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50 #include "gromacs/awh/read_params.h"
51 #include "gromacs/fileio/readinp.h"
52 #include "gromacs/fileio/warninp.h"
53 #include "gromacs/gmxlib/network.h"
54 #include "gromacs/gmxpreprocess/toputil.h"
55 #include "gromacs/math/functions.h"
56 #include "gromacs/math/units.h"
57 #include "gromacs/math/vec.h"
58 #include "gromacs/mdlib/calc_verletbuf.h"
59 #include "gromacs/mdrun/mdmodules.h"
60 #include "gromacs/mdtypes/inputrec.h"
61 #include "gromacs/mdtypes/md_enums.h"
62 #include "gromacs/mdtypes/pull_params.h"
63 #include "gromacs/options/options.h"
64 #include "gromacs/options/treesupport.h"
65 #include "gromacs/pbcutil/pbc.h"
66 #include "gromacs/selection/indexutil.h"
67 #include "gromacs/topology/block.h"
68 #include "gromacs/topology/ifunc.h"
69 #include "gromacs/topology/index.h"
70 #include "gromacs/topology/mtop_util.h"
71 #include "gromacs/topology/symtab.h"
72 #include "gromacs/topology/topology.h"
73 #include "gromacs/utility/cstringutil.h"
74 #include "gromacs/utility/exceptions.h"
75 #include "gromacs/utility/fatalerror.h"
76 #include "gromacs/utility/filestream.h"
77 #include "gromacs/utility/gmxassert.h"
78 #include "gromacs/utility/ikeyvaluetreeerror.h"
79 #include "gromacs/utility/keyvaluetree.h"
80 #include "gromacs/utility/keyvaluetreebuilder.h"
81 #include "gromacs/utility/keyvaluetreemdpwriter.h"
82 #include "gromacs/utility/keyvaluetreetransform.h"
83 #include "gromacs/utility/mdmodulenotification.h"
84 #include "gromacs/utility/smalloc.h"
85 #include "gromacs/utility/strconvert.h"
86 #include "gromacs/utility/stringcompare.h"
87 #include "gromacs/utility/stringutil.h"
88 #include "gromacs/utility/textwriter.h"
93 /* Resource parameters
94 * Do not change any of these until you read the instruction
95 * in readinp.h. Some cpp's do not take spaces after the backslash
96 * (like the c-shell), which will give you a very weird compiler
100 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.preProcessingNotifications_.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", c_pbcTypeNames[PbcType::Xyz].c_str());
594 CHECK(ir->pbcType != PbcType::Xyz);
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);
672 "The soft-core sc-r-power is %d and can only be 6. (sc-r-power 48 is no longer "
674 static_cast<int>(fep->sc_r_power));
675 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0);
678 "Can't use positive delta-lambda (%g) if initial state/lambda does not start at "
681 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
683 sprintf(err_buf, "Can't use positive delta-lambda (%g) with expanded ensemble simulations",
685 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
687 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
688 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
690 sprintf(err_buf, "Free-energy not implemented for Ewald");
691 CHECK(ir->coulombtype == eelEWALD);
693 /* check validty of lambda inputs */
694 if (fep->n_lambda == 0)
696 /* Clear output in case of no states:*/
697 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.",
698 fep->init_fep_state);
699 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
703 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d",
704 fep->init_fep_state, fep->n_lambda - 1);
705 CHECK((fep->init_fep_state >= fep->n_lambda));
709 "Lambda state must be set, either with init-lambda-state or with init-lambda");
710 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
713 "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with "
714 "init-lambda-state or with init-lambda, but not both",
715 fep->init_lambda, fep->init_fep_state);
716 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
719 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
723 for (i = 0; i < efptNR; i++)
725 if (fep->separate_dvdl[i])
730 if (n_lambda_terms > 1)
733 "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't "
734 "use init-lambda to set lambda state (except for slow growth). Use "
735 "init-lambda-state instead.");
736 warning(wi, warn_buf);
739 if (n_lambda_terms < 2 && fep->n_lambda > 0)
742 "init-lambda is deprecated for setting lambda state (except for slow "
743 "growth). Use init-lambda-state instead.");
747 for (j = 0; j < efptNR; j++)
749 for (i = 0; i < fep->n_lambda; i++)
751 sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i,
752 efpt_names[j], fep->all_lambda[j][i]);
753 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
757 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
759 for (i = 0; i < fep->n_lambda; i++)
762 "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while "
763 "coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to "
764 "crashes, and is not supported.",
765 i, fep->all_lambda[efptVDW][i], fep->all_lambda[efptCOUL][i]);
766 CHECK((fep->sc_alpha > 0)
767 && (((fep->all_lambda[efptCOUL][i] > 0.0) && (fep->all_lambda[efptCOUL][i] < 1.0))
768 && ((fep->all_lambda[efptVDW][i] > 0.0) && (fep->all_lambda[efptVDW][i] < 1.0))));
772 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
774 real sigma, lambda, r_sc;
777 /* Maximum estimate for A and B charges equal with lambda power 1 */
779 r_sc = std::pow(lambda * fep->sc_alpha * std::pow(sigma / ir->rcoulomb, fep->sc_r_power) + 1.0,
780 1.0 / fep->sc_r_power);
782 "With PME there is a minor soft core effect present at the cut-off, "
783 "proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on "
784 "energy conservation, but usually other effects dominate. With a common sigma "
785 "value of %g nm the fraction of the particle-particle potential at the cut-off "
786 "at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
787 fep->sc_r_power, sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
788 warning_note(wi, warn_buf);
791 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
792 be treated differently, but that's the next step */
794 for (i = 0; i < efptNR; i++)
796 for (j = 0; j < fep->n_lambda; j++)
798 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
799 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
804 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
808 /* checking equilibration of weights inputs for validity */
811 "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal "
813 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
814 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
817 "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to "
819 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
820 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
823 "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
824 expand->equil_steps, elmceq_names[elmceqSTEPS]);
825 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
828 "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
829 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
830 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
833 "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
834 expand->equil_ratio, elmceq_names[elmceqRATIO]);
835 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
838 "weight-equil-number-all-lambda (%d) must be a positive integer if "
839 "lmc-weights-equil=%s",
840 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
841 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
844 "weight-equil-number-samples (%d) must be a positive integer if "
845 "lmc-weights-equil=%s",
846 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
847 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
850 "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
851 expand->equil_steps, elmceq_names[elmceqSTEPS]);
852 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
854 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
855 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
856 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
858 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
859 expand->equil_ratio, elmceq_names[elmceqRATIO]);
860 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
862 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
863 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
864 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
866 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
867 CHECK((expand->lmc_repeats <= 0));
868 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
869 CHECK((expand->minvarmin <= 0));
870 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
871 CHECK((expand->c_range < 0));
873 "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != "
875 fep->init_fep_state, expand->lmc_forced_nstart);
876 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0)
877 && (expand->elmcmove != elmcmoveNO));
878 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
879 CHECK((expand->lmc_forced_nstart < 0));
880 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)",
881 fep->init_fep_state);
882 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
884 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
885 CHECK((expand->init_wl_delta < 0));
886 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
887 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
888 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
889 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
891 /* if there is no temperature control, we need to specify an MC temperature */
892 if (!integratorHasReferenceTemperature(ir) && (expand->elmcmove != elmcmoveNO)
893 && (expand->mc_temp <= 0.0))
896 "If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set "
897 "to a positive number");
898 warning_error(wi, err_buf);
900 if (expand->nstTij > 0)
902 sprintf(err_buf, "nstlog must be non-zero");
903 CHECK(ir->nstlog == 0);
904 // Avoid modulus by zero in the case that already triggered an error exit.
908 "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
909 expand->nstTij, ir->nstlog);
910 CHECK((expand->nstTij % ir->nstlog) != 0);
916 sprintf(err_buf, "walls only work with pbc=%s", c_pbcTypeNames[PbcType::XY].c_str());
917 CHECK(ir->nwall && ir->pbcType != PbcType::XY);
920 if (ir->pbcType != PbcType::Xyz && ir->nwall != 2)
922 if (ir->pbcType == PbcType::No)
924 if (ir->epc != epcNO)
926 warning(wi, "Turning off pressure coupling for vacuum system");
932 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
933 c_pbcTypeNames[ir->pbcType].c_str());
934 CHECK(ir->epc != epcNO);
936 sprintf(err_buf, "Can not have Ewald with pbc=%s", c_pbcTypeNames[ir->pbcType].c_str());
937 CHECK(EEL_FULL(ir->coulombtype));
939 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
940 c_pbcTypeNames[ir->pbcType].c_str());
941 CHECK(ir->eDispCorr != edispcNO);
944 if (ir->rlist == 0.0)
947 "can only have neighborlist cut-off zero (=infinite)\n"
948 "with coulombtype = %s or coulombtype = %s\n"
949 "without periodic boundary conditions (pbc = %s) and\n"
950 "rcoulomb and rvdw set to zero",
951 eel_names[eelCUT], eel_names[eelUSER], c_pbcTypeNames[PbcType::No].c_str());
952 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER))
953 || (ir->pbcType != PbcType::No) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
958 "Simulating without cut-offs can be (slightly) faster with nstlist=0, "
959 "nstype=simple and only one MPI rank");
964 if (ir->nstcomm == 0)
966 // TODO Change this behaviour. There should be exactly one way
967 // to turn off an algorithm.
968 ir->comm_mode = ecmNO;
970 if (ir->comm_mode != ecmNO)
974 // TODO Such input was once valid. Now that we've been
975 // helpful for a few years, we should reject such input,
976 // lest we have to support every historical decision
979 "If you want to remove the rotation around the center of mass, you should set "
980 "comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to "
981 "its absolute value");
982 ir->nstcomm = abs(ir->nstcomm);
985 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
988 "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting "
989 "nstcomm to nstcalcenergy");
990 ir->nstcomm = ir->nstcalcenergy;
993 if (ir->comm_mode == ecmANGULAR)
996 "Can not remove the rotation around the center of mass with periodic "
998 CHECK(ir->bPeriodicMols);
999 if (ir->pbcType != PbcType::No)
1002 "Removing the rotation around the center of mass in a periodic system, "
1003 "this can lead to artifacts. Only use this on a single (cluster of) "
1004 "molecules. This cluster should not cross periodic boundaries.");
1009 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->pbcType == PbcType::No && ir->comm_mode != ecmANGULAR)
1012 "Tumbling and flying ice-cubes: We are not removing rotation around center of mass "
1013 "in a non-periodic system. You should probably set comm_mode = ANGULAR or use "
1016 warning_note(wi, warn_buf);
1019 /* TEMPERATURE COUPLING */
1020 if (ir->etc == etcYES)
1022 ir->etc = etcBERENDSEN;
1024 "Old option for temperature coupling given: "
1025 "changing \"yes\" to \"Berendsen\"\n");
1028 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
1030 if (ir->opts.nhchainlength < 1)
1033 "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to "
1035 ir->opts.nhchainlength);
1036 ir->opts.nhchainlength = 1;
1037 warning(wi, warn_buf);
1040 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
1044 "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
1045 ir->opts.nhchainlength = 1;
1050 ir->opts.nhchainlength = 0;
1053 if (ir->eI == eiVVAK)
1056 "%s implemented primarily for validation, and requires nsttcouple = 1 and "
1059 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
1062 if (ETC_ANDERSEN(ir->etc))
1064 sprintf(err_buf, "%s temperature control not supported for integrator %s.",
1065 etcoupl_names[ir->etc], ei_names[ir->eI]);
1066 CHECK(!(EI_VV(ir->eI)));
1068 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
1071 "Center of mass removal not necessary for %s. All velocities of coupled "
1072 "groups are rerandomized periodically, so flying ice cube errors will not "
1074 etcoupl_names[ir->etc]);
1075 warning_note(wi, warn_buf);
1079 "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are "
1080 "randomized every time step",
1081 ir->nstcomm, etcoupl_names[ir->etc]);
1082 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
1085 if (ir->etc == etcBERENDSEN)
1088 "The %s thermostat does not generate the correct kinetic energy distribution. You "
1089 "might want to consider using the %s thermostat.",
1090 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
1091 warning_note(wi, warn_buf);
1094 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc)) && ir->epc == epcBERENDSEN)
1097 "Using Berendsen pressure coupling invalidates the "
1098 "true ensemble for the thermostat");
1099 warning(wi, warn_buf);
1102 /* PRESSURE COUPLING */
1103 if (ir->epc == epcISOTROPIC)
1105 ir->epc = epcBERENDSEN;
1107 "Old option for pressure coupling given: "
1108 "changing \"Isotropic\" to \"Berendsen\"\n");
1111 if (ir->epc != epcNO)
1113 dt_pcoupl = ir->nstpcouple * ir->delta_t;
1115 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1116 CHECK(ir->tau_p <= 0);
1118 if (ir->tau_p / dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10 * GMX_REAL_EPS)
1121 "For proper integration of the %s barostat, tau-p (%g) should be at least %d "
1122 "times larger than nstpcouple*dt (%g)",
1123 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1124 warning(wi, warn_buf);
1128 "compressibility must be > 0 when using pressure"
1130 EPCOUPLTYPE(ir->epc));
1131 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 || ir->compress[ZZ][ZZ] < 0
1132 || (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 && ir->compress[ZZ][XX] <= 0
1133 && ir->compress[ZZ][YY] <= 0));
1135 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1138 "You are generating velocities so I am assuming you "
1139 "are equilibrating a system. You are using "
1140 "%s pressure coupling, but this can be "
1141 "unstable for equilibration. If your system crashes, try "
1142 "equilibrating first with Berendsen pressure coupling. If "
1143 "you are not equilibrating the system, you can probably "
1144 "ignore this warning.",
1145 epcoupl_names[ir->epc]);
1146 warning(wi, warn_buf);
1152 if (ir->epc == epcMTTK)
1154 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1158 /* ELECTROSTATICS */
1159 /* More checks are in triple check (grompp.c) */
1161 if (ir->coulombtype == eelSWITCH)
1164 "coulombtype = %s is only for testing purposes and can lead to serious "
1165 "artifacts, advice: use coulombtype = %s",
1166 eel_names[ir->coulombtype], eel_names[eelRF_ZERO]);
1167 warning(wi, warn_buf);
1170 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1173 "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old "
1174 "format and exchanging epsilon-r and epsilon-rf",
1176 warning(wi, warn_buf);
1177 ir->epsilon_rf = ir->epsilon_r;
1178 ir->epsilon_r = 1.0;
1181 if (ir->epsilon_r == 0)
1184 "It is pointless to use long-range electrostatics with infinite relative "
1186 "Since you are effectively turning of electrostatics, a plain cutoff will be much "
1188 CHECK(EEL_FULL(ir->coulombtype));
1191 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1193 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1194 CHECK(ir->epsilon_r < 0);
1197 if (EEL_RF(ir->coulombtype))
1199 /* reaction field (at the cut-off) */
1201 if (ir->coulombtype == eelRF_ZERO && ir->epsilon_rf != 0)
1204 "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1205 eel_names[ir->coulombtype]);
1206 warning(wi, warn_buf);
1207 ir->epsilon_rf = 0.0;
1210 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1211 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) || (ir->epsilon_r == 0));
1212 if (ir->epsilon_rf == ir->epsilon_r)
1214 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1215 eel_names[ir->coulombtype]);
1216 warning(wi, warn_buf);
1219 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1220 * means the interaction is zero outside rcoulomb, but it helps to
1221 * provide accurate energy conservation.
1223 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1225 if (ir_coulomb_switched(ir))
1228 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the "
1229 "potential modifier options!",
1230 eel_names[ir->coulombtype]);
1231 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1235 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1238 "Explicit switch/shift coulomb interactions cannot be used in combination with a "
1239 "secondary coulomb-modifier.");
1240 CHECK(ir->coulomb_modifier != eintmodNONE);
1242 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1245 "Explicit switch/shift vdw interactions cannot be used in combination with a "
1246 "secondary vdw-modifier.");
1247 CHECK(ir->vdw_modifier != eintmodNONE);
1250 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT || ir->vdwtype == evdwSWITCH
1251 || ir->vdwtype == evdwSHIFT)
1254 "The switch/shift interaction settings are just for compatibility; you will get "
1256 "performance from applying potential modifiers to your interactions!\n");
1257 warning_note(wi, warn_buf);
1260 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1262 if (ir->rcoulomb_switch / ir->rcoulomb < 0.9499)
1264 real percentage = 100 * (ir->rcoulomb - ir->rcoulomb_switch) / ir->rcoulomb;
1266 "The switching range should be 5%% or less (currently %.2f%% using a switching "
1267 "range of %4f-%4f) for accurate electrostatic energies, energy conservation "
1268 "will be good regardless, since ewald_rtol = %g.",
1269 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1270 warning(wi, warn_buf);
1274 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1276 if (ir->rvdw_switch == 0)
1279 "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones "
1280 "potential. This suggests it was not set in the mdp, which can lead to large "
1281 "energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw "
1282 "switching range.");
1283 warning(wi, warn_buf);
1287 if (EEL_FULL(ir->coulombtype))
1289 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER
1290 || ir->coulombtype == eelPMEUSERSWITCH)
1292 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1293 eel_names[ir->coulombtype]);
1294 CHECK(ir->rcoulomb > ir->rlist);
1298 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1300 // TODO: Move these checks into the ewald module with the options class
1302 int orderMax = (ir->coulombtype == eelP3M_AD ? 8 : 12);
1304 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1306 sprintf(warn_buf, "With coulombtype = %s, you should have %d <= pme-order <= %d",
1307 eel_names[ir->coulombtype], orderMin, orderMax);
1308 warning_error(wi, warn_buf);
1312 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1314 if (ir->ewald_geometry == eewg3D)
1316 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1317 c_pbcTypeNames[ir->pbcType].c_str(), eewg_names[eewg3DC]);
1318 warning(wi, warn_buf);
1320 /* This check avoids extra pbc coding for exclusion corrections */
1321 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1322 CHECK(ir->wall_ewald_zfac < 2);
1324 if ((ir->ewald_geometry == eewg3DC) && (ir->pbcType != PbcType::XY) && EEL_FULL(ir->coulombtype))
1326 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1327 eel_names[ir->coulombtype], eewg_names[eewg3DC], c_pbcTypeNames[PbcType::XY].c_str());
1328 warning(wi, warn_buf);
1330 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1332 sprintf(err_buf, "Cannot have periodic molecules with epsilon_surface > 0");
1333 CHECK(ir->bPeriodicMols);
1334 sprintf(warn_buf, "With epsilon_surface > 0 all molecules should be neutral.");
1335 warning_note(wi, warn_buf);
1337 "With epsilon_surface > 0 you can only use domain decomposition "
1338 "when there are only small molecules with all bonds constrained (mdrun will check "
1340 warning_note(wi, warn_buf);
1343 if (ir_vdw_switched(ir))
1345 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1346 CHECK(ir->rvdw_switch >= ir->rvdw);
1348 if (ir->rvdw_switch < 0.5 * ir->rvdw)
1351 "You are applying a switch function to vdw forces or potentials from %g to %g "
1352 "nm, which is more than half the interaction range, whereas switch functions "
1353 "are intended to act only close to the cut-off.",
1354 ir->rvdw_switch, ir->rvdw);
1355 warning_note(wi, warn_buf);
1359 if (ir->vdwtype == evdwPME)
1361 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1363 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s and %s",
1364 evdw_names[ir->vdwtype], eintmod_names[eintmodPOTSHIFT], eintmod_names[eintmodNONE]);
1365 warning_error(wi, err_buf);
1369 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1372 "You have selected user tables with dispersion correction, the dispersion "
1373 "will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction "
1374 "between rvdw_switch and rvdw will not be double counted). Make sure that you "
1375 "really want dispersion correction to -C6/r^6.");
1378 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT) && ir->rvdw != 0)
1380 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1383 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1385 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1388 /* IMPLICIT SOLVENT */
1389 if (ir->coulombtype == eelGB_NOTUSED)
1391 sprintf(warn_buf, "Invalid option %s for coulombtype", eel_names[ir->coulombtype]);
1392 warning_error(wi, warn_buf);
1397 warning_error(wi, "QMMM is currently not supported");
1398 if (!EI_DYNAMICS(ir->eI))
1401 sprintf(buf, "QMMM is only supported with dynamics, not with integrator %s", ei_names[ir->eI]);
1402 warning_error(wi, buf);
1408 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1412 /* interpret a number of doubles from a string and put them in an array,
1413 after allocating space for them.
1414 str = the input string
1415 n = the (pre-allocated) number of doubles read
1416 r = the output array of doubles. */
1417 static void parse_n_real(char* str, int* n, real** r, warninp_t wi)
1419 auto values = gmx::splitString(str);
1423 for (int i = 0; i < *n; i++)
1427 (*r)[i] = gmx::fromString<real>(values[i]);
1429 catch (gmx::GromacsException&)
1431 warning_error(wi, "Invalid value " + values[i]
1432 + " in string in mdp file. Expected a real number.");
1438 static void do_fep_params(t_inputrec* ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
1441 int i, j, max_n_lambda, nweights, nfep[efptNR];
1442 t_lambda* fep = ir->fepvals;
1443 t_expanded* expand = ir->expandedvals;
1444 real** count_fep_lambdas;
1445 bool bOneLambda = TRUE;
1447 snew(count_fep_lambdas, efptNR);
1449 /* FEP input processing */
1450 /* first, identify the number of lambda values for each type.
1451 All that are nonzero must have the same number */
1453 for (i = 0; i < efptNR; i++)
1455 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
1458 /* now, determine the number of components. All must be either zero, or equal. */
1461 for (i = 0; i < efptNR; i++)
1463 if (nfep[i] > max_n_lambda)
1465 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1466 must have the same number if its not zero.*/
1471 for (i = 0; i < efptNR; i++)
1475 ir->fepvals->separate_dvdl[i] = FALSE;
1477 else if (nfep[i] == max_n_lambda)
1479 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute
1480 the derivative with respect to the temperature currently */
1482 ir->fepvals->separate_dvdl[i] = TRUE;
1488 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1490 nfep[i], efpt_names[i], max_n_lambda);
1493 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1494 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1496 /* the number of lambdas is the number we've read in, which is either zero
1497 or the same for all */
1498 fep->n_lambda = max_n_lambda;
1500 /* allocate space for the array of lambda values */
1501 snew(fep->all_lambda, efptNR);
1502 /* if init_lambda is defined, we need to set lambda */
1503 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1505 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1507 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1508 for (i = 0; i < efptNR; i++)
1510 snew(fep->all_lambda[i], fep->n_lambda);
1511 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1514 for (j = 0; j < fep->n_lambda; j++)
1516 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1518 sfree(count_fep_lambdas[i]);
1521 sfree(count_fep_lambdas);
1523 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1524 internal bookkeeping -- for now, init_lambda */
1526 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1528 for (i = 0; i < fep->n_lambda; i++)
1530 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1534 /* check to see if only a single component lambda is defined, and soft core is defined.
1535 In this case, turn on coulomb soft core */
1537 if (max_n_lambda == 0)
1543 for (i = 0; i < efptNR; i++)
1545 if ((nfep[i] != 0) && (i != efptFEP))
1551 if ((bOneLambda) && (fep->sc_alpha > 0))
1553 fep->bScCoul = TRUE;
1556 /* Fill in the others with the efptFEP if they are not explicitly
1557 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1558 they are all zero. */
1560 for (i = 0; i < efptNR; i++)
1562 if ((nfep[i] == 0) && (i != efptFEP))
1564 for (j = 0; j < fep->n_lambda; j++)
1566 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1572 /* now read in the weights */
1573 parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
1576 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1578 else if (nweights != fep->n_lambda)
1580 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1581 nweights, fep->n_lambda);
1583 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1585 expand->nstexpanded = fep->nstdhdl;
1586 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1591 static void do_simtemp_params(t_inputrec* ir)
1594 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1595 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1598 static void convertYesNos(warninp_t /*wi*/,
1599 gmx::ArrayRef<const std::string> inputs,
1600 const char* /*name*/,
1604 for (const auto& input : inputs)
1606 outputs[i] = gmx::equalCaseInsensitive(input, "Y", 1);
1611 template<typename T>
1612 void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
1615 for (const auto& input : inputs)
1619 outputs[i] = gmx::fromStdString<T>(input);
1621 catch (gmx::GromacsException&)
1623 auto message = gmx::formatString(
1624 "Invalid value for mdp option %s. %s should only consist of integers separated "
1627 warning_error(wi, message);
1633 static void convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, real* outputs)
1636 for (const auto& input : inputs)
1640 outputs[i] = gmx::fromString<real>(input);
1642 catch (gmx::GromacsException&)
1644 auto message = gmx::formatString(
1645 "Invalid value for mdp option %s. %s should only consist of real numbers "
1646 "separated by spaces.",
1648 warning_error(wi, message);
1654 static void convertRvecs(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, rvec* outputs)
1657 for (const auto& input : inputs)
1661 outputs[i][d] = gmx::fromString<real>(input);
1663 catch (gmx::GromacsException&)
1665 auto message = gmx::formatString(
1666 "Invalid value for mdp option %s. %s should only consist of real numbers "
1667 "separated by spaces.",
1669 warning_error(wi, message);
1680 static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
1682 opts->wall_atomtype[0] = nullptr;
1683 opts->wall_atomtype[1] = nullptr;
1685 ir->wall_atomtype[0] = -1;
1686 ir->wall_atomtype[1] = -1;
1687 ir->wall_density[0] = 0;
1688 ir->wall_density[1] = 0;
1692 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1693 if (wallAtomTypes.size() != size_t(ir->nwall))
1695 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %zu", ir->nwall,
1696 wallAtomTypes.size());
1698 for (int i = 0; i < ir->nwall; i++)
1700 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1703 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1705 auto wallDensity = gmx::splitString(wall_density);
1706 if (wallDensity.size() != size_t(ir->nwall))
1708 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %zu", ir->nwall,
1709 wallDensity.size());
1711 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1712 for (int i = 0; i < ir->nwall; i++)
1714 if (ir->wall_density[i] <= 0)
1716 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1723 static void add_wall_energrps(SimulationGroups* groups, int nwall, t_symtab* symtab)
1727 AtomGroupIndices* grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1728 for (int i = 0; i < nwall; i++)
1730 groups->groupNames.emplace_back(put_symtab(symtab, gmx::formatString("wall%d", i).c_str()));
1731 grps->emplace_back(groups->groupNames.size() - 1);
1736 static void read_expandedparams(std::vector<t_inpfile>* inp, t_expanded* expand, warninp_t wi)
1738 /* read expanded ensemble parameters */
1739 printStringNewline(inp, "expanded ensemble variables");
1740 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1741 expand->elamstats = get_eeenum(inp, "lmc-stats", elamstats_names, wi);
1742 expand->elmcmove = get_eeenum(inp, "lmc-move", elmcmove_names, wi);
1743 expand->elmceq = get_eeenum(inp, "lmc-weights-equil", elmceq_names, wi);
1744 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1745 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1746 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1747 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1748 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1749 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1750 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1751 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1752 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1753 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1754 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1755 expand->bSymmetrizedTMatrix =
1756 (get_eeenum(inp, "symmetrized-transition-matrix", yesno_names, wi) != 0);
1757 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1758 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1759 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1760 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1761 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1762 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1763 expand->bWLoneovert = (get_eeenum(inp, "wl-oneovert", yesno_names, wi) != 0);
1766 /*! \brief Return whether an end state with the given coupling-lambda
1767 * value describes fully-interacting VDW.
1769 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1770 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1772 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1774 return (couple_lambda_value == ecouplamVDW || couple_lambda_value == ecouplamVDWQ);
1780 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1783 explicit MdpErrorHandler(warninp_t wi) : wi_(wi), mapping_(nullptr) {}
1785 void setBackMapping(const gmx::IKeyValueTreeBackMapping& mapping) { mapping_ = &mapping; }
1787 bool onError(gmx::UserInputError* ex, const gmx::KeyValueTreePath& context) override
1790 gmx::formatString("Error in mdp option \"%s\":", getOptionName(context).c_str()));
1791 std::string message = gmx::formatExceptionMessageToString(*ex);
1792 warning_error(wi_, message.c_str());
1797 std::string getOptionName(const gmx::KeyValueTreePath& context)
1799 if (mapping_ != nullptr)
1801 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1802 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1805 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1810 const gmx::IKeyValueTreeBackMapping* mapping_;
1815 void get_ir(const char* mdparin,
1816 const char* mdparout,
1817 gmx::MDModules* mdModules,
1820 WriteMdpHeader writeMdpHeader,
1824 double dumdub[2][6];
1826 char warn_buf[STRLEN];
1827 t_lambda* fep = ir->fepvals;
1828 t_expanded* expand = ir->expandedvals;
1830 const char* no_names[] = { "no", nullptr };
1832 init_inputrec_strings();
1833 gmx::TextInputFile stream(mdparin);
1834 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1836 snew(dumstr[0], STRLEN);
1837 snew(dumstr[1], STRLEN);
1839 /* ignore the following deprecated commands */
1840 replace_inp_entry(inp, "title", nullptr);
1841 replace_inp_entry(inp, "cpp", nullptr);
1842 replace_inp_entry(inp, "domain-decomposition", nullptr);
1843 replace_inp_entry(inp, "andersen-seed", nullptr);
1844 replace_inp_entry(inp, "dihre", nullptr);
1845 replace_inp_entry(inp, "dihre-fc", nullptr);
1846 replace_inp_entry(inp, "dihre-tau", nullptr);
1847 replace_inp_entry(inp, "nstdihreout", nullptr);
1848 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1849 replace_inp_entry(inp, "optimize-fft", nullptr);
1850 replace_inp_entry(inp, "adress_type", nullptr);
1851 replace_inp_entry(inp, "adress_const_wf", nullptr);
1852 replace_inp_entry(inp, "adress_ex_width", nullptr);
1853 replace_inp_entry(inp, "adress_hy_width", nullptr);
1854 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1855 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1856 replace_inp_entry(inp, "adress_site", nullptr);
1857 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1858 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1859 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1860 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1861 replace_inp_entry(inp, "rlistlong", nullptr);
1862 replace_inp_entry(inp, "nstcalclr", nullptr);
1863 replace_inp_entry(inp, "pull-print-com2", nullptr);
1864 replace_inp_entry(inp, "gb-algorithm", nullptr);
1865 replace_inp_entry(inp, "nstgbradii", nullptr);
1866 replace_inp_entry(inp, "rgbradii", nullptr);
1867 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1868 replace_inp_entry(inp, "gb-saltconc", nullptr);
1869 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1870 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1871 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1872 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1873 replace_inp_entry(inp, "sa-algorithm", nullptr);
1874 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1875 replace_inp_entry(inp, "ns-type", nullptr);
1877 /* replace the following commands with the clearer new versions*/
1878 replace_inp_entry(inp, "unconstrained-start", "continuation");
1879 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1880 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1881 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1882 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1883 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1884 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1886 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1887 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1888 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1889 setStringEntry(&inp, "include", opts->include, nullptr);
1890 printStringNoNewline(
1891 &inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1892 setStringEntry(&inp, "define", opts->define, nullptr);
1894 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1895 ir->eI = get_eeenum(&inp, "integrator", ei_names, wi);
1896 printStringNoNewline(&inp, "Start time and timestep in ps");
1897 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1898 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1899 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1900 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1901 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1902 printStringNoNewline(
1903 &inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1904 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1905 printStringNoNewline(&inp, "mode for center of mass motion removal");
1906 ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
1907 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
1908 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
1909 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
1910 setStringEntry(&inp, "comm-grps", is->vcm, nullptr);
1912 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
1913 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
1914 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
1915 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
1918 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
1919 printStringNoNewline(&inp, "Force tolerance and initial step-size");
1920 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
1921 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
1922 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
1923 ir->niter = get_eint(&inp, "niter", 20, wi);
1924 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
1925 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
1926 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
1927 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
1928 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
1930 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
1931 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
1933 /* Output options */
1934 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
1935 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
1936 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
1937 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
1938 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
1939 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
1940 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
1941 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
1942 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
1943 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
1944 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
1945 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
1946 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
1947 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
1948 printStringNoNewline(&inp, "default, all atoms will be written.");
1949 setStringEntry(&inp, "compressed-x-grps", is->x_compressed_groups, nullptr);
1950 printStringNoNewline(&inp, "Selection of energy groups");
1951 setStringEntry(&inp, "energygrps", is->energy, nullptr);
1953 /* Neighbor searching */
1954 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
1955 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
1956 ir->cutoff_scheme = get_eeenum(&inp, "cutoff-scheme", ecutscheme_names, wi);
1957 printStringNoNewline(&inp, "nblist update frequency");
1958 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
1959 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
1960 // TODO This conversion should be removed when proper std:string handling will be added to get_eeenum(...), etc.
1961 std::vector<const char*> pbcTypesNamesChar;
1962 for (const auto& pbcTypeName : c_pbcTypeNames)
1964 pbcTypesNamesChar.push_back(pbcTypeName.c_str());
1966 ir->pbcType = static_cast<PbcType>(get_eeenum(&inp, "pbc", pbcTypesNamesChar.data(), wi));
1967 ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi) != 0;
1968 printStringNoNewline(&inp,
1969 "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1970 printStringNoNewline(&inp, "a value of -1 means: use rlist");
1971 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
1972 printStringNoNewline(&inp, "nblist cut-off");
1973 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
1974 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
1976 /* Electrostatics */
1977 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
1978 printStringNoNewline(&inp, "Method for doing electrostatics");
1979 ir->coulombtype = get_eeenum(&inp, "coulombtype", eel_names, wi);
1980 ir->coulomb_modifier = get_eeenum(&inp, "coulomb-modifier", eintmod_names, wi);
1981 printStringNoNewline(&inp, "cut-off lengths");
1982 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
1983 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
1984 printStringNoNewline(&inp,
1985 "Relative dielectric constant for the medium and the reaction field");
1986 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
1987 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
1988 printStringNoNewline(&inp, "Method for doing Van der Waals");
1989 ir->vdwtype = get_eeenum(&inp, "vdw-type", evdw_names, wi);
1990 ir->vdw_modifier = get_eeenum(&inp, "vdw-modifier", eintmod_names, wi);
1991 printStringNoNewline(&inp, "cut-off lengths");
1992 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
1993 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
1994 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
1995 ir->eDispCorr = get_eeenum(&inp, "DispCorr", edispc_names, wi);
1996 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
1997 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
1998 printStringNoNewline(&inp, "Separate tables between energy group pairs");
1999 setStringEntry(&inp, "energygrp-table", is->egptable, nullptr);
2000 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
2001 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
2002 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
2003 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
2004 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
2005 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
2006 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
2007 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
2008 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
2009 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
2010 ir->ljpme_combination_rule = get_eeenum(&inp, "lj-pme-comb-rule", eljpme_names, wi);
2011 ir->ewald_geometry = get_eeenum(&inp, "ewald-geometry", eewg_names, wi);
2012 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
2014 /* Implicit solvation is no longer supported, but we need grompp
2015 to be able to refuse old .mdp files that would have built a tpr
2016 to run it. Thus, only "no" is accepted. */
2017 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
2019 /* Coupling stuff */
2020 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
2021 printStringNoNewline(&inp, "Temperature coupling");
2022 ir->etc = get_eeenum(&inp, "tcoupl", etcoupl_names, wi);
2023 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
2024 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
2025 ir->bPrintNHChains = (get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi) != 0);
2026 printStringNoNewline(&inp, "Groups to couple separately");
2027 setStringEntry(&inp, "tc-grps", is->tcgrps, nullptr);
2028 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
2029 setStringEntry(&inp, "tau-t", is->tau_t, nullptr);
2030 setStringEntry(&inp, "ref-t", is->ref_t, nullptr);
2031 printStringNoNewline(&inp, "pressure coupling");
2032 ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
2033 ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
2034 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
2035 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
2036 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
2037 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
2038 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
2039 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
2040 ir->refcoord_scaling = get_eeenum(&inp, "refcoord-scaling", erefscaling_names, wi);
2043 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2044 ir->bQMMM = (get_eeenum(&inp, "QMMM", yesno_names, wi) != 0);
2045 printStringNoNewline(&inp, "Groups treated Quantum Mechanically");
2046 setStringEntry(&inp, "QMMM-grps", is->QMMM, nullptr);
2047 printStringNoNewline(&inp, "QM method");
2048 setStringEntry(&inp, "QMmethod", is->QMmethod, nullptr);
2049 printStringNoNewline(&inp, "QMMM scheme");
2050 ir->QMMMscheme = get_eeenum(&inp, "QMMMscheme", eQMMMscheme_names, wi);
2051 printStringNoNewline(&inp, "QM basisset");
2052 setStringEntry(&inp, "QMbasis", is->QMbasis, nullptr);
2053 printStringNoNewline(&inp, "QM charge");
2054 setStringEntry(&inp, "QMcharge", is->QMcharge, nullptr);
2055 printStringNoNewline(&inp, "QM multiplicity");
2056 setStringEntry(&inp, "QMmult", is->QMmult, nullptr);
2057 printStringNoNewline(&inp, "Surface Hopping");
2058 setStringEntry(&inp, "SH", is->bSH, nullptr);
2059 printStringNoNewline(&inp, "CAS space options");
2060 setStringEntry(&inp, "CASorbitals", is->CASorbitals, nullptr);
2061 setStringEntry(&inp, "CASelectrons", is->CASelectrons, nullptr);
2062 setStringEntry(&inp, "SAon", is->SAon, nullptr);
2063 setStringEntry(&inp, "SAoff", is->SAoff, nullptr);
2064 setStringEntry(&inp, "SAsteps", is->SAsteps, nullptr);
2065 printStringNoNewline(&inp, "Scale factor for MM charges");
2066 ir->scalefactor = get_ereal(&inp, "MMChargeScaleFactor", 1.0, wi);
2068 /* Simulated annealing */
2069 printStringNewline(&inp, "SIMULATED ANNEALING");
2070 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2071 setStringEntry(&inp, "annealing", is->anneal, nullptr);
2072 printStringNoNewline(&inp,
2073 "Number of time points to use for specifying annealing in each group");
2074 setStringEntry(&inp, "annealing-npoints", is->anneal_npoints, nullptr);
2075 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2076 setStringEntry(&inp, "annealing-time", is->anneal_time, nullptr);
2077 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2078 setStringEntry(&inp, "annealing-temp", is->anneal_temp, nullptr);
2081 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2082 opts->bGenVel = (get_eeenum(&inp, "gen-vel", yesno_names, wi) != 0);
2083 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2084 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2087 printStringNewline(&inp, "OPTIONS FOR BONDS");
2088 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2089 printStringNoNewline(&inp, "Type of constraint algorithm");
2090 ir->eConstrAlg = get_eeenum(&inp, "constraint-algorithm", econstr_names, wi);
2091 printStringNoNewline(&inp, "Do not constrain the start configuration");
2092 ir->bContinuation = (get_eeenum(&inp, "continuation", yesno_names, wi) != 0);
2093 printStringNoNewline(&inp,
2094 "Use successive overrelaxation to reduce the number of shake iterations");
2095 ir->bShakeSOR = (get_eeenum(&inp, "Shake-SOR", yesno_names, wi) != 0);
2096 printStringNoNewline(&inp, "Relative tolerance of shake");
2097 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2098 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2099 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2100 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2101 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2102 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2103 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2104 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2105 printStringNoNewline(&inp, "rotates over more degrees than");
2106 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2107 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2108 opts->bMorse = (get_eeenum(&inp, "morse", yesno_names, wi) != 0);
2110 /* Energy group exclusions */
2111 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2112 printStringNoNewline(
2113 &inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2114 setStringEntry(&inp, "energygrp-excl", is->egpexcl, nullptr);
2117 printStringNewline(&inp, "WALLS");
2118 printStringNoNewline(
2119 &inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2120 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2121 ir->wall_type = get_eeenum(&inp, "wall-type", ewt_names, wi);
2122 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2123 setStringEntry(&inp, "wall-atomtype", is->wall_atomtype, nullptr);
2124 setStringEntry(&inp, "wall-density", is->wall_density, nullptr);
2125 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2128 printStringNewline(&inp, "COM PULLING");
2129 ir->bPull = (get_eeenum(&inp, "pull", yesno_names, wi) != 0);
2133 is->pull_grp = read_pullparams(&inp, ir->pull, wi);
2137 NOTE: needs COM pulling input */
2138 printStringNewline(&inp, "AWH biasing");
2139 ir->bDoAwh = (get_eeenum(&inp, "awh", yesno_names, wi) != 0);
2142 ir->awhParams = gmx::readAwhParams(&inp, wi);
2145 /* Enforced rotation */
2146 printStringNewline(&inp, "ENFORCED ROTATION");
2147 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2148 ir->bRot = (get_eeenum(&inp, "rotation", yesno_names, wi) != 0);
2152 is->rot_grp = read_rotparams(&inp, ir->rot, wi);
2155 /* Interactive MD */
2157 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2158 setStringEntry(&inp, "IMD-group", is->imd_grp, nullptr);
2159 if (is->imd_grp[0] != '\0')
2166 printStringNewline(&inp, "NMR refinement stuff");
2167 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2168 ir->eDisre = get_eeenum(&inp, "disre", edisre_names, wi);
2169 printStringNoNewline(
2170 &inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2171 ir->eDisreWeighting = get_eeenum(&inp, "disre-weighting", edisreweighting_names, wi);
2172 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2173 ir->bDisreMixed = (get_eeenum(&inp, "disre-mixed", yesno_names, wi) != 0);
2174 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2175 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2176 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2177 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2178 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2179 opts->bOrire = (get_eeenum(&inp, "orire", yesno_names, wi) != 0);
2180 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2181 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2182 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2183 setStringEntry(&inp, "orire-fitgrp", is->orirefitgrp, nullptr);
2184 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2185 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2187 /* free energy variables */
2188 printStringNewline(&inp, "Free energy variables");
2189 ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
2190 setStringEntry(&inp, "couple-moltype", is->couple_moltype, nullptr);
2191 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2192 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2193 opts->bCoupleIntra = (get_eeenum(&inp, "couple-intramol", yesno_names, wi) != 0);
2195 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2197 it was not entered */
2198 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2199 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2200 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2201 setStringEntry(&inp, "fep-lambdas", is->fep_lambda[efptFEP], nullptr);
2202 setStringEntry(&inp, "mass-lambdas", is->fep_lambda[efptMASS], nullptr);
2203 setStringEntry(&inp, "coul-lambdas", is->fep_lambda[efptCOUL], nullptr);
2204 setStringEntry(&inp, "vdw-lambdas", is->fep_lambda[efptVDW], nullptr);
2205 setStringEntry(&inp, "bonded-lambdas", is->fep_lambda[efptBONDED], nullptr);
2206 setStringEntry(&inp, "restraint-lambdas", is->fep_lambda[efptRESTRAINT], nullptr);
2207 setStringEntry(&inp, "temperature-lambdas", is->fep_lambda[efptTEMPERATURE], nullptr);
2208 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2209 setStringEntry(&inp, "init-lambda-weights", is->lambda_weights, nullptr);
2210 fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
2211 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2212 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2213 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2214 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2215 fep->bScCoul = (get_eeenum(&inp, "sc-coul", yesno_names, wi) != 0);
2216 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2217 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2218 fep->separate_dhdl_file = get_eeenum(&inp, "separate-dhdl-file", separate_dhdl_file_names, wi);
2219 fep->dhdl_derivatives = get_eeenum(&inp, "dhdl-derivatives", dhdl_derivatives_names, wi);
2220 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2221 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2223 /* Non-equilibrium MD stuff */
2224 printStringNewline(&inp, "Non-equilibrium MD stuff");
2225 setStringEntry(&inp, "acc-grps", is->accgrps, nullptr);
2226 setStringEntry(&inp, "accelerate", is->acc, nullptr);
2227 setStringEntry(&inp, "freezegrps", is->freeze, nullptr);
2228 setStringEntry(&inp, "freezedim", is->frdim, nullptr);
2229 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2230 setStringEntry(&inp, "deform", is->deform, nullptr);
2232 /* simulated tempering variables */
2233 printStringNewline(&inp, "simulated tempering variables");
2234 ir->bSimTemp = (get_eeenum(&inp, "simulated-tempering", yesno_names, wi) != 0);
2235 ir->simtempvals->eSimTempScale = get_eeenum(&inp, "simulated-tempering-scaling", esimtemp_names, wi);
2236 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2237 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2239 /* expanded ensemble variables */
2240 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2242 read_expandedparams(&inp, expand, wi);
2245 /* Electric fields */
2247 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2248 gmx::KeyValueTreeTransformer transform;
2249 transform.rules()->addRule().keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2250 mdModules->initMdpTransform(transform.rules());
2251 for (const auto& path : transform.mappedPaths())
2253 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2254 mark_einp_set(inp, path[0].c_str());
2256 MdpErrorHandler errorHandler(wi);
2257 auto result = transform.transform(convertedValues, &errorHandler);
2258 ir->params = new gmx::KeyValueTreeObject(result.object());
2259 mdModules->adjustInputrecBasedOnModules(ir);
2260 errorHandler.setBackMapping(result.backMapping());
2261 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2264 /* Ion/water position swapping ("computational electrophysiology") */
2265 printStringNewline(&inp,
2266 "Ion/water position swapping for computational electrophysiology setups");
2267 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2268 ir->eSwapCoords = get_eeenum(&inp, "swapcoords", eSwapTypes_names, wi);
2269 if (ir->eSwapCoords != eswapNO)
2276 printStringNoNewline(&inp, "Swap attempt frequency");
2277 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2278 printStringNoNewline(&inp, "Number of ion types to be controlled");
2279 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2282 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2284 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2285 snew(ir->swap->grp, ir->swap->ngrp);
2286 for (i = 0; i < ir->swap->ngrp; i++)
2288 snew(ir->swap->grp[i].molname, STRLEN);
2290 printStringNoNewline(&inp,
2291 "Two index groups that contain the compartment-partitioning atoms");
2292 setStringEntry(&inp, "split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2293 setStringEntry(&inp, "split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2294 printStringNoNewline(&inp,
2295 "Use center of mass of split groups (yes/no), otherwise center of "
2296 "geometry is used");
2297 ir->swap->massw_split[0] = (get_eeenum(&inp, "massw-split0", yesno_names, wi) != 0);
2298 ir->swap->massw_split[1] = (get_eeenum(&inp, "massw-split1", yesno_names, wi) != 0);
2300 printStringNoNewline(&inp, "Name of solvent molecules");
2301 setStringEntry(&inp, "solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2303 printStringNoNewline(&inp,
2304 "Split cylinder: radius, upper and lower extension (nm) (this will "
2305 "define the channels)");
2306 printStringNoNewline(&inp,
2307 "Note that the split cylinder settings do not have an influence on "
2308 "the swapping protocol,");
2309 printStringNoNewline(
2311 "however, if correctly defined, the permeation events are recorded per channel");
2312 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2313 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2314 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2315 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2316 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2317 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2319 printStringNoNewline(
2321 "Average the number of ions per compartment over these many swap attempt steps");
2322 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2324 printStringNoNewline(
2325 &inp, "Names of the ion types that can be exchanged with solvent molecules,");
2326 printStringNoNewline(
2327 &inp, "and the requested number of ions of this type in compartments A and B");
2328 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2329 for (i = 0; i < nIonTypes; i++)
2331 int ig = eSwapFixedGrpNR + i;
2333 sprintf(buf, "iontype%d-name", i);
2334 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2335 sprintf(buf, "iontype%d-in-A", i);
2336 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2337 sprintf(buf, "iontype%d-in-B", i);
2338 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2341 printStringNoNewline(
2343 "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2344 printStringNoNewline(
2346 "at maximum distance (= bulk concentration) to the split group layers. However,");
2347 printStringNoNewline(&inp,
2348 "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk "
2349 "layer from the middle at 0.0");
2350 printStringNoNewline(&inp,
2351 "towards one of the compartment-partitioning layers (at +/- 1.0).");
2352 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2353 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2354 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2355 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0))
2357 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2360 printStringNoNewline(
2361 &inp, "Start to swap ions if threshold difference to requested count is reached");
2362 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2365 /* AdResS is no longer supported, but we need grompp to be able to
2366 refuse to process old .mdp files that used it. */
2367 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2369 /* User defined thingies */
2370 printStringNewline(&inp, "User defined thingies");
2371 setStringEntry(&inp, "user1-grps", is->user1, nullptr);
2372 setStringEntry(&inp, "user2-grps", is->user2, nullptr);
2373 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2374 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2375 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2376 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2377 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2378 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2379 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2380 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2384 gmx::TextOutputFile stream(mdparout);
2385 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2387 // Transform module data into a flat key-value tree for output.
2388 gmx::KeyValueTreeBuilder builder;
2389 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2390 mdModules->buildMdpOutput(&builderObject);
2392 gmx::TextWriter writer(&stream);
2393 writeKeyValueTreeAsMdp(&writer, builder.build());
2398 /* Process options if necessary */
2399 for (m = 0; m < 2; m++)
2401 for (i = 0; i < 2 * DIM; i++)
2410 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2414 "Pressure coupling incorrect number of values (I need exactly 1)");
2416 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2418 case epctSEMIISOTROPIC:
2419 case epctSURFACETENSION:
2420 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2424 "Pressure coupling incorrect number of values (I need exactly 2)");
2426 dumdub[m][YY] = dumdub[m][XX];
2428 case epctANISOTROPIC:
2429 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf", &(dumdub[m][XX]), &(dumdub[m][YY]),
2430 &(dumdub[m][ZZ]), &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5]))
2435 "Pressure coupling incorrect number of values (I need exactly 6)");
2439 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2440 epcoupltype_names[ir->epct]);
2444 clear_mat(ir->ref_p);
2445 clear_mat(ir->compress);
2446 for (i = 0; i < DIM; i++)
2448 ir->ref_p[i][i] = dumdub[1][i];
2449 ir->compress[i][i] = dumdub[0][i];
2451 if (ir->epct == epctANISOTROPIC)
2453 ir->ref_p[XX][YY] = dumdub[1][3];
2454 ir->ref_p[XX][ZZ] = dumdub[1][4];
2455 ir->ref_p[YY][ZZ] = dumdub[1][5];
2456 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2459 "All off-diagonal reference pressures are non-zero. Are you sure you want to "
2460 "apply a threefold shear stress?\n");
2462 ir->compress[XX][YY] = dumdub[0][3];
2463 ir->compress[XX][ZZ] = dumdub[0][4];
2464 ir->compress[YY][ZZ] = dumdub[0][5];
2465 for (i = 0; i < DIM; i++)
2467 for (m = 0; m < i; m++)
2469 ir->ref_p[i][m] = ir->ref_p[m][i];
2470 ir->compress[i][m] = ir->compress[m][i];
2475 if (ir->comm_mode == ecmNO)
2480 opts->couple_moltype = nullptr;
2481 if (strlen(is->couple_moltype) > 0)
2483 if (ir->efep != efepNO)
2485 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2486 if (opts->couple_lam0 == opts->couple_lam1)
2488 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2490 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
2494 "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
2501 "Free energy is turned off, so we will not decouple the molecule listed "
2505 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2506 if (ir->efep != efepNO)
2508 if (fep->delta_lambda > 0)
2510 ir->efep = efepSLOWGROWTH;
2514 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2516 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2518 "Old option for dhdl-print-energy given: "
2519 "changing \"yes\" to \"total\"\n");
2522 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2524 /* always print out the energy to dhdl if we are doing
2525 expanded ensemble, since we need the total energy for
2526 analysis if the temperature is changing. In some
2527 conditions one may only want the potential energy, so
2528 we will allow that if the appropriate mdp setting has
2529 been enabled. Otherwise, total it is:
2531 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2534 if ((ir->efep != efepNO) || ir->bSimTemp)
2536 ir->bExpanded = FALSE;
2537 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2539 ir->bExpanded = TRUE;
2541 do_fep_params(ir, is->fep_lambda, is->lambda_weights, wi);
2542 if (ir->bSimTemp) /* done after fep params */
2544 do_simtemp_params(ir);
2547 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2548 * setup and not on the old way of specifying the free-energy setup,
2549 * we should check for using soft-core when not needed, since that
2550 * can complicate the sampling significantly.
2551 * Note that we only check for the automated coupling setup.
2552 * If the (advanced) user does FEP through manual topology changes,
2553 * this check will not be triggered.
2555 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 && ir->fepvals->sc_alpha != 0
2556 && (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
2559 "You are using soft-core interactions while the Van der Waals interactions are "
2560 "not decoupled (note that the sc-coul option is only active when using lambda "
2561 "states). Although this will not lead to errors, you will need much more "
2562 "sampling than without soft-core interactions. Consider using sc-alpha=0.");
2567 ir->fepvals->n_lambda = 0;
2570 /* WALL PARAMETERS */
2572 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts, wi);
2574 /* ORIENTATION RESTRAINT PARAMETERS */
2576 if (opts->bOrire && gmx::splitString(is->orirefitgrp).size() != 1)
2578 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2581 /* DEFORMATION PARAMETERS */
2583 clear_mat(ir->deform);
2584 for (i = 0; i < 6; i++)
2589 double gmx_unused canary;
2590 int ndeform = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf %lf", &(dumdub[0][0]), &(dumdub[0][1]),
2591 &(dumdub[0][2]), &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]), &canary);
2593 if (strlen(is->deform) > 0 && ndeform != 6)
2596 wi, gmx::formatString(
2597 "Cannot parse exactly 6 box deformation velocities from string '%s'", is->deform)
2600 for (i = 0; i < 3; i++)
2602 ir->deform[i][i] = dumdub[0][i];
2604 ir->deform[YY][XX] = dumdub[0][3];
2605 ir->deform[ZZ][XX] = dumdub[0][4];
2606 ir->deform[ZZ][YY] = dumdub[0][5];
2607 if (ir->epc != epcNO)
2609 for (i = 0; i < 3; i++)
2611 for (j = 0; j <= i; j++)
2613 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2615 warning_error(wi, "A box element has deform set and compressibility > 0");
2619 for (i = 0; i < 3; i++)
2621 for (j = 0; j < i; j++)
2623 if (ir->deform[i][j] != 0)
2625 for (m = j; m < DIM; m++)
2627 if (ir->compress[m][j] != 0)
2630 "An off-diagonal box element has deform set while "
2631 "compressibility > 0 for the same component of another box "
2632 "vector, this might lead to spurious periodicity effects.");
2633 warning(wi, warn_buf);
2641 /* Ion/water position swapping checks */
2642 if (ir->eSwapCoords != eswapNO)
2644 if (ir->swap->nstswap < 1)
2646 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2648 if (ir->swap->nAverage < 1)
2650 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2652 if (ir->swap->threshold < 1.0)
2654 warning_error(wi, "Ion count threshold must be at least 1.\n");
2660 gmx::checkAwhParams(ir->awhParams, ir, wi);
2667 static int search_QMstring(const char* s, int ng, const char* gn[])
2669 /* same as normal search_string, but this one searches QM strings */
2672 for (i = 0; (i < ng); i++)
2674 if (gmx_strcasecmp(s, gn[i]) == 0)
2680 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2681 } /* search_QMstring */
2683 /* We would like gn to be const as well, but C doesn't allow this */
2684 /* TODO this is utility functionality (search for the index of a
2685 string in a collection), so should be refactored and located more
2687 int search_string(const char* s, int ng, char* gn[])
2691 for (i = 0; (i < ng); i++)
2693 if (gmx_strcasecmp(s, gn[i]) == 0)
2700 "Group %s referenced in the .mdp file was not found in the index file.\n"
2701 "Group names must match either [moleculetype] names or custom index group\n"
2702 "names, in which case you must supply an index file to the '-n' option\n"
2707 static void do_numbering(int natoms,
2708 SimulationGroups* groups,
2709 gmx::ArrayRef<std::string> groupsFromMdpFile,
2712 SimulationAtomGroupType gtype,
2718 unsigned short* cbuf;
2719 AtomGroupIndices* grps = &(groups->groups[gtype]);
2720 int j, gid, aj, ognr, ntot = 0;
2722 char warn_buf[STRLEN];
2724 title = shortName(gtype);
2727 /* Mark all id's as not set */
2728 for (int i = 0; (i < natoms); i++)
2733 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2735 /* Lookup the group name in the block structure */
2736 gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2737 if ((grptp != egrptpONE) || (i == 0))
2739 grps->emplace_back(gid);
2742 /* Now go over the atoms in the group */
2743 for (j = block->index[gid]; (j < block->index[gid + 1]); j++)
2748 /* Range checking */
2749 if ((aj < 0) || (aj >= natoms))
2751 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2753 /* Lookup up the old group number */
2757 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title,
2762 /* Store the group number in buffer */
2763 if (grptp == egrptpONE)
2776 /* Now check whether we have done all atoms */
2779 if (grptp == egrptpALL)
2781 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2783 else if (grptp == egrptpPART)
2785 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2786 warning_note(wi, warn_buf);
2788 /* Assign all atoms currently unassigned to a rest group */
2789 for (j = 0; (j < natoms); j++)
2791 if (cbuf[j] == NOGID)
2793 cbuf[j] = grps->size();
2796 if (grptp != egrptpPART)
2800 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title,
2803 /* Add group name "rest" */
2804 grps->emplace_back(restnm);
2806 /* Assign the rest name to all atoms not currently assigned to a group */
2807 for (j = 0; (j < natoms); j++)
2809 if (cbuf[j] == NOGID)
2811 // group size was not updated before this here, so need to use -1.
2812 cbuf[j] = grps->size() - 1;
2818 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2820 /* All atoms are part of one (or no) group, no index required */
2821 groups->groupNumbers[gtype].clear();
2825 for (int j = 0; (j < natoms); j++)
2827 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2834 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
2837 pull_params_t* pull;
2838 int natoms, imin, jmin;
2839 int * nrdf2, *na_vcm, na_tot;
2840 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2845 * First calc 3xnr-atoms for each group
2846 * then subtract half a degree of freedom for each constraint
2848 * Only atoms and nuclei contribute to the degrees of freedom...
2853 const SimulationGroups& groups = mtop->groups;
2854 natoms = mtop->natoms;
2856 /* Allocate one more for a possible rest group */
2857 /* We need to sum degrees of freedom into doubles,
2858 * since floats give too low nrdf's above 3 million atoms.
2860 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
2861 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2862 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2863 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2864 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2866 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
2870 for (gmx::index i = 0;
2871 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; i++)
2874 clear_ivec(dof_vcm[i]);
2876 nrdf_vcm_sub[i] = 0;
2878 snew(nrdf2, natoms);
2879 for (const AtomProxy atomP : AtomRange(*mtop))
2881 const t_atom& local = atomP.atom();
2882 int i = atomP.globalAtomNumber();
2884 if (local.ptype == eptAtom || local.ptype == eptNucleus)
2886 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
2887 for (int d = 0; d < DIM; d++)
2889 if (opts->nFreeze[g][d] == 0)
2891 /* Add one DOF for particle i (counted as 2*1) */
2893 /* VCM group i has dim d as a DOF */
2894 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
2898 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
2900 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
2906 for (const gmx_molblock_t& molb : mtop->molblock)
2908 const gmx_moltype_t& molt = mtop->moltype[molb.type];
2909 const t_atom* atom = molt.atoms.atom;
2910 for (int mol = 0; mol < molb.nmol; mol++)
2912 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2914 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
2915 for (int i = 0; i < molt.ilist[ftype].size();)
2917 /* Subtract degrees of freedom for the constraints,
2918 * if the particles still have degrees of freedom left.
2919 * If one of the particles is a vsite or a shell, then all
2920 * constraint motion will go there, but since they do not
2921 * contribute to the constraints the degrees of freedom do not
2924 int ai = as + ia[i + 1];
2925 int aj = as + ia[i + 2];
2926 if (((atom[ia[i + 1]].ptype == eptNucleus) || (atom[ia[i + 1]].ptype == eptAtom))
2927 && ((atom[ia[i + 2]].ptype == eptNucleus) || (atom[ia[i + 2]].ptype == eptAtom)))
2945 imin = std::min(imin, nrdf2[ai]);
2946 jmin = std::min(jmin, nrdf2[aj]);
2949 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2951 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
2953 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2955 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
2958 i += interaction_function[ftype].nratoms + 1;
2961 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
2962 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
2964 /* Subtract 1 dof from every atom in the SETTLE */
2965 for (int j = 0; j < 3; j++)
2967 int ai = as + ia[i + 1 + j];
2968 imin = std::min(2, nrdf2[ai]);
2970 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2972 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2977 as += molt.atoms.nr;
2983 /* Correct nrdf for the COM constraints.
2984 * We correct using the TC and VCM group of the first atom
2985 * in the reference and pull group. If atoms in one pull group
2986 * belong to different TC or VCM groups it is anyhow difficult
2987 * to determine the optimal nrdf assignment.
2991 for (int i = 0; i < pull->ncoord; i++)
2993 if (pull->coord[i].eType != epullCONSTRAINT)
3000 for (int j = 0; j < 2; j++)
3002 const t_pull_group* pgrp;
3004 pgrp = &pull->group[pull->coord[i].group[j]];
3008 /* Subtract 1/2 dof from each group */
3009 int ai = pgrp->ind[0];
3010 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3012 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3014 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
3017 "Center of mass pulling constraints caused the number of degrees "
3018 "of freedom for temperature coupling group %s to be negative",
3019 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
3020 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
3025 /* We need to subtract the whole DOF from group j=1 */
3032 if (ir->nstcomm != 0)
3034 GMX_RELEASE_ASSERT(!groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty(),
3035 "Expect at least one group when removing COM motion");
3037 /* We remove COM motion up to dim ndof_com() */
3038 const int ndim_rm_vcm = ndof_com(ir);
3040 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3041 * the number of degrees of freedom in each vcm group when COM
3042 * translation is removed and 6 when rotation is removed as well.
3043 * Note that we do not and should not include the rest group here.
3045 for (gmx::index j = 0;
3046 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]); j++)
3048 switch (ir->comm_mode)
3051 case ecmLINEAR_ACCELERATION_CORRECTION:
3052 nrdf_vcm_sub[j] = 0;
3053 for (int d = 0; d < ndim_rm_vcm; d++)
3061 case ecmANGULAR: nrdf_vcm_sub[j] = 6; break;
3062 default: gmx_incons("Checking comm_mode");
3066 for (gmx::index i = 0;
3067 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
3069 /* Count the number of atoms of TC group i for every VCM group */
3070 for (gmx::index j = 0;
3071 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3076 for (int ai = 0; ai < natoms; ai++)
3078 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3080 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3084 /* Correct for VCM removal according to the fraction of each VCM
3085 * group present in this TC group.
3087 nrdf_uc = nrdf_tc[i];
3089 for (gmx::index j = 0;
3090 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3092 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3094 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3095 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3100 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3102 opts->nrdf[i] = nrdf_tc[i];
3103 if (opts->nrdf[i] < 0)
3107 fprintf(stderr, "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3108 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]], opts->nrdf[i]);
3116 sfree(nrdf_vcm_sub);
3119 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3121 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3122 * But since this is much larger than STRLEN, such a line can not be parsed.
3123 * The real maximum is the number of names that fit in a string: STRLEN/2.
3125 #define EGP_MAX (STRLEN / 2)
3129 auto names = gmx::splitString(val);
3130 if (names.size() % 2 != 0)
3132 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3134 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3136 for (size_t i = 0; i < names.size() / 2; i++)
3138 // TODO this needs to be replaced by a solution using std::find_if
3142 names[2 * i].c_str(),
3143 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3149 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3154 names[2 * i + 1].c_str(),
3155 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3161 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3163 if ((j < nr) && (k < nr))
3165 ir->opts.egp_flags[nr * j + k] |= flag;
3166 ir->opts.egp_flags[nr * k + j] |= flag;
3175 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3177 int ig = -1, i = 0, gind;
3181 /* Just a quick check here, more thorough checks are in mdrun */
3182 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3184 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3187 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3188 for (ig = 0; ig < swap->ngrp; ig++)
3190 swapg = &swap->grp[ig];
3191 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3192 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3196 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3197 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap", swap->grp[ig].molname, swapg->nat);
3198 snew(swapg->ind, swapg->nat);
3199 for (i = 0; i < swapg->nat; i++)
3201 swapg->ind[i] = grps->a[grps->index[gind] + i];
3206 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3212 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3217 ig = search_string(IMDgname, grps->nr, gnames);
3218 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3220 if (IMDgroup->nat > 0)
3223 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3225 IMDgname, IMDgroup->nat);
3226 snew(IMDgroup->ind, IMDgroup->nat);
3227 for (i = 0; i < IMDgroup->nat; i++)
3229 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3234 /* Checks whether atoms are both part of a COM removal group and frozen.
3235 * If a fully frozen atom is part of a COM removal group, it is removed
3236 * from the COM removal group. A note is issued if such atoms are present.
3237 * A warning is issued for atom with one or two dimensions frozen that
3238 * are part of a COM removal group (mdrun would need to compute COM mass
3239 * per dimension to handle this correctly).
3240 * Also issues a warning when non-frozen atoms are not part of a COM
3241 * removal group while COM removal is active.
3243 static void checkAndUpdateVcmFreezeGroupConsistency(SimulationGroups* groups,
3245 const t_grpopts& opts,
3248 const int vcmRestGroup =
3249 std::max(int(groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()), 1);
3251 int numFullyFrozenVcmAtoms = 0;
3252 int numPartiallyFrozenVcmAtoms = 0;
3253 int numNonVcmAtoms = 0;
3254 for (int a = 0; a < numAtoms; a++)
3256 const int freezeGroup = getGroupType(*groups, SimulationAtomGroupType::Freeze, a);
3257 int numFrozenDims = 0;
3258 for (int d = 0; d < DIM; d++)
3260 numFrozenDims += opts.nFreeze[freezeGroup][d];
3263 const int vcmGroup = getGroupType(*groups, SimulationAtomGroupType::MassCenterVelocityRemoval, a);
3264 if (vcmGroup < vcmRestGroup)
3266 if (numFrozenDims == DIM)
3268 /* Do not remove COM motion for this fully frozen atom */
3269 if (groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
3271 groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(numAtoms, 0);
3273 groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
3274 numFullyFrozenVcmAtoms++;
3276 else if (numFrozenDims > 0)
3278 numPartiallyFrozenVcmAtoms++;
3281 else if (numFrozenDims < DIM)
3287 if (numFullyFrozenVcmAtoms > 0)
3289 std::string warningText = gmx::formatString(
3290 "There are %d atoms that are fully frozen and part of COMM removal group(s), "
3291 "removing these atoms from the COMM removal group(s)",
3292 numFullyFrozenVcmAtoms);
3293 warning_note(wi, warningText.c_str());
3295 if (numPartiallyFrozenVcmAtoms > 0 && numPartiallyFrozenVcmAtoms < numAtoms)
3297 std::string warningText = gmx::formatString(
3298 "There are %d atoms that are frozen along less then %d dimensions and part of COMM "
3299 "removal group(s), due to limitations in the code these still contribute to the "
3300 "mass of the COM along frozen dimensions and therefore the COMM correction will be "
3302 numPartiallyFrozenVcmAtoms, DIM);
3303 warning(wi, warningText.c_str());
3305 if (numNonVcmAtoms > 0)
3307 std::string warningText = gmx::formatString(
3308 "%d atoms are not part of any center of mass motion removal group.\n"
3309 "This may lead to artifacts.\n"
3310 "In most cases one should use one group for the whole system.",
3312 warning(wi, warningText.c_str());
3316 void do_index(const char* mdparin,
3320 const gmx::MdModulesNotifier& notifier,
3324 t_blocka* defaultIndexGroups;
3332 int i, j, k, restnm;
3333 bool bExcl, bTable, bAnneal;
3334 char warn_buf[STRLEN];
3338 fprintf(stderr, "processing index file...\n");
3342 snew(defaultIndexGroups, 1);
3343 snew(defaultIndexGroups->index, 1);
3345 atoms_all = gmx_mtop_global_atoms(mtop);
3346 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3347 done_atom(&atoms_all);
3351 defaultIndexGroups = init_index(ndx, &gnames);
3354 SimulationGroups* groups = &mtop->groups;
3355 natoms = mtop->natoms;
3356 symtab = &mtop->symtab;
3358 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3360 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3362 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3363 restnm = groups->groupNames.size() - 1;
3364 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3365 srenew(gnames, defaultIndexGroups->nr + 1);
3366 gnames[restnm] = *(groups->groupNames.back());
3368 set_warning_line(wi, mdparin, -1);
3370 auto temperatureCouplingTauValues = gmx::splitString(is->tau_t);
3371 auto temperatureCouplingReferenceValues = gmx::splitString(is->ref_t);
3372 auto temperatureCouplingGroupNames = gmx::splitString(is->tcgrps);
3373 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3374 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3377 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3379 temperatureCouplingGroupNames.size(), temperatureCouplingReferenceValues.size(),
3380 temperatureCouplingTauValues.size());
3383 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3384 do_numbering(natoms, groups, temperatureCouplingGroupNames, defaultIndexGroups, gnames,
3385 SimulationAtomGroupType::TemperatureCoupling, restnm,
3386 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3387 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3389 snew(ir->opts.nrdf, nr);
3390 snew(ir->opts.tau_t, nr);
3391 snew(ir->opts.ref_t, nr);
3392 if (ir->eI == eiBD && ir->bd_fric == 0)
3394 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3397 if (useReferenceTemperature)
3399 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3401 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3405 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3406 for (i = 0; (i < nr); i++)
3408 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3410 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3411 warning_error(wi, warn_buf);
3414 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3418 "tau-t = -1 is the value to signal that a group should not have "
3419 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3422 if (ir->opts.tau_t[i] >= 0)
3424 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3427 if (ir->etc != etcNO && ir->nsttcouple == -1)
3429 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3434 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3437 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3438 "md-vv; use either vrescale temperature with berendsen pressure or "
3439 "Nose-Hoover temperature with MTTK pressure");
3441 if (ir->epc == epcMTTK)
3443 if (ir->etc != etcNOSEHOOVER)
3446 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3451 if (ir->nstpcouple != ir->nsttcouple)
3453 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3454 ir->nstpcouple = ir->nsttcouple = mincouple;
3456 "for current Trotter decomposition methods with vv, nsttcouple and "
3457 "nstpcouple must be equal. Both have been reset to "
3458 "min(nsttcouple,nstpcouple) = %d",
3460 warning_note(wi, warn_buf);
3465 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3466 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3468 if (ETC_ANDERSEN(ir->etc))
3470 if (ir->nsttcouple != 1)
3474 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3475 "need for larger nsttcouple > 1, since no global parameters are computed. "
3476 "nsttcouple has been reset to 1");
3477 warning_note(wi, warn_buf);
3480 nstcmin = tcouple_min_integration_steps(ir->etc);
3483 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3486 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3487 "least %d times larger than nsttcouple*dt (%g)",
3488 ETCOUPLTYPE(ir->etc), tau_min, nstcmin, ir->nsttcouple * ir->delta_t);
3489 warning(wi, warn_buf);
3492 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3493 for (i = 0; (i < nr); i++)
3495 if (ir->opts.ref_t[i] < 0)
3497 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3500 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3501 if we are in this conditional) if mc_temp is negative */
3502 if (ir->expandedvals->mc_temp < 0)
3504 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3508 /* Simulated annealing for each group. There are nr groups */
3509 auto simulatedAnnealingGroupNames = gmx::splitString(is->anneal);
3510 if (simulatedAnnealingGroupNames.size() == 1
3511 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3513 simulatedAnnealingGroupNames.resize(0);
3515 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3517 gmx_fatal(FARGS, "Wrong number of annealing values: %zu (for %d groups)\n",
3518 simulatedAnnealingGroupNames.size(), nr);
3522 snew(ir->opts.annealing, nr);
3523 snew(ir->opts.anneal_npoints, nr);
3524 snew(ir->opts.anneal_time, nr);
3525 snew(ir->opts.anneal_temp, nr);
3526 for (i = 0; i < nr; i++)
3528 ir->opts.annealing[i] = eannNO;
3529 ir->opts.anneal_npoints[i] = 0;
3530 ir->opts.anneal_time[i] = nullptr;
3531 ir->opts.anneal_temp[i] = nullptr;
3533 if (!simulatedAnnealingGroupNames.empty())
3536 for (i = 0; i < nr; i++)
3538 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3540 ir->opts.annealing[i] = eannNO;
3542 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3544 ir->opts.annealing[i] = eannSINGLE;
3547 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3549 ir->opts.annealing[i] = eannPERIODIC;
3555 /* Read the other fields too */
3556 auto simulatedAnnealingPoints = gmx::splitString(is->anneal_npoints);
3557 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3559 gmx_fatal(FARGS, "Found %zu annealing-npoints values for %zu groups\n",
3560 simulatedAnnealingPoints.size(), simulatedAnnealingGroupNames.size());
3562 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3563 size_t numSimulatedAnnealingFields = 0;
3564 for (i = 0; i < nr; i++)
3566 if (ir->opts.anneal_npoints[i] == 1)
3570 "Please specify at least a start and an end point for annealing\n");
3572 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3573 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3574 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3577 auto simulatedAnnealingTimes = gmx::splitString(is->anneal_time);
3579 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3581 gmx_fatal(FARGS, "Found %zu annealing-time values, wanted %zu\n",
3582 simulatedAnnealingTimes.size(), numSimulatedAnnealingFields);
3584 auto simulatedAnnealingTemperatures = gmx::splitString(is->anneal_temp);
3585 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3587 gmx_fatal(FARGS, "Found %zu annealing-temp values, wanted %zu\n",
3588 simulatedAnnealingTemperatures.size(), numSimulatedAnnealingFields);
3591 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3592 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3593 convertReals(wi, simulatedAnnealingTimes, "anneal-time",
3594 allSimulatedAnnealingTimes.data());
3595 convertReals(wi, simulatedAnnealingTemperatures, "anneal-temp",
3596 allSimulatedAnnealingTemperatures.data());
3597 for (i = 0, k = 0; i < nr; i++)
3599 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3601 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3602 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3605 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3607 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3613 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3616 "Annealing timepoints out of order: t=%f comes after "
3618 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j - 1]);
3621 if (ir->opts.anneal_temp[i][j] < 0)
3623 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n",
3624 ir->opts.anneal_temp[i][j]);
3629 /* Print out some summary information, to make sure we got it right */
3630 for (i = 0; i < nr; i++)
3632 if (ir->opts.annealing[i] != eannNO)
3634 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3635 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3636 *(groups->groupNames[j]), eann_names[ir->opts.annealing[i]],
3637 ir->opts.anneal_npoints[i]);
3638 fprintf(stderr, "Time (ps) Temperature (K)\n");
3639 /* All terms except the last one */
3640 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3642 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3643 ir->opts.anneal_temp[i][j]);
3646 /* Finally the last one */
3647 j = ir->opts.anneal_npoints[i] - 1;
3648 if (ir->opts.annealing[i] == eannSINGLE)
3650 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j],
3651 ir->opts.anneal_temp[i][j]);
3655 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3656 ir->opts.anneal_temp[i][j]);
3657 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3660 "There is a temperature jump when your annealing "
3672 make_pull_groups(ir->pull, is->pull_grp, defaultIndexGroups, gnames);
3674 make_pull_coords(ir->pull);
3679 make_rotation_groups(ir->rot, is->rot_grp, defaultIndexGroups, gnames);
3682 if (ir->eSwapCoords != eswapNO)
3684 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3687 /* Make indices for IMD session */
3690 make_IMD_group(ir->imd, is->imd_grp, defaultIndexGroups, gnames);
3693 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3694 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3695 notifier.preProcessingNotifications_.notify(defaultIndexGroupsAndNames);
3697 auto accelerations = gmx::splitString(is->acc);
3698 auto accelerationGroupNames = gmx::splitString(is->accgrps);
3699 if (accelerationGroupNames.size() * DIM != accelerations.size())
3701 gmx_fatal(FARGS, "Invalid Acceleration input: %zu groups and %zu acc. values",
3702 accelerationGroupNames.size(), accelerations.size());
3704 do_numbering(natoms, groups, accelerationGroupNames, defaultIndexGroups, gnames,
3705 SimulationAtomGroupType::Acceleration, restnm, egrptpALL_GENREST, bVerbose, wi);
3706 nr = groups->groups[SimulationAtomGroupType::Acceleration].size();
3707 snew(ir->opts.acc, nr);
3708 ir->opts.ngacc = nr;
3710 convertRvecs(wi, accelerations, "anneal-time", ir->opts.acc);
3712 auto freezeDims = gmx::splitString(is->frdim);
3713 auto freezeGroupNames = gmx::splitString(is->freeze);
3714 if (freezeDims.size() != DIM * freezeGroupNames.size())
3716 gmx_fatal(FARGS, "Invalid Freezing input: %zu groups and %zu freeze values",
3717 freezeGroupNames.size(), freezeDims.size());
3719 do_numbering(natoms, groups, freezeGroupNames, defaultIndexGroups, gnames,
3720 SimulationAtomGroupType::Freeze, restnm, egrptpALL_GENREST, bVerbose, wi);
3721 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3722 ir->opts.ngfrz = nr;
3723 snew(ir->opts.nFreeze, nr);
3724 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3726 for (j = 0; (j < DIM); j++, k++)
3728 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3729 if (!ir->opts.nFreeze[i][j])
3731 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3734 "Please use Y(ES) or N(O) for freezedim only "
3736 freezeDims[k].c_str());
3737 warning(wi, warn_buf);
3742 for (; (i < nr); i++)
3744 for (j = 0; (j < DIM); j++)
3746 ir->opts.nFreeze[i][j] = 0;
3750 auto energyGroupNames = gmx::splitString(is->energy);
3751 do_numbering(natoms, groups, energyGroupNames, defaultIndexGroups, gnames,
3752 SimulationAtomGroupType::EnergyOutput, restnm, egrptpALL_GENREST, bVerbose, wi);
3753 add_wall_energrps(groups, ir->nwall, symtab);
3754 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3755 auto vcmGroupNames = gmx::splitString(is->vcm);
3756 do_numbering(natoms, groups, vcmGroupNames, defaultIndexGroups, gnames,
3757 SimulationAtomGroupType::MassCenterVelocityRemoval, restnm,
3758 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3760 if (ir->comm_mode != ecmNO)
3762 checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
3765 /* Now we have filled the freeze struct, so we can calculate NRDF */
3766 calc_nrdf(mtop, ir, gnames);
3768 auto user1GroupNames = gmx::splitString(is->user1);
3769 do_numbering(natoms, groups, user1GroupNames, defaultIndexGroups, gnames,
3770 SimulationAtomGroupType::User1, restnm, egrptpALL_GENREST, bVerbose, wi);
3771 auto user2GroupNames = gmx::splitString(is->user2);
3772 do_numbering(natoms, groups, user2GroupNames, defaultIndexGroups, gnames,
3773 SimulationAtomGroupType::User2, restnm, egrptpALL_GENREST, bVerbose, wi);
3774 auto compressedXGroupNames = gmx::splitString(is->x_compressed_groups);
3775 do_numbering(natoms, groups, compressedXGroupNames, defaultIndexGroups, gnames,
3776 SimulationAtomGroupType::CompressedPositionOutput, restnm, egrptpONE, bVerbose, wi);
3777 auto orirefFitGroupNames = gmx::splitString(is->orirefitgrp);
3778 do_numbering(natoms, groups, orirefFitGroupNames, defaultIndexGroups, gnames,
3779 SimulationAtomGroupType::OrientationRestraintsFit, restnm, egrptpALL_GENREST,
3782 /* QMMM input processing */
3783 auto qmGroupNames = gmx::splitString(is->QMMM);
3784 auto qmMethods = gmx::splitString(is->QMmethod);
3785 auto qmBasisSets = gmx::splitString(is->QMbasis);
3786 if (ir->eI != eiMimic)
3788 if (qmMethods.size() != qmGroupNames.size() || qmBasisSets.size() != qmGroupNames.size())
3791 "Invalid QMMM input: %zu groups %zu basissets"
3792 " and %zu methods\n",
3793 qmGroupNames.size(), qmBasisSets.size(), qmMethods.size());
3795 /* group rest, if any, is always MM! */
3796 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3797 SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
3798 nr = qmGroupNames.size(); /*atoms->grps[egcQMMM].nr;*/
3799 ir->opts.ngQM = qmGroupNames.size();
3800 snew(ir->opts.QMmethod, nr);
3801 snew(ir->opts.QMbasis, nr);
3802 for (i = 0; i < nr; i++)
3804 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3805 * converted to the corresponding enum in names.c
3807 ir->opts.QMmethod[i] = search_QMstring(qmMethods[i].c_str(), eQMmethodNR, eQMmethod_names);
3808 ir->opts.QMbasis[i] = search_QMstring(qmBasisSets[i].c_str(), eQMbasisNR, eQMbasis_names);
3810 auto qmMultiplicities = gmx::splitString(is->QMmult);
3811 auto qmCharges = gmx::splitString(is->QMcharge);
3812 auto qmbSH = gmx::splitString(is->bSH);
3813 snew(ir->opts.QMmult, nr);
3814 snew(ir->opts.QMcharge, nr);
3815 snew(ir->opts.bSH, nr);
3816 convertInts(wi, qmMultiplicities, "QMmult", ir->opts.QMmult);
3817 convertInts(wi, qmCharges, "QMcharge", ir->opts.QMcharge);
3818 convertYesNos(wi, qmbSH, "bSH", ir->opts.bSH);
3820 auto CASelectrons = gmx::splitString(is->CASelectrons);
3821 auto CASorbitals = gmx::splitString(is->CASorbitals);
3822 snew(ir->opts.CASelectrons, nr);
3823 snew(ir->opts.CASorbitals, nr);
3824 convertInts(wi, CASelectrons, "CASelectrons", ir->opts.CASelectrons);
3825 convertInts(wi, CASorbitals, "CASOrbitals", ir->opts.CASorbitals);
3827 auto SAon = gmx::splitString(is->SAon);
3828 auto SAoff = gmx::splitString(is->SAoff);
3829 auto SAsteps = gmx::splitString(is->SAsteps);
3830 snew(ir->opts.SAon, nr);
3831 snew(ir->opts.SAoff, nr);
3832 snew(ir->opts.SAsteps, nr);
3833 convertInts(wi, SAon, "SAon", ir->opts.SAon);
3834 convertInts(wi, SAoff, "SAoff", ir->opts.SAoff);
3835 convertInts(wi, SAsteps, "SAsteps", ir->opts.SAsteps);
3840 if (qmGroupNames.size() > 1)
3842 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
3844 /* group rest, if any, is always MM! */
3845 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3846 SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
3848 ir->opts.ngQM = qmGroupNames.size();
3851 /* end of QMMM input */
3855 for (auto group : gmx::keysOf(groups->groups))
3857 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
3858 for (const auto& entry : groups->groups[group])
3860 fprintf(stderr, " %s", *(groups->groupNames[entry]));
3862 fprintf(stderr, "\n");
3866 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3867 snew(ir->opts.egp_flags, nr * nr);
3869 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3870 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3872 warning_error(wi, "Energy group exclusions are currently not supported");
3874 if (bExcl && EEL_FULL(ir->coulombtype))
3876 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3879 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3880 if (bTable && !(ir->vdwtype == evdwUSER) && !(ir->coulombtype == eelUSER)
3881 && !(ir->coulombtype == eelPMEUSER) && !(ir->coulombtype == eelPMEUSERSWITCH))
3884 "Can only have energy group pair tables in combination with user tables for VdW "
3888 /* final check before going out of scope if simulated tempering variables
3889 * need to be set to default values.
3891 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
3893 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
3894 warning(wi, gmx::formatString(
3895 "the value for nstexpanded was not specified for "
3896 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
3897 "by default, but it is recommended to set it to an explicit value!",
3898 ir->expandedvals->nstexpanded));
3900 for (i = 0; (i < defaultIndexGroups->nr); i++)
3905 done_blocka(defaultIndexGroups);
3906 sfree(defaultIndexGroups);
3910 static void check_disre(const gmx_mtop_t* mtop)
3912 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3914 const gmx_ffparams_t& ffparams = mtop->ffparams;
3917 for (int i = 0; i < ffparams.numTypes(); i++)
3919 int ftype = ffparams.functype[i];
3920 if (ftype == F_DISRES)
3922 int label = ffparams.iparams[i].disres.label;
3923 if (label == old_label)
3925 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3934 "Found %d double distance restraint indices,\n"
3935 "probably the parameters for multiple pairs in one restraint "
3936 "are not identical\n",
3942 static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t* sys, const bool posres_only, ivec AbsRef)
3945 gmx_mtop_ilistloop_t iloop;
3947 const t_iparams* pr;
3954 for (d = 0; d < DIM; d++)
3956 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3958 /* Check for freeze groups */
3959 for (g = 0; g < ir->opts.ngfrz; g++)
3961 for (d = 0; d < DIM; d++)
3963 if (ir->opts.nFreeze[g][d] != 0)
3971 /* Check for position restraints */
3972 iloop = gmx_mtop_ilistloop_init(sys);
3973 while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
3975 if (nmol > 0 && (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3977 for (i = 0; i < (*ilist)[F_POSRES].size(); i += 2)
3979 pr = &sys->ffparams.iparams[(*ilist)[F_POSRES].iatoms[i]];
3980 for (d = 0; d < DIM; d++)
3982 if (pr->posres.fcA[d] != 0)
3988 for (i = 0; i < (*ilist)[F_FBPOSRES].size(); i += 2)
3990 /* Check for flat-bottom posres */
3991 pr = &sys->ffparams.iparams[(*ilist)[F_FBPOSRES].iatoms[i]];
3992 if (pr->fbposres.k != 0)
3994 switch (pr->fbposres.geom)
3996 case efbposresSPHERE: AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1; break;
3997 case efbposresCYLINDERX: AbsRef[YY] = AbsRef[ZZ] = 1; break;
3998 case efbposresCYLINDERY: AbsRef[XX] = AbsRef[ZZ] = 1; break;
3999 case efbposresCYLINDER:
4000 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
4001 case efbposresCYLINDERZ: AbsRef[XX] = AbsRef[YY] = 1; break;
4002 case efbposresX: /* d=XX */
4003 case efbposresY: /* d=YY */
4004 case efbposresZ: /* d=ZZ */
4005 d = pr->fbposres.geom - efbposresX;
4010 " Invalid geometry for flat-bottom position restraint.\n"
4011 "Expected nr between 1 and %d. Found %d\n",
4012 efbposresNR - 1, pr->fbposres.geom);
4019 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
4022 static void check_combination_rule_differences(const gmx_mtop_t* mtop,
4024 bool* bC6ParametersWorkWithGeometricRules,
4025 bool* bC6ParametersWorkWithLBRules,
4026 bool* bLBRulesPossible)
4028 int ntypes, tpi, tpj;
4031 double c6i, c6j, c12i, c12j;
4032 double c6, c6_geometric, c6_LB;
4033 double sigmai, sigmaj, epsi, epsj;
4034 bool bCanDoLBRules, bCanDoGeometricRules;
4037 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
4038 * force-field floating point parameters.
4041 ptr = getenv("GMX_LJCOMB_TOL");
4045 double gmx_unused canary;
4047 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
4050 "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
4055 *bC6ParametersWorkWithLBRules = TRUE;
4056 *bC6ParametersWorkWithGeometricRules = TRUE;
4057 bCanDoLBRules = TRUE;
4058 ntypes = mtop->ffparams.atnr;
4059 snew(typecount, ntypes);
4060 gmx_mtop_count_atomtypes(mtop, state, typecount);
4061 *bLBRulesPossible = TRUE;
4062 for (tpi = 0; tpi < ntypes; ++tpi)
4064 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
4065 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
4066 for (tpj = tpi; tpj < ntypes; ++tpj)
4068 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
4069 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
4070 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
4071 c6_geometric = std::sqrt(c6i * c6j);
4072 if (!gmx_numzero(c6_geometric))
4074 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4076 sigmai = gmx::sixthroot(c12i / c6i);
4077 sigmaj = gmx::sixthroot(c12j / c6j);
4078 epsi = c6i * c6i / (4.0 * c12i);
4079 epsj = c6j * c6j / (4.0 * c12j);
4080 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4084 *bLBRulesPossible = FALSE;
4085 c6_LB = c6_geometric;
4087 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4092 *bC6ParametersWorkWithLBRules = FALSE;
4095 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4097 if (!bCanDoGeometricRules)
4099 *bC6ParametersWorkWithGeometricRules = FALSE;
4106 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t* mtop, warninp_t wi)
4108 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4110 check_combination_rule_differences(mtop, 0, &bC6ParametersWorkWithGeometricRules,
4111 &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4112 if (ir->ljpme_combination_rule == eljpmeLB)
4114 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4117 "You are using arithmetic-geometric combination rules "
4118 "in LJ-PME, but your non-bonded C6 parameters do not "
4119 "follow these rules.");
4124 if (!bC6ParametersWorkWithGeometricRules)
4126 if (ir->eDispCorr != edispcNO)
4129 "You are using geometric combination rules in "
4130 "LJ-PME, but your non-bonded C6 parameters do "
4131 "not follow these rules. "
4132 "This will introduce very small errors in the forces and energies in "
4133 "your simulations. Dispersion correction will correct total energy "
4134 "and/or pressure for isotropic systems, but not forces or surface "
4140 "You are using geometric combination rules in "
4141 "LJ-PME, but your non-bonded C6 parameters do "
4142 "not follow these rules. "
4143 "This will introduce very small errors in the forces and energies in "
4144 "your simulations. If your system is homogeneous, consider using "
4145 "dispersion correction "
4146 "for the total energy and pressure.");
4152 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4154 char err_buf[STRLEN];
4159 gmx_mtop_atomloop_block_t aloopb;
4161 char warn_buf[STRLEN];
4163 set_warning_line(wi, mdparin, -1);
4165 if (absolute_reference(ir, sys, false, AbsRef))
4168 "Removing center of mass motion in the presence of position restraints might "
4169 "cause artifacts. When you are using position restraints to equilibrate a "
4170 "macro-molecule, the artifacts are usually negligible.");
4173 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 && ir->nstlist > 1
4174 && ((EI_MD(ir->eI) || EI_SD(ir->eI)) && (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4176 /* Check if a too small Verlet buffer might potentially
4177 * cause more drift than the thermostat can couple off.
4179 /* Temperature error fraction for warning and suggestion */
4180 const real T_error_warn = 0.002;
4181 const real T_error_suggest = 0.001;
4182 /* For safety: 2 DOF per atom (typical with constraints) */
4183 const real nrdf_at = 2;
4184 real T, tau, max_T_error;
4189 for (i = 0; i < ir->opts.ngtc; i++)
4191 T = std::max(T, ir->opts.ref_t[i]);
4192 tau = std::max(tau, ir->opts.tau_t[i]);
4196 /* This is a worst case estimate of the temperature error,
4197 * assuming perfect buffer estimation and no cancelation
4198 * of errors. The factor 0.5 is because energy distributes
4199 * equally over Ekin and Epot.
4201 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * BOLTZ * T);
4202 if (max_T_error > T_error_warn)
4205 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4206 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4207 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4208 "%.0e or decrease tau_t.",
4209 ir->verletbuf_tol, T, tau, 100 * max_T_error, 100 * T_error_suggest,
4210 ir->verletbuf_tol * T_error_suggest / max_T_error);
4211 warning(wi, warn_buf);
4216 if (ETC_ANDERSEN(ir->etc))
4220 for (i = 0; i < ir->opts.ngtc; i++)
4223 "all tau_t must currently be equal using Andersen temperature control, "
4224 "violated for group %d",
4226 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4228 "all tau_t must be positive using Andersen temperature control, "
4230 i, ir->opts.tau_t[i]);
4231 CHECK(ir->opts.tau_t[i] < 0);
4234 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4236 for (i = 0; i < ir->opts.ngtc; i++)
4238 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4240 "tau_t/delta_t for group %d for temperature control method %s must be a "
4241 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4242 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4244 i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
4245 CHECK(nsteps % ir->nstcomm != 0);
4250 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD && ir->comm_mode == ecmNO
4251 && !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) && !ETC_ANDERSEN(ir->etc))
4254 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4255 "rounding errors can lead to build up of kinetic energy of the center of mass");
4258 if (ir->epc == epcPARRINELLORAHMAN && ir->etc == etcNOSEHOOVER)
4261 for (int g = 0; g < ir->opts.ngtc; g++)
4263 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4265 if (ir->tau_p < 1.9 * tau_t_max)
4267 std::string message = gmx::formatString(
4268 "With %s T-coupling and %s p-coupling, "
4269 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4270 etcoupl_names[ir->etc], epcoupl_names[ir->epc], "tau-p", ir->tau_p, "tau-t",
4272 warning(wi, message.c_str());
4276 /* Check for pressure coupling with absolute position restraints */
4277 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4279 absolute_reference(ir, sys, TRUE, AbsRef);
4281 for (m = 0; m < DIM; m++)
4283 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4286 "You are using pressure coupling with absolute position restraints, "
4287 "this will give artifacts. Use the refcoord_scaling option.");
4295 aloopb = gmx_mtop_atomloop_block_init(sys);
4297 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4299 if (atom->q != 0 || atom->qB != 0)
4307 if (EEL_FULL(ir->coulombtype))
4310 "You are using full electrostatics treatment %s for a system without charges.\n"
4311 "This costs a lot of performance for just processing zeros, consider using %s "
4313 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4314 warning(wi, err_buf);
4319 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
4322 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4323 "You might want to consider using %s electrostatics.\n",
4325 warning_note(wi, err_buf);
4329 /* Check if combination rules used in LJ-PME are the same as in the force field */
4330 if (EVDW_PME(ir->vdwtype))
4332 check_combination_rules(ir, sys, wi);
4335 /* Generalized reaction field */
4336 if (ir->coulombtype == eelGRF_NOTUSED)
4339 "Generalized reaction-field electrostatics is no longer supported. "
4340 "You can use normal reaction-field instead and compute the reaction-field "
4341 "constant by hand.");
4345 for (int i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4347 for (m = 0; (m < DIM); m++)
4349 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4358 snew(mgrp, sys->groups.groups[SimulationAtomGroupType::Acceleration].size());
4359 for (const AtomProxy atomP : AtomRange(*sys))
4361 const t_atom& local = atomP.atom();
4362 int i = atomP.globalAtomNumber();
4363 mgrp[getGroupType(sys->groups, SimulationAtomGroupType::Acceleration, i)] += local.m;
4366 for (i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4368 for (m = 0; (m < DIM); m++)
4370 acc[m] += ir->opts.acc[i][m] * mgrp[i];
4374 for (m = 0; (m < DIM); m++)
4376 if (fabs(acc[m]) > 1e-6)
4378 const char* dim[DIM] = { "X", "Y", "Z" };
4379 fprintf(stderr, "Net Acceleration in %s direction, will %s be corrected\n", dim[m],
4380 ir->nstcomm != 0 ? "" : "not");
4381 if (ir->nstcomm != 0 && m < ndof_com(ir))
4385 (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4387 ir->opts.acc[i][m] -= acc[m];
4395 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0
4396 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4398 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4406 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4408 if (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0)
4410 absolute_reference(ir, sys, FALSE, AbsRef);
4411 for (m = 0; m < DIM; m++)
4413 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4416 "You are using an absolute reference for pulling, but the rest of "
4417 "the system does not have an absolute reference. This will lead to "
4426 for (i = 0; i < 3; i++)
4428 for (m = 0; m <= i; m++)
4430 if ((ir->epc != epcNO && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4432 for (c = 0; c < ir->pull->ncoord; c++)
4434 if (ir->pull->coord[c].eGeom == epullgDIRPBC && ir->pull->coord[c].vec[m] != 0)
4437 "Can not have dynamic box while using pull geometry '%s' "
4439 EPULLGEOM(ir->pull->coord[c].eGeom), 'x' + m);
4450 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4452 char warn_buf[STRLEN];
4455 ptr = check_box(ir->pbcType, box);
4458 warning_error(wi, ptr);
4461 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4463 if (ir->shake_tol <= 0.0)
4465 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4466 warning_error(wi, warn_buf);
4470 if ((ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4472 /* If we have Lincs constraints: */
4473 if (ir->eI == eiMD && ir->etc == etcNO && ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4476 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4477 warning_note(wi, warn_buf);
4480 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4483 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4485 warning_note(wi, warn_buf);
4487 if (ir->epc == epcMTTK)
4489 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4493 if (bHasAnyConstraints && ir->epc == epcMTTK)
4495 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4498 if (ir->LincsWarnAngle > 90.0)
4500 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4501 warning(wi, warn_buf);
4502 ir->LincsWarnAngle = 90.0;
4505 if (ir->pbcType != PbcType::No)
4507 if (ir->nstlist == 0)
4510 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4511 "atoms might cause the simulation to crash.");
4513 if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
4516 "ERROR: The cut-off length is longer than half the shortest box vector or "
4517 "longer than the smallest box diagonal element. Increase the box size or "
4518 "decrease rlist.\n");
4519 warning_error(wi, warn_buf);