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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");
1407 // cosine acceleration is only supported in leap-frog
1408 if (ir->cos_accel != 0.0 && ir->eI != eiMD)
1410 warning_error(wi, "cos-acceleration is only supported by integrator = md");
1414 /* interpret a number of doubles from a string and put them in an array,
1415 after allocating space for them.
1416 str = the input string
1417 n = the (pre-allocated) number of doubles read
1418 r = the output array of doubles. */
1419 static void parse_n_real(char* str, int* n, real** r, warninp_t wi)
1421 auto values = gmx::splitString(str);
1425 for (int i = 0; i < *n; i++)
1429 (*r)[i] = gmx::fromString<real>(values[i]);
1431 catch (gmx::GromacsException&)
1433 warning_error(wi, "Invalid value " + values[i]
1434 + " in string in mdp file. Expected a real number.");
1440 static void do_fep_params(t_inputrec* ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
1443 int i, j, max_n_lambda, nweights, nfep[efptNR];
1444 t_lambda* fep = ir->fepvals;
1445 t_expanded* expand = ir->expandedvals;
1446 real** count_fep_lambdas;
1447 bool bOneLambda = TRUE;
1449 snew(count_fep_lambdas, efptNR);
1451 /* FEP input processing */
1452 /* first, identify the number of lambda values for each type.
1453 All that are nonzero must have the same number */
1455 for (i = 0; i < efptNR; i++)
1457 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
1460 /* now, determine the number of components. All must be either zero, or equal. */
1463 for (i = 0; i < efptNR; i++)
1465 if (nfep[i] > max_n_lambda)
1467 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1468 must have the same number if its not zero.*/
1473 for (i = 0; i < efptNR; i++)
1477 ir->fepvals->separate_dvdl[i] = FALSE;
1479 else if (nfep[i] == max_n_lambda)
1481 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute
1482 the derivative with respect to the temperature currently */
1484 ir->fepvals->separate_dvdl[i] = TRUE;
1490 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1492 nfep[i], efpt_names[i], max_n_lambda);
1495 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1496 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1498 /* the number of lambdas is the number we've read in, which is either zero
1499 or the same for all */
1500 fep->n_lambda = max_n_lambda;
1502 /* allocate space for the array of lambda values */
1503 snew(fep->all_lambda, efptNR);
1504 /* if init_lambda is defined, we need to set lambda */
1505 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1507 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1509 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1510 for (i = 0; i < efptNR; i++)
1512 snew(fep->all_lambda[i], fep->n_lambda);
1513 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1516 for (j = 0; j < fep->n_lambda; j++)
1518 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1520 sfree(count_fep_lambdas[i]);
1523 sfree(count_fep_lambdas);
1525 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1526 internal bookkeeping -- for now, init_lambda */
1528 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1530 for (i = 0; i < fep->n_lambda; i++)
1532 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1536 /* check to see if only a single component lambda is defined, and soft core is defined.
1537 In this case, turn on coulomb soft core */
1539 if (max_n_lambda == 0)
1545 for (i = 0; i < efptNR; i++)
1547 if ((nfep[i] != 0) && (i != efptFEP))
1553 if ((bOneLambda) && (fep->sc_alpha > 0))
1555 fep->bScCoul = TRUE;
1558 /* Fill in the others with the efptFEP if they are not explicitly
1559 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1560 they are all zero. */
1562 for (i = 0; i < efptNR; i++)
1564 if ((nfep[i] == 0) && (i != efptFEP))
1566 for (j = 0; j < fep->n_lambda; j++)
1568 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1574 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1575 if (fep->sc_r_power == 48)
1577 if (fep->sc_alpha > 0.1)
1580 "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004",
1585 /* now read in the weights */
1586 parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
1589 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1591 else if (nweights != fep->n_lambda)
1593 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1594 nweights, fep->n_lambda);
1596 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1598 expand->nstexpanded = fep->nstdhdl;
1599 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1604 static void do_simtemp_params(t_inputrec* ir)
1607 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1608 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1611 static void convertYesNos(warninp_t /*wi*/,
1612 gmx::ArrayRef<const std::string> inputs,
1613 const char* /*name*/,
1617 for (const auto& input : inputs)
1619 outputs[i] = gmx::equalCaseInsensitive(input, "Y", 1);
1624 template<typename T>
1625 void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
1628 for (const auto& input : inputs)
1632 outputs[i] = gmx::fromStdString<T>(input);
1634 catch (gmx::GromacsException&)
1636 auto message = gmx::formatString(
1637 "Invalid value for mdp option %s. %s should only consist of integers separated "
1640 warning_error(wi, message);
1646 static void convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, real* outputs)
1649 for (const auto& input : inputs)
1653 outputs[i] = gmx::fromString<real>(input);
1655 catch (gmx::GromacsException&)
1657 auto message = gmx::formatString(
1658 "Invalid value for mdp option %s. %s should only consist of real numbers "
1659 "separated by spaces.",
1661 warning_error(wi, message);
1667 static void convertRvecs(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, rvec* outputs)
1670 for (const auto& input : inputs)
1674 outputs[i][d] = gmx::fromString<real>(input);
1676 catch (gmx::GromacsException&)
1678 auto message = gmx::formatString(
1679 "Invalid value for mdp option %s. %s should only consist of real numbers "
1680 "separated by spaces.",
1682 warning_error(wi, message);
1693 static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
1695 opts->wall_atomtype[0] = nullptr;
1696 opts->wall_atomtype[1] = nullptr;
1698 ir->wall_atomtype[0] = -1;
1699 ir->wall_atomtype[1] = -1;
1700 ir->wall_density[0] = 0;
1701 ir->wall_density[1] = 0;
1705 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1706 if (wallAtomTypes.size() != size_t(ir->nwall))
1708 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %zu", ir->nwall,
1709 wallAtomTypes.size());
1711 for (int i = 0; i < ir->nwall; i++)
1713 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1716 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1718 auto wallDensity = gmx::splitString(wall_density);
1719 if (wallDensity.size() != size_t(ir->nwall))
1721 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %zu", ir->nwall,
1722 wallDensity.size());
1724 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1725 for (int i = 0; i < ir->nwall; i++)
1727 if (ir->wall_density[i] <= 0)
1729 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1736 static void add_wall_energrps(SimulationGroups* groups, int nwall, t_symtab* symtab)
1740 AtomGroupIndices* grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1741 for (int i = 0; i < nwall; i++)
1743 groups->groupNames.emplace_back(put_symtab(symtab, gmx::formatString("wall%d", i).c_str()));
1744 grps->emplace_back(groups->groupNames.size() - 1);
1749 static void read_expandedparams(std::vector<t_inpfile>* inp, t_expanded* expand, warninp_t wi)
1751 /* read expanded ensemble parameters */
1752 printStringNewline(inp, "expanded ensemble variables");
1753 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1754 expand->elamstats = get_eeenum(inp, "lmc-stats", elamstats_names, wi);
1755 expand->elmcmove = get_eeenum(inp, "lmc-move", elmcmove_names, wi);
1756 expand->elmceq = get_eeenum(inp, "lmc-weights-equil", elmceq_names, wi);
1757 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1758 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1759 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1760 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1761 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1762 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1763 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1764 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1765 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1766 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1767 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1768 expand->bSymmetrizedTMatrix =
1769 (get_eeenum(inp, "symmetrized-transition-matrix", yesno_names, wi) != 0);
1770 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1771 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1772 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1773 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1774 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1775 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1776 expand->bWLoneovert = (get_eeenum(inp, "wl-oneovert", yesno_names, wi) != 0);
1779 /*! \brief Return whether an end state with the given coupling-lambda
1780 * value describes fully-interacting VDW.
1782 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1783 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1785 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1787 return (couple_lambda_value == ecouplamVDW || couple_lambda_value == ecouplamVDWQ);
1793 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1796 explicit MdpErrorHandler(warninp_t wi) : wi_(wi), mapping_(nullptr) {}
1798 void setBackMapping(const gmx::IKeyValueTreeBackMapping& mapping) { mapping_ = &mapping; }
1800 bool onError(gmx::UserInputError* ex, const gmx::KeyValueTreePath& context) override
1803 gmx::formatString("Error in mdp option \"%s\":", getOptionName(context).c_str()));
1804 std::string message = gmx::formatExceptionMessageToString(*ex);
1805 warning_error(wi_, message.c_str());
1810 std::string getOptionName(const gmx::KeyValueTreePath& context)
1812 if (mapping_ != nullptr)
1814 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1815 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1818 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1823 const gmx::IKeyValueTreeBackMapping* mapping_;
1828 void get_ir(const char* mdparin,
1829 const char* mdparout,
1830 gmx::MDModules* mdModules,
1833 WriteMdpHeader writeMdpHeader,
1837 double dumdub[2][6];
1839 char warn_buf[STRLEN];
1840 t_lambda* fep = ir->fepvals;
1841 t_expanded* expand = ir->expandedvals;
1843 const char* no_names[] = { "no", nullptr };
1845 init_inputrec_strings();
1846 gmx::TextInputFile stream(mdparin);
1847 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1849 snew(dumstr[0], STRLEN);
1850 snew(dumstr[1], STRLEN);
1852 /* ignore the following deprecated commands */
1853 replace_inp_entry(inp, "title", nullptr);
1854 replace_inp_entry(inp, "cpp", nullptr);
1855 replace_inp_entry(inp, "domain-decomposition", nullptr);
1856 replace_inp_entry(inp, "andersen-seed", nullptr);
1857 replace_inp_entry(inp, "dihre", nullptr);
1858 replace_inp_entry(inp, "dihre-fc", nullptr);
1859 replace_inp_entry(inp, "dihre-tau", nullptr);
1860 replace_inp_entry(inp, "nstdihreout", nullptr);
1861 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1862 replace_inp_entry(inp, "optimize-fft", nullptr);
1863 replace_inp_entry(inp, "adress_type", nullptr);
1864 replace_inp_entry(inp, "adress_const_wf", nullptr);
1865 replace_inp_entry(inp, "adress_ex_width", nullptr);
1866 replace_inp_entry(inp, "adress_hy_width", nullptr);
1867 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1868 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1869 replace_inp_entry(inp, "adress_site", nullptr);
1870 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1871 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1872 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1873 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1874 replace_inp_entry(inp, "rlistlong", nullptr);
1875 replace_inp_entry(inp, "nstcalclr", nullptr);
1876 replace_inp_entry(inp, "pull-print-com2", nullptr);
1877 replace_inp_entry(inp, "gb-algorithm", nullptr);
1878 replace_inp_entry(inp, "nstgbradii", nullptr);
1879 replace_inp_entry(inp, "rgbradii", nullptr);
1880 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1881 replace_inp_entry(inp, "gb-saltconc", nullptr);
1882 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1883 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1884 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1885 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1886 replace_inp_entry(inp, "sa-algorithm", nullptr);
1887 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1888 replace_inp_entry(inp, "ns-type", nullptr);
1890 /* replace the following commands with the clearer new versions*/
1891 replace_inp_entry(inp, "unconstrained-start", "continuation");
1892 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1893 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1894 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1895 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1896 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1897 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1899 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1900 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1901 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1902 setStringEntry(&inp, "include", opts->include, nullptr);
1903 printStringNoNewline(
1904 &inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1905 setStringEntry(&inp, "define", opts->define, nullptr);
1907 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1908 ir->eI = get_eeenum(&inp, "integrator", ei_names, wi);
1909 printStringNoNewline(&inp, "Start time and timestep in ps");
1910 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1911 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1912 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1913 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1914 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1915 printStringNoNewline(
1916 &inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1917 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1918 printStringNoNewline(&inp, "mode for center of mass motion removal");
1919 ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
1920 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
1921 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
1922 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
1923 setStringEntry(&inp, "comm-grps", is->vcm, nullptr);
1925 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
1926 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
1927 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
1928 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
1931 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
1932 printStringNoNewline(&inp, "Force tolerance and initial step-size");
1933 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
1934 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
1935 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
1936 ir->niter = get_eint(&inp, "niter", 20, wi);
1937 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
1938 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
1939 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
1940 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
1941 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
1943 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
1944 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
1946 /* Output options */
1947 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
1948 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
1949 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
1950 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
1951 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
1952 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
1953 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
1954 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
1955 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
1956 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
1957 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
1958 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
1959 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
1960 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
1961 printStringNoNewline(&inp, "default, all atoms will be written.");
1962 setStringEntry(&inp, "compressed-x-grps", is->x_compressed_groups, nullptr);
1963 printStringNoNewline(&inp, "Selection of energy groups");
1964 setStringEntry(&inp, "energygrps", is->energy, nullptr);
1966 /* Neighbor searching */
1967 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
1968 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
1969 ir->cutoff_scheme = get_eeenum(&inp, "cutoff-scheme", ecutscheme_names, wi);
1970 printStringNoNewline(&inp, "nblist update frequency");
1971 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
1972 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
1973 ir->ePBC = get_eeenum(&inp, "pbc", epbc_names, wi);
1974 ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi) != 0;
1975 printStringNoNewline(&inp,
1976 "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1977 printStringNoNewline(&inp, "a value of -1 means: use rlist");
1978 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
1979 printStringNoNewline(&inp, "nblist cut-off");
1980 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
1981 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
1983 /* Electrostatics */
1984 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
1985 printStringNoNewline(&inp, "Method for doing electrostatics");
1986 ir->coulombtype = get_eeenum(&inp, "coulombtype", eel_names, wi);
1987 ir->coulomb_modifier = get_eeenum(&inp, "coulomb-modifier", eintmod_names, wi);
1988 printStringNoNewline(&inp, "cut-off lengths");
1989 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
1990 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
1991 printStringNoNewline(&inp,
1992 "Relative dielectric constant for the medium and the reaction field");
1993 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
1994 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
1995 printStringNoNewline(&inp, "Method for doing Van der Waals");
1996 ir->vdwtype = get_eeenum(&inp, "vdw-type", evdw_names, wi);
1997 ir->vdw_modifier = get_eeenum(&inp, "vdw-modifier", eintmod_names, wi);
1998 printStringNoNewline(&inp, "cut-off lengths");
1999 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
2000 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
2001 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
2002 ir->eDispCorr = get_eeenum(&inp, "DispCorr", edispc_names, wi);
2003 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
2004 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
2005 printStringNoNewline(&inp, "Separate tables between energy group pairs");
2006 setStringEntry(&inp, "energygrp-table", is->egptable, nullptr);
2007 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
2008 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
2009 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
2010 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
2011 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
2012 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
2013 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
2014 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
2015 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
2016 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
2017 ir->ljpme_combination_rule = get_eeenum(&inp, "lj-pme-comb-rule", eljpme_names, wi);
2018 ir->ewald_geometry = get_eeenum(&inp, "ewald-geometry", eewg_names, wi);
2019 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
2021 /* Implicit solvation is no longer supported, but we need grompp
2022 to be able to refuse old .mdp files that would have built a tpr
2023 to run it. Thus, only "no" is accepted. */
2024 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
2026 /* Coupling stuff */
2027 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
2028 printStringNoNewline(&inp, "Temperature coupling");
2029 ir->etc = get_eeenum(&inp, "tcoupl", etcoupl_names, wi);
2030 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
2031 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
2032 ir->bPrintNHChains = (get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi) != 0);
2033 printStringNoNewline(&inp, "Groups to couple separately");
2034 setStringEntry(&inp, "tc-grps", is->tcgrps, nullptr);
2035 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
2036 setStringEntry(&inp, "tau-t", is->tau_t, nullptr);
2037 setStringEntry(&inp, "ref-t", is->ref_t, nullptr);
2038 printStringNoNewline(&inp, "pressure coupling");
2039 ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
2040 ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
2041 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
2042 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
2043 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
2044 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
2045 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
2046 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
2047 ir->refcoord_scaling = get_eeenum(&inp, "refcoord-scaling", erefscaling_names, wi);
2050 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2051 ir->bQMMM = (get_eeenum(&inp, "QMMM", yesno_names, wi) != 0);
2052 printStringNoNewline(&inp, "Groups treated Quantum Mechanically");
2053 setStringEntry(&inp, "QMMM-grps", is->QMMM, nullptr);
2054 printStringNoNewline(&inp, "QM method");
2055 setStringEntry(&inp, "QMmethod", is->QMmethod, nullptr);
2056 printStringNoNewline(&inp, "QMMM scheme");
2057 ir->QMMMscheme = get_eeenum(&inp, "QMMMscheme", eQMMMscheme_names, wi);
2058 printStringNoNewline(&inp, "QM basisset");
2059 setStringEntry(&inp, "QMbasis", is->QMbasis, nullptr);
2060 printStringNoNewline(&inp, "QM charge");
2061 setStringEntry(&inp, "QMcharge", is->QMcharge, nullptr);
2062 printStringNoNewline(&inp, "QM multiplicity");
2063 setStringEntry(&inp, "QMmult", is->QMmult, nullptr);
2064 printStringNoNewline(&inp, "Surface Hopping");
2065 setStringEntry(&inp, "SH", is->bSH, nullptr);
2066 printStringNoNewline(&inp, "CAS space options");
2067 setStringEntry(&inp, "CASorbitals", is->CASorbitals, nullptr);
2068 setStringEntry(&inp, "CASelectrons", is->CASelectrons, nullptr);
2069 setStringEntry(&inp, "SAon", is->SAon, nullptr);
2070 setStringEntry(&inp, "SAoff", is->SAoff, nullptr);
2071 setStringEntry(&inp, "SAsteps", is->SAsteps, nullptr);
2072 printStringNoNewline(&inp, "Scale factor for MM charges");
2073 ir->scalefactor = get_ereal(&inp, "MMChargeScaleFactor", 1.0, wi);
2075 /* Simulated annealing */
2076 printStringNewline(&inp, "SIMULATED ANNEALING");
2077 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2078 setStringEntry(&inp, "annealing", is->anneal, nullptr);
2079 printStringNoNewline(&inp,
2080 "Number of time points to use for specifying annealing in each group");
2081 setStringEntry(&inp, "annealing-npoints", is->anneal_npoints, nullptr);
2082 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2083 setStringEntry(&inp, "annealing-time", is->anneal_time, nullptr);
2084 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2085 setStringEntry(&inp, "annealing-temp", is->anneal_temp, nullptr);
2088 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2089 opts->bGenVel = (get_eeenum(&inp, "gen-vel", yesno_names, wi) != 0);
2090 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2091 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2094 printStringNewline(&inp, "OPTIONS FOR BONDS");
2095 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2096 printStringNoNewline(&inp, "Type of constraint algorithm");
2097 ir->eConstrAlg = get_eeenum(&inp, "constraint-algorithm", econstr_names, wi);
2098 printStringNoNewline(&inp, "Do not constrain the start configuration");
2099 ir->bContinuation = (get_eeenum(&inp, "continuation", yesno_names, wi) != 0);
2100 printStringNoNewline(&inp,
2101 "Use successive overrelaxation to reduce the number of shake iterations");
2102 ir->bShakeSOR = (get_eeenum(&inp, "Shake-SOR", yesno_names, wi) != 0);
2103 printStringNoNewline(&inp, "Relative tolerance of shake");
2104 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2105 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2106 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2107 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2108 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2109 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2110 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2111 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2112 printStringNoNewline(&inp, "rotates over more degrees than");
2113 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2114 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2115 opts->bMorse = (get_eeenum(&inp, "morse", yesno_names, wi) != 0);
2117 /* Energy group exclusions */
2118 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2119 printStringNoNewline(
2120 &inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2121 setStringEntry(&inp, "energygrp-excl", is->egpexcl, nullptr);
2124 printStringNewline(&inp, "WALLS");
2125 printStringNoNewline(
2126 &inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2127 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2128 ir->wall_type = get_eeenum(&inp, "wall-type", ewt_names, wi);
2129 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2130 setStringEntry(&inp, "wall-atomtype", is->wall_atomtype, nullptr);
2131 setStringEntry(&inp, "wall-density", is->wall_density, nullptr);
2132 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2135 printStringNewline(&inp, "COM PULLING");
2136 ir->bPull = (get_eeenum(&inp, "pull", yesno_names, wi) != 0);
2140 is->pull_grp = read_pullparams(&inp, ir->pull, wi);
2144 NOTE: needs COM pulling input */
2145 printStringNewline(&inp, "AWH biasing");
2146 ir->bDoAwh = (get_eeenum(&inp, "awh", yesno_names, wi) != 0);
2151 ir->awhParams = gmx::readAndCheckAwhParams(&inp, ir, wi);
2155 gmx_fatal(FARGS, "AWH biasing is only compatible with COM pulling turned on");
2159 /* Enforced rotation */
2160 printStringNewline(&inp, "ENFORCED ROTATION");
2161 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2162 ir->bRot = (get_eeenum(&inp, "rotation", yesno_names, wi) != 0);
2166 is->rot_grp = read_rotparams(&inp, ir->rot, wi);
2169 /* Interactive MD */
2171 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2172 setStringEntry(&inp, "IMD-group", is->imd_grp, nullptr);
2173 if (is->imd_grp[0] != '\0')
2180 printStringNewline(&inp, "NMR refinement stuff");
2181 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2182 ir->eDisre = get_eeenum(&inp, "disre", edisre_names, wi);
2183 printStringNoNewline(
2184 &inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2185 ir->eDisreWeighting = get_eeenum(&inp, "disre-weighting", edisreweighting_names, wi);
2186 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2187 ir->bDisreMixed = (get_eeenum(&inp, "disre-mixed", yesno_names, wi) != 0);
2188 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2189 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2190 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2191 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2192 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2193 opts->bOrire = (get_eeenum(&inp, "orire", yesno_names, wi) != 0);
2194 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2195 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2196 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2197 setStringEntry(&inp, "orire-fitgrp", is->orirefitgrp, nullptr);
2198 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2199 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2201 /* free energy variables */
2202 printStringNewline(&inp, "Free energy variables");
2203 ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
2204 setStringEntry(&inp, "couple-moltype", is->couple_moltype, nullptr);
2205 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2206 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2207 opts->bCoupleIntra = (get_eeenum(&inp, "couple-intramol", yesno_names, wi) != 0);
2209 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2211 it was not entered */
2212 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2213 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2214 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2215 setStringEntry(&inp, "fep-lambdas", is->fep_lambda[efptFEP], nullptr);
2216 setStringEntry(&inp, "mass-lambdas", is->fep_lambda[efptMASS], nullptr);
2217 setStringEntry(&inp, "coul-lambdas", is->fep_lambda[efptCOUL], nullptr);
2218 setStringEntry(&inp, "vdw-lambdas", is->fep_lambda[efptVDW], nullptr);
2219 setStringEntry(&inp, "bonded-lambdas", is->fep_lambda[efptBONDED], nullptr);
2220 setStringEntry(&inp, "restraint-lambdas", is->fep_lambda[efptRESTRAINT], nullptr);
2221 setStringEntry(&inp, "temperature-lambdas", is->fep_lambda[efptTEMPERATURE], nullptr);
2222 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2223 setStringEntry(&inp, "init-lambda-weights", is->lambda_weights, nullptr);
2224 fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
2225 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2226 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2227 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2228 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2229 fep->bScCoul = (get_eeenum(&inp, "sc-coul", yesno_names, wi) != 0);
2230 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2231 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2232 fep->separate_dhdl_file = get_eeenum(&inp, "separate-dhdl-file", separate_dhdl_file_names, wi);
2233 fep->dhdl_derivatives = get_eeenum(&inp, "dhdl-derivatives", dhdl_derivatives_names, wi);
2234 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2235 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2237 /* Non-equilibrium MD stuff */
2238 printStringNewline(&inp, "Non-equilibrium MD stuff");
2239 setStringEntry(&inp, "acc-grps", is->accgrps, nullptr);
2240 setStringEntry(&inp, "accelerate", is->acc, nullptr);
2241 setStringEntry(&inp, "freezegrps", is->freeze, nullptr);
2242 setStringEntry(&inp, "freezedim", is->frdim, nullptr);
2243 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2244 setStringEntry(&inp, "deform", is->deform, nullptr);
2246 /* simulated tempering variables */
2247 printStringNewline(&inp, "simulated tempering variables");
2248 ir->bSimTemp = (get_eeenum(&inp, "simulated-tempering", yesno_names, wi) != 0);
2249 ir->simtempvals->eSimTempScale = get_eeenum(&inp, "simulated-tempering-scaling", esimtemp_names, wi);
2250 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2251 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2253 /* expanded ensemble variables */
2254 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2256 read_expandedparams(&inp, expand, wi);
2259 /* Electric fields */
2261 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2262 gmx::KeyValueTreeTransformer transform;
2263 transform.rules()->addRule().keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2264 mdModules->initMdpTransform(transform.rules());
2265 for (const auto& path : transform.mappedPaths())
2267 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2268 mark_einp_set(inp, path[0].c_str());
2270 MdpErrorHandler errorHandler(wi);
2271 auto result = transform.transform(convertedValues, &errorHandler);
2272 ir->params = new gmx::KeyValueTreeObject(result.object());
2273 mdModules->adjustInputrecBasedOnModules(ir);
2274 errorHandler.setBackMapping(result.backMapping());
2275 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2278 /* Ion/water position swapping ("computational electrophysiology") */
2279 printStringNewline(&inp,
2280 "Ion/water position swapping for computational electrophysiology setups");
2281 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2282 ir->eSwapCoords = get_eeenum(&inp, "swapcoords", eSwapTypes_names, wi);
2283 if (ir->eSwapCoords != eswapNO)
2290 printStringNoNewline(&inp, "Swap attempt frequency");
2291 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2292 printStringNoNewline(&inp, "Number of ion types to be controlled");
2293 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2296 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2298 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2299 snew(ir->swap->grp, ir->swap->ngrp);
2300 for (i = 0; i < ir->swap->ngrp; i++)
2302 snew(ir->swap->grp[i].molname, STRLEN);
2304 printStringNoNewline(&inp,
2305 "Two index groups that contain the compartment-partitioning atoms");
2306 setStringEntry(&inp, "split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2307 setStringEntry(&inp, "split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2308 printStringNoNewline(&inp,
2309 "Use center of mass of split groups (yes/no), otherwise center of "
2310 "geometry is used");
2311 ir->swap->massw_split[0] = (get_eeenum(&inp, "massw-split0", yesno_names, wi) != 0);
2312 ir->swap->massw_split[1] = (get_eeenum(&inp, "massw-split1", yesno_names, wi) != 0);
2314 printStringNoNewline(&inp, "Name of solvent molecules");
2315 setStringEntry(&inp, "solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2317 printStringNoNewline(&inp,
2318 "Split cylinder: radius, upper and lower extension (nm) (this will "
2319 "define the channels)");
2320 printStringNoNewline(&inp,
2321 "Note that the split cylinder settings do not have an influence on "
2322 "the swapping protocol,");
2323 printStringNoNewline(
2325 "however, if correctly defined, the permeation events are recorded per channel");
2326 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2327 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2328 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2329 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2330 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2331 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2333 printStringNoNewline(
2335 "Average the number of ions per compartment over these many swap attempt steps");
2336 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2338 printStringNoNewline(
2339 &inp, "Names of the ion types that can be exchanged with solvent molecules,");
2340 printStringNoNewline(
2341 &inp, "and the requested number of ions of this type in compartments A and B");
2342 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2343 for (i = 0; i < nIonTypes; i++)
2345 int ig = eSwapFixedGrpNR + i;
2347 sprintf(buf, "iontype%d-name", i);
2348 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2349 sprintf(buf, "iontype%d-in-A", i);
2350 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2351 sprintf(buf, "iontype%d-in-B", i);
2352 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2355 printStringNoNewline(
2357 "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2358 printStringNoNewline(
2360 "at maximum distance (= bulk concentration) to the split group layers. However,");
2361 printStringNoNewline(&inp,
2362 "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk "
2363 "layer from the middle at 0.0");
2364 printStringNoNewline(&inp,
2365 "towards one of the compartment-partitioning layers (at +/- 1.0).");
2366 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2367 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2368 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2369 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0))
2371 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2374 printStringNoNewline(
2375 &inp, "Start to swap ions if threshold difference to requested count is reached");
2376 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2379 /* AdResS is no longer supported, but we need grompp to be able to
2380 refuse to process old .mdp files that used it. */
2381 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2383 /* User defined thingies */
2384 printStringNewline(&inp, "User defined thingies");
2385 setStringEntry(&inp, "user1-grps", is->user1, nullptr);
2386 setStringEntry(&inp, "user2-grps", is->user2, nullptr);
2387 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2388 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2389 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2390 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2391 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2392 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2393 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2394 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2398 gmx::TextOutputFile stream(mdparout);
2399 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2401 // Transform module data into a flat key-value tree for output.
2402 gmx::KeyValueTreeBuilder builder;
2403 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2404 mdModules->buildMdpOutput(&builderObject);
2406 gmx::TextWriter writer(&stream);
2407 writeKeyValueTreeAsMdp(&writer, builder.build());
2412 /* Process options if necessary */
2413 for (m = 0; m < 2; m++)
2415 for (i = 0; i < 2 * DIM; i++)
2424 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2428 "Pressure coupling incorrect number of values (I need exactly 1)");
2430 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2432 case epctSEMIISOTROPIC:
2433 case epctSURFACETENSION:
2434 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2438 "Pressure coupling incorrect number of values (I need exactly 2)");
2440 dumdub[m][YY] = dumdub[m][XX];
2442 case epctANISOTROPIC:
2443 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf", &(dumdub[m][XX]), &(dumdub[m][YY]),
2444 &(dumdub[m][ZZ]), &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5]))
2449 "Pressure coupling incorrect number of values (I need exactly 6)");
2453 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2454 epcoupltype_names[ir->epct]);
2458 clear_mat(ir->ref_p);
2459 clear_mat(ir->compress);
2460 for (i = 0; i < DIM; i++)
2462 ir->ref_p[i][i] = dumdub[1][i];
2463 ir->compress[i][i] = dumdub[0][i];
2465 if (ir->epct == epctANISOTROPIC)
2467 ir->ref_p[XX][YY] = dumdub[1][3];
2468 ir->ref_p[XX][ZZ] = dumdub[1][4];
2469 ir->ref_p[YY][ZZ] = dumdub[1][5];
2470 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2473 "All off-diagonal reference pressures are non-zero. Are you sure you want to "
2474 "apply a threefold shear stress?\n");
2476 ir->compress[XX][YY] = dumdub[0][3];
2477 ir->compress[XX][ZZ] = dumdub[0][4];
2478 ir->compress[YY][ZZ] = dumdub[0][5];
2479 for (i = 0; i < DIM; i++)
2481 for (m = 0; m < i; m++)
2483 ir->ref_p[i][m] = ir->ref_p[m][i];
2484 ir->compress[i][m] = ir->compress[m][i];
2489 if (ir->comm_mode == ecmNO)
2494 opts->couple_moltype = nullptr;
2495 if (strlen(is->couple_moltype) > 0)
2497 if (ir->efep != efepNO)
2499 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2500 if (opts->couple_lam0 == opts->couple_lam1)
2502 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2504 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
2508 "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
2515 "Free energy is turned off, so we will not decouple the molecule listed "
2519 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2520 if (ir->efep != efepNO)
2522 if (fep->delta_lambda > 0)
2524 ir->efep = efepSLOWGROWTH;
2528 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2530 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2532 "Old option for dhdl-print-energy given: "
2533 "changing \"yes\" to \"total\"\n");
2536 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2538 /* always print out the energy to dhdl if we are doing
2539 expanded ensemble, since we need the total energy for
2540 analysis if the temperature is changing. In some
2541 conditions one may only want the potential energy, so
2542 we will allow that if the appropriate mdp setting has
2543 been enabled. Otherwise, total it is:
2545 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2548 if ((ir->efep != efepNO) || ir->bSimTemp)
2550 ir->bExpanded = FALSE;
2551 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2553 ir->bExpanded = TRUE;
2555 do_fep_params(ir, is->fep_lambda, is->lambda_weights, wi);
2556 if (ir->bSimTemp) /* done after fep params */
2558 do_simtemp_params(ir);
2561 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2562 * setup and not on the old way of specifying the free-energy setup,
2563 * we should check for using soft-core when not needed, since that
2564 * can complicate the sampling significantly.
2565 * Note that we only check for the automated coupling setup.
2566 * If the (advanced) user does FEP through manual topology changes,
2567 * this check will not be triggered.
2569 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 && ir->fepvals->sc_alpha != 0
2570 && (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
2573 "You are using soft-core interactions while the Van der Waals interactions are "
2574 "not decoupled (note that the sc-coul option is only active when using lambda "
2575 "states). Although this will not lead to errors, you will need much more "
2576 "sampling than without soft-core interactions. Consider using sc-alpha=0.");
2581 ir->fepvals->n_lambda = 0;
2584 /* WALL PARAMETERS */
2586 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts, wi);
2588 /* ORIENTATION RESTRAINT PARAMETERS */
2590 if (opts->bOrire && gmx::splitString(is->orirefitgrp).size() != 1)
2592 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2595 /* DEFORMATION PARAMETERS */
2597 clear_mat(ir->deform);
2598 for (i = 0; i < 6; i++)
2603 double gmx_unused canary;
2604 int ndeform = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf %lf", &(dumdub[0][0]), &(dumdub[0][1]),
2605 &(dumdub[0][2]), &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]), &canary);
2607 if (strlen(is->deform) > 0 && ndeform != 6)
2610 wi, gmx::formatString(
2611 "Cannot parse exactly 6 box deformation velocities from string '%s'", is->deform)
2614 for (i = 0; i < 3; i++)
2616 ir->deform[i][i] = dumdub[0][i];
2618 ir->deform[YY][XX] = dumdub[0][3];
2619 ir->deform[ZZ][XX] = dumdub[0][4];
2620 ir->deform[ZZ][YY] = dumdub[0][5];
2621 if (ir->epc != epcNO)
2623 for (i = 0; i < 3; i++)
2625 for (j = 0; j <= i; j++)
2627 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2629 warning_error(wi, "A box element has deform set and compressibility > 0");
2633 for (i = 0; i < 3; i++)
2635 for (j = 0; j < i; j++)
2637 if (ir->deform[i][j] != 0)
2639 for (m = j; m < DIM; m++)
2641 if (ir->compress[m][j] != 0)
2644 "An off-diagonal box element has deform set while "
2645 "compressibility > 0 for the same component of another box "
2646 "vector, this might lead to spurious periodicity effects.");
2647 warning(wi, warn_buf);
2655 /* Ion/water position swapping checks */
2656 if (ir->eSwapCoords != eswapNO)
2658 if (ir->swap->nstswap < 1)
2660 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2662 if (ir->swap->nAverage < 1)
2664 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2666 if (ir->swap->threshold < 1.0)
2668 warning_error(wi, "Ion count threshold must be at least 1.\n");
2676 static int search_QMstring(const char* s, int ng, const char* gn[])
2678 /* same as normal search_string, but this one searches QM strings */
2681 for (i = 0; (i < ng); i++)
2683 if (gmx_strcasecmp(s, gn[i]) == 0)
2689 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2690 } /* search_QMstring */
2692 /* We would like gn to be const as well, but C doesn't allow this */
2693 /* TODO this is utility functionality (search for the index of a
2694 string in a collection), so should be refactored and located more
2696 int search_string(const char* s, int ng, char* gn[])
2700 for (i = 0; (i < ng); i++)
2702 if (gmx_strcasecmp(s, gn[i]) == 0)
2709 "Group %s referenced in the .mdp file was not found in the index file.\n"
2710 "Group names must match either [moleculetype] names or custom index group\n"
2711 "names, in which case you must supply an index file to the '-n' option\n"
2716 static void atomGroupRangeValidation(int natoms, int groupIndex, const t_blocka& block)
2718 /* Now go over the atoms in the group */
2719 for (int j = block.index[groupIndex]; (j < block.index[groupIndex + 1]); j++)
2721 int aj = block.a[j];
2723 /* Range checking */
2724 if ((aj < 0) || (aj >= natoms))
2726 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2731 static void do_numbering(int natoms,
2732 SimulationGroups* groups,
2733 gmx::ArrayRef<std::string> groupsFromMdpFile,
2736 SimulationAtomGroupType gtype,
2742 unsigned short* cbuf;
2743 AtomGroupIndices* grps = &(groups->groups[gtype]);
2746 char warn_buf[STRLEN];
2748 title = shortName(gtype);
2751 /* Mark all id's as not set */
2752 for (int i = 0; (i < natoms); i++)
2757 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2759 /* Lookup the group name in the block structure */
2760 const int gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2761 if ((grptp != egrptpONE) || (i == 0))
2763 grps->emplace_back(gid);
2765 GMX_ASSERT(block, "Can't have a nullptr block");
2766 atomGroupRangeValidation(natoms, gid, *block);
2767 /* Now go over the atoms in the group */
2768 for (int j = block->index[gid]; (j < block->index[gid + 1]); j++)
2770 const int aj = block->a[j];
2771 /* Lookup up the old group number */
2772 const int ognr = cbuf[aj];
2775 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title,
2780 /* Store the group number in buffer */
2781 if (grptp == egrptpONE)
2794 /* Now check whether we have done all atoms */
2797 if (grptp == egrptpALL)
2799 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2801 else if (grptp == egrptpPART)
2803 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2804 warning_note(wi, warn_buf);
2806 /* Assign all atoms currently unassigned to a rest group */
2807 for (int j = 0; (j < natoms); j++)
2809 if (cbuf[j] == NOGID)
2811 cbuf[j] = grps->size();
2814 if (grptp != egrptpPART)
2818 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title,
2821 /* Add group name "rest" */
2822 grps->emplace_back(restnm);
2824 /* Assign the rest name to all atoms not currently assigned to a group */
2825 for (int j = 0; (j < natoms); j++)
2827 if (cbuf[j] == NOGID)
2829 // group size was not updated before this here, so need to use -1.
2830 cbuf[j] = grps->size() - 1;
2836 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2838 /* All atoms are part of one (or no) group, no index required */
2839 groups->groupNumbers[gtype].clear();
2843 for (int j = 0; (j < natoms); j++)
2845 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2852 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
2855 pull_params_t* pull;
2856 int natoms, imin, jmin;
2857 int * nrdf2, *na_vcm, na_tot;
2858 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2863 * First calc 3xnr-atoms for each group
2864 * then subtract half a degree of freedom for each constraint
2866 * Only atoms and nuclei contribute to the degrees of freedom...
2871 const SimulationGroups& groups = mtop->groups;
2872 natoms = mtop->natoms;
2874 /* Allocate one more for a possible rest group */
2875 /* We need to sum degrees of freedom into doubles,
2876 * since floats give too low nrdf's above 3 million atoms.
2878 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
2879 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2880 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2881 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2882 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2884 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
2888 for (gmx::index i = 0;
2889 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; i++)
2892 clear_ivec(dof_vcm[i]);
2894 nrdf_vcm_sub[i] = 0;
2896 snew(nrdf2, natoms);
2897 for (const AtomProxy atomP : AtomRange(*mtop))
2899 const t_atom& local = atomP.atom();
2900 int i = atomP.globalAtomNumber();
2902 if (local.ptype == eptAtom || local.ptype == eptNucleus)
2904 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
2905 for (int d = 0; d < DIM; d++)
2907 if (opts->nFreeze[g][d] == 0)
2909 /* Add one DOF for particle i (counted as 2*1) */
2911 /* VCM group i has dim d as a DOF */
2912 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
2916 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
2918 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
2924 for (const gmx_molblock_t& molb : mtop->molblock)
2926 const gmx_moltype_t& molt = mtop->moltype[molb.type];
2927 const t_atom* atom = molt.atoms.atom;
2928 for (int mol = 0; mol < molb.nmol; mol++)
2930 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2932 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
2933 for (int i = 0; i < molt.ilist[ftype].size();)
2935 /* Subtract degrees of freedom for the constraints,
2936 * if the particles still have degrees of freedom left.
2937 * If one of the particles is a vsite or a shell, then all
2938 * constraint motion will go there, but since they do not
2939 * contribute to the constraints the degrees of freedom do not
2942 int ai = as + ia[i + 1];
2943 int aj = as + ia[i + 2];
2944 if (((atom[ia[i + 1]].ptype == eptNucleus) || (atom[ia[i + 1]].ptype == eptAtom))
2945 && ((atom[ia[i + 2]].ptype == eptNucleus) || (atom[ia[i + 2]].ptype == eptAtom)))
2963 imin = std::min(imin, nrdf2[ai]);
2964 jmin = std::min(jmin, nrdf2[aj]);
2967 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2969 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
2971 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2973 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
2976 i += interaction_function[ftype].nratoms + 1;
2979 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
2980 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
2982 /* Subtract 1 dof from every atom in the SETTLE */
2983 for (int j = 0; j < 3; j++)
2985 int ai = as + ia[i + 1 + j];
2986 imin = std::min(2, nrdf2[ai]);
2988 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2990 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2995 as += molt.atoms.nr;
3001 /* Correct nrdf for the COM constraints.
3002 * We correct using the TC and VCM group of the first atom
3003 * in the reference and pull group. If atoms in one pull group
3004 * belong to different TC or VCM groups it is anyhow difficult
3005 * to determine the optimal nrdf assignment.
3009 for (int i = 0; i < pull->ncoord; i++)
3011 if (pull->coord[i].eType != epullCONSTRAINT)
3018 for (int j = 0; j < 2; j++)
3020 const t_pull_group* pgrp;
3022 pgrp = &pull->group[pull->coord[i].group[j]];
3026 /* Subtract 1/2 dof from each group */
3027 int ai = pgrp->ind[0];
3028 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3030 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3032 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
3035 "Center of mass pulling constraints caused the number of degrees "
3036 "of freedom for temperature coupling group %s to be negative",
3037 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
3038 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
3043 /* We need to subtract the whole DOF from group j=1 */
3050 if (ir->nstcomm != 0)
3052 GMX_RELEASE_ASSERT(!groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty(),
3053 "Expect at least one group when removing COM motion");
3055 /* We remove COM motion up to dim ndof_com() */
3056 const int ndim_rm_vcm = ndof_com(ir);
3058 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3059 * the number of degrees of freedom in each vcm group when COM
3060 * translation is removed and 6 when rotation is removed as well.
3061 * Note that we do not and should not include the rest group here.
3063 for (gmx::index j = 0;
3064 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]); j++)
3066 switch (ir->comm_mode)
3069 case ecmLINEAR_ACCELERATION_CORRECTION:
3070 nrdf_vcm_sub[j] = 0;
3071 for (int d = 0; d < ndim_rm_vcm; d++)
3079 case ecmANGULAR: nrdf_vcm_sub[j] = 6; break;
3080 default: gmx_incons("Checking comm_mode");
3084 for (gmx::index i = 0;
3085 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
3087 /* Count the number of atoms of TC group i for every VCM group */
3088 for (gmx::index j = 0;
3089 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3094 for (int ai = 0; ai < natoms; ai++)
3096 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3098 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3102 /* Correct for VCM removal according to the fraction of each VCM
3103 * group present in this TC group.
3105 nrdf_uc = nrdf_tc[i];
3107 for (gmx::index j = 0;
3108 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3110 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3112 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3113 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3118 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3120 opts->nrdf[i] = nrdf_tc[i];
3121 if (opts->nrdf[i] < 0)
3125 fprintf(stderr, "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3126 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]], opts->nrdf[i]);
3134 sfree(nrdf_vcm_sub);
3137 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3139 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3140 * But since this is much larger than STRLEN, such a line can not be parsed.
3141 * The real maximum is the number of names that fit in a string: STRLEN/2.
3143 #define EGP_MAX (STRLEN / 2)
3147 auto names = gmx::splitString(val);
3148 if (names.size() % 2 != 0)
3150 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3152 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3154 for (size_t i = 0; i < names.size() / 2; i++)
3156 // TODO this needs to be replaced by a solution using std::find_if
3160 names[2 * i].c_str(),
3161 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3167 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3172 names[2 * i + 1].c_str(),
3173 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3179 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3181 if ((j < nr) && (k < nr))
3183 ir->opts.egp_flags[nr * j + k] |= flag;
3184 ir->opts.egp_flags[nr * k + j] |= flag;
3193 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3195 int ig = -1, i = 0, gind;
3199 /* Just a quick check here, more thorough checks are in mdrun */
3200 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3202 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3205 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3206 for (ig = 0; ig < swap->ngrp; ig++)
3208 swapg = &swap->grp[ig];
3209 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3210 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3214 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3215 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap", swap->grp[ig].molname, swapg->nat);
3216 snew(swapg->ind, swapg->nat);
3217 for (i = 0; i < swapg->nat; i++)
3219 swapg->ind[i] = grps->a[grps->index[gind] + i];
3224 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3230 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3235 ig = search_string(IMDgname, grps->nr, gnames);
3236 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3238 if (IMDgroup->nat > 0)
3241 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3243 IMDgname, IMDgroup->nat);
3244 snew(IMDgroup->ind, IMDgroup->nat);
3245 for (i = 0; i < IMDgroup->nat; i++)
3247 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3252 /* Checks whether atoms are both part of a COM removal group and frozen.
3253 * If a fully frozen atom is part of a COM removal group, it is removed
3254 * from the COM removal group. A note is issued if such atoms are present.
3255 * A warning is issued for atom with one or two dimensions frozen that
3256 * are part of a COM removal group (mdrun would need to compute COM mass
3257 * per dimension to handle this correctly).
3258 * Also issues a warning when non-frozen atoms are not part of a COM
3259 * removal group while COM removal is active.
3261 static void checkAndUpdateVcmFreezeGroupConsistency(SimulationGroups* groups,
3263 const t_grpopts& opts,
3266 const int vcmRestGroup =
3267 std::max(int(groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()), 1);
3269 int numFullyFrozenVcmAtoms = 0;
3270 int numPartiallyFrozenVcmAtoms = 0;
3271 int numNonVcmAtoms = 0;
3272 for (int a = 0; a < numAtoms; a++)
3274 const int freezeGroup = getGroupType(*groups, SimulationAtomGroupType::Freeze, a);
3275 int numFrozenDims = 0;
3276 for (int d = 0; d < DIM; d++)
3278 numFrozenDims += opts.nFreeze[freezeGroup][d];
3281 const int vcmGroup = getGroupType(*groups, SimulationAtomGroupType::MassCenterVelocityRemoval, a);
3282 if (vcmGroup < vcmRestGroup)
3284 if (numFrozenDims == DIM)
3286 /* Do not remove COM motion for this fully frozen atom */
3287 if (groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
3289 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(
3292 groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
3293 numFullyFrozenVcmAtoms++;
3295 else if (numFrozenDims > 0)
3297 numPartiallyFrozenVcmAtoms++;
3300 else if (numFrozenDims < DIM)
3306 if (numFullyFrozenVcmAtoms > 0)
3308 std::string warningText = gmx::formatString(
3309 "There are %d atoms that are fully frozen and part of COMM removal group(s), "
3310 "removing these atoms from the COMM removal group(s)",
3311 numFullyFrozenVcmAtoms);
3312 warning_note(wi, warningText.c_str());
3314 if (numPartiallyFrozenVcmAtoms > 0 && numPartiallyFrozenVcmAtoms < numAtoms)
3316 std::string warningText = gmx::formatString(
3317 "There are %d atoms that are frozen along less then %d dimensions and part of COMM "
3318 "removal group(s), due to limitations in the code these still contribute to the "
3319 "mass of the COM along frozen dimensions and therefore the COMM correction will be "
3321 numPartiallyFrozenVcmAtoms, DIM);
3322 warning(wi, warningText.c_str());
3324 if (numNonVcmAtoms > 0)
3326 std::string warningText = gmx::formatString(
3327 "%d atoms are not part of any center of mass motion removal group.\n"
3328 "This may lead to artifacts.\n"
3329 "In most cases one should use one group for the whole system.",
3331 warning(wi, warningText.c_str());
3335 void do_index(const char* mdparin,
3339 const gmx::MdModulesNotifier& notifier,
3343 t_blocka* defaultIndexGroups;
3351 int i, j, k, restnm;
3352 bool bExcl, bTable, bAnneal;
3353 char warn_buf[STRLEN];
3357 fprintf(stderr, "processing index file...\n");
3361 snew(defaultIndexGroups, 1);
3362 snew(defaultIndexGroups->index, 1);
3364 atoms_all = gmx_mtop_global_atoms(mtop);
3365 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3366 done_atom(&atoms_all);
3370 defaultIndexGroups = init_index(ndx, &gnames);
3373 SimulationGroups* groups = &mtop->groups;
3374 natoms = mtop->natoms;
3375 symtab = &mtop->symtab;
3377 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3379 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3381 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3382 restnm = groups->groupNames.size() - 1;
3383 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3384 srenew(gnames, defaultIndexGroups->nr + 1);
3385 gnames[restnm] = *(groups->groupNames.back());
3387 set_warning_line(wi, mdparin, -1);
3389 auto temperatureCouplingTauValues = gmx::splitString(is->tau_t);
3390 auto temperatureCouplingReferenceValues = gmx::splitString(is->ref_t);
3391 auto temperatureCouplingGroupNames = gmx::splitString(is->tcgrps);
3392 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3393 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3396 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3398 temperatureCouplingGroupNames.size(), temperatureCouplingReferenceValues.size(),
3399 temperatureCouplingTauValues.size());
3402 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3403 do_numbering(natoms, groups, temperatureCouplingGroupNames, defaultIndexGroups, gnames,
3404 SimulationAtomGroupType::TemperatureCoupling, restnm,
3405 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3406 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3408 snew(ir->opts.nrdf, nr);
3409 snew(ir->opts.tau_t, nr);
3410 snew(ir->opts.ref_t, nr);
3411 if (ir->eI == eiBD && ir->bd_fric == 0)
3413 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3416 if (useReferenceTemperature)
3418 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3420 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3424 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3425 for (i = 0; (i < nr); i++)
3427 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3429 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3430 warning_error(wi, warn_buf);
3433 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3437 "tau-t = -1 is the value to signal that a group should not have "
3438 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3441 if (ir->opts.tau_t[i] >= 0)
3443 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3446 if (ir->etc != etcNO && ir->nsttcouple == -1)
3448 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3453 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3456 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3457 "md-vv; use either vrescale temperature with berendsen pressure or "
3458 "Nose-Hoover temperature with MTTK pressure");
3460 if (ir->epc == epcMTTK)
3462 if (ir->etc != etcNOSEHOOVER)
3465 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3470 if (ir->nstpcouple != ir->nsttcouple)
3472 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3473 ir->nstpcouple = ir->nsttcouple = mincouple;
3475 "for current Trotter decomposition methods with vv, nsttcouple and "
3476 "nstpcouple must be equal. Both have been reset to "
3477 "min(nsttcouple,nstpcouple) = %d",
3479 warning_note(wi, warn_buf);
3484 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3485 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3487 if (ETC_ANDERSEN(ir->etc))
3489 if (ir->nsttcouple != 1)
3493 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3494 "need for larger nsttcouple > 1, since no global parameters are computed. "
3495 "nsttcouple has been reset to 1");
3496 warning_note(wi, warn_buf);
3499 nstcmin = tcouple_min_integration_steps(ir->etc);
3502 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3505 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3506 "least %d times larger than nsttcouple*dt (%g)",
3507 ETCOUPLTYPE(ir->etc), tau_min, nstcmin, ir->nsttcouple * ir->delta_t);
3508 warning(wi, warn_buf);
3511 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3512 for (i = 0; (i < nr); i++)
3514 if (ir->opts.ref_t[i] < 0)
3516 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3519 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3520 if we are in this conditional) if mc_temp is negative */
3521 if (ir->expandedvals->mc_temp < 0)
3523 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3527 /* Simulated annealing for each group. There are nr groups */
3528 auto simulatedAnnealingGroupNames = gmx::splitString(is->anneal);
3529 if (simulatedAnnealingGroupNames.size() == 1
3530 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3532 simulatedAnnealingGroupNames.resize(0);
3534 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3536 gmx_fatal(FARGS, "Wrong number of annealing values: %zu (for %d groups)\n",
3537 simulatedAnnealingGroupNames.size(), nr);
3541 snew(ir->opts.annealing, nr);
3542 snew(ir->opts.anneal_npoints, nr);
3543 snew(ir->opts.anneal_time, nr);
3544 snew(ir->opts.anneal_temp, nr);
3545 for (i = 0; i < nr; i++)
3547 ir->opts.annealing[i] = eannNO;
3548 ir->opts.anneal_npoints[i] = 0;
3549 ir->opts.anneal_time[i] = nullptr;
3550 ir->opts.anneal_temp[i] = nullptr;
3552 if (!simulatedAnnealingGroupNames.empty())
3555 for (i = 0; i < nr; i++)
3557 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3559 ir->opts.annealing[i] = eannNO;
3561 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3563 ir->opts.annealing[i] = eannSINGLE;
3566 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3568 ir->opts.annealing[i] = eannPERIODIC;
3574 /* Read the other fields too */
3575 auto simulatedAnnealingPoints = gmx::splitString(is->anneal_npoints);
3576 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3578 gmx_fatal(FARGS, "Found %zu annealing-npoints values for %zu groups\n",
3579 simulatedAnnealingPoints.size(), simulatedAnnealingGroupNames.size());
3581 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3582 size_t numSimulatedAnnealingFields = 0;
3583 for (i = 0; i < nr; i++)
3585 if (ir->opts.anneal_npoints[i] == 1)
3589 "Please specify at least a start and an end point for annealing\n");
3591 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3592 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3593 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3596 auto simulatedAnnealingTimes = gmx::splitString(is->anneal_time);
3598 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3600 gmx_fatal(FARGS, "Found %zu annealing-time values, wanted %zu\n",
3601 simulatedAnnealingTimes.size(), numSimulatedAnnealingFields);
3603 auto simulatedAnnealingTemperatures = gmx::splitString(is->anneal_temp);
3604 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3606 gmx_fatal(FARGS, "Found %zu annealing-temp values, wanted %zu\n",
3607 simulatedAnnealingTemperatures.size(), numSimulatedAnnealingFields);
3610 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3611 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3612 convertReals(wi, simulatedAnnealingTimes, "anneal-time",
3613 allSimulatedAnnealingTimes.data());
3614 convertReals(wi, simulatedAnnealingTemperatures, "anneal-temp",
3615 allSimulatedAnnealingTemperatures.data());
3616 for (i = 0, k = 0; i < nr; i++)
3618 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3620 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3621 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3624 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3626 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3632 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3635 "Annealing timepoints out of order: t=%f comes after "
3637 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j - 1]);
3640 if (ir->opts.anneal_temp[i][j] < 0)
3642 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n",
3643 ir->opts.anneal_temp[i][j]);
3648 /* Print out some summary information, to make sure we got it right */
3649 for (i = 0; i < nr; i++)
3651 if (ir->opts.annealing[i] != eannNO)
3653 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3654 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3655 *(groups->groupNames[j]), eann_names[ir->opts.annealing[i]],
3656 ir->opts.anneal_npoints[i]);
3657 fprintf(stderr, "Time (ps) Temperature (K)\n");
3658 /* All terms except the last one */
3659 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3661 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3662 ir->opts.anneal_temp[i][j]);
3665 /* Finally the last one */
3666 j = ir->opts.anneal_npoints[i] - 1;
3667 if (ir->opts.annealing[i] == eannSINGLE)
3669 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j],
3670 ir->opts.anneal_temp[i][j]);
3674 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3675 ir->opts.anneal_temp[i][j]);
3676 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3679 "There is a temperature jump when your annealing "
3691 for (int i = 1; i < ir->pull->ngroup; i++)
3693 const int gid = search_string(is->pull_grp[i], defaultIndexGroups->nr, gnames);
3694 GMX_ASSERT(defaultIndexGroups, "Must have initialized default index groups");
3695 atomGroupRangeValidation(natoms, gid, *defaultIndexGroups);
3698 make_pull_groups(ir->pull, is->pull_grp, defaultIndexGroups, gnames);
3700 make_pull_coords(ir->pull);
3705 make_rotation_groups(ir->rot, is->rot_grp, defaultIndexGroups, gnames);
3708 if (ir->eSwapCoords != eswapNO)
3710 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3713 /* Make indices for IMD session */
3716 make_IMD_group(ir->imd, is->imd_grp, defaultIndexGroups, gnames);
3719 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3720 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3721 notifier.notifier_.notify(defaultIndexGroupsAndNames);
3723 auto accelerations = gmx::splitString(is->acc);
3724 auto accelerationGroupNames = gmx::splitString(is->accgrps);
3725 if (accelerationGroupNames.size() * DIM != accelerations.size())
3727 gmx_fatal(FARGS, "Invalid Acceleration input: %zu groups and %zu acc. values",
3728 accelerationGroupNames.size(), accelerations.size());
3730 do_numbering(natoms, groups, accelerationGroupNames, defaultIndexGroups, gnames,
3731 SimulationAtomGroupType::Acceleration, restnm, egrptpALL_GENREST, bVerbose, wi);
3732 nr = groups->groups[SimulationAtomGroupType::Acceleration].size();
3733 snew(ir->opts.acc, nr);
3734 ir->opts.ngacc = nr;
3736 convertRvecs(wi, accelerations, "anneal-time", ir->opts.acc);
3738 auto freezeDims = gmx::splitString(is->frdim);
3739 auto freezeGroupNames = gmx::splitString(is->freeze);
3740 if (freezeDims.size() != DIM * freezeGroupNames.size())
3742 gmx_fatal(FARGS, "Invalid Freezing input: %zu groups and %zu freeze values",
3743 freezeGroupNames.size(), freezeDims.size());
3745 do_numbering(natoms, groups, freezeGroupNames, defaultIndexGroups, gnames,
3746 SimulationAtomGroupType::Freeze, restnm, egrptpALL_GENREST, bVerbose, wi);
3747 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3748 ir->opts.ngfrz = nr;
3749 snew(ir->opts.nFreeze, nr);
3750 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3752 for (j = 0; (j < DIM); j++, k++)
3754 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3755 if (!ir->opts.nFreeze[i][j])
3757 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3760 "Please use Y(ES) or N(O) for freezedim only "
3762 freezeDims[k].c_str());
3763 warning(wi, warn_buf);
3768 for (; (i < nr); i++)
3770 for (j = 0; (j < DIM); j++)
3772 ir->opts.nFreeze[i][j] = 0;
3776 auto energyGroupNames = gmx::splitString(is->energy);
3777 do_numbering(natoms, groups, energyGroupNames, defaultIndexGroups, gnames,
3778 SimulationAtomGroupType::EnergyOutput, restnm, egrptpALL_GENREST, bVerbose, wi);
3779 add_wall_energrps(groups, ir->nwall, symtab);
3780 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3781 auto vcmGroupNames = gmx::splitString(is->vcm);
3782 do_numbering(natoms, groups, vcmGroupNames, defaultIndexGroups, gnames,
3783 SimulationAtomGroupType::MassCenterVelocityRemoval, restnm,
3784 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3786 if (ir->comm_mode != ecmNO)
3788 checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
3791 /* Now we have filled the freeze struct, so we can calculate NRDF */
3792 calc_nrdf(mtop, ir, gnames);
3794 auto user1GroupNames = gmx::splitString(is->user1);
3795 do_numbering(natoms, groups, user1GroupNames, defaultIndexGroups, gnames,
3796 SimulationAtomGroupType::User1, restnm, egrptpALL_GENREST, bVerbose, wi);
3797 auto user2GroupNames = gmx::splitString(is->user2);
3798 do_numbering(natoms, groups, user2GroupNames, defaultIndexGroups, gnames,
3799 SimulationAtomGroupType::User2, restnm, egrptpALL_GENREST, bVerbose, wi);
3800 auto compressedXGroupNames = gmx::splitString(is->x_compressed_groups);
3801 do_numbering(natoms, groups, compressedXGroupNames, defaultIndexGroups, gnames,
3802 SimulationAtomGroupType::CompressedPositionOutput, restnm, egrptpONE, bVerbose, wi);
3803 auto orirefFitGroupNames = gmx::splitString(is->orirefitgrp);
3804 do_numbering(natoms, groups, orirefFitGroupNames, defaultIndexGroups, gnames,
3805 SimulationAtomGroupType::OrientationRestraintsFit, restnm, egrptpALL_GENREST,
3808 /* QMMM input processing */
3809 auto qmGroupNames = gmx::splitString(is->QMMM);
3810 auto qmMethods = gmx::splitString(is->QMmethod);
3811 auto qmBasisSets = gmx::splitString(is->QMbasis);
3812 if (ir->eI != eiMimic)
3814 if (qmMethods.size() != qmGroupNames.size() || qmBasisSets.size() != qmGroupNames.size())
3817 "Invalid QMMM input: %zu groups %zu basissets"
3818 " and %zu methods\n",
3819 qmGroupNames.size(), qmBasisSets.size(), qmMethods.size());
3821 /* group rest, if any, is always MM! */
3822 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3823 SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
3824 nr = qmGroupNames.size(); /*atoms->grps[egcQMMM].nr;*/
3825 ir->opts.ngQM = qmGroupNames.size();
3826 snew(ir->opts.QMmethod, nr);
3827 snew(ir->opts.QMbasis, nr);
3828 for (i = 0; i < nr; i++)
3830 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3831 * converted to the corresponding enum in names.c
3833 ir->opts.QMmethod[i] = search_QMstring(qmMethods[i].c_str(), eQMmethodNR, eQMmethod_names);
3834 ir->opts.QMbasis[i] = search_QMstring(qmBasisSets[i].c_str(), eQMbasisNR, eQMbasis_names);
3836 auto qmMultiplicities = gmx::splitString(is->QMmult);
3837 auto qmCharges = gmx::splitString(is->QMcharge);
3838 auto qmbSH = gmx::splitString(is->bSH);
3839 snew(ir->opts.QMmult, nr);
3840 snew(ir->opts.QMcharge, nr);
3841 snew(ir->opts.bSH, nr);
3842 convertInts(wi, qmMultiplicities, "QMmult", ir->opts.QMmult);
3843 convertInts(wi, qmCharges, "QMcharge", ir->opts.QMcharge);
3844 convertYesNos(wi, qmbSH, "bSH", ir->opts.bSH);
3846 auto CASelectrons = gmx::splitString(is->CASelectrons);
3847 auto CASorbitals = gmx::splitString(is->CASorbitals);
3848 snew(ir->opts.CASelectrons, nr);
3849 snew(ir->opts.CASorbitals, nr);
3850 convertInts(wi, CASelectrons, "CASelectrons", ir->opts.CASelectrons);
3851 convertInts(wi, CASorbitals, "CASOrbitals", ir->opts.CASorbitals);
3853 auto SAon = gmx::splitString(is->SAon);
3854 auto SAoff = gmx::splitString(is->SAoff);
3855 auto SAsteps = gmx::splitString(is->SAsteps);
3856 snew(ir->opts.SAon, nr);
3857 snew(ir->opts.SAoff, nr);
3858 snew(ir->opts.SAsteps, nr);
3859 convertInts(wi, SAon, "SAon", ir->opts.SAon);
3860 convertInts(wi, SAoff, "SAoff", ir->opts.SAoff);
3861 convertInts(wi, SAsteps, "SAsteps", ir->opts.SAsteps);
3866 if (qmGroupNames.size() > 1)
3868 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
3870 /* group rest, if any, is always MM! */
3871 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3872 SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
3874 ir->opts.ngQM = qmGroupNames.size();
3877 /* end of QMMM input */
3881 for (auto group : gmx::keysOf(groups->groups))
3883 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
3884 for (const auto& entry : groups->groups[group])
3886 fprintf(stderr, " %s", *(groups->groupNames[entry]));
3888 fprintf(stderr, "\n");
3892 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3893 snew(ir->opts.egp_flags, nr * nr);
3895 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3896 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3898 warning_error(wi, "Energy group exclusions are currently not supported");
3900 if (bExcl && EEL_FULL(ir->coulombtype))
3902 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3905 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3906 if (bTable && !(ir->vdwtype == evdwUSER) && !(ir->coulombtype == eelUSER)
3907 && !(ir->coulombtype == eelPMEUSER) && !(ir->coulombtype == eelPMEUSERSWITCH))
3910 "Can only have energy group pair tables in combination with user tables for VdW "
3914 /* final check before going out of scope if simulated tempering variables
3915 * need to be set to default values.
3917 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
3919 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
3920 warning(wi, gmx::formatString(
3921 "the value for nstexpanded was not specified for "
3922 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
3923 "by default, but it is recommended to set it to an explicit value!",
3924 ir->expandedvals->nstexpanded));
3926 for (i = 0; (i < defaultIndexGroups->nr); i++)
3931 done_blocka(defaultIndexGroups);
3932 sfree(defaultIndexGroups);
3936 static void check_disre(const gmx_mtop_t* mtop)
3938 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3940 const gmx_ffparams_t& ffparams = mtop->ffparams;
3943 for (int i = 0; i < ffparams.numTypes(); i++)
3945 int ftype = ffparams.functype[i];
3946 if (ftype == F_DISRES)
3948 int label = ffparams.iparams[i].disres.label;
3949 if (label == old_label)
3951 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3960 "Found %d double distance restraint indices,\n"
3961 "probably the parameters for multiple pairs in one restraint "
3962 "are not identical\n",
3968 static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t* sys, const bool posres_only, ivec AbsRef)
3971 gmx_mtop_ilistloop_t iloop;
3973 const t_iparams* pr;
3980 for (d = 0; d < DIM; d++)
3982 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3984 /* Check for freeze groups */
3985 for (g = 0; g < ir->opts.ngfrz; g++)
3987 for (d = 0; d < DIM; d++)
3989 if (ir->opts.nFreeze[g][d] != 0)
3997 /* Check for position restraints */
3998 iloop = gmx_mtop_ilistloop_init(sys);
3999 while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
4001 if (nmol > 0 && (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
4003 for (i = 0; i < (*ilist)[F_POSRES].size(); i += 2)
4005 pr = &sys->ffparams.iparams[(*ilist)[F_POSRES].iatoms[i]];
4006 for (d = 0; d < DIM; d++)
4008 if (pr->posres.fcA[d] != 0)
4014 for (i = 0; i < (*ilist)[F_FBPOSRES].size(); i += 2)
4016 /* Check for flat-bottom posres */
4017 pr = &sys->ffparams.iparams[(*ilist)[F_FBPOSRES].iatoms[i]];
4018 if (pr->fbposres.k != 0)
4020 switch (pr->fbposres.geom)
4022 case efbposresSPHERE: AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1; break;
4023 case efbposresCYLINDERX: AbsRef[YY] = AbsRef[ZZ] = 1; break;
4024 case efbposresCYLINDERY: AbsRef[XX] = AbsRef[ZZ] = 1; break;
4025 case efbposresCYLINDER:
4026 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
4027 case efbposresCYLINDERZ: AbsRef[XX] = AbsRef[YY] = 1; break;
4028 case efbposresX: /* d=XX */
4029 case efbposresY: /* d=YY */
4030 case efbposresZ: /* d=ZZ */
4031 d = pr->fbposres.geom - efbposresX;
4036 " Invalid geometry for flat-bottom position restraint.\n"
4037 "Expected nr between 1 and %d. Found %d\n",
4038 efbposresNR - 1, pr->fbposres.geom);
4045 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
4048 static void check_combination_rule_differences(const gmx_mtop_t* mtop,
4050 bool* bC6ParametersWorkWithGeometricRules,
4051 bool* bC6ParametersWorkWithLBRules,
4052 bool* bLBRulesPossible)
4054 int ntypes, tpi, tpj;
4057 double c6i, c6j, c12i, c12j;
4058 double c6, c6_geometric, c6_LB;
4059 double sigmai, sigmaj, epsi, epsj;
4060 bool bCanDoLBRules, bCanDoGeometricRules;
4063 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
4064 * force-field floating point parameters.
4067 ptr = getenv("GMX_LJCOMB_TOL");
4071 double gmx_unused canary;
4073 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
4076 "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
4081 *bC6ParametersWorkWithLBRules = TRUE;
4082 *bC6ParametersWorkWithGeometricRules = TRUE;
4083 bCanDoLBRules = TRUE;
4084 ntypes = mtop->ffparams.atnr;
4085 snew(typecount, ntypes);
4086 gmx_mtop_count_atomtypes(mtop, state, typecount);
4087 *bLBRulesPossible = TRUE;
4088 for (tpi = 0; tpi < ntypes; ++tpi)
4090 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
4091 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
4092 for (tpj = tpi; tpj < ntypes; ++tpj)
4094 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
4095 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
4096 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
4097 c6_geometric = std::sqrt(c6i * c6j);
4098 if (!gmx_numzero(c6_geometric))
4100 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4102 sigmai = gmx::sixthroot(c12i / c6i);
4103 sigmaj = gmx::sixthroot(c12j / c6j);
4104 epsi = c6i * c6i / (4.0 * c12i);
4105 epsj = c6j * c6j / (4.0 * c12j);
4106 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4110 *bLBRulesPossible = FALSE;
4111 c6_LB = c6_geometric;
4113 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4118 *bC6ParametersWorkWithLBRules = FALSE;
4121 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4123 if (!bCanDoGeometricRules)
4125 *bC6ParametersWorkWithGeometricRules = FALSE;
4132 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t* mtop, warninp_t wi)
4134 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4136 check_combination_rule_differences(mtop, 0, &bC6ParametersWorkWithGeometricRules,
4137 &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4138 if (ir->ljpme_combination_rule == eljpmeLB)
4140 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4143 "You are using arithmetic-geometric combination rules "
4144 "in LJ-PME, but your non-bonded C6 parameters do not "
4145 "follow these rules.");
4150 if (!bC6ParametersWorkWithGeometricRules)
4152 if (ir->eDispCorr != edispcNO)
4155 "You are using geometric combination rules in "
4156 "LJ-PME, but your non-bonded C6 parameters do "
4157 "not follow these rules. "
4158 "This will introduce very small errors in the forces and energies in "
4159 "your simulations. Dispersion correction will correct total energy "
4160 "and/or pressure for isotropic systems, but not forces or surface "
4166 "You are using geometric combination rules in "
4167 "LJ-PME, but your non-bonded C6 parameters do "
4168 "not follow these rules. "
4169 "This will introduce very small errors in the forces and energies in "
4170 "your simulations. If your system is homogeneous, consider using "
4171 "dispersion correction "
4172 "for the total energy and pressure.");
4178 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4180 char err_buf[STRLEN];
4185 gmx_mtop_atomloop_block_t aloopb;
4187 char warn_buf[STRLEN];
4189 set_warning_line(wi, mdparin, -1);
4191 if (absolute_reference(ir, sys, false, AbsRef))
4194 "Removing center of mass motion in the presence of position restraints might "
4195 "cause artifacts. When you are using position restraints to equilibrate a "
4196 "macro-molecule, the artifacts are usually negligible.");
4199 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 && ir->nstlist > 1
4200 && ((EI_MD(ir->eI) || EI_SD(ir->eI)) && (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4202 /* Check if a too small Verlet buffer might potentially
4203 * cause more drift than the thermostat can couple off.
4205 /* Temperature error fraction for warning and suggestion */
4206 const real T_error_warn = 0.002;
4207 const real T_error_suggest = 0.001;
4208 /* For safety: 2 DOF per atom (typical with constraints) */
4209 const real nrdf_at = 2;
4210 real T, tau, max_T_error;
4215 for (i = 0; i < ir->opts.ngtc; i++)
4217 T = std::max(T, ir->opts.ref_t[i]);
4218 tau = std::max(tau, ir->opts.tau_t[i]);
4222 /* This is a worst case estimate of the temperature error,
4223 * assuming perfect buffer estimation and no cancelation
4224 * of errors. The factor 0.5 is because energy distributes
4225 * equally over Ekin and Epot.
4227 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * BOLTZ * T);
4228 if (max_T_error > T_error_warn)
4231 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4232 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4233 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4234 "%.0e or decrease tau_t.",
4235 ir->verletbuf_tol, T, tau, 100 * max_T_error, 100 * T_error_suggest,
4236 ir->verletbuf_tol * T_error_suggest / max_T_error);
4237 warning(wi, warn_buf);
4242 if (ETC_ANDERSEN(ir->etc))
4246 for (i = 0; i < ir->opts.ngtc; i++)
4249 "all tau_t must currently be equal using Andersen temperature control, "
4250 "violated for group %d",
4252 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4254 "all tau_t must be positive using Andersen temperature control, "
4256 i, ir->opts.tau_t[i]);
4257 CHECK(ir->opts.tau_t[i] < 0);
4260 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4262 for (i = 0; i < ir->opts.ngtc; i++)
4264 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4266 "tau_t/delta_t for group %d for temperature control method %s must be a "
4267 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4268 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4270 i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
4271 CHECK(nsteps % ir->nstcomm != 0);
4276 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD && ir->comm_mode == ecmNO
4277 && !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) && !ETC_ANDERSEN(ir->etc))
4280 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4281 "rounding errors can lead to build up of kinetic energy of the center of mass");
4284 if (ir->epc == epcPARRINELLORAHMAN && ir->etc == etcNOSEHOOVER)
4287 for (int g = 0; g < ir->opts.ngtc; g++)
4289 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4291 if (ir->tau_p < 1.9 * tau_t_max)
4293 std::string message = gmx::formatString(
4294 "With %s T-coupling and %s p-coupling, "
4295 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4296 etcoupl_names[ir->etc], epcoupl_names[ir->epc], "tau-p", ir->tau_p, "tau-t",
4298 warning(wi, message.c_str());
4302 /* Check for pressure coupling with absolute position restraints */
4303 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4305 absolute_reference(ir, sys, TRUE, AbsRef);
4307 for (m = 0; m < DIM; m++)
4309 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4312 "You are using pressure coupling with absolute position restraints, "
4313 "this will give artifacts. Use the refcoord_scaling option.");
4321 aloopb = gmx_mtop_atomloop_block_init(sys);
4323 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4325 if (atom->q != 0 || atom->qB != 0)
4333 if (EEL_FULL(ir->coulombtype))
4336 "You are using full electrostatics treatment %s for a system without charges.\n"
4337 "This costs a lot of performance for just processing zeros, consider using %s "
4339 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4340 warning(wi, err_buf);
4345 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
4348 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4349 "You might want to consider using %s electrostatics.\n",
4351 warning_note(wi, err_buf);
4355 /* Check if combination rules used in LJ-PME are the same as in the force field */
4356 if (EVDW_PME(ir->vdwtype))
4358 check_combination_rules(ir, sys, wi);
4361 /* Generalized reaction field */
4362 if (ir->coulombtype == eelGRF_NOTUSED)
4365 "Generalized reaction-field electrostatics is no longer supported. "
4366 "You can use normal reaction-field instead and compute the reaction-field "
4367 "constant by hand.");
4371 for (int i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4373 for (m = 0; (m < DIM); m++)
4375 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4384 snew(mgrp, sys->groups.groups[SimulationAtomGroupType::Acceleration].size());
4385 for (const AtomProxy atomP : AtomRange(*sys))
4387 const t_atom& local = atomP.atom();
4388 int i = atomP.globalAtomNumber();
4389 mgrp[getGroupType(sys->groups, SimulationAtomGroupType::Acceleration, i)] += local.m;
4392 for (i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4394 for (m = 0; (m < DIM); m++)
4396 acc[m] += ir->opts.acc[i][m] * mgrp[i];
4400 for (m = 0; (m < DIM); m++)
4402 if (fabs(acc[m]) > 1e-6)
4404 const char* dim[DIM] = { "X", "Y", "Z" };
4405 fprintf(stderr, "Net Acceleration in %s direction, will %s be corrected\n", dim[m],
4406 ir->nstcomm != 0 ? "" : "not");
4407 if (ir->nstcomm != 0 && m < ndof_com(ir))
4411 (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4413 ir->opts.acc[i][m] -= acc[m];
4421 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0
4422 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4424 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4432 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4434 if (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0)
4436 absolute_reference(ir, sys, FALSE, AbsRef);
4437 for (m = 0; m < DIM; m++)
4439 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4442 "You are using an absolute reference for pulling, but the rest of "
4443 "the system does not have an absolute reference. This will lead to "
4452 for (i = 0; i < 3; i++)
4454 for (m = 0; m <= i; m++)
4456 if ((ir->epc != epcNO && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4458 for (c = 0; c < ir->pull->ncoord; c++)
4460 if (ir->pull->coord[c].eGeom == epullgDIRPBC && ir->pull->coord[c].vec[m] != 0)
4463 "Can not have dynamic box while using pull geometry '%s' "
4465 EPULLGEOM(ir->pull->coord[c].eGeom), 'x' + m);
4476 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4478 char warn_buf[STRLEN];
4481 ptr = check_box(ir->ePBC, box);
4484 warning_error(wi, ptr);
4487 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4489 if (ir->shake_tol <= 0.0)
4491 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4492 warning_error(wi, warn_buf);
4496 if ((ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4498 /* If we have Lincs constraints: */
4499 if (ir->eI == eiMD && ir->etc == etcNO && ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4502 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4503 warning_note(wi, warn_buf);
4506 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4509 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4511 warning_note(wi, warn_buf);
4513 if (ir->epc == epcMTTK)
4515 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4519 if (bHasAnyConstraints && ir->epc == epcMTTK)
4521 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4524 if (ir->LincsWarnAngle > 90.0)
4526 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4527 warning(wi, warn_buf);
4528 ir->LincsWarnAngle = 90.0;
4531 if (ir->ePBC != epbcNONE)
4533 if (ir->nstlist == 0)
4536 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4537 "atoms might cause the simulation to crash.");
4539 if (gmx::square(ir->rlist) >= max_cutoff2(ir->ePBC, box))
4542 "ERROR: The cut-off length is longer than half the shortest box vector or "
4543 "longer than the smallest box diagonal element. Increase the box size or "
4544 "decrease rlist.\n");
4545 warning_error(wi, warn_buf);