->nsttcouple == -1)
3397 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3402 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3405 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3406 "md-vv; use either vrescale temperature with berendsen pressure or "
3407 "Nose-Hoover temperature with MTTK pressure");
3409 if (ir->epc == epcMTTK)
3411 if (ir->etc != etcNOSEHOOVER)
3414 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3419 if (ir->nstpcouple != ir->nsttcouple)
3421 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3422 ir->nstpcouple = ir->nsttcouple = mincouple;
3424 "for current Trotter decomposition methods with vv, nsttcouple and "
3425 "nstpcouple must be equal. Both have been reset to "
3426 "min(nsttcouple,nstpcouple) = %d",
3428 warning_note(wi, warn_buf);
3433 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3434 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3436 if (ETC_ANDERSEN(ir->etc))
3438 if (ir->nsttcouple != 1)
3442 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3443 "need for larger nsttcouple > 1, since no global parameters are computed. "
3444 "nsttcouple has been reset to 1");
3445 warning_note(wi, warn_buf);
3448 nstcmin = tcouple_min_integration_steps(ir->etc);
3451 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3454 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3455 "least %d times larger than nsttcouple*dt (%g)",
3456 ETCOUPLTYPE(ir->etc), tau_min, nstcmin, ir->nsttcouple * ir->delta_t);
3457 warning(wi, warn_buf);
3460 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3461 for (i = 0; (i < nr); i++)
3463 if (ir->opts.ref_t[i] < 0)
3465 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3468 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3469 if we are in this conditional) if mc_temp is negative */
3470 if (ir->expandedvals->mc_temp < 0)
3472 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3476 /* Simulated annealing for each group. There are nr groups */
3477 auto simulatedAnnealingGroupNames = gmx::splitString(inputrecStrings->anneal);
3478 if (simulatedAnnealingGroupNames.size() == 1
3479 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3481 simulatedAnnealingGroupNames.resize(0);
3483 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3485 gmx_fatal(FARGS, "Wrong number of annealing values: %zu (for %d groups)\n",
3486 simulatedAnnealingGroupNames.size(), nr);
3490 snew(ir->opts.annealing, nr);
3491 snew(ir->opts.anneal_npoints, nr);
3492 snew(ir->opts.anneal_time, nr);
3493 snew(ir->opts.anneal_temp, nr);
3494 for (i = 0; i < nr; i++)
3496 ir->opts.annealing[i] = eannNO;
3497 ir->opts.anneal_npoints[i] = 0;
3498 ir->opts.anneal_time[i] = nullptr;
3499 ir->opts.anneal_temp[i] = nullptr;
3501 if (!simulatedAnnealingGroupNames.empty())
3504 for (i = 0; i < nr; i++)
3506 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3508 ir->opts.annealing[i] = eannNO;
3510 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3512 ir->opts.annealing[i] = eannSINGLE;
3515 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3517 ir->opts.annealing[i] = eannPERIODIC;
3523 /* Read the other fields too */
3524 auto simulatedAnnealingPoints = gmx::splitString(inputrecStrings->anneal_npoints);
3525 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3527 gmx_fatal(FARGS, "Found %zu annealing-npoints values for %zu groups\n",
3528 simulatedAnnealingPoints.size(), simulatedAnnealingGroupNames.size());
3530 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3531 size_t numSimulatedAnnealingFields = 0;
3532 for (i = 0; i < nr; i++)
3534 if (ir->opts.anneal_npoints[i] == 1)
3538 "Please specify at least a start and an end point for annealing\n");
3540 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3541 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3542 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3545 auto simulatedAnnealingTimes = gmx::splitString(inputrecStrings->anneal_time);
3547 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3549 gmx_fatal(FARGS, "Found %zu annealing-time values, wanted %zu\n",
3550 simulatedAnnealingTimes.size(), numSimulatedAnnealingFields);
3552 auto simulatedAnnealingTemperatures = gmx::splitString(inputrecStrings->anneal_temp);
3553 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3555 gmx_fatal(FARGS, "Found %zu annealing-temp values, wanted %zu\n",
3556 simulatedAnnealingTemperatures.size(), numSimulatedAnnealingFields);
3559 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3560 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3561 convertReals(wi, simulatedAnnealingTimes, "anneal-time",
3562 allSimulatedAnnealingTimes.data());
3563 convertReals(wi, simulatedAnnealingTemperatures, "anneal-temp",
3564 allSimulatedAnnealingTemperatures.data());
3565 for (i = 0, k = 0; i < nr; i++)
3567 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3569 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3570 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3573 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3575 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3581 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3584 "Annealing timepoints out of order: t=%f comes after "
3586 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j - 1]);
3589 if (ir->opts.anneal_temp[i][j] < 0)
3591 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n",
3592 ir->opts.anneal_temp[i][j]);
3597 /* Print out some summary information, to make sure we got it right */
3598 for (i = 0; i < nr; i++)
3600 if (ir->opts.annealing[i] != eannNO)
3602 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3603 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3604 *(groups->groupNames[j]), eann_names[ir->opts.annealing[i]],
3605 ir->opts.anneal_npoints[i]);
3606 fprintf(stderr, "Time (ps) Temperature (K)\n");
3607 /* All terms except the last one */
3608 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3610 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3611 ir->opts.anneal_temp[i][j]);
3614 /* Finally the last one */
3615 j = ir->opts.anneal_npoints[i] - 1;
3616 if (ir->opts.annealing[i] == eannSINGLE)
3618 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j],
3619 ir->opts.anneal_temp[i][j]);
3623 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3624 ir->opts.anneal_temp[i][j]);
3625 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3628 "There is a temperature jump when your annealing "
3640 make_pull_groups(ir->pull, inputrecStrings->pullGroupNames, defaultIndexGroups, gnames);
3642 make_pull_coords(ir->pull);
3647 make_rotation_groups(ir->rot, inputrecStrings->rotateGroupNames, defaultIndexGroups, gnames);
3650 if (ir->eSwapCoords != eswapNO)
3652 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3655 /* Make indices for IMD session */
3658 make_IMD_group(ir->imd, inputrecStrings->imd_grp, defaultIndexGroups, gnames);
3661 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3662 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3663 notifier.preProcessingNotifications_.notify(defaultIndexGroupsAndNames);
3665 auto accelerations = gmx::splitString(inputrecStrings->acc);
3666 auto accelerationGroupNames = gmx::splitString(inputrecStrings->accgrps);
3667 if (accelerationGroupNames.size() * DIM != accelerations.size())
3669 gmx_fatal(FARGS, "Invalid Acceleration input: %zu groups and %zu acc. values",
3670 accelerationGroupNames.size(), accelerations.size());
3672 do_numbering(natoms, groups, accelerationGroupNames, defaultIndexGroups, gnames,
3673 SimulationAtomGroupType::Acceleration, restnm, egrptpALL_GENREST, bVerbose, wi);
3674 nr = groups->groups[SimulationAtomGroupType::Acceleration].size();
3675 snew(ir->opts.acc, nr);
3676 ir->opts.ngacc = nr;
3678 convertRvecs(wi, accelerations, "anneal-time", ir->opts.acc);
3680 auto freezeDims = gmx::splitString(inputrecStrings->frdim);
3681 auto freezeGroupNames = gmx::splitString(inputrecStrings->freeze);
3682 if (freezeDims.size() != DIM * freezeGroupNames.size())
3684 gmx_fatal(FARGS, "Invalid Freezing input: %zu groups and %zu freeze values",
3685 freezeGroupNames.size(), freezeDims.size());
3687 do_numbering(natoms, groups, freezeGroupNames, defaultIndexGroups, gnames,
3688 SimulationAtomGroupType::Freeze, restnm, egrptpALL_GENREST, bVerbose, wi);
3689 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3690 ir->opts.ngfrz = nr;
3691 snew(ir->opts.nFreeze, nr);
3692 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3694 for (j = 0; (j < DIM); j++, k++)
3696 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3697 if (!ir->opts.nFreeze[i][j])
3699 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3702 "Please use Y(ES) or N(O) for freezedim only "
3704 freezeDims[k].c_str());
3705 warning(wi, warn_buf);
3710 for (; (i < nr); i++)
3712 for (j = 0; (j < DIM); j++)
3714 ir->opts.nFreeze[i][j] = 0;
3718 auto energyGroupNames = gmx::splitString(inputrecStrings->energy);
3719 do_numbering(natoms, groups, energyGroupNames, defaultIndexGroups, gnames,
3720 SimulationAtomGroupType::EnergyOutput, restnm, egrptpALL_GENREST, bVerbose, wi);
3721 add_wall_energrps(groups, ir->nwall, symtab);
3722 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3723 auto vcmGroupNames = gmx::splitString(inputrecStrings->vcm);
3724 do_numbering(natoms, groups, vcmGroupNames, defaultIndexGroups, gnames,
3725 SimulationAtomGroupType::MassCenterVelocityRemoval, restnm,
3726 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3728 if (ir->comm_mode != ecmNO)
3730 checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
3733 /* Now we have filled the freeze struct, so we can calculate NRDF */
3734 calc_nrdf(mtop, ir, gnames);
3736 auto user1GroupNames = gmx::splitString(inputrecStrings->user1);
3737 do_numbering(natoms, groups, user1GroupNames, defaultIndexGroups, gnames,
3738 SimulationAtomGroupType::User1, restnm, egrptpALL_GENREST, bVerbose, wi);
3739 auto user2GroupNames = gmx::splitString(inputrecStrings->user2);
3740 do_numbering(natoms, groups, user2GroupNames, defaultIndexGroups, gnames,
3741 SimulationAtomGroupType::User2, restnm, egrptpALL_GENREST, bVerbose, wi);
3742 auto compressedXGroupNames = gmx::splitString(inputrecStrings->x_compressed_groups);
3743 do_numbering(natoms, groups, compressedXGroupNames, defaultIndexGroups, gnames,
3744 SimulationAtomGroupType::CompressedPositionOutput, restnm, egrptpONE, bVerbose, wi);
3745 auto orirefFitGroupNames = gmx::splitString(inputrecStrings->orirefitgrp);
3746 do_numbering(natoms, groups, orirefFitGroupNames, defaultIndexGroups, gnames,
3747 SimulationAtomGroupType::OrientationRestraintsFit, restnm, egrptpALL_GENREST,
3750 /* MiMiC QMMM input processing */
3751 auto qmGroupNames = gmx::splitString(inputrecStrings->QMMM);
3752 if (qmGroupNames.size() > 1)
3754 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
3756 /* group rest, if any, is always MM! */
3757 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3758 SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
3759 ir->opts.ngQM = qmGroupNames.size();
3761 /* end of MiMiC QMMM input */
3765 for (auto group : gmx::keysOf(groups->groups))
3767 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
3768 for (const auto& entry : groups->groups[group])
3770 fprintf(stderr, " %s", *(groups->groupNames[entry]));
3772 fprintf(stderr, "\n");
3776 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3777 snew(ir->opts.egp_flags, nr * nr);
3779 bExcl = do_egp_flag(ir, groups, "energygrp-excl", inputrecStrings->egpexcl, EGP_EXCL);
3780 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3782 warning_error(wi, "Energy group exclusions are currently not supported");
3784 if (bExcl && EEL_FULL(ir->coulombtype))
3786 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3789 bTable = do_egp_flag(ir, groups, "energygrp-table", inputrecStrings->egptable, EGP_TABLE);
3790 if (bTable && !(ir->vdwtype == evdwUSER) && !(ir->coulombtype == eelUSER)
3791 && !(ir->coulombtype == eelPMEUSER) && !(ir->coulombtype == eelPMEUSERSWITCH))
3794 "Can only have energy group pair tables in combination with user tables for VdW "
3798 /* final check before going out of scope if simulated tempering variables
3799 * need to be set to default values.
3801 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
3803 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
3804 warning(wi, gmx::formatString(
3805 "the value for nstexpanded was not specified for "
3806 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
3807 "by default, but it is recommended to set it to an explicit value!",
3808 ir->expandedvals->nstexpanded));
3810 for (i = 0; (i < defaultIndexGroups->nr); i++)
3815 done_blocka(defaultIndexGroups);
3816 sfree(defaultIndexGroups);
3820 static void check_disre(const gmx_mtop_t* mtop)
3822 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3824 const gmx_ffparams_t& ffparams = mtop->ffparams;
3827 for (int i = 0; i < ffparams.numTypes(); i++)
3829 int ftype = ffparams.functype[i];
3830 if (ftype == F_DISRES)
3832 int label = ffparams.iparams[i].disres.label;
3833 if (label == old_label)
3835 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3844 "Found %d double distance restraint indices,\n"
3845 "probably the parameters for multiple pairs in one restraint "
3846 "are not identical\n",
3852 static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t* sys, const bool posres_only, ivec AbsRef)
3855 gmx_mtop_ilistloop_t iloop;
3857 const t_iparams* pr;
3864 for (d = 0; d < DIM; d++)
3866 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3868 /* Check for freeze groups */
3869 for (g = 0; g < ir->opts.ngfrz; g++)
3871 for (d = 0; d < DIM; d++)
3873 if (ir->opts.nFreeze[g][d] != 0)
3881 /* Check for position restraints */
3882 iloop = gmx_mtop_ilistloop_init(sys);
3883 while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
3885 if (nmol > 0 && (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3887 for (i = 0; i < (*ilist)[F_POSRES].size(); i += 2)
3889 pr = &sys->ffparams.iparams[(*ilist)[F_POSRES].iatoms[i]];
3890 for (d = 0; d < DIM; d++)
3892 if (pr->posres.fcA[d] != 0)
3898 for (i = 0; i < (*ilist)[F_FBPOSRES].size(); i += 2)
3900 /* Check for flat-bottom posres */
3901 pr = &sys->ffparams.iparams[(*ilist)[F_FBPOSRES].iatoms[i]];
3902 if (pr->fbposres.k != 0)
3904 switch (pr->fbposres.geom)
3906 case efbposresSPHERE: AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1; break;
3907 case efbposresCYLINDERX: AbsRef[YY] = AbsRef[ZZ] = 1; break;
3908 case efbposresCYLINDERY: AbsRef[XX] = AbsRef[ZZ] = 1; break;
3909 case efbposresCYLINDER:
3910 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3911 case efbposresCYLINDERZ: AbsRef[XX] = AbsRef[YY] = 1; break;
3912 case efbposresX: /* d=XX */
3913 case efbposresY: /* d=YY */
3914 case efbposresZ: /* d=ZZ */
3915 d = pr->fbposres.geom - efbposresX;
3920 " Invalid geometry for flat-bottom position restraint.\n"
3921 "Expected nr between 1 and %d. Found %d\n",
3922 efbposresNR - 1, pr->fbposres.geom);
3929 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3932 static void check_combination_rule_differences(const gmx_mtop_t* mtop,
3934 bool* bC6ParametersWorkWithGeometricRules,
3935 bool* bC6ParametersWorkWithLBRules,
3936 bool* bLBRulesPossible)
3938 int ntypes, tpi, tpj;
3941 double c6i, c6j, c12i, c12j;
3942 double c6, c6_geometric, c6_LB;
3943 double sigmai, sigmaj, epsi, epsj;
3944 bool bCanDoLBRules, bCanDoGeometricRules;
3947 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3948 * force-field floating point parameters.
3951 ptr = getenv("GMX_LJCOMB_TOL");
3955 double gmx_unused canary;
3957 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
3960 "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
3965 *bC6ParametersWorkWithLBRules = TRUE;
3966 *bC6ParametersWorkWithGeometricRules = TRUE;
3967 bCanDoLBRules = TRUE;
3968 ntypes = mtop->ffparams.atnr;
3969 snew(typecount, ntypes);
3970 gmx_mtop_count_atomtypes(mtop, state, typecount);
3971 *bLBRulesPossible = TRUE;
3972 for (tpi = 0; tpi < ntypes; ++tpi)
3974 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3975 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3976 for (tpj = tpi; tpj < ntypes; ++tpj)
3978 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3979 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3980 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3981 c6_geometric = std::sqrt(c6i * c6j);
3982 if (!gmx_numzero(c6_geometric))
3984 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3986 sigmai = gmx::sixthroot(c12i / c6i);
3987 sigmaj = gmx::sixthroot(c12j / c6j);
3988 epsi = c6i * c6i / (4.0 * c12i);
3989 epsj = c6j * c6j / (4.0 * c12j);
3990 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
3994 *bLBRulesPossible = FALSE;
3995 c6_LB = c6_geometric;
3997 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4002 *bC6ParametersWorkWithLBRules = FALSE;
4005 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4007 if (!bCanDoGeometricRules)
4009 *bC6ParametersWorkWithGeometricRules = FALSE;
4016 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t* mtop, warninp_t wi)
4018 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4020 check_combination_rule_differences(mtop, 0, &bC6ParametersWorkWithGeometricRules,
4021 &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4022 if (ir->ljpme_combination_rule == eljpmeLB)
4024 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4027 "You are using arithmetic-geometric combination rules "
4028 "in LJ-PME, but your non-bonded C6 parameters do not "
4029 "follow these rules.");
4034 if (!bC6ParametersWorkWithGeometricRules)
4036 if (ir->eDispCorr != edispcNO)
4039 "You are using geometric combination rules in "
4040 "LJ-PME, but your non-bonded C6 parameters do "
4041 "not follow these rules. "
4042 "This will introduce very small errors in the forces and energies in "
4043 "your simulations. Dispersion correction will correct total energy "
4044 "and/or pressure for isotropic systems, but not forces or surface "
4050 "You are using geometric combination rules in "
4051 "LJ-PME, but your non-bonded C6 parameters do "
4052 "not follow these rules. "
4053 "This will introduce very small errors in the forces and energies in "
4054 "your simulations. If your system is homogeneous, consider using "
4055 "dispersion correction "
4056 "for the total energy and pressure.");
4062 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4064 char err_buf[STRLEN];
4069 gmx_mtop_atomloop_block_t aloopb;
4071 char warn_buf[STRLEN];
4073 set_warning_line(wi, mdparin, -1);
4075 if (absolute_reference(ir, sys, false, AbsRef))
4078 "Removing center of mass motion in the presence of position restraints might "
4079 "cause artifacts. When you are using position restraints to equilibrate a "
4080 "macro-molecule, the artifacts are usually negligible.");
4083 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 && ir->nstlist > 1
4084 && ((EI_MD(ir->eI) || EI_SD(ir->eI)) && (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4086 /* Check if a too small Verlet buffer might potentially
4087 * cause more drift than the thermostat can couple off.
4089 /* Temperature error fraction for warning and suggestion */
4090 const real T_error_warn = 0.002;
4091 const real T_error_suggest = 0.001;
4092 /* For safety: 2 DOF per atom (typical with constraints) */
4093 const real nrdf_at = 2;
4094 real T, tau, max_T_error;
4099 for (i = 0; i < ir->opts.ngtc; i++)
4101 T = std::max(T, ir->opts.ref_t[i]);
4102 tau = std::max(tau, ir->opts.tau_t[i]);
4106 /* This is a worst case estimate of the temperature error,
4107 * assuming perfect buffer estimation and no cancelation
4108 * of errors. The factor 0.5 is because energy distributes
4109 * equally over Ekin and Epot.
4111 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * BOLTZ * T);
4112 if (max_T_error > T_error_warn)
4115 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4116 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4117 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4118 "%.0e or decrease tau_t.",
4119 ir->verletbuf_tol, T, tau, 100 * max_T_error, 100 * T_error_suggest,
4120 ir->verletbuf_tol * T_error_suggest / max_T_error);
4121 warning(wi, warn_buf);
4126 if (ETC_ANDERSEN(ir->etc))
4130 for (i = 0; i < ir->opts.ngtc; i++)
4133 "all tau_t must currently be equal using Andersen temperature control, "
4134 "violated for group %d",
4136 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4138 "all tau_t must be positive using Andersen temperature control, "
4140 i, ir->opts.tau_t[i]);
4141 CHECK(ir->opts.tau_t[i] < 0);
4144 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4146 for (i = 0; i < ir->opts.ngtc; i++)
4148 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4150 "tau_t/delta_t for group %d for temperature control method %s must be a "
4151 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4152 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4154 i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
4155 CHECK(nsteps % ir->nstcomm != 0);
4160 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD && ir->comm_mode == ecmNO
4161 && !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) && !ETC_ANDERSEN(ir->etc))
4164 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4165 "rounding errors can lead to build up of kinetic energy of the center of mass");
4168 if (ir->epc == epcPARRINELLORAHMAN && ir->etc == etcNOSEHOOVER)
4171 for (int g = 0; g < ir->opts.ngtc; g++)
4173 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4175 if (ir->tau_p < 1.9 * tau_t_max)
4177 std::string message = gmx::formatString(
4178 "With %s T-coupling and %s p-coupling, "
4179 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4180 etcoupl_names[ir->etc], epcoupl_names[ir->epc], "tau-p", ir->tau_p, "tau-t",
4182 warning(wi, message.c_str());
4186 /* Check for pressure coupling with absolute position restraints */
4187 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4189 absolute_reference(ir, sys, TRUE, AbsRef);
4191 for (m = 0; m < DIM; m++)
4193 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4196 "You are using pressure coupling with absolute position restraints, "
4197 "this will give artifacts. Use the refcoord_scaling option.");
4205 aloopb = gmx_mtop_atomloop_block_init(sys);
4207 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4209 if (atom->q != 0 || atom->qB != 0)
4217 if (EEL_FULL(ir->coulombtype))
4220 "You are using full electrostatics treatment %s for a system without charges.\n"
4221 "This costs a lot of performance for just processing zeros, consider using %s "
4223 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4224 warning(wi, err_buf);
4229 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
4232 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4233 "You might want to consider using %s electrostatics.\n",
4235 warning_note(wi, err_buf);
4239 /* Check if combination rules used in LJ-PME are the same as in the force field */
4240 if (EVDW_PME(ir->vdwtype))
4242 check_combination_rules(ir, sys, wi);
4245 /* Generalized reaction field */
4246 if (ir->coulombtype == eelGRF_NOTUSED)
4249 "Generalized reaction-field electrostatics is no longer supported. "
4250 "You can use normal reaction-field instead and compute the reaction-field "
4251 "constant by hand.");
4255 for (int i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4257 for (m = 0; (m < DIM); m++)
4259 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4268 snew(mgrp, sys->groups.groups[SimulationAtomGroupType::Acceleration].size());
4269 for (const AtomProxy atomP : AtomRange(*sys))
4271 const t_atom& local = atomP.atom();
4272 int i = atomP.globalAtomNumber();
4273 mgrp[getGroupType(sys->groups, SimulationAtomGroupType::Acceleration, i)] += local.m;
4276 for (i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4278 for (m = 0; (m < DIM); m++)
4280 acc[m] += ir->opts.acc[i][m] * mgrp[i];
4284 for (m = 0; (m < DIM); m++)
4286 if (fabs(acc[m]) > 1e-6)
4288 const char* dim[DIM] = { "X", "Y", "Z" };
4289 fprintf(stderr, "Net Acceleration in %s direction, will %s be corrected\n", dim[m],
4290 ir->nstcomm != 0 ? "" : "not");
4291 if (ir->nstcomm != 0 && m < ndof_com(ir))
4295 (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4297 ir->opts.acc[i][m] -= acc[m];
4305 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0
4306 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4308 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4316 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4318 if (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0)
4320 absolute_reference(ir, sys, FALSE, AbsRef);
4321 for (m = 0; m < DIM; m++)
4323 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4326 "You are using an absolute reference for pulling, but the rest of "
4327 "the system does not have an absolute reference. This will lead to "
4336 for (i = 0; i < 3; i++)
4338 for (m = 0; m <= i; m++)
4340 if ((ir->epc != epcNO && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4342 for (c = 0; c < ir->pull->ncoord; c++)
4344 if (ir->pull->coord[c].eGeom == epullgDIRPBC && ir->pull->coord[c].vec[m] != 0)
4347 "Can not have dynamic box while using pull geometry '%s' "
4349 EPULLGEOM(ir->pull->coord[c].eGeom), 'x' + m);
4360 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4362 char warn_buf[STRLEN];
4365 ptr = check_box(ir->pbcType, box);
4368 warning_error(wi, ptr);
4371 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4373 if (ir->shake_tol <= 0.0)
4375 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4376 warning_error(wi, warn_buf);
4380 if ((ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4382 /* If we have Lincs constraints: */
4383 if (ir->eI == eiMD && ir->etc == etcNO && ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4386 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4387 warning_note(wi, warn_buf);
4390 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4393 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4395 warning_note(wi, warn_buf);
4397 if (ir->epc == epcMTTK)
4399 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4403 if (bHasAnyConstraints && ir->epc == epcMTTK)
4405 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4408 if (ir->LincsWarnAngle > 90.0)
4410 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4411 warning(wi, warn_buf);
4412 ir->LincsWarnAngle = 90.0;
4415 if (ir->pbcType != PbcType::No)
4417 if (ir->nstlist == 0)
4420 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4421 "atoms might cause the simulation to crash.");
4423 if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
4426 "ERROR: The cut-off length is longer than half the shortest box vector or "
4427 "longer than the smallest box diagonal element. Increase the box size or "
4428 "decrease rlist.\n");
4429 warning_error(wi, warn_buf);