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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);
2144 ir->awhParams = gmx::readAndCheckAwhParams(&inp, ir, wi);
2148 gmx_fatal(FARGS, "AWH biasing is only compatible with COM pulling turned on");
2152 /* Enforced rotation */
2153 printStringNewline(&inp, "ENFORCED ROTATION");
2154 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2155 ir->bRot = (get_eeenum(&inp, "rotation", yesno_names, wi) != 0);
2159 is->rot_grp = read_rotparams(&inp, ir->rot, wi);
2162 /* Interactive MD */
2164 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2165 setStringEntry(&inp, "IMD-group", is->imd_grp, nullptr);
2166 if (is->imd_grp[0] != '\0')
2173 printStringNewline(&inp, "NMR refinement stuff");
2174 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2175 ir->eDisre = get_eeenum(&inp, "disre", edisre_names, wi);
2176 printStringNoNewline(
2177 &inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2178 ir->eDisreWeighting = get_eeenum(&inp, "disre-weighting", edisreweighting_names, wi);
2179 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2180 ir->bDisreMixed = (get_eeenum(&inp, "disre-mixed", yesno_names, wi) != 0);
2181 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2182 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2183 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2184 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2185 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2186 opts->bOrire = (get_eeenum(&inp, "orire", yesno_names, wi) != 0);
2187 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2188 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2189 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2190 setStringEntry(&inp, "orire-fitgrp", is->orirefitgrp, nullptr);
2191 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2192 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2194 /* free energy variables */
2195 printStringNewline(&inp, "Free energy variables");
2196 ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
2197 setStringEntry(&inp, "couple-moltype", is->couple_moltype, nullptr);
2198 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2199 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2200 opts->bCoupleIntra = (get_eeenum(&inp, "couple-intramol", yesno_names, wi) != 0);
2202 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2204 it was not entered */
2205 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2206 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2207 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2208 setStringEntry(&inp, "fep-lambdas", is->fep_lambda[efptFEP], nullptr);
2209 setStringEntry(&inp, "mass-lambdas", is->fep_lambda[efptMASS], nullptr);
2210 setStringEntry(&inp, "coul-lambdas", is->fep_lambda[efptCOUL], nullptr);
2211 setStringEntry(&inp, "vdw-lambdas", is->fep_lambda[efptVDW], nullptr);
2212 setStringEntry(&inp, "bonded-lambdas", is->fep_lambda[efptBONDED], nullptr);
2213 setStringEntry(&inp, "restraint-lambdas", is->fep_lambda[efptRESTRAINT], nullptr);
2214 setStringEntry(&inp, "temperature-lambdas", is->fep_lambda[efptTEMPERATURE], nullptr);
2215 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2216 setStringEntry(&inp, "init-lambda-weights", is->lambda_weights, nullptr);
2217 fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
2218 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2219 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2220 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2221 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2222 fep->bScCoul = (get_eeenum(&inp, "sc-coul", yesno_names, wi) != 0);
2223 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2224 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2225 fep->separate_dhdl_file = get_eeenum(&inp, "separate-dhdl-file", separate_dhdl_file_names, wi);
2226 fep->dhdl_derivatives = get_eeenum(&inp, "dhdl-derivatives", dhdl_derivatives_names, wi);
2227 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2228 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2230 /* Non-equilibrium MD stuff */
2231 printStringNewline(&inp, "Non-equilibrium MD stuff");
2232 setStringEntry(&inp, "acc-grps", is->accgrps, nullptr);
2233 setStringEntry(&inp, "accelerate", is->acc, nullptr);
2234 setStringEntry(&inp, "freezegrps", is->freeze, nullptr);
2235 setStringEntry(&inp, "freezedim", is->frdim, nullptr);
2236 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2237 setStringEntry(&inp, "deform", is->deform, nullptr);
2239 /* simulated tempering variables */
2240 printStringNewline(&inp, "simulated tempering variables");
2241 ir->bSimTemp = (get_eeenum(&inp, "simulated-tempering", yesno_names, wi) != 0);
2242 ir->simtempvals->eSimTempScale = get_eeenum(&inp, "simulated-tempering-scaling", esimtemp_names, wi);
2243 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2244 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2246 /* expanded ensemble variables */
2247 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2249 read_expandedparams(&inp, expand, wi);
2252 /* Electric fields */
2254 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2255 gmx::KeyValueTreeTransformer transform;
2256 transform.rules()->addRule().keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2257 mdModules->initMdpTransform(transform.rules());
2258 for (const auto& path : transform.mappedPaths())
2260 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2261 mark_einp_set(inp, path[0].c_str());
2263 MdpErrorHandler errorHandler(wi);
2264 auto result = transform.transform(convertedValues, &errorHandler);
2265 ir->params = new gmx::KeyValueTreeObject(result.object());
2266 mdModules->adjustInputrecBasedOnModules(ir);
2267 errorHandler.setBackMapping(result.backMapping());
2268 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2271 /* Ion/water position swapping ("computational electrophysiology") */
2272 printStringNewline(&inp,
2273 "Ion/water position swapping for computational electrophysiology setups");
2274 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2275 ir->eSwapCoords = get_eeenum(&inp, "swapcoords", eSwapTypes_names, wi);
2276 if (ir->eSwapCoords != eswapNO)
2283 printStringNoNewline(&inp, "Swap attempt frequency");
2284 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2285 printStringNoNewline(&inp, "Number of ion types to be controlled");
2286 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2289 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2291 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2292 snew(ir->swap->grp, ir->swap->ngrp);
2293 for (i = 0; i < ir->swap->ngrp; i++)
2295 snew(ir->swap->grp[i].molname, STRLEN);
2297 printStringNoNewline(&inp,
2298 "Two index groups that contain the compartment-partitioning atoms");
2299 setStringEntry(&inp, "split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2300 setStringEntry(&inp, "split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2301 printStringNoNewline(&inp,
2302 "Use center of mass of split groups (yes/no), otherwise center of "
2303 "geometry is used");
2304 ir->swap->massw_split[0] = (get_eeenum(&inp, "massw-split0", yesno_names, wi) != 0);
2305 ir->swap->massw_split[1] = (get_eeenum(&inp, "massw-split1", yesno_names, wi) != 0);
2307 printStringNoNewline(&inp, "Name of solvent molecules");
2308 setStringEntry(&inp, "solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2310 printStringNoNewline(&inp,
2311 "Split cylinder: radius, upper and lower extension (nm) (this will "
2312 "define the channels)");
2313 printStringNoNewline(&inp,
2314 "Note that the split cylinder settings do not have an influence on "
2315 "the swapping protocol,");
2316 printStringNoNewline(
2318 "however, if correctly defined, the permeation events are recorded per channel");
2319 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2320 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2321 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2322 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2323 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2324 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2326 printStringNoNewline(
2328 "Average the number of ions per compartment over these many swap attempt steps");
2329 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2331 printStringNoNewline(
2332 &inp, "Names of the ion types that can be exchanged with solvent molecules,");
2333 printStringNoNewline(
2334 &inp, "and the requested number of ions of this type in compartments A and B");
2335 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2336 for (i = 0; i < nIonTypes; i++)
2338 int ig = eSwapFixedGrpNR + i;
2340 sprintf(buf, "iontype%d-name", i);
2341 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2342 sprintf(buf, "iontype%d-in-A", i);
2343 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2344 sprintf(buf, "iontype%d-in-B", i);
2345 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2348 printStringNoNewline(
2350 "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2351 printStringNoNewline(
2353 "at maximum distance (= bulk concentration) to the split group layers. However,");
2354 printStringNoNewline(&inp,
2355 "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk "
2356 "layer from the middle at 0.0");
2357 printStringNoNewline(&inp,
2358 "towards one of the compartment-partitioning layers (at +/- 1.0).");
2359 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2360 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2361 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2362 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0))
2364 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2367 printStringNoNewline(
2368 &inp, "Start to swap ions if threshold difference to requested count is reached");
2369 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2372 /* AdResS is no longer supported, but we need grompp to be able to
2373 refuse to process old .mdp files that used it. */
2374 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2376 /* User defined thingies */
2377 printStringNewline(&inp, "User defined thingies");
2378 setStringEntry(&inp, "user1-grps", is->user1, nullptr);
2379 setStringEntry(&inp, "user2-grps", is->user2, nullptr);
2380 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2381 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2382 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2383 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2384 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2385 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2386 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2387 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2391 gmx::TextOutputFile stream(mdparout);
2392 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2394 // Transform module data into a flat key-value tree for output.
2395 gmx::KeyValueTreeBuilder builder;
2396 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2397 mdModules->buildMdpOutput(&builderObject);
2399 gmx::TextWriter writer(&stream);
2400 writeKeyValueTreeAsMdp(&writer, builder.build());
2405 /* Process options if necessary */
2406 for (m = 0; m < 2; m++)
2408 for (i = 0; i < 2 * DIM; i++)
2417 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2421 "Pressure coupling incorrect number of values (I need exactly 1)");
2423 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2425 case epctSEMIISOTROPIC:
2426 case epctSURFACETENSION:
2427 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2431 "Pressure coupling incorrect number of values (I need exactly 2)");
2433 dumdub[m][YY] = dumdub[m][XX];
2435 case epctANISOTROPIC:
2436 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf", &(dumdub[m][XX]), &(dumdub[m][YY]),
2437 &(dumdub[m][ZZ]), &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5]))
2442 "Pressure coupling incorrect number of values (I need exactly 6)");
2446 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2447 epcoupltype_names[ir->epct]);
2451 clear_mat(ir->ref_p);
2452 clear_mat(ir->compress);
2453 for (i = 0; i < DIM; i++)
2455 ir->ref_p[i][i] = dumdub[1][i];
2456 ir->compress[i][i] = dumdub[0][i];
2458 if (ir->epct == epctANISOTROPIC)
2460 ir->ref_p[XX][YY] = dumdub[1][3];
2461 ir->ref_p[XX][ZZ] = dumdub[1][4];
2462 ir->ref_p[YY][ZZ] = dumdub[1][5];
2463 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2466 "All off-diagonal reference pressures are non-zero. Are you sure you want to "
2467 "apply a threefold shear stress?\n");
2469 ir->compress[XX][YY] = dumdub[0][3];
2470 ir->compress[XX][ZZ] = dumdub[0][4];
2471 ir->compress[YY][ZZ] = dumdub[0][5];
2472 for (i = 0; i < DIM; i++)
2474 for (m = 0; m < i; m++)
2476 ir->ref_p[i][m] = ir->ref_p[m][i];
2477 ir->compress[i][m] = ir->compress[m][i];
2482 if (ir->comm_mode == ecmNO)
2487 opts->couple_moltype = nullptr;
2488 if (strlen(is->couple_moltype) > 0)
2490 if (ir->efep != efepNO)
2492 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2493 if (opts->couple_lam0 == opts->couple_lam1)
2495 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2497 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
2501 "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
2508 "Free energy is turned off, so we will not decouple the molecule listed "
2512 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2513 if (ir->efep != efepNO)
2515 if (fep->delta_lambda > 0)
2517 ir->efep = efepSLOWGROWTH;
2521 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2523 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2525 "Old option for dhdl-print-energy given: "
2526 "changing \"yes\" to \"total\"\n");
2529 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2531 /* always print out the energy to dhdl if we are doing
2532 expanded ensemble, since we need the total energy for
2533 analysis if the temperature is changing. In some
2534 conditions one may only want the potential energy, so
2535 we will allow that if the appropriate mdp setting has
2536 been enabled. Otherwise, total it is:
2538 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2541 if ((ir->efep != efepNO) || ir->bSimTemp)
2543 ir->bExpanded = FALSE;
2544 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2546 ir->bExpanded = TRUE;
2548 do_fep_params(ir, is->fep_lambda, is->lambda_weights, wi);
2549 if (ir->bSimTemp) /* done after fep params */
2551 do_simtemp_params(ir);
2554 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2555 * setup and not on the old way of specifying the free-energy setup,
2556 * we should check for using soft-core when not needed, since that
2557 * can complicate the sampling significantly.
2558 * Note that we only check for the automated coupling setup.
2559 * If the (advanced) user does FEP through manual topology changes,
2560 * this check will not be triggered.
2562 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 && ir->fepvals->sc_alpha != 0
2563 && (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
2566 "You are using soft-core interactions while the Van der Waals interactions are "
2567 "not decoupled (note that the sc-coul option is only active when using lambda "
2568 "states). Although this will not lead to errors, you will need much more "
2569 "sampling than without soft-core interactions. Consider using sc-alpha=0.");
2574 ir->fepvals->n_lambda = 0;
2577 /* WALL PARAMETERS */
2579 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts, wi);
2581 /* ORIENTATION RESTRAINT PARAMETERS */
2583 if (opts->bOrire && gmx::splitString(is->orirefitgrp).size() != 1)
2585 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2588 /* DEFORMATION PARAMETERS */
2590 clear_mat(ir->deform);
2591 for (i = 0; i < 6; i++)
2596 double gmx_unused canary;
2597 int ndeform = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf %lf", &(dumdub[0][0]), &(dumdub[0][1]),
2598 &(dumdub[0][2]), &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]), &canary);
2600 if (strlen(is->deform) > 0 && ndeform != 6)
2603 wi, gmx::formatString(
2604 "Cannot parse exactly 6 box deformation velocities from string '%s'", is->deform)
2607 for (i = 0; i < 3; i++)
2609 ir->deform[i][i] = dumdub[0][i];
2611 ir->deform[YY][XX] = dumdub[0][3];
2612 ir->deform[ZZ][XX] = dumdub[0][4];
2613 ir->deform[ZZ][YY] = dumdub[0][5];
2614 if (ir->epc != epcNO)
2616 for (i = 0; i < 3; i++)
2618 for (j = 0; j <= i; j++)
2620 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2622 warning_error(wi, "A box element has deform set and compressibility > 0");
2626 for (i = 0; i < 3; i++)
2628 for (j = 0; j < i; j++)
2630 if (ir->deform[i][j] != 0)
2632 for (m = j; m < DIM; m++)
2634 if (ir->compress[m][j] != 0)
2637 "An off-diagonal box element has deform set while "
2638 "compressibility > 0 for the same component of another box "
2639 "vector, this might lead to spurious periodicity effects.");
2640 warning(wi, warn_buf);
2648 /* Ion/water position swapping checks */
2649 if (ir->eSwapCoords != eswapNO)
2651 if (ir->swap->nstswap < 1)
2653 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2655 if (ir->swap->nAverage < 1)
2657 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2659 if (ir->swap->threshold < 1.0)
2661 warning_error(wi, "Ion count threshold must be at least 1.\n");
2669 static int search_QMstring(const char* s, int ng, const char* gn[])
2671 /* same as normal search_string, but this one searches QM strings */
2674 for (i = 0; (i < ng); i++)
2676 if (gmx_strcasecmp(s, gn[i]) == 0)
2682 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2683 } /* search_QMstring */
2685 /* We would like gn to be const as well, but C doesn't allow this */
2686 /* TODO this is utility functionality (search for the index of a
2687 string in a collection), so should be refactored and located more
2689 int search_string(const char* s, int ng, char* gn[])
2693 for (i = 0; (i < ng); i++)
2695 if (gmx_strcasecmp(s, gn[i]) == 0)
2702 "Group %s referenced in the .mdp file was not found in the index file.\n"
2703 "Group names must match either [moleculetype] names or custom index group\n"
2704 "names, in which case you must supply an index file to the '-n' option\n"
2709 static void do_numbering(int natoms,
2710 SimulationGroups* groups,
2711 gmx::ArrayRef<std::string> groupsFromMdpFile,
2714 SimulationAtomGroupType gtype,
2720 unsigned short* cbuf;
2721 AtomGroupIndices* grps = &(groups->groups[gtype]);
2722 int j, gid, aj, ognr, ntot = 0;
2724 char warn_buf[STRLEN];
2726 title = shortName(gtype);
2729 /* Mark all id's as not set */
2730 for (int i = 0; (i < natoms); i++)
2735 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2737 /* Lookup the group name in the block structure */
2738 gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2739 if ((grptp != egrptpONE) || (i == 0))
2741 grps->emplace_back(gid);
2744 /* Now go over the atoms in the group */
2745 for (j = block->index[gid]; (j < block->index[gid + 1]); j++)
2750 /* Range checking */
2751 if ((aj < 0) || (aj >= natoms))
2753 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2755 /* Lookup up the old group number */
2759 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title,
2764 /* Store the group number in buffer */
2765 if (grptp == egrptpONE)
2778 /* Now check whether we have done all atoms */
2781 if (grptp == egrptpALL)
2783 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2785 else if (grptp == egrptpPART)
2787 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2788 warning_note(wi, warn_buf);
2790 /* Assign all atoms currently unassigned to a rest group */
2791 for (j = 0; (j < natoms); j++)
2793 if (cbuf[j] == NOGID)
2795 cbuf[j] = grps->size();
2798 if (grptp != egrptpPART)
2802 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title,
2805 /* Add group name "rest" */
2806 grps->emplace_back(restnm);
2808 /* Assign the rest name to all atoms not currently assigned to a group */
2809 for (j = 0; (j < natoms); j++)
2811 if (cbuf[j] == NOGID)
2813 // group size was not updated before this here, so need to use -1.
2814 cbuf[j] = grps->size() - 1;
2820 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2822 /* All atoms are part of one (or no) group, no index required */
2823 groups->groupNumbers[gtype].clear();
2827 for (int j = 0; (j < natoms); j++)
2829 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2836 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
2839 pull_params_t* pull;
2840 int natoms, imin, jmin;
2841 int * nrdf2, *na_vcm, na_tot;
2842 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2847 * First calc 3xnr-atoms for each group
2848 * then subtract half a degree of freedom for each constraint
2850 * Only atoms and nuclei contribute to the degrees of freedom...
2855 const SimulationGroups& groups = mtop->groups;
2856 natoms = mtop->natoms;
2858 /* Allocate one more for a possible rest group */
2859 /* We need to sum degrees of freedom into doubles,
2860 * since floats give too low nrdf's above 3 million atoms.
2862 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
2863 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2864 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2865 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2866 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2868 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
2872 for (gmx::index i = 0;
2873 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; i++)
2876 clear_ivec(dof_vcm[i]);
2878 nrdf_vcm_sub[i] = 0;
2880 snew(nrdf2, natoms);
2881 for (const AtomProxy atomP : AtomRange(*mtop))
2883 const t_atom& local = atomP.atom();
2884 int i = atomP.globalAtomNumber();
2886 if (local.ptype == eptAtom || local.ptype == eptNucleus)
2888 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
2889 for (int d = 0; d < DIM; d++)
2891 if (opts->nFreeze[g][d] == 0)
2893 /* Add one DOF for particle i (counted as 2*1) */
2895 /* VCM group i has dim d as a DOF */
2896 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
2900 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
2902 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
2908 for (const gmx_molblock_t& molb : mtop->molblock)
2910 const gmx_moltype_t& molt = mtop->moltype[molb.type];
2911 const t_atom* atom = molt.atoms.atom;
2912 for (int mol = 0; mol < molb.nmol; mol++)
2914 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2916 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
2917 for (int i = 0; i < molt.ilist[ftype].size();)
2919 /* Subtract degrees of freedom for the constraints,
2920 * if the particles still have degrees of freedom left.
2921 * If one of the particles is a vsite or a shell, then all
2922 * constraint motion will go there, but since they do not
2923 * contribute to the constraints the degrees of freedom do not
2926 int ai = as + ia[i + 1];
2927 int aj = as + ia[i + 2];
2928 if (((atom[ia[i + 1]].ptype == eptNucleus) || (atom[ia[i + 1]].ptype == eptAtom))
2929 && ((atom[ia[i + 2]].ptype == eptNucleus) || (atom[ia[i + 2]].ptype == eptAtom)))
2947 imin = std::min(imin, nrdf2[ai]);
2948 jmin = std::min(jmin, nrdf2[aj]);
2951 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2953 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
2955 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2957 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
2960 i += interaction_function[ftype].nratoms + 1;
2963 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
2964 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
2966 /* Subtract 1 dof from every atom in the SETTLE */
2967 for (int j = 0; j < 3; j++)
2969 int ai = as + ia[i + 1 + j];
2970 imin = std::min(2, nrdf2[ai]);
2972 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2974 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2979 as += molt.atoms.nr;
2985 /* Correct nrdf for the COM constraints.
2986 * We correct using the TC and VCM group of the first atom
2987 * in the reference and pull group. If atoms in one pull group
2988 * belong to different TC or VCM groups it is anyhow difficult
2989 * to determine the optimal nrdf assignment.
2993 for (int i = 0; i < pull->ncoord; i++)
2995 if (pull->coord[i].eType != epullCONSTRAINT)
3002 for (int j = 0; j < 2; j++)
3004 const t_pull_group* pgrp;
3006 pgrp = &pull->group[pull->coord[i].group[j]];
3010 /* Subtract 1/2 dof from each group */
3011 int ai = pgrp->ind[0];
3012 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3014 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3016 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
3019 "Center of mass pulling constraints caused the number of degrees "
3020 "of freedom for temperature coupling group %s to be negative",
3021 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
3022 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
3027 /* We need to subtract the whole DOF from group j=1 */
3034 if (ir->nstcomm != 0)
3036 GMX_RELEASE_ASSERT(!groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty(),
3037 "Expect at least one group when removing COM motion");
3039 /* We remove COM motion up to dim ndof_com() */
3040 const int ndim_rm_vcm = ndof_com(ir);
3042 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3043 * the number of degrees of freedom in each vcm group when COM
3044 * translation is removed and 6 when rotation is removed as well.
3045 * Note that we do not and should not include the rest group here.
3047 for (gmx::index j = 0;
3048 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]); j++)
3050 switch (ir->comm_mode)
3053 case ecmLINEAR_ACCELERATION_CORRECTION:
3054 nrdf_vcm_sub[j] = 0;
3055 for (int d = 0; d < ndim_rm_vcm; d++)
3063 case ecmANGULAR: nrdf_vcm_sub[j] = 6; break;
3064 default: gmx_incons("Checking comm_mode");
3068 for (gmx::index i = 0;
3069 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
3071 /* Count the number of atoms of TC group i for every VCM group */
3072 for (gmx::index j = 0;
3073 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3078 for (int ai = 0; ai < natoms; ai++)
3080 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3082 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3086 /* Correct for VCM removal according to the fraction of each VCM
3087 * group present in this TC group.
3089 nrdf_uc = nrdf_tc[i];
3091 for (gmx::index j = 0;
3092 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3094 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3096 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3097 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3102 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3104 opts->nrdf[i] = nrdf_tc[i];
3105 if (opts->nrdf[i] < 0)
3109 fprintf(stderr, "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3110 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]], opts->nrdf[i]);
3118 sfree(nrdf_vcm_sub);
3121 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3123 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3124 * But since this is much larger than STRLEN, such a line can not be parsed.
3125 * The real maximum is the number of names that fit in a string: STRLEN/2.
3127 #define EGP_MAX (STRLEN / 2)
3131 auto names = gmx::splitString(val);
3132 if (names.size() % 2 != 0)
3134 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3136 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3138 for (size_t i = 0; i < names.size() / 2; i++)
3140 // TODO this needs to be replaced by a solution using std::find_if
3144 names[2 * i].c_str(),
3145 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3151 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3156 names[2 * i + 1].c_str(),
3157 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3163 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3165 if ((j < nr) && (k < nr))
3167 ir->opts.egp_flags[nr * j + k] |= flag;
3168 ir->opts.egp_flags[nr * k + j] |= flag;
3177 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3179 int ig = -1, i = 0, gind;
3183 /* Just a quick check here, more thorough checks are in mdrun */
3184 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3186 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3189 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3190 for (ig = 0; ig < swap->ngrp; ig++)
3192 swapg = &swap->grp[ig];
3193 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3194 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3198 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3199 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap", swap->grp[ig].molname, swapg->nat);
3200 snew(swapg->ind, swapg->nat);
3201 for (i = 0; i < swapg->nat; i++)
3203 swapg->ind[i] = grps->a[grps->index[gind] + i];
3208 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3214 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3219 ig = search_string(IMDgname, grps->nr, gnames);
3220 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3222 if (IMDgroup->nat > 0)
3225 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3227 IMDgname, IMDgroup->nat);
3228 snew(IMDgroup->ind, IMDgroup->nat);
3229 for (i = 0; i < IMDgroup->nat; i++)
3231 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3236 /* Checks whether atoms are both part of a COM removal group and frozen.
3237 * If a fully frozen atom is part of a COM removal group, it is removed
3238 * from the COM removal group. A note is issued if such atoms are present.
3239 * A warning is issued for atom with one or two dimensions frozen that
3240 * are part of a COM removal group (mdrun would need to compute COM mass
3241 * per dimension to handle this correctly).
3242 * Also issues a warning when non-frozen atoms are not part of a COM
3243 * removal group while COM removal is active.
3245 static void checkAndUpdateVcmFreezeGroupConsistency(SimulationGroups* groups,
3247 const t_grpopts& opts,
3250 const int vcmRestGroup =
3251 std::max(int(groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()), 1);
3253 int numFullyFrozenVcmAtoms = 0;
3254 int numPartiallyFrozenVcmAtoms = 0;
3255 int numNonVcmAtoms = 0;
3256 for (int a = 0; a < numAtoms; a++)
3258 const int freezeGroup = getGroupType(*groups, SimulationAtomGroupType::Freeze, a);
3259 int numFrozenDims = 0;
3260 for (int d = 0; d < DIM; d++)
3262 numFrozenDims += opts.nFreeze[freezeGroup][d];
3265 const int vcmGroup = getGroupType(*groups, SimulationAtomGroupType::MassCenterVelocityRemoval, a);
3266 if (vcmGroup < vcmRestGroup)
3268 if (numFrozenDims == DIM)
3270 /* Do not remove COM motion for this fully frozen atom */
3271 if (groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
3273 groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(numAtoms, 0);
3275 groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
3276 numFullyFrozenVcmAtoms++;
3278 else if (numFrozenDims > 0)
3280 numPartiallyFrozenVcmAtoms++;
3283 else if (numFrozenDims < DIM)
3289 if (numFullyFrozenVcmAtoms > 0)
3291 std::string warningText = gmx::formatString(
3292 "There are %d atoms that are fully frozen and part of COMM removal group(s), "
3293 "removing these atoms from the COMM removal group(s)",
3294 numFullyFrozenVcmAtoms);
3295 warning_note(wi, warningText.c_str());
3297 if (numPartiallyFrozenVcmAtoms > 0 && numPartiallyFrozenVcmAtoms < numAtoms)
3299 std::string warningText = gmx::formatString(
3300 "There are %d atoms that are frozen along less then %d dimensions and part of COMM "
3301 "removal group(s), due to limitations in the code these still contribute to the "
3302 "mass of the COM along frozen dimensions and therefore the COMM correction will be "
3304 numPartiallyFrozenVcmAtoms, DIM);
3305 warning(wi, warningText.c_str());
3307 if (numNonVcmAtoms > 0)
3309 std::string warningText = gmx::formatString(
3310 "%d atoms are not part of any center of mass motion removal group.\n"
3311 "This may lead to artifacts.\n"
3312 "In most cases one should use one group for the whole system.",
3314 warning(wi, warningText.c_str());
3318 void do_index(const char* mdparin,
3322 const gmx::MdModulesNotifier& notifier,
3326 t_blocka* defaultIndexGroups;
3334 int i, j, k, restnm;
3335 bool bExcl, bTable, bAnneal;
3336 char warn_buf[STRLEN];
3340 fprintf(stderr, "processing index file...\n");
3344 snew(defaultIndexGroups, 1);
3345 snew(defaultIndexGroups->index, 1);
3347 atoms_all = gmx_mtop_global_atoms(mtop);
3348 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3349 done_atom(&atoms_all);
3353 defaultIndexGroups = init_index(ndx, &gnames);
3356 SimulationGroups* groups = &mtop->groups;
3357 natoms = mtop->natoms;
3358 symtab = &mtop->symtab;
3360 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3362 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3364 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3365 restnm = groups->groupNames.size() - 1;
3366 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3367 srenew(gnames, defaultIndexGroups->nr + 1);
3368 gnames[restnm] = *(groups->groupNames.back());
3370 set_warning_line(wi, mdparin, -1);
3372 auto temperatureCouplingTauValues = gmx::splitString(is->tau_t);
3373 auto temperatureCouplingReferenceValues = gmx::splitString(is->ref_t);
3374 auto temperatureCouplingGroupNames = gmx::splitString(is->tcgrps);
3375 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3376 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3379 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3381 temperatureCouplingGroupNames.size(), temperatureCouplingReferenceValues.size(),
3382 temperatureCouplingTauValues.size());
3385 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3386 do_numbering(natoms, groups, temperatureCouplingGroupNames, defaultIndexGroups, gnames,
3387 SimulationAtomGroupType::TemperatureCoupling, restnm,
3388 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3389 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3391 snew(ir->opts.nrdf, nr);
3392 snew(ir->opts.tau_t, nr);
3393 snew(ir->opts.ref_t, nr);
3394 if (ir->eI == eiBD && ir->bd_fric == 0)
3396 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3399 if (useReferenceTemperature)
3401 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3403 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3407 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3408 for (i = 0; (i < nr); i++)
3410 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3412 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3413 warning_error(wi, warn_buf);
3416 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3420 "tau-t = -1 is the value to signal that a group should not have "
3421 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3424 if (ir->opts.tau_t[i] >= 0)
3426 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3429 if (ir->etc != etcNO && ir->nsttcouple == -1)
3431 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3436 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3439 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3440 "md-vv; use either vrescale temperature with berendsen pressure or "
3441 "Nose-Hoover temperature with MTTK pressure");
3443 if (ir->epc == epcMTTK)
3445 if (ir->etc != etcNOSEHOOVER)
3448 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3453 if (ir->nstpcouple != ir->nsttcouple)
3455 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3456 ir->nstpcouple = ir->nsttcouple = mincouple;
3458 "for current Trotter decomposition methods with vv, nsttcouple and "
3459 "nstpcouple must be equal. Both have been reset to "
3460 "min(nsttcouple,nstpcouple) = %d",
3462 warning_note(wi, warn_buf);
3467 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3468 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3470 if (ETC_ANDERSEN(ir->etc))
3472 if (ir->nsttcouple != 1)
3476 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3477 "need for larger nsttcouple > 1, since no global parameters are computed. "
3478 "nsttcouple has been reset to 1");
3479 warning_note(wi, warn_buf);
3482 nstcmin = tcouple_min_integration_steps(ir->etc);
3485 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3488 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3489 "least %d times larger than nsttcouple*dt (%g)",
3490 ETCOUPLTYPE(ir->etc), tau_min, nstcmin, ir->nsttcouple * ir->delta_t);
3491 warning(wi, warn_buf);
3494 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3495 for (i = 0; (i < nr); i++)
3497 if (ir->opts.ref_t[i] < 0)
3499 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3502 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3503 if we are in this conditional) if mc_temp is negative */
3504 if (ir->expandedvals->mc_temp < 0)
3506 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3510 /* Simulated annealing for each group. There are nr groups */
3511 auto simulatedAnnealingGroupNames = gmx::splitString(is->anneal);
3512 if (simulatedAnnealingGroupNames.size() == 1
3513 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3515 simulatedAnnealingGroupNames.resize(0);
3517 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3519 gmx_fatal(FARGS, "Wrong number of annealing values: %zu (for %d groups)\n",
3520 simulatedAnnealingGroupNames.size(), nr);
3524 snew(ir->opts.annealing, nr);
3525 snew(ir->opts.anneal_npoints, nr);
3526 snew(ir->opts.anneal_time, nr);
3527 snew(ir->opts.anneal_temp, nr);
3528 for (i = 0; i < nr; i++)
3530 ir->opts.annealing[i] = eannNO;
3531 ir->opts.anneal_npoints[i] = 0;
3532 ir->opts.anneal_time[i] = nullptr;
3533 ir->opts.anneal_temp[i] = nullptr;
3535 if (!simulatedAnnealingGroupNames.empty())
3538 for (i = 0; i < nr; i++)
3540 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3542 ir->opts.annealing[i] = eannNO;
3544 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3546 ir->opts.annealing[i] = eannSINGLE;
3549 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3551 ir->opts.annealing[i] = eannPERIODIC;
3557 /* Read the other fields too */
3558 auto simulatedAnnealingPoints = gmx::splitString(is->anneal_npoints);
3559 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3561 gmx_fatal(FARGS, "Found %zu annealing-npoints values for %zu groups\n",
3562 simulatedAnnealingPoints.size(), simulatedAnnealingGroupNames.size());
3564 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3565 size_t numSimulatedAnnealingFields = 0;
3566 for (i = 0; i < nr; i++)
3568 if (ir->opts.anneal_npoints[i] == 1)
3572 "Please specify at least a start and an end point for annealing\n");
3574 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3575 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3576 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3579 auto simulatedAnnealingTimes = gmx::splitString(is->anneal_time);
3581 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3583 gmx_fatal(FARGS, "Found %zu annealing-time values, wanted %zu\n",
3584 simulatedAnnealingTimes.size(), numSimulatedAnnealingFields);
3586 auto simulatedAnnealingTemperatures = gmx::splitString(is->anneal_temp);
3587 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3589 gmx_fatal(FARGS, "Found %zu annealing-temp values, wanted %zu\n",
3590 simulatedAnnealingTemperatures.size(), numSimulatedAnnealingFields);
3593 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3594 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3595 convertReals(wi, simulatedAnnealingTimes, "anneal-time",
3596 allSimulatedAnnealingTimes.data());
3597 convertReals(wi, simulatedAnnealingTemperatures, "anneal-temp",
3598 allSimulatedAnnealingTemperatures.data());
3599 for (i = 0, k = 0; i < nr; i++)
3601 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3603 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3604 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3607 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3609 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3615 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3618 "Annealing timepoints out of order: t=%f comes after "
3620 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j - 1]);
3623 if (ir->opts.anneal_temp[i][j] < 0)
3625 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n",
3626 ir->opts.anneal_temp[i][j]);
3631 /* Print out some summary information, to make sure we got it right */
3632 for (i = 0; i < nr; i++)
3634 if (ir->opts.annealing[i] != eannNO)
3636 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3637 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3638 *(groups->groupNames[j]), eann_names[ir->opts.annealing[i]],
3639 ir->opts.anneal_npoints[i]);
3640 fprintf(stderr, "Time (ps) Temperature (K)\n");
3641 /* All terms except the last one */
3642 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3644 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3645 ir->opts.anneal_temp[i][j]);
3648 /* Finally the last one */
3649 j = ir->opts.anneal_npoints[i] - 1;
3650 if (ir->opts.annealing[i] == eannSINGLE)
3652 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j],
3653 ir->opts.anneal_temp[i][j]);
3657 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3658 ir->opts.anneal_temp[i][j]);
3659 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3662 "There is a temperature jump when your annealing "
3674 make_pull_groups(ir->pull, is->pull_grp, defaultIndexGroups, gnames);
3676 make_pull_coords(ir->pull);
3681 make_rotation_groups(ir->rot, is->rot_grp, defaultIndexGroups, gnames);
3684 if (ir->eSwapCoords != eswapNO)
3686 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3689 /* Make indices for IMD session */
3692 make_IMD_group(ir->imd, is->imd_grp, defaultIndexGroups, gnames);
3695 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3696 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3697 notifier.preProcessingNotifications_.notify(defaultIndexGroupsAndNames);
3699 auto accelerations = gmx::splitString(is->acc);
3700 auto accelerationGroupNames = gmx::splitString(is->accgrps);
3701 if (accelerationGroupNames.size() * DIM != accelerations.size())
3703 gmx_fatal(FARGS, "Invalid Acceleration input: %zu groups and %zu acc. values",
3704 accelerationGroupNames.size(), accelerations.size());
3706 do_numbering(natoms, groups, accelerationGroupNames, defaultIndexGroups, gnames,
3707 SimulationAtomGroupType::Acceleration, restnm, egrptpALL_GENREST, bVerbose, wi);
3708 nr = groups->groups[SimulationAtomGroupType::Acceleration].size();
3709 snew(ir->opts.acc, nr);
3710 ir->opts.ngacc = nr;
3712 convertRvecs(wi, accelerations, "anneal-time", ir->opts.acc);
3714 auto freezeDims = gmx::splitString(is->frdim);
3715 auto freezeGroupNames = gmx::splitString(is->freeze);
3716 if (freezeDims.size() != DIM * freezeGroupNames.size())
3718 gmx_fatal(FARGS, "Invalid Freezing input: %zu groups and %zu freeze values",
3719 freezeGroupNames.size(), freezeDims.size());
3721 do_numbering(natoms, groups, freezeGroupNames, defaultIndexGroups, gnames,
3722 SimulationAtomGroupType::Freeze, restnm, egrptpALL_GENREST, bVerbose, wi);
3723 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3724 ir->opts.ngfrz = nr;
3725 snew(ir->opts.nFreeze, nr);
3726 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3728 for (j = 0; (j < DIM); j++, k++)
3730 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3731 if (!ir->opts.nFreeze[i][j])
3733 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3736 "Please use Y(ES) or N(O) for freezedim only "
3738 freezeDims[k].c_str());
3739 warning(wi, warn_buf);
3744 for (; (i < nr); i++)
3746 for (j = 0; (j < DIM); j++)
3748 ir->opts.nFreeze[i][j] = 0;
3752 auto energyGroupNames = gmx::splitString(is->energy);
3753 do_numbering(natoms, groups, energyGroupNames, defaultIndexGroups, gnames,
3754 SimulationAtomGroupType::EnergyOutput, restnm, egrptpALL_GENREST, bVerbose, wi);
3755 add_wall_energrps(groups, ir->nwall, symtab);
3756 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3757 auto vcmGroupNames = gmx::splitString(is->vcm);
3758 do_numbering(natoms, groups, vcmGroupNames, defaultIndexGroups, gnames,
3759 SimulationAtomGroupType::MassCenterVelocityRemoval, restnm,
3760 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3762 if (ir->comm_mode != ecmNO)
3764 checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
3767 /* Now we have filled the freeze struct, so we can calculate NRDF */
3768 calc_nrdf(mtop, ir, gnames);
3770 auto user1GroupNames = gmx::splitString(is->user1);
3771 do_numbering(natoms, groups, user1GroupNames, defaultIndexGroups, gnames,
3772 SimulationAtomGroupType::User1, restnm, egrptpALL_GENREST, bVerbose, wi);
3773 auto user2GroupNames = gmx::splitString(is->user2);
3774 do_numbering(natoms, groups, user2GroupNames, defaultIndexGroups, gnames,
3775 SimulationAtomGroupType::User2, restnm, egrptpALL_GENREST, bVerbose, wi);
3776 auto compressedXGroupNames = gmx::splitString(is->x_compressed_groups);
3777 do_numbering(natoms, groups, compressedXGroupNames, defaultIndexGroups, gnames,
3778 SimulationAtomGroupType::CompressedPositionOutput, restnm, egrptpONE, bVerbose, wi);
3779 auto orirefFitGroupNames = gmx::splitString(is->orirefitgrp);
3780 do_numbering(natoms, groups, orirefFitGroupNames, defaultIndexGroups, gnames,
3781 SimulationAtomGroupType::OrientationRestraintsFit, restnm, egrptpALL_GENREST,
3784 /* QMMM input processing */
3785 auto qmGroupNames = gmx::splitString(is->QMMM);
3786 auto qmMethods = gmx::splitString(is->QMmethod);
3787 auto qmBasisSets = gmx::splitString(is->QMbasis);
3788 if (ir->eI != eiMimic)
3790 if (qmMethods.size() != qmGroupNames.size() || qmBasisSets.size() != qmGroupNames.size())
3793 "Invalid QMMM input: %zu groups %zu basissets"
3794 " and %zu methods\n",
3795 qmGroupNames.size(), qmBasisSets.size(), qmMethods.size());
3797 /* group rest, if any, is always MM! */
3798 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3799 SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
3800 nr = qmGroupNames.size(); /*atoms->grps[egcQMMM].nr;*/
3801 ir->opts.ngQM = qmGroupNames.size();
3802 snew(ir->opts.QMmethod, nr);
3803 snew(ir->opts.QMbasis, nr);
3804 for (i = 0; i < nr; i++)
3806 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3807 * converted to the corresponding enum in names.c
3809 ir->opts.QMmethod[i] = search_QMstring(qmMethods[i].c_str(), eQMmethodNR, eQMmethod_names);
3810 ir->opts.QMbasis[i] = search_QMstring(qmBasisSets[i].c_str(), eQMbasisNR, eQMbasis_names);
3812 auto qmMultiplicities = gmx::splitString(is->QMmult);
3813 auto qmCharges = gmx::splitString(is->QMcharge);
3814 auto qmbSH = gmx::splitString(is->bSH);
3815 snew(ir->opts.QMmult, nr);
3816 snew(ir->opts.QMcharge, nr);
3817 snew(ir->opts.bSH, nr);
3818 convertInts(wi, qmMultiplicities, "QMmult", ir->opts.QMmult);
3819 convertInts(wi, qmCharges, "QMcharge", ir->opts.QMcharge);
3820 convertYesNos(wi, qmbSH, "bSH", ir->opts.bSH);
3822 auto CASelectrons = gmx::splitString(is->CASelectrons);
3823 auto CASorbitals = gmx::splitString(is->CASorbitals);
3824 snew(ir->opts.CASelectrons, nr);
3825 snew(ir->opts.CASorbitals, nr);
3826 convertInts(wi, CASelectrons, "CASelectrons", ir->opts.CASelectrons);
3827 convertInts(wi, CASorbitals, "CASOrbitals", ir->opts.CASorbitals);
3829 auto SAon = gmx::splitString(is->SAon);
3830 auto SAoff = gmx::splitString(is->SAoff);
3831 auto SAsteps = gmx::splitString(is->SAsteps);
3832 snew(ir->opts.SAon, nr);
3833 snew(ir->opts.SAoff, nr);
3834 snew(ir->opts.SAsteps, nr);
3835 convertInts(wi, SAon, "SAon", ir->opts.SAon);
3836 convertInts(wi, SAoff, "SAoff", ir->opts.SAoff);
3837 convertInts(wi, SAsteps, "SAsteps", ir->opts.SAsteps);
3842 if (qmGroupNames.size() > 1)
3844 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
3846 /* group rest, if any, is always MM! */
3847 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3848 SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
3850 ir->opts.ngQM = qmGroupNames.size();
3853 /* end of QMMM input */
3857 for (auto group : gmx::keysOf(groups->groups))
3859 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
3860 for (const auto& entry : groups->groups[group])
3862 fprintf(stderr, " %s", *(groups->groupNames[entry]));
3864 fprintf(stderr, "\n");
3868 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3869 snew(ir->opts.egp_flags, nr * nr);
3871 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3872 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3874 warning_error(wi, "Energy group exclusions are currently not supported");
3876 if (bExcl && EEL_FULL(ir->coulombtype))
3878 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3881 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3882 if (bTable && !(ir->vdwtype == evdwUSER) && !(ir->coulombtype == eelUSER)
3883 && !(ir->coulombtype == eelPMEUSER) && !(ir->coulombtype == eelPMEUSERSWITCH))
3886 "Can only have energy group pair tables in combination with user tables for VdW "
3890 /* final check before going out of scope if simulated tempering variables
3891 * need to be set to default values.
3893 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
3895 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
3896 warning(wi, gmx::formatString(
3897 "the value for nstexpanded was not specified for "
3898 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
3899 "by default, but it is recommended to set it to an explicit value!",
3900 ir->expandedvals->nstexpanded));
3902 for (i = 0; (i < defaultIndexGroups->nr); i++)
3907 done_blocka(defaultIndexGroups);
3908 sfree(defaultIndexGroups);
3912 static void check_disre(const gmx_mtop_t* mtop)
3914 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3916 const gmx_ffparams_t& ffparams = mtop->ffparams;
3919 for (int i = 0; i < ffparams.numTypes(); i++)
3921 int ftype = ffparams.functype[i];
3922 if (ftype == F_DISRES)
3924 int label = ffparams.iparams[i].disres.label;
3925 if (label == old_label)
3927 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3936 "Found %d double distance restraint indices,\n"
3937 "probably the parameters for multiple pairs in one restraint "
3938 "are not identical\n",
3944 static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t* sys, const bool posres_only, ivec AbsRef)
3947 gmx_mtop_ilistloop_t iloop;
3949 const t_iparams* pr;
3956 for (d = 0; d < DIM; d++)
3958 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3960 /* Check for freeze groups */
3961 for (g = 0; g < ir->opts.ngfrz; g++)
3963 for (d = 0; d < DIM; d++)
3965 if (ir->opts.nFreeze[g][d] != 0)
3973 /* Check for position restraints */
3974 iloop = gmx_mtop_ilistloop_init(sys);
3975 while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
3977 if (nmol > 0 && (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3979 for (i = 0; i < (*ilist)[F_POSRES].size(); i += 2)
3981 pr = &sys->ffparams.iparams[(*ilist)[F_POSRES].iatoms[i]];
3982 for (d = 0; d < DIM; d++)
3984 if (pr->posres.fcA[d] != 0)
3990 for (i = 0; i < (*ilist)[F_FBPOSRES].size(); i += 2)
3992 /* Check for flat-bottom posres */
3993 pr = &sys->ffparams.iparams[(*ilist)[F_FBPOSRES].iatoms[i]];
3994 if (pr->fbposres.k != 0)
3996 switch (pr->fbposres.geom)
3998 case efbposresSPHERE: AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1; break;
3999 case efbposresCYLINDERX: AbsRef[YY] = AbsRef[ZZ] = 1; break;
4000 case efbposresCYLINDERY: AbsRef[XX] = AbsRef[ZZ] = 1; break;
4001 case efbposresCYLINDER:
4002 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
4003 case efbposresCYLINDERZ: AbsRef[XX] = AbsRef[YY] = 1; break;
4004 case efbposresX: /* d=XX */
4005 case efbposresY: /* d=YY */
4006 case efbposresZ: /* d=ZZ */
4007 d = pr->fbposres.geom - efbposresX;
4012 " Invalid geometry for flat-bottom position restraint.\n"
4013 "Expected nr between 1 and %d. Found %d\n",
4014 efbposresNR - 1, pr->fbposres.geom);
4021 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
4024 static void check_combination_rule_differences(const gmx_mtop_t* mtop,
4026 bool* bC6ParametersWorkWithGeometricRules,
4027 bool* bC6ParametersWorkWithLBRules,
4028 bool* bLBRulesPossible)
4030 int ntypes, tpi, tpj;
4033 double c6i, c6j, c12i, c12j;
4034 double c6, c6_geometric, c6_LB;
4035 double sigmai, sigmaj, epsi, epsj;
4036 bool bCanDoLBRules, bCanDoGeometricRules;
4039 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
4040 * force-field floating point parameters.
4043 ptr = getenv("GMX_LJCOMB_TOL");
4047 double gmx_unused canary;
4049 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
4052 "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
4057 *bC6ParametersWorkWithLBRules = TRUE;
4058 *bC6ParametersWorkWithGeometricRules = TRUE;
4059 bCanDoLBRules = TRUE;
4060 ntypes = mtop->ffparams.atnr;
4061 snew(typecount, ntypes);
4062 gmx_mtop_count_atomtypes(mtop, state, typecount);
4063 *bLBRulesPossible = TRUE;
4064 for (tpi = 0; tpi < ntypes; ++tpi)
4066 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
4067 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
4068 for (tpj = tpi; tpj < ntypes; ++tpj)
4070 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
4071 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
4072 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
4073 c6_geometric = std::sqrt(c6i * c6j);
4074 if (!gmx_numzero(c6_geometric))
4076 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4078 sigmai = gmx::sixthroot(c12i / c6i);
4079 sigmaj = gmx::sixthroot(c12j / c6j);
4080 epsi = c6i * c6i / (4.0 * c12i);
4081 epsj = c6j * c6j / (4.0 * c12j);
4082 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4086 *bLBRulesPossible = FALSE;
4087 c6_LB = c6_geometric;
4089 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4094 *bC6ParametersWorkWithLBRules = FALSE;
4097 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4099 if (!bCanDoGeometricRules)
4101 *bC6ParametersWorkWithGeometricRules = FALSE;
4108 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t* mtop, warninp_t wi)
4110 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4112 check_combination_rule_differences(mtop, 0, &bC6ParametersWorkWithGeometricRules,
4113 &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4114 if (ir->ljpme_combination_rule == eljpmeLB)
4116 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4119 "You are using arithmetic-geometric combination rules "
4120 "in LJ-PME, but your non-bonded C6 parameters do not "
4121 "follow these rules.");
4126 if (!bC6ParametersWorkWithGeometricRules)
4128 if (ir->eDispCorr != edispcNO)
4131 "You are using geometric combination rules in "
4132 "LJ-PME, but your non-bonded C6 parameters do "
4133 "not follow these rules. "
4134 "This will introduce very small errors in the forces and energies in "
4135 "your simulations. Dispersion correction will correct total energy "
4136 "and/or pressure for isotropic systems, but not forces or surface "
4142 "You are using geometric combination rules in "
4143 "LJ-PME, but your non-bonded C6 parameters do "
4144 "not follow these rules. "
4145 "This will introduce very small errors in the forces and energies in "
4146 "your simulations. If your system is homogeneous, consider using "
4147 "dispersion correction "
4148 "for the total energy and pressure.");
4154 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4156 char err_buf[STRLEN];
4161 gmx_mtop_atomloop_block_t aloopb;
4163 char warn_buf[STRLEN];
4165 set_warning_line(wi, mdparin, -1);
4167 if (absolute_reference(ir, sys, false, AbsRef))
4170 "Removing center of mass motion in the presence of position restraints might "
4171 "cause artifacts. When you are using position restraints to equilibrate a "
4172 "macro-molecule, the artifacts are usually negligible.");
4175 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 && ir->nstlist > 1
4176 && ((EI_MD(ir->eI) || EI_SD(ir->eI)) && (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4178 /* Check if a too small Verlet buffer might potentially
4179 * cause more drift than the thermostat can couple off.
4181 /* Temperature error fraction for warning and suggestion */
4182 const real T_error_warn = 0.002;
4183 const real T_error_suggest = 0.001;
4184 /* For safety: 2 DOF per atom (typical with constraints) */
4185 const real nrdf_at = 2;
4186 real T, tau, max_T_error;
4191 for (i = 0; i < ir->opts.ngtc; i++)
4193 T = std::max(T, ir->opts.ref_t[i]);
4194 tau = std::max(tau, ir->opts.tau_t[i]);
4198 /* This is a worst case estimate of the temperature error,
4199 * assuming perfect buffer estimation and no cancelation
4200 * of errors. The factor 0.5 is because energy distributes
4201 * equally over Ekin and Epot.
4203 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * BOLTZ * T);
4204 if (max_T_error > T_error_warn)
4207 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4208 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4209 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4210 "%.0e or decrease tau_t.",
4211 ir->verletbuf_tol, T, tau, 100 * max_T_error, 100 * T_error_suggest,
4212 ir->verletbuf_tol * T_error_suggest / max_T_error);
4213 warning(wi, warn_buf);
4218 if (ETC_ANDERSEN(ir->etc))
4222 for (i = 0; i < ir->opts.ngtc; i++)
4225 "all tau_t must currently be equal using Andersen temperature control, "
4226 "violated for group %d",
4228 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4230 "all tau_t must be positive using Andersen temperature control, "
4232 i, ir->opts.tau_t[i]);
4233 CHECK(ir->opts.tau_t[i] < 0);
4236 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4238 for (i = 0; i < ir->opts.ngtc; i++)
4240 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4242 "tau_t/delta_t for group %d for temperature control method %s must be a "
4243 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4244 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4246 i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
4247 CHECK(nsteps % ir->nstcomm != 0);
4252 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD && ir->comm_mode == ecmNO
4253 && !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) && !ETC_ANDERSEN(ir->etc))
4256 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4257 "rounding errors can lead to build up of kinetic energy of the center of mass");
4260 if (ir->epc == epcPARRINELLORAHMAN && ir->etc == etcNOSEHOOVER)
4263 for (int g = 0; g < ir->opts.ngtc; g++)
4265 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4267 if (ir->tau_p < 1.9 * tau_t_max)
4269 std::string message = gmx::formatString(
4270 "With %s T-coupling and %s p-coupling, "
4271 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4272 etcoupl_names[ir->etc], epcoupl_names[ir->epc], "tau-p", ir->tau_p, "tau-t",
4274 warning(wi, message.c_str());
4278 /* Check for pressure coupling with absolute position restraints */
4279 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4281 absolute_reference(ir, sys, TRUE, AbsRef);
4283 for (m = 0; m < DIM; m++)
4285 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4288 "You are using pressure coupling with absolute position restraints, "
4289 "this will give artifacts. Use the refcoord_scaling option.");
4297 aloopb = gmx_mtop_atomloop_block_init(sys);
4299 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4301 if (atom->q != 0 || atom->qB != 0)
4309 if (EEL_FULL(ir->coulombtype))
4312 "You are using full electrostatics treatment %s for a system without charges.\n"
4313 "This costs a lot of performance for just processing zeros, consider using %s "
4315 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4316 warning(wi, err_buf);
4321 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
4324 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4325 "You might want to consider using %s electrostatics.\n",
4327 warning_note(wi, err_buf);
4331 /* Check if combination rules used in LJ-PME are the same as in the force field */
4332 if (EVDW_PME(ir->vdwtype))
4334 check_combination_rules(ir, sys, wi);
4337 /* Generalized reaction field */
4338 if (ir->coulombtype == eelGRF_NOTUSED)
4341 "Generalized reaction-field electrostatics is no longer supported. "
4342 "You can use normal reaction-field instead and compute the reaction-field "
4343 "constant by hand.");
4347 for (int i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4349 for (m = 0; (m < DIM); m++)
4351 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4360 snew(mgrp, sys->groups.groups[SimulationAtomGroupType::Acceleration].size());
4361 for (const AtomProxy atomP : AtomRange(*sys))
4363 const t_atom& local = atomP.atom();
4364 int i = atomP.globalAtomNumber();
4365 mgrp[getGroupType(sys->groups, SimulationAtomGroupType::Acceleration, i)] += local.m;
4368 for (i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4370 for (m = 0; (m < DIM); m++)
4372 acc[m] += ir->opts.acc[i][m] * mgrp[i];
4376 for (m = 0; (m < DIM); m++)
4378 if (fabs(acc[m]) > 1e-6)
4380 const char* dim[DIM] = { "X", "Y", "Z" };
4381 fprintf(stderr, "Net Acceleration in %s direction, will %s be corrected\n", dim[m],
4382 ir->nstcomm != 0 ? "" : "not");
4383 if (ir->nstcomm != 0 && m < ndof_com(ir))
4387 (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4389 ir->opts.acc[i][m] -= acc[m];
4397 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0
4398 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4400 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4408 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4410 if (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0)
4412 absolute_reference(ir, sys, FALSE, AbsRef);
4413 for (m = 0; m < DIM; m++)
4415 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4418 "You are using an absolute reference for pulling, but the rest of "
4419 "the system does not have an absolute reference. This will lead to "
4428 for (i = 0; i < 3; i++)
4430 for (m = 0; m <= i; m++)
4432 if ((ir->epc != epcNO && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4434 for (c = 0; c < ir->pull->ncoord; c++)
4436 if (ir->pull->coord[c].eGeom == epullgDIRPBC && ir->pull->coord[c].vec[m] != 0)
4439 "Can not have dynamic box while using pull geometry '%s' "
4441 EPULLGEOM(ir->pull->coord[c].eGeom), 'x' + m);
4452 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4454 char warn_buf[STRLEN];
4457 ptr = check_box(ir->pbcType, box);
4460 warning_error(wi, ptr);
4463 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4465 if (ir->shake_tol <= 0.0)
4467 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4468 warning_error(wi, warn_buf);
4472 if ((ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4474 /* If we have Lincs constraints: */
4475 if (ir->eI == eiMD && ir->etc == etcNO && ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4478 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4479 warning_note(wi, warn_buf);
4482 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4485 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4487 warning_note(wi, warn_buf);
4489 if (ir->epc == epcMTTK)
4491 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4495 if (bHasAnyConstraints && ir->epc == epcMTTK)
4497 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4500 if (ir->LincsWarnAngle > 90.0)
4502 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4503 warning(wi, warn_buf);
4504 ir->LincsWarnAngle = 90.0;
4507 if (ir->pbcType != PbcType::No)
4509 if (ir->nstlist == 0)
4512 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4513 "atoms might cause the simulation to crash.");
4515 if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
4518 "ERROR: The cut-off length is longer than half the shortest box vector or "
4519 "longer than the smallest box diagonal element. Increase the box size or "
4520 "decrease rlist.\n");
4521 warning_error(wi, warn_buf);