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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/arrayref.h"
73 #include "gromacs/utility/cstringutil.h"
74 #include "gromacs/utility/exceptions.h"
75 #include "gromacs/utility/fatalerror.h"
76 #include "gromacs/utility/filestream.h"
77 #include "gromacs/utility/gmxassert.h"
78 #include "gromacs/utility/ikeyvaluetreeerror.h"
79 #include "gromacs/utility/keyvaluetree.h"
80 #include "gromacs/utility/keyvaluetreebuilder.h"
81 #include "gromacs/utility/keyvaluetreemdpwriter.h"
82 #include "gromacs/utility/keyvaluetreetransform.h"
83 #include "gromacs/utility/mdmodulenotification.h"
84 #include "gromacs/utility/smalloc.h"
85 #include "gromacs/utility/strconvert.h"
86 #include "gromacs/utility/stringcompare.h"
87 #include "gromacs/utility/stringutil.h"
88 #include "gromacs/utility/textwriter.h"
93 /* Resource parameters
94 * Do not change any of these until you read the instruction
95 * in readinp.h. Some cpp's do not take spaces after the backslash
96 * (like the c-shell), which will give you a very weird compiler
100 typedef struct t_inputrec_strings
102 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN], acc[STRLEN], accgrps[STRLEN], freeze[STRLEN],
103 frdim[STRLEN], energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN],
104 x_compressed_groups[STRLEN], couple_moltype[STRLEN], orirefitgrp[STRLEN],
105 egptable[STRLEN], egpexcl[STRLEN], wall_atomtype[STRLEN], wall_density[STRLEN],
106 deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
107 char fep_lambda[efptNR][STRLEN];
108 char lambda_weights[STRLEN];
111 char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
112 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN], bSH[STRLEN],
113 CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN], SAoff[STRLEN], SAsteps[STRLEN];
115 } gmx_inputrec_strings;
117 static gmx_inputrec_strings* is = nullptr;
119 void init_inputrec_strings()
124 "Attempted to call init_inputrec_strings before calling done_inputrec_strings. "
125 "Only one inputrec (i.e. .mdp file) can be parsed at a time.");
130 void done_inputrec_strings()
139 egrptpALL, /* All particles have to be a member of a group. */
140 egrptpALL_GENREST, /* A rest group with name is generated for particles *
141 * that are not part of any group. */
142 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
143 * for the rest group. */
144 egrptpONE /* Merge all selected groups into one group, *
145 * make a rest group for the remaining particles. */
148 static const char* constraints[eshNR + 1] = { "none", "h-bonds", "all-bonds",
149 "h-angles", "all-angles", nullptr };
151 static const char* couple_lam[ecouplamNR + 1] = { "vdw-q", "vdw", "q", "none", nullptr };
153 static void GetSimTemps(int ntemps, t_simtemp* simtemp, double* temperature_lambdas)
158 for (i = 0; i < ntemps; i++)
160 /* simple linear scaling -- allows more control */
161 if (simtemp->eSimTempScale == esimtempLINEAR)
163 simtemp->temperatures[i] =
165 + (simtemp->simtemp_high - simtemp->simtemp_low) * temperature_lambdas[i];
167 else if (simtemp->eSimTempScale
168 == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
170 simtemp->temperatures[i] = simtemp->simtemp_low
171 * std::pow(simtemp->simtemp_high / simtemp->simtemp_low,
172 static_cast<real>((1.0 * i) / (ntemps - 1)));
174 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
176 simtemp->temperatures[i] = simtemp->simtemp_low
177 + (simtemp->simtemp_high - simtemp->simtemp_low)
178 * (std::expm1(temperature_lambdas[i]) / std::expm1(1.0));
183 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
184 gmx_fatal(FARGS, "%s", errorstr);
190 static void _low_check(bool b, const char* s, warninp_t wi)
194 warning_error(wi, s);
198 static void check_nst(const char* desc_nst, int nst, const char* desc_p, int* p, warninp_t wi)
202 if (*p > 0 && *p % nst != 0)
204 /* Round up to the next multiple of nst */
205 *p = ((*p) / nst + 1) * nst;
206 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n", desc_p, desc_nst, desc_p, *p);
211 static int lcd(int n1, int n2)
216 for (i = 2; (i <= n1 && i <= n2); i++)
218 if (n1 % i == 0 && n2 % i == 0)
227 //! Convert legacy mdp entries to modern ones.
228 static void process_interaction_modifier(int* eintmod)
230 if (*eintmod == eintmodPOTSHIFT_VERLET_UNSUPPORTED)
232 *eintmod = eintmodPOTSHIFT;
236 void check_ir(const char* mdparin,
237 const gmx::MdModulesNotifier& mdModulesNotifier,
241 /* Check internal consistency.
242 * NOTE: index groups are not set here yet, don't check things
243 * like temperature coupling group options here, but in triple_check
246 /* Strange macro: first one fills the err_buf, and then one can check
247 * the condition, which will print the message and increase the error
250 #define CHECK(b) _low_check(b, err_buf, wi)
251 char err_buf[256], warn_buf[STRLEN];
254 t_lambda* fep = ir->fepvals;
255 t_expanded* expand = ir->expandedvals;
257 set_warning_line(wi, mdparin, -1);
259 if (ir->coulombtype == eelRF_NEC_UNSUPPORTED)
261 sprintf(warn_buf, "%s electrostatics is no longer supported", eel_names[eelRF_NEC_UNSUPPORTED]);
262 warning_error(wi, warn_buf);
265 /* BASIC CUT-OFF STUFF */
266 if (ir->rcoulomb < 0)
268 warning_error(wi, "rcoulomb should be >= 0");
272 warning_error(wi, "rvdw should be >= 0");
274 if (ir->rlist < 0 && !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
276 warning_error(wi, "rlist should be >= 0");
279 "nstlist can not be smaller than 0. (If you were trying to use the heuristic "
280 "neighbour-list update scheme for efficient buffering for improved energy "
281 "conservation, please use the Verlet cut-off scheme instead.)");
282 CHECK(ir->nstlist < 0);
284 process_interaction_modifier(&ir->coulomb_modifier);
285 process_interaction_modifier(&ir->vdw_modifier);
287 if (ir->cutoff_scheme == ecutsGROUP)
290 "The group cutoff scheme has been removed since GROMACS 2020. "
291 "Please use the Verlet cutoff scheme.");
293 if (ir->cutoff_scheme == ecutsVERLET)
297 /* Normal Verlet type neighbor-list, currently only limited feature support */
298 if (inputrec2nboundeddim(ir) < 3)
300 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
303 // We don't (yet) have general Verlet kernels for rcoulomb!=rvdw
304 if (ir->rcoulomb != ir->rvdw)
306 // Since we have PME coulomb + LJ cut-off kernels with rcoulomb>rvdw
307 // for PME load balancing, we can support this exception.
308 bool bUsesPmeTwinRangeKernel = (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == evdwCUT
309 && ir->rcoulomb > ir->rvdw);
310 if (!bUsesPmeTwinRangeKernel)
313 "With Verlet lists rcoulomb!=rvdw is not supported (except for "
314 "rcoulomb>rvdw with PME electrostatics)");
318 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
320 if (ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT)
322 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
325 "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and "
327 evdw_names[ir->vdwtype], evdw_names[evdwCUT], eintmod_names[ir->vdw_modifier]);
328 warning_note(wi, warn_buf);
330 ir->vdwtype = evdwCUT;
334 sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s",
335 evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
336 warning_error(wi, warn_buf);
340 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
343 "With Verlet lists only cut-off and PME LJ interactions are supported");
345 if (!(ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype) || EEL_PME(ir->coulombtype)
346 || ir->coulombtype == eelEWALD))
349 "With Verlet lists only cut-off, reaction-field, PME and Ewald "
350 "electrostatics are supported");
352 if (!(ir->coulomb_modifier == eintmodNONE || ir->coulomb_modifier == eintmodPOTSHIFT))
354 sprintf(warn_buf, "coulomb_modifier=%s is not supported", eintmod_names[ir->coulomb_modifier]);
355 warning_error(wi, warn_buf);
358 if (EEL_USER(ir->coulombtype))
360 sprintf(warn_buf, "Coulomb type %s is not supported with the verlet scheme",
361 eel_names[ir->coulombtype]);
362 warning_error(wi, warn_buf);
365 if (ir->nstlist <= 0)
367 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
370 if (ir->nstlist < 10)
373 "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note "
374 "that with the Verlet scheme, nstlist has no effect on the accuracy of "
378 rc_max = std::max(ir->rvdw, ir->rcoulomb);
382 /* With TPI we set the pairlist cut-off later using the radius of the insterted molecule */
383 ir->verletbuf_tol = 0;
386 else if (ir->verletbuf_tol <= 0)
388 if (ir->verletbuf_tol == 0)
390 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
393 if (ir->rlist < rc_max)
396 "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
399 if (ir->rlist == rc_max && ir->nstlist > 1)
403 "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet "
404 "buffer. The cluster pair list does have a buffering effect, but choosing "
405 "a larger rlist might be necessary for good energy conservation.");
410 if (ir->rlist > rc_max)
413 "You have set rlist larger than the interaction cut-off, but you also "
414 "have verlet-buffer-tolerance > 0. Will set rlist using "
415 "verlet-buffer-tolerance.");
418 if (ir->nstlist == 1)
420 /* No buffer required */
425 if (EI_DYNAMICS(ir->eI))
427 if (inputrec2nboundeddim(ir) < 3)
430 "The box volume is required for calculating rlist from the "
431 "energy drift with verlet-buffer-tolerance > 0. You are "
432 "using at least one unbounded dimension, so no volume can be "
433 "computed. Either use a finite box, or set rlist yourself "
434 "together with verlet-buffer-tolerance = -1.");
436 /* Set rlist temporarily so we can continue processing */
441 /* Set the buffer to 5% of the cut-off */
442 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics) * rc_max;
448 /* GENERAL INTEGRATOR STUFF */
451 if (ir->etc != etcNO)
453 if (EI_RANDOM(ir->eI))
456 "Setting tcoupl from '%s' to 'no'. %s handles temperature coupling "
457 "implicitly. See the documentation for more information on which "
458 "parameters affect temperature for %s.",
459 etcoupl_names[ir->etc], ei_names[ir->eI], ei_names[ir->eI]);
464 "Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to "
466 etcoupl_names[ir->etc], ei_names[ir->eI]);
468 warning_note(wi, warn_buf);
472 if (ir->eI == eiVVAK)
475 "Integrator method %s is implemented primarily for validation purposes; for "
476 "molecular dynamics, you should probably be using %s or %s",
477 ei_names[eiVVAK], ei_names[eiMD], ei_names[eiVV]);
478 warning_note(wi, warn_buf);
480 if (!EI_DYNAMICS(ir->eI))
482 if (ir->epc != epcNO)
485 "Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.",
486 epcoupl_names[ir->epc], ei_names[ir->eI]);
487 warning_note(wi, warn_buf);
491 if (EI_DYNAMICS(ir->eI))
493 if (ir->nstcalcenergy < 0)
495 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
496 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
498 /* nstcalcenergy larger than nstener does not make sense.
499 * We ideally want nstcalcenergy=nstener.
503 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
507 ir->nstcalcenergy = ir->nstenergy;
511 else if ((ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy)
512 || (ir->efep != efepNO && ir->fepvals->nstdhdl > 0
513 && (ir->nstcalcenergy > ir->fepvals->nstdhdl)))
516 const char* nsten = "nstenergy";
517 const char* nstdh = "nstdhdl";
518 const char* min_name = nsten;
519 int min_nst = ir->nstenergy;
521 /* find the smallest of ( nstenergy, nstdhdl ) */
522 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0
523 && (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
525 min_nst = ir->fepvals->nstdhdl;
528 /* If the user sets nstenergy small, we should respect that */
529 sprintf(warn_buf, "Setting nstcalcenergy (%d) equal to %s (%d)", ir->nstcalcenergy,
531 warning_note(wi, warn_buf);
532 ir->nstcalcenergy = min_nst;
535 if (ir->epc != epcNO)
537 if (ir->nstpcouple < 0)
539 ir->nstpcouple = ir_optimal_nstpcouple(ir);
543 if (ir->nstcalcenergy > 0)
545 if (ir->efep != efepNO)
547 /* nstdhdl should be a multiple of nstcalcenergy */
548 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstdhdl", &ir->fepvals->nstdhdl, wi);
552 /* nstexpanded should be a multiple of nstcalcenergy */
553 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstexpanded",
554 &ir->expandedvals->nstexpanded, wi);
556 /* for storing exact averages nstenergy should be
557 * a multiple of nstcalcenergy
559 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstenergy", &ir->nstenergy, wi);
562 // Inquire all MdModules, if their parameters match with the energy
563 // calculation frequency
564 gmx::EnergyCalculationFrequencyErrors energyCalculationFrequencyErrors(ir->nstcalcenergy);
565 mdModulesNotifier.notifier_.notify(&energyCalculationFrequencyErrors);
567 // Emit all errors from the energy calculation frequency checks
568 for (const std::string& energyFrequencyErrorMessage :
569 energyCalculationFrequencyErrors.errorMessages())
571 warning_error(wi, energyFrequencyErrorMessage);
575 if (ir->nsteps == 0 && !ir->bContinuation)
578 "For a correct single-point energy evaluation with nsteps = 0, use "
579 "continuation = yes to avoid constraining the input coordinates.");
583 if ((EI_SD(ir->eI) || ir->eI == eiBD) && ir->bContinuation && ir->ld_seed != -1)
586 "You are doing a continuation with SD or BD, make sure that ld_seed is "
587 "different from the previous run (using ld_seed=-1 will ensure this)");
593 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
594 CHECK(ir->ePBC != epbcXYZ);
595 sprintf(err_buf, "with TPI nstlist should be larger than zero");
596 CHECK(ir->nstlist <= 0);
597 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
598 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
602 if ((opts->nshake > 0) && (opts->bMorse))
604 sprintf(warn_buf, "Using morse bond-potentials while constraining bonds is useless");
605 warning(wi, warn_buf);
608 if ((EI_SD(ir->eI) || ir->eI == eiBD) && ir->bContinuation && ir->ld_seed != -1)
611 "You are doing a continuation with SD or BD, make sure that ld_seed is "
612 "different from the previous run (using ld_seed=-1 will ensure this)");
614 /* verify simulated tempering options */
618 bool bAllTempZero = TRUE;
619 for (i = 0; i < fep->n_lambda; i++)
621 sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i,
622 efpt_names[efptTEMPERATURE], fep->all_lambda[efptTEMPERATURE][i]);
623 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
624 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
626 bAllTempZero = FALSE;
629 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
630 CHECK(bAllTempZero == TRUE);
632 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
633 CHECK(ir->eI != eiVV);
635 /* check compatability of the temperature coupling with simulated tempering */
637 if (ir->etc == etcNOSEHOOVER)
640 "Nose-Hoover based temperature control such as [%s] my not be "
641 "entirelyconsistent with simulated tempering",
642 etcoupl_names[ir->etc]);
643 warning_note(wi, warn_buf);
646 /* check that the temperatures make sense */
649 "Higher simulated tempering temperature (%g) must be >= than the simulated "
650 "tempering lower temperature (%g)",
651 ir->simtempvals->simtemp_high, ir->simtempvals->simtemp_low);
652 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
654 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero",
655 ir->simtempvals->simtemp_high);
656 CHECK(ir->simtempvals->simtemp_high <= 0);
658 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero",
659 ir->simtempvals->simtemp_low);
660 CHECK(ir->simtempvals->simtemp_low <= 0);
663 /* verify free energy options */
665 if (ir->efep != efepNO)
668 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2", fep->sc_power);
669 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
671 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
672 static_cast<int>(fep->sc_r_power));
673 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
676 "Can't use positive delta-lambda (%g) if initial state/lambda does not start at "
679 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
681 sprintf(err_buf, "Can't use positive delta-lambda (%g) with expanded ensemble simulations",
683 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
685 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
686 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
688 sprintf(err_buf, "Free-energy not implemented for Ewald");
689 CHECK(ir->coulombtype == eelEWALD);
691 /* check validty of lambda inputs */
692 if (fep->n_lambda == 0)
694 /* Clear output in case of no states:*/
695 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.",
696 fep->init_fep_state);
697 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
701 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d",
702 fep->init_fep_state, fep->n_lambda - 1);
703 CHECK((fep->init_fep_state >= fep->n_lambda));
707 "Lambda state must be set, either with init-lambda-state or with init-lambda");
708 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
711 "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with "
712 "init-lambda-state or with init-lambda, but not both",
713 fep->init_lambda, fep->init_fep_state);
714 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
717 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
721 for (i = 0; i < efptNR; i++)
723 if (fep->separate_dvdl[i])
728 if (n_lambda_terms > 1)
731 "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't "
732 "use init-lambda to set lambda state (except for slow growth). Use "
733 "init-lambda-state instead.");
734 warning(wi, warn_buf);
737 if (n_lambda_terms < 2 && fep->n_lambda > 0)
740 "init-lambda is deprecated for setting lambda state (except for slow "
741 "growth). Use init-lambda-state instead.");
745 for (j = 0; j < efptNR; j++)
747 for (i = 0; i < fep->n_lambda; i++)
749 sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i,
750 efpt_names[j], fep->all_lambda[j][i]);
751 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
755 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
757 for (i = 0; i < fep->n_lambda; i++)
760 "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while "
761 "coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to "
762 "crashes, and is not supported.",
763 i, fep->all_lambda[efptVDW][i], fep->all_lambda[efptCOUL][i]);
764 CHECK((fep->sc_alpha > 0)
765 && (((fep->all_lambda[efptCOUL][i] > 0.0) && (fep->all_lambda[efptCOUL][i] < 1.0))
766 && ((fep->all_lambda[efptVDW][i] > 0.0) && (fep->all_lambda[efptVDW][i] < 1.0))));
770 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
772 real sigma, lambda, r_sc;
775 /* Maximum estimate for A and B charges equal with lambda power 1 */
777 r_sc = std::pow(lambda * fep->sc_alpha * std::pow(sigma / ir->rcoulomb, fep->sc_r_power) + 1.0,
778 1.0 / fep->sc_r_power);
780 "With PME there is a minor soft core effect present at the cut-off, "
781 "proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on "
782 "energy conservation, but usually other effects dominate. With a common sigma "
783 "value of %g nm the fraction of the particle-particle potential at the cut-off "
784 "at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
785 fep->sc_r_power, sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
786 warning_note(wi, warn_buf);
789 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
790 be treated differently, but that's the next step */
792 for (i = 0; i < efptNR; i++)
794 for (j = 0; j < fep->n_lambda; j++)
796 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
797 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
802 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
806 /* checking equilibration of weights inputs for validity */
809 "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal "
811 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
812 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
815 "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to "
817 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
818 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
821 "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
822 expand->equil_steps, elmceq_names[elmceqSTEPS]);
823 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
826 "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
827 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
828 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
831 "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
832 expand->equil_ratio, elmceq_names[elmceqRATIO]);
833 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
836 "weight-equil-number-all-lambda (%d) must be a positive integer if "
837 "lmc-weights-equil=%s",
838 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
839 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
842 "weight-equil-number-samples (%d) must be a positive integer if "
843 "lmc-weights-equil=%s",
844 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
845 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
848 "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
849 expand->equil_steps, elmceq_names[elmceqSTEPS]);
850 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
852 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
853 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
854 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
856 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
857 expand->equil_ratio, elmceq_names[elmceqRATIO]);
858 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
860 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
861 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
862 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
864 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
865 CHECK((expand->lmc_repeats <= 0));
866 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
867 CHECK((expand->minvarmin <= 0));
868 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
869 CHECK((expand->c_range < 0));
871 "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != "
873 fep->init_fep_state, expand->lmc_forced_nstart);
874 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0)
875 && (expand->elmcmove != elmcmoveNO));
876 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
877 CHECK((expand->lmc_forced_nstart < 0));
878 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)",
879 fep->init_fep_state);
880 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
882 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
883 CHECK((expand->init_wl_delta < 0));
884 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
885 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
886 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
887 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
889 /* if there is no temperature control, we need to specify an MC temperature */
890 if (!integratorHasReferenceTemperature(ir) && (expand->elmcmove != elmcmoveNO)
891 && (expand->mc_temp <= 0.0))
894 "If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set "
895 "to a positive number");
896 warning_error(wi, err_buf);
898 if (expand->nstTij > 0)
900 sprintf(err_buf, "nstlog must be non-zero");
901 CHECK(ir->nstlog == 0);
902 // Avoid modulus by zero in the case that already triggered an error exit.
906 "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
907 expand->nstTij, ir->nstlog);
908 CHECK((expand->nstTij % ir->nstlog) != 0);
914 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
915 CHECK(ir->nwall && ir->ePBC != epbcXY);
918 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
920 if (ir->ePBC == epbcNONE)
922 if (ir->epc != epcNO)
924 warning(wi, "Turning off pressure coupling for vacuum system");
930 sprintf(err_buf, "Can not have pressure coupling with pbc=%s", epbc_names[ir->ePBC]);
931 CHECK(ir->epc != epcNO);
933 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
934 CHECK(EEL_FULL(ir->coulombtype));
936 sprintf(err_buf, "Can not have dispersion correction with pbc=%s", epbc_names[ir->ePBC]);
937 CHECK(ir->eDispCorr != edispcNO);
940 if (ir->rlist == 0.0)
943 "can only have neighborlist cut-off zero (=infinite)\n"
944 "with coulombtype = %s or coulombtype = %s\n"
945 "without periodic boundary conditions (pbc = %s) and\n"
946 "rcoulomb and rvdw set to zero",
947 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
948 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER))
949 || (ir->ePBC != epbcNONE) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
954 "Simulating without cut-offs can be (slightly) faster with nstlist=0, "
955 "nstype=simple and only one MPI rank");
960 if (ir->nstcomm == 0)
962 // TODO Change this behaviour. There should be exactly one way
963 // to turn off an algorithm.
964 ir->comm_mode = ecmNO;
966 if (ir->comm_mode != ecmNO)
970 // TODO Such input was once valid. Now that we've been
971 // helpful for a few years, we should reject such input,
972 // lest we have to support every historical decision
975 "If you want to remove the rotation around the center of mass, you should set "
976 "comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to "
977 "its absolute value");
978 ir->nstcomm = abs(ir->nstcomm);
981 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
984 "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting "
985 "nstcomm to nstcalcenergy");
986 ir->nstcomm = ir->nstcalcenergy;
989 if (ir->comm_mode == ecmANGULAR)
992 "Can not remove the rotation around the center of mass with periodic "
994 CHECK(ir->bPeriodicMols);
995 if (ir->ePBC != epbcNONE)
998 "Removing the rotation around the center of mass in a periodic system, "
999 "this can lead to artifacts. Only use this on a single (cluster of) "
1000 "molecules. This cluster should not cross periodic boundaries.");
1005 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
1008 "Tumbling and flying ice-cubes: We are not removing rotation around center of mass "
1009 "in a non-periodic system. You should probably set comm_mode = ANGULAR or use "
1012 warning_note(wi, warn_buf);
1015 /* TEMPERATURE COUPLING */
1016 if (ir->etc == etcYES)
1018 ir->etc = etcBERENDSEN;
1020 "Old option for temperature coupling given: "
1021 "changing \"yes\" to \"Berendsen\"\n");
1024 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
1026 if (ir->opts.nhchainlength < 1)
1029 "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to "
1031 ir->opts.nhchainlength);
1032 ir->opts.nhchainlength = 1;
1033 warning(wi, warn_buf);
1036 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
1040 "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
1041 ir->opts.nhchainlength = 1;
1046 ir->opts.nhchainlength = 0;
1049 if (ir->eI == eiVVAK)
1052 "%s implemented primarily for validation, and requires nsttcouple = 1 and "
1055 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
1058 if (ETC_ANDERSEN(ir->etc))
1060 sprintf(err_buf, "%s temperature control not supported for integrator %s.",
1061 etcoupl_names[ir->etc], ei_names[ir->eI]);
1062 CHECK(!(EI_VV(ir->eI)));
1064 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
1067 "Center of mass removal not necessary for %s. All velocities of coupled "
1068 "groups are rerandomized periodically, so flying ice cube errors will not "
1070 etcoupl_names[ir->etc]);
1071 warning_note(wi, warn_buf);
1075 "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are "
1076 "randomized every time step",
1077 ir->nstcomm, etcoupl_names[ir->etc]);
1078 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
1081 if (ir->etc == etcBERENDSEN)
1084 "The %s thermostat does not generate the correct kinetic energy distribution. You "
1085 "might want to consider using the %s thermostat.",
1086 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
1087 warning_note(wi, warn_buf);
1090 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc)) && ir->epc == epcBERENDSEN)
1093 "Using Berendsen pressure coupling invalidates the "
1094 "true ensemble for the thermostat");
1095 warning(wi, warn_buf);
1098 /* PRESSURE COUPLING */
1099 if (ir->epc == epcISOTROPIC)
1101 ir->epc = epcBERENDSEN;
1103 "Old option for pressure coupling given: "
1104 "changing \"Isotropic\" to \"Berendsen\"\n");
1107 if (ir->epc != epcNO)
1109 dt_pcoupl = ir->nstpcouple * ir->delta_t;
1111 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1112 CHECK(ir->tau_p <= 0);
1114 if (ir->tau_p / dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10 * GMX_REAL_EPS)
1117 "For proper integration of the %s barostat, tau-p (%g) should be at least %d "
1118 "times larger than nstpcouple*dt (%g)",
1119 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1120 warning(wi, warn_buf);
1124 "compressibility must be > 0 when using pressure"
1126 EPCOUPLTYPE(ir->epc));
1127 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 || ir->compress[ZZ][ZZ] < 0
1128 || (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 && ir->compress[ZZ][XX] <= 0
1129 && ir->compress[ZZ][YY] <= 0));
1131 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1134 "You are generating velocities so I am assuming you "
1135 "are equilibrating a system. You are using "
1136 "%s pressure coupling, but this can be "
1137 "unstable for equilibration. If your system crashes, try "
1138 "equilibrating first with Berendsen pressure coupling. If "
1139 "you are not equilibrating the system, you can probably "
1140 "ignore this warning.",
1141 epcoupl_names[ir->epc]);
1142 warning(wi, warn_buf);
1148 if (ir->epc == epcMTTK)
1150 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1154 /* ELECTROSTATICS */
1155 /* More checks are in triple check (grompp.c) */
1157 if (ir->coulombtype == eelSWITCH)
1160 "coulombtype = %s is only for testing purposes and can lead to serious "
1161 "artifacts, advice: use coulombtype = %s",
1162 eel_names[ir->coulombtype], eel_names[eelRF_ZERO]);
1163 warning(wi, warn_buf);
1166 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1169 "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old "
1170 "format and exchanging epsilon-r and epsilon-rf",
1172 warning(wi, warn_buf);
1173 ir->epsilon_rf = ir->epsilon_r;
1174 ir->epsilon_r = 1.0;
1177 if (ir->epsilon_r == 0)
1180 "It is pointless to use long-range electrostatics with infinite relative "
1182 "Since you are effectively turning of electrostatics, a plain cutoff will be much "
1184 CHECK(EEL_FULL(ir->coulombtype));
1187 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1189 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1190 CHECK(ir->epsilon_r < 0);
1193 if (EEL_RF(ir->coulombtype))
1195 /* reaction field (at the cut-off) */
1197 if (ir->coulombtype == eelRF_ZERO && ir->epsilon_rf != 0)
1200 "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1201 eel_names[ir->coulombtype]);
1202 warning(wi, warn_buf);
1203 ir->epsilon_rf = 0.0;
1206 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1207 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) || (ir->epsilon_r == 0));
1208 if (ir->epsilon_rf == ir->epsilon_r)
1210 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1211 eel_names[ir->coulombtype]);
1212 warning(wi, warn_buf);
1215 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1216 * means the interaction is zero outside rcoulomb, but it helps to
1217 * provide accurate energy conservation.
1219 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1221 if (ir_coulomb_switched(ir))
1224 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the "
1225 "potential modifier options!",
1226 eel_names[ir->coulombtype]);
1227 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1231 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1234 "Explicit switch/shift coulomb interactions cannot be used in combination with a "
1235 "secondary coulomb-modifier.");
1236 CHECK(ir->coulomb_modifier != eintmodNONE);
1238 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1241 "Explicit switch/shift vdw interactions cannot be used in combination with a "
1242 "secondary vdw-modifier.");
1243 CHECK(ir->vdw_modifier != eintmodNONE);
1246 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT || ir->vdwtype == evdwSWITCH
1247 || ir->vdwtype == evdwSHIFT)
1250 "The switch/shift interaction settings are just for compatibility; you will get "
1252 "performance from applying potential modifiers to your interactions!\n");
1253 warning_note(wi, warn_buf);
1256 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1258 if (ir->rcoulomb_switch / ir->rcoulomb < 0.9499)
1260 real percentage = 100 * (ir->rcoulomb - ir->rcoulomb_switch) / ir->rcoulomb;
1262 "The switching range should be 5%% or less (currently %.2f%% using a switching "
1263 "range of %4f-%4f) for accurate electrostatic energies, energy conservation "
1264 "will be good regardless, since ewald_rtol = %g.",
1265 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1266 warning(wi, warn_buf);
1270 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1272 if (ir->rvdw_switch == 0)
1275 "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones "
1276 "potential. This suggests it was not set in the mdp, which can lead to large "
1277 "energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw "
1278 "switching range.");
1279 warning(wi, warn_buf);
1283 if (EEL_FULL(ir->coulombtype))
1285 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER
1286 || ir->coulombtype == eelPMEUSERSWITCH)
1288 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1289 eel_names[ir->coulombtype]);
1290 CHECK(ir->rcoulomb > ir->rlist);
1294 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1296 // TODO: Move these checks into the ewald module with the options class
1298 int orderMax = (ir->coulombtype == eelP3M_AD ? 8 : 12);
1300 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1302 sprintf(warn_buf, "With coulombtype = %s, you should have %d <= pme-order <= %d",
1303 eel_names[ir->coulombtype], orderMin, orderMax);
1304 warning_error(wi, warn_buf);
1308 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1310 if (ir->ewald_geometry == eewg3D)
1312 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s", epbc_names[ir->ePBC],
1313 eewg_names[eewg3DC]);
1314 warning(wi, warn_buf);
1316 /* This check avoids extra pbc coding for exclusion corrections */
1317 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1318 CHECK(ir->wall_ewald_zfac < 2);
1320 if ((ir->ewald_geometry == eewg3DC) && (ir->ePBC != epbcXY) && EEL_FULL(ir->coulombtype))
1322 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1323 eel_names[ir->coulombtype], eewg_names[eewg3DC], epbc_names[epbcXY]);
1324 warning(wi, warn_buf);
1326 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1328 sprintf(err_buf, "Cannot have periodic molecules with epsilon_surface > 0");
1329 CHECK(ir->bPeriodicMols);
1330 sprintf(warn_buf, "With epsilon_surface > 0 all molecules should be neutral.");
1331 warning_note(wi, warn_buf);
1333 "With epsilon_surface > 0 you can only use domain decomposition "
1334 "when there are only small molecules with all bonds constrained (mdrun will check "
1336 warning_note(wi, warn_buf);
1339 if (ir_vdw_switched(ir))
1341 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1342 CHECK(ir->rvdw_switch >= ir->rvdw);
1344 if (ir->rvdw_switch < 0.5 * ir->rvdw)
1347 "You are applying a switch function to vdw forces or potentials from %g to %g "
1348 "nm, which is more than half the interaction range, whereas switch functions "
1349 "are intended to act only close to the cut-off.",
1350 ir->rvdw_switch, ir->rvdw);
1351 warning_note(wi, warn_buf);
1355 if (ir->vdwtype == evdwPME)
1357 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1359 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s and %s",
1360 evdw_names[ir->vdwtype], eintmod_names[eintmodPOTSHIFT], eintmod_names[eintmodNONE]);
1361 warning_error(wi, err_buf);
1365 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1368 "You have selected user tables with dispersion correction, the dispersion "
1369 "will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction "
1370 "between rvdw_switch and rvdw will not be double counted). Make sure that you "
1371 "really want dispersion correction to -C6/r^6.");
1374 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT) && ir->rvdw != 0)
1376 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1379 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1381 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1384 /* IMPLICIT SOLVENT */
1385 if (ir->coulombtype == eelGB_NOTUSED)
1387 sprintf(warn_buf, "Invalid option %s for coulombtype", eel_names[ir->coulombtype]);
1388 warning_error(wi, warn_buf);
1393 warning_error(wi, "QMMM is currently not supported");
1394 if (!EI_DYNAMICS(ir->eI))
1397 sprintf(buf, "QMMM is only supported with dynamics, not with integrator %s", ei_names[ir->eI]);
1398 warning_error(wi, buf);
1404 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1408 /* interpret a number of doubles from a string and put them in an array,
1409 after allocating space for them.
1410 str = the input string
1411 n = the (pre-allocated) number of doubles read
1412 r = the output array of doubles. */
1413 static void parse_n_real(char* str, int* n, real** r, warninp_t wi)
1415 auto values = gmx::splitString(str);
1419 for (int i = 0; i < *n; i++)
1423 (*r)[i] = gmx::fromString<real>(values[i]);
1425 catch (gmx::GromacsException&)
1427 warning_error(wi, "Invalid value " + values[i]
1428 + " in string in mdp file. Expected a real number.");
1434 static void do_fep_params(t_inputrec* ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
1437 int i, j, max_n_lambda, nweights, nfep[efptNR];
1438 t_lambda* fep = ir->fepvals;
1439 t_expanded* expand = ir->expandedvals;
1440 real** count_fep_lambdas;
1441 bool bOneLambda = TRUE;
1443 snew(count_fep_lambdas, efptNR);
1445 /* FEP input processing */
1446 /* first, identify the number of lambda values for each type.
1447 All that are nonzero must have the same number */
1449 for (i = 0; i < efptNR; i++)
1451 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
1454 /* now, determine the number of components. All must be either zero, or equal. */
1457 for (i = 0; i < efptNR; i++)
1459 if (nfep[i] > max_n_lambda)
1461 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1462 must have the same number if its not zero.*/
1467 for (i = 0; i < efptNR; i++)
1471 ir->fepvals->separate_dvdl[i] = FALSE;
1473 else if (nfep[i] == max_n_lambda)
1475 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute
1476 the derivative with respect to the temperature currently */
1478 ir->fepvals->separate_dvdl[i] = TRUE;
1484 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1486 nfep[i], efpt_names[i], max_n_lambda);
1489 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1490 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1492 /* the number of lambdas is the number we've read in, which is either zero
1493 or the same for all */
1494 fep->n_lambda = max_n_lambda;
1496 /* allocate space for the array of lambda values */
1497 snew(fep->all_lambda, efptNR);
1498 /* if init_lambda is defined, we need to set lambda */
1499 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1501 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1503 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1504 for (i = 0; i < efptNR; i++)
1506 snew(fep->all_lambda[i], fep->n_lambda);
1507 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1510 for (j = 0; j < fep->n_lambda; j++)
1512 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1514 sfree(count_fep_lambdas[i]);
1517 sfree(count_fep_lambdas);
1519 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1520 internal bookkeeping -- for now, init_lambda */
1522 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1524 for (i = 0; i < fep->n_lambda; i++)
1526 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1530 /* check to see if only a single component lambda is defined, and soft core is defined.
1531 In this case, turn on coulomb soft core */
1533 if (max_n_lambda == 0)
1539 for (i = 0; i < efptNR; i++)
1541 if ((nfep[i] != 0) && (i != efptFEP))
1547 if ((bOneLambda) && (fep->sc_alpha > 0))
1549 fep->bScCoul = TRUE;
1552 /* Fill in the others with the efptFEP if they are not explicitly
1553 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1554 they are all zero. */
1556 for (i = 0; i < efptNR; i++)
1558 if ((nfep[i] == 0) && (i != efptFEP))
1560 for (j = 0; j < fep->n_lambda; j++)
1562 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1568 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1569 if (fep->sc_r_power == 48)
1571 if (fep->sc_alpha > 0.1)
1574 "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004",
1579 /* now read in the weights */
1580 parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
1583 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1585 else if (nweights != fep->n_lambda)
1587 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1588 nweights, fep->n_lambda);
1590 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1592 expand->nstexpanded = fep->nstdhdl;
1593 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1598 static void do_simtemp_params(t_inputrec* ir)
1601 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1602 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1605 static void convertYesNos(warninp_t /*wi*/,
1606 gmx::ArrayRef<const std::string> inputs,
1607 const char* /*name*/,
1611 for (const auto& input : inputs)
1613 outputs[i] = gmx::equalCaseInsensitive(input, "Y", 1);
1618 template<typename T>
1619 void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
1622 for (const auto& input : inputs)
1626 outputs[i] = gmx::fromStdString<T>(input);
1628 catch (gmx::GromacsException&)
1630 auto message = gmx::formatString(
1631 "Invalid value for mdp option %s. %s should only consist of integers separated "
1634 warning_error(wi, message);
1640 static void convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, real* outputs)
1643 for (const auto& input : inputs)
1647 outputs[i] = gmx::fromString<real>(input);
1649 catch (gmx::GromacsException&)
1651 auto message = gmx::formatString(
1652 "Invalid value for mdp option %s. %s should only consist of real numbers "
1653 "separated by spaces.",
1655 warning_error(wi, message);
1661 static void convertRvecs(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, rvec* outputs)
1664 for (const auto& input : inputs)
1668 outputs[i][d] = gmx::fromString<real>(input);
1670 catch (gmx::GromacsException&)
1672 auto message = gmx::formatString(
1673 "Invalid value for mdp option %s. %s should only consist of real numbers "
1674 "separated by spaces.",
1676 warning_error(wi, message);
1687 static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
1689 opts->wall_atomtype[0] = nullptr;
1690 opts->wall_atomtype[1] = nullptr;
1692 ir->wall_atomtype[0] = -1;
1693 ir->wall_atomtype[1] = -1;
1694 ir->wall_density[0] = 0;
1695 ir->wall_density[1] = 0;
1699 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1700 if (wallAtomTypes.size() != size_t(ir->nwall))
1702 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %zu", ir->nwall,
1703 wallAtomTypes.size());
1705 for (int i = 0; i < ir->nwall; i++)
1707 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1710 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1712 auto wallDensity = gmx::splitString(wall_density);
1713 if (wallDensity.size() != size_t(ir->nwall))
1715 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %zu", ir->nwall,
1716 wallDensity.size());
1718 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1719 for (int i = 0; i < ir->nwall; i++)
1721 if (ir->wall_density[i] <= 0)
1723 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1730 static void add_wall_energrps(SimulationGroups* groups, int nwall, t_symtab* symtab)
1734 AtomGroupIndices* grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1735 for (int i = 0; i < nwall; i++)
1737 groups->groupNames.emplace_back(put_symtab(symtab, gmx::formatString("wall%d", i).c_str()));
1738 grps->emplace_back(groups->groupNames.size() - 1);
1743 static void read_expandedparams(std::vector<t_inpfile>* inp, t_expanded* expand, warninp_t wi)
1745 /* read expanded ensemble parameters */
1746 printStringNewline(inp, "expanded ensemble variables");
1747 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1748 expand->elamstats = get_eeenum(inp, "lmc-stats", elamstats_names, wi);
1749 expand->elmcmove = get_eeenum(inp, "lmc-move", elmcmove_names, wi);
1750 expand->elmceq = get_eeenum(inp, "lmc-weights-equil", elmceq_names, wi);
1751 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1752 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1753 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1754 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1755 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1756 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1757 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1758 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1759 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1760 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1761 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1762 expand->bSymmetrizedTMatrix =
1763 (get_eeenum(inp, "symmetrized-transition-matrix", yesno_names, wi) != 0);
1764 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1765 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1766 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1767 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1768 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1769 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1770 expand->bWLoneovert = (get_eeenum(inp, "wl-oneovert", yesno_names, wi) != 0);
1773 /*! \brief Return whether an end state with the given coupling-lambda
1774 * value describes fully-interacting VDW.
1776 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1777 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1779 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1781 return (couple_lambda_value == ecouplamVDW || couple_lambda_value == ecouplamVDWQ);
1787 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1790 explicit MdpErrorHandler(warninp_t wi) : wi_(wi), mapping_(nullptr) {}
1792 void setBackMapping(const gmx::IKeyValueTreeBackMapping& mapping) { mapping_ = &mapping; }
1794 bool onError(gmx::UserInputError* ex, const gmx::KeyValueTreePath& context) override
1797 gmx::formatString("Error in mdp option \"%s\":", getOptionName(context).c_str()));
1798 std::string message = gmx::formatExceptionMessageToString(*ex);
1799 warning_error(wi_, message.c_str());
1804 std::string getOptionName(const gmx::KeyValueTreePath& context)
1806 if (mapping_ != nullptr)
1808 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1809 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1812 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1817 const gmx::IKeyValueTreeBackMapping* mapping_;
1822 void get_ir(const char* mdparin,
1823 const char* mdparout,
1824 gmx::MDModules* mdModules,
1827 WriteMdpHeader writeMdpHeader,
1831 double dumdub[2][6];
1833 char warn_buf[STRLEN];
1834 t_lambda* fep = ir->fepvals;
1835 t_expanded* expand = ir->expandedvals;
1837 const char* no_names[] = { "no", nullptr };
1839 init_inputrec_strings();
1840 gmx::TextInputFile stream(mdparin);
1841 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1843 snew(dumstr[0], STRLEN);
1844 snew(dumstr[1], STRLEN);
1846 /* ignore the following deprecated commands */
1847 replace_inp_entry(inp, "title", nullptr);
1848 replace_inp_entry(inp, "cpp", nullptr);
1849 replace_inp_entry(inp, "domain-decomposition", nullptr);
1850 replace_inp_entry(inp, "andersen-seed", nullptr);
1851 replace_inp_entry(inp, "dihre", nullptr);
1852 replace_inp_entry(inp, "dihre-fc", nullptr);
1853 replace_inp_entry(inp, "dihre-tau", nullptr);
1854 replace_inp_entry(inp, "nstdihreout", nullptr);
1855 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1856 replace_inp_entry(inp, "optimize-fft", nullptr);
1857 replace_inp_entry(inp, "adress_type", nullptr);
1858 replace_inp_entry(inp, "adress_const_wf", nullptr);
1859 replace_inp_entry(inp, "adress_ex_width", nullptr);
1860 replace_inp_entry(inp, "adress_hy_width", nullptr);
1861 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1862 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1863 replace_inp_entry(inp, "adress_site", nullptr);
1864 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1865 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1866 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1867 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1868 replace_inp_entry(inp, "rlistlong", nullptr);
1869 replace_inp_entry(inp, "nstcalclr", nullptr);
1870 replace_inp_entry(inp, "pull-print-com2", nullptr);
1871 replace_inp_entry(inp, "gb-algorithm", nullptr);
1872 replace_inp_entry(inp, "nstgbradii", nullptr);
1873 replace_inp_entry(inp, "rgbradii", nullptr);
1874 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1875 replace_inp_entry(inp, "gb-saltconc", nullptr);
1876 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1877 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1878 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1879 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1880 replace_inp_entry(inp, "sa-algorithm", nullptr);
1881 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1882 replace_inp_entry(inp, "ns-type", nullptr);
1884 /* replace the following commands with the clearer new versions*/
1885 replace_inp_entry(inp, "unconstrained-start", "continuation");
1886 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1887 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1888 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1889 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1890 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1891 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1893 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1894 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1895 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1896 setStringEntry(&inp, "include", opts->include, nullptr);
1897 printStringNoNewline(
1898 &inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1899 setStringEntry(&inp, "define", opts->define, nullptr);
1901 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1902 ir->eI = get_eeenum(&inp, "integrator", ei_names, wi);
1903 printStringNoNewline(&inp, "Start time and timestep in ps");
1904 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1905 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1906 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1907 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1908 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1909 printStringNoNewline(
1910 &inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1911 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1912 printStringNoNewline(&inp, "mode for center of mass motion removal");
1913 ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
1914 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
1915 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
1916 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
1917 setStringEntry(&inp, "comm-grps", is->vcm, nullptr);
1919 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
1920 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
1921 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
1922 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
1925 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
1926 printStringNoNewline(&inp, "Force tolerance and initial step-size");
1927 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
1928 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
1929 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
1930 ir->niter = get_eint(&inp, "niter", 20, wi);
1931 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
1932 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
1933 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
1934 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
1935 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
1937 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
1938 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
1940 /* Output options */
1941 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
1942 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
1943 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
1944 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
1945 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
1946 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
1947 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
1948 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
1949 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
1950 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
1951 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
1952 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
1953 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
1954 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
1955 printStringNoNewline(&inp, "default, all atoms will be written.");
1956 setStringEntry(&inp, "compressed-x-grps", is->x_compressed_groups, nullptr);
1957 printStringNoNewline(&inp, "Selection of energy groups");
1958 setStringEntry(&inp, "energygrps", is->energy, nullptr);
1960 /* Neighbor searching */
1961 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
1962 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
1963 ir->cutoff_scheme = get_eeenum(&inp, "cutoff-scheme", ecutscheme_names, wi);
1964 printStringNoNewline(&inp, "nblist update frequency");
1965 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
1966 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
1967 ir->ePBC = get_eeenum(&inp, "pbc", epbc_names, wi);
1968 ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi) != 0;
1969 printStringNoNewline(&inp,
1970 "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1971 printStringNoNewline(&inp, "a value of -1 means: use rlist");
1972 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
1973 printStringNoNewline(&inp, "nblist cut-off");
1974 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
1975 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
1977 /* Electrostatics */
1978 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
1979 printStringNoNewline(&inp, "Method for doing electrostatics");
1980 ir->coulombtype = get_eeenum(&inp, "coulombtype", eel_names, wi);
1981 ir->coulomb_modifier = get_eeenum(&inp, "coulomb-modifier", eintmod_names, wi);
1982 printStringNoNewline(&inp, "cut-off lengths");
1983 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
1984 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
1985 printStringNoNewline(&inp,
1986 "Relative dielectric constant for the medium and the reaction field");
1987 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
1988 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
1989 printStringNoNewline(&inp, "Method for doing Van der Waals");
1990 ir->vdwtype = get_eeenum(&inp, "vdw-type", evdw_names, wi);
1991 ir->vdw_modifier = get_eeenum(&inp, "vdw-modifier", eintmod_names, wi);
1992 printStringNoNewline(&inp, "cut-off lengths");
1993 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
1994 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
1995 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
1996 ir->eDispCorr = get_eeenum(&inp, "DispCorr", edispc_names, wi);
1997 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
1998 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
1999 printStringNoNewline(&inp, "Separate tables between energy group pairs");
2000 setStringEntry(&inp, "energygrp-table", is->egptable, nullptr);
2001 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
2002 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
2003 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
2004 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
2005 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
2006 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
2007 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
2008 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
2009 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
2010 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
2011 ir->ljpme_combination_rule = get_eeenum(&inp, "lj-pme-comb-rule", eljpme_names, wi);
2012 ir->ewald_geometry = get_eeenum(&inp, "ewald-geometry", eewg_names, wi);
2013 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
2015 /* Implicit solvation is no longer supported, but we need grompp
2016 to be able to refuse old .mdp files that would have built a tpr
2017 to run it. Thus, only "no" is accepted. */
2018 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
2020 /* Coupling stuff */
2021 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
2022 printStringNoNewline(&inp, "Temperature coupling");
2023 ir->etc = get_eeenum(&inp, "tcoupl", etcoupl_names, wi);
2024 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
2025 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
2026 ir->bPrintNHChains = (get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi) != 0);
2027 printStringNoNewline(&inp, "Groups to couple separately");
2028 setStringEntry(&inp, "tc-grps", is->tcgrps, nullptr);
2029 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
2030 setStringEntry(&inp, "tau-t", is->tau_t, nullptr);
2031 setStringEntry(&inp, "ref-t", is->ref_t, nullptr);
2032 printStringNoNewline(&inp, "pressure coupling");
2033 ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
2034 ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
2035 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
2036 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
2037 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
2038 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
2039 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
2040 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
2041 ir->refcoord_scaling = get_eeenum(&inp, "refcoord-scaling", erefscaling_names, wi);
2044 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2045 ir->bQMMM = (get_eeenum(&inp, "QMMM", yesno_names, wi) != 0);
2046 printStringNoNewline(&inp, "Groups treated Quantum Mechanically");
2047 setStringEntry(&inp, "QMMM-grps", is->QMMM, nullptr);
2048 printStringNoNewline(&inp, "QM method");
2049 setStringEntry(&inp, "QMmethod", is->QMmethod, nullptr);
2050 printStringNoNewline(&inp, "QMMM scheme");
2051 ir->QMMMscheme = get_eeenum(&inp, "QMMMscheme", eQMMMscheme_names, wi);
2052 printStringNoNewline(&inp, "QM basisset");
2053 setStringEntry(&inp, "QMbasis", is->QMbasis, nullptr);
2054 printStringNoNewline(&inp, "QM charge");
2055 setStringEntry(&inp, "QMcharge", is->QMcharge, nullptr);
2056 printStringNoNewline(&inp, "QM multiplicity");
2057 setStringEntry(&inp, "QMmult", is->QMmult, nullptr);
2058 printStringNoNewline(&inp, "Surface Hopping");
2059 setStringEntry(&inp, "SH", is->bSH, nullptr);
2060 printStringNoNewline(&inp, "CAS space options");
2061 setStringEntry(&inp, "CASorbitals", is->CASorbitals, nullptr);
2062 setStringEntry(&inp, "CASelectrons", is->CASelectrons, nullptr);
2063 setStringEntry(&inp, "SAon", is->SAon, nullptr);
2064 setStringEntry(&inp, "SAoff", is->SAoff, nullptr);
2065 setStringEntry(&inp, "SAsteps", is->SAsteps, nullptr);
2066 printStringNoNewline(&inp, "Scale factor for MM charges");
2067 ir->scalefactor = get_ereal(&inp, "MMChargeScaleFactor", 1.0, wi);
2069 /* Simulated annealing */
2070 printStringNewline(&inp, "SIMULATED ANNEALING");
2071 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2072 setStringEntry(&inp, "annealing", is->anneal, nullptr);
2073 printStringNoNewline(&inp,
2074 "Number of time points to use for specifying annealing in each group");
2075 setStringEntry(&inp, "annealing-npoints", is->anneal_npoints, nullptr);
2076 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2077 setStringEntry(&inp, "annealing-time", is->anneal_time, nullptr);
2078 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2079 setStringEntry(&inp, "annealing-temp", is->anneal_temp, nullptr);
2082 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2083 opts->bGenVel = (get_eeenum(&inp, "gen-vel", yesno_names, wi) != 0);
2084 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2085 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2088 printStringNewline(&inp, "OPTIONS FOR BONDS");
2089 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2090 printStringNoNewline(&inp, "Type of constraint algorithm");
2091 ir->eConstrAlg = get_eeenum(&inp, "constraint-algorithm", econstr_names, wi);
2092 printStringNoNewline(&inp, "Do not constrain the start configuration");
2093 ir->bContinuation = (get_eeenum(&inp, "continuation", yesno_names, wi) != 0);
2094 printStringNoNewline(&inp,
2095 "Use successive overrelaxation to reduce the number of shake iterations");
2096 ir->bShakeSOR = (get_eeenum(&inp, "Shake-SOR", yesno_names, wi) != 0);
2097 printStringNoNewline(&inp, "Relative tolerance of shake");
2098 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2099 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2100 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2101 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2102 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2103 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2104 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2105 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2106 printStringNoNewline(&inp, "rotates over more degrees than");
2107 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2108 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2109 opts->bMorse = (get_eeenum(&inp, "morse", yesno_names, wi) != 0);
2111 /* Energy group exclusions */
2112 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2113 printStringNoNewline(
2114 &inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2115 setStringEntry(&inp, "energygrp-excl", is->egpexcl, nullptr);
2118 printStringNewline(&inp, "WALLS");
2119 printStringNoNewline(
2120 &inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2121 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2122 ir->wall_type = get_eeenum(&inp, "wall-type", ewt_names, wi);
2123 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2124 setStringEntry(&inp, "wall-atomtype", is->wall_atomtype, nullptr);
2125 setStringEntry(&inp, "wall-density", is->wall_density, nullptr);
2126 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2129 printStringNewline(&inp, "COM PULLING");
2130 ir->bPull = (get_eeenum(&inp, "pull", yesno_names, wi) != 0);
2134 is->pull_grp = read_pullparams(&inp, ir->pull, wi);
2138 NOTE: needs COM pulling input */
2139 printStringNewline(&inp, "AWH biasing");
2140 ir->bDoAwh = (get_eeenum(&inp, "awh", yesno_names, wi) != 0);
2145 ir->awhParams = gmx::readAndCheckAwhParams(&inp, ir, wi);
2149 gmx_fatal(FARGS, "AWH biasing is only compatible with COM pulling turned on");
2153 /* Enforced rotation */
2154 printStringNewline(&inp, "ENFORCED ROTATION");
2155 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2156 ir->bRot = (get_eeenum(&inp, "rotation", yesno_names, wi) != 0);
2160 is->rot_grp = read_rotparams(&inp, ir->rot, wi);
2163 /* Interactive MD */
2165 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2166 setStringEntry(&inp, "IMD-group", is->imd_grp, nullptr);
2167 if (is->imd_grp[0] != '\0')
2174 printStringNewline(&inp, "NMR refinement stuff");
2175 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2176 ir->eDisre = get_eeenum(&inp, "disre", edisre_names, wi);
2177 printStringNoNewline(
2178 &inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2179 ir->eDisreWeighting = get_eeenum(&inp, "disre-weighting", edisreweighting_names, wi);
2180 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2181 ir->bDisreMixed = (get_eeenum(&inp, "disre-mixed", yesno_names, wi) != 0);
2182 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2183 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2184 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2185 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2186 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2187 opts->bOrire = (get_eeenum(&inp, "orire", yesno_names, wi) != 0);
2188 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2189 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2190 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2191 setStringEntry(&inp, "orire-fitgrp", is->orirefitgrp, nullptr);
2192 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2193 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2195 /* free energy variables */
2196 printStringNewline(&inp, "Free energy variables");
2197 ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
2198 setStringEntry(&inp, "couple-moltype", is->couple_moltype, nullptr);
2199 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2200 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2201 opts->bCoupleIntra = (get_eeenum(&inp, "couple-intramol", yesno_names, wi) != 0);
2203 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2205 it was not entered */
2206 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2207 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2208 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2209 setStringEntry(&inp, "fep-lambdas", is->fep_lambda[efptFEP], nullptr);
2210 setStringEntry(&inp, "mass-lambdas", is->fep_lambda[efptMASS], nullptr);
2211 setStringEntry(&inp, "coul-lambdas", is->fep_lambda[efptCOUL], nullptr);
2212 setStringEntry(&inp, "vdw-lambdas", is->fep_lambda[efptVDW], nullptr);
2213 setStringEntry(&inp, "bonded-lambdas", is->fep_lambda[efptBONDED], nullptr);
2214 setStringEntry(&inp, "restraint-lambdas", is->fep_lambda[efptRESTRAINT], nullptr);
2215 setStringEntry(&inp, "temperature-lambdas", is->fep_lambda[efptTEMPERATURE], nullptr);
2216 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2217 setStringEntry(&inp, "init-lambda-weights", is->lambda_weights, nullptr);
2218 fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
2219 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2220 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2221 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2222 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2223 fep->bScCoul = (get_eeenum(&inp, "sc-coul", yesno_names, wi) != 0);
2224 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2225 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2226 fep->separate_dhdl_file = get_eeenum(&inp, "separate-dhdl-file", separate_dhdl_file_names, wi);
2227 fep->dhdl_derivatives = get_eeenum(&inp, "dhdl-derivatives", dhdl_derivatives_names, wi);
2228 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2229 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2231 /* Non-equilibrium MD stuff */
2232 printStringNewline(&inp, "Non-equilibrium MD stuff");
2233 setStringEntry(&inp, "acc-grps", is->accgrps, nullptr);
2234 setStringEntry(&inp, "accelerate", is->acc, nullptr);
2235 setStringEntry(&inp, "freezegrps", is->freeze, nullptr);
2236 setStringEntry(&inp, "freezedim", is->frdim, nullptr);
2237 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2238 setStringEntry(&inp, "deform", is->deform, nullptr);
2240 /* simulated tempering variables */
2241 printStringNewline(&inp, "simulated tempering variables");
2242 ir->bSimTemp = (get_eeenum(&inp, "simulated-tempering", yesno_names, wi) != 0);
2243 ir->simtempvals->eSimTempScale = get_eeenum(&inp, "simulated-tempering-scaling", esimtemp_names, wi);
2244 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2245 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2247 /* expanded ensemble variables */
2248 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2250 read_expandedparams(&inp, expand, wi);
2253 /* Electric fields */
2255 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2256 gmx::KeyValueTreeTransformer transform;
2257 transform.rules()->addRule().keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2258 mdModules->initMdpTransform(transform.rules());
2259 for (const auto& path : transform.mappedPaths())
2261 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2262 mark_einp_set(inp, path[0].c_str());
2264 MdpErrorHandler errorHandler(wi);
2265 auto result = transform.transform(convertedValues, &errorHandler);
2266 ir->params = new gmx::KeyValueTreeObject(result.object());
2267 mdModules->adjustInputrecBasedOnModules(ir);
2268 errorHandler.setBackMapping(result.backMapping());
2269 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2272 /* Ion/water position swapping ("computational electrophysiology") */
2273 printStringNewline(&inp,
2274 "Ion/water position swapping for computational electrophysiology setups");
2275 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2276 ir->eSwapCoords = get_eeenum(&inp, "swapcoords", eSwapTypes_names, wi);
2277 if (ir->eSwapCoords != eswapNO)
2284 printStringNoNewline(&inp, "Swap attempt frequency");
2285 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2286 printStringNoNewline(&inp, "Number of ion types to be controlled");
2287 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2290 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2292 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2293 snew(ir->swap->grp, ir->swap->ngrp);
2294 for (i = 0; i < ir->swap->ngrp; i++)
2296 snew(ir->swap->grp[i].molname, STRLEN);
2298 printStringNoNewline(&inp,
2299 "Two index groups that contain the compartment-partitioning atoms");
2300 setStringEntry(&inp, "split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2301 setStringEntry(&inp, "split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2302 printStringNoNewline(&inp,
2303 "Use center of mass of split groups (yes/no), otherwise center of "
2304 "geometry is used");
2305 ir->swap->massw_split[0] = (get_eeenum(&inp, "massw-split0", yesno_names, wi) != 0);
2306 ir->swap->massw_split[1] = (get_eeenum(&inp, "massw-split1", yesno_names, wi) != 0);
2308 printStringNoNewline(&inp, "Name of solvent molecules");
2309 setStringEntry(&inp, "solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2311 printStringNoNewline(&inp,
2312 "Split cylinder: radius, upper and lower extension (nm) (this will "
2313 "define the channels)");
2314 printStringNoNewline(&inp,
2315 "Note that the split cylinder settings do not have an influence on "
2316 "the swapping protocol,");
2317 printStringNoNewline(
2319 "however, if correctly defined, the permeation events are recorded per channel");
2320 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2321 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2322 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2323 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2324 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2325 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2327 printStringNoNewline(
2329 "Average the number of ions per compartment over these many swap attempt steps");
2330 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2332 printStringNoNewline(
2333 &inp, "Names of the ion types that can be exchanged with solvent molecules,");
2334 printStringNoNewline(
2335 &inp, "and the requested number of ions of this type in compartments A and B");
2336 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2337 for (i = 0; i < nIonTypes; i++)
2339 int ig = eSwapFixedGrpNR + i;
2341 sprintf(buf, "iontype%d-name", i);
2342 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2343 sprintf(buf, "iontype%d-in-A", i);
2344 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2345 sprintf(buf, "iontype%d-in-B", i);
2346 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2349 printStringNoNewline(
2351 "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2352 printStringNoNewline(
2354 "at maximum distance (= bulk concentration) to the split group layers. However,");
2355 printStringNoNewline(&inp,
2356 "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk "
2357 "layer from the middle at 0.0");
2358 printStringNoNewline(&inp,
2359 "towards one of the compartment-partitioning layers (at +/- 1.0).");
2360 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2361 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2362 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2363 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0))
2365 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2368 printStringNoNewline(
2369 &inp, "Start to swap ions if threshold difference to requested count is reached");
2370 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2373 /* AdResS is no longer supported, but we need grompp to be able to
2374 refuse to process old .mdp files that used it. */
2375 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2377 /* User defined thingies */
2378 printStringNewline(&inp, "User defined thingies");
2379 setStringEntry(&inp, "user1-grps", is->user1, nullptr);
2380 setStringEntry(&inp, "user2-grps", is->user2, nullptr);
2381 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2382 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2383 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2384 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2385 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2386 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2387 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2388 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2392 gmx::TextOutputFile stream(mdparout);
2393 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2395 // Transform module data into a flat key-value tree for output.
2396 gmx::KeyValueTreeBuilder builder;
2397 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2398 mdModules->buildMdpOutput(&builderObject);
2400 gmx::TextWriter writer(&stream);
2401 writeKeyValueTreeAsMdp(&writer, builder.build());
2406 /* Process options if necessary */
2407 for (m = 0; m < 2; m++)
2409 for (i = 0; i < 2 * DIM; i++)
2418 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2422 "Pressure coupling incorrect number of values (I need exactly 1)");
2424 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2426 case epctSEMIISOTROPIC:
2427 case epctSURFACETENSION:
2428 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2432 "Pressure coupling incorrect number of values (I need exactly 2)");
2434 dumdub[m][YY] = dumdub[m][XX];
2436 case epctANISOTROPIC:
2437 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf", &(dumdub[m][XX]), &(dumdub[m][YY]),
2438 &(dumdub[m][ZZ]), &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5]))
2443 "Pressure coupling incorrect number of values (I need exactly 6)");
2447 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2448 epcoupltype_names[ir->epct]);
2452 clear_mat(ir->ref_p);
2453 clear_mat(ir->compress);
2454 for (i = 0; i < DIM; i++)
2456 ir->ref_p[i][i] = dumdub[1][i];
2457 ir->compress[i][i] = dumdub[0][i];
2459 if (ir->epct == epctANISOTROPIC)
2461 ir->ref_p[XX][YY] = dumdub[1][3];
2462 ir->ref_p[XX][ZZ] = dumdub[1][4];
2463 ir->ref_p[YY][ZZ] = dumdub[1][5];
2464 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2467 "All off-diagonal reference pressures are non-zero. Are you sure you want to "
2468 "apply a threefold shear stress?\n");
2470 ir->compress[XX][YY] = dumdub[0][3];
2471 ir->compress[XX][ZZ] = dumdub[0][4];
2472 ir->compress[YY][ZZ] = dumdub[0][5];
2473 for (i = 0; i < DIM; i++)
2475 for (m = 0; m < i; m++)
2477 ir->ref_p[i][m] = ir->ref_p[m][i];
2478 ir->compress[i][m] = ir->compress[m][i];
2483 if (ir->comm_mode == ecmNO)
2488 opts->couple_moltype = nullptr;
2489 if (strlen(is->couple_moltype) > 0)
2491 if (ir->efep != efepNO)
2493 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2494 if (opts->couple_lam0 == opts->couple_lam1)
2496 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2498 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
2502 "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
2509 "Free energy is turned off, so we will not decouple the molecule listed "
2513 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2514 if (ir->efep != efepNO)
2516 if (fep->delta_lambda > 0)
2518 ir->efep = efepSLOWGROWTH;
2522 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2524 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2526 "Old option for dhdl-print-energy given: "
2527 "changing \"yes\" to \"total\"\n");
2530 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2532 /* always print out the energy to dhdl if we are doing
2533 expanded ensemble, since we need the total energy for
2534 analysis if the temperature is changing. In some
2535 conditions one may only want the potential energy, so
2536 we will allow that if the appropriate mdp setting has
2537 been enabled. Otherwise, total it is:
2539 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2542 if ((ir->efep != efepNO) || ir->bSimTemp)
2544 ir->bExpanded = FALSE;
2545 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2547 ir->bExpanded = TRUE;
2549 do_fep_params(ir, is->fep_lambda, is->lambda_weights, wi);
2550 if (ir->bSimTemp) /* done after fep params */
2552 do_simtemp_params(ir);
2555 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2556 * setup and not on the old way of specifying the free-energy setup,
2557 * we should check for using soft-core when not needed, since that
2558 * can complicate the sampling significantly.
2559 * Note that we only check for the automated coupling setup.
2560 * If the (advanced) user does FEP through manual topology changes,
2561 * this check will not be triggered.
2563 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 && ir->fepvals->sc_alpha != 0
2564 && (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
2567 "You are using soft-core interactions while the Van der Waals interactions are "
2568 "not decoupled (note that the sc-coul option is only active when using lambda "
2569 "states). Although this will not lead to errors, you will need much more "
2570 "sampling than without soft-core interactions. Consider using sc-alpha=0.");
2575 ir->fepvals->n_lambda = 0;
2578 /* WALL PARAMETERS */
2580 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts, wi);
2582 /* ORIENTATION RESTRAINT PARAMETERS */
2584 if (opts->bOrire && gmx::splitString(is->orirefitgrp).size() != 1)
2586 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2589 /* DEFORMATION PARAMETERS */
2591 clear_mat(ir->deform);
2592 for (i = 0; i < 6; i++)
2597 double gmx_unused canary;
2598 int ndeform = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf %lf", &(dumdub[0][0]), &(dumdub[0][1]),
2599 &(dumdub[0][2]), &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]), &canary);
2601 if (strlen(is->deform) > 0 && ndeform != 6)
2604 wi, gmx::formatString(
2605 "Cannot parse exactly 6 box deformation velocities from string '%s'", is->deform)
2608 for (i = 0; i < 3; i++)
2610 ir->deform[i][i] = dumdub[0][i];
2612 ir->deform[YY][XX] = dumdub[0][3];
2613 ir->deform[ZZ][XX] = dumdub[0][4];
2614 ir->deform[ZZ][YY] = dumdub[0][5];
2615 if (ir->epc != epcNO)
2617 for (i = 0; i < 3; i++)
2619 for (j = 0; j <= i; j++)
2621 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2623 warning_error(wi, "A box element has deform set and compressibility > 0");
2627 for (i = 0; i < 3; i++)
2629 for (j = 0; j < i; j++)
2631 if (ir->deform[i][j] != 0)
2633 for (m = j; m < DIM; m++)
2635 if (ir->compress[m][j] != 0)
2638 "An off-diagonal box element has deform set while "
2639 "compressibility > 0 for the same component of another box "
2640 "vector, this might lead to spurious periodicity effects.");
2641 warning(wi, warn_buf);
2649 /* Ion/water position swapping checks */
2650 if (ir->eSwapCoords != eswapNO)
2652 if (ir->swap->nstswap < 1)
2654 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2656 if (ir->swap->nAverage < 1)
2658 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2660 if (ir->swap->threshold < 1.0)
2662 warning_error(wi, "Ion count threshold must be at least 1.\n");
2670 static int search_QMstring(const char* s, int ng, const char* gn[])
2672 /* same as normal search_string, but this one searches QM strings */
2675 for (i = 0; (i < ng); i++)
2677 if (gmx_strcasecmp(s, gn[i]) == 0)
2683 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2684 } /* search_QMstring */
2686 /* We would like gn to be const as well, but C doesn't allow this */
2687 /* TODO this is utility functionality (search for the index of a
2688 string in a collection), so should be refactored and located more
2690 int search_string(const char* s, int ng, char* gn[])
2694 for (i = 0; (i < ng); i++)
2696 if (gmx_strcasecmp(s, gn[i]) == 0)
2703 "Group %s referenced in the .mdp file was not found in the index file.\n"
2704 "Group names must match either [moleculetype] names or custom index group\n"
2705 "names, in which case you must supply an index file to the '-n' option\n"
2710 static void atomGroupRangeValidation(int natoms, int groupIndex, const t_blocka& block)
2712 /* Now go over the atoms in the group */
2713 for (int j = block.index[groupIndex]; (j < block.index[groupIndex + 1]); j++)
2715 int aj = block.a[j];
2717 /* Range checking */
2718 if ((aj < 0) || (aj >= natoms))
2720 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2725 static void do_numbering(int natoms,
2726 SimulationGroups* groups,
2727 gmx::ArrayRef<std::string> groupsFromMdpFile,
2730 SimulationAtomGroupType gtype,
2736 unsigned short* cbuf;
2737 AtomGroupIndices* grps = &(groups->groups[gtype]);
2740 char warn_buf[STRLEN];
2742 title = shortName(gtype);
2745 /* Mark all id's as not set */
2746 for (int i = 0; (i < natoms); i++)
2751 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2753 /* Lookup the group name in the block structure */
2754 const int gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2755 if ((grptp != egrptpONE) || (i == 0))
2757 grps->emplace_back(gid);
2759 GMX_ASSERT(block, "Can't have a nullptr block");
2760 atomGroupRangeValidation(natoms, gid, *block);
2761 /* Now go over the atoms in the group */
2762 for (int j = block->index[gid]; (j < block->index[gid + 1]); j++)
2764 const int aj = block->a[j];
2765 /* Lookup up the old group number */
2766 const int ognr = cbuf[aj];
2769 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title,
2774 /* Store the group number in buffer */
2775 if (grptp == egrptpONE)
2788 /* Now check whether we have done all atoms */
2791 if (grptp == egrptpALL)
2793 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2795 else if (grptp == egrptpPART)
2797 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2798 warning_note(wi, warn_buf);
2800 /* Assign all atoms currently unassigned to a rest group */
2801 for (int j = 0; (j < natoms); j++)
2803 if (cbuf[j] == NOGID)
2805 cbuf[j] = grps->size();
2808 if (grptp != egrptpPART)
2812 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title,
2815 /* Add group name "rest" */
2816 grps->emplace_back(restnm);
2818 /* Assign the rest name to all atoms not currently assigned to a group */
2819 for (int j = 0; (j < natoms); j++)
2821 if (cbuf[j] == NOGID)
2823 // group size was not updated before this here, so need to use -1.
2824 cbuf[j] = grps->size() - 1;
2830 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2832 /* All atoms are part of one (or no) group, no index required */
2833 groups->groupNumbers[gtype].clear();
2837 for (int j = 0; (j < natoms); j++)
2839 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2846 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
2849 pull_params_t* pull;
2850 int natoms, imin, jmin;
2851 int * nrdf2, *na_vcm, na_tot;
2852 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2857 * First calc 3xnr-atoms for each group
2858 * then subtract half a degree of freedom for each constraint
2860 * Only atoms and nuclei contribute to the degrees of freedom...
2865 const SimulationGroups& groups = mtop->groups;
2866 natoms = mtop->natoms;
2868 /* Allocate one more for a possible rest group */
2869 /* We need to sum degrees of freedom into doubles,
2870 * since floats give too low nrdf's above 3 million atoms.
2872 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
2873 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2874 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2875 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2876 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2878 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
2882 for (gmx::index i = 0;
2883 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; i++)
2886 clear_ivec(dof_vcm[i]);
2888 nrdf_vcm_sub[i] = 0;
2890 snew(nrdf2, natoms);
2891 for (const AtomProxy atomP : AtomRange(*mtop))
2893 const t_atom& local = atomP.atom();
2894 int i = atomP.globalAtomNumber();
2896 if (local.ptype == eptAtom || local.ptype == eptNucleus)
2898 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
2899 for (int d = 0; d < DIM; d++)
2901 if (opts->nFreeze[g][d] == 0)
2903 /* Add one DOF for particle i (counted as 2*1) */
2905 /* VCM group i has dim d as a DOF */
2906 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
2910 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
2912 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
2918 for (const gmx_molblock_t& molb : mtop->molblock)
2920 const gmx_moltype_t& molt = mtop->moltype[molb.type];
2921 const t_atom* atom = molt.atoms.atom;
2922 for (int mol = 0; mol < molb.nmol; mol++)
2924 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2926 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
2927 for (int i = 0; i < molt.ilist[ftype].size();)
2929 /* Subtract degrees of freedom for the constraints,
2930 * if the particles still have degrees of freedom left.
2931 * If one of the particles is a vsite or a shell, then all
2932 * constraint motion will go there, but since they do not
2933 * contribute to the constraints the degrees of freedom do not
2936 int ai = as + ia[i + 1];
2937 int aj = as + ia[i + 2];
2938 if (((atom[ia[i + 1]].ptype == eptNucleus) || (atom[ia[i + 1]].ptype == eptAtom))
2939 && ((atom[ia[i + 2]].ptype == eptNucleus) || (atom[ia[i + 2]].ptype == eptAtom)))
2957 imin = std::min(imin, nrdf2[ai]);
2958 jmin = std::min(jmin, nrdf2[aj]);
2961 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2963 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
2965 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2967 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
2970 i += interaction_function[ftype].nratoms + 1;
2973 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
2974 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
2976 /* Subtract 1 dof from every atom in the SETTLE */
2977 for (int j = 0; j < 3; j++)
2979 int ai = as + ia[i + 1 + j];
2980 imin = std::min(2, nrdf2[ai]);
2982 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2984 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2989 as += molt.atoms.nr;
2995 /* Correct nrdf for the COM constraints.
2996 * We correct using the TC and VCM group of the first atom
2997 * in the reference and pull group. If atoms in one pull group
2998 * belong to different TC or VCM groups it is anyhow difficult
2999 * to determine the optimal nrdf assignment.
3003 for (int i = 0; i < pull->ncoord; i++)
3005 if (pull->coord[i].eType != epullCONSTRAINT)
3012 for (int j = 0; j < 2; j++)
3014 const t_pull_group* pgrp;
3016 pgrp = &pull->group[pull->coord[i].group[j]];
3020 /* Subtract 1/2 dof from each group */
3021 int ai = pgrp->ind[0];
3022 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3024 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3026 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
3029 "Center of mass pulling constraints caused the number of degrees "
3030 "of freedom for temperature coupling group %s to be negative",
3031 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
3032 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
3037 /* We need to subtract the whole DOF from group j=1 */
3044 if (ir->nstcomm != 0)
3046 GMX_RELEASE_ASSERT(!groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty(),
3047 "Expect at least one group when removing COM motion");
3049 /* We remove COM motion up to dim ndof_com() */
3050 const int ndim_rm_vcm = ndof_com(ir);
3052 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3053 * the number of degrees of freedom in each vcm group when COM
3054 * translation is removed and 6 when rotation is removed as well.
3055 * Note that we do not and should not include the rest group here.
3057 for (gmx::index j = 0;
3058 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]); j++)
3060 switch (ir->comm_mode)
3063 case ecmLINEAR_ACCELERATION_CORRECTION:
3064 nrdf_vcm_sub[j] = 0;
3065 for (int d = 0; d < ndim_rm_vcm; d++)
3073 case ecmANGULAR: nrdf_vcm_sub[j] = 6; break;
3074 default: gmx_incons("Checking comm_mode");
3078 for (gmx::index i = 0;
3079 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
3081 /* Count the number of atoms of TC group i for every VCM group */
3082 for (gmx::index j = 0;
3083 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3088 for (int ai = 0; ai < natoms; ai++)
3090 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3092 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3096 /* Correct for VCM removal according to the fraction of each VCM
3097 * group present in this TC group.
3099 nrdf_uc = nrdf_tc[i];
3101 for (gmx::index j = 0;
3102 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3104 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3106 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3107 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3112 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3114 opts->nrdf[i] = nrdf_tc[i];
3115 if (opts->nrdf[i] < 0)
3119 fprintf(stderr, "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3120 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]], opts->nrdf[i]);
3128 sfree(nrdf_vcm_sub);
3131 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3133 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3134 * But since this is much larger than STRLEN, such a line can not be parsed.
3135 * The real maximum is the number of names that fit in a string: STRLEN/2.
3137 #define EGP_MAX (STRLEN / 2)
3141 auto names = gmx::splitString(val);
3142 if (names.size() % 2 != 0)
3144 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3146 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3148 for (size_t i = 0; i < names.size() / 2; i++)
3150 // TODO this needs to be replaced by a solution using std::find_if
3154 names[2 * i].c_str(),
3155 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3161 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3166 names[2 * i + 1].c_str(),
3167 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3173 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3175 if ((j < nr) && (k < nr))
3177 ir->opts.egp_flags[nr * j + k] |= flag;
3178 ir->opts.egp_flags[nr * k + j] |= flag;
3187 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3189 int ig = -1, i = 0, gind;
3193 /* Just a quick check here, more thorough checks are in mdrun */
3194 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3196 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3199 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3200 for (ig = 0; ig < swap->ngrp; ig++)
3202 swapg = &swap->grp[ig];
3203 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3204 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3208 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3209 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap", swap->grp[ig].molname, swapg->nat);
3210 snew(swapg->ind, swapg->nat);
3211 for (i = 0; i < swapg->nat; i++)
3213 swapg->ind[i] = grps->a[grps->index[gind] + i];
3218 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3224 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3229 ig = search_string(IMDgname, grps->nr, gnames);
3230 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3232 if (IMDgroup->nat > 0)
3235 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3237 IMDgname, IMDgroup->nat);
3238 snew(IMDgroup->ind, IMDgroup->nat);
3239 for (i = 0; i < IMDgroup->nat; i++)
3241 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3246 /* Checks whether atoms are both part of a COM removal group and frozen.
3247 * If a fully frozen atom is part of a COM removal group, it is removed
3248 * from the COM removal group. A note is issued if such atoms are present.
3249 * A warning is issued for atom with one or two dimensions frozen that
3250 * are part of a COM removal group (mdrun would need to compute COM mass
3251 * per dimension to handle this correctly).
3252 * Also issues a warning when non-frozen atoms are not part of a COM
3253 * removal group while COM removal is active.
3255 static void checkAndUpdateVcmFreezeGroupConsistency(SimulationGroups* groups,
3257 const t_grpopts& opts,
3260 const int vcmRestGroup =
3261 std::max(int(groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()), 1);
3263 int numFullyFrozenVcmAtoms = 0;
3264 int numPartiallyFrozenVcmAtoms = 0;
3265 int numNonVcmAtoms = 0;
3266 for (int a = 0; a < numAtoms; a++)
3268 const int freezeGroup = getGroupType(*groups, SimulationAtomGroupType::Freeze, a);
3269 int numFrozenDims = 0;
3270 for (int d = 0; d < DIM; d++)
3272 numFrozenDims += opts.nFreeze[freezeGroup][d];
3275 const int vcmGroup = getGroupType(*groups, SimulationAtomGroupType::MassCenterVelocityRemoval, a);
3276 if (vcmGroup < vcmRestGroup)
3278 if (numFrozenDims == DIM)
3280 /* Do not remove COM motion for this fully frozen atom */
3281 if (groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
3283 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(
3286 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
3287 numFullyFrozenVcmAtoms++;
3289 else if (numFrozenDims > 0)
3291 numPartiallyFrozenVcmAtoms++;
3294 else if (numFrozenDims < DIM)
3300 if (numFullyFrozenVcmAtoms > 0)
3302 std::string warningText = gmx::formatString(
3303 "There are %d atoms that are fully frozen and part of COMM removal group(s), "
3304 "removing these atoms from the COMM removal group(s)",
3305 numFullyFrozenVcmAtoms);
3306 warning_note(wi, warningText.c_str());
3308 if (numPartiallyFrozenVcmAtoms > 0 && numPartiallyFrozenVcmAtoms < numAtoms)
3310 std::string warningText = gmx::formatString(
3311 "There are %d atoms that are frozen along less then %d dimensions and part of COMM "
3312 "removal group(s), due to limitations in the code these still contribute to the "
3313 "mass of the COM along frozen dimensions and therefore the COMM correction will be "
3315 numPartiallyFrozenVcmAtoms, DIM);
3316 warning(wi, warningText.c_str());
3318 if (numNonVcmAtoms > 0)
3320 std::string warningText = gmx::formatString(
3321 "%d atoms are not part of any center of mass motion removal group.\n"
3322 "This may lead to artifacts.\n"
3323 "In most cases one should use one group for the whole system.",
3325 warning(wi, warningText.c_str());
3329 void do_index(const char* mdparin,
3333 const gmx::MdModulesNotifier& notifier,
3337 t_blocka* defaultIndexGroups;
3345 int i, j, k, restnm;
3346 bool bExcl, bTable, bAnneal;
3347 char warn_buf[STRLEN];
3351 fprintf(stderr, "processing index file...\n");
3355 snew(defaultIndexGroups, 1);
3356 snew(defaultIndexGroups->index, 1);
3358 atoms_all = gmx_mtop_global_atoms(mtop);
3359 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3360 done_atom(&atoms_all);
3364 defaultIndexGroups = init_index(ndx, &gnames);
3367 SimulationGroups* groups = &mtop->groups;
3368 natoms = mtop->natoms;
3369 symtab = &mtop->symtab;
3371 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3373 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3375 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3376 restnm = groups->groupNames.size() - 1;
3377 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3378 srenew(gnames, defaultIndexGroups->nr + 1);
3379 gnames[restnm] = *(groups->groupNames.back());
3381 set_warning_line(wi, mdparin, -1);
3383 auto temperatureCouplingTauValues = gmx::splitString(is->tau_t);
3384 auto temperatureCouplingReferenceValues = gmx::splitString(is->ref_t);
3385 auto temperatureCouplingGroupNames = gmx::splitString(is->tcgrps);
3386 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3387 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3390 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3392 temperatureCouplingGroupNames.size(), temperatureCouplingReferenceValues.size(),
3393 temperatureCouplingTauValues.size());
3396 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3397 do_numbering(natoms, groups, temperatureCouplingGroupNames, defaultIndexGroups, gnames,
3398 SimulationAtomGroupType::TemperatureCoupling, restnm,
3399 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3400 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3402 snew(ir->opts.nrdf, nr);
3403 snew(ir->opts.tau_t, nr);
3404 snew(ir->opts.ref_t, nr);
3405 if (ir->eI == eiBD && ir->bd_fric == 0)
3407 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3410 if (useReferenceTemperature)
3412 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3414 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3418 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3419 for (i = 0; (i < nr); i++)
3421 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3423 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3424 warning_error(wi, warn_buf);
3427 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3431 "tau-t = -1 is the value to signal that a group should not have "
3432 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3435 if (ir->opts.tau_t[i] >= 0)
3437 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3440 if (ir->etc != etcNO && ir->nsttcouple == -1)
3442 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3447 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3450 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3451 "md-vv; use either vrescale temperature with berendsen pressure or "
3452 "Nose-Hoover temperature with MTTK pressure");
3454 if (ir->epc == epcMTTK)
3456 if (ir->etc != etcNOSEHOOVER)
3459 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3464 if (ir->nstpcouple != ir->nsttcouple)
3466 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3467 ir->nstpcouple = ir->nsttcouple = mincouple;
3469 "for current Trotter decomposition methods with vv, nsttcouple and "
3470 "nstpcouple must be equal. Both have been reset to "
3471 "min(nsttcouple,nstpcouple) = %d",
3473 warning_note(wi, warn_buf);
3478 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3479 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3481 if (ETC_ANDERSEN(ir->etc))
3483 if (ir->nsttcouple != 1)
3487 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3488 "need for larger nsttcouple > 1, since no global parameters are computed. "
3489 "nsttcouple has been reset to 1");
3490 warning_note(wi, warn_buf);
3493 nstcmin = tcouple_min_integration_steps(ir->etc);
3496 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3499 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3500 "least %d times larger than nsttcouple*dt (%g)",
3501 ETCOUPLTYPE(ir->etc), tau_min, nstcmin, ir->nsttcouple * ir->delta_t);
3502 warning(wi, warn_buf);
3505 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3506 for (i = 0; (i < nr); i++)
3508 if (ir->opts.ref_t[i] < 0)
3510 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3513 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3514 if we are in this conditional) if mc_temp is negative */
3515 if (ir->expandedvals->mc_temp < 0)
3517 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3521 /* Simulated annealing for each group. There are nr groups */
3522 auto simulatedAnnealingGroupNames = gmx::splitString(is->anneal);
3523 if (simulatedAnnealingGroupNames.size() == 1
3524 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3526 simulatedAnnealingGroupNames.resize(0);
3528 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3530 gmx_fatal(FARGS, "Wrong number of annealing values: %zu (for %d groups)\n",
3531 simulatedAnnealingGroupNames.size(), nr);
3535 snew(ir->opts.annealing, nr);
3536 snew(ir->opts.anneal_npoints, nr);
3537 snew(ir->opts.anneal_time, nr);
3538 snew(ir->opts.anneal_temp, nr);
3539 for (i = 0; i < nr; i++)
3541 ir->opts.annealing[i] = eannNO;
3542 ir->opts.anneal_npoints[i] = 0;
3543 ir->opts.anneal_time[i] = nullptr;
3544 ir->opts.anneal_temp[i] = nullptr;
3546 if (!simulatedAnnealingGroupNames.empty())
3549 for (i = 0; i < nr; i++)
3551 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3553 ir->opts.annealing[i] = eannNO;
3555 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3557 ir->opts.annealing[i] = eannSINGLE;
3560 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3562 ir->opts.annealing[i] = eannPERIODIC;
3568 /* Read the other fields too */
3569 auto simulatedAnnealingPoints = gmx::splitString(is->anneal_npoints);
3570 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3572 gmx_fatal(FARGS, "Found %zu annealing-npoints values for %zu groups\n",
3573 simulatedAnnealingPoints.size(), simulatedAnnealingGroupNames.size());
3575 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3576 size_t numSimulatedAnnealingFields = 0;
3577 for (i = 0; i < nr; i++)
3579 if (ir->opts.anneal_npoints[i] == 1)
3583 "Please specify at least a start and an end point for annealing\n");
3585 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3586 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3587 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3590 auto simulatedAnnealingTimes = gmx::splitString(is->anneal_time);
3592 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3594 gmx_fatal(FARGS, "Found %zu annealing-time values, wanted %zu\n",
3595 simulatedAnnealingTimes.size(), numSimulatedAnnealingFields);
3597 auto simulatedAnnealingTemperatures = gmx::splitString(is->anneal_temp);
3598 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3600 gmx_fatal(FARGS, "Found %zu annealing-temp values, wanted %zu\n",
3601 simulatedAnnealingTemperatures.size(), numSimulatedAnnealingFields);
3604 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3605 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3606 convertReals(wi, simulatedAnnealingTimes, "anneal-time",
3607 allSimulatedAnnealingTimes.data());
3608 convertReals(wi, simulatedAnnealingTemperatures, "anneal-temp",
3609 allSimulatedAnnealingTemperatures.data());
3610 for (i = 0, k = 0; i < nr; i++)
3612 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3614 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3615 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3618 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3620 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3626 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3629 "Annealing timepoints out of order: t=%f comes after "
3631 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j - 1]);
3634 if (ir->opts.anneal_temp[i][j] < 0)
3636 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n",
3637 ir->opts.anneal_temp[i][j]);
3642 /* Print out some summary information, to make sure we got it right */
3643 for (i = 0; i < nr; i++)
3645 if (ir->opts.annealing[i] != eannNO)
3647 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3648 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3649 *(groups->groupNames[j]), eann_names[ir->opts.annealing[i]],
3650 ir->opts.anneal_npoints[i]);
3651 fprintf(stderr, "Time (ps) Temperature (K)\n");
3652 /* All terms except the last one */
3653 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3655 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3656 ir->opts.anneal_temp[i][j]);
3659 /* Finally the last one */
3660 j = ir->opts.anneal_npoints[i] - 1;
3661 if (ir->opts.annealing[i] == eannSINGLE)
3663 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j],
3664 ir->opts.anneal_temp[i][j]);
3668 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3669 ir->opts.anneal_temp[i][j]);
3670 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3673 "There is a temperature jump when your annealing "
3685 for (int i = 1; i < ir->pull->ngroup; i++)
3687 const int gid = search_string(is->pull_grp[i], defaultIndexGroups->nr, gnames);
3688 GMX_ASSERT(defaultIndexGroups, "Must have initialized default index groups");
3689 atomGroupRangeValidation(natoms, gid, *defaultIndexGroups);
3692 make_pull_groups(ir->pull, is->pull_grp, defaultIndexGroups, gnames);
3694 make_pull_coords(ir->pull);
3699 make_rotation_groups(ir->rot, is->rot_grp, defaultIndexGroups, gnames);
3702 if (ir->eSwapCoords != eswapNO)
3704 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3707 /* Make indices for IMD session */
3710 make_IMD_group(ir->imd, is->imd_grp, defaultIndexGroups, gnames);
3713 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3714 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3715 notifier.notifier_.notify(defaultIndexGroupsAndNames);
3717 auto accelerations = gmx::splitString(is->acc);
3718 auto accelerationGroupNames = gmx::splitString(is->accgrps);
3719 if (accelerationGroupNames.size() * DIM != accelerations.size())
3721 gmx_fatal(FARGS, "Invalid Acceleration input: %zu groups and %zu acc. values",
3722 accelerationGroupNames.size(), accelerations.size());
3724 do_numbering(natoms, groups, accelerationGroupNames, defaultIndexGroups, gnames,
3725 SimulationAtomGroupType::Acceleration, restnm, egrptpALL_GENREST, bVerbose, wi);
3726 nr = groups->groups[SimulationAtomGroupType::Acceleration].size();
3727 snew(ir->opts.acc, nr);
3728 ir->opts.ngacc = nr;
3730 convertRvecs(wi, accelerations, "anneal-time", ir->opts.acc);
3732 auto freezeDims = gmx::splitString(is->frdim);
3733 auto freezeGroupNames = gmx::splitString(is->freeze);
3734 if (freezeDims.size() != DIM * freezeGroupNames.size())
3736 gmx_fatal(FARGS, "Invalid Freezing input: %zu groups and %zu freeze values",
3737 freezeGroupNames.size(), freezeDims.size());
3739 do_numbering(natoms, groups, freezeGroupNames, defaultIndexGroups, gnames,
3740 SimulationAtomGroupType::Freeze, restnm, egrptpALL_GENREST, bVerbose, wi);
3741 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3742 ir->opts.ngfrz = nr;
3743 snew(ir->opts.nFreeze, nr);
3744 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3746 for (j = 0; (j < DIM); j++, k++)
3748 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3749 if (!ir->opts.nFreeze[i][j])
3751 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3754 "Please use Y(ES) or N(O) for freezedim only "
3756 freezeDims[k].c_str());
3757 warning(wi, warn_buf);
3762 for (; (i < nr); i++)
3764 for (j = 0; (j < DIM); j++)
3766 ir->opts.nFreeze[i][j] = 0;
3770 auto energyGroupNames = gmx::splitString(is->energy);
3771 do_numbering(natoms, groups, energyGroupNames, defaultIndexGroups, gnames,
3772 SimulationAtomGroupType::EnergyOutput, restnm, egrptpALL_GENREST, bVerbose, wi);
3773 add_wall_energrps(groups, ir->nwall, symtab);
3774 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3775 auto vcmGroupNames = gmx::splitString(is->vcm);
3776 do_numbering(natoms, groups, vcmGroupNames, defaultIndexGroups, gnames,
3777 SimulationAtomGroupType::MassCenterVelocityRemoval, restnm,
3778 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3780 if (ir->comm_mode != ecmNO)
3782 checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
3785 /* Now we have filled the freeze struct, so we can calculate NRDF */
3786 calc_nrdf(mtop, ir, gnames);
3788 auto user1GroupNames = gmx::splitString(is->user1);
3789 do_numbering(natoms, groups, user1GroupNames, defaultIndexGroups, gnames,
3790 SimulationAtomGroupType::User1, restnm, egrptpALL_GENREST, bVerbose, wi);
3791 auto user2GroupNames = gmx::splitString(is->user2);
3792 do_numbering(natoms, groups, user2GroupNames, defaultIndexGroups, gnames,
3793 SimulationAtomGroupType::User2, restnm, egrptpALL_GENREST, bVerbose, wi);
3794 auto compressedXGroupNames = gmx::splitString(is->x_compressed_groups);
3795 do_numbering(natoms, groups, compressedXGroupNames, defaultIndexGroups, gnames,
3796 SimulationAtomGroupType::CompressedPositionOutput, restnm, egrptpONE, bVerbose, wi);
3797 auto orirefFitGroupNames = gmx::splitString(is->orirefitgrp);
3798 do_numbering(natoms, groups, orirefFitGroupNames, defaultIndexGroups, gnames,
3799 SimulationAtomGroupType::OrientationRestraintsFit, restnm, egrptpALL_GENREST,
3802 /* QMMM input processing */
3803 auto qmGroupNames = gmx::splitString(is->QMMM);
3804 auto qmMethods = gmx::splitString(is->QMmethod);
3805 auto qmBasisSets = gmx::splitString(is->QMbasis);
3806 if (ir->eI != eiMimic)
3808 if (qmMethods.size() != qmGroupNames.size() || qmBasisSets.size() != qmGroupNames.size())
3811 "Invalid QMMM input: %zu groups %zu basissets"
3812 " and %zu methods\n",
3813 qmGroupNames.size(), qmBasisSets.size(), qmMethods.size());
3815 /* group rest, if any, is always MM! */
3816 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3817 SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
3818 nr = qmGroupNames.size(); /*atoms->grps[egcQMMM].nr;*/
3819 ir->opts.ngQM = qmGroupNames.size();
3820 snew(ir->opts.QMmethod, nr);
3821 snew(ir->opts.QMbasis, nr);
3822 for (i = 0; i < nr; i++)
3824 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3825 * converted to the corresponding enum in names.c
3827 ir->opts.QMmethod[i] = search_QMstring(qmMethods[i].c_str(), eQMmethodNR, eQMmethod_names);
3828 ir->opts.QMbasis[i] = search_QMstring(qmBasisSets[i].c_str(), eQMbasisNR, eQMbasis_names);
3830 auto qmMultiplicities = gmx::splitString(is->QMmult);
3831 auto qmCharges = gmx::splitString(is->QMcharge);
3832 auto qmbSH = gmx::splitString(is->bSH);
3833 snew(ir->opts.QMmult, nr);
3834 snew(ir->opts.QMcharge, nr);
3835 snew(ir->opts.bSH, nr);
3836 convertInts(wi, qmMultiplicities, "QMmult", ir->opts.QMmult);
3837 convertInts(wi, qmCharges, "QMcharge", ir->opts.QMcharge);
3838 convertYesNos(wi, qmbSH, "bSH", ir->opts.bSH);
3840 auto CASelectrons = gmx::splitString(is->CASelectrons);
3841 auto CASorbitals = gmx::splitString(is->CASorbitals);
3842 snew(ir->opts.CASelectrons, nr);
3843 snew(ir->opts.CASorbitals, nr);
3844 convertInts(wi, CASelectrons, "CASelectrons", ir->opts.CASelectrons);
3845 convertInts(wi, CASorbitals, "CASOrbitals", ir->opts.CASorbitals);
3847 auto SAon = gmx::splitString(is->SAon);
3848 auto SAoff = gmx::splitString(is->SAoff);
3849 auto SAsteps = gmx::splitString(is->SAsteps);
3850 snew(ir->opts.SAon, nr);
3851 snew(ir->opts.SAoff, nr);
3852 snew(ir->opts.SAsteps, nr);
3853 convertInts(wi, SAon, "SAon", ir->opts.SAon);
3854 convertInts(wi, SAoff, "SAoff", ir->opts.SAoff);
3855 convertInts(wi, SAsteps, "SAsteps", ir->opts.SAsteps);
3860 if (qmGroupNames.size() > 1)
3862 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
3864 /* group rest, if any, is always MM! */
3865 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3866 SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
3868 ir->opts.ngQM = qmGroupNames.size();
3871 /* end of QMMM input */
3875 for (auto group : gmx::keysOf(groups->groups))
3877 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
3878 for (const auto& entry : groups->groups[group])
3880 fprintf(stderr, " %s", *(groups->groupNames[entry]));
3882 fprintf(stderr, "\n");
3886 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3887 snew(ir->opts.egp_flags, nr * nr);
3889 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3890 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3892 warning_error(wi, "Energy group exclusions are currently not supported");
3894 if (bExcl && EEL_FULL(ir->coulombtype))
3896 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3899 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3900 if (bTable && !(ir->vdwtype == evdwUSER) && !(ir->coulombtype == eelUSER)
3901 && !(ir->coulombtype == eelPMEUSER) && !(ir->coulombtype == eelPMEUSERSWITCH))
3904 "Can only have energy group pair tables in combination with user tables for VdW "
3908 /* final check before going out of scope if simulated tempering variables
3909 * need to be set to default values.
3911 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
3913 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
3914 warning(wi, gmx::formatString(
3915 "the value for nstexpanded was not specified for "
3916 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
3917 "by default, but it is recommended to set it to an explicit value!",
3918 ir->expandedvals->nstexpanded));
3920 for (i = 0; (i < defaultIndexGroups->nr); i++)
3925 done_blocka(defaultIndexGroups);
3926 sfree(defaultIndexGroups);
3930 static void check_disre(const gmx_mtop_t* mtop)
3932 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3934 const gmx_ffparams_t& ffparams = mtop->ffparams;
3937 for (int i = 0; i < ffparams.numTypes(); i++)
3939 int ftype = ffparams.functype[i];
3940 if (ftype == F_DISRES)
3942 int label = ffparams.iparams[i].disres.label;
3943 if (label == old_label)
3945 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3954 "Found %d double distance restraint indices,\n"
3955 "probably the parameters for multiple pairs in one restraint "
3956 "are not identical\n",
3962 static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t* sys, const bool posres_only, ivec AbsRef)
3965 gmx_mtop_ilistloop_t iloop;
3967 const t_iparams* pr;
3974 for (d = 0; d < DIM; d++)
3976 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3978 /* Check for freeze groups */
3979 for (g = 0; g < ir->opts.ngfrz; g++)
3981 for (d = 0; d < DIM; d++)
3983 if (ir->opts.nFreeze[g][d] != 0)
3991 /* Check for position restraints */
3992 iloop = gmx_mtop_ilistloop_init(sys);
3993 while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
3995 if (nmol > 0 && (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3997 for (i = 0; i < (*ilist)[F_POSRES].size(); i += 2)
3999 pr = &sys->ffparams.iparams[(*ilist)[F_POSRES].iatoms[i]];
4000 for (d = 0; d < DIM; d++)
4002 if (pr->posres.fcA[d] != 0)
4008 for (i = 0; i < (*ilist)[F_FBPOSRES].size(); i += 2)
4010 /* Check for flat-bottom posres */
4011 pr = &sys->ffparams.iparams[(*ilist)[F_FBPOSRES].iatoms[i]];
4012 if (pr->fbposres.k != 0)
4014 switch (pr->fbposres.geom)
4016 case efbposresSPHERE: AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1; break;
4017 case efbposresCYLINDERX: AbsRef[YY] = AbsRef[ZZ] = 1; break;
4018 case efbposresCYLINDERY: AbsRef[XX] = AbsRef[ZZ] = 1; break;
4019 case efbposresCYLINDER:
4020 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
4021 case efbposresCYLINDERZ: AbsRef[XX] = AbsRef[YY] = 1; break;
4022 case efbposresX: /* d=XX */
4023 case efbposresY: /* d=YY */
4024 case efbposresZ: /* d=ZZ */
4025 d = pr->fbposres.geom - efbposresX;
4030 " Invalid geometry for flat-bottom position restraint.\n"
4031 "Expected nr between 1 and %d. Found %d\n",
4032 efbposresNR - 1, pr->fbposres.geom);
4039 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
4042 static void check_combination_rule_differences(const gmx_mtop_t* mtop,
4044 bool* bC6ParametersWorkWithGeometricRules,
4045 bool* bC6ParametersWorkWithLBRules,
4046 bool* bLBRulesPossible)
4048 int ntypes, tpi, tpj;
4051 double c6i, c6j, c12i, c12j;
4052 double c6, c6_geometric, c6_LB;
4053 double sigmai, sigmaj, epsi, epsj;
4054 bool bCanDoLBRules, bCanDoGeometricRules;
4057 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
4058 * force-field floating point parameters.
4061 ptr = getenv("GMX_LJCOMB_TOL");
4065 double gmx_unused canary;
4067 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
4070 "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
4075 *bC6ParametersWorkWithLBRules = TRUE;
4076 *bC6ParametersWorkWithGeometricRules = TRUE;
4077 bCanDoLBRules = TRUE;
4078 ntypes = mtop->ffparams.atnr;
4079 snew(typecount, ntypes);
4080 gmx_mtop_count_atomtypes(mtop, state, typecount);
4081 *bLBRulesPossible = TRUE;
4082 for (tpi = 0; tpi < ntypes; ++tpi)
4084 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
4085 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
4086 for (tpj = tpi; tpj < ntypes; ++tpj)
4088 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
4089 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
4090 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
4091 c6_geometric = std::sqrt(c6i * c6j);
4092 if (!gmx_numzero(c6_geometric))
4094 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4096 sigmai = gmx::sixthroot(c12i / c6i);
4097 sigmaj = gmx::sixthroot(c12j / c6j);
4098 epsi = c6i * c6i / (4.0 * c12i);
4099 epsj = c6j * c6j / (4.0 * c12j);
4100 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4104 *bLBRulesPossible = FALSE;
4105 c6_LB = c6_geometric;
4107 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4112 *bC6ParametersWorkWithLBRules = FALSE;
4115 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4117 if (!bCanDoGeometricRules)
4119 *bC6ParametersWorkWithGeometricRules = FALSE;
4126 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t* mtop, warninp_t wi)
4128 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4130 check_combination_rule_differences(mtop, 0, &bC6ParametersWorkWithGeometricRules,
4131 &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4132 if (ir->ljpme_combination_rule == eljpmeLB)
4134 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4137 "You are using arithmetic-geometric combination rules "
4138 "in LJ-PME, but your non-bonded C6 parameters do not "
4139 "follow these rules.");
4144 if (!bC6ParametersWorkWithGeometricRules)
4146 if (ir->eDispCorr != edispcNO)
4149 "You are using geometric combination rules in "
4150 "LJ-PME, but your non-bonded C6 parameters do "
4151 "not follow these rules. "
4152 "This will introduce very small errors in the forces and energies in "
4153 "your simulations. Dispersion correction will correct total energy "
4154 "and/or pressure for isotropic systems, but not forces or surface "
4160 "You are using geometric combination rules in "
4161 "LJ-PME, but your non-bonded C6 parameters do "
4162 "not follow these rules. "
4163 "This will introduce very small errors in the forces and energies in "
4164 "your simulations. If your system is homogeneous, consider using "
4165 "dispersion correction "
4166 "for the total energy and pressure.");
4172 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4174 char err_buf[STRLEN];
4179 gmx_mtop_atomloop_block_t aloopb;
4181 char warn_buf[STRLEN];
4183 set_warning_line(wi, mdparin, -1);
4185 if (absolute_reference(ir, sys, false, AbsRef))
4188 "Removing center of mass motion in the presence of position restraints might "
4189 "cause artifacts. When you are using position restraints to equilibrate a "
4190 "macro-molecule, the artifacts are usually negligible.");
4193 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 && ir->nstlist > 1
4194 && ((EI_MD(ir->eI) || EI_SD(ir->eI)) && (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4196 /* Check if a too small Verlet buffer might potentially
4197 * cause more drift than the thermostat can couple off.
4199 /* Temperature error fraction for warning and suggestion */
4200 const real T_error_warn = 0.002;
4201 const real T_error_suggest = 0.001;
4202 /* For safety: 2 DOF per atom (typical with constraints) */
4203 const real nrdf_at = 2;
4204 real T, tau, max_T_error;
4209 for (i = 0; i < ir->opts.ngtc; i++)
4211 T = std::max(T, ir->opts.ref_t[i]);
4212 tau = std::max(tau, ir->opts.tau_t[i]);
4216 /* This is a worst case estimate of the temperature error,
4217 * assuming perfect buffer estimation and no cancelation
4218 * of errors. The factor 0.5 is because energy distributes
4219 * equally over Ekin and Epot.
4221 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * BOLTZ * T);
4222 if (max_T_error > T_error_warn)
4225 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4226 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4227 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4228 "%.0e or decrease tau_t.",
4229 ir->verletbuf_tol, T, tau, 100 * max_T_error, 100 * T_error_suggest,
4230 ir->verletbuf_tol * T_error_suggest / max_T_error);
4231 warning(wi, warn_buf);
4236 if (ETC_ANDERSEN(ir->etc))
4240 for (i = 0; i < ir->opts.ngtc; i++)
4243 "all tau_t must currently be equal using Andersen temperature control, "
4244 "violated for group %d",
4246 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4248 "all tau_t must be positive using Andersen temperature control, "
4250 i, ir->opts.tau_t[i]);
4251 CHECK(ir->opts.tau_t[i] < 0);
4254 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4256 for (i = 0; i < ir->opts.ngtc; i++)
4258 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4260 "tau_t/delta_t for group %d for temperature control method %s must be a "
4261 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4262 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4264 i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
4265 CHECK(nsteps % ir->nstcomm != 0);
4270 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD && ir->comm_mode == ecmNO
4271 && !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) && !ETC_ANDERSEN(ir->etc))
4274 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4275 "rounding errors can lead to build up of kinetic energy of the center of mass");
4278 if (ir->epc == epcPARRINELLORAHMAN && ir->etc == etcNOSEHOOVER)
4281 for (int g = 0; g < ir->opts.ngtc; g++)
4283 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4285 if (ir->tau_p < 1.9 * tau_t_max)
4287 std::string message = gmx::formatString(
4288 "With %s T-coupling and %s p-coupling, "
4289 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4290 etcoupl_names[ir->etc], epcoupl_names[ir->epc], "tau-p", ir->tau_p, "tau-t",
4292 warning(wi, message.c_str());
4296 /* Check for pressure coupling with absolute position restraints */
4297 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4299 absolute_reference(ir, sys, TRUE, AbsRef);
4301 for (m = 0; m < DIM; m++)
4303 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4306 "You are using pressure coupling with absolute position restraints, "
4307 "this will give artifacts. Use the refcoord_scaling option.");
4315 aloopb = gmx_mtop_atomloop_block_init(sys);
4317 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4319 if (atom->q != 0 || atom->qB != 0)
4327 if (EEL_FULL(ir->coulombtype))
4330 "You are using full electrostatics treatment %s for a system without charges.\n"
4331 "This costs a lot of performance for just processing zeros, consider using %s "
4333 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4334 warning(wi, err_buf);
4339 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
4342 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4343 "You might want to consider using %s electrostatics.\n",
4345 warning_note(wi, err_buf);
4349 /* Check if combination rules used in LJ-PME are the same as in the force field */
4350 if (EVDW_PME(ir->vdwtype))
4352 check_combination_rules(ir, sys, wi);
4355 /* Generalized reaction field */
4356 if (ir->coulombtype == eelGRF_NOTUSED)
4359 "Generalized reaction-field electrostatics is no longer supported. "
4360 "You can use normal reaction-field instead and compute the reaction-field "
4361 "constant by hand.");
4365 for (int i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4367 for (m = 0; (m < DIM); m++)
4369 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4378 snew(mgrp, sys->groups.groups[SimulationAtomGroupType::Acceleration].size());
4379 for (const AtomProxy atomP : AtomRange(*sys))
4381 const t_atom& local = atomP.atom();
4382 int i = atomP.globalAtomNumber();
4383 mgrp[getGroupType(sys->groups, SimulationAtomGroupType::Acceleration, i)] += local.m;
4386 for (i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4388 for (m = 0; (m < DIM); m++)
4390 acc[m] += ir->opts.acc[i][m] * mgrp[i];
4394 for (m = 0; (m < DIM); m++)
4396 if (fabs(acc[m]) > 1e-6)
4398 const char* dim[DIM] = { "X", "Y", "Z" };
4399 fprintf(stderr, "Net Acceleration in %s direction, will %s be corrected\n", dim[m],
4400 ir->nstcomm != 0 ? "" : "not");
4401 if (ir->nstcomm != 0 && m < ndof_com(ir))
4405 (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4407 ir->opts.acc[i][m] -= acc[m];
4415 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0
4416 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4418 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4426 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4428 if (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0)
4430 absolute_reference(ir, sys, FALSE, AbsRef);
4431 for (m = 0; m < DIM; m++)
4433 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4436 "You are using an absolute reference for pulling, but the rest of "
4437 "the system does not have an absolute reference. This will lead to "
4446 for (i = 0; i < 3; i++)
4448 for (m = 0; m <= i; m++)
4450 if ((ir->epc != epcNO && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4452 for (c = 0; c < ir->pull->ncoord; c++)
4454 if (ir->pull->coord[c].eGeom == epullgDIRPBC && ir->pull->coord[c].vec[m] != 0)
4457 "Can not have dynamic box while using pull geometry '%s' "
4459 EPULLGEOM(ir->pull->coord[c].eGeom), 'x' + m);
4470 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4472 char warn_buf[STRLEN];
4475 ptr = check_box(ir->ePBC, box);
4478 warning_error(wi, ptr);
4481 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4483 if (ir->shake_tol <= 0.0)
4485 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4486 warning_error(wi, warn_buf);
4490 if ((ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4492 /* If we have Lincs constraints: */
4493 if (ir->eI == eiMD && ir->etc == etcNO && ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4496 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4497 warning_note(wi, warn_buf);
4500 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4503 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4505 warning_note(wi, warn_buf);
4507 if (ir->epc == epcMTTK)
4509 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4513 if (bHasAnyConstraints && ir->epc == epcMTTK)
4515 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4518 if (ir->LincsWarnAngle > 90.0)
4520 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4521 warning(wi, warn_buf);
4522 ir->LincsWarnAngle = 90.0;
4525 if (ir->ePBC != epbcNONE)
4527 if (ir->nstlist == 0)
4530 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4531 "atoms might cause the simulation to crash.");
4533 if (gmx::square(ir->rlist) >= max_cutoff2(ir->ePBC, box))
4536 "ERROR: The cut-off length is longer than half the shortest box vector or "
4537 "longer than the smallest box diagonal element. Increase the box size or "
4538 "decrease rlist.\n");
4539 warning_error(wi, warn_buf);