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49 #include "gromacs/awh/read_params.h"
50 #include "gromacs/fileio/readinp.h"
51 #include "gromacs/fileio/warninp.h"
52 #include "gromacs/gmxlib/network.h"
53 #include "gromacs/gmxpreprocess/toputil.h"
54 #include "gromacs/math/functions.h"
55 #include "gromacs/math/units.h"
56 #include "gromacs/math/vec.h"
57 #include "gromacs/mdlib/calc_verletbuf.h"
58 #include "gromacs/mdrun/mdmodules.h"
59 #include "gromacs/mdtypes/inputrec.h"
60 #include "gromacs/mdtypes/md_enums.h"
61 #include "gromacs/mdtypes/pull_params.h"
62 #include "gromacs/options/options.h"
63 #include "gromacs/options/treesupport.h"
64 #include "gromacs/pbcutil/pbc.h"
65 #include "gromacs/selection/indexutil.h"
66 #include "gromacs/topology/block.h"
67 #include "gromacs/topology/ifunc.h"
68 #include "gromacs/topology/index.h"
69 #include "gromacs/topology/mtop_util.h"
70 #include "gromacs/topology/symtab.h"
71 #include "gromacs/topology/topology.h"
72 #include "gromacs/utility/cstringutil.h"
73 #include "gromacs/utility/exceptions.h"
74 #include "gromacs/utility/fatalerror.h"
75 #include "gromacs/utility/filestream.h"
76 #include "gromacs/utility/gmxassert.h"
77 #include "gromacs/utility/ikeyvaluetreeerror.h"
78 #include "gromacs/utility/keyvaluetree.h"
79 #include "gromacs/utility/keyvaluetreebuilder.h"
80 #include "gromacs/utility/keyvaluetreemdpwriter.h"
81 #include "gromacs/utility/keyvaluetreetransform.h"
82 #include "gromacs/utility/mdmodulenotification.h"
83 #include "gromacs/utility/smalloc.h"
84 #include "gromacs/utility/strconvert.h"
85 #include "gromacs/utility/stringcompare.h"
86 #include "gromacs/utility/stringutil.h"
87 #include "gromacs/utility/textwriter.h"
92 /* Resource parameters
93 * Do not change any of these until you read the instruction
94 * in readinp.h. Some cpp's do not take spaces after the backslash
95 * (like the c-shell), which will give you a very weird compiler
99 typedef struct t_inputrec_strings
101 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN], acc[STRLEN], accgrps[STRLEN], freeze[STRLEN],
102 frdim[STRLEN], energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN],
103 x_compressed_groups[STRLEN], couple_moltype[STRLEN], orirefitgrp[STRLEN],
104 egptable[STRLEN], egpexcl[STRLEN], wall_atomtype[STRLEN], wall_density[STRLEN],
105 deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
106 char fep_lambda[efptNR][STRLEN];
107 char lambda_weights[STRLEN];
110 char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
111 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN], bSH[STRLEN],
112 CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN], SAoff[STRLEN], SAsteps[STRLEN];
114 } gmx_inputrec_strings;
116 static gmx_inputrec_strings* is = 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.");
129 void done_inputrec_strings()
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.notifier_.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, "QMMM is currently not supported");
1397 if (!EI_DYNAMICS(ir->eI))
1400 sprintf(buf, "QMMM is only supported with dynamics, not with integrator %s", ei_names[ir->eI]);
1401 warning_error(wi, buf);
1407 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1411 /* interpret a number of doubles from a string and put them in an array,
1412 after allocating space for them.
1413 str = the input string
1414 n = the (pre-allocated) number of doubles read
1415 r = the output array of doubles. */
1416 static void parse_n_real(char* str, int* n, real** r, warninp_t wi)
1418 auto values = gmx::splitString(str);
1422 for (int i = 0; i < *n; i++)
1426 (*r)[i] = gmx::fromString<real>(values[i]);
1428 catch (gmx::GromacsException&)
1430 warning_error(wi, "Invalid value " + values[i]
1431 + " in string in mdp file. Expected a real number.");
1437 static void do_fep_params(t_inputrec* ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
1440 int i, j, max_n_lambda, nweights, nfep[efptNR];
1441 t_lambda* fep = ir->fepvals;
1442 t_expanded* expand = ir->expandedvals;
1443 real** count_fep_lambdas;
1444 bool bOneLambda = TRUE;
1446 snew(count_fep_lambdas, efptNR);
1448 /* FEP input processing */
1449 /* first, identify the number of lambda values for each type.
1450 All that are nonzero must have the same number */
1452 for (i = 0; i < efptNR; i++)
1454 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
1457 /* now, determine the number of components. All must be either zero, or equal. */
1460 for (i = 0; i < efptNR; i++)
1462 if (nfep[i] > max_n_lambda)
1464 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1465 must have the same number if its not zero.*/
1470 for (i = 0; i < efptNR; i++)
1474 ir->fepvals->separate_dvdl[i] = FALSE;
1476 else if (nfep[i] == max_n_lambda)
1478 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute
1479 the derivative with respect to the temperature currently */
1481 ir->fepvals->separate_dvdl[i] = TRUE;
1487 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1489 nfep[i], efpt_names[i], max_n_lambda);
1492 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1493 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1495 /* the number of lambdas is the number we've read in, which is either zero
1496 or the same for all */
1497 fep->n_lambda = max_n_lambda;
1499 /* allocate space for the array of lambda values */
1500 snew(fep->all_lambda, efptNR);
1501 /* if init_lambda is defined, we need to set lambda */
1502 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1504 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1506 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1507 for (i = 0; i < efptNR; i++)
1509 snew(fep->all_lambda[i], fep->n_lambda);
1510 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1513 for (j = 0; j < fep->n_lambda; j++)
1515 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1517 sfree(count_fep_lambdas[i]);
1520 sfree(count_fep_lambdas);
1522 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1523 internal bookkeeping -- for now, init_lambda */
1525 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1527 for (i = 0; i < fep->n_lambda; i++)
1529 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1533 /* check to see if only a single component lambda is defined, and soft core is defined.
1534 In this case, turn on coulomb soft core */
1536 if (max_n_lambda == 0)
1542 for (i = 0; i < efptNR; i++)
1544 if ((nfep[i] != 0) && (i != efptFEP))
1550 if ((bOneLambda) && (fep->sc_alpha > 0))
1552 fep->bScCoul = TRUE;
1555 /* Fill in the others with the efptFEP if they are not explicitly
1556 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1557 they are all zero. */
1559 for (i = 0; i < efptNR; i++)
1561 if ((nfep[i] == 0) && (i != efptFEP))
1563 for (j = 0; j < fep->n_lambda; j++)
1565 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1571 /* now read in the weights */
1572 parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
1575 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1577 else if (nweights != fep->n_lambda)
1579 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1580 nweights, fep->n_lambda);
1582 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1584 expand->nstexpanded = fep->nstdhdl;
1585 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1590 static void do_simtemp_params(t_inputrec* ir)
1593 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1594 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1597 static void convertYesNos(warninp_t /*wi*/,
1598 gmx::ArrayRef<const std::string> inputs,
1599 const char* /*name*/,
1603 for (const auto& input : inputs)
1605 outputs[i] = gmx::equalCaseInsensitive(input, "Y", 1);
1610 template<typename T>
1611 void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
1614 for (const auto& input : inputs)
1618 outputs[i] = gmx::fromStdString<T>(input);
1620 catch (gmx::GromacsException&)
1622 auto message = gmx::formatString(
1623 "Invalid value for mdp option %s. %s should only consist of integers separated "
1626 warning_error(wi, message);
1632 static void convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, real* outputs)
1635 for (const auto& input : inputs)
1639 outputs[i] = gmx::fromString<real>(input);
1641 catch (gmx::GromacsException&)
1643 auto message = gmx::formatString(
1644 "Invalid value for mdp option %s. %s should only consist of real numbers "
1645 "separated by spaces.",
1647 warning_error(wi, message);
1653 static void convertRvecs(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, rvec* outputs)
1656 for (const auto& input : inputs)
1660 outputs[i][d] = gmx::fromString<real>(input);
1662 catch (gmx::GromacsException&)
1664 auto message = gmx::formatString(
1665 "Invalid value for mdp option %s. %s should only consist of real numbers "
1666 "separated by spaces.",
1668 warning_error(wi, message);
1679 static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
1681 opts->wall_atomtype[0] = nullptr;
1682 opts->wall_atomtype[1] = nullptr;
1684 ir->wall_atomtype[0] = -1;
1685 ir->wall_atomtype[1] = -1;
1686 ir->wall_density[0] = 0;
1687 ir->wall_density[1] = 0;
1691 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1692 if (wallAtomTypes.size() != size_t(ir->nwall))
1694 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %zu", ir->nwall,
1695 wallAtomTypes.size());
1697 for (int i = 0; i < ir->nwall; i++)
1699 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1702 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1704 auto wallDensity = gmx::splitString(wall_density);
1705 if (wallDensity.size() != size_t(ir->nwall))
1707 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %zu", ir->nwall,
1708 wallDensity.size());
1710 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1711 for (int i = 0; i < ir->nwall; i++)
1713 if (ir->wall_density[i] <= 0)
1715 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1722 static void add_wall_energrps(SimulationGroups* groups, int nwall, t_symtab* symtab)
1726 AtomGroupIndices* grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1727 for (int i = 0; i < nwall; i++)
1729 groups->groupNames.emplace_back(put_symtab(symtab, gmx::formatString("wall%d", i).c_str()));
1730 grps->emplace_back(groups->groupNames.size() - 1);
1735 static void read_expandedparams(std::vector<t_inpfile>* inp, t_expanded* expand, warninp_t wi)
1737 /* read expanded ensemble parameters */
1738 printStringNewline(inp, "expanded ensemble variables");
1739 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1740 expand->elamstats = get_eeenum(inp, "lmc-stats", elamstats_names, wi);
1741 expand->elmcmove = get_eeenum(inp, "lmc-move", elmcmove_names, wi);
1742 expand->elmceq = get_eeenum(inp, "lmc-weights-equil", elmceq_names, wi);
1743 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1744 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1745 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1746 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1747 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1748 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1749 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1750 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1751 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1752 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1753 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1754 expand->bSymmetrizedTMatrix =
1755 (get_eeenum(inp, "symmetrized-transition-matrix", yesno_names, wi) != 0);
1756 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1757 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1758 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1759 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1760 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1761 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1762 expand->bWLoneovert = (get_eeenum(inp, "wl-oneovert", yesno_names, wi) != 0);
1765 /*! \brief Return whether an end state with the given coupling-lambda
1766 * value describes fully-interacting VDW.
1768 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1769 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1771 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1773 return (couple_lambda_value == ecouplamVDW || couple_lambda_value == ecouplamVDWQ);
1779 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1782 explicit MdpErrorHandler(warninp_t wi) : wi_(wi), mapping_(nullptr) {}
1784 void setBackMapping(const gmx::IKeyValueTreeBackMapping& mapping) { mapping_ = &mapping; }
1786 bool onError(gmx::UserInputError* ex, const gmx::KeyValueTreePath& context) override
1789 gmx::formatString("Error in mdp option \"%s\":", getOptionName(context).c_str()));
1790 std::string message = gmx::formatExceptionMessageToString(*ex);
1791 warning_error(wi_, message.c_str());
1796 std::string getOptionName(const gmx::KeyValueTreePath& context)
1798 if (mapping_ != nullptr)
1800 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1801 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1804 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1809 const gmx::IKeyValueTreeBackMapping* mapping_;
1814 void get_ir(const char* mdparin,
1815 const char* mdparout,
1816 gmx::MDModules* mdModules,
1819 WriteMdpHeader writeMdpHeader,
1823 double dumdub[2][6];
1825 char warn_buf[STRLEN];
1826 t_lambda* fep = ir->fepvals;
1827 t_expanded* expand = ir->expandedvals;
1829 const char* no_names[] = { "no", nullptr };
1831 init_inputrec_strings();
1832 gmx::TextInputFile stream(mdparin);
1833 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1835 snew(dumstr[0], STRLEN);
1836 snew(dumstr[1], STRLEN);
1838 /* ignore the following deprecated commands */
1839 replace_inp_entry(inp, "title", nullptr);
1840 replace_inp_entry(inp, "cpp", nullptr);
1841 replace_inp_entry(inp, "domain-decomposition", nullptr);
1842 replace_inp_entry(inp, "andersen-seed", nullptr);
1843 replace_inp_entry(inp, "dihre", nullptr);
1844 replace_inp_entry(inp, "dihre-fc", nullptr);
1845 replace_inp_entry(inp, "dihre-tau", nullptr);
1846 replace_inp_entry(inp, "nstdihreout", nullptr);
1847 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1848 replace_inp_entry(inp, "optimize-fft", nullptr);
1849 replace_inp_entry(inp, "adress_type", nullptr);
1850 replace_inp_entry(inp, "adress_const_wf", nullptr);
1851 replace_inp_entry(inp, "adress_ex_width", nullptr);
1852 replace_inp_entry(inp, "adress_hy_width", nullptr);
1853 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1854 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1855 replace_inp_entry(inp, "adress_site", nullptr);
1856 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1857 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1858 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1859 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1860 replace_inp_entry(inp, "rlistlong", nullptr);
1861 replace_inp_entry(inp, "nstcalclr", nullptr);
1862 replace_inp_entry(inp, "pull-print-com2", nullptr);
1863 replace_inp_entry(inp, "gb-algorithm", nullptr);
1864 replace_inp_entry(inp, "nstgbradii", nullptr);
1865 replace_inp_entry(inp, "rgbradii", nullptr);
1866 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1867 replace_inp_entry(inp, "gb-saltconc", nullptr);
1868 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1869 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1870 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1871 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1872 replace_inp_entry(inp, "sa-algorithm", nullptr);
1873 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1874 replace_inp_entry(inp, "ns-type", nullptr);
1876 /* replace the following commands with the clearer new versions*/
1877 replace_inp_entry(inp, "unconstrained-start", "continuation");
1878 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1879 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1880 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1881 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1882 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1883 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1885 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1886 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1887 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1888 setStringEntry(&inp, "include", opts->include, nullptr);
1889 printStringNoNewline(
1890 &inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1891 setStringEntry(&inp, "define", opts->define, nullptr);
1893 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1894 ir->eI = get_eeenum(&inp, "integrator", ei_names, wi);
1895 printStringNoNewline(&inp, "Start time and timestep in ps");
1896 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1897 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1898 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1899 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1900 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1901 printStringNoNewline(
1902 &inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1903 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1904 printStringNoNewline(&inp, "mode for center of mass motion removal");
1905 ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
1906 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
1907 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
1908 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
1909 setStringEntry(&inp, "comm-grps", is->vcm, nullptr);
1911 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
1912 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
1913 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
1914 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
1917 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
1918 printStringNoNewline(&inp, "Force tolerance and initial step-size");
1919 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
1920 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
1921 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
1922 ir->niter = get_eint(&inp, "niter", 20, wi);
1923 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
1924 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
1925 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
1926 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
1927 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
1929 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
1930 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
1932 /* Output options */
1933 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
1934 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
1935 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
1936 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
1937 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
1938 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
1939 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
1940 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
1941 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
1942 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
1943 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
1944 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
1945 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
1946 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
1947 printStringNoNewline(&inp, "default, all atoms will be written.");
1948 setStringEntry(&inp, "compressed-x-grps", is->x_compressed_groups, nullptr);
1949 printStringNoNewline(&inp, "Selection of energy groups");
1950 setStringEntry(&inp, "energygrps", is->energy, nullptr);
1952 /* Neighbor searching */
1953 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
1954 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
1955 ir->cutoff_scheme = get_eeenum(&inp, "cutoff-scheme", ecutscheme_names, wi);
1956 printStringNoNewline(&inp, "nblist update frequency");
1957 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
1958 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
1959 // TODO This conversion should be removed when proper std:string handling will be added to get_eeenum(...), etc.
1960 std::vector<const char*> pbcTypesNamesChar;
1961 for (const auto& pbcTypeName : c_pbcTypeNames)
1963 pbcTypesNamesChar.push_back(pbcTypeName.c_str());
1965 ir->pbcType = static_cast<PbcType>(get_eeenum(&inp, "pbc", pbcTypesNamesChar.data(), wi));
1966 ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi) != 0;
1967 printStringNoNewline(&inp,
1968 "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1969 printStringNoNewline(&inp, "a value of -1 means: use rlist");
1970 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
1971 printStringNoNewline(&inp, "nblist cut-off");
1972 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
1973 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
1975 /* Electrostatics */
1976 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
1977 printStringNoNewline(&inp, "Method for doing electrostatics");
1978 ir->coulombtype = get_eeenum(&inp, "coulombtype", eel_names, wi);
1979 ir->coulomb_modifier = get_eeenum(&inp, "coulomb-modifier", eintmod_names, wi);
1980 printStringNoNewline(&inp, "cut-off lengths");
1981 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
1982 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
1983 printStringNoNewline(&inp,
1984 "Relative dielectric constant for the medium and the reaction field");
1985 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
1986 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
1987 printStringNoNewline(&inp, "Method for doing Van der Waals");
1988 ir->vdwtype = get_eeenum(&inp, "vdw-type", evdw_names, wi);
1989 ir->vdw_modifier = get_eeenum(&inp, "vdw-modifier", eintmod_names, wi);
1990 printStringNoNewline(&inp, "cut-off lengths");
1991 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
1992 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
1993 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
1994 ir->eDispCorr = get_eeenum(&inp, "DispCorr", edispc_names, wi);
1995 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
1996 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
1997 printStringNoNewline(&inp, "Separate tables between energy group pairs");
1998 setStringEntry(&inp, "energygrp-table", is->egptable, nullptr);
1999 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
2000 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
2001 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
2002 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
2003 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
2004 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
2005 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
2006 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
2007 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
2008 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
2009 ir->ljpme_combination_rule = get_eeenum(&inp, "lj-pme-comb-rule", eljpme_names, wi);
2010 ir->ewald_geometry = get_eeenum(&inp, "ewald-geometry", eewg_names, wi);
2011 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
2013 /* Implicit solvation is no longer supported, but we need grompp
2014 to be able to refuse old .mdp files that would have built a tpr
2015 to run it. Thus, only "no" is accepted. */
2016 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
2018 /* Coupling stuff */
2019 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
2020 printStringNoNewline(&inp, "Temperature coupling");
2021 ir->etc = get_eeenum(&inp, "tcoupl", etcoupl_names, wi);
2022 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
2023 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
2024 ir->bPrintNHChains = (get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi) != 0);
2025 printStringNoNewline(&inp, "Groups to couple separately");
2026 setStringEntry(&inp, "tc-grps", is->tcgrps, nullptr);
2027 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
2028 setStringEntry(&inp, "tau-t", is->tau_t, nullptr);
2029 setStringEntry(&inp, "ref-t", is->ref_t, nullptr);
2030 printStringNoNewline(&inp, "pressure coupling");
2031 ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
2032 ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
2033 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
2034 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
2035 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
2036 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
2037 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
2038 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
2039 ir->refcoord_scaling = get_eeenum(&inp, "refcoord-scaling", erefscaling_names, wi);
2042 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2043 ir->bQMMM = (get_eeenum(&inp, "QMMM", yesno_names, wi) != 0);
2044 printStringNoNewline(&inp, "Groups treated Quantum Mechanically");
2045 setStringEntry(&inp, "QMMM-grps", is->QMMM, nullptr);
2046 printStringNoNewline(&inp, "QM method");
2047 setStringEntry(&inp, "QMmethod", is->QMmethod, nullptr);
2048 printStringNoNewline(&inp, "QMMM scheme");
2049 ir->QMMMscheme = get_eeenum(&inp, "QMMMscheme", eQMMMscheme_names, wi);
2050 printStringNoNewline(&inp, "QM basisset");
2051 setStringEntry(&inp, "QMbasis", is->QMbasis, nullptr);
2052 printStringNoNewline(&inp, "QM charge");
2053 setStringEntry(&inp, "QMcharge", is->QMcharge, nullptr);
2054 printStringNoNewline(&inp, "QM multiplicity");
2055 setStringEntry(&inp, "QMmult", is->QMmult, nullptr);
2056 printStringNoNewline(&inp, "Surface Hopping");
2057 setStringEntry(&inp, "SH", is->bSH, nullptr);
2058 printStringNoNewline(&inp, "CAS space options");
2059 setStringEntry(&inp, "CASorbitals", is->CASorbitals, nullptr);
2060 setStringEntry(&inp, "CASelectrons", is->CASelectrons, nullptr);
2061 setStringEntry(&inp, "SAon", is->SAon, nullptr);
2062 setStringEntry(&inp, "SAoff", is->SAoff, nullptr);
2063 setStringEntry(&inp, "SAsteps", is->SAsteps, nullptr);
2064 printStringNoNewline(&inp, "Scale factor for MM charges");
2065 ir->scalefactor = get_ereal(&inp, "MMChargeScaleFactor", 1.0, wi);
2067 /* Simulated annealing */
2068 printStringNewline(&inp, "SIMULATED ANNEALING");
2069 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2070 setStringEntry(&inp, "annealing", is->anneal, nullptr);
2071 printStringNoNewline(&inp,
2072 "Number of time points to use for specifying annealing in each group");
2073 setStringEntry(&inp, "annealing-npoints", is->anneal_npoints, nullptr);
2074 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2075 setStringEntry(&inp, "annealing-time", is->anneal_time, nullptr);
2076 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2077 setStringEntry(&inp, "annealing-temp", is->anneal_temp, nullptr);
2080 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2081 opts->bGenVel = (get_eeenum(&inp, "gen-vel", yesno_names, wi) != 0);
2082 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2083 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2086 printStringNewline(&inp, "OPTIONS FOR BONDS");
2087 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2088 printStringNoNewline(&inp, "Type of constraint algorithm");
2089 ir->eConstrAlg = get_eeenum(&inp, "constraint-algorithm", econstr_names, wi);
2090 printStringNoNewline(&inp, "Do not constrain the start configuration");
2091 ir->bContinuation = (get_eeenum(&inp, "continuation", yesno_names, wi) != 0);
2092 printStringNoNewline(&inp,
2093 "Use successive overrelaxation to reduce the number of shake iterations");
2094 ir->bShakeSOR = (get_eeenum(&inp, "Shake-SOR", yesno_names, wi) != 0);
2095 printStringNoNewline(&inp, "Relative tolerance of shake");
2096 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2097 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2098 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2099 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2100 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2101 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2102 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2103 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2104 printStringNoNewline(&inp, "rotates over more degrees than");
2105 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2106 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2107 opts->bMorse = (get_eeenum(&inp, "morse", yesno_names, wi) != 0);
2109 /* Energy group exclusions */
2110 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2111 printStringNoNewline(
2112 &inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2113 setStringEntry(&inp, "energygrp-excl", is->egpexcl, nullptr);
2116 printStringNewline(&inp, "WALLS");
2117 printStringNoNewline(
2118 &inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2119 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2120 ir->wall_type = get_eeenum(&inp, "wall-type", ewt_names, wi);
2121 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2122 setStringEntry(&inp, "wall-atomtype", is->wall_atomtype, nullptr);
2123 setStringEntry(&inp, "wall-density", is->wall_density, nullptr);
2124 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2127 printStringNewline(&inp, "COM PULLING");
2128 ir->bPull = (get_eeenum(&inp, "pull", yesno_names, wi) != 0);
2132 is->pull_grp = read_pullparams(&inp, ir->pull, wi);
2136 NOTE: needs COM pulling input */
2137 printStringNewline(&inp, "AWH biasing");
2138 ir->bDoAwh = (get_eeenum(&inp, "awh", yesno_names, wi) != 0);
2143 ir->awhParams = gmx::readAndCheckAwhParams(&inp, ir, wi);
2147 gmx_fatal(FARGS, "AWH biasing is only compatible with COM pulling turned on");
2151 /* Enforced rotation */
2152 printStringNewline(&inp, "ENFORCED ROTATION");
2153 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2154 ir->bRot = (get_eeenum(&inp, "rotation", yesno_names, wi) != 0);
2158 is->rot_grp = read_rotparams(&inp, ir->rot, wi);
2161 /* Interactive MD */
2163 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2164 setStringEntry(&inp, "IMD-group", is->imd_grp, nullptr);
2165 if (is->imd_grp[0] != '\0')
2172 printStringNewline(&inp, "NMR refinement stuff");
2173 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2174 ir->eDisre = get_eeenum(&inp, "disre", edisre_names, wi);
2175 printStringNoNewline(
2176 &inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2177 ir->eDisreWeighting = get_eeenum(&inp, "disre-weighting", edisreweighting_names, wi);
2178 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2179 ir->bDisreMixed = (get_eeenum(&inp, "disre-mixed", yesno_names, wi) != 0);
2180 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2181 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2182 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2183 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2184 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2185 opts->bOrire = (get_eeenum(&inp, "orire", yesno_names, wi) != 0);
2186 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2187 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2188 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2189 setStringEntry(&inp, "orire-fitgrp", is->orirefitgrp, nullptr);
2190 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2191 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2193 /* free energy variables */
2194 printStringNewline(&inp, "Free energy variables");
2195 ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
2196 setStringEntry(&inp, "couple-moltype", is->couple_moltype, nullptr);
2197 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2198 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2199 opts->bCoupleIntra = (get_eeenum(&inp, "couple-intramol", yesno_names, wi) != 0);
2201 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2203 it was not entered */
2204 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2205 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2206 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2207 setStringEntry(&inp, "fep-lambdas", is->fep_lambda[efptFEP], nullptr);
2208 setStringEntry(&inp, "mass-lambdas", is->fep_lambda[efptMASS], nullptr);
2209 setStringEntry(&inp, "coul-lambdas", is->fep_lambda[efptCOUL], nullptr);
2210 setStringEntry(&inp, "vdw-lambdas", is->fep_lambda[efptVDW], nullptr);
2211 setStringEntry(&inp, "bonded-lambdas", is->fep_lambda[efptBONDED], nullptr);
2212 setStringEntry(&inp, "restraint-lambdas", is->fep_lambda[efptRESTRAINT], nullptr);
2213 setStringEntry(&inp, "temperature-lambdas", is->fep_lambda[efptTEMPERATURE], nullptr);
2214 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2215 setStringEntry(&inp, "init-lambda-weights", is->lambda_weights, nullptr);
2216 fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
2217 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2218 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2219 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2220 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2221 fep->bScCoul = (get_eeenum(&inp, "sc-coul", yesno_names, wi) != 0);
2222 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2223 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2224 fep->separate_dhdl_file = get_eeenum(&inp, "separate-dhdl-file", separate_dhdl_file_names, wi);
2225 fep->dhdl_derivatives = get_eeenum(&inp, "dhdl-derivatives", dhdl_derivatives_names, wi);
2226 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2227 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2229 /* Non-equilibrium MD stuff */
2230 printStringNewline(&inp, "Non-equilibrium MD stuff");
2231 setStringEntry(&inp, "acc-grps", is->accgrps, nullptr);
2232 setStringEntry(&inp, "accelerate", is->acc, nullptr);
2233 setStringEntry(&inp, "freezegrps", is->freeze, nullptr);
2234 setStringEntry(&inp, "freezedim", is->frdim, nullptr);
2235 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2236 setStringEntry(&inp, "deform", is->deform, nullptr);
2238 /* simulated tempering variables */
2239 printStringNewline(&inp, "simulated tempering variables");
2240 ir->bSimTemp = (get_eeenum(&inp, "simulated-tempering", yesno_names, wi) != 0);
2241 ir->simtempvals->eSimTempScale = get_eeenum(&inp, "simulated-tempering-scaling", esimtemp_names, wi);
2242 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2243 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2245 /* expanded ensemble variables */
2246 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2248 read_expandedparams(&inp, expand, wi);
2251 /* Electric fields */
2253 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2254 gmx::KeyValueTreeTransformer transform;
2255 transform.rules()->addRule().keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2256 mdModules->initMdpTransform(transform.rules());
2257 for (const auto& path : transform.mappedPaths())
2259 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2260 mark_einp_set(inp, path[0].c_str());
2262 MdpErrorHandler errorHandler(wi);
2263 auto result = transform.transform(convertedValues, &errorHandler);
2264 ir->params = new gmx::KeyValueTreeObject(result.object());
2265 mdModules->adjustInputrecBasedOnModules(ir);
2266 errorHandler.setBackMapping(result.backMapping());
2267 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2270 /* Ion/water position swapping ("computational electrophysiology") */
2271 printStringNewline(&inp,
2272 "Ion/water position swapping for computational electrophysiology setups");
2273 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2274 ir->eSwapCoords = get_eeenum(&inp, "swapcoords", eSwapTypes_names, wi);
2275 if (ir->eSwapCoords != eswapNO)
2282 printStringNoNewline(&inp, "Swap attempt frequency");
2283 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2284 printStringNoNewline(&inp, "Number of ion types to be controlled");
2285 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2288 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2290 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2291 snew(ir->swap->grp, ir->swap->ngrp);
2292 for (i = 0; i < ir->swap->ngrp; i++)
2294 snew(ir->swap->grp[i].molname, STRLEN);
2296 printStringNoNewline(&inp,
2297 "Two index groups that contain the compartment-partitioning atoms");
2298 setStringEntry(&inp, "split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2299 setStringEntry(&inp, "split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2300 printStringNoNewline(&inp,
2301 "Use center of mass of split groups (yes/no), otherwise center of "
2302 "geometry is used");
2303 ir->swap->massw_split[0] = (get_eeenum(&inp, "massw-split0", yesno_names, wi) != 0);
2304 ir->swap->massw_split[1] = (get_eeenum(&inp, "massw-split1", yesno_names, wi) != 0);
2306 printStringNoNewline(&inp, "Name of solvent molecules");
2307 setStringEntry(&inp, "solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2309 printStringNoNewline(&inp,
2310 "Split cylinder: radius, upper and lower extension (nm) (this will "
2311 "define the channels)");
2312 printStringNoNewline(&inp,
2313 "Note that the split cylinder settings do not have an influence on "
2314 "the swapping protocol,");
2315 printStringNoNewline(
2317 "however, if correctly defined, the permeation events are recorded per channel");
2318 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2319 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2320 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2321 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2322 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2323 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2325 printStringNoNewline(
2327 "Average the number of ions per compartment over these many swap attempt steps");
2328 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2330 printStringNoNewline(
2331 &inp, "Names of the ion types that can be exchanged with solvent molecules,");
2332 printStringNoNewline(
2333 &inp, "and the requested number of ions of this type in compartments A and B");
2334 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2335 for (i = 0; i < nIonTypes; i++)
2337 int ig = eSwapFixedGrpNR + i;
2339 sprintf(buf, "iontype%d-name", i);
2340 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2341 sprintf(buf, "iontype%d-in-A", i);
2342 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2343 sprintf(buf, "iontype%d-in-B", i);
2344 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2347 printStringNoNewline(
2349 "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2350 printStringNoNewline(
2352 "at maximum distance (= bulk concentration) to the split group layers. However,");
2353 printStringNoNewline(&inp,
2354 "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk "
2355 "layer from the middle at 0.0");
2356 printStringNoNewline(&inp,
2357 "towards one of the compartment-partitioning layers (at +/- 1.0).");
2358 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2359 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2360 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2361 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0))
2363 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2366 printStringNoNewline(
2367 &inp, "Start to swap ions if threshold difference to requested count is reached");
2368 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2371 /* AdResS is no longer supported, but we need grompp to be able to
2372 refuse to process old .mdp files that used it. */
2373 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2375 /* User defined thingies */
2376 printStringNewline(&inp, "User defined thingies");
2377 setStringEntry(&inp, "user1-grps", is->user1, nullptr);
2378 setStringEntry(&inp, "user2-grps", is->user2, nullptr);
2379 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2380 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2381 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2382 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2383 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2384 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2385 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2386 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2390 gmx::TextOutputFile stream(mdparout);
2391 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2393 // Transform module data into a flat key-value tree for output.
2394 gmx::KeyValueTreeBuilder builder;
2395 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2396 mdModules->buildMdpOutput(&builderObject);
2398 gmx::TextWriter writer(&stream);
2399 writeKeyValueTreeAsMdp(&writer, builder.build());
2404 /* Process options if necessary */
2405 for (m = 0; m < 2; m++)
2407 for (i = 0; i < 2 * DIM; i++)
2416 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2420 "Pressure coupling incorrect number of values (I need exactly 1)");
2422 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2424 case epctSEMIISOTROPIC:
2425 case epctSURFACETENSION:
2426 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2430 "Pressure coupling incorrect number of values (I need exactly 2)");
2432 dumdub[m][YY] = dumdub[m][XX];
2434 case epctANISOTROPIC:
2435 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf", &(dumdub[m][XX]), &(dumdub[m][YY]),
2436 &(dumdub[m][ZZ]), &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5]))
2441 "Pressure coupling incorrect number of values (I need exactly 6)");
2445 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2446 epcoupltype_names[ir->epct]);
2450 clear_mat(ir->ref_p);
2451 clear_mat(ir->compress);
2452 for (i = 0; i < DIM; i++)
2454 ir->ref_p[i][i] = dumdub[1][i];
2455 ir->compress[i][i] = dumdub[0][i];
2457 if (ir->epct == epctANISOTROPIC)
2459 ir->ref_p[XX][YY] = dumdub[1][3];
2460 ir->ref_p[XX][ZZ] = dumdub[1][4];
2461 ir->ref_p[YY][ZZ] = dumdub[1][5];
2462 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2465 "All off-diagonal reference pressures are non-zero. Are you sure you want to "
2466 "apply a threefold shear stress?\n");
2468 ir->compress[XX][YY] = dumdub[0][3];
2469 ir->compress[XX][ZZ] = dumdub[0][4];
2470 ir->compress[YY][ZZ] = dumdub[0][5];
2471 for (i = 0; i < DIM; i++)
2473 for (m = 0; m < i; m++)
2475 ir->ref_p[i][m] = ir->ref_p[m][i];
2476 ir->compress[i][m] = ir->compress[m][i];
2481 if (ir->comm_mode == ecmNO)
2486 opts->couple_moltype = nullptr;
2487 if (strlen(is->couple_moltype) > 0)
2489 if (ir->efep != efepNO)
2491 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2492 if (opts->couple_lam0 == opts->couple_lam1)
2494 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2496 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
2500 "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
2507 "Free energy is turned off, so we will not decouple the molecule listed "
2511 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2512 if (ir->efep != efepNO)
2514 if (fep->delta_lambda > 0)
2516 ir->efep = efepSLOWGROWTH;
2520 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2522 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2524 "Old option for dhdl-print-energy given: "
2525 "changing \"yes\" to \"total\"\n");
2528 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2530 /* always print out the energy to dhdl if we are doing
2531 expanded ensemble, since we need the total energy for
2532 analysis if the temperature is changing. In some
2533 conditions one may only want the potential energy, so
2534 we will allow that if the appropriate mdp setting has
2535 been enabled. Otherwise, total it is:
2537 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2540 if ((ir->efep != efepNO) || ir->bSimTemp)
2542 ir->bExpanded = FALSE;
2543 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2545 ir->bExpanded = TRUE;
2547 do_fep_params(ir, is->fep_lambda, is->lambda_weights, wi);
2548 if (ir->bSimTemp) /* done after fep params */
2550 do_simtemp_params(ir);
2553 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2554 * setup and not on the old way of specifying the free-energy setup,
2555 * we should check for using soft-core when not needed, since that
2556 * can complicate the sampling significantly.
2557 * Note that we only check for the automated coupling setup.
2558 * If the (advanced) user does FEP through manual topology changes,
2559 * this check will not be triggered.
2561 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 && ir->fepvals->sc_alpha != 0
2562 && (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
2565 "You are using soft-core interactions while the Van der Waals interactions are "
2566 "not decoupled (note that the sc-coul option is only active when using lambda "
2567 "states). Although this will not lead to errors, you will need much more "
2568 "sampling than without soft-core interactions. Consider using sc-alpha=0.");
2573 ir->fepvals->n_lambda = 0;
2576 /* WALL PARAMETERS */
2578 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts, wi);
2580 /* ORIENTATION RESTRAINT PARAMETERS */
2582 if (opts->bOrire && gmx::splitString(is->orirefitgrp).size() != 1)
2584 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2587 /* DEFORMATION PARAMETERS */
2589 clear_mat(ir->deform);
2590 for (i = 0; i < 6; i++)
2595 double gmx_unused canary;
2596 int ndeform = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf %lf", &(dumdub[0][0]), &(dumdub[0][1]),
2597 &(dumdub[0][2]), &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]), &canary);
2599 if (strlen(is->deform) > 0 && ndeform != 6)
2602 wi, gmx::formatString(
2603 "Cannot parse exactly 6 box deformation velocities from string '%s'", is->deform)
2606 for (i = 0; i < 3; i++)
2608 ir->deform[i][i] = dumdub[0][i];
2610 ir->deform[YY][XX] = dumdub[0][3];
2611 ir->deform[ZZ][XX] = dumdub[0][4];
2612 ir->deform[ZZ][YY] = dumdub[0][5];
2613 if (ir->epc != epcNO)
2615 for (i = 0; i < 3; i++)
2617 for (j = 0; j <= i; j++)
2619 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2621 warning_error(wi, "A box element has deform set and compressibility > 0");
2625 for (i = 0; i < 3; i++)
2627 for (j = 0; j < i; j++)
2629 if (ir->deform[i][j] != 0)
2631 for (m = j; m < DIM; m++)
2633 if (ir->compress[m][j] != 0)
2636 "An off-diagonal box element has deform set while "
2637 "compressibility > 0 for the same component of another box "
2638 "vector, this might lead to spurious periodicity effects.");
2639 warning(wi, warn_buf);
2647 /* Ion/water position swapping checks */
2648 if (ir->eSwapCoords != eswapNO)
2650 if (ir->swap->nstswap < 1)
2652 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2654 if (ir->swap->nAverage < 1)
2656 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2658 if (ir->swap->threshold < 1.0)
2660 warning_error(wi, "Ion count threshold must be at least 1.\n");
2668 static int search_QMstring(const char* s, int ng, const char* gn[])
2670 /* same as normal search_string, but this one searches QM strings */
2673 for (i = 0; (i < ng); i++)
2675 if (gmx_strcasecmp(s, gn[i]) == 0)
2681 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2682 } /* search_QMstring */
2684 /* We would like gn to be const as well, but C doesn't allow this */
2685 /* TODO this is utility functionality (search for the index of a
2686 string in a collection), so should be refactored and located more
2688 int search_string(const char* s, int ng, char* gn[])
2692 for (i = 0; (i < ng); i++)
2694 if (gmx_strcasecmp(s, gn[i]) == 0)
2701 "Group %s referenced in the .mdp file was not found in the index file.\n"
2702 "Group names must match either [moleculetype] names or custom index group\n"
2703 "names, in which case you must supply an index file to the '-n' option\n"
2708 static bool do_numbering(int natoms,
2709 SimulationGroups* groups,
2710 gmx::ArrayRef<std::string> groupsFromMdpFile,
2713 SimulationAtomGroupType gtype,
2719 unsigned short* cbuf;
2720 AtomGroupIndices* grps = &(groups->groups[gtype]);
2721 int j, gid, aj, ognr, ntot = 0;
2724 char warn_buf[STRLEN];
2726 title = shortName(gtype);
2729 /* Mark all id's as not set */
2730 for (int i = 0; (i < natoms); i++)
2735 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2737 /* Lookup the group name in the block structure */
2738 gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2739 if ((grptp != egrptpONE) || (i == 0))
2741 grps->emplace_back(gid);
2744 /* Now go over the atoms in the group */
2745 for (j = block->index[gid]; (j < block->index[gid + 1]); j++)
2750 /* Range checking */
2751 if ((aj < 0) || (aj >= natoms))
2753 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2755 /* Lookup up the old group number */
2759 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title,
2764 /* Store the group number in buffer */
2765 if (grptp == egrptpONE)
2778 /* Now check whether we have done all atoms */
2782 if (grptp == egrptpALL)
2784 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2786 else if (grptp == egrptpPART)
2788 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2789 warning_note(wi, warn_buf);
2791 /* Assign all atoms currently unassigned to a rest group */
2792 for (j = 0; (j < natoms); j++)
2794 if (cbuf[j] == NOGID)
2796 cbuf[j] = grps->size();
2800 if (grptp != egrptpPART)
2804 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title,
2807 /* Add group name "rest" */
2808 grps->emplace_back(restnm);
2810 /* Assign the rest name to all atoms not currently assigned to a group */
2811 for (j = 0; (j < natoms); j++)
2813 if (cbuf[j] == NOGID)
2815 // group size was not updated before this here, so need to use -1.
2816 cbuf[j] = grps->size() - 1;
2822 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2824 /* All atoms are part of one (or no) group, no index required */
2825 groups->groupNumbers[gtype].clear();
2829 for (int j = 0; (j < natoms); j++)
2831 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2837 return (bRest && grptp == egrptpPART);
2840 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
2843 pull_params_t* pull;
2844 int natoms, imin, jmin;
2845 int * nrdf2, *na_vcm, na_tot;
2846 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2851 * First calc 3xnr-atoms for each group
2852 * then subtract half a degree of freedom for each constraint
2854 * Only atoms and nuclei contribute to the degrees of freedom...
2859 const SimulationGroups& groups = mtop->groups;
2860 natoms = mtop->natoms;
2862 /* Allocate one more for a possible rest group */
2863 /* We need to sum degrees of freedom into doubles,
2864 * since floats give too low nrdf's above 3 million atoms.
2866 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
2867 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2868 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2869 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2870 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2872 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
2876 for (gmx::index i = 0;
2877 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; i++)
2880 clear_ivec(dof_vcm[i]);
2882 nrdf_vcm_sub[i] = 0;
2884 snew(nrdf2, natoms);
2885 for (const AtomProxy atomP : AtomRange(*mtop))
2887 const t_atom& local = atomP.atom();
2888 int i = atomP.globalAtomNumber();
2890 if (local.ptype == eptAtom || local.ptype == eptNucleus)
2892 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
2893 for (int d = 0; d < DIM; d++)
2895 if (opts->nFreeze[g][d] == 0)
2897 /* Add one DOF for particle i (counted as 2*1) */
2899 /* VCM group i has dim d as a DOF */
2900 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
2904 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
2906 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
2912 for (const gmx_molblock_t& molb : mtop->molblock)
2914 const gmx_moltype_t& molt = mtop->moltype[molb.type];
2915 const t_atom* atom = molt.atoms.atom;
2916 for (int mol = 0; mol < molb.nmol; mol++)
2918 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2920 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
2921 for (int i = 0; i < molt.ilist[ftype].size();)
2923 /* Subtract degrees of freedom for the constraints,
2924 * if the particles still have degrees of freedom left.
2925 * If one of the particles is a vsite or a shell, then all
2926 * constraint motion will go there, but since they do not
2927 * contribute to the constraints the degrees of freedom do not
2930 int ai = as + ia[i + 1];
2931 int aj = as + ia[i + 2];
2932 if (((atom[ia[i + 1]].ptype == eptNucleus) || (atom[ia[i + 1]].ptype == eptAtom))
2933 && ((atom[ia[i + 2]].ptype == eptNucleus) || (atom[ia[i + 2]].ptype == eptAtom)))
2951 imin = std::min(imin, nrdf2[ai]);
2952 jmin = std::min(jmin, nrdf2[aj]);
2955 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2957 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
2959 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2961 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
2964 i += interaction_function[ftype].nratoms + 1;
2967 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
2968 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
2970 /* Subtract 1 dof from every atom in the SETTLE */
2971 for (int j = 0; j < 3; j++)
2973 int ai = as + ia[i + 1 + j];
2974 imin = std::min(2, nrdf2[ai]);
2976 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2978 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2983 as += molt.atoms.nr;
2989 /* Correct nrdf for the COM constraints.
2990 * We correct using the TC and VCM group of the first atom
2991 * in the reference and pull group. If atoms in one pull group
2992 * belong to different TC or VCM groups it is anyhow difficult
2993 * to determine the optimal nrdf assignment.
2997 for (int i = 0; i < pull->ncoord; i++)
2999 if (pull->coord[i].eType != epullCONSTRAINT)
3006 for (int j = 0; j < 2; j++)
3008 const t_pull_group* pgrp;
3010 pgrp = &pull->group[pull->coord[i].group[j]];
3014 /* Subtract 1/2 dof from each group */
3015 int ai = pgrp->ind[0];
3016 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3018 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3020 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
3023 "Center of mass pulling constraints caused the number of degrees "
3024 "of freedom for temperature coupling group %s to be negative",
3025 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
3026 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
3031 /* We need to subtract the whole DOF from group j=1 */
3038 if (ir->nstcomm != 0)
3042 /* We remove COM motion up to dim ndof_com() */
3043 ndim_rm_vcm = ndof_com(ir);
3045 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3046 * the number of degrees of freedom in each vcm group when COM
3047 * translation is removed and 6 when rotation is removed as well.
3049 for (gmx::index j = 0;
3050 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3052 switch (ir->comm_mode)
3055 case ecmLINEAR_ACCELERATION_CORRECTION:
3056 nrdf_vcm_sub[j] = 0;
3057 for (int d = 0; d < ndim_rm_vcm; d++)
3065 case ecmANGULAR: nrdf_vcm_sub[j] = 6; break;
3066 default: gmx_incons("Checking comm_mode");
3070 for (gmx::index i = 0;
3071 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
3073 /* Count the number of atoms of TC group i for every VCM group */
3074 for (gmx::index j = 0;
3075 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3080 for (int ai = 0; ai < natoms; ai++)
3082 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3084 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3088 /* Correct for VCM removal according to the fraction of each VCM
3089 * group present in this TC group.
3091 nrdf_uc = nrdf_tc[i];
3093 for (gmx::index j = 0;
3094 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3096 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3098 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3099 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3104 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3106 opts->nrdf[i] = nrdf_tc[i];
3107 if (opts->nrdf[i] < 0)
3111 fprintf(stderr, "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3112 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]], opts->nrdf[i]);
3120 sfree(nrdf_vcm_sub);
3123 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3125 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3126 * But since this is much larger than STRLEN, such a line can not be parsed.
3127 * The real maximum is the number of names that fit in a string: STRLEN/2.
3129 #define EGP_MAX (STRLEN / 2)
3133 auto names = gmx::splitString(val);
3134 if (names.size() % 2 != 0)
3136 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3138 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3140 for (size_t i = 0; i < names.size() / 2; i++)
3142 // TODO this needs to be replaced by a solution using std::find_if
3146 names[2 * i].c_str(),
3147 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3153 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3158 names[2 * i + 1].c_str(),
3159 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3165 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3167 if ((j < nr) && (k < nr))
3169 ir->opts.egp_flags[nr * j + k] |= flag;
3170 ir->opts.egp_flags[nr * k + j] |= flag;
3179 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3181 int ig = -1, i = 0, gind;
3185 /* Just a quick check here, more thorough checks are in mdrun */
3186 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3188 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3191 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3192 for (ig = 0; ig < swap->ngrp; ig++)
3194 swapg = &swap->grp[ig];
3195 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3196 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3200 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3201 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap", swap->grp[ig].molname, swapg->nat);
3202 snew(swapg->ind, swapg->nat);
3203 for (i = 0; i < swapg->nat; i++)
3205 swapg->ind[i] = grps->a[grps->index[gind] + i];
3210 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3216 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3221 ig = search_string(IMDgname, grps->nr, gnames);
3222 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3224 if (IMDgroup->nat > 0)
3227 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3229 IMDgname, IMDgroup->nat);
3230 snew(IMDgroup->ind, IMDgroup->nat);
3231 for (i = 0; i < IMDgroup->nat; i++)
3233 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3238 void do_index(const char* mdparin,
3242 const gmx::MdModulesNotifier& notifier,
3246 t_blocka* defaultIndexGroups;
3250 char warnbuf[STRLEN], **gnames;
3254 int i, j, k, restnm;
3255 bool bExcl, bTable, bAnneal, bRest;
3256 char warn_buf[STRLEN];
3260 fprintf(stderr, "processing index file...\n");
3264 snew(defaultIndexGroups, 1);
3265 snew(defaultIndexGroups->index, 1);
3267 atoms_all = gmx_mtop_global_atoms(mtop);
3268 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3269 done_atom(&atoms_all);
3273 defaultIndexGroups = init_index(ndx, &gnames);
3276 SimulationGroups* groups = &mtop->groups;
3277 natoms = mtop->natoms;
3278 symtab = &mtop->symtab;
3280 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3282 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3284 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3285 restnm = groups->groupNames.size() - 1;
3286 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3287 srenew(gnames, defaultIndexGroups->nr + 1);
3288 gnames[restnm] = *(groups->groupNames.back());
3290 set_warning_line(wi, mdparin, -1);
3292 auto temperatureCouplingTauValues = gmx::splitString(is->tau_t);
3293 auto temperatureCouplingReferenceValues = gmx::splitString(is->ref_t);
3294 auto temperatureCouplingGroupNames = gmx::splitString(is->tcgrps);
3295 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3296 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3299 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3301 temperatureCouplingGroupNames.size(), temperatureCouplingReferenceValues.size(),
3302 temperatureCouplingTauValues.size());
3305 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3306 do_numbering(natoms, groups, temperatureCouplingGroupNames, defaultIndexGroups, gnames,
3307 SimulationAtomGroupType::TemperatureCoupling, restnm,
3308 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3309 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3311 snew(ir->opts.nrdf, nr);
3312 snew(ir->opts.tau_t, nr);
3313 snew(ir->opts.ref_t, nr);
3314 if (ir->eI == eiBD && ir->bd_fric == 0)
3316 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3319 if (useReferenceTemperature)
3321 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3323 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3327 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3328 for (i = 0; (i < nr); i++)
3330 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3332 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3333 warning_error(wi, warn_buf);
3336 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3340 "tau-t = -1 is the value to signal that a group should not have "
3341 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3344 if (ir->opts.tau_t[i] >= 0)
3346 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3349 if (ir->etc != etcNO && ir->nsttcouple == -1)
3351 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3356 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3359 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3360 "md-vv; use either vrescale temperature with berendsen pressure or "
3361 "Nose-Hoover temperature with MTTK pressure");
3363 if (ir->epc == epcMTTK)
3365 if (ir->etc != etcNOSEHOOVER)
3368 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3373 if (ir->nstpcouple != ir->nsttcouple)
3375 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3376 ir->nstpcouple = ir->nsttcouple = mincouple;
3378 "for current Trotter decomposition methods with vv, nsttcouple and "
3379 "nstpcouple must be equal. Both have been reset to "
3380 "min(nsttcouple,nstpcouple) = %d",
3382 warning_note(wi, warn_buf);
3387 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3388 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3390 if (ETC_ANDERSEN(ir->etc))
3392 if (ir->nsttcouple != 1)
3396 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3397 "need for larger nsttcouple > 1, since no global parameters are computed. "
3398 "nsttcouple has been reset to 1");
3399 warning_note(wi, warn_buf);
3402 nstcmin = tcouple_min_integration_steps(ir->etc);
3405 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3408 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3409 "least %d times larger than nsttcouple*dt (%g)",
3410 ETCOUPLTYPE(ir->etc), tau_min, nstcmin, ir->nsttcouple * ir->delta_t);
3411 warning(wi, warn_buf);
3414 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3415 for (i = 0; (i < nr); i++)
3417 if (ir->opts.ref_t[i] < 0)
3419 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3422 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3423 if we are in this conditional) if mc_temp is negative */
3424 if (ir->expandedvals->mc_temp < 0)
3426 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3430 /* Simulated annealing for each group. There are nr groups */
3431 auto simulatedAnnealingGroupNames = gmx::splitString(is->anneal);
3432 if (simulatedAnnealingGroupNames.size() == 1
3433 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3435 simulatedAnnealingGroupNames.resize(0);
3437 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3439 gmx_fatal(FARGS, "Wrong number of annealing values: %zu (for %d groups)\n",
3440 simulatedAnnealingGroupNames.size(), nr);
3444 snew(ir->opts.annealing, nr);
3445 snew(ir->opts.anneal_npoints, nr);
3446 snew(ir->opts.anneal_time, nr);
3447 snew(ir->opts.anneal_temp, nr);
3448 for (i = 0; i < nr; i++)
3450 ir->opts.annealing[i] = eannNO;
3451 ir->opts.anneal_npoints[i] = 0;
3452 ir->opts.anneal_time[i] = nullptr;
3453 ir->opts.anneal_temp[i] = nullptr;
3455 if (!simulatedAnnealingGroupNames.empty())
3458 for (i = 0; i < nr; i++)
3460 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3462 ir->opts.annealing[i] = eannNO;
3464 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3466 ir->opts.annealing[i] = eannSINGLE;
3469 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3471 ir->opts.annealing[i] = eannPERIODIC;
3477 /* Read the other fields too */
3478 auto simulatedAnnealingPoints = gmx::splitString(is->anneal_npoints);
3479 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3481 gmx_fatal(FARGS, "Found %zu annealing-npoints values for %zu groups\n",
3482 simulatedAnnealingPoints.size(), simulatedAnnealingGroupNames.size());
3484 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3485 size_t numSimulatedAnnealingFields = 0;
3486 for (i = 0; i < nr; i++)
3488 if (ir->opts.anneal_npoints[i] == 1)
3492 "Please specify at least a start and an end point for annealing\n");
3494 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3495 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3496 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3499 auto simulatedAnnealingTimes = gmx::splitString(is->anneal_time);
3501 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3503 gmx_fatal(FARGS, "Found %zu annealing-time values, wanted %zu\n",
3504 simulatedAnnealingTimes.size(), numSimulatedAnnealingFields);
3506 auto simulatedAnnealingTemperatures = gmx::splitString(is->anneal_temp);
3507 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3509 gmx_fatal(FARGS, "Found %zu annealing-temp values, wanted %zu\n",
3510 simulatedAnnealingTemperatures.size(), numSimulatedAnnealingFields);
3513 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3514 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3515 convertReals(wi, simulatedAnnealingTimes, "anneal-time",
3516 allSimulatedAnnealingTimes.data());
3517 convertReals(wi, simulatedAnnealingTemperatures, "anneal-temp",
3518 allSimulatedAnnealingTemperatures.data());
3519 for (i = 0, k = 0; i < nr; i++)
3521 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3523 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3524 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3527 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3529 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3535 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3538 "Annealing timepoints out of order: t=%f comes after "
3540 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j - 1]);
3543 if (ir->opts.anneal_temp[i][j] < 0)
3545 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n",
3546 ir->opts.anneal_temp[i][j]);
3551 /* Print out some summary information, to make sure we got it right */
3552 for (i = 0; i < nr; i++)
3554 if (ir->opts.annealing[i] != eannNO)
3556 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3557 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3558 *(groups->groupNames[j]), eann_names[ir->opts.annealing[i]],
3559 ir->opts.anneal_npoints[i]);
3560 fprintf(stderr, "Time (ps) Temperature (K)\n");
3561 /* All terms except the last one */
3562 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3564 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3565 ir->opts.anneal_temp[i][j]);
3568 /* Finally the last one */
3569 j = ir->opts.anneal_npoints[i] - 1;
3570 if (ir->opts.annealing[i] == eannSINGLE)
3572 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j],
3573 ir->opts.anneal_temp[i][j]);
3577 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3578 ir->opts.anneal_temp[i][j]);
3579 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3582 "There is a temperature jump when your annealing "
3594 make_pull_groups(ir->pull, is->pull_grp, defaultIndexGroups, gnames);
3596 make_pull_coords(ir->pull);
3601 make_rotation_groups(ir->rot, is->rot_grp, defaultIndexGroups, gnames);
3604 if (ir->eSwapCoords != eswapNO)
3606 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3609 /* Make indices for IMD session */
3612 make_IMD_group(ir->imd, is->imd_grp, defaultIndexGroups, gnames);
3615 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3616 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3617 notifier.notifier_.notify(defaultIndexGroupsAndNames);
3619 auto accelerations = gmx::splitString(is->acc);
3620 auto accelerationGroupNames = gmx::splitString(is->accgrps);
3621 if (accelerationGroupNames.size() * DIM != accelerations.size())
3623 gmx_fatal(FARGS, "Invalid Acceleration input: %zu groups and %zu acc. values",
3624 accelerationGroupNames.size(), accelerations.size());
3626 do_numbering(natoms, groups, accelerationGroupNames, defaultIndexGroups, gnames,
3627 SimulationAtomGroupType::Acceleration, restnm, egrptpALL_GENREST, bVerbose, wi);
3628 nr = groups->groups[SimulationAtomGroupType::Acceleration].size();
3629 snew(ir->opts.acc, nr);
3630 ir->opts.ngacc = nr;
3632 convertRvecs(wi, accelerations, "anneal-time", ir->opts.acc);
3634 auto freezeDims = gmx::splitString(is->frdim);
3635 auto freezeGroupNames = gmx::splitString(is->freeze);
3636 if (freezeDims.size() != DIM * freezeGroupNames.size())
3638 gmx_fatal(FARGS, "Invalid Freezing input: %zu groups and %zu freeze values",
3639 freezeGroupNames.size(), freezeDims.size());
3641 do_numbering(natoms, groups, freezeGroupNames, defaultIndexGroups, gnames,
3642 SimulationAtomGroupType::Freeze, restnm, egrptpALL_GENREST, bVerbose, wi);
3643 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3644 ir->opts.ngfrz = nr;
3645 snew(ir->opts.nFreeze, nr);
3646 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3648 for (j = 0; (j < DIM); j++, k++)
3650 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3651 if (!ir->opts.nFreeze[i][j])
3653 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3656 "Please use Y(ES) or N(O) for freezedim only "
3658 freezeDims[k].c_str());
3659 warning(wi, warn_buf);
3664 for (; (i < nr); i++)
3666 for (j = 0; (j < DIM); j++)
3668 ir->opts.nFreeze[i][j] = 0;
3672 auto energyGroupNames = gmx::splitString(is->energy);
3673 do_numbering(natoms, groups, energyGroupNames, defaultIndexGroups, gnames,
3674 SimulationAtomGroupType::EnergyOutput, restnm, egrptpALL_GENREST, bVerbose, wi);
3675 add_wall_energrps(groups, ir->nwall, symtab);
3676 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3677 auto vcmGroupNames = gmx::splitString(is->vcm);
3678 bRest = do_numbering(natoms, groups, vcmGroupNames, defaultIndexGroups, gnames,
3679 SimulationAtomGroupType::MassCenterVelocityRemoval, restnm,
3680 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3684 "Some atoms are not part of any center of mass motion removal group.\n"
3685 "This may lead to artifacts.\n"
3686 "In most cases one should use one group for the whole system.");
3689 /* Now we have filled the freeze struct, so we can calculate NRDF */
3690 calc_nrdf(mtop, ir, gnames);
3692 auto user1GroupNames = gmx::splitString(is->user1);
3693 do_numbering(natoms, groups, user1GroupNames, defaultIndexGroups, gnames,
3694 SimulationAtomGroupType::User1, restnm, egrptpALL_GENREST, bVerbose, wi);
3695 auto user2GroupNames = gmx::splitString(is->user2);
3696 do_numbering(natoms, groups, user2GroupNames, defaultIndexGroups, gnames,
3697 SimulationAtomGroupType::User2, restnm, egrptpALL_GENREST, bVerbose, wi);
3698 auto compressedXGroupNames = gmx::splitString(is->x_compressed_groups);
3699 do_numbering(natoms, groups, compressedXGroupNames, defaultIndexGroups, gnames,
3700 SimulationAtomGroupType::CompressedPositionOutput, restnm, egrptpONE, bVerbose, wi);
3701 auto orirefFitGroupNames = gmx::splitString(is->orirefitgrp);
3702 do_numbering(natoms, groups, orirefFitGroupNames, defaultIndexGroups, gnames,
3703 SimulationAtomGroupType::OrientationRestraintsFit, restnm, egrptpALL_GENREST,
3706 /* QMMM input processing */
3707 auto qmGroupNames = gmx::splitString(is->QMMM);
3708 auto qmMethods = gmx::splitString(is->QMmethod);
3709 auto qmBasisSets = gmx::splitString(is->QMbasis);
3710 if (ir->eI != eiMimic)
3712 if (qmMethods.size() != qmGroupNames.size() || qmBasisSets.size() != qmGroupNames.size())
3715 "Invalid QMMM input: %zu groups %zu basissets"
3716 " and %zu methods\n",
3717 qmGroupNames.size(), qmBasisSets.size(), qmMethods.size());
3719 /* group rest, if any, is always MM! */
3720 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3721 SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
3722 nr = qmGroupNames.size(); /*atoms->grps[egcQMMM].nr;*/
3723 ir->opts.ngQM = qmGroupNames.size();
3724 snew(ir->opts.QMmethod, nr);
3725 snew(ir->opts.QMbasis, nr);
3726 for (i = 0; i < nr; i++)
3728 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3729 * converted to the corresponding enum in names.c
3731 ir->opts.QMmethod[i] = search_QMstring(qmMethods[i].c_str(), eQMmethodNR, eQMmethod_names);
3732 ir->opts.QMbasis[i] = search_QMstring(qmBasisSets[i].c_str(), eQMbasisNR, eQMbasis_names);
3734 auto qmMultiplicities = gmx::splitString(is->QMmult);
3735 auto qmCharges = gmx::splitString(is->QMcharge);
3736 auto qmbSH = gmx::splitString(is->bSH);
3737 snew(ir->opts.QMmult, nr);
3738 snew(ir->opts.QMcharge, nr);
3739 snew(ir->opts.bSH, nr);
3740 convertInts(wi, qmMultiplicities, "QMmult", ir->opts.QMmult);
3741 convertInts(wi, qmCharges, "QMcharge", ir->opts.QMcharge);
3742 convertYesNos(wi, qmbSH, "bSH", ir->opts.bSH);
3744 auto CASelectrons = gmx::splitString(is->CASelectrons);
3745 auto CASorbitals = gmx::splitString(is->CASorbitals);
3746 snew(ir->opts.CASelectrons, nr);
3747 snew(ir->opts.CASorbitals, nr);
3748 convertInts(wi, CASelectrons, "CASelectrons", ir->opts.CASelectrons);
3749 convertInts(wi, CASorbitals, "CASOrbitals", ir->opts.CASorbitals);
3751 auto SAon = gmx::splitString(is->SAon);
3752 auto SAoff = gmx::splitString(is->SAoff);
3753 auto SAsteps = gmx::splitString(is->SAsteps);
3754 snew(ir->opts.SAon, nr);
3755 snew(ir->opts.SAoff, nr);
3756 snew(ir->opts.SAsteps, nr);
3757 convertInts(wi, SAon, "SAon", ir->opts.SAon);
3758 convertInts(wi, SAoff, "SAoff", ir->opts.SAoff);
3759 convertInts(wi, SAsteps, "SAsteps", ir->opts.SAsteps);
3764 if (qmGroupNames.size() > 1)
3766 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
3768 /* group rest, if any, is always MM! */
3769 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3770 SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
3772 ir->opts.ngQM = qmGroupNames.size();
3775 /* end of QMMM input */
3779 for (auto group : gmx::keysOf(groups->groups))
3781 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
3782 for (const auto& entry : groups->groups[group])
3784 fprintf(stderr, " %s", *(groups->groupNames[entry]));
3786 fprintf(stderr, "\n");
3790 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3791 snew(ir->opts.egp_flags, nr * nr);
3793 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3794 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3796 warning_error(wi, "Energy group exclusions are currently not supported");
3798 if (bExcl && EEL_FULL(ir->coulombtype))
3800 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3803 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3804 if (bTable && !(ir->vdwtype == evdwUSER) && !(ir->coulombtype == eelUSER)
3805 && !(ir->coulombtype == eelPMEUSER) && !(ir->coulombtype == eelPMEUSERSWITCH))
3808 "Can only have energy group pair tables in combination with user tables for VdW "
3812 /* final check before going out of scope if simulated tempering variables
3813 * need to be set to default values.
3815 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
3817 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
3818 warning(wi, gmx::formatString(
3819 "the value for nstexpanded was not specified for "
3820 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
3821 "by default, but it is recommended to set it to an explicit value!",
3822 ir->expandedvals->nstexpanded));
3824 for (i = 0; (i < defaultIndexGroups->nr); i++)
3829 done_blocka(defaultIndexGroups);
3830 sfree(defaultIndexGroups);
3834 static void check_disre(const gmx_mtop_t* mtop)
3836 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3838 const gmx_ffparams_t& ffparams = mtop->ffparams;
3841 for (int i = 0; i < ffparams.numTypes(); i++)
3843 int ftype = ffparams.functype[i];
3844 if (ftype == F_DISRES)
3846 int label = ffparams.iparams[i].disres.label;
3847 if (label == old_label)
3849 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3858 "Found %d double distance restraint indices,\n"
3859 "probably the parameters for multiple pairs in one restraint "
3860 "are not identical\n",
3866 static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t* sys, const bool posres_only, ivec AbsRef)
3869 gmx_mtop_ilistloop_t iloop;
3871 const t_iparams* pr;
3878 for (d = 0; d < DIM; d++)
3880 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3882 /* Check for freeze groups */
3883 for (g = 0; g < ir->opts.ngfrz; g++)
3885 for (d = 0; d < DIM; d++)
3887 if (ir->opts.nFreeze[g][d] != 0)
3895 /* Check for position restraints */
3896 iloop = gmx_mtop_ilistloop_init(sys);
3897 while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
3899 if (nmol > 0 && (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3901 for (i = 0; i < (*ilist)[F_POSRES].size(); i += 2)
3903 pr = &sys->ffparams.iparams[(*ilist)[F_POSRES].iatoms[i]];
3904 for (d = 0; d < DIM; d++)
3906 if (pr->posres.fcA[d] != 0)
3912 for (i = 0; i < (*ilist)[F_FBPOSRES].size(); i += 2)
3914 /* Check for flat-bottom posres */
3915 pr = &sys->ffparams.iparams[(*ilist)[F_FBPOSRES].iatoms[i]];
3916 if (pr->fbposres.k != 0)
3918 switch (pr->fbposres.geom)
3920 case efbposresSPHERE: AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1; break;
3921 case efbposresCYLINDERX: AbsRef[YY] = AbsRef[ZZ] = 1; break;
3922 case efbposresCYLINDERY: AbsRef[XX] = AbsRef[ZZ] = 1; break;
3923 case efbposresCYLINDER:
3924 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3925 case efbposresCYLINDERZ: AbsRef[XX] = AbsRef[YY] = 1; break;
3926 case efbposresX: /* d=XX */
3927 case efbposresY: /* d=YY */
3928 case efbposresZ: /* d=ZZ */
3929 d = pr->fbposres.geom - efbposresX;
3934 " Invalid geometry for flat-bottom position restraint.\n"
3935 "Expected nr between 1 and %d. Found %d\n",
3936 efbposresNR - 1, pr->fbposres.geom);
3943 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3946 static void check_combination_rule_differences(const gmx_mtop_t* mtop,
3948 bool* bC6ParametersWorkWithGeometricRules,
3949 bool* bC6ParametersWorkWithLBRules,
3950 bool* bLBRulesPossible)
3952 int ntypes, tpi, tpj;
3955 double c6i, c6j, c12i, c12j;
3956 double c6, c6_geometric, c6_LB;
3957 double sigmai, sigmaj, epsi, epsj;
3958 bool bCanDoLBRules, bCanDoGeometricRules;
3961 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3962 * force-field floating point parameters.
3965 ptr = getenv("GMX_LJCOMB_TOL");
3969 double gmx_unused canary;
3971 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
3974 "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
3979 *bC6ParametersWorkWithLBRules = TRUE;
3980 *bC6ParametersWorkWithGeometricRules = TRUE;
3981 bCanDoLBRules = TRUE;
3982 ntypes = mtop->ffparams.atnr;
3983 snew(typecount, ntypes);
3984 gmx_mtop_count_atomtypes(mtop, state, typecount);
3985 *bLBRulesPossible = TRUE;
3986 for (tpi = 0; tpi < ntypes; ++tpi)
3988 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3989 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3990 for (tpj = tpi; tpj < ntypes; ++tpj)
3992 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3993 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3994 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3995 c6_geometric = std::sqrt(c6i * c6j);
3996 if (!gmx_numzero(c6_geometric))
3998 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4000 sigmai = gmx::sixthroot(c12i / c6i);
4001 sigmaj = gmx::sixthroot(c12j / c6j);
4002 epsi = c6i * c6i / (4.0 * c12i);
4003 epsj = c6j * c6j / (4.0 * c12j);
4004 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4008 *bLBRulesPossible = FALSE;
4009 c6_LB = c6_geometric;
4011 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4016 *bC6ParametersWorkWithLBRules = FALSE;
4019 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4021 if (!bCanDoGeometricRules)
4023 *bC6ParametersWorkWithGeometricRules = FALSE;
4030 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t* mtop, warninp_t wi)
4032 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4034 check_combination_rule_differences(mtop, 0, &bC6ParametersWorkWithGeometricRules,
4035 &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4036 if (ir->ljpme_combination_rule == eljpmeLB)
4038 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4041 "You are using arithmetic-geometric combination rules "
4042 "in LJ-PME, but your non-bonded C6 parameters do not "
4043 "follow these rules.");
4048 if (!bC6ParametersWorkWithGeometricRules)
4050 if (ir->eDispCorr != edispcNO)
4053 "You are using geometric combination rules in "
4054 "LJ-PME, but your non-bonded C6 parameters do "
4055 "not follow these rules. "
4056 "This will introduce very small errors in the forces and energies in "
4057 "your simulations. Dispersion correction will correct total energy "
4058 "and/or pressure for isotropic systems, but not forces or surface "
4064 "You are using geometric combination rules in "
4065 "LJ-PME, but your non-bonded C6 parameters do "
4066 "not follow these rules. "
4067 "This will introduce very small errors in the forces and energies in "
4068 "your simulations. If your system is homogeneous, consider using "
4069 "dispersion correction "
4070 "for the total energy and pressure.");
4076 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4078 char err_buf[STRLEN];
4083 gmx_mtop_atomloop_block_t aloopb;
4085 char warn_buf[STRLEN];
4087 set_warning_line(wi, mdparin, -1);
4089 if (absolute_reference(ir, sys, false, AbsRef))
4092 "Removing center of mass motion in the presence of position restraints might "
4096 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 && ir->nstlist > 1
4097 && ((EI_MD(ir->eI) || EI_SD(ir->eI)) && (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4099 /* Check if a too small Verlet buffer might potentially
4100 * cause more drift than the thermostat can couple off.
4102 /* Temperature error fraction for warning and suggestion */
4103 const real T_error_warn = 0.002;
4104 const real T_error_suggest = 0.001;
4105 /* For safety: 2 DOF per atom (typical with constraints) */
4106 const real nrdf_at = 2;
4107 real T, tau, max_T_error;
4112 for (i = 0; i < ir->opts.ngtc; i++)
4114 T = std::max(T, ir->opts.ref_t[i]);
4115 tau = std::max(tau, ir->opts.tau_t[i]);
4119 /* This is a worst case estimate of the temperature error,
4120 * assuming perfect buffer estimation and no cancelation
4121 * of errors. The factor 0.5 is because energy distributes
4122 * equally over Ekin and Epot.
4124 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * BOLTZ * T);
4125 if (max_T_error > T_error_warn)
4128 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4129 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4130 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4131 "%.0e or decrease tau_t.",
4132 ir->verletbuf_tol, T, tau, 100 * max_T_error, 100 * T_error_suggest,
4133 ir->verletbuf_tol * T_error_suggest / max_T_error);
4134 warning(wi, warn_buf);
4139 if (ETC_ANDERSEN(ir->etc))
4143 for (i = 0; i < ir->opts.ngtc; i++)
4146 "all tau_t must currently be equal using Andersen temperature control, "
4147 "violated for group %d",
4149 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4151 "all tau_t must be positive using Andersen temperature control, "
4153 i, ir->opts.tau_t[i]);
4154 CHECK(ir->opts.tau_t[i] < 0);
4157 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4159 for (i = 0; i < ir->opts.ngtc; i++)
4161 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4163 "tau_t/delta_t for group %d for temperature control method %s must be a "
4164 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4165 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4167 i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
4168 CHECK(nsteps % ir->nstcomm != 0);
4173 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD && ir->comm_mode == ecmNO
4174 && !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) && !ETC_ANDERSEN(ir->etc))
4177 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4178 "rounding errors can lead to build up of kinetic energy of the center of mass");
4181 if (ir->epc == epcPARRINELLORAHMAN && ir->etc == etcNOSEHOOVER)
4184 for (int g = 0; g < ir->opts.ngtc; g++)
4186 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4188 if (ir->tau_p < 1.9 * tau_t_max)
4190 std::string message = gmx::formatString(
4191 "With %s T-coupling and %s p-coupling, "
4192 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4193 etcoupl_names[ir->etc], epcoupl_names[ir->epc], "tau-p", ir->tau_p, "tau-t",
4195 warning(wi, message.c_str());
4199 /* Check for pressure coupling with absolute position restraints */
4200 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4202 absolute_reference(ir, sys, TRUE, AbsRef);
4204 for (m = 0; m < DIM; m++)
4206 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4209 "You are using pressure coupling with absolute position restraints, "
4210 "this will give artifacts. Use the refcoord_scaling option.");
4218 aloopb = gmx_mtop_atomloop_block_init(sys);
4220 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4222 if (atom->q != 0 || atom->qB != 0)
4230 if (EEL_FULL(ir->coulombtype))
4233 "You are using full electrostatics treatment %s for a system without charges.\n"
4234 "This costs a lot of performance for just processing zeros, consider using %s "
4236 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4237 warning(wi, err_buf);
4242 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
4245 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4246 "You might want to consider using %s electrostatics.\n",
4248 warning_note(wi, err_buf);
4252 /* Check if combination rules used in LJ-PME are the same as in the force field */
4253 if (EVDW_PME(ir->vdwtype))
4255 check_combination_rules(ir, sys, wi);
4258 /* Generalized reaction field */
4259 if (ir->coulombtype == eelGRF_NOTUSED)
4262 "Generalized reaction-field electrostatics is no longer supported. "
4263 "You can use normal reaction-field instead and compute the reaction-field "
4264 "constant by hand.");
4268 for (int i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4270 for (m = 0; (m < DIM); m++)
4272 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4281 snew(mgrp, sys->groups.groups[SimulationAtomGroupType::Acceleration].size());
4282 for (const AtomProxy atomP : AtomRange(*sys))
4284 const t_atom& local = atomP.atom();
4285 int i = atomP.globalAtomNumber();
4286 mgrp[getGroupType(sys->groups, SimulationAtomGroupType::Acceleration, i)] += local.m;
4289 for (i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4291 for (m = 0; (m < DIM); m++)
4293 acc[m] += ir->opts.acc[i][m] * mgrp[i];
4297 for (m = 0; (m < DIM); m++)
4299 if (fabs(acc[m]) > 1e-6)
4301 const char* dim[DIM] = { "X", "Y", "Z" };
4302 fprintf(stderr, "Net Acceleration in %s direction, will %s be corrected\n", dim[m],
4303 ir->nstcomm != 0 ? "" : "not");
4304 if (ir->nstcomm != 0 && m < ndof_com(ir))
4308 (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4310 ir->opts.acc[i][m] -= acc[m];
4318 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0
4319 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4321 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4329 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4331 if (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0)
4333 absolute_reference(ir, sys, FALSE, AbsRef);
4334 for (m = 0; m < DIM; m++)
4336 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4339 "You are using an absolute reference for pulling, but the rest of "
4340 "the system does not have an absolute reference. This will lead to "
4349 for (i = 0; i < 3; i++)
4351 for (m = 0; m <= i; m++)
4353 if ((ir->epc != epcNO && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4355 for (c = 0; c < ir->pull->ncoord; c++)
4357 if (ir->pull->coord[c].eGeom == epullgDIRPBC && ir->pull->coord[c].vec[m] != 0)
4360 "Can not have dynamic box while using pull geometry '%s' "
4362 EPULLGEOM(ir->pull->coord[c].eGeom), 'x' + m);
4373 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4375 char warn_buf[STRLEN];
4378 ptr = check_box(ir->pbcType, box);
4381 warning_error(wi, ptr);
4384 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4386 if (ir->shake_tol <= 0.0)
4388 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4389 warning_error(wi, warn_buf);
4393 if ((ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4395 /* If we have Lincs constraints: */
4396 if (ir->eI == eiMD && ir->etc == etcNO && ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4399 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4400 warning_note(wi, warn_buf);
4403 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4406 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4408 warning_note(wi, warn_buf);
4410 if (ir->epc == epcMTTK)
4412 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4416 if (bHasAnyConstraints && ir->epc == epcMTTK)
4418 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4421 if (ir->LincsWarnAngle > 90.0)
4423 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4424 warning(wi, warn_buf);
4425 ir->LincsWarnAngle = 90.0;
4428 if (ir->pbcType != PbcType::No)
4430 if (ir->nstlist == 0)
4433 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4434 "atoms might cause the simulation to crash.");
4436 if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
4439 "ERROR: The cut-off length is longer than half the shortest box vector or "
4440 "longer than the smallest box diagonal element. Increase the box size or "
4441 "decrease rlist.\n");
4442 warning_error(wi, warn_buf);