2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013-2019,2020, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
49 #include "gromacs/awh/read_params.h"
50 #include "gromacs/fileio/readinp.h"
51 #include "gromacs/fileio/warninp.h"
52 #include "gromacs/gmxlib/network.h"
53 #include "gromacs/gmxpreprocess/toputil.h"
54 #include "gromacs/math/functions.h"
55 #include "gromacs/math/units.h"
56 #include "gromacs/math/vec.h"
57 #include "gromacs/mdlib/calc_verletbuf.h"
58 #include "gromacs/mdrun/mdmodules.h"
59 #include "gromacs/mdtypes/inputrec.h"
60 #include "gromacs/mdtypes/md_enums.h"
61 #include "gromacs/mdtypes/pull_params.h"
62 #include "gromacs/options/options.h"
63 #include "gromacs/options/treesupport.h"
64 #include "gromacs/pbcutil/pbc.h"
65 #include "gromacs/selection/indexutil.h"
66 #include "gromacs/topology/block.h"
67 #include "gromacs/topology/ifunc.h"
68 #include "gromacs/topology/index.h"
69 #include "gromacs/topology/mtop_util.h"
70 #include "gromacs/topology/symtab.h"
71 #include "gromacs/topology/topology.h"
72 #include "gromacs/utility/cstringutil.h"
73 #include "gromacs/utility/exceptions.h"
74 #include "gromacs/utility/fatalerror.h"
75 #include "gromacs/utility/filestream.h"
76 #include "gromacs/utility/gmxassert.h"
77 #include "gromacs/utility/ikeyvaluetreeerror.h"
78 #include "gromacs/utility/keyvaluetree.h"
79 #include "gromacs/utility/keyvaluetreebuilder.h"
80 #include "gromacs/utility/keyvaluetreemdpwriter.h"
81 #include "gromacs/utility/keyvaluetreetransform.h"
82 #include "gromacs/utility/mdmodulenotification.h"
83 #include "gromacs/utility/smalloc.h"
84 #include "gromacs/utility/strconvert.h"
85 #include "gromacs/utility/stringcompare.h"
86 #include "gromacs/utility/stringutil.h"
87 #include "gromacs/utility/textwriter.h"
92 /* Resource parameters
93 * Do not change any of these until you read the instruction
94 * in readinp.h. Some cpp's do not take spaces after the backslash
95 * (like the c-shell), which will give you a very weird compiler
99 typedef struct t_inputrec_strings
101 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN], acc[STRLEN], accgrps[STRLEN], freeze[STRLEN],
102 frdim[STRLEN], energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN],
103 x_compressed_groups[STRLEN], couple_moltype[STRLEN], orirefitgrp[STRLEN],
104 egptable[STRLEN], egpexcl[STRLEN], wall_atomtype[STRLEN], wall_density[STRLEN],
105 deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
106 char fep_lambda[efptNR][STRLEN];
107 char lambda_weights[STRLEN];
110 char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
111 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN], bSH[STRLEN],
112 CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN], SAoff[STRLEN], SAsteps[STRLEN];
114 } gmx_inputrec_strings;
116 static gmx_inputrec_strings* is = nullptr;
118 void init_inputrec_strings()
123 "Attempted to call init_inputrec_strings before calling done_inputrec_strings. "
124 "Only one inputrec (i.e. .mdp file) can be parsed at a time.");
129 void done_inputrec_strings()
138 egrptpALL, /* All particles have to be a member of a group. */
139 egrptpALL_GENREST, /* A rest group with name is generated for particles *
140 * that are not part of any group. */
141 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
142 * for the rest group. */
143 egrptpONE /* Merge all selected groups into one group, *
144 * make a rest group for the remaining particles. */
147 static const char* constraints[eshNR + 1] = { "none", "h-bonds", "all-bonds",
148 "h-angles", "all-angles", nullptr };
150 static const char* couple_lam[ecouplamNR + 1] = { "vdw-q", "vdw", "q", "none", nullptr };
152 static void GetSimTemps(int ntemps, t_simtemp* simtemp, double* temperature_lambdas)
157 for (i = 0; i < ntemps; i++)
159 /* simple linear scaling -- allows more control */
160 if (simtemp->eSimTempScale == esimtempLINEAR)
162 simtemp->temperatures[i] =
164 + (simtemp->simtemp_high - simtemp->simtemp_low) * temperature_lambdas[i];
166 else if (simtemp->eSimTempScale
167 == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
169 simtemp->temperatures[i] = simtemp->simtemp_low
170 * std::pow(simtemp->simtemp_high / simtemp->simtemp_low,
171 static_cast<real>((1.0 * i) / (ntemps - 1)));
173 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
175 simtemp->temperatures[i] = simtemp->simtemp_low
176 + (simtemp->simtemp_high - simtemp->simtemp_low)
177 * (std::expm1(temperature_lambdas[i]) / std::expm1(1.0));
182 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
183 gmx_fatal(FARGS, "%s", errorstr);
189 static void _low_check(bool b, const char* s, warninp_t wi)
193 warning_error(wi, s);
197 static void check_nst(const char* desc_nst, int nst, const char* desc_p, int* p, warninp_t wi)
201 if (*p > 0 && *p % nst != 0)
203 /* Round up to the next multiple of nst */
204 *p = ((*p) / nst + 1) * nst;
205 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n", desc_p, desc_nst, desc_p, *p);
210 static int lcd(int n1, int n2)
215 for (i = 2; (i <= n1 && i <= n2); i++)
217 if (n1 % i == 0 && n2 % i == 0)
226 //! Convert legacy mdp entries to modern ones.
227 static void process_interaction_modifier(int* eintmod)
229 if (*eintmod == eintmodPOTSHIFT_VERLET_UNSUPPORTED)
231 *eintmod = eintmodPOTSHIFT;
235 void check_ir(const char* mdparin,
236 const gmx::MdModulesNotifier& mdModulesNotifier,
240 /* Check internal consistency.
241 * NOTE: index groups are not set here yet, don't check things
242 * like temperature coupling group options here, but in triple_check
245 /* Strange macro: first one fills the err_buf, and then one can check
246 * the condition, which will print the message and increase the error
249 #define CHECK(b) _low_check(b, err_buf, wi)
250 char err_buf[256], warn_buf[STRLEN];
253 t_lambda* fep = ir->fepvals;
254 t_expanded* expand = ir->expandedvals;
256 set_warning_line(wi, mdparin, -1);
258 if (ir->coulombtype == eelRF_NEC_UNSUPPORTED)
260 sprintf(warn_buf, "%s electrostatics is no longer supported", eel_names[eelRF_NEC_UNSUPPORTED]);
261 warning_error(wi, warn_buf);
264 /* BASIC CUT-OFF STUFF */
265 if (ir->rcoulomb < 0)
267 warning_error(wi, "rcoulomb should be >= 0");
271 warning_error(wi, "rvdw should be >= 0");
273 if (ir->rlist < 0 && !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
275 warning_error(wi, "rlist should be >= 0");
278 "nstlist can not be smaller than 0. (If you were trying to use the heuristic "
279 "neighbour-list update scheme for efficient buffering for improved energy "
280 "conservation, please use the Verlet cut-off scheme instead.)");
281 CHECK(ir->nstlist < 0);
283 process_interaction_modifier(&ir->coulomb_modifier);
284 process_interaction_modifier(&ir->vdw_modifier);
286 if (ir->cutoff_scheme == ecutsGROUP)
289 "The group cutoff scheme has been removed since GROMACS 2020. "
290 "Please use the Verlet cutoff scheme.");
292 if (ir->cutoff_scheme == ecutsVERLET)
296 /* Normal Verlet type neighbor-list, currently only limited feature support */
297 if (inputrec2nboundeddim(ir) < 3)
299 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
302 // We don't (yet) have general Verlet kernels for rcoulomb!=rvdw
303 if (ir->rcoulomb != ir->rvdw)
305 // Since we have PME coulomb + LJ cut-off kernels with rcoulomb>rvdw
306 // for PME load balancing, we can support this exception.
307 bool bUsesPmeTwinRangeKernel = (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == evdwCUT
308 && ir->rcoulomb > ir->rvdw);
309 if (!bUsesPmeTwinRangeKernel)
312 "With Verlet lists rcoulomb!=rvdw is not supported (except for "
313 "rcoulomb>rvdw with PME electrostatics)");
317 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
319 if (ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT)
321 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
324 "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and "
326 evdw_names[ir->vdwtype], evdw_names[evdwCUT], eintmod_names[ir->vdw_modifier]);
327 warning_note(wi, warn_buf);
329 ir->vdwtype = evdwCUT;
333 sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s",
334 evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
335 warning_error(wi, warn_buf);
339 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
342 "With Verlet lists only cut-off and PME LJ interactions are supported");
344 if (!(ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype) || EEL_PME(ir->coulombtype)
345 || ir->coulombtype == eelEWALD))
348 "With Verlet lists only cut-off, reaction-field, PME and Ewald "
349 "electrostatics are supported");
351 if (!(ir->coulomb_modifier == eintmodNONE || ir->coulomb_modifier == eintmodPOTSHIFT))
353 sprintf(warn_buf, "coulomb_modifier=%s is not supported", eintmod_names[ir->coulomb_modifier]);
354 warning_error(wi, warn_buf);
357 if (EEL_USER(ir->coulombtype))
359 sprintf(warn_buf, "Coulomb type %s is not supported with the verlet scheme",
360 eel_names[ir->coulombtype]);
361 warning_error(wi, warn_buf);
364 if (ir->nstlist <= 0)
366 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
369 if (ir->nstlist < 10)
372 "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note "
373 "that with the Verlet scheme, nstlist has no effect on the accuracy of "
377 rc_max = std::max(ir->rvdw, ir->rcoulomb);
381 /* With TPI we set the pairlist cut-off later using the radius of the insterted molecule */
382 ir->verletbuf_tol = 0;
385 else if (ir->verletbuf_tol <= 0)
387 if (ir->verletbuf_tol == 0)
389 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
392 if (ir->rlist < rc_max)
395 "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
398 if (ir->rlist == rc_max && ir->nstlist > 1)
402 "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet "
403 "buffer. The cluster pair list does have a buffering effect, but choosing "
404 "a larger rlist might be necessary for good energy conservation.");
409 if (ir->rlist > rc_max)
412 "You have set rlist larger than the interaction cut-off, but you also "
413 "have verlet-buffer-tolerance > 0. Will set rlist using "
414 "verlet-buffer-tolerance.");
417 if (ir->nstlist == 1)
419 /* No buffer required */
424 if (EI_DYNAMICS(ir->eI))
426 if (inputrec2nboundeddim(ir) < 3)
429 "The box volume is required for calculating rlist from the "
430 "energy drift with verlet-buffer-tolerance > 0. You are "
431 "using at least one unbounded dimension, so no volume can be "
432 "computed. Either use a finite box, or set rlist yourself "
433 "together with verlet-buffer-tolerance = -1.");
435 /* Set rlist temporarily so we can continue processing */
440 /* Set the buffer to 5% of the cut-off */
441 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics) * rc_max;
447 /* GENERAL INTEGRATOR STUFF */
450 if (ir->etc != etcNO)
452 if (EI_RANDOM(ir->eI))
455 "Setting tcoupl from '%s' to 'no'. %s handles temperature coupling "
456 "implicitly. See the documentation for more information on which "
457 "parameters affect temperature for %s.",
458 etcoupl_names[ir->etc], ei_names[ir->eI], ei_names[ir->eI]);
463 "Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to "
465 etcoupl_names[ir->etc], ei_names[ir->eI]);
467 warning_note(wi, warn_buf);
471 if (ir->eI == eiVVAK)
474 "Integrator method %s is implemented primarily for validation purposes; for "
475 "molecular dynamics, you should probably be using %s or %s",
476 ei_names[eiVVAK], ei_names[eiMD], ei_names[eiVV]);
477 warning_note(wi, warn_buf);
479 if (!EI_DYNAMICS(ir->eI))
481 if (ir->epc != epcNO)
484 "Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.",
485 epcoupl_names[ir->epc], ei_names[ir->eI]);
486 warning_note(wi, warn_buf);
490 if (EI_DYNAMICS(ir->eI))
492 if (ir->nstcalcenergy < 0)
494 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
495 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
497 /* nstcalcenergy larger than nstener does not make sense.
498 * We ideally want nstcalcenergy=nstener.
502 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
506 ir->nstcalcenergy = ir->nstenergy;
510 else if ((ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy)
511 || (ir->efep != efepNO && ir->fepvals->nstdhdl > 0
512 && (ir->nstcalcenergy > ir->fepvals->nstdhdl)))
515 const char* nsten = "nstenergy";
516 const char* nstdh = "nstdhdl";
517 const char* min_name = nsten;
518 int min_nst = ir->nstenergy;
520 /* find the smallest of ( nstenergy, nstdhdl ) */
521 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0
522 && (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
524 min_nst = ir->fepvals->nstdhdl;
527 /* If the user sets nstenergy small, we should respect that */
528 sprintf(warn_buf, "Setting nstcalcenergy (%d) equal to %s (%d)", ir->nstcalcenergy,
530 warning_note(wi, warn_buf);
531 ir->nstcalcenergy = min_nst;
534 if (ir->epc != epcNO)
536 if (ir->nstpcouple < 0)
538 ir->nstpcouple = ir_optimal_nstpcouple(ir);
542 if (ir->nstcalcenergy > 0)
544 if (ir->efep != efepNO)
546 /* nstdhdl should be a multiple of nstcalcenergy */
547 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstdhdl", &ir->fepvals->nstdhdl, wi);
551 /* nstexpanded should be a multiple of nstcalcenergy */
552 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstexpanded",
553 &ir->expandedvals->nstexpanded, wi);
555 /* for storing exact averages nstenergy should be
556 * a multiple of nstcalcenergy
558 check_nst("nstcalcenergy", ir->nstcalcenergy, "nstenergy", &ir->nstenergy, wi);
561 // Inquire all MdModules, if their parameters match with the energy
562 // calculation frequency
563 gmx::EnergyCalculationFrequencyErrors energyCalculationFrequencyErrors(ir->nstcalcenergy);
564 mdModulesNotifier.notifier_.notify(&energyCalculationFrequencyErrors);
566 // Emit all errors from the energy calculation frequency checks
567 for (const std::string& energyFrequencyErrorMessage :
568 energyCalculationFrequencyErrors.errorMessages())
570 warning_error(wi, energyFrequencyErrorMessage);
574 if (ir->nsteps == 0 && !ir->bContinuation)
577 "For a correct single-point energy evaluation with nsteps = 0, use "
578 "continuation = yes to avoid constraining the input coordinates.");
582 if ((EI_SD(ir->eI) || ir->eI == eiBD) && ir->bContinuation && ir->ld_seed != -1)
585 "You are doing a continuation with SD or BD, make sure that ld_seed is "
586 "different from the previous run (using ld_seed=-1 will ensure this)");
592 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
593 CHECK(ir->ePBC != epbcXYZ);
594 sprintf(err_buf, "with TPI nstlist should be larger than zero");
595 CHECK(ir->nstlist <= 0);
596 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
597 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
601 if ((opts->nshake > 0) && (opts->bMorse))
603 sprintf(warn_buf, "Using morse bond-potentials while constraining bonds is useless");
604 warning(wi, warn_buf);
607 if ((EI_SD(ir->eI) || ir->eI == eiBD) && ir->bContinuation && ir->ld_seed != -1)
610 "You are doing a continuation with SD or BD, make sure that ld_seed is "
611 "different from the previous run (using ld_seed=-1 will ensure this)");
613 /* verify simulated tempering options */
617 bool bAllTempZero = TRUE;
618 for (i = 0; i < fep->n_lambda; i++)
620 sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i,
621 efpt_names[efptTEMPERATURE], fep->all_lambda[efptTEMPERATURE][i]);
622 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
623 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
625 bAllTempZero = FALSE;
628 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
629 CHECK(bAllTempZero == TRUE);
631 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
632 CHECK(ir->eI != eiVV);
634 /* check compatability of the temperature coupling with simulated tempering */
636 if (ir->etc == etcNOSEHOOVER)
639 "Nose-Hoover based temperature control such as [%s] my not be "
640 "entirelyconsistent with simulated tempering",
641 etcoupl_names[ir->etc]);
642 warning_note(wi, warn_buf);
645 /* check that the temperatures make sense */
648 "Higher simulated tempering temperature (%g) must be >= than the simulated "
649 "tempering lower temperature (%g)",
650 ir->simtempvals->simtemp_high, ir->simtempvals->simtemp_low);
651 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
653 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero",
654 ir->simtempvals->simtemp_high);
655 CHECK(ir->simtempvals->simtemp_high <= 0);
657 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero",
658 ir->simtempvals->simtemp_low);
659 CHECK(ir->simtempvals->simtemp_low <= 0);
662 /* verify free energy options */
664 if (ir->efep != efepNO)
667 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2", fep->sc_power);
668 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
670 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
671 static_cast<int>(fep->sc_r_power));
672 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
675 "Can't use positive delta-lambda (%g) if initial state/lambda does not start at "
678 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
680 sprintf(err_buf, "Can't use positive delta-lambda (%g) with expanded ensemble simulations",
682 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
684 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
685 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
687 sprintf(err_buf, "Free-energy not implemented for Ewald");
688 CHECK(ir->coulombtype == eelEWALD);
690 /* check validty of lambda inputs */
691 if (fep->n_lambda == 0)
693 /* Clear output in case of no states:*/
694 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.",
695 fep->init_fep_state);
696 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
700 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d",
701 fep->init_fep_state, fep->n_lambda - 1);
702 CHECK((fep->init_fep_state >= fep->n_lambda));
706 "Lambda state must be set, either with init-lambda-state or with init-lambda");
707 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
710 "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with "
711 "init-lambda-state or with init-lambda, but not both",
712 fep->init_lambda, fep->init_fep_state);
713 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
716 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
720 for (i = 0; i < efptNR; i++)
722 if (fep->separate_dvdl[i])
727 if (n_lambda_terms > 1)
730 "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't "
731 "use init-lambda to set lambda state (except for slow growth). Use "
732 "init-lambda-state instead.");
733 warning(wi, warn_buf);
736 if (n_lambda_terms < 2 && fep->n_lambda > 0)
739 "init-lambda is deprecated for setting lambda state (except for slow "
740 "growth). Use init-lambda-state instead.");
744 for (j = 0; j < efptNR; j++)
746 for (i = 0; i < fep->n_lambda; i++)
748 sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i,
749 efpt_names[j], fep->all_lambda[j][i]);
750 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
754 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
756 for (i = 0; i < fep->n_lambda; i++)
759 "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while "
760 "coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to "
761 "crashes, and is not supported.",
762 i, fep->all_lambda[efptVDW][i], fep->all_lambda[efptCOUL][i]);
763 CHECK((fep->sc_alpha > 0)
764 && (((fep->all_lambda[efptCOUL][i] > 0.0) && (fep->all_lambda[efptCOUL][i] < 1.0))
765 && ((fep->all_lambda[efptVDW][i] > 0.0) && (fep->all_lambda[efptVDW][i] < 1.0))));
769 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
771 real sigma, lambda, r_sc;
774 /* Maximum estimate for A and B charges equal with lambda power 1 */
776 r_sc = std::pow(lambda * fep->sc_alpha * std::pow(sigma / ir->rcoulomb, fep->sc_r_power) + 1.0,
777 1.0 / fep->sc_r_power);
779 "With PME there is a minor soft core effect present at the cut-off, "
780 "proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on "
781 "energy conservation, but usually other effects dominate. With a common sigma "
782 "value of %g nm the fraction of the particle-particle potential at the cut-off "
783 "at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
784 fep->sc_r_power, sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
785 warning_note(wi, warn_buf);
788 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
789 be treated differently, but that's the next step */
791 for (i = 0; i < efptNR; i++)
793 for (j = 0; j < fep->n_lambda; j++)
795 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
796 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
801 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
805 /* checking equilibration of weights inputs for validity */
808 "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal "
810 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
811 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
814 "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to "
816 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
817 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
820 "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
821 expand->equil_steps, elmceq_names[elmceqSTEPS]);
822 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
825 "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
826 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
827 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
830 "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
831 expand->equil_ratio, elmceq_names[elmceqRATIO]);
832 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
835 "weight-equil-number-all-lambda (%d) must be a positive integer if "
836 "lmc-weights-equil=%s",
837 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
838 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
841 "weight-equil-number-samples (%d) must be a positive integer if "
842 "lmc-weights-equil=%s",
843 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
844 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
847 "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
848 expand->equil_steps, elmceq_names[elmceqSTEPS]);
849 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
851 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
852 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
853 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
855 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
856 expand->equil_ratio, elmceq_names[elmceqRATIO]);
857 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
859 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
860 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
861 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
863 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
864 CHECK((expand->lmc_repeats <= 0));
865 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
866 CHECK((expand->minvarmin <= 0));
867 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
868 CHECK((expand->c_range < 0));
870 "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != "
872 fep->init_fep_state, expand->lmc_forced_nstart);
873 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0)
874 && (expand->elmcmove != elmcmoveNO));
875 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
876 CHECK((expand->lmc_forced_nstart < 0));
877 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)",
878 fep->init_fep_state);
879 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
881 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
882 CHECK((expand->init_wl_delta < 0));
883 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
884 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
885 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
886 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
888 /* if there is no temperature control, we need to specify an MC temperature */
889 if (!integratorHasReferenceTemperature(ir) && (expand->elmcmove != elmcmoveNO)
890 && (expand->mc_temp <= 0.0))
893 "If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set "
894 "to a positive number");
895 warning_error(wi, err_buf);
897 if (expand->nstTij > 0)
899 sprintf(err_buf, "nstlog must be non-zero");
900 CHECK(ir->nstlog == 0);
901 // Avoid modulus by zero in the case that already triggered an error exit.
905 "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
906 expand->nstTij, ir->nstlog);
907 CHECK((expand->nstTij % ir->nstlog) != 0);
913 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
914 CHECK(ir->nwall && ir->ePBC != epbcXY);
917 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
919 if (ir->ePBC == epbcNONE)
921 if (ir->epc != epcNO)
923 warning(wi, "Turning off pressure coupling for vacuum system");
929 sprintf(err_buf, "Can not have pressure coupling with pbc=%s", epbc_names[ir->ePBC]);
930 CHECK(ir->epc != epcNO);
932 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
933 CHECK(EEL_FULL(ir->coulombtype));
935 sprintf(err_buf, "Can not have dispersion correction with pbc=%s", epbc_names[ir->ePBC]);
936 CHECK(ir->eDispCorr != edispcNO);
939 if (ir->rlist == 0.0)
942 "can only have neighborlist cut-off zero (=infinite)\n"
943 "with coulombtype = %s or coulombtype = %s\n"
944 "without periodic boundary conditions (pbc = %s) and\n"
945 "rcoulomb and rvdw set to zero",
946 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
947 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER))
948 || (ir->ePBC != epbcNONE) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
953 "Simulating without cut-offs can be (slightly) faster with nstlist=0, "
954 "nstype=simple and only one MPI rank");
959 if (ir->nstcomm == 0)
961 // TODO Change this behaviour. There should be exactly one way
962 // to turn off an algorithm.
963 ir->comm_mode = ecmNO;
965 if (ir->comm_mode != ecmNO)
969 // TODO Such input was once valid. Now that we've been
970 // helpful for a few years, we should reject such input,
971 // lest we have to support every historical decision
974 "If you want to remove the rotation around the center of mass, you should set "
975 "comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to "
976 "its absolute value");
977 ir->nstcomm = abs(ir->nstcomm);
980 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
983 "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting "
984 "nstcomm to nstcalcenergy");
985 ir->nstcomm = ir->nstcalcenergy;
988 if (ir->comm_mode == ecmANGULAR)
991 "Can not remove the rotation around the center of mass with periodic "
993 CHECK(ir->bPeriodicMols);
994 if (ir->ePBC != epbcNONE)
997 "Removing the rotation around the center of mass in a periodic system, "
998 "this can lead to artifacts. Only use this on a single (cluster of) "
999 "molecules. This cluster should not cross periodic boundaries.");
1004 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
1007 "Tumbling and flying ice-cubes: We are not removing rotation around center of mass "
1008 "in a non-periodic system. You should probably set comm_mode = ANGULAR or use "
1011 warning_note(wi, warn_buf);
1014 /* TEMPERATURE COUPLING */
1015 if (ir->etc == etcYES)
1017 ir->etc = etcBERENDSEN;
1019 "Old option for temperature coupling given: "
1020 "changing \"yes\" to \"Berendsen\"\n");
1023 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
1025 if (ir->opts.nhchainlength < 1)
1028 "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to "
1030 ir->opts.nhchainlength);
1031 ir->opts.nhchainlength = 1;
1032 warning(wi, warn_buf);
1035 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
1039 "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
1040 ir->opts.nhchainlength = 1;
1045 ir->opts.nhchainlength = 0;
1048 if (ir->eI == eiVVAK)
1051 "%s implemented primarily for validation, and requires nsttcouple = 1 and "
1054 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
1057 if (ETC_ANDERSEN(ir->etc))
1059 sprintf(err_buf, "%s temperature control not supported for integrator %s.",
1060 etcoupl_names[ir->etc], ei_names[ir->eI]);
1061 CHECK(!(EI_VV(ir->eI)));
1063 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
1066 "Center of mass removal not necessary for %s. All velocities of coupled "
1067 "groups are rerandomized periodically, so flying ice cube errors will not "
1069 etcoupl_names[ir->etc]);
1070 warning_note(wi, warn_buf);
1074 "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are "
1075 "randomized every time step",
1076 ir->nstcomm, etcoupl_names[ir->etc]);
1077 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
1080 if (ir->etc == etcBERENDSEN)
1083 "The %s thermostat does not generate the correct kinetic energy distribution. You "
1084 "might want to consider using the %s thermostat.",
1085 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
1086 warning_note(wi, warn_buf);
1089 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc)) && ir->epc == epcBERENDSEN)
1092 "Using Berendsen pressure coupling invalidates the "
1093 "true ensemble for the thermostat");
1094 warning(wi, warn_buf);
1097 /* PRESSURE COUPLING */
1098 if (ir->epc == epcISOTROPIC)
1100 ir->epc = epcBERENDSEN;
1102 "Old option for pressure coupling given: "
1103 "changing \"Isotropic\" to \"Berendsen\"\n");
1106 if (ir->epc != epcNO)
1108 dt_pcoupl = ir->nstpcouple * ir->delta_t;
1110 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1111 CHECK(ir->tau_p <= 0);
1113 if (ir->tau_p / dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10 * GMX_REAL_EPS)
1116 "For proper integration of the %s barostat, tau-p (%g) should be at least %d "
1117 "times larger than nstpcouple*dt (%g)",
1118 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1119 warning(wi, warn_buf);
1123 "compressibility must be > 0 when using pressure"
1125 EPCOUPLTYPE(ir->epc));
1126 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 || ir->compress[ZZ][ZZ] < 0
1127 || (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 && ir->compress[ZZ][XX] <= 0
1128 && ir->compress[ZZ][YY] <= 0));
1130 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1133 "You are generating velocities so I am assuming you "
1134 "are equilibrating a system. You are using "
1135 "%s pressure coupling, but this can be "
1136 "unstable for equilibration. If your system crashes, try "
1137 "equilibrating first with Berendsen pressure coupling. If "
1138 "you are not equilibrating the system, you can probably "
1139 "ignore this warning.",
1140 epcoupl_names[ir->epc]);
1141 warning(wi, warn_buf);
1147 if (ir->epc == epcMTTK)
1149 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1153 /* ELECTROSTATICS */
1154 /* More checks are in triple check (grompp.c) */
1156 if (ir->coulombtype == eelSWITCH)
1159 "coulombtype = %s is only for testing purposes and can lead to serious "
1160 "artifacts, advice: use coulombtype = %s",
1161 eel_names[ir->coulombtype], eel_names[eelRF_ZERO]);
1162 warning(wi, warn_buf);
1165 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1168 "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old "
1169 "format and exchanging epsilon-r and epsilon-rf",
1171 warning(wi, warn_buf);
1172 ir->epsilon_rf = ir->epsilon_r;
1173 ir->epsilon_r = 1.0;
1176 if (ir->epsilon_r == 0)
1179 "It is pointless to use long-range electrostatics with infinite relative "
1181 "Since you are effectively turning of electrostatics, a plain cutoff will be much "
1183 CHECK(EEL_FULL(ir->coulombtype));
1186 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1188 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1189 CHECK(ir->epsilon_r < 0);
1192 if (EEL_RF(ir->coulombtype))
1194 /* reaction field (at the cut-off) */
1196 if (ir->coulombtype == eelRF_ZERO && ir->epsilon_rf != 0)
1199 "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1200 eel_names[ir->coulombtype]);
1201 warning(wi, warn_buf);
1202 ir->epsilon_rf = 0.0;
1205 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1206 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) || (ir->epsilon_r == 0));
1207 if (ir->epsilon_rf == ir->epsilon_r)
1209 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1210 eel_names[ir->coulombtype]);
1211 warning(wi, warn_buf);
1214 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1215 * means the interaction is zero outside rcoulomb, but it helps to
1216 * provide accurate energy conservation.
1218 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1220 if (ir_coulomb_switched(ir))
1223 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the "
1224 "potential modifier options!",
1225 eel_names[ir->coulombtype]);
1226 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1230 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1233 "Explicit switch/shift coulomb interactions cannot be used in combination with a "
1234 "secondary coulomb-modifier.");
1235 CHECK(ir->coulomb_modifier != eintmodNONE);
1237 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1240 "Explicit switch/shift vdw interactions cannot be used in combination with a "
1241 "secondary vdw-modifier.");
1242 CHECK(ir->vdw_modifier != eintmodNONE);
1245 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT || ir->vdwtype == evdwSWITCH
1246 || ir->vdwtype == evdwSHIFT)
1249 "The switch/shift interaction settings are just for compatibility; you will get "
1251 "performance from applying potential modifiers to your interactions!\n");
1252 warning_note(wi, warn_buf);
1255 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1257 if (ir->rcoulomb_switch / ir->rcoulomb < 0.9499)
1259 real percentage = 100 * (ir->rcoulomb - ir->rcoulomb_switch) / ir->rcoulomb;
1261 "The switching range should be 5%% or less (currently %.2f%% using a switching "
1262 "range of %4f-%4f) for accurate electrostatic energies, energy conservation "
1263 "will be good regardless, since ewald_rtol = %g.",
1264 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1265 warning(wi, warn_buf);
1269 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1271 if (ir->rvdw_switch == 0)
1274 "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones "
1275 "potential. This suggests it was not set in the mdp, which can lead to large "
1276 "energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw "
1277 "switching range.");
1278 warning(wi, warn_buf);
1282 if (EEL_FULL(ir->coulombtype))
1284 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER
1285 || ir->coulombtype == eelPMEUSERSWITCH)
1287 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1288 eel_names[ir->coulombtype]);
1289 CHECK(ir->rcoulomb > ir->rlist);
1293 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1295 // TODO: Move these checks into the ewald module with the options class
1297 int orderMax = (ir->coulombtype == eelP3M_AD ? 8 : 12);
1299 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1301 sprintf(warn_buf, "With coulombtype = %s, you should have %d <= pme-order <= %d",
1302 eel_names[ir->coulombtype], orderMin, orderMax);
1303 warning_error(wi, warn_buf);
1307 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1309 if (ir->ewald_geometry == eewg3D)
1311 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s", epbc_names[ir->ePBC],
1312 eewg_names[eewg3DC]);
1313 warning(wi, warn_buf);
1315 /* This check avoids extra pbc coding for exclusion corrections */
1316 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1317 CHECK(ir->wall_ewald_zfac < 2);
1319 if ((ir->ewald_geometry == eewg3DC) && (ir->ePBC != epbcXY) && EEL_FULL(ir->coulombtype))
1321 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1322 eel_names[ir->coulombtype], eewg_names[eewg3DC], epbc_names[epbcXY]);
1323 warning(wi, warn_buf);
1325 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1327 sprintf(err_buf, "Cannot have periodic molecules with epsilon_surface > 0");
1328 CHECK(ir->bPeriodicMols);
1329 sprintf(warn_buf, "With epsilon_surface > 0 all molecules should be neutral.");
1330 warning_note(wi, warn_buf);
1332 "With epsilon_surface > 0 you can only use domain decomposition "
1333 "when there are only small molecules with all bonds constrained (mdrun will check "
1335 warning_note(wi, warn_buf);
1338 if (ir_vdw_switched(ir))
1340 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1341 CHECK(ir->rvdw_switch >= ir->rvdw);
1343 if (ir->rvdw_switch < 0.5 * ir->rvdw)
1346 "You are applying a switch function to vdw forces or potentials from %g to %g "
1347 "nm, which is more than half the interaction range, whereas switch functions "
1348 "are intended to act only close to the cut-off.",
1349 ir->rvdw_switch, ir->rvdw);
1350 warning_note(wi, warn_buf);
1354 if (ir->vdwtype == evdwPME)
1356 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1358 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s and %s",
1359 evdw_names[ir->vdwtype], eintmod_names[eintmodPOTSHIFT], eintmod_names[eintmodNONE]);
1360 warning_error(wi, err_buf);
1364 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1367 "You have selected user tables with dispersion correction, the dispersion "
1368 "will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction "
1369 "between rvdw_switch and rvdw will not be double counted). Make sure that you "
1370 "really want dispersion correction to -C6/r^6.");
1373 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT) && ir->rvdw != 0)
1375 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1378 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1380 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1383 /* IMPLICIT SOLVENT */
1384 if (ir->coulombtype == eelGB_NOTUSED)
1386 sprintf(warn_buf, "Invalid option %s for coulombtype", eel_names[ir->coulombtype]);
1387 warning_error(wi, warn_buf);
1392 warning_error(wi, "QMMM is currently not supported");
1393 if (!EI_DYNAMICS(ir->eI))
1396 sprintf(buf, "QMMM is only supported with dynamics, not with integrator %s", ei_names[ir->eI]);
1397 warning_error(wi, buf);
1403 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1407 /* interpret a number of doubles from a string and put them in an array,
1408 after allocating space for them.
1409 str = the input string
1410 n = the (pre-allocated) number of doubles read
1411 r = the output array of doubles. */
1412 static void parse_n_real(char* str, int* n, real** r, warninp_t wi)
1414 auto values = gmx::splitString(str);
1418 for (int i = 0; i < *n; i++)
1422 (*r)[i] = gmx::fromString<real>(values[i]);
1424 catch (gmx::GromacsException&)
1426 warning_error(wi, "Invalid value " + values[i]
1427 + " in string in mdp file. Expected a real number.");
1433 static void do_fep_params(t_inputrec* ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
1436 int i, j, max_n_lambda, nweights, nfep[efptNR];
1437 t_lambda* fep = ir->fepvals;
1438 t_expanded* expand = ir->expandedvals;
1439 real** count_fep_lambdas;
1440 bool bOneLambda = TRUE;
1442 snew(count_fep_lambdas, efptNR);
1444 /* FEP input processing */
1445 /* first, identify the number of lambda values for each type.
1446 All that are nonzero must have the same number */
1448 for (i = 0; i < efptNR; i++)
1450 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
1453 /* now, determine the number of components. All must be either zero, or equal. */
1456 for (i = 0; i < efptNR; i++)
1458 if (nfep[i] > max_n_lambda)
1460 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1461 must have the same number if its not zero.*/
1466 for (i = 0; i < efptNR; i++)
1470 ir->fepvals->separate_dvdl[i] = FALSE;
1472 else if (nfep[i] == max_n_lambda)
1474 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute
1475 the derivative with respect to the temperature currently */
1477 ir->fepvals->separate_dvdl[i] = TRUE;
1483 "Number of lambdas (%d) for FEP type %s not equal to number of other types "
1485 nfep[i], efpt_names[i], max_n_lambda);
1488 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1489 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1491 /* the number of lambdas is the number we've read in, which is either zero
1492 or the same for all */
1493 fep->n_lambda = max_n_lambda;
1495 /* allocate space for the array of lambda values */
1496 snew(fep->all_lambda, efptNR);
1497 /* if init_lambda is defined, we need to set lambda */
1498 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1500 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1502 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1503 for (i = 0; i < efptNR; i++)
1505 snew(fep->all_lambda[i], fep->n_lambda);
1506 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1509 for (j = 0; j < fep->n_lambda; j++)
1511 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1513 sfree(count_fep_lambdas[i]);
1516 sfree(count_fep_lambdas);
1518 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for
1519 internal bookkeeping -- for now, init_lambda */
1521 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1523 for (i = 0; i < fep->n_lambda; i++)
1525 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1529 /* check to see if only a single component lambda is defined, and soft core is defined.
1530 In this case, turn on coulomb soft core */
1532 if (max_n_lambda == 0)
1538 for (i = 0; i < efptNR; i++)
1540 if ((nfep[i] != 0) && (i != efptFEP))
1546 if ((bOneLambda) && (fep->sc_alpha > 0))
1548 fep->bScCoul = TRUE;
1551 /* Fill in the others with the efptFEP if they are not explicitly
1552 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1553 they are all zero. */
1555 for (i = 0; i < efptNR; i++)
1557 if ((nfep[i] == 0) && (i != efptFEP))
1559 for (j = 0; j < fep->n_lambda; j++)
1561 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1567 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1568 if (fep->sc_r_power == 48)
1570 if (fep->sc_alpha > 0.1)
1573 "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004",
1578 /* now read in the weights */
1579 parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
1582 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1584 else if (nweights != fep->n_lambda)
1586 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1587 nweights, fep->n_lambda);
1589 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1591 expand->nstexpanded = fep->nstdhdl;
1592 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1597 static void do_simtemp_params(t_inputrec* ir)
1600 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1601 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1604 static void convertYesNos(warninp_t /*wi*/,
1605 gmx::ArrayRef<const std::string> inputs,
1606 const char* /*name*/,
1610 for (const auto& input : inputs)
1612 outputs[i] = gmx::equalCaseInsensitive(input, "Y", 1);
1617 template<typename T>
1618 void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
1621 for (const auto& input : inputs)
1625 outputs[i] = gmx::fromStdString<T>(input);
1627 catch (gmx::GromacsException&)
1629 auto message = gmx::formatString(
1630 "Invalid value for mdp option %s. %s should only consist of integers separated "
1633 warning_error(wi, message);
1639 static void convertReals(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, real* outputs)
1642 for (const auto& input : inputs)
1646 outputs[i] = gmx::fromString<real>(input);
1648 catch (gmx::GromacsException&)
1650 auto message = gmx::formatString(
1651 "Invalid value for mdp option %s. %s should only consist of real numbers "
1652 "separated by spaces.",
1654 warning_error(wi, message);
1660 static void convertRvecs(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, rvec* outputs)
1663 for (const auto& input : inputs)
1667 outputs[i][d] = gmx::fromString<real>(input);
1669 catch (gmx::GromacsException&)
1671 auto message = gmx::formatString(
1672 "Invalid value for mdp option %s. %s should only consist of real numbers "
1673 "separated by spaces.",
1675 warning_error(wi, message);
1686 static void do_wall_params(t_inputrec* ir, char* wall_atomtype, char* wall_density, t_gromppopts* opts, warninp_t wi)
1688 opts->wall_atomtype[0] = nullptr;
1689 opts->wall_atomtype[1] = nullptr;
1691 ir->wall_atomtype[0] = -1;
1692 ir->wall_atomtype[1] = -1;
1693 ir->wall_density[0] = 0;
1694 ir->wall_density[1] = 0;
1698 auto wallAtomTypes = gmx::splitString(wall_atomtype);
1699 if (wallAtomTypes.size() != size_t(ir->nwall))
1701 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %zu", ir->nwall,
1702 wallAtomTypes.size());
1704 for (int i = 0; i < ir->nwall; i++)
1706 opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
1709 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1711 auto wallDensity = gmx::splitString(wall_density);
1712 if (wallDensity.size() != size_t(ir->nwall))
1714 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %zu", ir->nwall,
1715 wallDensity.size());
1717 convertReals(wi, wallDensity, "wall-density", ir->wall_density);
1718 for (int i = 0; i < ir->nwall; i++)
1720 if (ir->wall_density[i] <= 0)
1722 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, ir->wall_density[i]);
1729 static void add_wall_energrps(SimulationGroups* groups, int nwall, t_symtab* symtab)
1733 AtomGroupIndices* grps = &(groups->groups[SimulationAtomGroupType::EnergyOutput]);
1734 for (int i = 0; i < nwall; i++)
1736 groups->groupNames.emplace_back(put_symtab(symtab, gmx::formatString("wall%d", i).c_str()));
1737 grps->emplace_back(groups->groupNames.size() - 1);
1742 static void read_expandedparams(std::vector<t_inpfile>* inp, t_expanded* expand, warninp_t wi)
1744 /* read expanded ensemble parameters */
1745 printStringNewline(inp, "expanded ensemble variables");
1746 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1747 expand->elamstats = get_eeenum(inp, "lmc-stats", elamstats_names, wi);
1748 expand->elmcmove = get_eeenum(inp, "lmc-move", elmcmove_names, wi);
1749 expand->elmceq = get_eeenum(inp, "lmc-weights-equil", elmceq_names, wi);
1750 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1751 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1752 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1753 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1754 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1755 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1756 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1757 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1758 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1759 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1760 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1761 expand->bSymmetrizedTMatrix =
1762 (get_eeenum(inp, "symmetrized-transition-matrix", yesno_names, wi) != 0);
1763 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1764 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1765 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1766 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1767 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1768 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1769 expand->bWLoneovert = (get_eeenum(inp, "wl-oneovert", yesno_names, wi) != 0);
1772 /*! \brief Return whether an end state with the given coupling-lambda
1773 * value describes fully-interacting VDW.
1775 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1776 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1778 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1780 return (couple_lambda_value == ecouplamVDW || couple_lambda_value == ecouplamVDWQ);
1786 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1789 explicit MdpErrorHandler(warninp_t wi) : wi_(wi), mapping_(nullptr) {}
1791 void setBackMapping(const gmx::IKeyValueTreeBackMapping& mapping) { mapping_ = &mapping; }
1793 bool onError(gmx::UserInputError* ex, const gmx::KeyValueTreePath& context) override
1796 gmx::formatString("Error in mdp option \"%s\":", getOptionName(context).c_str()));
1797 std::string message = gmx::formatExceptionMessageToString(*ex);
1798 warning_error(wi_, message.c_str());
1803 std::string getOptionName(const gmx::KeyValueTreePath& context)
1805 if (mapping_ != nullptr)
1807 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1808 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1811 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1816 const gmx::IKeyValueTreeBackMapping* mapping_;
1821 void get_ir(const char* mdparin,
1822 const char* mdparout,
1823 gmx::MDModules* mdModules,
1826 WriteMdpHeader writeMdpHeader,
1830 double dumdub[2][6];
1832 char warn_buf[STRLEN];
1833 t_lambda* fep = ir->fepvals;
1834 t_expanded* expand = ir->expandedvals;
1836 const char* no_names[] = { "no", nullptr };
1838 init_inputrec_strings();
1839 gmx::TextInputFile stream(mdparin);
1840 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1842 snew(dumstr[0], STRLEN);
1843 snew(dumstr[1], STRLEN);
1845 /* ignore the following deprecated commands */
1846 replace_inp_entry(inp, "title", nullptr);
1847 replace_inp_entry(inp, "cpp", nullptr);
1848 replace_inp_entry(inp, "domain-decomposition", nullptr);
1849 replace_inp_entry(inp, "andersen-seed", nullptr);
1850 replace_inp_entry(inp, "dihre", nullptr);
1851 replace_inp_entry(inp, "dihre-fc", nullptr);
1852 replace_inp_entry(inp, "dihre-tau", nullptr);
1853 replace_inp_entry(inp, "nstdihreout", nullptr);
1854 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1855 replace_inp_entry(inp, "optimize-fft", nullptr);
1856 replace_inp_entry(inp, "adress_type", nullptr);
1857 replace_inp_entry(inp, "adress_const_wf", nullptr);
1858 replace_inp_entry(inp, "adress_ex_width", nullptr);
1859 replace_inp_entry(inp, "adress_hy_width", nullptr);
1860 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1861 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1862 replace_inp_entry(inp, "adress_site", nullptr);
1863 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1864 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1865 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1866 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1867 replace_inp_entry(inp, "rlistlong", nullptr);
1868 replace_inp_entry(inp, "nstcalclr", nullptr);
1869 replace_inp_entry(inp, "pull-print-com2", nullptr);
1870 replace_inp_entry(inp, "gb-algorithm", nullptr);
1871 replace_inp_entry(inp, "nstgbradii", nullptr);
1872 replace_inp_entry(inp, "rgbradii", nullptr);
1873 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1874 replace_inp_entry(inp, "gb-saltconc", nullptr);
1875 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1876 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1877 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1878 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1879 replace_inp_entry(inp, "sa-algorithm", nullptr);
1880 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1881 replace_inp_entry(inp, "ns-type", nullptr);
1883 /* replace the following commands with the clearer new versions*/
1884 replace_inp_entry(inp, "unconstrained-start", "continuation");
1885 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1886 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1887 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1888 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1889 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1890 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1892 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1893 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1894 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1895 setStringEntry(&inp, "include", opts->include, nullptr);
1896 printStringNoNewline(
1897 &inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1898 setStringEntry(&inp, "define", opts->define, nullptr);
1900 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1901 ir->eI = get_eeenum(&inp, "integrator", ei_names, wi);
1902 printStringNoNewline(&inp, "Start time and timestep in ps");
1903 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1904 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1905 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1906 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1907 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1908 printStringNoNewline(
1909 &inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1910 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1911 printStringNoNewline(&inp, "mode for center of mass motion removal");
1912 ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
1913 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
1914 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
1915 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
1916 setStringEntry(&inp, "comm-grps", is->vcm, nullptr);
1918 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
1919 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
1920 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
1921 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
1924 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
1925 printStringNoNewline(&inp, "Force tolerance and initial step-size");
1926 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
1927 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
1928 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
1929 ir->niter = get_eint(&inp, "niter", 20, wi);
1930 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
1931 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
1932 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
1933 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
1934 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
1936 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
1937 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
1939 /* Output options */
1940 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
1941 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
1942 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
1943 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
1944 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
1945 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
1946 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
1947 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
1948 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
1949 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
1950 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
1951 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
1952 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
1953 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
1954 printStringNoNewline(&inp, "default, all atoms will be written.");
1955 setStringEntry(&inp, "compressed-x-grps", is->x_compressed_groups, nullptr);
1956 printStringNoNewline(&inp, "Selection of energy groups");
1957 setStringEntry(&inp, "energygrps", is->energy, nullptr);
1959 /* Neighbor searching */
1960 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
1961 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs)");
1962 ir->cutoff_scheme = get_eeenum(&inp, "cutoff-scheme", ecutscheme_names, wi);
1963 printStringNoNewline(&inp, "nblist update frequency");
1964 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
1965 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
1966 ir->ePBC = get_eeenum(&inp, "pbc", epbc_names, wi);
1967 ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi) != 0;
1968 printStringNoNewline(&inp,
1969 "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1970 printStringNoNewline(&inp, "a value of -1 means: use rlist");
1971 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
1972 printStringNoNewline(&inp, "nblist cut-off");
1973 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
1974 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
1976 /* Electrostatics */
1977 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
1978 printStringNoNewline(&inp, "Method for doing electrostatics");
1979 ir->coulombtype = get_eeenum(&inp, "coulombtype", eel_names, wi);
1980 ir->coulomb_modifier = get_eeenum(&inp, "coulomb-modifier", eintmod_names, wi);
1981 printStringNoNewline(&inp, "cut-off lengths");
1982 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
1983 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
1984 printStringNoNewline(&inp,
1985 "Relative dielectric constant for the medium and the reaction field");
1986 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
1987 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
1988 printStringNoNewline(&inp, "Method for doing Van der Waals");
1989 ir->vdwtype = get_eeenum(&inp, "vdw-type", evdw_names, wi);
1990 ir->vdw_modifier = get_eeenum(&inp, "vdw-modifier", eintmod_names, wi);
1991 printStringNoNewline(&inp, "cut-off lengths");
1992 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
1993 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
1994 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
1995 ir->eDispCorr = get_eeenum(&inp, "DispCorr", edispc_names, wi);
1996 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
1997 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
1998 printStringNoNewline(&inp, "Separate tables between energy group pairs");
1999 setStringEntry(&inp, "energygrp-table", is->egptable, nullptr);
2000 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
2001 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
2002 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
2003 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
2004 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
2005 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
2006 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
2007 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
2008 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
2009 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
2010 ir->ljpme_combination_rule = get_eeenum(&inp, "lj-pme-comb-rule", eljpme_names, wi);
2011 ir->ewald_geometry = get_eeenum(&inp, "ewald-geometry", eewg_names, wi);
2012 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
2014 /* Implicit solvation is no longer supported, but we need grompp
2015 to be able to refuse old .mdp files that would have built a tpr
2016 to run it. Thus, only "no" is accepted. */
2017 ir->implicit_solvent = (get_eeenum(&inp, "implicit-solvent", no_names, wi) != 0);
2019 /* Coupling stuff */
2020 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
2021 printStringNoNewline(&inp, "Temperature coupling");
2022 ir->etc = get_eeenum(&inp, "tcoupl", etcoupl_names, wi);
2023 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
2024 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
2025 ir->bPrintNHChains = (get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi) != 0);
2026 printStringNoNewline(&inp, "Groups to couple separately");
2027 setStringEntry(&inp, "tc-grps", is->tcgrps, nullptr);
2028 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
2029 setStringEntry(&inp, "tau-t", is->tau_t, nullptr);
2030 setStringEntry(&inp, "ref-t", is->ref_t, nullptr);
2031 printStringNoNewline(&inp, "pressure coupling");
2032 ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
2033 ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
2034 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
2035 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
2036 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
2037 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
2038 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
2039 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
2040 ir->refcoord_scaling = get_eeenum(&inp, "refcoord-scaling", erefscaling_names, wi);
2043 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
2044 ir->bQMMM = (get_eeenum(&inp, "QMMM", yesno_names, wi) != 0);
2045 printStringNoNewline(&inp, "Groups treated Quantum Mechanically");
2046 setStringEntry(&inp, "QMMM-grps", is->QMMM, nullptr);
2047 printStringNoNewline(&inp, "QM method");
2048 setStringEntry(&inp, "QMmethod", is->QMmethod, nullptr);
2049 printStringNoNewline(&inp, "QMMM scheme");
2050 ir->QMMMscheme = get_eeenum(&inp, "QMMMscheme", eQMMMscheme_names, wi);
2051 printStringNoNewline(&inp, "QM basisset");
2052 setStringEntry(&inp, "QMbasis", is->QMbasis, nullptr);
2053 printStringNoNewline(&inp, "QM charge");
2054 setStringEntry(&inp, "QMcharge", is->QMcharge, nullptr);
2055 printStringNoNewline(&inp, "QM multiplicity");
2056 setStringEntry(&inp, "QMmult", is->QMmult, nullptr);
2057 printStringNoNewline(&inp, "Surface Hopping");
2058 setStringEntry(&inp, "SH", is->bSH, nullptr);
2059 printStringNoNewline(&inp, "CAS space options");
2060 setStringEntry(&inp, "CASorbitals", is->CASorbitals, nullptr);
2061 setStringEntry(&inp, "CASelectrons", is->CASelectrons, nullptr);
2062 setStringEntry(&inp, "SAon", is->SAon, nullptr);
2063 setStringEntry(&inp, "SAoff", is->SAoff, nullptr);
2064 setStringEntry(&inp, "SAsteps", is->SAsteps, nullptr);
2065 printStringNoNewline(&inp, "Scale factor for MM charges");
2066 ir->scalefactor = get_ereal(&inp, "MMChargeScaleFactor", 1.0, wi);
2068 /* Simulated annealing */
2069 printStringNewline(&inp, "SIMULATED ANNEALING");
2070 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2071 setStringEntry(&inp, "annealing", is->anneal, nullptr);
2072 printStringNoNewline(&inp,
2073 "Number of time points to use for specifying annealing in each group");
2074 setStringEntry(&inp, "annealing-npoints", is->anneal_npoints, nullptr);
2075 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2076 setStringEntry(&inp, "annealing-time", is->anneal_time, nullptr);
2077 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2078 setStringEntry(&inp, "annealing-temp", is->anneal_temp, nullptr);
2081 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2082 opts->bGenVel = (get_eeenum(&inp, "gen-vel", yesno_names, wi) != 0);
2083 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2084 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2087 printStringNewline(&inp, "OPTIONS FOR BONDS");
2088 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2089 printStringNoNewline(&inp, "Type of constraint algorithm");
2090 ir->eConstrAlg = get_eeenum(&inp, "constraint-algorithm", econstr_names, wi);
2091 printStringNoNewline(&inp, "Do not constrain the start configuration");
2092 ir->bContinuation = (get_eeenum(&inp, "continuation", yesno_names, wi) != 0);
2093 printStringNoNewline(&inp,
2094 "Use successive overrelaxation to reduce the number of shake iterations");
2095 ir->bShakeSOR = (get_eeenum(&inp, "Shake-SOR", yesno_names, wi) != 0);
2096 printStringNoNewline(&inp, "Relative tolerance of shake");
2097 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2098 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2099 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2100 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2101 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2102 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2103 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2104 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2105 printStringNoNewline(&inp, "rotates over more degrees than");
2106 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2107 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2108 opts->bMorse = (get_eeenum(&inp, "morse", yesno_names, wi) != 0);
2110 /* Energy group exclusions */
2111 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2112 printStringNoNewline(
2113 &inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2114 setStringEntry(&inp, "energygrp-excl", is->egpexcl, nullptr);
2117 printStringNewline(&inp, "WALLS");
2118 printStringNoNewline(
2119 &inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2120 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2121 ir->wall_type = get_eeenum(&inp, "wall-type", ewt_names, wi);
2122 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2123 setStringEntry(&inp, "wall-atomtype", is->wall_atomtype, nullptr);
2124 setStringEntry(&inp, "wall-density", is->wall_density, nullptr);
2125 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2128 printStringNewline(&inp, "COM PULLING");
2129 ir->bPull = (get_eeenum(&inp, "pull", yesno_names, wi) != 0);
2133 is->pull_grp = read_pullparams(&inp, ir->pull, wi);
2137 NOTE: needs COM pulling input */
2138 printStringNewline(&inp, "AWH biasing");
2139 ir->bDoAwh = (get_eeenum(&inp, "awh", yesno_names, wi) != 0);
2144 ir->awhParams = gmx::readAndCheckAwhParams(&inp, ir, wi);
2148 gmx_fatal(FARGS, "AWH biasing is only compatible with COM pulling turned on");
2152 /* Enforced rotation */
2153 printStringNewline(&inp, "ENFORCED ROTATION");
2154 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2155 ir->bRot = (get_eeenum(&inp, "rotation", yesno_names, wi) != 0);
2159 is->rot_grp = read_rotparams(&inp, ir->rot, wi);
2162 /* Interactive MD */
2164 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2165 setStringEntry(&inp, "IMD-group", is->imd_grp, nullptr);
2166 if (is->imd_grp[0] != '\0')
2173 printStringNewline(&inp, "NMR refinement stuff");
2174 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2175 ir->eDisre = get_eeenum(&inp, "disre", edisre_names, wi);
2176 printStringNoNewline(
2177 &inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2178 ir->eDisreWeighting = get_eeenum(&inp, "disre-weighting", edisreweighting_names, wi);
2179 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2180 ir->bDisreMixed = (get_eeenum(&inp, "disre-mixed", yesno_names, wi) != 0);
2181 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2182 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2183 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2184 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2185 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2186 opts->bOrire = (get_eeenum(&inp, "orire", yesno_names, wi) != 0);
2187 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2188 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2189 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2190 setStringEntry(&inp, "orire-fitgrp", is->orirefitgrp, nullptr);
2191 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2192 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2194 /* free energy variables */
2195 printStringNewline(&inp, "Free energy variables");
2196 ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
2197 setStringEntry(&inp, "couple-moltype", is->couple_moltype, nullptr);
2198 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2199 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2200 opts->bCoupleIntra = (get_eeenum(&inp, "couple-intramol", yesno_names, wi) != 0);
2202 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2204 it was not entered */
2205 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2206 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2207 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2208 setStringEntry(&inp, "fep-lambdas", is->fep_lambda[efptFEP], nullptr);
2209 setStringEntry(&inp, "mass-lambdas", is->fep_lambda[efptMASS], nullptr);
2210 setStringEntry(&inp, "coul-lambdas", is->fep_lambda[efptCOUL], nullptr);
2211 setStringEntry(&inp, "vdw-lambdas", is->fep_lambda[efptVDW], nullptr);
2212 setStringEntry(&inp, "bonded-lambdas", is->fep_lambda[efptBONDED], nullptr);
2213 setStringEntry(&inp, "restraint-lambdas", is->fep_lambda[efptRESTRAINT], nullptr);
2214 setStringEntry(&inp, "temperature-lambdas", is->fep_lambda[efptTEMPERATURE], nullptr);
2215 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2216 setStringEntry(&inp, "init-lambda-weights", is->lambda_weights, nullptr);
2217 fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
2218 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2219 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2220 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2221 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2222 fep->bScCoul = (get_eeenum(&inp, "sc-coul", yesno_names, wi) != 0);
2223 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2224 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2225 fep->separate_dhdl_file = get_eeenum(&inp, "separate-dhdl-file", separate_dhdl_file_names, wi);
2226 fep->dhdl_derivatives = get_eeenum(&inp, "dhdl-derivatives", dhdl_derivatives_names, wi);
2227 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2228 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2230 /* Non-equilibrium MD stuff */
2231 printStringNewline(&inp, "Non-equilibrium MD stuff");
2232 setStringEntry(&inp, "acc-grps", is->accgrps, nullptr);
2233 setStringEntry(&inp, "accelerate", is->acc, nullptr);
2234 setStringEntry(&inp, "freezegrps", is->freeze, nullptr);
2235 setStringEntry(&inp, "freezedim", is->frdim, nullptr);
2236 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2237 setStringEntry(&inp, "deform", is->deform, nullptr);
2239 /* simulated tempering variables */
2240 printStringNewline(&inp, "simulated tempering variables");
2241 ir->bSimTemp = (get_eeenum(&inp, "simulated-tempering", yesno_names, wi) != 0);
2242 ir->simtempvals->eSimTempScale = get_eeenum(&inp, "simulated-tempering-scaling", esimtemp_names, wi);
2243 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2244 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2246 /* expanded ensemble variables */
2247 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2249 read_expandedparams(&inp, expand, wi);
2252 /* Electric fields */
2254 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2255 gmx::KeyValueTreeTransformer transform;
2256 transform.rules()->addRule().keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2257 mdModules->initMdpTransform(transform.rules());
2258 for (const auto& path : transform.mappedPaths())
2260 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2261 mark_einp_set(inp, path[0].c_str());
2263 MdpErrorHandler errorHandler(wi);
2264 auto result = transform.transform(convertedValues, &errorHandler);
2265 ir->params = new gmx::KeyValueTreeObject(result.object());
2266 mdModules->adjustInputrecBasedOnModules(ir);
2267 errorHandler.setBackMapping(result.backMapping());
2268 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2271 /* Ion/water position swapping ("computational electrophysiology") */
2272 printStringNewline(&inp,
2273 "Ion/water position swapping for computational electrophysiology setups");
2274 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2275 ir->eSwapCoords = get_eeenum(&inp, "swapcoords", eSwapTypes_names, wi);
2276 if (ir->eSwapCoords != eswapNO)
2283 printStringNoNewline(&inp, "Swap attempt frequency");
2284 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2285 printStringNoNewline(&inp, "Number of ion types to be controlled");
2286 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2289 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2291 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2292 snew(ir->swap->grp, ir->swap->ngrp);
2293 for (i = 0; i < ir->swap->ngrp; i++)
2295 snew(ir->swap->grp[i].molname, STRLEN);
2297 printStringNoNewline(&inp,
2298 "Two index groups that contain the compartment-partitioning atoms");
2299 setStringEntry(&inp, "split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2300 setStringEntry(&inp, "split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2301 printStringNoNewline(&inp,
2302 "Use center of mass of split groups (yes/no), otherwise center of "
2303 "geometry is used");
2304 ir->swap->massw_split[0] = (get_eeenum(&inp, "massw-split0", yesno_names, wi) != 0);
2305 ir->swap->massw_split[1] = (get_eeenum(&inp, "massw-split1", yesno_names, wi) != 0);
2307 printStringNoNewline(&inp, "Name of solvent molecules");
2308 setStringEntry(&inp, "solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2310 printStringNoNewline(&inp,
2311 "Split cylinder: radius, upper and lower extension (nm) (this will "
2312 "define the channels)");
2313 printStringNoNewline(&inp,
2314 "Note that the split cylinder settings do not have an influence on "
2315 "the swapping protocol,");
2316 printStringNoNewline(
2318 "however, if correctly defined, the permeation events are recorded per channel");
2319 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2320 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2321 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2322 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2323 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2324 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2326 printStringNoNewline(
2328 "Average the number of ions per compartment over these many swap attempt steps");
2329 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2331 printStringNoNewline(
2332 &inp, "Names of the ion types that can be exchanged with solvent molecules,");
2333 printStringNoNewline(
2334 &inp, "and the requested number of ions of this type in compartments A and B");
2335 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2336 for (i = 0; i < nIonTypes; i++)
2338 int ig = eSwapFixedGrpNR + i;
2340 sprintf(buf, "iontype%d-name", i);
2341 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2342 sprintf(buf, "iontype%d-in-A", i);
2343 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2344 sprintf(buf, "iontype%d-in-B", i);
2345 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2348 printStringNoNewline(
2350 "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2351 printStringNoNewline(
2353 "at maximum distance (= bulk concentration) to the split group layers. However,");
2354 printStringNoNewline(&inp,
2355 "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk "
2356 "layer from the middle at 0.0");
2357 printStringNoNewline(&inp,
2358 "towards one of the compartment-partitioning layers (at +/- 1.0).");
2359 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2360 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2361 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2362 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0))
2364 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2367 printStringNoNewline(
2368 &inp, "Start to swap ions if threshold difference to requested count is reached");
2369 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2372 /* AdResS is no longer supported, but we need grompp to be able to
2373 refuse to process old .mdp files that used it. */
2374 ir->bAdress = (get_eeenum(&inp, "adress", no_names, wi) != 0);
2376 /* User defined thingies */
2377 printStringNewline(&inp, "User defined thingies");
2378 setStringEntry(&inp, "user1-grps", is->user1, nullptr);
2379 setStringEntry(&inp, "user2-grps", is->user2, nullptr);
2380 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2381 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2382 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2383 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2384 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2385 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2386 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2387 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2391 gmx::TextOutputFile stream(mdparout);
2392 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2394 // Transform module data into a flat key-value tree for output.
2395 gmx::KeyValueTreeBuilder builder;
2396 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2397 mdModules->buildMdpOutput(&builderObject);
2399 gmx::TextWriter writer(&stream);
2400 writeKeyValueTreeAsMdp(&writer, builder.build());
2405 /* Process options if necessary */
2406 for (m = 0; m < 2; m++)
2408 for (i = 0; i < 2 * DIM; i++)
2417 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2421 "Pressure coupling incorrect number of values (I need exactly 1)");
2423 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2425 case epctSEMIISOTROPIC:
2426 case epctSURFACETENSION:
2427 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2431 "Pressure coupling incorrect number of values (I need exactly 2)");
2433 dumdub[m][YY] = dumdub[m][XX];
2435 case epctANISOTROPIC:
2436 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf", &(dumdub[m][XX]), &(dumdub[m][YY]),
2437 &(dumdub[m][ZZ]), &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5]))
2442 "Pressure coupling incorrect number of values (I need exactly 6)");
2446 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2447 epcoupltype_names[ir->epct]);
2451 clear_mat(ir->ref_p);
2452 clear_mat(ir->compress);
2453 for (i = 0; i < DIM; i++)
2455 ir->ref_p[i][i] = dumdub[1][i];
2456 ir->compress[i][i] = dumdub[0][i];
2458 if (ir->epct == epctANISOTROPIC)
2460 ir->ref_p[XX][YY] = dumdub[1][3];
2461 ir->ref_p[XX][ZZ] = dumdub[1][4];
2462 ir->ref_p[YY][ZZ] = dumdub[1][5];
2463 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2466 "All off-diagonal reference pressures are non-zero. Are you sure you want to "
2467 "apply a threefold shear stress?\n");
2469 ir->compress[XX][YY] = dumdub[0][3];
2470 ir->compress[XX][ZZ] = dumdub[0][4];
2471 ir->compress[YY][ZZ] = dumdub[0][5];
2472 for (i = 0; i < DIM; i++)
2474 for (m = 0; m < i; m++)
2476 ir->ref_p[i][m] = ir->ref_p[m][i];
2477 ir->compress[i][m] = ir->compress[m][i];
2482 if (ir->comm_mode == ecmNO)
2487 opts->couple_moltype = nullptr;
2488 if (strlen(is->couple_moltype) > 0)
2490 if (ir->efep != efepNO)
2492 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2493 if (opts->couple_lam0 == opts->couple_lam1)
2495 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2497 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
2501 "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
2508 "Free energy is turned off, so we will not decouple the molecule listed "
2512 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2513 if (ir->efep != efepNO)
2515 if (fep->delta_lambda > 0)
2517 ir->efep = efepSLOWGROWTH;
2521 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2523 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2525 "Old option for dhdl-print-energy given: "
2526 "changing \"yes\" to \"total\"\n");
2529 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2531 /* always print out the energy to dhdl if we are doing
2532 expanded ensemble, since we need the total energy for
2533 analysis if the temperature is changing. In some
2534 conditions one may only want the potential energy, so
2535 we will allow that if the appropriate mdp setting has
2536 been enabled. Otherwise, total it is:
2538 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2541 if ((ir->efep != efepNO) || ir->bSimTemp)
2543 ir->bExpanded = FALSE;
2544 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2546 ir->bExpanded = TRUE;
2548 do_fep_params(ir, is->fep_lambda, is->lambda_weights, wi);
2549 if (ir->bSimTemp) /* done after fep params */
2551 do_simtemp_params(ir);
2554 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2555 * setup and not on the old way of specifying the free-energy setup,
2556 * we should check for using soft-core when not needed, since that
2557 * can complicate the sampling significantly.
2558 * Note that we only check for the automated coupling setup.
2559 * If the (advanced) user does FEP through manual topology changes,
2560 * this check will not be triggered.
2562 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 && ir->fepvals->sc_alpha != 0
2563 && (couple_lambda_has_vdw_on(opts->couple_lam0) && couple_lambda_has_vdw_on(opts->couple_lam1)))
2566 "You are using soft-core interactions while the Van der Waals interactions are "
2567 "not decoupled (note that the sc-coul option is only active when using lambda "
2568 "states). Although this will not lead to errors, you will need much more "
2569 "sampling than without soft-core interactions. Consider using sc-alpha=0.");
2574 ir->fepvals->n_lambda = 0;
2577 /* WALL PARAMETERS */
2579 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts, wi);
2581 /* ORIENTATION RESTRAINT PARAMETERS */
2583 if (opts->bOrire && gmx::splitString(is->orirefitgrp).size() != 1)
2585 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2588 /* DEFORMATION PARAMETERS */
2590 clear_mat(ir->deform);
2591 for (i = 0; i < 6; i++)
2596 double gmx_unused canary;
2597 int ndeform = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf %lf", &(dumdub[0][0]), &(dumdub[0][1]),
2598 &(dumdub[0][2]), &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]), &canary);
2600 if (strlen(is->deform) > 0 && ndeform != 6)
2603 wi, gmx::formatString(
2604 "Cannot parse exactly 6 box deformation velocities from string '%s'", is->deform)
2607 for (i = 0; i < 3; i++)
2609 ir->deform[i][i] = dumdub[0][i];
2611 ir->deform[YY][XX] = dumdub[0][3];
2612 ir->deform[ZZ][XX] = dumdub[0][4];
2613 ir->deform[ZZ][YY] = dumdub[0][5];
2614 if (ir->epc != epcNO)
2616 for (i = 0; i < 3; i++)
2618 for (j = 0; j <= i; j++)
2620 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2622 warning_error(wi, "A box element has deform set and compressibility > 0");
2626 for (i = 0; i < 3; i++)
2628 for (j = 0; j < i; j++)
2630 if (ir->deform[i][j] != 0)
2632 for (m = j; m < DIM; m++)
2634 if (ir->compress[m][j] != 0)
2637 "An off-diagonal box element has deform set while "
2638 "compressibility > 0 for the same component of another box "
2639 "vector, this might lead to spurious periodicity effects.");
2640 warning(wi, warn_buf);
2648 /* Ion/water position swapping checks */
2649 if (ir->eSwapCoords != eswapNO)
2651 if (ir->swap->nstswap < 1)
2653 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2655 if (ir->swap->nAverage < 1)
2657 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2659 if (ir->swap->threshold < 1.0)
2661 warning_error(wi, "Ion count threshold must be at least 1.\n");
2669 static int search_QMstring(const char* s, int ng, const char* gn[])
2671 /* same as normal search_string, but this one searches QM strings */
2674 for (i = 0; (i < ng); i++)
2676 if (gmx_strcasecmp(s, gn[i]) == 0)
2682 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2683 } /* search_QMstring */
2685 /* We would like gn to be const as well, but C doesn't allow this */
2686 /* TODO this is utility functionality (search for the index of a
2687 string in a collection), so should be refactored and located more
2689 int search_string(const char* s, int ng, char* gn[])
2693 for (i = 0; (i < ng); i++)
2695 if (gmx_strcasecmp(s, gn[i]) == 0)
2702 "Group %s referenced in the .mdp file was not found in the index file.\n"
2703 "Group names must match either [moleculetype] names or custom index group\n"
2704 "names, in which case you must supply an index file to the '-n' option\n"
2709 static bool do_numbering(int natoms,
2710 SimulationGroups* groups,
2711 gmx::ArrayRef<std::string> groupsFromMdpFile,
2714 SimulationAtomGroupType gtype,
2720 unsigned short* cbuf;
2721 AtomGroupIndices* grps = &(groups->groups[gtype]);
2722 int j, gid, aj, ognr, ntot = 0;
2725 char warn_buf[STRLEN];
2727 title = shortName(gtype);
2730 /* Mark all id's as not set */
2731 for (int i = 0; (i < natoms); i++)
2736 for (int i = 0; i != groupsFromMdpFile.ssize(); ++i)
2738 /* Lookup the group name in the block structure */
2739 gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
2740 if ((grptp != egrptpONE) || (i == 0))
2742 grps->emplace_back(gid);
2745 /* Now go over the atoms in the group */
2746 for (j = block->index[gid]; (j < block->index[gid + 1]); j++)
2751 /* Range checking */
2752 if ((aj < 0) || (aj >= natoms))
2754 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj + 1);
2756 /* Lookup up the old group number */
2760 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)", aj + 1, title,
2765 /* Store the group number in buffer */
2766 if (grptp == egrptpONE)
2779 /* Now check whether we have done all atoms */
2783 if (grptp == egrptpALL)
2785 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2787 else if (grptp == egrptpPART)
2789 sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
2790 warning_note(wi, warn_buf);
2792 /* Assign all atoms currently unassigned to a rest group */
2793 for (j = 0; (j < natoms); j++)
2795 if (cbuf[j] == NOGID)
2797 cbuf[j] = grps->size();
2801 if (grptp != egrptpPART)
2805 fprintf(stderr, "Making dummy/rest group for %s containing %d elements\n", title,
2808 /* Add group name "rest" */
2809 grps->emplace_back(restnm);
2811 /* Assign the rest name to all atoms not currently assigned to a group */
2812 for (j = 0; (j < natoms); j++)
2814 if (cbuf[j] == NOGID)
2816 // group size was not updated before this here, so need to use -1.
2817 cbuf[j] = grps->size() - 1;
2823 if (grps->size() == 1 && (ntot == 0 || ntot == natoms))
2825 /* All atoms are part of one (or no) group, no index required */
2826 groups->groupNumbers[gtype].clear();
2830 for (int j = 0; (j < natoms); j++)
2832 groups->groupNumbers[gtype].emplace_back(cbuf[j]);
2838 return (bRest && grptp == egrptpPART);
2841 static void calc_nrdf(const gmx_mtop_t* mtop, t_inputrec* ir, char** gnames)
2844 pull_params_t* pull;
2845 int natoms, imin, jmin;
2846 int * nrdf2, *na_vcm, na_tot;
2847 double * nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2852 * First calc 3xnr-atoms for each group
2853 * then subtract half a degree of freedom for each constraint
2855 * Only atoms and nuclei contribute to the degrees of freedom...
2860 const SimulationGroups& groups = mtop->groups;
2861 natoms = mtop->natoms;
2863 /* Allocate one more for a possible rest group */
2864 /* We need to sum degrees of freedom into doubles,
2865 * since floats give too low nrdf's above 3 million atoms.
2867 snew(nrdf_tc, groups.groups[SimulationAtomGroupType::TemperatureCoupling].size() + 1);
2868 snew(nrdf_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2869 snew(dof_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2870 snew(na_vcm, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2871 snew(nrdf_vcm_sub, groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval].size() + 1);
2873 for (gmx::index i = 0; i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
2877 for (gmx::index i = 0;
2878 i < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; i++)
2881 clear_ivec(dof_vcm[i]);
2883 nrdf_vcm_sub[i] = 0;
2885 snew(nrdf2, natoms);
2886 for (const AtomProxy atomP : AtomRange(*mtop))
2888 const t_atom& local = atomP.atom();
2889 int i = atomP.globalAtomNumber();
2891 if (local.ptype == eptAtom || local.ptype == eptNucleus)
2893 int g = getGroupType(groups, SimulationAtomGroupType::Freeze, i);
2894 for (int d = 0; d < DIM; d++)
2896 if (opts->nFreeze[g][d] == 0)
2898 /* Add one DOF for particle i (counted as 2*1) */
2900 /* VCM group i has dim d as a DOF */
2901 dof_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)][d] =
2905 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, i)] +=
2907 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i)] +=
2913 for (const gmx_molblock_t& molb : mtop->molblock)
2915 const gmx_moltype_t& molt = mtop->moltype[molb.type];
2916 const t_atom* atom = molt.atoms.atom;
2917 for (int mol = 0; mol < molb.nmol; mol++)
2919 for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2921 gmx::ArrayRef<const int> ia = molt.ilist[ftype].iatoms;
2922 for (int i = 0; i < molt.ilist[ftype].size();)
2924 /* Subtract degrees of freedom for the constraints,
2925 * if the particles still have degrees of freedom left.
2926 * If one of the particles is a vsite or a shell, then all
2927 * constraint motion will go there, but since they do not
2928 * contribute to the constraints the degrees of freedom do not
2931 int ai = as + ia[i + 1];
2932 int aj = as + ia[i + 2];
2933 if (((atom[ia[i + 1]].ptype == eptNucleus) || (atom[ia[i + 1]].ptype == eptAtom))
2934 && ((atom[ia[i + 2]].ptype == eptNucleus) || (atom[ia[i + 2]].ptype == eptAtom)))
2952 imin = std::min(imin, nrdf2[ai]);
2953 jmin = std::min(jmin, nrdf2[aj]);
2956 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2958 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, aj)] -=
2960 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2962 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, aj)] -=
2965 i += interaction_function[ftype].nratoms + 1;
2968 gmx::ArrayRef<const int> ia = molt.ilist[F_SETTLE].iatoms;
2969 for (int i = 0; i < molt.ilist[F_SETTLE].size();)
2971 /* Subtract 1 dof from every atom in the SETTLE */
2972 for (int j = 0; j < 3; j++)
2974 int ai = as + ia[i + 1 + j];
2975 imin = std::min(2, nrdf2[ai]);
2977 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
2979 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
2984 as += molt.atoms.nr;
2990 /* Correct nrdf for the COM constraints.
2991 * We correct using the TC and VCM group of the first atom
2992 * in the reference and pull group. If atoms in one pull group
2993 * belong to different TC or VCM groups it is anyhow difficult
2994 * to determine the optimal nrdf assignment.
2998 for (int i = 0; i < pull->ncoord; i++)
3000 if (pull->coord[i].eType != epullCONSTRAINT)
3007 for (int j = 0; j < 2; j++)
3009 const t_pull_group* pgrp;
3011 pgrp = &pull->group[pull->coord[i].group[j]];
3015 /* Subtract 1/2 dof from each group */
3016 int ai = pgrp->ind[0];
3017 nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] -=
3019 nrdf_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)] -=
3021 if (nrdf_tc[getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai)] < 0)
3024 "Center of mass pulling constraints caused the number of degrees "
3025 "of freedom for temperature coupling group %s to be negative",
3026 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][getGroupType(
3027 groups, SimulationAtomGroupType::TemperatureCoupling, ai)]]);
3032 /* We need to subtract the whole DOF from group j=1 */
3039 if (ir->nstcomm != 0)
3043 /* We remove COM motion up to dim ndof_com() */
3044 ndim_rm_vcm = ndof_com(ir);
3046 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3047 * the number of degrees of freedom in each vcm group when COM
3048 * translation is removed and 6 when rotation is removed as well.
3050 for (gmx::index j = 0;
3051 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3053 switch (ir->comm_mode)
3056 case ecmLINEAR_ACCELERATION_CORRECTION:
3057 nrdf_vcm_sub[j] = 0;
3058 for (int d = 0; d < ndim_rm_vcm; d++)
3066 case ecmANGULAR: nrdf_vcm_sub[j] = 6; break;
3067 default: gmx_incons("Checking comm_mode");
3071 for (gmx::index i = 0;
3072 i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling]); i++)
3074 /* Count the number of atoms of TC group i for every VCM group */
3075 for (gmx::index j = 0;
3076 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3081 for (int ai = 0; ai < natoms; ai++)
3083 if (getGroupType(groups, SimulationAtomGroupType::TemperatureCoupling, ai) == i)
3085 na_vcm[getGroupType(groups, SimulationAtomGroupType::MassCenterVelocityRemoval, ai)]++;
3089 /* Correct for VCM removal according to the fraction of each VCM
3090 * group present in this TC group.
3092 nrdf_uc = nrdf_tc[i];
3094 for (gmx::index j = 0;
3095 j < gmx::ssize(groups.groups[SimulationAtomGroupType::MassCenterVelocityRemoval]) + 1; j++)
3097 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3099 nrdf_tc[i] += nrdf_uc * (static_cast<double>(na_vcm[j]) / static_cast<double>(na_tot))
3100 * (nrdf_vcm[j] - nrdf_vcm_sub[j]) / nrdf_vcm[j];
3105 for (int i = 0; (i < gmx::ssize(groups.groups[SimulationAtomGroupType::TemperatureCoupling])); i++)
3107 opts->nrdf[i] = nrdf_tc[i];
3108 if (opts->nrdf[i] < 0)
3112 fprintf(stderr, "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3113 gnames[groups.groups[SimulationAtomGroupType::TemperatureCoupling][i]], opts->nrdf[i]);
3121 sfree(nrdf_vcm_sub);
3124 static bool do_egp_flag(t_inputrec* ir, SimulationGroups* groups, const char* option, const char* val, int flag)
3126 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3127 * But since this is much larger than STRLEN, such a line can not be parsed.
3128 * The real maximum is the number of names that fit in a string: STRLEN/2.
3130 #define EGP_MAX (STRLEN / 2)
3134 auto names = gmx::splitString(val);
3135 if (names.size() % 2 != 0)
3137 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3139 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3141 for (size_t i = 0; i < names.size() / 2; i++)
3143 // TODO this needs to be replaced by a solution using std::find_if
3147 names[2 * i].c_str(),
3148 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
3154 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i].c_str(), option);
3159 names[2 * i + 1].c_str(),
3160 *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
3166 gmx_fatal(FARGS, "%s in %s is not an energy group\n", names[2 * i + 1].c_str(), option);
3168 if ((j < nr) && (k < nr))
3170 ir->opts.egp_flags[nr * j + k] |= flag;
3171 ir->opts.egp_flags[nr * k + j] |= flag;
3180 static void make_swap_groups(t_swapcoords* swap, t_blocka* grps, char** gnames)
3182 int ig = -1, i = 0, gind;
3186 /* Just a quick check here, more thorough checks are in mdrun */
3187 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3189 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3192 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3193 for (ig = 0; ig < swap->ngrp; ig++)
3195 swapg = &swap->grp[ig];
3196 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3197 swapg->nat = grps->index[gind + 1] - grps->index[gind];
3201 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3202 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap", swap->grp[ig].molname, swapg->nat);
3203 snew(swapg->ind, swapg->nat);
3204 for (i = 0; i < swapg->nat; i++)
3206 swapg->ind[i] = grps->a[grps->index[gind] + i];
3211 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3217 static void make_IMD_group(t_IMD* IMDgroup, char* IMDgname, t_blocka* grps, char** gnames)
3222 ig = search_string(IMDgname, grps->nr, gnames);
3223 IMDgroup->nat = grps->index[ig + 1] - grps->index[ig];
3225 if (IMDgroup->nat > 0)
3228 "Group '%s' with %d atoms can be activated for interactive molecular dynamics "
3230 IMDgname, IMDgroup->nat);
3231 snew(IMDgroup->ind, IMDgroup->nat);
3232 for (i = 0; i < IMDgroup->nat; i++)
3234 IMDgroup->ind[i] = grps->a[grps->index[ig] + i];
3239 void do_index(const char* mdparin,
3243 const gmx::MdModulesNotifier& notifier,
3247 t_blocka* defaultIndexGroups;
3251 char warnbuf[STRLEN], **gnames;
3255 int i, j, k, restnm;
3256 bool bExcl, bTable, bAnneal, bRest;
3257 char warn_buf[STRLEN];
3261 fprintf(stderr, "processing index file...\n");
3265 snew(defaultIndexGroups, 1);
3266 snew(defaultIndexGroups->index, 1);
3268 atoms_all = gmx_mtop_global_atoms(mtop);
3269 analyse(&atoms_all, defaultIndexGroups, &gnames, FALSE, TRUE);
3270 done_atom(&atoms_all);
3274 defaultIndexGroups = init_index(ndx, &gnames);
3277 SimulationGroups* groups = &mtop->groups;
3278 natoms = mtop->natoms;
3279 symtab = &mtop->symtab;
3281 for (int i = 0; (i < defaultIndexGroups->nr); i++)
3283 groups->groupNames.emplace_back(put_symtab(symtab, gnames[i]));
3285 groups->groupNames.emplace_back(put_symtab(symtab, "rest"));
3286 restnm = groups->groupNames.size() - 1;
3287 GMX_RELEASE_ASSERT(restnm == defaultIndexGroups->nr, "Size of allocations must match");
3288 srenew(gnames, defaultIndexGroups->nr + 1);
3289 gnames[restnm] = *(groups->groupNames.back());
3291 set_warning_line(wi, mdparin, -1);
3293 auto temperatureCouplingTauValues = gmx::splitString(is->tau_t);
3294 auto temperatureCouplingReferenceValues = gmx::splitString(is->ref_t);
3295 auto temperatureCouplingGroupNames = gmx::splitString(is->tcgrps);
3296 if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
3297 || temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
3300 "Invalid T coupling input: %zu groups, %zu ref-t values and "
3302 temperatureCouplingGroupNames.size(), temperatureCouplingReferenceValues.size(),
3303 temperatureCouplingTauValues.size());
3306 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3307 do_numbering(natoms, groups, temperatureCouplingGroupNames, defaultIndexGroups, gnames,
3308 SimulationAtomGroupType::TemperatureCoupling, restnm,
3309 useReferenceTemperature ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3310 nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
3312 snew(ir->opts.nrdf, nr);
3313 snew(ir->opts.tau_t, nr);
3314 snew(ir->opts.ref_t, nr);
3315 if (ir->eI == eiBD && ir->bd_fric == 0)
3317 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3320 if (useReferenceTemperature)
3322 if (size_t(nr) != temperatureCouplingReferenceValues.size())
3324 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3328 convertReals(wi, temperatureCouplingTauValues, "tau-t", ir->opts.tau_t);
3329 for (i = 0; (i < nr); i++)
3331 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3333 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3334 warning_error(wi, warn_buf);
3337 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3341 "tau-t = -1 is the value to signal that a group should not have "
3342 "temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3345 if (ir->opts.tau_t[i] >= 0)
3347 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3350 if (ir->etc != etcNO && ir->nsttcouple == -1)
3352 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3357 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3360 "Cannot do Nose-Hoover temperature with Berendsen pressure control with "
3361 "md-vv; use either vrescale temperature with berendsen pressure or "
3362 "Nose-Hoover temperature with MTTK pressure");
3364 if (ir->epc == epcMTTK)
3366 if (ir->etc != etcNOSEHOOVER)
3369 "Cannot do MTTK pressure coupling without Nose-Hoover temperature "
3374 if (ir->nstpcouple != ir->nsttcouple)
3376 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3377 ir->nstpcouple = ir->nsttcouple = mincouple;
3379 "for current Trotter decomposition methods with vv, nsttcouple and "
3380 "nstpcouple must be equal. Both have been reset to "
3381 "min(nsttcouple,nstpcouple) = %d",
3383 warning_note(wi, warn_buf);
3388 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3389 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3391 if (ETC_ANDERSEN(ir->etc))
3393 if (ir->nsttcouple != 1)
3397 "Andersen temperature control methods assume nsttcouple = 1; there is no "
3398 "need for larger nsttcouple > 1, since no global parameters are computed. "
3399 "nsttcouple has been reset to 1");
3400 warning_note(wi, warn_buf);
3403 nstcmin = tcouple_min_integration_steps(ir->etc);
3406 if (tau_min / (ir->delta_t * ir->nsttcouple) < nstcmin - 10 * GMX_REAL_EPS)
3409 "For proper integration of the %s thermostat, tau-t (%g) should be at "
3410 "least %d times larger than nsttcouple*dt (%g)",
3411 ETCOUPLTYPE(ir->etc), tau_min, nstcmin, ir->nsttcouple * ir->delta_t);
3412 warning(wi, warn_buf);
3415 convertReals(wi, temperatureCouplingReferenceValues, "ref-t", ir->opts.ref_t);
3416 for (i = 0; (i < nr); i++)
3418 if (ir->opts.ref_t[i] < 0)
3420 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3423 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3424 if we are in this conditional) if mc_temp is negative */
3425 if (ir->expandedvals->mc_temp < 0)
3427 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3431 /* Simulated annealing for each group. There are nr groups */
3432 auto simulatedAnnealingGroupNames = gmx::splitString(is->anneal);
3433 if (simulatedAnnealingGroupNames.size() == 1
3434 && gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
3436 simulatedAnnealingGroupNames.resize(0);
3438 if (!simulatedAnnealingGroupNames.empty() && gmx::ssize(simulatedAnnealingGroupNames) != nr)
3440 gmx_fatal(FARGS, "Wrong number of annealing values: %zu (for %d groups)\n",
3441 simulatedAnnealingGroupNames.size(), nr);
3445 snew(ir->opts.annealing, nr);
3446 snew(ir->opts.anneal_npoints, nr);
3447 snew(ir->opts.anneal_time, nr);
3448 snew(ir->opts.anneal_temp, nr);
3449 for (i = 0; i < nr; i++)
3451 ir->opts.annealing[i] = eannNO;
3452 ir->opts.anneal_npoints[i] = 0;
3453 ir->opts.anneal_time[i] = nullptr;
3454 ir->opts.anneal_temp[i] = nullptr;
3456 if (!simulatedAnnealingGroupNames.empty())
3459 for (i = 0; i < nr; i++)
3461 if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "N", 1))
3463 ir->opts.annealing[i] = eannNO;
3465 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "S", 1))
3467 ir->opts.annealing[i] = eannSINGLE;
3470 else if (gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[i], "P", 1))
3472 ir->opts.annealing[i] = eannPERIODIC;
3478 /* Read the other fields too */
3479 auto simulatedAnnealingPoints = gmx::splitString(is->anneal_npoints);
3480 if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
3482 gmx_fatal(FARGS, "Found %zu annealing-npoints values for %zu groups\n",
3483 simulatedAnnealingPoints.size(), simulatedAnnealingGroupNames.size());
3485 convertInts(wi, simulatedAnnealingPoints, "annealing points", ir->opts.anneal_npoints);
3486 size_t numSimulatedAnnealingFields = 0;
3487 for (i = 0; i < nr; i++)
3489 if (ir->opts.anneal_npoints[i] == 1)
3493 "Please specify at least a start and an end point for annealing\n");
3495 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3496 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3497 numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
3500 auto simulatedAnnealingTimes = gmx::splitString(is->anneal_time);
3502 if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
3504 gmx_fatal(FARGS, "Found %zu annealing-time values, wanted %zu\n",
3505 simulatedAnnealingTimes.size(), numSimulatedAnnealingFields);
3507 auto simulatedAnnealingTemperatures = gmx::splitString(is->anneal_temp);
3508 if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
3510 gmx_fatal(FARGS, "Found %zu annealing-temp values, wanted %zu\n",
3511 simulatedAnnealingTemperatures.size(), numSimulatedAnnealingFields);
3514 std::vector<real> allSimulatedAnnealingTimes(numSimulatedAnnealingFields);
3515 std::vector<real> allSimulatedAnnealingTemperatures(numSimulatedAnnealingFields);
3516 convertReals(wi, simulatedAnnealingTimes, "anneal-time",
3517 allSimulatedAnnealingTimes.data());
3518 convertReals(wi, simulatedAnnealingTemperatures, "anneal-temp",
3519 allSimulatedAnnealingTemperatures.data());
3520 for (i = 0, k = 0; i < nr; i++)
3522 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3524 ir->opts.anneal_time[i][j] = allSimulatedAnnealingTimes[k];
3525 ir->opts.anneal_temp[i][j] = allSimulatedAnnealingTemperatures[k];
3528 if (ir->opts.anneal_time[i][0] > (ir->init_t + GMX_REAL_EPS))
3530 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3536 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j - 1])
3539 "Annealing timepoints out of order: t=%f comes after "
3541 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j - 1]);
3544 if (ir->opts.anneal_temp[i][j] < 0)
3546 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n",
3547 ir->opts.anneal_temp[i][j]);
3552 /* Print out some summary information, to make sure we got it right */
3553 for (i = 0; i < nr; i++)
3555 if (ir->opts.annealing[i] != eannNO)
3557 j = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
3558 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3559 *(groups->groupNames[j]), eann_names[ir->opts.annealing[i]],
3560 ir->opts.anneal_npoints[i]);
3561 fprintf(stderr, "Time (ps) Temperature (K)\n");
3562 /* All terms except the last one */
3563 for (j = 0; j < (ir->opts.anneal_npoints[i] - 1); j++)
3565 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3566 ir->opts.anneal_temp[i][j]);
3569 /* Finally the last one */
3570 j = ir->opts.anneal_npoints[i] - 1;
3571 if (ir->opts.annealing[i] == eannSINGLE)
3573 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j],
3574 ir->opts.anneal_temp[i][j]);
3578 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j],
3579 ir->opts.anneal_temp[i][j]);
3580 if (std::fabs(ir->opts.anneal_temp[i][j] - ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3583 "There is a temperature jump when your annealing "
3595 make_pull_groups(ir->pull, is->pull_grp, defaultIndexGroups, gnames);
3597 make_pull_coords(ir->pull);
3602 make_rotation_groups(ir->rot, is->rot_grp, defaultIndexGroups, gnames);
3605 if (ir->eSwapCoords != eswapNO)
3607 make_swap_groups(ir->swap, defaultIndexGroups, gnames);
3610 /* Make indices for IMD session */
3613 make_IMD_group(ir->imd, is->imd_grp, defaultIndexGroups, gnames);
3616 gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
3617 *defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
3618 notifier.notifier_.notify(defaultIndexGroupsAndNames);
3620 auto accelerations = gmx::splitString(is->acc);
3621 auto accelerationGroupNames = gmx::splitString(is->accgrps);
3622 if (accelerationGroupNames.size() * DIM != accelerations.size())
3624 gmx_fatal(FARGS, "Invalid Acceleration input: %zu groups and %zu acc. values",
3625 accelerationGroupNames.size(), accelerations.size());
3627 do_numbering(natoms, groups, accelerationGroupNames, defaultIndexGroups, gnames,
3628 SimulationAtomGroupType::Acceleration, restnm, egrptpALL_GENREST, bVerbose, wi);
3629 nr = groups->groups[SimulationAtomGroupType::Acceleration].size();
3630 snew(ir->opts.acc, nr);
3631 ir->opts.ngacc = nr;
3633 convertRvecs(wi, accelerations, "anneal-time", ir->opts.acc);
3635 auto freezeDims = gmx::splitString(is->frdim);
3636 auto freezeGroupNames = gmx::splitString(is->freeze);
3637 if (freezeDims.size() != DIM * freezeGroupNames.size())
3639 gmx_fatal(FARGS, "Invalid Freezing input: %zu groups and %zu freeze values",
3640 freezeGroupNames.size(), freezeDims.size());
3642 do_numbering(natoms, groups, freezeGroupNames, defaultIndexGroups, gnames,
3643 SimulationAtomGroupType::Freeze, restnm, egrptpALL_GENREST, bVerbose, wi);
3644 nr = groups->groups[SimulationAtomGroupType::Freeze].size();
3645 ir->opts.ngfrz = nr;
3646 snew(ir->opts.nFreeze, nr);
3647 for (i = k = 0; (size_t(i) < freezeGroupNames.size()); i++)
3649 for (j = 0; (j < DIM); j++, k++)
3651 ir->opts.nFreeze[i][j] = static_cast<int>(gmx::equalCaseInsensitive(freezeDims[k], "Y", 1));
3652 if (!ir->opts.nFreeze[i][j])
3654 if (!gmx::equalCaseInsensitive(freezeDims[k], "N", 1))
3657 "Please use Y(ES) or N(O) for freezedim only "
3659 freezeDims[k].c_str());
3660 warning(wi, warn_buf);
3665 for (; (i < nr); i++)
3667 for (j = 0; (j < DIM); j++)
3669 ir->opts.nFreeze[i][j] = 0;
3673 auto energyGroupNames = gmx::splitString(is->energy);
3674 do_numbering(natoms, groups, energyGroupNames, defaultIndexGroups, gnames,
3675 SimulationAtomGroupType::EnergyOutput, restnm, egrptpALL_GENREST, bVerbose, wi);
3676 add_wall_energrps(groups, ir->nwall, symtab);
3677 ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3678 auto vcmGroupNames = gmx::splitString(is->vcm);
3679 bRest = do_numbering(natoms, groups, vcmGroupNames, defaultIndexGroups, gnames,
3680 SimulationAtomGroupType::MassCenterVelocityRemoval, restnm,
3681 vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3685 "Some atoms are not part of any center of mass motion removal group.\n"
3686 "This may lead to artifacts.\n"
3687 "In most cases one should use one group for the whole system.");
3690 /* Now we have filled the freeze struct, so we can calculate NRDF */
3691 calc_nrdf(mtop, ir, gnames);
3693 auto user1GroupNames = gmx::splitString(is->user1);
3694 do_numbering(natoms, groups, user1GroupNames, defaultIndexGroups, gnames,
3695 SimulationAtomGroupType::User1, restnm, egrptpALL_GENREST, bVerbose, wi);
3696 auto user2GroupNames = gmx::splitString(is->user2);
3697 do_numbering(natoms, groups, user2GroupNames, defaultIndexGroups, gnames,
3698 SimulationAtomGroupType::User2, restnm, egrptpALL_GENREST, bVerbose, wi);
3699 auto compressedXGroupNames = gmx::splitString(is->x_compressed_groups);
3700 do_numbering(natoms, groups, compressedXGroupNames, defaultIndexGroups, gnames,
3701 SimulationAtomGroupType::CompressedPositionOutput, restnm, egrptpONE, bVerbose, wi);
3702 auto orirefFitGroupNames = gmx::splitString(is->orirefitgrp);
3703 do_numbering(natoms, groups, orirefFitGroupNames, defaultIndexGroups, gnames,
3704 SimulationAtomGroupType::OrientationRestraintsFit, restnm, egrptpALL_GENREST,
3707 /* QMMM input processing */
3708 auto qmGroupNames = gmx::splitString(is->QMMM);
3709 auto qmMethods = gmx::splitString(is->QMmethod);
3710 auto qmBasisSets = gmx::splitString(is->QMbasis);
3711 if (ir->eI != eiMimic)
3713 if (qmMethods.size() != qmGroupNames.size() || qmBasisSets.size() != qmGroupNames.size())
3716 "Invalid QMMM input: %zu groups %zu basissets"
3717 " and %zu methods\n",
3718 qmGroupNames.size(), qmBasisSets.size(), qmMethods.size());
3720 /* group rest, if any, is always MM! */
3721 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3722 SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
3723 nr = qmGroupNames.size(); /*atoms->grps[egcQMMM].nr;*/
3724 ir->opts.ngQM = qmGroupNames.size();
3725 snew(ir->opts.QMmethod, nr);
3726 snew(ir->opts.QMbasis, nr);
3727 for (i = 0; i < nr; i++)
3729 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3730 * converted to the corresponding enum in names.c
3732 ir->opts.QMmethod[i] = search_QMstring(qmMethods[i].c_str(), eQMmethodNR, eQMmethod_names);
3733 ir->opts.QMbasis[i] = search_QMstring(qmBasisSets[i].c_str(), eQMbasisNR, eQMbasis_names);
3735 auto qmMultiplicities = gmx::splitString(is->QMmult);
3736 auto qmCharges = gmx::splitString(is->QMcharge);
3737 auto qmbSH = gmx::splitString(is->bSH);
3738 snew(ir->opts.QMmult, nr);
3739 snew(ir->opts.QMcharge, nr);
3740 snew(ir->opts.bSH, nr);
3741 convertInts(wi, qmMultiplicities, "QMmult", ir->opts.QMmult);
3742 convertInts(wi, qmCharges, "QMcharge", ir->opts.QMcharge);
3743 convertYesNos(wi, qmbSH, "bSH", ir->opts.bSH);
3745 auto CASelectrons = gmx::splitString(is->CASelectrons);
3746 auto CASorbitals = gmx::splitString(is->CASorbitals);
3747 snew(ir->opts.CASelectrons, nr);
3748 snew(ir->opts.CASorbitals, nr);
3749 convertInts(wi, CASelectrons, "CASelectrons", ir->opts.CASelectrons);
3750 convertInts(wi, CASorbitals, "CASOrbitals", ir->opts.CASorbitals);
3752 auto SAon = gmx::splitString(is->SAon);
3753 auto SAoff = gmx::splitString(is->SAoff);
3754 auto SAsteps = gmx::splitString(is->SAsteps);
3755 snew(ir->opts.SAon, nr);
3756 snew(ir->opts.SAoff, nr);
3757 snew(ir->opts.SAsteps, nr);
3758 convertInts(wi, SAon, "SAon", ir->opts.SAon);
3759 convertInts(wi, SAoff, "SAoff", ir->opts.SAoff);
3760 convertInts(wi, SAsteps, "SAsteps", ir->opts.SAsteps);
3765 if (qmGroupNames.size() > 1)
3767 gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
3769 /* group rest, if any, is always MM! */
3770 do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
3771 SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
3773 ir->opts.ngQM = qmGroupNames.size();
3776 /* end of QMMM input */
3780 for (auto group : gmx::keysOf(groups->groups))
3782 fprintf(stderr, "%-16s has %zu element(s):", shortName(group), groups->groups[group].size());
3783 for (const auto& entry : groups->groups[group])
3785 fprintf(stderr, " %s", *(groups->groupNames[entry]));
3787 fprintf(stderr, "\n");
3791 nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
3792 snew(ir->opts.egp_flags, nr * nr);
3794 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3795 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3797 warning_error(wi, "Energy group exclusions are currently not supported");
3799 if (bExcl && EEL_FULL(ir->coulombtype))
3801 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3804 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3805 if (bTable && !(ir->vdwtype == evdwUSER) && !(ir->coulombtype == eelUSER)
3806 && !(ir->coulombtype == eelPMEUSER) && !(ir->coulombtype == eelPMEUSERSWITCH))
3809 "Can only have energy group pair tables in combination with user tables for VdW "
3813 /* final check before going out of scope if simulated tempering variables
3814 * need to be set to default values.
3816 if ((ir->expandedvals->nstexpanded < 0) && ir->bSimTemp)
3818 ir->expandedvals->nstexpanded = 2 * static_cast<int>(ir->opts.tau_t[0] / ir->delta_t);
3819 warning(wi, gmx::formatString(
3820 "the value for nstexpanded was not specified for "
3821 " expanded ensemble simulated tempering. It is set to 2*tau_t (%d) "
3822 "by default, but it is recommended to set it to an explicit value!",
3823 ir->expandedvals->nstexpanded));
3825 for (i = 0; (i < defaultIndexGroups->nr); i++)
3830 done_blocka(defaultIndexGroups);
3831 sfree(defaultIndexGroups);
3835 static void check_disre(const gmx_mtop_t* mtop)
3837 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3839 const gmx_ffparams_t& ffparams = mtop->ffparams;
3842 for (int i = 0; i < ffparams.numTypes(); i++)
3844 int ftype = ffparams.functype[i];
3845 if (ftype == F_DISRES)
3847 int label = ffparams.iparams[i].disres.label;
3848 if (label == old_label)
3850 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3859 "Found %d double distance restraint indices,\n"
3860 "probably the parameters for multiple pairs in one restraint "
3861 "are not identical\n",
3867 static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t* sys, const bool posres_only, ivec AbsRef)
3870 gmx_mtop_ilistloop_t iloop;
3872 const t_iparams* pr;
3879 for (d = 0; d < DIM; d++)
3881 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3883 /* Check for freeze groups */
3884 for (g = 0; g < ir->opts.ngfrz; g++)
3886 for (d = 0; d < DIM; d++)
3888 if (ir->opts.nFreeze[g][d] != 0)
3896 /* Check for position restraints */
3897 iloop = gmx_mtop_ilistloop_init(sys);
3898 while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
3900 if (nmol > 0 && (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3902 for (i = 0; i < (*ilist)[F_POSRES].size(); i += 2)
3904 pr = &sys->ffparams.iparams[(*ilist)[F_POSRES].iatoms[i]];
3905 for (d = 0; d < DIM; d++)
3907 if (pr->posres.fcA[d] != 0)
3913 for (i = 0; i < (*ilist)[F_FBPOSRES].size(); i += 2)
3915 /* Check for flat-bottom posres */
3916 pr = &sys->ffparams.iparams[(*ilist)[F_FBPOSRES].iatoms[i]];
3917 if (pr->fbposres.k != 0)
3919 switch (pr->fbposres.geom)
3921 case efbposresSPHERE: AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1; break;
3922 case efbposresCYLINDERX: AbsRef[YY] = AbsRef[ZZ] = 1; break;
3923 case efbposresCYLINDERY: AbsRef[XX] = AbsRef[ZZ] = 1; break;
3924 case efbposresCYLINDER:
3925 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3926 case efbposresCYLINDERZ: AbsRef[XX] = AbsRef[YY] = 1; break;
3927 case efbposresX: /* d=XX */
3928 case efbposresY: /* d=YY */
3929 case efbposresZ: /* d=ZZ */
3930 d = pr->fbposres.geom - efbposresX;
3935 " Invalid geometry for flat-bottom position restraint.\n"
3936 "Expected nr between 1 and %d. Found %d\n",
3937 efbposresNR - 1, pr->fbposres.geom);
3944 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3947 static void check_combination_rule_differences(const gmx_mtop_t* mtop,
3949 bool* bC6ParametersWorkWithGeometricRules,
3950 bool* bC6ParametersWorkWithLBRules,
3951 bool* bLBRulesPossible)
3953 int ntypes, tpi, tpj;
3956 double c6i, c6j, c12i, c12j;
3957 double c6, c6_geometric, c6_LB;
3958 double sigmai, sigmaj, epsi, epsj;
3959 bool bCanDoLBRules, bCanDoGeometricRules;
3962 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3963 * force-field floating point parameters.
3966 ptr = getenv("GMX_LJCOMB_TOL");
3970 double gmx_unused canary;
3972 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
3975 "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
3980 *bC6ParametersWorkWithLBRules = TRUE;
3981 *bC6ParametersWorkWithGeometricRules = TRUE;
3982 bCanDoLBRules = TRUE;
3983 ntypes = mtop->ffparams.atnr;
3984 snew(typecount, ntypes);
3985 gmx_mtop_count_atomtypes(mtop, state, typecount);
3986 *bLBRulesPossible = TRUE;
3987 for (tpi = 0; tpi < ntypes; ++tpi)
3989 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3990 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3991 for (tpj = tpi; tpj < ntypes; ++tpj)
3993 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3994 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3995 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3996 c6_geometric = std::sqrt(c6i * c6j);
3997 if (!gmx_numzero(c6_geometric))
3999 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4001 sigmai = gmx::sixthroot(c12i / c6i);
4002 sigmaj = gmx::sixthroot(c12j / c6j);
4003 epsi = c6i * c6i / (4.0 * c12i);
4004 epsj = c6j * c6j / (4.0 * c12j);
4005 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4009 *bLBRulesPossible = FALSE;
4010 c6_LB = c6_geometric;
4012 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4017 *bC6ParametersWorkWithLBRules = FALSE;
4020 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4022 if (!bCanDoGeometricRules)
4024 *bC6ParametersWorkWithGeometricRules = FALSE;
4031 static void check_combination_rules(const t_inputrec* ir, const gmx_mtop_t* mtop, warninp_t wi)
4033 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4035 check_combination_rule_differences(mtop, 0, &bC6ParametersWorkWithGeometricRules,
4036 &bC6ParametersWorkWithLBRules, &bLBRulesPossible);
4037 if (ir->ljpme_combination_rule == eljpmeLB)
4039 if (!bC6ParametersWorkWithLBRules || !bLBRulesPossible)
4042 "You are using arithmetic-geometric combination rules "
4043 "in LJ-PME, but your non-bonded C6 parameters do not "
4044 "follow these rules.");
4049 if (!bC6ParametersWorkWithGeometricRules)
4051 if (ir->eDispCorr != edispcNO)
4054 "You are using geometric combination rules in "
4055 "LJ-PME, but your non-bonded C6 parameters do "
4056 "not follow these rules. "
4057 "This will introduce very small errors in the forces and energies in "
4058 "your simulations. Dispersion correction will correct total energy "
4059 "and/or pressure for isotropic systems, but not forces or surface "
4065 "You are using geometric combination rules in "
4066 "LJ-PME, but your non-bonded C6 parameters do "
4067 "not follow these rules. "
4068 "This will introduce very small errors in the forces and energies in "
4069 "your simulations. If your system is homogeneous, consider using "
4070 "dispersion correction "
4071 "for the total energy and pressure.");
4077 void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
4079 char err_buf[STRLEN];
4084 gmx_mtop_atomloop_block_t aloopb;
4086 char warn_buf[STRLEN];
4088 set_warning_line(wi, mdparin, -1);
4090 if (absolute_reference(ir, sys, false, AbsRef))
4093 "Removing center of mass motion in the presence of position restraints might "
4097 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 && ir->nstlist > 1
4098 && ((EI_MD(ir->eI) || EI_SD(ir->eI)) && (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4100 /* Check if a too small Verlet buffer might potentially
4101 * cause more drift than the thermostat can couple off.
4103 /* Temperature error fraction for warning and suggestion */
4104 const real T_error_warn = 0.002;
4105 const real T_error_suggest = 0.001;
4106 /* For safety: 2 DOF per atom (typical with constraints) */
4107 const real nrdf_at = 2;
4108 real T, tau, max_T_error;
4113 for (i = 0; i < ir->opts.ngtc; i++)
4115 T = std::max(T, ir->opts.ref_t[i]);
4116 tau = std::max(tau, ir->opts.tau_t[i]);
4120 /* This is a worst case estimate of the temperature error,
4121 * assuming perfect buffer estimation and no cancelation
4122 * of errors. The factor 0.5 is because energy distributes
4123 * equally over Ekin and Epot.
4125 max_T_error = 0.5 * tau * ir->verletbuf_tol / (nrdf_at * BOLTZ * T);
4126 if (max_T_error > T_error_warn)
4129 "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature "
4130 "of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. "
4131 "To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to "
4132 "%.0e or decrease tau_t.",
4133 ir->verletbuf_tol, T, tau, 100 * max_T_error, 100 * T_error_suggest,
4134 ir->verletbuf_tol * T_error_suggest / max_T_error);
4135 warning(wi, warn_buf);
4140 if (ETC_ANDERSEN(ir->etc))
4144 for (i = 0; i < ir->opts.ngtc; i++)
4147 "all tau_t must currently be equal using Andersen temperature control, "
4148 "violated for group %d",
4150 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4152 "all tau_t must be positive using Andersen temperature control, "
4154 i, ir->opts.tau_t[i]);
4155 CHECK(ir->opts.tau_t[i] < 0);
4158 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4160 for (i = 0; i < ir->opts.ngtc; i++)
4162 int nsteps = gmx::roundToInt(ir->opts.tau_t[i] / ir->delta_t);
4164 "tau_t/delta_t for group %d for temperature control method %s must be a "
4165 "multiple of nstcomm (%d), as velocities of atoms in coupled groups are "
4166 "randomized every time step. The input tau_t (%8.3f) leads to %d steps per "
4168 i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
4169 CHECK(nsteps % ir->nstcomm != 0);
4174 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD && ir->comm_mode == ecmNO
4175 && !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) && !ETC_ANDERSEN(ir->etc))
4178 "You are not using center of mass motion removal (mdp option comm-mode), numerical "
4179 "rounding errors can lead to build up of kinetic energy of the center of mass");
4182 if (ir->epc == epcPARRINELLORAHMAN && ir->etc == etcNOSEHOOVER)
4185 for (int g = 0; g < ir->opts.ngtc; g++)
4187 tau_t_max = std::max(tau_t_max, ir->opts.tau_t[g]);
4189 if (ir->tau_p < 1.9 * tau_t_max)
4191 std::string message = gmx::formatString(
4192 "With %s T-coupling and %s p-coupling, "
4193 "%s (%g) should be at least twice as large as %s (%g) to avoid resonances",
4194 etcoupl_names[ir->etc], epcoupl_names[ir->epc], "tau-p", ir->tau_p, "tau-t",
4196 warning(wi, message.c_str());
4200 /* Check for pressure coupling with absolute position restraints */
4201 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4203 absolute_reference(ir, sys, TRUE, AbsRef);
4205 for (m = 0; m < DIM; m++)
4207 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4210 "You are using pressure coupling with absolute position restraints, "
4211 "this will give artifacts. Use the refcoord_scaling option.");
4219 aloopb = gmx_mtop_atomloop_block_init(sys);
4221 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4223 if (atom->q != 0 || atom->qB != 0)
4231 if (EEL_FULL(ir->coulombtype))
4234 "You are using full electrostatics treatment %s for a system without charges.\n"
4235 "This costs a lot of performance for just processing zeros, consider using %s "
4237 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4238 warning(wi, err_buf);
4243 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
4246 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4247 "You might want to consider using %s electrostatics.\n",
4249 warning_note(wi, err_buf);
4253 /* Check if combination rules used in LJ-PME are the same as in the force field */
4254 if (EVDW_PME(ir->vdwtype))
4256 check_combination_rules(ir, sys, wi);
4259 /* Generalized reaction field */
4260 if (ir->coulombtype == eelGRF_NOTUSED)
4263 "Generalized reaction-field electrostatics is no longer supported. "
4264 "You can use normal reaction-field instead and compute the reaction-field "
4265 "constant by hand.");
4269 for (int i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4271 for (m = 0; (m < DIM); m++)
4273 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4282 snew(mgrp, sys->groups.groups[SimulationAtomGroupType::Acceleration].size());
4283 for (const AtomProxy atomP : AtomRange(*sys))
4285 const t_atom& local = atomP.atom();
4286 int i = atomP.globalAtomNumber();
4287 mgrp[getGroupType(sys->groups, SimulationAtomGroupType::Acceleration, i)] += local.m;
4290 for (i = 0; (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4292 for (m = 0; (m < DIM); m++)
4294 acc[m] += ir->opts.acc[i][m] * mgrp[i];
4298 for (m = 0; (m < DIM); m++)
4300 if (fabs(acc[m]) > 1e-6)
4302 const char* dim[DIM] = { "X", "Y", "Z" };
4303 fprintf(stderr, "Net Acceleration in %s direction, will %s be corrected\n", dim[m],
4304 ir->nstcomm != 0 ? "" : "not");
4305 if (ir->nstcomm != 0 && m < ndof_com(ir))
4309 (i < gmx::ssize(sys->groups.groups[SimulationAtomGroupType::Acceleration])); i++)
4311 ir->opts.acc[i][m] -= acc[m];
4319 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0
4320 && !gmx_within_tol(sys->ffparams.reppow, 12.0, 10 * GMX_DOUBLE_EPS))
4322 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4330 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4332 if (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0)
4334 absolute_reference(ir, sys, FALSE, AbsRef);
4335 for (m = 0; m < DIM; m++)
4337 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4340 "You are using an absolute reference for pulling, but the rest of "
4341 "the system does not have an absolute reference. This will lead to "
4350 for (i = 0; i < 3; i++)
4352 for (m = 0; m <= i; m++)
4354 if ((ir->epc != epcNO && ir->compress[i][m] != 0) || ir->deform[i][m] != 0)
4356 for (c = 0; c < ir->pull->ncoord; c++)
4358 if (ir->pull->coord[c].eGeom == epullgDIRPBC && ir->pull->coord[c].vec[m] != 0)
4361 "Can not have dynamic box while using pull geometry '%s' "
4363 EPULLGEOM(ir->pull->coord[c].eGeom), 'x' + m);
4374 void double_check(t_inputrec* ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, warninp_t wi)
4376 char warn_buf[STRLEN];
4379 ptr = check_box(ir->ePBC, box);
4382 warning_error(wi, ptr);
4385 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4387 if (ir->shake_tol <= 0.0)
4389 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n", ir->shake_tol);
4390 warning_error(wi, warn_buf);
4394 if ((ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4396 /* If we have Lincs constraints: */
4397 if (ir->eI == eiMD && ir->etc == etcNO && ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4400 "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4401 warning_note(wi, warn_buf);
4404 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4407 "For accurate %s with LINCS constraints, lincs-order should be 8 or more.",
4409 warning_note(wi, warn_buf);
4411 if (ir->epc == epcMTTK)
4413 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4417 if (bHasAnyConstraints && ir->epc == epcMTTK)
4419 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4422 if (ir->LincsWarnAngle > 90.0)
4424 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4425 warning(wi, warn_buf);
4426 ir->LincsWarnAngle = 90.0;
4429 if (ir->ePBC != epbcNONE)
4431 if (ir->nstlist == 0)
4434 "With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
4435 "atoms might cause the simulation to crash.");
4437 if (gmx::square(ir->rlist) >= max_cutoff2(ir->ePBC, box))
4440 "ERROR: The cut-off length is longer than half the shortest box vector or "
4441 "longer than the smallest box diagonal element. Increase the box size or "
4442 "decrease rlist.\n");
4443 warning_error(wi, warn_buf);