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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, "The QMMM integration you are trying to use is no longer supported");
1402 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1406 /* interpret a number of doubles from a string and put them in an array,
1407 after allocating space for them.
1408 str = the input string
1409 n = the (pre-allocated) number of doubles read
1410 r = the output array of doubles. */
1411 static void parse_n_real(char* str, int* n, real** r, warninp_t wi)
1413 auto values = gmx::splitString(str);
1417 for (int i = 0; i < *n; i++)
1421 (*r)[i] = gmx::fromString<real>(values[i]);
1423 catch (gmx::GromacsException&)
1425 warning_error(wi, "Invalid value " + values[i]
1426 + " in string in mdp file. Expected a real number.");
1432 static void do_fep_params(t_inputrec* ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
1435 int i, j, max_n_lambda, nweights, nfep[efptNR];
1436 t_lambda* fep = ir->fepvals;
1437 t_expanded* expand = ir->expandedvals;
1438 real** count_fep_lambdas;
1439 bool bOneLambda = TRUE;
1441 snew(count_fep_lambdas, efptNR);
1443 /* FEP input processing */
1444 /* first, identify the number of lambda values for each type.
1445 All that are nonzero must have the same number */
1447 for (i = 0; i < efptNR; i++)
1449 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
1452 /* now, determine the number of components. All must be either zero, or equal. */
1455 for (i = 0; i < efptNR; i++)
1457 if (nfep[i] > max_n_lambda)
1459 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1460 must have the same number if its not zero.*/
1465 for (i = 0; i < efptNR; i++)
1469 ir->fepvals->separate_dvdl[i] = FALSE;
1471 else if (nfep[i] == max_n_lambda)
1473 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute
1474 the derivative with respect to the temperature currently */
1476 ir->fepvals->separate_dvdl[i] = TRUE;
1482 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1484 nfep[i], efpt_names[i], max_n_lambda);
1487 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1488 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1490 /* the number of lambdas is the number we've read in, which is either zero
1491 or the same for all */
1492 fep->n_lambda = max_n_lambda;
1494 /* allocate space for the array of lambda values */
1495 snew(fep->all_lambda, efptNR);
1496 /* if init_lambda is defined, we need to set lambda */
1497 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1499 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1501 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1502 for (i = 0; i < efptNR; i++)
1504 snew(fep->all_lambda[i], fep->n_lambda);
1505 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1508 for (j = 0; j < fep->n_lambda; j++)
1510 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1512 sfree(count_fep_lambdas[i]);
1515 sfree(count_fep_lambdas);
1517 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1518 internal bookkeeping -- for now, init_lambda */
1520 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1522 for (i = 0; i < fep->n_lambda; i++)
1524 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1528 /* check to see if only a single component lambda is defined, and soft core is defined.
1529 In this case, turn on coulomb soft core */
1531 if (max_n_lambda == 0)
1537 for (i = 0; i < efptNR; i++)
1539 if ((nfep[i] != 0) && (i != efptFEP))
1545 if ((bOneLambda) && (fep->sc_alpha > 0))
1547 fep->bScCoul = TRUE;
1550 /* Fill in the others with the efptFEP if they are not explicitly
1551 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1552 they are all zero. */
1554 for (i = 0; i < efptNR; i++)
1556 if ((nfep[i] == 0) && (i != efptFEP))
1558 for (j = 0; j < fep->n_lambda; j++)
1560 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1566 /* now read in the weights */
1567 parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
1570 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1572 else if (nweights != fep->n_lambda)
1574 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1575 nweights, fep->n_lambda);
1577 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1579 expand->nstexpanded = fep->nstdhdl;
1580 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1585 static void do_simtemp_params(t_inputrec* ir)
1588 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1589 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1592 template<typename T>
1593 void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
1596 for (const auto& input : inputs)
1600 outputs[i] = gmx::fromStdString<T>(input);
1602 catch (gmx::GromacsException&)
1604 auto message = gmx::formatString(
1605 "Invalid value for mdp option %s. %s should only consist of integers separated "
1608 warning_error(wi, message);
1614 static void convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, real* outputs)
1617 for (const auto& input : inputs)
1621 outputs[i] = gmx::fromString<real>(input);
1623 catch (gmx::GromacsException&)
1625 auto message = gmx::formatString(
1626 "Invalid value for mdp option %s. %s should only consist of real numbers "
1627 "separated by spaces.",
1629 warning_error(wi, message);
1635 static void convertRvecs(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, rvec* outputs)
1638 for (const auto& input : inputs)
1642 outputs[i][d] = gmx::fromString<real>(input);
1644 catch (gmx::GromacsException&)
1646 auto message = gmx::formatString(
1647 "Invalid value for mdp option %s. %s should only consist of real numbers "
1648 "separated by spaces.",
1650 warning_error(wi, message);
1661 static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
1663 opts->wall_atomtype[0] = nullptr;
1664 opts->wall_atomtype[1] = nullptr;
1666 ir->wall_atomtype[0] = -1;
1667 ir->wall_atomtype[1] = -1;
1668 ir->wall_density[0] = 0;
1669 ir->wall_density[1] = 0;
1673 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1674 if (wallAtomTypes.size() != size_t(ir->nwall))
1676 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %zu", ir->nwall,
1677 wallAtomTypes.size());
1679 for (int i = 0; i < ir->nwall; i++)
1681 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1684 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1686 auto wallDensity = gmx::splitString(wall_density);
1687 if (wallDensity.size() != size_t(ir->nwall))
1689 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %zu", ir->nwall,
1690 wallDensity.size());
1692 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1693 for (int i = 0; i < ir->nwall; i++)
1695 if (ir->wall_density[i] <= 0)
1697 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1704 static void add_wall_energrps(SimulationGroups* groups, int nwall, t_symtab* symtab)
1708 AtomGroupIndices* grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1709 for (int i = 0; i < nwall; i++)
1711 groups->groupNames.emplace_back(put_symtab(symtab, gmx::formatString("wall%d", i).c_str()));
1712 grps->emplace_back(groups->groupNames.size() - 1);
1717 static void read_expandedparams(std::vector<t_inpfile>* inp, t_expanded* expand, warninp_t wi)
1719 /* read expanded ensemble parameters */
1720 printStringNewline(inp, "expanded ensemble variables");
1721 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1722 expand->elamstats = get_eeenum(inp, "lmc-stats", elamstats_names, wi);
1723 expand->elmcmove = get_eeenum(inp, "lmc-move", elmcmove_names, wi);
1724 expand->elmceq = get_eeenum(inp, "lmc-weights-equil", elmceq_names, wi);
1725 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1726 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1727 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1728 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1729 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1730 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1731 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1732 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1733 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1734 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1735 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1736 expand->bSymmetrizedTMatrix =
1737 (get_eeenum(inp, "symmetrized-transition-matrix", yesno_names, wi) != 0);
1738 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1739 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1740 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1741 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1742 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1743 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1744 expand->bWLoneovert = (get_eeenum(inp, "wl-oneovert", yesno_names, wi) != 0);
1747 /*! \brief Return whether an end state with the given coupling-lambda
1748 * value describes fully-interacting VDW.
1750 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1751 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1753 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1755 return (couple_lambda_value == ecouplamVDW || couple_lambda_value == ecouplamVDWQ);
1761 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1764 explicit MdpErrorHandler(warninp_t wi) : wi_(wi), mapping_(nullptr) {}
1766 void setBackMapping(const gmx::IKeyValueTreeBackMapping& mapping) { mapping_ = &mapping; }
1768 bool onError(gmx::UserInputError* ex, const gmx::KeyValueTreePath& context) override
1771 gmx::formatString("Error in mdp option \"%s\":", getOptionName(context).c_str()));
1772 std::string message = gmx::formatExceptionMessageToString(*ex);
1773 warning_error(wi_, message.c_str());
1778 std::string getOptionName(const gmx::KeyValueTreePath& context)
1780 if (mapping_ != nullptr)
1782 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1783 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1786 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1791 const gmx::IKeyValueTreeBackMapping* mapping_;
1796 void get_ir(const char* mdparin,
1797 const char* mdparout,
1798 gmx::MDModules* mdModules,
1801 WriteMdpHeader writeMdpHeader,
1805 double dumdub[2][6];
1807 char warn_buf[STRLEN];
1808 t_lambda* fep = ir->fepvals;
1809 t_expanded* expand = ir->expandedvals;
1811 const char* no_names[] = { "no", nullptr };
1813 init_inputrec_strings();
1814 gmx::TextInputFile stream(mdparin);
1815 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1817 snew(dumstr[0], STRLEN);
1818 snew(dumstr[1], STRLEN);
1820 /* ignore the following deprecated commands */
1821 replace_inp_entry(inp, "title", nullptr);
1822 replace_inp_entry(inp, "cpp", nullptr);
1823 replace_inp_entry(inp, "domain-decomposition", nullptr);
1824 replace_inp_entry(inp, "andersen-seed", nullptr);
1825 replace_inp_entry(inp, "dihre", nullptr);
1826 replace_inp_entry(inp, "dihre-fc", nullptr);
1827 replace_inp_entry(inp, "dihre-tau", nullptr);
1828 replace_inp_entry(inp, "nstdihreout", nullptr);
1829 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1830 replace_inp_entry(inp, "optimize-fft", nullptr);
1831 replace_inp_entry(inp, "adress_type", nullptr);
1832 replace_inp_entry(inp, "adress_const_wf", nullptr);
1833 replace_inp_entry(inp, "adress_ex_width", nullptr);
1834 replace_inp_entry(inp, "adress_hy_width", nullptr);
1835 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1836 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1837 replace_inp_entry(inp, "adress_site", nullptr);
1838 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1839 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1840 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1841 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1842 replace_inp_entry(inp, "rlistlong", nullptr);
1843 replace_inp_entry(inp, "nstcalclr", nullptr);
1844 replace_inp_entry(inp, "pull-print-com2", nullptr);
1845 replace_inp_entry(inp, "gb-algorithm", nullptr);
1846 replace_inp_entry(inp, "nstgbradii", nullptr);
1847 replace_inp_entry(inp, "rgbradii", nullptr);
1848 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1849 replace_inp_entry(inp, "gb-saltconc", nullptr);
1850 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1851 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1852 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1853 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1854 replace_inp_entry(inp, "sa-algorithm", nullptr);
1855 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1856 replace_inp_entry(inp, "ns-type", nullptr);
1858 /* replace the following commands with the clearer new versions*/
1859 replace_inp_entry(inp, "unconstrained-start", "continuation");
1860 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1861 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1862 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1863 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1864 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1865 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1867 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1868 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1869 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1870 setStringEntry(&inp, "include", opts->include, nullptr);
1871 printStringNoNewline(
1872 &inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1873 setStringEntry(&inp, "define", opts->define, nullptr);
1875 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1876 ir->eI = get_eeenum(&inp, "integrator", ei_names, wi);
1877 printStringNoNewline(&inp, "Start time and timestep in ps");
1878 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1879 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1880 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1881 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1882 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1883 printStringNoNewline(
1884 &inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1885 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1886 printStringNoNewline(&inp, "mode for center of mass motion removal");
1887 ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
1888 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
1889 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
1890 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
1891 setStringEntry(&inp, "comm-grps", is->vcm, nullptr);
1893 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
1894 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
1895 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
1896 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
1899 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
1900 printStringNoNewline(&inp, "Force tolerance and initial step-size");
1901 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
1902 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
1903 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
1904 ir->niter = get_eint(&inp, "niter", 20, wi);
1905 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
1906 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
1907 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
1908 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
1909 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
1911 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
1912 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
1914 /* Output options */
1915 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
1916 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
1917 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
1918 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
1919 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
1920 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
1921 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
1922 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
1923 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
1924 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
1925 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
1926 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
1927 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
1928 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
1929 printStringNoNewline(&inp, "default, all atoms will be written.");
1930 setStringEntry(&inp, "compressed-x-grps", is->x_compressed_groups, nullptr);
1931 printStringNoNewline(&inp, "Selection of energy groups");
1932 setStringEntry(&inp, "energygrps", is->energy, nullptr);
1934 /* Neighbor searching */
1935 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
1936 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
1937 ir->cutoff_scheme = get_eeenum(&inp, "cutoff-scheme", ecutscheme_names, wi);
1938 printStringNoNewline(&inp, "nblist update frequency");
1939 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
1940 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
1941 // TODO This conversion should be removed when proper std:string handling will be added to get_eeenum(...), etc.
1942 std::vector<const char*> pbcTypesNamesChar;
1943 for (const auto& pbcTypeName : c_pbcTypeNames)
1945 pbcTypesNamesChar.push_back(pbcTypeName.c_str());
1947 ir->pbcType = static_cast<PbcType>(get_eeenum(&inp, "pbc", pbcTypesNamesChar.data(), wi));
1948 ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi) != 0;
1949 printStringNoNewline(&inp,
1950 "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1951 printStringNoNewline(&inp, "a value of -1 means: use rlist");
1952 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
1953 printStringNoNewline(&inp, "nblist cut-off");
1954 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
1955 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
1957 /* Electrostatics */
1958 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
1959 printStringNoNewline(&inp, "Method for doing electrostatics");
1960 ir->coulombtype = get_eeenum(&inp, "coulombtype", eel_names, wi);
1961 ir->coulomb_modifier = get_eeenum(&inp, "coulomb-modifier", eintmod_names, wi);
1962 printStringNoNewline(&inp, "cut-off lengths");
1963 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
1964 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
1965 printStringNoNewline(&inp,
1966 "Relative dielectric constant for the medium and the reaction field");
1967 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
1968 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
1969 printStringNoNewline(&inp, "Method for doing Van der Waals");
1970 ir->vdwtype = get_eeenum(&inp, "vdw-type", evdw_names, wi);
1971 ir->vdw_modifier = get_eeenum(&inp, "vdw-modifier", eintmod_names, wi);
1972 printStringNoNewline(&inp, "cut-off lengths");
1973 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
1974 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
1975 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
1976 ir->eDispCorr = get_eeenum(&inp, "DispCorr", edispc_names, wi);
1977 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
1978 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
1979 printStringNoNewline(&inp, "Separate tables between energy group pairs");
1980 setStringEntry(&inp, "energygrp-table", is->egptable, nullptr);
1981 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
1982 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
1983 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
1984 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
1985 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
1986 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
1987 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
1988 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
1989 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
1990 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
1991 ir->ljpme_combination_rule = get_eeenum(&inp, "lj-pme-comb-rule", eljpme_names, wi);
1992 ir->ewald_geometry = get_eeenum(&inp, "ewald-geometry", eewg_names, wi);
1993 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
1995 /* Implicit solvation is no longer supported, but we need grompp
1996 to be able to refuse old .mdp files that would have built a tpr
1997 to run it. Thus, only "no" is accepted. */
1998 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
2000 /* Coupling stuff */
2001 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
2002 printStringNoNewline(&inp, "Temperature coupling");
2003 ir->etc = get_eeenum(&inp, "tcoupl", etcoupl_names, wi);
2004 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
2005 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
2006 ir->bPrintNHChains = (get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi) != 0);
2007 printStringNoNewline(&inp, "Groups to couple separately");
2008 setStringEntry(&inp, "tc-grps", is->tcgrps, nullptr);
2009 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
2010 setStringEntry(&inp, "tau-t", is->tau_t, nullptr);
2011 setStringEntry(&inp, "ref-t", is->ref_t, nullptr);
2012 printStringNoNewline(&inp, "pressure coupling");
2013 ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
2014 ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
2015 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
2016 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
2017 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
2018 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
2019 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
2020 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
2021 ir->refcoord_scaling = get_eeenum(&inp, "refcoord-scaling", erefscaling_names, wi);
2024 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2025 ir->bQMMM = (get_eeenum(&inp, "QMMM", yesno_names, wi) != 0);
2026 printStringNoNewline(&inp, "Groups treated Quantum Mechanically");
2027 setStringEntry(&inp, "QMMM-grps", is->QMMM, nullptr);
2028 printStringNoNewline(&inp, "QM method");
2029 setStringEntry(&inp, "QMmethod", is->QMmethod, nullptr);
2030 printStringNoNewline(&inp, "QMMM scheme");
2031 const char* noQMMMSchemeName = "normal";
2032 get_eeenum(&inp, "QMMMscheme", &noQMMMSchemeName, wi);
2033 printStringNoNewline(&inp, "QM basisset");
2034 setStringEntry(&inp, "QMbasis", is->QMbasis, nullptr);
2035 printStringNoNewline(&inp, "QM charge");
2036 setStringEntry(&inp, "QMcharge", is->QMcharge, nullptr);
2037 printStringNoNewline(&inp, "QM multiplicity");
2038 setStringEntry(&inp, "QMmult", is->QMmult, nullptr);
2039 printStringNoNewline(&inp, "Surface Hopping");
2040 setStringEntry(&inp, "SH", is->bSH, nullptr);
2041 printStringNoNewline(&inp, "CAS space options");
2042 setStringEntry(&inp, "CASorbitals", is->CASorbitals, nullptr);
2043 setStringEntry(&inp, "CASelectrons", is->CASelectrons, nullptr);
2044 setStringEntry(&inp, "SAon", is->SAon, nullptr);
2045 setStringEntry(&inp, "SAoff", is->SAoff, nullptr);
2046 setStringEntry(&inp, "SAsteps", is->SAsteps, nullptr);
2047 printStringNoNewline(&inp, "Scale factor for MM charges");
2048 get_ereal(&inp, "MMChargeScaleFactor", 1.0, wi);
2050 /* Simulated annealing */
2051 printStringNewline(&inp, "SIMULATED ANNEALING");
2052 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2053 setStringEntry(&inp, "annealing", is->anneal, nullptr);
2054 printStringNoNewline(&inp,
2055 "Number of time points to use for specifying annealing in each group");
2056 setStringEntry(&inp, "annealing-npoints", is->anneal_npoints, nullptr);
2057 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2058 setStringEntry(&inp, "annealing-time", is->anneal_time, nullptr);
2059 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2060 setStringEntry(&inp, "annealing-temp", is->anneal_temp, nullptr);
2063 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2064 opts->bGenVel = (get_eeenum(&inp, "gen-vel", yesno_names, wi) != 0);
2065 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2066 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2069 printStringNewline(&inp, "OPTIONS FOR BONDS");
2070 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2071 printStringNoNewline(&inp, "Type of constraint algorithm");
2072 ir->eConstrAlg = get_eeenum(&inp, "constraint-algorithm", econstr_names, wi);
2073 printStringNoNewline(&inp, "Do not constrain the start configuration");
2074 ir->bContinuation = (get_eeenum(&inp, "continuation", yesno_names, wi) != 0);
2075 printStringNoNewline(&inp,
2076 "Use successive overrelaxation to reduce the number of shake iterations");
2077 ir->bShakeSOR = (get_eeenum(&inp, "Shake-SOR", yesno_names, wi) != 0);
2078 printStringNoNewline(&inp, "Relative tolerance of shake");
2079 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2080 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2081 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2082 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2083 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2084 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2085 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2086 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2087 printStringNoNewline(&inp, "rotates over more degrees than");
2088 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2089 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2090 opts->bMorse = (get_eeenum(&inp, "morse", yesno_names, wi) != 0);
2092 /* Energy group exclusions */
2093 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2094 printStringNoNewline(
2095 &inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2096 setStringEntry(&inp, "energygrp-excl", is->egpexcl, nullptr);
2099 printStringNewline(&inp, "WALLS");
2100 printStringNoNewline(
2101 &inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2102 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2103 ir->wall_type = get_eeenum(&inp, "wall-type", ewt_names, wi);
2104 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2105 setStringEntry(&inp, "wall-atomtype", is->wall_atomtype, nullptr);
2106 setStringEntry(&inp, "wall-density", is->wall_density, nullptr);
2107 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2110 printStringNewline(&inp, "COM PULLING");
2111 ir->bPull = (get_eeenum(&inp, "pull", yesno_names, wi) != 0);
2115 is->pull_grp = read_pullparams(&inp, ir->pull, wi);
2119 NOTE: needs COM pulling input */
2120 printStringNewline(&inp, "AWH biasing");
2121 ir->bDoAwh = (get_eeenum(&inp, "awh", yesno_names, wi) != 0);
2124 ir->awhParams = gmx::readAwhParams(&inp, wi);
2127 /* Enforced rotation */
2128 printStringNewline(&inp, "ENFORCED ROTATION");
2129 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2130 ir->bRot = (get_eeenum(&inp, "rotation", yesno_names, wi) != 0);
2134 is->rot_grp = read_rotparams(&inp, ir->rot, wi);
2137 /* Interactive MD */
2139 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2140 setStringEntry(&inp, "IMD-group", is->imd_grp, nullptr);
2141 if (is->imd_grp[0] != '\0')
2148 printStringNewline(&inp, "NMR refinement stuff");
2149 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2150 ir->eDisre = get_eeenum(&inp, "disre", edisre_names, wi);
2151 printStringNoNewline(
2152 &inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2153 ir->eDisreWeighting = get_eeenum(&inp, "disre-weighting", edisreweighting_names, wi);
2154 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2155 ir->bDisreMixed = (get_eeenum(&inp, "disre-mixed", yesno_names, wi) != 0);
2156 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2157 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2158 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2159 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2160 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2161 opts->bOrire = (get_eeenum(&inp, "orire", yesno_names, wi) != 0);
2162 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2163 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2164 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2165 setStringEntry(&inp, "orire-fitgrp", is->orirefitgrp, nullptr);
2166 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2167 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2169 /* free energy variables */
2170 printStringNewline(&inp, "Free energy variables");
2171 ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
2172 setStringEntry(&inp, "couple-moltype", is->couple_moltype, nullptr);
2173 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2174 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2175 opts->bCoupleIntra = (get_eeenum(&inp, "couple-intramol", yesno_names, wi) != 0);
2177 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2179 it was not entered */
2180 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2181 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2182 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2183 setStringEntry(&inp, "fep-lambdas", is->fep_lambda[efptFEP], nullptr);
2184 setStringEntry(&inp, "mass-lambdas", is->fep_lambda[efptMASS], nullptr);
2185 setStringEntry(&inp, "coul-lambdas", is->fep_lambda[efptCOUL], nullptr);
2186 setStringEntry(&inp, "vdw-lambdas", is->fep_lambda[efptVDW], nullptr);
2187 setStringEntry(&inp, "bonded-lambdas", is->fep_lambda[efptBONDED], nullptr);
2188 setStringEntry(&inp, "restraint-lambdas", is->fep_lambda[efptRESTRAINT], nullptr);
2189 setStringEntry(&inp, "temperature-lambdas", is->fep_lambda[efptTEMPERATURE], nullptr);
2190 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2191 setStringEntry(&inp, "init-lambda-weights", is->lambda_weights, nullptr);
2192 fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
2193 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2194 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2195 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2196 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2197 fep->bScCoul = (get_eeenum(&inp, "sc-coul", yesno_names, wi) != 0);
2198 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2199 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2200 fep->separate_dhdl_file = get_eeenum(&inp, "separate-dhdl-file", separate_dhdl_file_names, wi);
2201 fep->dhdl_derivatives = get_eeenum(&inp, "dhdl-derivatives", dhdl_derivatives_names, wi);
2202 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2203 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2205 /* Non-equilibrium MD stuff */
2206 printStringNewline(&inp, "Non-equilibrium MD stuff");
2207 setStringEntry(&inp, "acc-grps", is->accgrps, nullptr);
2208 setStringEntry(&inp, "accelerate", is->acc, nullptr);
2209 setStringEntry(&inp, "freezegrps", is->freeze, nullptr);
2210 setStringEntry(&inp, "freezedim", is->frdim, nullptr);
2211 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2212 setStringEntry(&inp, "deform", is->deform, nullptr);
2214 /* simulated tempering variables */
2215 printStringNewline(&inp, "simulated tempering variables");
2216 ir->bSimTemp = (get_eeenum(&inp, "simulated-tempering", yesno_names, wi) != 0);
2217 ir->simtempvals->eSimTempScale = get_eeenum(&inp, "simulated-tempering-scaling", esimtemp_names, wi);
2218 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2219 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2221 /* expanded ensemble variables */
2222 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2224 read_expandedparams(&inp, expand, wi);
2227 /* Electric fields */
2229 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2230 gmx::KeyValueTreeTransformer transform;
2231 transform.rules()->addRule().keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2232 mdModules->initMdpTransform(transform.rules());
2233 for (const auto& path : transform.mappedPaths())
2235 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2236 mark_einp_set(inp, path[0].c_str());
2238 MdpErrorHandler errorHandler(wi);
2239 auto result = transform.transform(convertedValues, &errorHandler);
2240 ir->params = new gmx::KeyValueTreeObject(result.object());
2241 mdModules->adjustInputrecBasedOnModules(ir);
2242 errorHandler.setBackMapping(result.backMapping());
2243 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2246 /* Ion/water position swapping ("computational electrophysiology") */
2247 printStringNewline(&inp,
2248 "Ion/water position swapping for computational electrophysiology setups");
2249 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2250 ir->eSwapCoords = get_eeenum(&inp, "swapcoords", eSwapTypes_names, wi);
2251 if (ir->eSwapCoords != eswapNO)
2258 printStringNoNewline(&inp, "Swap attempt frequency");
2259 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2260 printStringNoNewline(&inp, "Number of ion types to be controlled");
2261 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2264 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2266 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2267 snew(ir->swap->grp, ir->swap->ngrp);
2268 for (i = 0; i < ir->swap->ngrp; i++)
2270 snew(ir->swap->grp[i].molname, STRLEN);
2272 printStringNoNewline(&inp,
2273 "Two index groups that contain the compartment-partitioning atoms");
2274 setStringEntry(&inp, "split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2275 setStringEntry(&inp, "split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2276 printStringNoNewline(&inp,
2277 "Use center of mass of split groups (yes/no), otherwise center of "
2278 "geometry is used");
2279 ir->swap->massw_split[0] = (get_eeenum(&inp, "massw-split0", yesno_names, wi) != 0);
2280 ir->swap->massw_split[1] = (get_eeenum(&inp, "massw-split1", yesno_names, wi) != 0);
2282 printStringNoNewline(&inp, "Name of solvent molecules");
2283 setStringEntry(&inp, "solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2285 printStringNoNewline(&inp,
2286 "Split cylinder: radius, upper and lower extension (nm) (this will "
2287 "define the channels)");
2288 printStringNoNewline(&inp,
2289 "Note that the split cylinder settings do not have an influence on "
2290 "the swapping protocol,");
2291 printStringNoNewline(
2293 "however, if correctly defined, the permeation events are recorded per channel");
2294 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2295 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2296 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2297 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2298 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2299 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2301 printStringNoNewline(
2303 "Average the number of ions per compartment over these many swap attempt steps");
2304 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2306 printStringNoNewline(
2307 &inp, "Names of the ion types that can be exchanged with solvent molecules,");
2308 printStringNoNewline(
2309 &inp, "and the requested number of ions of this type in compartments A and B");
2310 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2311 for (i = 0; i < nIonTypes; i++)
2313 int ig = eSwapFixedGrpNR + i;
2315 sprintf(buf, "iontype%d-name", i);
2316 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2317 sprintf(buf, "iontype%d-in-A", i);
2318 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2319 sprintf(buf, "iontype%d-in-B", i);
2320 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2323 printStringNoNewline(
2325 "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2326 printStringNoNewline(
2328 "at maximum distance (= bulk concentration) to the split group layers. However,");
2329 printStringNoNewline(&inp,
2330 "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk "
2331 "layer from the middle at 0.0");
2332 printStringNoNewline(&inp,
2333 "towards one of the compartment-partitioning layers (at +/- 1.0).");
2334 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2335 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2336 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2337 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0))
2339 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2342 printStringNoNewline(
2343 &inp, "Start to swap ions if threshold difference to requested count is reached");
2344 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2347 /* AdResS is no longer supported, but we need grompp to be able to
2348 refuse to process old .mdp files that used it. */
2349 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2351 /* User defined thingies */
2352 printStringNewline(&inp, "User defined thingies");
2353 setStringEntry(&inp, "user1-grps", is->user1, nullptr);
2354 setStringEntry(&inp, "user2-grps", is->user2, nullptr);
2355 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2356 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2357 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2358 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2359 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2360 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2361 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2362 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2366 gmx::TextOutputFile stream(mdparout);
2367 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2369 // Transform module data into a flat key-value tree for output.
2370 gmx::KeyValueTreeBuilder builder;
2371 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2372 mdModules->buildMdpOutput(&builderObject);
2374 gmx::TextWriter writer(&stream);
2375 writeKeyValueTreeAsMdp(&writer, builder.build());
2380 /* Process options if necessary */
2381 for (m = 0; m < 2; m++)
2383 for (i = 0; i < 2 * DIM; i++)
2392 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2396 "Pressure coupling incorrect number of values (I need exactly 1)");
2398 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2400 case epctSEMIISOTROPIC:
2401 case epctSURFACETENSION:
2402 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2406 "Pressure coupling incorrect number of values (I need exactly 2)");
2408 dumdub[m][YY] = dumdub[m][XX];
2410 case epctANISOTROPIC:
2411 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf", &(dumdub[m][XX]), &(dumdub[m][YY]),
2412 &(dumdub[m][ZZ]), &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5]))
2417 "Pressure coupling incorrect number of values (I need exactly 6)");
2421 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2422 epcoupltype_names[ir->epct]);
2426 clear_mat(ir->ref_p);
2427 clear_mat(ir->compress);
2428 for (i = 0; i < DIM; i++)
2430 ir->ref_p[i][i] = dumdub[1][i];
2431 ir->compress[i][i] = dumdub[0][i];
2433 if (ir->epct == epctANISOTROPIC)
2435 ir->ref_p[XX][YY] = dumdub[1][3];
2436 ir->ref_p[XX][ZZ] = dumdub[1][4];
2437 ir->ref_p[YY][ZZ] = dumdub[1][5];
2438 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2441 "All off-diagonal reference pressures are non-zero. Are you sure you want to "
2442 "apply a threefold shear stress?\n");
2444 ir->compress[XX][YY] = dumdub[0][3];
2445 ir->compress[XX][ZZ] = dumdub[0][4];
2446 ir->compress[YY][ZZ] = dumdub[0][5];
2447 for (i = 0; i < DIM; i++)
2449 for (m = 0; m < i; m++)
2451 ir->ref_p[i][m] = ir->ref_p[m][i];
2452 ir->compress[i][m] = ir->compress[m][i];
2457 if (ir->comm_mode == ecmNO)
2462 opts->couple_moltype = nullptr;
2463 if (strlen(is->couple_moltype) > 0)
2465 if (ir->efep != efepNO)
2467 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2468 if (opts->couple_lam0 == opts->couple_lam1)
2470 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2472 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
2476 "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
2483 "Free energy is turned off, so we will not decouple the molecule listed "
2487 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2488 if (ir->efep != efepNO)
2490 if (fep->delta_lambda > 0)
2492 ir->efep = efepSLOWGROWTH;
2496 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2498 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2500 "Old option for dhdl-print-energy given: "
2501 "changing \"yes\" to \"total\"\n");
2504 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2506 /* always print out the energy to dhdl if we are doing
2507 expanded ensemble, since we need the total energy for
2508 analysis if the temperature is changing. In some
2509 conditions one may only want the potential energy, so
2510 we will allow that if the appropriate mdp setting has
2511 been enabled. Otherwise, total it is:
2513 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2516 if ((ir->efep != efepNO) || ir->bSimTemp)
2518 ir->bExpanded = FALSE;
2519 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2521 ir->bExpanded = TRUE;
2523 do_fep_params(ir, is->fep_lambda, is->lambda_weights, wi);
2524 if (ir->bSimTemp) /* done after fep params */
2526 do_simtemp_params(ir);
2529 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2530 * setup and not on the old way of specifying the free-energy setup,
2531 * we should check for using soft-core when not needed, since that
2532 * can complicate the sampling significantly.
2533 * Note that we only check for the automated coupling setup.
2534 * If the (advanced) user does FEP through manual topology changes,
2535 * this check will not be triggered.
2537 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 && ir->fepvals->sc_alpha != 0
2538 && (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
2541 "You are using soft-core interactions while the Van der Waals interactions are "
2542 "not decoupled (note that the sc-coul option is only active when using lambda "
2543 "states). Although this will not lead to errors, you will need much more "
2544 "sampling than without soft-core interactions. Consider using sc-alpha=0.");
2549 ir->fepvals->n_lambda = 0;
2552 /* WALL PARAMETERS */
2554 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts, wi);
2556 /* ORIENTATION RESTRAINT PARAMETERS */
2558 if (opts->bOrire && gmx::splitString(is->orirefitgrp).size() != 1)
2560 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2563 /* DEFORMATION PARAMETERS */
2565 clear_mat(ir->deform);
2566 for (i = 0; i < 6; i++)
2571 double gmx_unused canary;
2572 int ndeform = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf %lf", &(dumdub[0][0]), &(dumdub[0][1]),
2573 &(dumdub[0][2]), &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]), &canary);
2575 if (strlen(is->deform) > 0 && ndeform != 6)
2578 wi, gmx::formatString(
2579 "Cannot parse exactly 6 box deformation velocities from string '%s'", is->deform)
2582 for (i = 0; i < 3; i++)
2584 ir->deform[i][i] = dumdub[0][i];
2586 ir->deform[YY][XX] = dumdub[0][3];
2587 ir->deform[ZZ][XX] = dumdub[0][4];
2588 ir->deform[ZZ][YY] = dumdub[0][5];
2589 if (ir->epc != epcNO)
2591 for (i = 0; i < 3; i++)
2593 for (j = 0; j <= i; j++)
2595 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2597 warning_error(wi, "A box element has deform set and compressibility > 0");
2601 for (i = 0; i < 3; i++)
2603 for (j = 0; j < i; j++)
2605 if (ir->deform[i][j] != 0)
2607 for (m = j; m < DIM; m++)
2609 if (ir->compress[m][j] != 0)
2612 "An off-diagonal box element has deform set while "
2613 "compressibility > 0 for the same component of another box "
2614 "vector, this might lead to spurious periodicity effects.");
2615 warning(wi, warn_buf);
2623 /* Ion/water position swapping checks */
2624 if (ir->eSwapCoords != eswapNO)
2626 if (ir->swap->nstswap < 1)
2628 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2630 if (ir->swap->nAverage < 1)
2632 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2634 if (ir->swap->threshold < 1.0)
2636 warning_error(wi, "Ion count threshold must be at least 1.\n");
2642 gmx::checkAwhParams(ir->awhParams, ir, wi);
2649 /* We would like gn to be const as well, but C doesn't allow this */
2650 /* TODO this is utility functionality (search for the index of a
2651 string in a collection), so should be refactored and located more
2653 int search_string(const char* s, int ng, char* gn[])
2657 for (i = 0; (i < ng); i++)
2659 if (gmx_strcasecmp(s, gn[i]) == 0)
2666 "Group %s referenced in the .mdp file was not found in the index file.\n"
2667 "Group names must match either [moleculetype] names or custom index group\n"
2668 "names, in which case you must supply an index file to the '-n' option\n"
2673 static void do_numbering(int natoms,
2674 SimulationGroups* groups,
2675 gmx::ArrayRef<std::string> groupsFromMdpFile,
2678 SimulationAtomGroupType gtype,
2684 unsigned short* cbuf;
2685 AtomGroupIndices* grps = &(groups->groups[gtype]);
2686 int j, gid, aj, ognr, ntot = 0;
2688 char warn_buf[STRLEN];
2690 title = shortName(gtype);
2693 /* Mark all id's as not set */
2694 for (int i = 0; (i < natoms); i++)
2699 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2701 /* Lookup the group name in the block structure */
2702 gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2703 if ((grptp != egrptpONE) || (i == 0))
2705 grps->emplace_back(gid);
2708 /* Now go over the atoms in the group */
2709 for (j = block->index[gid]; (j < block->index[gid + 1]); j++)
2714 /* Range checking */
2715 if ((aj < 0) || (aj >= natoms))
2717 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2719 /* Lookup up the old group number */
2723 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title,
2728 /* Store the group number in buffer */
2729 if (grptp == egrptpONE)
2742 /* Now check whether we have done all atoms */
2745 if (grptp == egrptpALL)
2747 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2749 else if (grptp == egrptpPART)
2751 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2752 warning_note(wi, warn_buf);
2754 /* Assign all atoms currently unassigned to a rest group */
2755 for (j = 0; (j < natoms); j++)
2757 if (cbuf[j] == NOGID)
2759 cbuf[j] = grps->size();
2762 if (grptp != egrptpPART)
2766 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title,
2769 /* Add group name "rest" */
2770 grps->emplace_back(restnm);
2772 /* Assign the rest name to all atoms not currently assigned to a group */
2773 for (j = 0; (j < natoms); j++)
2775 if (cbuf[j] == NOGID)
2777 // group size was not updated before this here, so need to use -1.
2778 cbuf[j] = grps->size() - 1;
2784 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2786 /* All atoms are part of one (or no) group, no index required */
2787 groups->groupNumbers[gtype].clear();
2791 for (int j = 0; (j < natoms); j++)
2793 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2800 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
2803 pull_params_t* pull;
2804 int natoms, imin, jmin;
2805 int * nrdf2, *na_vcm, na_tot;
2806 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2811 * First calc 3xnr-atoms for each group
2812 * then subtract half a degree of freedom for each constraint
2814 * Only atoms and nuclei contribute to the degrees of freedom...
2819 const SimulationGroups& groups = mtop->groups;
2820 natoms = mtop->natoms;
2822 /* Allocate one more for a possible rest group */
2823 /* We need to sum degrees of freedom into doubles,
2824 * since floats give too low nrdf's above 3 million atoms.
2826 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
2827 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2828 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2829 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2830 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2832 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
2836 for (gmx::index i = 0;
2837 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; i++)
2840 clear_ivec(dof_vcm[i]);
2842 nrdf_vcm_sub[i] = 0;
2844 snew(nrdf2, natoms);
2845 for (const AtomProxy atomP : AtomRange(*mtop))
2847 const t_atom& local = atomP.atom();
2848 int i = atomP.globalAtomNumber();
2850 if (local.ptype == eptAtom || local.ptype == eptNucleus)
2852 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
2853 for (int d = 0; d < DIM; d++)
2855 if (opts->nFreeze[g][d] == 0)
2857 /* Add one DOF for particle i (counted as 2*1) */
2859 /* VCM group i has dim d as a DOF */
2860 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
2864 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
2866 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
2872 for (const gmx_molblock_t& molb : mtop->molblock)
2874 const gmx_moltype_t& molt = mtop->moltype[molb.type];
2875 const t_atom* atom = molt.atoms.atom;
2876 for (int mol = 0; mol < molb.nmol; mol++)
2878 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2880 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
2881 for (int i = 0; i < molt.ilist[ftype].size();)
2883 /* Subtract degrees of freedom for the constraints,
2884 * if the particles still have degrees of freedom left.
2885 * If one of the particles is a vsite or a shell, then all
2886 * constraint motion will go there, but since they do not
2887 * contribute to the constraints the degrees of freedom do not
2890 int ai = as + ia[i + 1];
2891 int aj = as + ia[i + 2];
2892 if (((atom[ia[i + 1]].ptype == eptNucleus) || (atom[ia[i + 1]].ptype == eptAtom))
2893 && ((atom[ia[i + 2]].ptype == eptNucleus) || (atom[ia[i + 2]].ptype == eptAtom)))
2911 imin = std::min(imin, nrdf2[ai]);
2912 jmin = std::min(jmin, nrdf2[aj]);
2915 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2917 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
2919 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2921 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
2924 i += interaction_function[ftype].nratoms + 1;
2927 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
2928 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
2930 /* Subtract 1 dof from every atom in the SETTLE */
2931 for (int j = 0; j < 3; j++)
2933 int ai = as + ia[i + 1 + j];
2934 imin = std::min(2, nrdf2[ai]);
2936 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2938 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2943 as += molt.atoms.nr;
2949 /* Correct nrdf for the COM constraints.
2950 * We correct using the TC and VCM group of the first atom
2951 * in the reference and pull group. If atoms in one pull group
2952 * belong to different TC or VCM groups it is anyhow difficult
2953 * to determine the optimal nrdf assignment.
2957 for (int i = 0; i < pull->ncoord; i++)
2959 if (pull->coord[i].eType != epullCONSTRAINT)
2966 for (int j = 0; j < 2; j++)
2968 const t_pull_group* pgrp;
2970 pgrp = &pull->group[pull->coord[i].group[j]];
2974 /* Subtract 1/2 dof from each group */
2975 int ai = pgrp->ind[0];
2976 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2978 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2980 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
2983 "Center of mass pulling constraints caused the number of degrees "
2984 "of freedom for temperature coupling group %s to be negative",
2985 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
2986 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
2991 /* We need to subtract the whole DOF from group j=1 */
2998 if (ir->nstcomm != 0)
3000 GMX_RELEASE_ASSERT(!groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty(),
3001 "Expect at least one group when removing COM motion");
3003 /* We remove COM motion up to dim ndof_com() */
3004 const int ndim_rm_vcm = ndof_com(ir);
3006 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3007 * the number of degrees of freedom in each vcm group when COM
3008 * translation is removed and 6 when rotation is removed as well.
3009 * Note that we do not and should not include the rest group here.
3011 for (gmx::index j = 0;
3012 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]); j++)
3014 switch (ir->comm_mode)
3017 case ecmLINEAR_ACCELERATION_CORRECTION:
3018 nrdf_vcm_sub[j] = 0;
3019 for (int d = 0; d < ndim_rm_vcm; d++)
3027 case ecmANGULAR: nrdf_vcm_sub[j] = 6; break;
3028 default: gmx_incons("Checking comm_mode");
3032 for (gmx::index i = 0;
3033 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
3035 /* Count the number of atoms of TC group i for every VCM group */
3036 for (gmx::index j = 0;
3037 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3042 for (int ai = 0; ai < natoms; ai++)
3044 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3046 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3050 /* Correct for VCM removal according to the fraction of each VCM
3051 * group present in this TC group.
3053 nrdf_uc = nrdf_tc[i];
3055 for (gmx::index j = 0;
3056 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3058 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3060 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3061 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3066 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3068 opts->nrdf[i] = nrdf_tc[i];
3069 if (opts->nrdf[i] < 0)
3073 fprintf(stderr, "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3074 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]], opts->nrdf[i]);
3082 sfree(nrdf_vcm_sub);
3085 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3087 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3088 * But since this is much larger than STRLEN, such a line can not be parsed.
3089 * The real maximum is the number of names that fit in a string: STRLEN/2.
3091 #define EGP_MAX (STRLEN / 2)
3095 auto names = gmx::splitString(val);
3096 if (names.size() % 2 != 0)
3098 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3100 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3102 for (size_t i = 0; i < names.size() / 2; i++)
3104 // TODO this needs to be replaced by a solution using std::find_if
3108 names[2 * i].c_str(),
3109 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3115 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3120 names[2 * i + 1].c_str(),
3121 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3127 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3129 if ((j < nr) && (k < nr))
3131 ir->opts.egp_flags[nr * j + k] |= flag;
3132 ir->opts.egp_flags[nr * k + j] |= flag;
3141 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3143 int ig = -1, i = 0, gind;
3147 /* Just a quick check here, more thorough checks are in mdrun */
3148 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3150 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3153 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3154 for (ig = 0; ig < swap->ngrp; ig++)
3156 swapg = &swap->grp[ig];
3157 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3158 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3162 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3163 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap", swap->grp[ig].molname, swapg->nat);
3164 snew(swapg->ind, swapg->nat);
3165 for (i = 0; i < swapg->nat; i++)
3167 swapg->ind[i] = grps->a[grps->index[gind] + i];
3172 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3178 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3183 ig = search_string(IMDgname, grps->nr, gnames);
3184 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3186 if (IMDgroup->nat > 0)
3189 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3191 IMDgname, IMDgroup->nat);
3192 snew(IMDgroup->ind, IMDgroup->nat);
3193 for (i = 0; i < IMDgroup->nat; i++)
3195 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3200 /* Checks whether atoms are both part of a COM removal group and frozen.
3201 * If a fully frozen atom is part of a COM removal group, it is removed
3202 * from the COM removal group. A note is issued if such atoms are present.
3203 * A warning is issued for atom with one or two dimensions frozen that
3204 * are part of a COM removal group (mdrun would need to compute COM mass
3205 * per dimension to handle this correctly).
3206 * Also issues a warning when non-frozen atoms are not part of a COM
3207 * removal group while COM removal is active.
3209 static void checkAndUpdateVcmFreezeGroupConsistency(SimulationGroups* groups,
3211 const t_grpopts& opts,
3214 const int vcmRestGroup =
3215 std::max(int(groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size()), 1);
3217 int numFullyFrozenVcmAtoms = 0;
3218 int numPartiallyFrozenVcmAtoms = 0;
3219 int numNonVcmAtoms = 0;
3220 for (int a = 0; a < numAtoms; a++)
3222 const int freezeGroup = getGroupType(*groups, SimulationAtomGroupType::Freeze, a);
3223 int numFrozenDims = 0;
3224 for (int d = 0; d < DIM; d++)
3226 numFrozenDims += opts.nFreeze[freezeGroup][d];
3229 const int vcmGroup = getGroupType(*groups, SimulationAtomGroupType::MassCenterVelocityRemoval, a);
3230 if (vcmGroup < vcmRestGroup)
3232 if (numFrozenDims == DIM)
3234 /* Do not remove COM motion for this fully frozen atom */
3235 if (groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
3237 groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(numAtoms, 0);
3239 groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
3240 numFullyFrozenVcmAtoms++;
3242 else if (numFrozenDims > 0)
3244 numPartiallyFrozenVcmAtoms++;
3247 else if (numFrozenDims < DIM)
3253 if (numFullyFrozenVcmAtoms > 0)
3255 std::string warningText = gmx::formatString(
3256 "There are %d atoms that are fully frozen and part of COMM removal group(s), "
3257 "removing these atoms from the COMM removal group(s)",
3258 numFullyFrozenVcmAtoms);
3259 warning_note(wi, warningText.c_str());
3261 if (numPartiallyFrozenVcmAtoms > 0 && numPartiallyFrozenVcmAtoms < numAtoms)
3263 std::string warningText = gmx::formatString(
3264 "There are %d atoms that are frozen along less then %d dimensions and part of COMM "
3265 "removal group(s), due to limitations in the code these still contribute to the "
3266 "mass of the COM along frozen dimensions and therefore the COMM correction will be "
3268 numPartiallyFrozenVcmAtoms, DIM);
3269 warning(wi, warningText.c_str());
3271 if (numNonVcmAtoms > 0)
3273 std::string warningText = gmx::formatString(
3274 "%d atoms are not part of any center of mass motion removal group.\n"
3275 "This may lead to artifacts.\n"
3276 "In most cases one should use one group for the whole system.",
3278 warning(wi, warningText.c_str());
3282 void do_index(const char* mdparin,
3286 const gmx::MdModulesNotifier& notifier,
3290 t_blocka* defaultIndexGroups;
3298 int i, j, k, restnm;
3299 bool bExcl, bTable, bAnneal;
3300 char warn_buf[STRLEN];
3304 fprintf(stderr, "processing index file...\n");
3308 snew(defaultIndexGroups, 1);
3309 snew(defaultIndexGroups->index, 1);
3311 atoms_all = gmx_mtop_global_atoms(mtop);
3312 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3313 done_atom(&atoms_all);
3317 defaultIndexGroups = init_index(ndx, &gnames);
3320 SimulationGroups* groups = &mtop->groups;
3321 natoms = mtop->natoms;
3322 symtab = &mtop->symtab;
3324 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3326 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3328 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3329 restnm = groups->groupNames.size() - 1;
3330 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3331 srenew(gnames, defaultIndexGroups->nr + 1);
3332 gnames[restnm] = *(groups->groupNames.back());
3334 set_warning_line(wi, mdparin, -1);
3336 auto temperatureCouplingTauValues = gmx::splitString(is->tau_t);
3337 auto temperatureCouplingReferenceValues = gmx::splitString(is->ref_t);
3338 auto temperatureCouplingGroupNames = gmx::splitString(is->tcgrps);
3339 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3340 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3343 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3345 temperatureCouplingGroupNames.size(), temperatureCouplingReferenceValues.size(),
3346 temperatureCouplingTauValues.size());
3349 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3350 do_numbering(natoms, groups, temperatureCouplingGroupNames, defaultIndexGroups, gnames,
3351 SimulationAtomGroupType::TemperatureCoupling, restnm,
3352 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3353 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3355 snew(ir->opts.nrdf, nr);
3356 snew(ir->opts.tau_t, nr);
3357 snew(ir->opts.ref_t, nr);
3358 if (ir->eI == eiBD && ir->bd_fric == 0)
3360 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3363 if (useReferenceTemperature)
3365 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3367 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3371 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3372 for (i = 0; (i < nr); i++)
3374 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3376 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3377 warning_error(wi, warn_buf);
3380 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3384 "tau-t = -1 is the value to signal that a group should not have "
3385 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3388 if (ir->opts.tau_t[i] >= 0)
3390 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3393 if (ir->etc != etcNO && ir->nsttcouple == -1)
3395 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3400 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3403 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3404 "md-vv; use either vrescale temperature with berendsen pressure or "
3405 "Nose-Hoover temperature with MTTK pressure");
3407 if (ir->epc == epcMTTK)
3409 if (ir->etc != etcNOSEHOOVER)
3412 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3417 if (ir->nstpcouple != ir->nsttcouple)
3419 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3420 ir->nstpcouple = ir->nsttcouple = mincouple;
3422 "for current Trotter decomposition methods with vv, nsttcouple and "
3423 "nstpcouple must be equal. Both have been reset to "
3424 "min(nsttcouple,nstpcouple) = %d",
3426 warning_note(wi, warn_buf);
3431 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3432 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3434 if (ETC_ANDERSEN(ir->etc))
3436 if (ir->nsttcouple != 1)
3440 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3441 "need for larger nsttcouple > 1, since no global parameters are computed. "
3442 "nsttcouple has been reset to 1");
3443 warning_note(wi, warn_buf);
3446 nstcmin = tcouple_min_integration_steps(ir->etc);
3449 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3452 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3453 "least %d times larger than nsttcouple*dt (%g)",
3454 ETCOUPLTYPE(ir->etc), tau_min, nstcmin, ir->nsttcouple * ir->delta_t);
3455 warning(wi, warn_buf);
3458 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3459 for (i = 0; (i < nr); i++)
3461 if (ir->opts.ref_t[i] < 0)
3463 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3466 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3467 if we are in this conditional) if mc_temp is negative */
3468 if (ir->expandedvals->mc_temp < 0)
3470 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3474 /* Simulated annealing for each group. There are nr groups */
3475 auto simulatedAnnealingGroupNames = gmx::splitString(is->anneal);
3476 if (simulatedAnnealingGroupNames.size() == 1
3477 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3479 simulatedAnnealingGroupNames.resize(0);
3481 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3483 gmx_fatal(FARGS, "Wrong number of annealing values: %zu (for %d groups)\n",
3484 simulatedAnnealingGroupNames.size(), nr);
3488 snew(ir->opts.annealing, nr);
3489 snew(ir->opts.anneal_npoints, nr);
3490 snew(ir->opts.anneal_time, nr);
3491 snew(ir->opts.anneal_temp, nr);
3492 for (i = 0; i < nr; i++)
3494 ir->opts.annealing[i] = eannNO;
3495 ir->opts.anneal_npoints[i] = 0;
3496 ir->opts.anneal_time[i] = nullptr;
3497 ir->opts.anneal_temp[i] = nullptr;
3499 if (!simulatedAnnealingGroupNames.empty())
3502 for (i = 0; i < nr; i++)
3504 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3506 ir->opts.annealing[i] = eannNO;
3508 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3510 ir->opts.annealing[i] = eannSINGLE;
3513 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3515 ir->opts.annealing[i] = eannPERIODIC;
3521 /* Read the other fields too */
3522 auto simulatedAnnealingPoints = gmx::splitString(is->anneal_npoints);
3523 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3525 gmx_fatal(FARGS, "Found %zu annealing-npoints values for %zu groups\n",
3526 simulatedAnnealingPoints.size(), simulatedAnnealingGroupNames.size());
3528 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3529 size_t numSimulatedAnnealingFields = 0;
3530 for (i = 0; i < nr; i++)
3532 if (ir->opts.anneal_npoints[i] == 1)
3536 "Please specify at least a start and an end point for annealing\n");
3538 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3539 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3540 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3543 auto simulatedAnnealingTimes = gmx::splitString(is->anneal_time);
3545 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3547 gmx_fatal(FARGS, "Found %zu annealing-time values, wanted %zu\n",
3548 simulatedAnnealingTimes.size(), numSimulatedAnnealingFields);
3550 auto simulatedAnnealingTemperatures = gmx::splitString(is->anneal_temp);
3551 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3553 gmx_fatal(FARGS, "Found %zu annealing-temp values, wanted %zu\n",
3554 simulatedAnnealingTemperatures.size(), numSimulatedAnnealingFields);
3557 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3558 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3559 convertReals(wi, simulatedAnnealingTimes, "anneal-time",
3560 allSimulatedAnnealingTimes.data());
3561 convertReals(wi, simulatedAnnealingTemperatures, "anneal-temp",
3562 allSimulatedAnnealingTemperatures.data());
3563 for (i = 0, k = 0; i < nr; i++)
3565 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3567 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3568 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3571 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3573 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3579 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3582 "Annealing timepoints out of order: t=%f comes after "
3584 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j - 1]);
3587 if (ir->opts.anneal_temp[i][j] < 0)
3589 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n",
3590 ir->opts.anneal_temp[i][j]);
3595 /* Print out some summary information, to make sure we got it right */
3596 for (i = 0; i < nr; i++)
3598 if (ir->opts.annealing[i] != eannNO)
3600 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3601 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3602 *(groups->groupNames[j]), eann_names[ir->opts.annealing[i]],
3603 ir->opts.anneal_npoints[i]);
3604 fprintf(stderr, "Time (ps) Temperature (K)\n");
3605 /* All terms except the last one */
3606 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3608 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3609 ir->opts.anneal_temp[i][j]);
3612 /* Finally the last one */
3613 j = ir->opts.anneal_npoints[i] - 1;
3614 if (ir->opts.annealing[i] == eannSINGLE)
3616 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j],
3617 ir->opts.anneal_temp[i][j]);
3621 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3622 ir->opts.anneal_temp[i][j]);
3623 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3626 "There is a temperature jump when your annealing "
3638 make_pull_groups(ir->pull, is->pull_grp, defaultIndexGroups, gnames);
3640 make_pull_coords(ir->pull);
3645 make_rotation_groups(ir->rot, is->rot_grp, defaultIndexGroups, gnames);
3648 if (ir->eSwapCoords != eswapNO)
3650 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3653 /* Make indices for IMD session */
3656 make_IMD_group(ir->imd, is->imd_grp, defaultIndexGroups, gnames);
3659 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3660 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3661 notifier.preProcessingNotifications_.notify(defaultIndexGroupsAndNames);
3663 auto accelerations = gmx::splitString(is->acc);
3664 auto accelerationGroupNames = gmx::splitString(is->accgrps);
3665 if (accelerationGroupNames.size() * DIM != accelerations.size())
3667 gmx_fatal(FARGS, "Invalid Acceleration input: %zu groups and %zu acc. values",
3668 accelerationGroupNames.size(), accelerations.size());
3670 do_numbering(natoms, groups, accelerationGroupNames, defaultIndexGroups, gnames,
3671 SimulationAtomGroupType::Acceleration, restnm, egrptpALL_GENREST, bVerbose, wi);
3672 nr = groups->groups[SimulationAtomGroupType::Acceleration].size();
3673 snew(ir->opts.acc, nr);
3674 ir->opts.ngacc = nr;
3676 convertRvecs(wi, accelerations, "anneal-time", ir->opts.acc);
3678 auto freezeDims = gmx::splitString(is->frdim);
3679 auto freezeGroupNames = gmx::splitString(is->freeze);
3680 if (freezeDims.size() != DIM * freezeGroupNames.size())
3682 gmx_fatal(FARGS, "Invalid Freezing input: %zu groups and %zu freeze values",
3683 freezeGroupNames.size(), freezeDims.size());
3685 do_numbering(natoms, groups, freezeGroupNames, defaultIndexGroups, gnames,
3686 SimulationAtomGroupType::Freeze, restnm, egrptpALL_GENREST, bVerbose, wi);
3687 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3688 ir->opts.ngfrz = nr;
3689 snew(ir->opts.nFreeze, nr);
3690 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3692 for (j = 0; (j < DIM); j++, k++)
3694 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3695 if (!ir->opts.nFreeze[i][j])
3697 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3700 "Please use Y(ES) or N(O) for freezedim only "
3702 freezeDims[k].c_str());
3703 warning(wi, warn_buf);
3708 for (; (i < nr); i++)
3710 for (j = 0; (j < DIM); j++)
3712 ir->opts.nFreeze[i][j] = 0;
3716 auto energyGroupNames = gmx::splitString(is->energy);
3717 do_numbering(natoms, groups, energyGroupNames, defaultIndexGroups, gnames,
3718 SimulationAtomGroupType::EnergyOutput, restnm, egrptpALL_GENREST, bVerbose, wi);
3719 add_wall_energrps(groups, ir->nwall, symtab);
3720 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3721 auto vcmGroupNames = gmx::splitString(is->vcm);
3722 do_numbering(natoms, groups, vcmGroupNames, defaultIndexGroups, gnames,
3723 SimulationAtomGroupType::MassCenterVelocityRemoval, restnm,
3724 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3726 if (ir->comm_mode != ecmNO)
3728 checkAndUpdateVcmFreezeGroupConsistency(groups, natoms, ir->opts, wi);
3731 /* Now we have filled the freeze struct, so we can calculate NRDF */
3732 calc_nrdf(mtop, ir, gnames);
3734 auto user1GroupNames = gmx::splitString(is->user1);
3735 do_numbering(natoms, groups, user1GroupNames, defaultIndexGroups, gnames,
3736 SimulationAtomGroupType::User1, restnm, egrptpALL_GENREST, bVerbose, wi);
3737 auto user2GroupNames = gmx::splitString(is->user2);
3738 do_numbering(natoms, groups, user2GroupNames, defaultIndexGroups, gnames,
3739 SimulationAtomGroupType::User2, restnm, egrptpALL_GENREST, bVerbose, wi);
3740 auto compressedXGroupNames = gmx::splitString(is->x_compressed_groups);
3741 do_numbering(natoms, groups, compressedXGroupNames, defaultIndexGroups, gnames,
3742 SimulationAtomGroupType::CompressedPositionOutput, restnm, egrptpONE, bVerbose, wi);
3743 auto orirefFitGroupNames = gmx::splitString(is->orirefitgrp);
3744 do_numbering(natoms, groups, orirefFitGroupNames, defaultIndexGroups, gnames,
3745 SimulationAtomGroupType::OrientationRestraintsFit, restnm, egrptpALL_GENREST,
3748 /* MiMiC QMMM input processing */
3749 auto qmGroupNames = gmx::splitString(is->QMMM);
3750 if (qmGroupNames.size() > 1)
3752 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
3754 /* group rest, if any, is always MM! */
3755 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3756 SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
3757 ir->opts.ngQM = qmGroupNames.size();
3759 /* end of MiMiC QMMM input */
3763 for (auto group : gmx::keysOf(groups->groups))
3765 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
3766 for (const auto& entry : groups->groups[group])
3768 fprintf(stderr, " %s", *(groups->groupNames[entry]));
3770 fprintf(stderr, "\n");
3774 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3775 snew(ir->opts.egp_flags, nr * nr);
3777 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3778 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3780 warning_error(wi, "Energy group exclusions are currently not supported");
3782 if (bExcl && EEL_FULL(ir->coulombtype))
3784 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3787 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3788 if (bTable && !(ir->vdwtype == evdwUSER) && !(ir->coulombtype == eelUSER)
3789 && !(ir->coulombtype == eelPMEUSER) && !(ir->coulombtype == eelPMEUSERSWITCH))
3792 "Can only have energy group pair tables in combination with user tables for VdW "
3796 /* final check before going out of scope if simulated tempering variables
3797 * need to be set to default values.
3799 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
3801 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
3802 warning(wi, gmx::formatString(
3803 "the value for nstexpanded was not specified for "
3804 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
3805 "by default, but it is recommended to set it to an explicit value!",
3806 ir->expandedvals->nstexpanded));
3808 for (i = 0; (i < defaultIndexGroups->nr); i++)
3813 done_blocka(defaultIndexGroups);
3814 sfree(defaultIndexGroups);
3818 static void check_disre(const gmx_mtop_t* mtop)
3820 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3822 const gmx_ffparams_t& ffparams = mtop->ffparams;
3825 for (int i = 0; i < ffparams.numTypes(); i++)
3827 int ftype = ffparams.functype[i];
3828 if (ftype == F_DISRES)
3830 int label = ffparams.iparams[i].disres.label;
3831 if (label == old_label)
3833 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3842 "Found %d double distance restraint indices,\n"
3843 "probably the parameters for multiple pairs in one restraint "
3844 "are not identical\n",
3850 static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t* sys, const bool posres_only, ivec AbsRef)
3853 gmx_mtop_ilistloop_t iloop;
3855 const t_iparams* pr;
3862 for (d = 0; d < DIM; d++)
3864 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3866 /* Check for freeze groups */
3867 for (g = 0; g < ir->opts.ngfrz; g++)
3869 for (d = 0; d < DIM; d++)
3871 if (ir->opts.nFreeze[g][d] != 0)
3879 /* Check for position restraints */
3880 iloop = gmx_mtop_ilistloop_init(sys);
3881 while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
3883 if (nmol > 0 && (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3885 for (i = 0; i < (*ilist)[F_POSRES].size(); i += 2)
3887 pr = &sys->ffparams.iparams[(*ilist)[F_POSRES].iatoms[i]];
3888 for (d = 0; d < DIM; d++)
3890 if (pr->posres.fcA[d] != 0)
3896 for (i = 0; i < (*ilist)[F_FBPOSRES].size(); i += 2)
3898 /* Check for flat-bottom posres */
3899 pr = &sys->ffparams.iparams[(*ilist)[F_FBPOSRES].iatoms[i]];
3900 if (pr->fbposres.k != 0)
3902 switch (pr->fbposres.geom)
3904 case efbposresSPHERE: AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1; break;
3905 case efbposresCYLINDERX: AbsRef[YY] = AbsRef[ZZ] = 1; break;
3906 case efbposresCYLINDERY: AbsRef[XX] = AbsRef[ZZ] = 1; break;
3907 case efbposresCYLINDER:
3908 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3909 case efbposresCYLINDERZ: AbsRef[XX] = AbsRef[YY] = 1; break;
3910 case efbposresX: /* d=XX */
3911 case efbposresY: /* d=YY */
3912 case efbposresZ: /* d=ZZ */
3913 d = pr->fbposres.geom - efbposresX;
3918 " Invalid geometry for flat-bottom position restraint.\n"
3919 "Expected nr between 1 and %d. Found %d\n",
3920 efbposresNR - 1, pr->fbposres.geom);
3927 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3930 static void check_combination_rule_differences(const gmx_mtop_t* mtop,
3932 bool* bC6ParametersWorkWithGeometricRules,
3933 bool* bC6ParametersWorkWithLBRules,
3934 bool* bLBRulesPossible)
3936 int ntypes, tpi, tpj;
3939 double c6i, c6j, c12i, c12j;
3940 double c6, c6_geometric, c6_LB;
3941 double sigmai, sigmaj, epsi, epsj;
3942 bool bCanDoLBRules, bCanDoGeometricRules;
3945 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3946 * force-field floating point parameters.
3949 ptr = getenv("GMX_LJCOMB_TOL");
3953 double gmx_unused canary;
3955 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
3958 "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
3963 *bC6ParametersWorkWithLBRules = TRUE;
3964 *bC6ParametersWorkWithGeometricRules = TRUE;
3965 bCanDoLBRules = TRUE;
3966 ntypes = mtop->ffparams.atnr;
3967 snew(typecount, ntypes);
3968 gmx_mtop_count_atomtypes(mtop, state, typecount);
3969 *bLBRulesPossible = TRUE;
3970 for (tpi = 0; tpi < ntypes; ++tpi)
3972 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3973 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3974 for (tpj = tpi; tpj < ntypes; ++tpj)
3976 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3977 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3978 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3979 c6_geometric = std::sqrt(c6i * c6j);
3980 if (!gmx_numzero(c6_geometric))
3982 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3984 sigmai = gmx::sixthroot(c12i / c6i);
3985 sigmaj = gmx::sixthroot(c12j / c6j);
3986 epsi = c6i * c6i / (4.0 * c12i);
3987 epsj = c6j * c6j / (4.0 * c12j);
3988 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
3992 *bLBRulesPossible = FALSE;
3993 c6_LB = c6_geometric;
3995 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4000 *bC6ParametersWorkWithLBRules = FALSE;
4003 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4005 if (!bCanDoGeometricRules)
4007 *bC6ParametersWorkWithGeometricRules = FALSE;
4014 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t* mtop, warninp_t wi)
4016 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4018 check_combination_rule_differences(mtop, 0, &bC6ParametersWorkWithGeometricRules,
4019 &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4020 if (ir->ljpme_combination_rule == eljpmeLB)
4022 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4025 "You are using arithmetic-geometric combination rules "
4026 "in LJ-PME, but your non-bonded C6 parameters do not "
4027 "follow these rules.");
4032 if (!bC6ParametersWorkWithGeometricRules)
4034 if (ir->eDispCorr != edispcNO)
4037 "You are using geometric combination rules in "
4038 "LJ-PME, but your non-bonded C6 parameters do "
4039 "not follow these rules. "
4040 "This will introduce very small errors in the forces and energies in "
4041 "your simulations. Dispersion correction will correct total energy "
4042 "and/or pressure for isotropic systems, but not forces or surface "
4048 "You are using geometric combination rules in "
4049 "LJ-PME, but your non-bonded C6 parameters do "
4050 "not follow these rules. "
4051 "This will introduce very small errors in the forces and energies in "
4052 "your simulations. If your system is homogeneous, consider using "
4053 "dispersion correction "
4054 "for the total energy and pressure.");
4060 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4062 char err_buf[STRLEN];
4067 gmx_mtop_atomloop_block_t aloopb;
4069 char warn_buf[STRLEN];
4071 set_warning_line(wi, mdparin, -1);
4073 if (absolute_reference(ir, sys, false, AbsRef))
4076 "Removing center of mass motion in the presence of position restraints might "
4077 "cause artifacts. When you are using position restraints to equilibrate a "
4078 "macro-molecule, the artifacts are usually negligible.");
4081 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 && ir->nstlist > 1
4082 && ((EI_MD(ir->eI) || EI_SD(ir->eI)) && (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4084 /* Check if a too small Verlet buffer might potentially
4085 * cause more drift than the thermostat can couple off.
4087 /* Temperature error fraction for warning and suggestion */
4088 const real T_error_warn = 0.002;
4089 const real T_error_suggest = 0.001;
4090 /* For safety: 2 DOF per atom (typical with constraints) */
4091 const real nrdf_at = 2;
4092 real T, tau, max_T_error;
4097 for (i = 0; i < ir->opts.ngtc; i++)
4099 T = std::max(T, ir->opts.ref_t[i]);
4100 tau = std::max(tau, ir->opts.tau_t[i]);
4104 /* This is a worst case estimate of the temperature error,
4105 * assuming perfect buffer estimation and no cancelation
4106 * of errors. The factor 0.5 is because energy distributes
4107 * equally over Ekin and Epot.
4109 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * BOLTZ * T);
4110 if (max_T_error > T_error_warn)
4113 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4114 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4115 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4116 "%.0e or decrease tau_t.",
4117 ir->verletbuf_tol, T, tau, 100 * max_T_error, 100 * T_error_suggest,
4118 ir->verletbuf_tol * T_error_suggest / max_T_error);
4119 warning(wi, warn_buf);
4124 if (ETC_ANDERSEN(ir->etc))
4128 for (i = 0; i < ir->opts.ngtc; i++)
4131 "all tau_t must currently be equal using Andersen temperature control, "
4132 "violated for group %d",
4134 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4136 "all tau_t must be positive using Andersen temperature control, "
4138 i, ir->opts.tau_t[i]);
4139 CHECK(ir->opts.tau_t[i] < 0);
4142 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4144 for (i = 0; i < ir->opts.ngtc; i++)
4146 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4148 "tau_t/delta_t for group %d for temperature control method %s must be a "
4149 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4150 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4152 i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
4153 CHECK(nsteps % ir->nstcomm != 0);
4158 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD && ir->comm_mode == ecmNO
4159 && !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) && !ETC_ANDERSEN(ir->etc))
4162 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4163 "rounding errors can lead to build up of kinetic energy of the center of mass");
4166 if (ir->epc == epcPARRINELLORAHMAN && ir->etc == etcNOSEHOOVER)
4169 for (int g = 0; g < ir->opts.ngtc; g++)
4171 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4173 if (ir->tau_p < 1.9 * tau_t_max)
4175 std::string message = gmx::formatString(
4176 "With %s T-coupling and %s p-coupling, "
4177 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4178 etcoupl_names[ir->etc], epcoupl_names[ir->epc], "tau-p", ir->tau_p, "tau-t",
4180 warning(wi, message.c_str());
4184 /* Check for pressure coupling with absolute position restraints */
4185 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4187 absolute_reference(ir, sys, TRUE, AbsRef);
4189 for (m = 0; m < DIM; m++)
4191 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4194 "You are using pressure coupling with absolute position restraints, "
4195 "this will give artifacts. Use the refcoord_scaling option.");
4203 aloopb = gmx_mtop_atomloop_block_init(sys);
4205 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4207 if (atom->q != 0 || atom->qB != 0)
4215 if (EEL_FULL(ir->coulombtype))
4218 "You are using full electrostatics treatment %s for a system without charges.\n"
4219 "This costs a lot of performance for just processing zeros, consider using %s "
4221 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4222 warning(wi, err_buf);
4227 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
4230 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4231 "You might want to consider using %s electrostatics.\n",
4233 warning_note(wi, err_buf);
4237 /* Check if combination rules used in LJ-PME are the same as in the force field */
4238 if (EVDW_PME(ir->vdwtype))
4240 check_combination_rules(ir, sys, wi);
4243 /* Generalized reaction field */
4244 if (ir->coulombtype == eelGRF_NOTUSED)
4247 "Generalized reaction-field electrostatics is no longer supported. "
4248 "You can use normal reaction-field instead and compute the reaction-field "
4249 "constant by hand.");
4253 for (int i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4255 for (m = 0; (m < DIM); m++)
4257 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4266 snew(mgrp, sys->groups.groups[SimulationAtomGroupType::Acceleration].size());
4267 for (const AtomProxy atomP : AtomRange(*sys))
4269 const t_atom& local = atomP.atom();
4270 int i = atomP.globalAtomNumber();
4271 mgrp[getGroupType(sys->groups, SimulationAtomGroupType::Acceleration, i)] += local.m;
4274 for (i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4276 for (m = 0; (m < DIM); m++)
4278 acc[m] += ir->opts.acc[i][m] * mgrp[i];
4282 for (m = 0; (m < DIM); m++)
4284 if (fabs(acc[m]) > 1e-6)
4286 const char* dim[DIM] = { "X", "Y", "Z" };
4287 fprintf(stderr, "Net Acceleration in %s direction, will %s be corrected\n", dim[m],
4288 ir->nstcomm != 0 ? "" : "not");
4289 if (ir->nstcomm != 0 && m < ndof_com(ir))
4293 (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4295 ir->opts.acc[i][m] -= acc[m];
4303 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0
4304 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4306 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4314 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4316 if (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0)
4318 absolute_reference(ir, sys, FALSE, AbsRef);
4319 for (m = 0; m < DIM; m++)
4321 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4324 "You are using an absolute reference for pulling, but the rest of "
4325 "the system does not have an absolute reference. This will lead to "
4334 for (i = 0; i < 3; i++)
4336 for (m = 0; m <= i; m++)
4338 if ((ir->epc != epcNO && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4340 for (c = 0; c < ir->pull->ncoord; c++)
4342 if (ir->pull->coord[c].eGeom == epullgDIRPBC && ir->pull->coord[c].vec[m] != 0)
4345 "Can not have dynamic box while using pull geometry '%s' "
4347 EPULLGEOM(ir->pull->coord[c].eGeom), 'x' + m);
4358 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4360 char warn_buf[STRLEN];
4363 ptr = check_box(ir->pbcType, box);
4366 warning_error(wi, ptr);
4369 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4371 if (ir->shake_tol <= 0.0)
4373 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4374 warning_error(wi, warn_buf);
4378 if ((ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4380 /* If we have Lincs constraints: */
4381 if (ir->eI == eiMD && ir->etc == etcNO && ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4384 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4385 warning_note(wi, warn_buf);
4388 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4391 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4393 warning_note(wi, warn_buf);
4395 if (ir->epc == epcMTTK)
4397 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4401 if (bHasAnyConstraints && ir->epc == epcMTTK)
4403 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4406 if (ir->LincsWarnAngle > 90.0)
4408 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4409 warning(wi, warn_buf);
4410 ir->LincsWarnAngle = 90.0;
4413 if (ir->pbcType != PbcType::No)
4415 if (ir->nstlist == 0)
4418 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4419 "atoms might cause the simulation to crash.");
4421 if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
4424 "ERROR: The cut-off length is longer than half the shortest box vector or "
4425 "longer than the smallest box diagonal element. Increase the box size or "
4426 "decrease rlist.\n");
4427 warning_error(wi, warn_buf);