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50 #include "gromacs/awh/read-params.h"
51 #include "gromacs/fileio/readinp.h"
52 #include "gromacs/fileio/warninp.h"
53 #include "gromacs/gmxlib/chargegroup.h"
54 #include "gromacs/gmxlib/network.h"
55 #include "gromacs/gmxpreprocess/keyvaluetreemdpwriter.h"
56 #include "gromacs/gmxpreprocess/toputil.h"
57 #include "gromacs/math/functions.h"
58 #include "gromacs/math/units.h"
59 #include "gromacs/math/vec.h"
60 #include "gromacs/mdlib/calc_verletbuf.h"
61 #include "gromacs/mdrunutility/mdmodules.h"
62 #include "gromacs/mdtypes/inputrec.h"
63 #include "gromacs/mdtypes/md_enums.h"
64 #include "gromacs/mdtypes/pull-params.h"
65 #include "gromacs/options/options.h"
66 #include "gromacs/options/treesupport.h"
67 #include "gromacs/pbcutil/pbc.h"
68 #include "gromacs/topology/block.h"
69 #include "gromacs/topology/ifunc.h"
70 #include "gromacs/topology/index.h"
71 #include "gromacs/topology/mtop_util.h"
72 #include "gromacs/topology/symtab.h"
73 #include "gromacs/topology/topology.h"
74 #include "gromacs/utility/cstringutil.h"
75 #include "gromacs/utility/exceptions.h"
76 #include "gromacs/utility/fatalerror.h"
77 #include "gromacs/utility/filestream.h"
78 #include "gromacs/utility/gmxassert.h"
79 #include "gromacs/utility/ikeyvaluetreeerror.h"
80 #include "gromacs/utility/keyvaluetree.h"
81 #include "gromacs/utility/keyvaluetreebuilder.h"
82 #include "gromacs/utility/keyvaluetreetransform.h"
83 #include "gromacs/utility/smalloc.h"
84 #include "gromacs/utility/stringcompare.h"
85 #include "gromacs/utility/stringutil.h"
86 #include "gromacs/utility/textwriter.h"
91 /* Resource parameters
92 * Do not change any of these until you read the instruction
93 * in readinp.h. Some cpp's do not take spaces after the backslash
94 * (like the c-shell), which will give you a very weird compiler
98 typedef struct t_inputrec_strings
100 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN],
101 acc[STRLEN], accgrps[STRLEN], freeze[STRLEN], frdim[STRLEN],
102 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
103 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
104 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN],
106 char fep_lambda[efptNR][STRLEN];
107 char lambda_weights[STRLEN];
110 char anneal[STRLEN], anneal_npoints[STRLEN],
111 anneal_time[STRLEN], anneal_temp[STRLEN];
112 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
113 bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
114 SAoff[STRLEN], SAsteps[STRLEN];
116 } gmx_inputrec_strings;
118 static gmx_inputrec_strings *is = nullptr;
120 void init_inputrec_strings()
124 gmx_incons("Attempted to call init_inputrec_strings before calling done_inputrec_strings. Only one inputrec (i.e. .mdp file) can be parsed at a time.");
129 void done_inputrec_strings()
137 egrptpALL, /* All particles have to be a member of a group. */
138 egrptpALL_GENREST, /* A rest group with name is generated for particles *
139 * that are not part of any group. */
140 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
141 * for the rest group. */
142 egrptpONE /* Merge all selected groups into one group, *
143 * make a rest group for the remaining particles. */
146 static const char *constraints[eshNR+1] = {
147 "none", "h-bonds", "all-bonds", "h-angles", "all-angles", nullptr
150 static const char *couple_lam[ecouplamNR+1] = {
151 "vdw-q", "vdw", "q", "none", nullptr
154 static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
159 for (i = 0; i < ntemps; i++)
161 /* simple linear scaling -- allows more control */
162 if (simtemp->eSimTempScale == esimtempLINEAR)
164 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*temperature_lambdas[i];
166 else if (simtemp->eSimTempScale == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
168 simtemp->temperatures[i] = simtemp->simtemp_low * std::pow(simtemp->simtemp_high/simtemp->simtemp_low, static_cast<real>((1.0*i)/(ntemps-1)));
170 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
172 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*(std::expm1(temperature_lambdas[i])/std::expm1(1.0));
177 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
178 gmx_fatal(FARGS, "%s", errorstr);
185 static void _low_check(bool b, const char *s, warninp_t wi)
189 warning_error(wi, s);
193 static void check_nst(const char *desc_nst, int nst,
194 const char *desc_p, int *p,
199 if (*p > 0 && *p % nst != 0)
201 /* Round up to the next multiple of nst */
202 *p = ((*p)/nst + 1)*nst;
203 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n",
204 desc_p, desc_nst, desc_p, *p);
209 static bool ir_NVE(const t_inputrec *ir)
211 return (EI_MD(ir->eI) && ir->etc == etcNO);
214 static int lcd(int n1, int n2)
219 for (i = 2; (i <= n1 && i <= n2); i++)
221 if (n1 % i == 0 && n2 % i == 0)
230 static void process_interaction_modifier(const t_inputrec *ir, int *eintmod)
232 if (*eintmod == eintmodPOTSHIFT_VERLET)
234 if (ir->cutoff_scheme == ecutsVERLET)
236 *eintmod = eintmodPOTSHIFT;
240 *eintmod = eintmodNONE;
245 void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
247 /* Check internal consistency.
248 * NOTE: index groups are not set here yet, don't check things
249 * like temperature coupling group options here, but in triple_check
252 /* Strange macro: first one fills the err_buf, and then one can check
253 * the condition, which will print the message and increase the error
256 #define CHECK(b) _low_check(b, err_buf, wi)
257 char err_buf[256], warn_buf[STRLEN];
260 t_lambda *fep = ir->fepvals;
261 t_expanded *expand = ir->expandedvals;
263 set_warning_line(wi, mdparin, -1);
265 if (ir->coulombtype == eelRF_NEC_UNSUPPORTED)
267 sprintf(warn_buf, "%s electrostatics is no longer supported",
268 eel_names[eelRF_NEC_UNSUPPORTED]);
269 warning_error(wi, warn_buf);
272 /* BASIC CUT-OFF STUFF */
273 if (ir->rcoulomb < 0)
275 warning_error(wi, "rcoulomb should be >= 0");
279 warning_error(wi, "rvdw should be >= 0");
282 !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
284 warning_error(wi, "rlist should be >= 0");
286 sprintf(err_buf, "nstlist can not be smaller than 0. (If you were trying to use the heuristic neighbour-list update scheme for efficient buffering for improved energy conservation, please use the Verlet cut-off scheme instead.)");
287 CHECK(ir->nstlist < 0);
289 process_interaction_modifier(ir, &ir->coulomb_modifier);
290 process_interaction_modifier(ir, &ir->vdw_modifier);
292 if (ir->cutoff_scheme == ecutsGROUP)
295 "The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future "
296 "release when all interaction forms are supported for the verlet scheme. The verlet "
297 "scheme already scales better, and it is compatible with GPUs and other accelerators.");
299 if (ir->rlist > 0 && ir->rlist < ir->rcoulomb)
301 gmx_fatal(FARGS, "rcoulomb must not be greater than rlist (twin-range schemes are not supported)");
303 if (ir->rlist > 0 && ir->rlist < ir->rvdw)
305 gmx_fatal(FARGS, "rvdw must not be greater than rlist (twin-range schemes are not supported)");
308 if (ir->rlist == 0 && ir->ePBC != epbcNONE)
310 warning_error(wi, "Can not have an infinite cut-off with PBC");
314 if (ir->cutoff_scheme == ecutsVERLET)
318 /* Normal Verlet type neighbor-list, currently only limited feature support */
319 if (inputrec2nboundeddim(ir) < 3)
321 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
324 // We don't (yet) have general Verlet kernels for rcoulomb!=rvdw
325 if (ir->rcoulomb != ir->rvdw)
327 // Since we have PME coulomb + LJ cut-off kernels with rcoulomb>rvdw
328 // for PME load balancing, we can support this exception.
329 bool bUsesPmeTwinRangeKernel = (EEL_PME_EWALD(ir->coulombtype) &&
330 ir->vdwtype == evdwCUT &&
331 ir->rcoulomb > ir->rvdw);
332 if (!bUsesPmeTwinRangeKernel)
334 warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported (except for rcoulomb>rvdw with PME electrostatics)");
338 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
340 if (ir->vdw_modifier == eintmodNONE ||
341 ir->vdw_modifier == eintmodPOTSHIFT)
343 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
345 sprintf(warn_buf, "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], evdw_names[evdwCUT], eintmod_names[ir->vdw_modifier]);
346 warning_note(wi, warn_buf);
348 ir->vdwtype = evdwCUT;
352 sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
353 warning_error(wi, warn_buf);
357 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
359 warning_error(wi, "With Verlet lists only cut-off and PME LJ interactions are supported");
361 if (!(ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype) ||
362 EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
364 warning_error(wi, "With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
366 if (!(ir->coulomb_modifier == eintmodNONE ||
367 ir->coulomb_modifier == eintmodPOTSHIFT))
369 sprintf(warn_buf, "coulomb_modifier=%s is not supported with the Verlet cut-off scheme", eintmod_names[ir->coulomb_modifier]);
370 warning_error(wi, warn_buf);
373 if (EEL_USER(ir->coulombtype))
375 sprintf(warn_buf, "Coulomb type %s is not supported with the verlet scheme", eel_names[ir->coulombtype]);
376 warning_error(wi, warn_buf);
379 if (ir->nstlist <= 0)
381 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
384 if (ir->nstlist < 10)
386 warning_note(wi, "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation.");
389 rc_max = std::max(ir->rvdw, ir->rcoulomb);
391 if (ir->verletbuf_tol <= 0)
393 if (ir->verletbuf_tol == 0)
395 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
398 if (ir->rlist < rc_max)
400 warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
403 if (ir->rlist == rc_max && ir->nstlist > 1)
405 warning_note(wi, "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet buffer. The cluster pair list does have a buffering effect, but choosing a larger rlist might be necessary for good energy conservation.");
410 if (ir->rlist > rc_max)
412 warning_note(wi, "You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance.");
415 if (ir->nstlist == 1)
417 /* No buffer required */
422 if (EI_DYNAMICS(ir->eI))
424 if (inputrec2nboundeddim(ir) < 3)
426 warning_error(wi, "The box volume is required for calculating rlist from the energy drift with verlet-buffer-tolerance > 0. You are using at least one unbounded dimension, so no volume can be computed. Either use a finite box, or set rlist yourself together with verlet-buffer-tolerance = -1.");
428 /* Set rlist temporarily so we can continue processing */
433 /* Set the buffer to 5% of the cut-off */
434 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
440 /* GENERAL INTEGRATOR STUFF */
443 if (ir->etc != etcNO)
445 if (EI_RANDOM(ir->eI))
447 sprintf(warn_buf, "Setting tcoupl from '%s' to 'no'. %s handles temperature coupling implicitly. See the documentation for more information on which parameters affect temperature for %s.", etcoupl_names[ir->etc], ei_names[ir->eI], ei_names[ir->eI]);
451 sprintf(warn_buf, "Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
453 warning_note(wi, warn_buf);
457 if (ir->eI == eiVVAK)
459 sprintf(warn_buf, "Integrator method %s is implemented primarily for validation purposes; for molecular dynamics, you should probably be using %s or %s", ei_names[eiVVAK], ei_names[eiMD], ei_names[eiVV]);
460 warning_note(wi, warn_buf);
462 if (!EI_DYNAMICS(ir->eI))
464 if (ir->epc != epcNO)
466 sprintf(warn_buf, "Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.", epcoupl_names[ir->epc], ei_names[ir->eI]);
467 warning_note(wi, warn_buf);
471 if (EI_DYNAMICS(ir->eI))
473 if (ir->nstcalcenergy < 0)
475 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
476 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
478 /* nstcalcenergy larger than nstener does not make sense.
479 * We ideally want nstcalcenergy=nstener.
483 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
487 ir->nstcalcenergy = ir->nstenergy;
491 else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
492 (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
493 (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
496 const char *nsten = "nstenergy";
497 const char *nstdh = "nstdhdl";
498 const char *min_name = nsten;
499 int min_nst = ir->nstenergy;
501 /* find the smallest of ( nstenergy, nstdhdl ) */
502 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
503 (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
505 min_nst = ir->fepvals->nstdhdl;
508 /* If the user sets nstenergy small, we should respect that */
510 "Setting nstcalcenergy (%d) equal to %s (%d)",
511 ir->nstcalcenergy, min_name, min_nst);
512 warning_note(wi, warn_buf);
513 ir->nstcalcenergy = min_nst;
516 if (ir->epc != epcNO)
518 if (ir->nstpcouple < 0)
520 ir->nstpcouple = ir_optimal_nstpcouple(ir);
524 if (ir->nstcalcenergy > 0)
526 if (ir->efep != efepNO)
528 /* nstdhdl should be a multiple of nstcalcenergy */
529 check_nst("nstcalcenergy", ir->nstcalcenergy,
530 "nstdhdl", &ir->fepvals->nstdhdl, wi);
531 /* nstexpanded should be a multiple of nstcalcenergy */
532 check_nst("nstcalcenergy", ir->nstcalcenergy,
533 "nstexpanded", &ir->expandedvals->nstexpanded, wi);
535 /* for storing exact averages nstenergy should be
536 * a multiple of nstcalcenergy
538 check_nst("nstcalcenergy", ir->nstcalcenergy,
539 "nstenergy", &ir->nstenergy, wi);
543 if (ir->nsteps == 0 && !ir->bContinuation)
545 warning_note(wi, "For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates.");
549 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
550 ir->bContinuation && ir->ld_seed != -1)
552 warning_note(wi, "You are doing a continuation with SD or BD, make sure that ld_seed is different from the previous run (using ld_seed=-1 will ensure this)");
558 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
559 CHECK(ir->ePBC != epbcXYZ);
560 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
561 CHECK(ir->ns_type != ensGRID);
562 sprintf(err_buf, "with TPI nstlist should be larger than zero");
563 CHECK(ir->nstlist <= 0);
564 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
565 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
566 sprintf(err_buf, "TPI does not work (yet) with the Verlet cut-off scheme");
567 CHECK(ir->cutoff_scheme == ecutsVERLET);
571 if ( (opts->nshake > 0) && (opts->bMorse) )
574 "Using morse bond-potentials while constraining bonds is useless");
575 warning(wi, warn_buf);
578 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
579 ir->bContinuation && ir->ld_seed != -1)
581 warning_note(wi, "You are doing a continuation with SD or BD, make sure that ld_seed is different from the previous run (using ld_seed=-1 will ensure this)");
583 /* verify simulated tempering options */
587 bool bAllTempZero = TRUE;
588 for (i = 0; i < fep->n_lambda; i++)
590 sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i, efpt_names[efptTEMPERATURE], fep->all_lambda[efptTEMPERATURE][i]);
591 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
592 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
594 bAllTempZero = FALSE;
597 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
598 CHECK(bAllTempZero == TRUE);
600 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
601 CHECK(ir->eI != eiVV);
603 /* check compatability of the temperature coupling with simulated tempering */
605 if (ir->etc == etcNOSEHOOVER)
607 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
608 warning_note(wi, warn_buf);
611 /* check that the temperatures make sense */
613 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= than the simulated tempering lower temperature (%g)", ir->simtempvals->simtemp_high, ir->simtempvals->simtemp_low);
614 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
616 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
617 CHECK(ir->simtempvals->simtemp_high <= 0);
619 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
620 CHECK(ir->simtempvals->simtemp_low <= 0);
623 /* verify free energy options */
625 if (ir->efep != efepNO)
628 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
630 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
632 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
633 static_cast<int>(fep->sc_r_power));
634 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
636 sprintf(err_buf, "Can't use positive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
637 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
639 sprintf(err_buf, "Can't use positive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
640 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
642 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
643 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
645 sprintf(err_buf, "Free-energy not implemented for Ewald");
646 CHECK(ir->coulombtype == eelEWALD);
648 /* check validty of lambda inputs */
649 if (fep->n_lambda == 0)
651 /* Clear output in case of no states:*/
652 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
653 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
657 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
658 CHECK((fep->init_fep_state >= fep->n_lambda));
661 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
662 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
664 sprintf(err_buf, "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with init-lambda-state or with init-lambda, but not both",
665 fep->init_lambda, fep->init_fep_state);
666 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
670 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
674 for (i = 0; i < efptNR; i++)
676 if (fep->separate_dvdl[i])
681 if (n_lambda_terms > 1)
683 sprintf(warn_buf, "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't use init-lambda to set lambda state (except for slow growth). Use init-lambda-state instead.");
684 warning(wi, warn_buf);
687 if (n_lambda_terms < 2 && fep->n_lambda > 0)
690 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
694 for (j = 0; j < efptNR; j++)
696 for (i = 0; i < fep->n_lambda; i++)
698 sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i, efpt_names[j], fep->all_lambda[j][i]);
699 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
703 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
705 for (i = 0; i < fep->n_lambda; i++)
707 sprintf(err_buf, "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to crashes, and is not supported.", i, fep->all_lambda[efptVDW][i],
708 fep->all_lambda[efptCOUL][i]);
709 CHECK((fep->sc_alpha > 0) &&
710 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
711 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
712 ((fep->all_lambda[efptVDW][i] > 0.0) &&
713 (fep->all_lambda[efptVDW][i] < 1.0))));
717 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
719 real sigma, lambda, r_sc;
722 /* Maximum estimate for A and B charges equal with lambda power 1 */
724 r_sc = std::pow(lambda*fep->sc_alpha*std::pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
725 sprintf(warn_buf, "With PME there is a minor soft core effect present at the cut-off, proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on energy conservation, but usually other effects dominate. With a common sigma value of %g nm the fraction of the particle-particle potential at the cut-off at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
727 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
728 warning_note(wi, warn_buf);
731 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
732 be treated differently, but that's the next step */
734 for (i = 0; i < efptNR; i++)
736 for (j = 0; j < fep->n_lambda; j++)
738 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
739 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
744 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
748 /* checking equilibration of weights inputs for validity */
750 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
751 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
752 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
754 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
755 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
756 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
758 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
759 expand->equil_steps, elmceq_names[elmceqSTEPS]);
760 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
762 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
763 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
764 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
766 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
767 expand->equil_ratio, elmceq_names[elmceqRATIO]);
768 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
770 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
771 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
772 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
774 sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
775 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
776 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
778 sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
779 expand->equil_steps, elmceq_names[elmceqSTEPS]);
780 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
782 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
783 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
784 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
786 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
787 expand->equil_ratio, elmceq_names[elmceqRATIO]);
788 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
790 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
791 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
792 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
794 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
795 CHECK((expand->lmc_repeats <= 0));
796 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
797 CHECK((expand->minvarmin <= 0));
798 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
799 CHECK((expand->c_range < 0));
800 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
801 fep->init_fep_state, expand->lmc_forced_nstart);
802 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
803 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
804 CHECK((expand->lmc_forced_nstart < 0));
805 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
806 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
808 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
809 CHECK((expand->init_wl_delta < 0));
810 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
811 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
812 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
813 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
815 /* if there is no temperature control, we need to specify an MC temperature */
816 if (!integratorHasReferenceTemperature(ir) && (expand->elmcmove != elmcmoveNO) && (expand->mc_temp <= 0.0))
818 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!='no', mc_temp must be set to a positive number");
819 warning_error(wi, err_buf);
821 if (expand->nstTij > 0)
823 sprintf(err_buf, "nstlog must be non-zero");
824 CHECK(ir->nstlog == 0);
825 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
826 expand->nstTij, ir->nstlog);
827 CHECK((expand->nstTij % ir->nstlog) != 0);
832 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
833 CHECK(ir->nwall && ir->ePBC != epbcXY);
836 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
838 if (ir->ePBC == epbcNONE)
840 if (ir->epc != epcNO)
842 warning(wi, "Turning off pressure coupling for vacuum system");
848 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
849 epbc_names[ir->ePBC]);
850 CHECK(ir->epc != epcNO);
852 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
853 CHECK(EEL_FULL(ir->coulombtype));
855 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
856 epbc_names[ir->ePBC]);
857 CHECK(ir->eDispCorr != edispcNO);
860 if (ir->rlist == 0.0)
862 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
863 "with coulombtype = %s or coulombtype = %s\n"
864 "without periodic boundary conditions (pbc = %s) and\n"
865 "rcoulomb and rvdw set to zero",
866 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
867 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
868 (ir->ePBC != epbcNONE) ||
869 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
873 warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
878 if (ir->nstcomm == 0)
880 ir->comm_mode = ecmNO;
882 if (ir->comm_mode != ecmNO)
886 warning(wi, "If you want to remove the rotation around the center of mass, you should set comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to its absolute value");
887 ir->nstcomm = abs(ir->nstcomm);
890 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
892 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
893 ir->nstcomm = ir->nstcalcenergy;
896 if (ir->comm_mode == ecmANGULAR)
898 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
899 CHECK(ir->bPeriodicMols);
900 if (ir->ePBC != epbcNONE)
902 warning(wi, "Removing the rotation around the center of mass in a periodic system, this can lead to artifacts. Only use this on a single (cluster of) molecules. This cluster should not cross periodic boundaries.");
907 if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
909 sprintf(warn_buf, "Tumbling and flying ice-cubes: We are not removing rotation around center of mass in a non-periodic system. You should probably set comm_mode = ANGULAR or use integrator = %s.", ei_names[eiSD1]);
910 warning_note(wi, warn_buf);
913 /* TEMPERATURE COUPLING */
914 if (ir->etc == etcYES)
916 ir->etc = etcBERENDSEN;
917 warning_note(wi, "Old option for temperature coupling given: "
918 "changing \"yes\" to \"Berendsen\"\n");
921 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
923 if (ir->opts.nhchainlength < 1)
925 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
926 ir->opts.nhchainlength = 1;
927 warning(wi, warn_buf);
930 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
932 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
933 ir->opts.nhchainlength = 1;
938 ir->opts.nhchainlength = 0;
941 if (ir->eI == eiVVAK)
943 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
945 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
948 if (ETC_ANDERSEN(ir->etc))
950 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
951 CHECK(!(EI_VV(ir->eI)));
953 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
955 sprintf(warn_buf, "Center of mass removal not necessary for %s. All velocities of coupled groups are rerandomized periodically, so flying ice cube errors will not occur.", etcoupl_names[ir->etc]);
956 warning_note(wi, warn_buf);
959 sprintf(err_buf, "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are randomized every time step", ir->nstcomm, etcoupl_names[ir->etc]);
960 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
963 if (ir->etc == etcBERENDSEN)
965 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
966 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
967 warning_note(wi, warn_buf);
970 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
971 && ir->epc == epcBERENDSEN)
973 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
974 "true ensemble for the thermostat");
975 warning(wi, warn_buf);
978 /* PRESSURE COUPLING */
979 if (ir->epc == epcISOTROPIC)
981 ir->epc = epcBERENDSEN;
982 warning_note(wi, "Old option for pressure coupling given: "
983 "changing \"Isotropic\" to \"Berendsen\"\n");
986 if (ir->epc != epcNO)
988 dt_pcoupl = ir->nstpcouple*ir->delta_t;
990 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
991 CHECK(ir->tau_p <= 0);
993 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10*GMX_REAL_EPS)
995 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
996 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
997 warning(wi, warn_buf);
1000 sprintf(err_buf, "compressibility must be > 0 when using pressure"
1001 " coupling %s\n", EPCOUPLTYPE(ir->epc));
1002 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
1003 ir->compress[ZZ][ZZ] < 0 ||
1004 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
1005 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
1007 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1010 "You are generating velocities so I am assuming you "
1011 "are equilibrating a system. You are using "
1012 "%s pressure coupling, but this can be "
1013 "unstable for equilibration. If your system crashes, try "
1014 "equilibrating first with Berendsen pressure coupling. If "
1015 "you are not equilibrating the system, you can probably "
1016 "ignore this warning.",
1017 epcoupl_names[ir->epc]);
1018 warning(wi, warn_buf);
1024 if (ir->epc > epcNO)
1026 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1028 warning_error(wi, "for md-vv and md-vv-avek, can only use Berendsen and Martyna-Tuckerman-Tobias-Klein (MTTK) equations for pressure control; MTTK is equivalent to Parrinello-Rahman.");
1034 if (ir->epc == epcMTTK)
1036 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1040 /* ELECTROSTATICS */
1041 /* More checks are in triple check (grompp.c) */
1043 if (ir->coulombtype == eelSWITCH)
1045 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1046 "artifacts, advice: use coulombtype = %s",
1047 eel_names[ir->coulombtype],
1048 eel_names[eelRF_ZERO]);
1049 warning(wi, warn_buf);
1052 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1054 sprintf(warn_buf, "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old format and exchanging epsilon-r and epsilon-rf", ir->epsilon_r);
1055 warning(wi, warn_buf);
1056 ir->epsilon_rf = ir->epsilon_r;
1057 ir->epsilon_r = 1.0;
1060 if (ir->epsilon_r == 0)
1063 "It is pointless to use long-range electrostatics with infinite relative permittivity."
1064 "Since you are effectively turning of electrostatics, a plain cutoff will be much faster.");
1065 CHECK(EEL_FULL(ir->coulombtype));
1068 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1070 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1071 CHECK(ir->epsilon_r < 0);
1074 if (EEL_RF(ir->coulombtype))
1076 /* reaction field (at the cut-off) */
1078 if (ir->coulombtype == eelRF_ZERO && ir->epsilon_rf != 0)
1080 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1081 eel_names[ir->coulombtype]);
1082 warning(wi, warn_buf);
1083 ir->epsilon_rf = 0.0;
1086 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1087 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1088 (ir->epsilon_r == 0));
1089 if (ir->epsilon_rf == ir->epsilon_r)
1091 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1092 eel_names[ir->coulombtype]);
1093 warning(wi, warn_buf);
1096 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1097 * means the interaction is zero outside rcoulomb, but it helps to
1098 * provide accurate energy conservation.
1100 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1102 if (ir_coulomb_switched(ir))
1105 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1106 eel_names[ir->coulombtype]);
1107 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1110 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1112 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1114 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1115 eel_names[ir->coulombtype]);
1116 CHECK(ir->rlist > ir->rcoulomb);
1120 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1123 "Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier.");
1124 CHECK( ir->coulomb_modifier != eintmodNONE);
1126 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1129 "Explicit switch/shift vdw interactions cannot be used in combination with a secondary vdw-modifier.");
1130 CHECK( ir->vdw_modifier != eintmodNONE);
1133 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1134 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1137 "The switch/shift interaction settings are just for compatibility; you will get better "
1138 "performance from applying potential modifiers to your interactions!\n");
1139 warning_note(wi, warn_buf);
1142 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1144 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1146 real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
1147 sprintf(warn_buf, "The switching range should be 5%% or less (currently %.2f%% using a switching range of %4f-%4f) for accurate electrostatic energies, energy conservation will be good regardless, since ewald_rtol = %g.",
1148 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1149 warning(wi, warn_buf);
1153 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1155 if (ir->rvdw_switch == 0)
1157 sprintf(warn_buf, "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones potential. This suggests it was not set in the mdp, which can lead to large energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw switching range.");
1158 warning(wi, warn_buf);
1162 if (EEL_FULL(ir->coulombtype))
1164 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1165 ir->coulombtype == eelPMEUSERSWITCH)
1167 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1168 eel_names[ir->coulombtype]);
1169 CHECK(ir->rcoulomb > ir->rlist);
1171 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1173 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1176 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist.\n"
1177 "For optimal energy conservation,consider using\n"
1178 "a potential modifier.", eel_names[ir->coulombtype]);
1179 CHECK(ir->rcoulomb != ir->rlist);
1184 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1186 // TODO: Move these checks into the ewald module with the options class
1188 int orderMax = (ir->coulombtype == eelP3M_AD ? 8 : 12);
1190 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1192 sprintf(warn_buf, "With coulombtype = %s, you should have %d <= pme-order <= %d", eel_names[ir->coulombtype], orderMin, orderMax);
1193 warning_error(wi, warn_buf);
1197 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1199 if (ir->ewald_geometry == eewg3D)
1201 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1202 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1203 warning(wi, warn_buf);
1205 /* This check avoids extra pbc coding for exclusion corrections */
1206 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1207 CHECK(ir->wall_ewald_zfac < 2);
1209 if ((ir->ewald_geometry == eewg3DC) && (ir->ePBC != epbcXY) &&
1210 EEL_FULL(ir->coulombtype))
1212 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1213 eel_names[ir->coulombtype], eewg_names[eewg3DC], epbc_names[epbcXY]);
1214 warning(wi, warn_buf);
1216 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1218 if (ir->cutoff_scheme == ecutsVERLET)
1220 sprintf(warn_buf, "Since molecules/charge groups are broken using the Verlet scheme, you can not use a dipole correction to the %s electrostatics.",
1221 eel_names[ir->coulombtype]);
1222 warning(wi, warn_buf);
1226 sprintf(warn_buf, "Dipole corrections to %s electrostatics only work if all charge groups that can cross PBC boundaries are dipoles. If this is not the case set epsilon_surface to 0",
1227 eel_names[ir->coulombtype]);
1228 warning_note(wi, warn_buf);
1232 if (ir_vdw_switched(ir))
1234 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1235 CHECK(ir->rvdw_switch >= ir->rvdw);
1237 if (ir->rvdw_switch < 0.5*ir->rvdw)
1239 sprintf(warn_buf, "You are applying a switch function to vdw forces or potentials from %g to %g nm, which is more than half the interaction range, whereas switch functions are intended to act only close to the cut-off.",
1240 ir->rvdw_switch, ir->rvdw);
1241 warning_note(wi, warn_buf);
1244 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1246 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1248 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1249 CHECK(ir->rlist > ir->rvdw);
1253 if (ir->vdwtype == evdwPME)
1255 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1257 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s and %s",
1258 evdw_names[ir->vdwtype],
1259 eintmod_names[eintmodPOTSHIFT],
1260 eintmod_names[eintmodNONE]);
1261 warning_error(wi, err_buf);
1265 if (ir->cutoff_scheme == ecutsGROUP)
1267 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1268 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)))
1270 warning_note(wi, "With exact cut-offs, rlist should be "
1271 "larger than rcoulomb and rvdw, so that there "
1272 "is a buffer region for particle motion "
1273 "between neighborsearch steps");
1276 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlist <= ir->rcoulomb)
1278 sprintf(warn_buf, "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb.");
1279 warning_note(wi, warn_buf);
1281 if (ir_vdw_switched(ir) && (ir->rlist <= ir->rvdw))
1283 sprintf(warn_buf, "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw.");
1284 warning_note(wi, warn_buf);
1288 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1290 warning_note(wi, "You have selected user tables with dispersion correction, the dispersion will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction between rvdw_switch and rvdw will not be double counted). Make sure that you really want dispersion correction to -C6/r^6.");
1293 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1296 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1299 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1301 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1304 /* ENERGY CONSERVATION */
1305 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1307 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1309 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1310 evdw_names[evdwSHIFT]);
1311 warning_note(wi, warn_buf);
1313 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1315 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1316 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1317 warning_note(wi, warn_buf);
1321 /* IMPLICIT SOLVENT */
1322 if (ir->coulombtype == eelGB_NOTUSED)
1324 sprintf(warn_buf, "Invalid option %s for coulombtype",
1325 eel_names[ir->coulombtype]);
1326 warning_error(wi, warn_buf);
1331 if (ir->cutoff_scheme != ecutsGROUP)
1333 warning_error(wi, "QMMM is currently only supported with cutoff-scheme=group");
1335 if (!EI_DYNAMICS(ir->eI))
1338 sprintf(buf, "QMMM is only supported with dynamics, not with integrator %s", ei_names[ir->eI]);
1339 warning_error(wi, buf);
1345 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1349 /* count the number of text elemets separated by whitespace in a string.
1350 str = the input string
1351 maxptr = the maximum number of allowed elements
1352 ptr = the output array of pointers to the first character of each element
1353 returns: the number of elements. */
1354 int str_nelem(const char *str, int maxptr, char *ptr[])
1359 copy0 = gmx_strdup(str);
1362 while (*copy != '\0')
1366 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1374 while ((*copy != '\0') && !isspace(*copy))
1393 /* interpret a number of doubles from a string and put them in an array,
1394 after allocating space for them.
1395 str = the input string
1396 n = the (pre-allocated) number of doubles read
1397 r = the output array of doubles. */
1398 static void parse_n_real(char *str, int *n, real **r, warninp_t wi)
1403 char warn_buf[STRLEN];
1405 *n = str_nelem(str, MAXPTR, ptr);
1408 for (i = 0; i < *n; i++)
1410 (*r)[i] = strtod(ptr[i], &endptr);
1413 sprintf(warn_buf, "Invalid value %s in string in mdp file. Expected a real number.", ptr[i]);
1414 warning_error(wi, warn_buf);
1419 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
1422 int i, j, max_n_lambda, nweights, nfep[efptNR];
1423 t_lambda *fep = ir->fepvals;
1424 t_expanded *expand = ir->expandedvals;
1425 real **count_fep_lambdas;
1426 bool bOneLambda = TRUE;
1428 snew(count_fep_lambdas, efptNR);
1430 /* FEP input processing */
1431 /* first, identify the number of lambda values for each type.
1432 All that are nonzero must have the same number */
1434 for (i = 0; i < efptNR; i++)
1436 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
1439 /* now, determine the number of components. All must be either zero, or equal. */
1442 for (i = 0; i < efptNR; i++)
1444 if (nfep[i] > max_n_lambda)
1446 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1447 must have the same number if its not zero.*/
1452 for (i = 0; i < efptNR; i++)
1456 ir->fepvals->separate_dvdl[i] = FALSE;
1458 else if (nfep[i] == max_n_lambda)
1460 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1461 respect to the temperature currently */
1463 ir->fepvals->separate_dvdl[i] = TRUE;
1468 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1469 nfep[i], efpt_names[i], max_n_lambda);
1472 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1473 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1475 /* the number of lambdas is the number we've read in, which is either zero
1476 or the same for all */
1477 fep->n_lambda = max_n_lambda;
1479 /* allocate space for the array of lambda values */
1480 snew(fep->all_lambda, efptNR);
1481 /* if init_lambda is defined, we need to set lambda */
1482 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1484 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1486 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1487 for (i = 0; i < efptNR; i++)
1489 snew(fep->all_lambda[i], fep->n_lambda);
1490 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1493 for (j = 0; j < fep->n_lambda; j++)
1495 fep->all_lambda[i][j] = static_cast<double>(count_fep_lambdas[i][j]);
1497 sfree(count_fep_lambdas[i]);
1500 sfree(count_fep_lambdas);
1502 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1503 bookkeeping -- for now, init_lambda */
1505 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1507 for (i = 0; i < fep->n_lambda; i++)
1509 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1513 /* check to see if only a single component lambda is defined, and soft core is defined.
1514 In this case, turn on coulomb soft core */
1516 if (max_n_lambda == 0)
1522 for (i = 0; i < efptNR; i++)
1524 if ((nfep[i] != 0) && (i != efptFEP))
1530 if ((bOneLambda) && (fep->sc_alpha > 0))
1532 fep->bScCoul = TRUE;
1535 /* Fill in the others with the efptFEP if they are not explicitly
1536 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1537 they are all zero. */
1539 for (i = 0; i < efptNR; i++)
1541 if ((nfep[i] == 0) && (i != efptFEP))
1543 for (j = 0; j < fep->n_lambda; j++)
1545 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1551 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1552 if (fep->sc_r_power == 48)
1554 if (fep->sc_alpha > 0.1)
1556 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1560 /* now read in the weights */
1561 parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
1564 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1566 else if (nweights != fep->n_lambda)
1568 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1569 nweights, fep->n_lambda);
1571 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1573 expand->nstexpanded = fep->nstdhdl;
1574 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1576 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1578 expand->nstexpanded = 2*static_cast<int>(ir->opts.tau_t[0]/ir->delta_t);
1579 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1580 2*tau_t just to be careful so it's not to frequent */
1585 static void do_simtemp_params(t_inputrec *ir)
1588 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1589 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1592 static void do_wall_params(t_inputrec *ir,
1593 char *wall_atomtype, char *wall_density,
1597 char *names[MAXPTR];
1600 opts->wall_atomtype[0] = nullptr;
1601 opts->wall_atomtype[1] = nullptr;
1603 ir->wall_atomtype[0] = -1;
1604 ir->wall_atomtype[1] = -1;
1605 ir->wall_density[0] = 0;
1606 ir->wall_density[1] = 0;
1610 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1611 if (nstr != ir->nwall)
1613 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1616 for (i = 0; i < ir->nwall; i++)
1618 opts->wall_atomtype[i] = gmx_strdup(names[i]);
1621 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1623 nstr = str_nelem(wall_density, MAXPTR, names);
1624 if (nstr != ir->nwall)
1626 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1628 for (i = 0; i < ir->nwall; i++)
1630 if (sscanf(names[i], "%lf", &dbl) != 1)
1632 gmx_fatal(FARGS, "Could not parse wall-density value from string '%s'", names[i]);
1636 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1638 ir->wall_density[i] = dbl;
1644 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1652 srenew(groups->grpname, groups->ngrpname+nwall);
1653 grps = &(groups->grps[egcENER]);
1654 srenew(grps->nm_ind, grps->nr+nwall);
1655 for (i = 0; i < nwall; i++)
1657 sprintf(str, "wall%d", i);
1658 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1659 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1664 static void read_expandedparams(std::vector<t_inpfile> *inp,
1665 t_expanded *expand, warninp_t wi)
1667 /* read expanded ensemble parameters */
1668 printStringNewline(inp, "expanded ensemble variables");
1669 expand->nstexpanded = get_eint(inp, "nstexpanded", -1, wi);
1670 expand->elamstats = get_eeenum(inp, "lmc-stats", elamstats_names, wi);
1671 expand->elmcmove = get_eeenum(inp, "lmc-move", elmcmove_names, wi);
1672 expand->elmceq = get_eeenum(inp, "lmc-weights-equil", elmceq_names, wi);
1673 expand->equil_n_at_lam = get_eint(inp, "weight-equil-number-all-lambda", -1, wi);
1674 expand->equil_samples = get_eint(inp, "weight-equil-number-samples", -1, wi);
1675 expand->equil_steps = get_eint(inp, "weight-equil-number-steps", -1, wi);
1676 expand->equil_wl_delta = get_ereal(inp, "weight-equil-wl-delta", -1, wi);
1677 expand->equil_ratio = get_ereal(inp, "weight-equil-count-ratio", -1, wi);
1678 printStringNewline(inp, "Seed for Monte Carlo in lambda space");
1679 expand->lmc_seed = get_eint(inp, "lmc-seed", -1, wi);
1680 expand->mc_temp = get_ereal(inp, "mc-temperature", -1, wi);
1681 expand->lmc_repeats = get_eint(inp, "lmc-repeats", 1, wi);
1682 expand->gibbsdeltalam = get_eint(inp, "lmc-gibbsdelta", -1, wi);
1683 expand->lmc_forced_nstart = get_eint(inp, "lmc-forced-nstart", 0, wi);
1684 expand->bSymmetrizedTMatrix = get_eeenum(inp, "symmetrized-transition-matrix", yesno_names, wi);
1685 expand->nstTij = get_eint(inp, "nst-transition-matrix", -1, wi);
1686 expand->minvarmin = get_eint(inp, "mininum-var-min", 100, wi); /*default is reasonable */
1687 expand->c_range = get_eint(inp, "weight-c-range", 0, wi); /* default is just C=0 */
1688 expand->wl_scale = get_ereal(inp, "wl-scale", 0.8, wi);
1689 expand->wl_ratio = get_ereal(inp, "wl-ratio", 0.8, wi);
1690 expand->init_wl_delta = get_ereal(inp, "init-wl-delta", 1.0, wi);
1691 expand->bWLoneovert = get_eeenum(inp, "wl-oneovert", yesno_names, wi);
1694 /*! \brief Return whether an end state with the given coupling-lambda
1695 * value describes fully-interacting VDW.
1697 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1698 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1700 static bool couple_lambda_has_vdw_on(int couple_lambda_value)
1702 return (couple_lambda_value == ecouplamVDW ||
1703 couple_lambda_value == ecouplamVDWQ);
1709 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1712 explicit MdpErrorHandler(warninp_t wi)
1713 : wi_(wi), mapping_(nullptr)
1717 void setBackMapping(const gmx::IKeyValueTreeBackMapping &mapping)
1719 mapping_ = &mapping;
1722 virtual bool onError(gmx::UserInputError *ex, const gmx::KeyValueTreePath &context)
1724 ex->prependContext(gmx::formatString("Error in mdp option \"%s\":",
1725 getOptionName(context).c_str()));
1726 std::string message = gmx::formatExceptionMessageToString(*ex);
1727 warning_error(wi_, message.c_str());
1732 std::string getOptionName(const gmx::KeyValueTreePath &context)
1734 if (mapping_ != nullptr)
1736 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1737 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1740 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1745 const gmx::IKeyValueTreeBackMapping *mapping_;
1750 void get_ir(const char *mdparin, const char *mdparout,
1751 gmx::MDModules *mdModules, t_inputrec *ir, t_gromppopts *opts,
1752 WriteMdpHeader writeMdpHeader, warninp_t wi)
1755 double dumdub[2][6];
1757 char warn_buf[STRLEN];
1758 t_lambda *fep = ir->fepvals;
1759 t_expanded *expand = ir->expandedvals;
1761 const char *no_names[] = { "no", nullptr };
1763 init_inputrec_strings();
1764 gmx::TextInputFile stream(mdparin);
1765 std::vector<t_inpfile> inp = read_inpfile(&stream, mdparin, wi);
1767 snew(dumstr[0], STRLEN);
1768 snew(dumstr[1], STRLEN);
1770 if (-1 == search_einp(inp, "cutoff-scheme"))
1773 "%s did not specify a value for the .mdp option "
1774 "\"cutoff-scheme\". Probably it was first intended for use "
1775 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1776 "introduced, but the group scheme was still the default. "
1777 "The default is now the Verlet scheme, so you will observe "
1778 "different behaviour.", mdparin);
1779 warning_note(wi, warn_buf);
1782 /* ignore the following deprecated commands */
1783 replace_inp_entry(inp, "title", nullptr);
1784 replace_inp_entry(inp, "cpp", nullptr);
1785 replace_inp_entry(inp, "domain-decomposition", nullptr);
1786 replace_inp_entry(inp, "andersen-seed", nullptr);
1787 replace_inp_entry(inp, "dihre", nullptr);
1788 replace_inp_entry(inp, "dihre-fc", nullptr);
1789 replace_inp_entry(inp, "dihre-tau", nullptr);
1790 replace_inp_entry(inp, "nstdihreout", nullptr);
1791 replace_inp_entry(inp, "nstcheckpoint", nullptr);
1792 replace_inp_entry(inp, "optimize-fft", nullptr);
1793 replace_inp_entry(inp, "adress_type", nullptr);
1794 replace_inp_entry(inp, "adress_const_wf", nullptr);
1795 replace_inp_entry(inp, "adress_ex_width", nullptr);
1796 replace_inp_entry(inp, "adress_hy_width", nullptr);
1797 replace_inp_entry(inp, "adress_ex_forcecap", nullptr);
1798 replace_inp_entry(inp, "adress_interface_correction", nullptr);
1799 replace_inp_entry(inp, "adress_site", nullptr);
1800 replace_inp_entry(inp, "adress_reference_coords", nullptr);
1801 replace_inp_entry(inp, "adress_tf_grp_names", nullptr);
1802 replace_inp_entry(inp, "adress_cg_grp_names", nullptr);
1803 replace_inp_entry(inp, "adress_do_hybridpairs", nullptr);
1804 replace_inp_entry(inp, "rlistlong", nullptr);
1805 replace_inp_entry(inp, "nstcalclr", nullptr);
1806 replace_inp_entry(inp, "pull-print-com2", nullptr);
1807 replace_inp_entry(inp, "gb-algorithm", nullptr);
1808 replace_inp_entry(inp, "nstgbradii", nullptr);
1809 replace_inp_entry(inp, "rgbradii", nullptr);
1810 replace_inp_entry(inp, "gb-epsilon-solvent", nullptr);
1811 replace_inp_entry(inp, "gb-saltconc", nullptr);
1812 replace_inp_entry(inp, "gb-obc-alpha", nullptr);
1813 replace_inp_entry(inp, "gb-obc-beta", nullptr);
1814 replace_inp_entry(inp, "gb-obc-gamma", nullptr);
1815 replace_inp_entry(inp, "gb-dielectric-offset", nullptr);
1816 replace_inp_entry(inp, "sa-algorithm", nullptr);
1817 replace_inp_entry(inp, "sa-surface-tension", nullptr);
1819 /* replace the following commands with the clearer new versions*/
1820 replace_inp_entry(inp, "unconstrained-start", "continuation");
1821 replace_inp_entry(inp, "foreign-lambda", "fep-lambdas");
1822 replace_inp_entry(inp, "verlet-buffer-drift", "verlet-buffer-tolerance");
1823 replace_inp_entry(inp, "nstxtcout", "nstxout-compressed");
1824 replace_inp_entry(inp, "xtc-grps", "compressed-x-grps");
1825 replace_inp_entry(inp, "xtc-precision", "compressed-x-precision");
1826 replace_inp_entry(inp, "pull-print-com1", "pull-print-com");
1828 printStringNewline(&inp, "VARIOUS PREPROCESSING OPTIONS");
1829 printStringNoNewline(&inp, "Preprocessor information: use cpp syntax.");
1830 printStringNoNewline(&inp, "e.g.: -I/home/joe/doe -I/home/mary/roe");
1831 setStringEntry(&inp, "include", opts->include, nullptr);
1832 printStringNoNewline(&inp, "e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1833 setStringEntry(&inp, "define", opts->define, nullptr);
1835 printStringNewline(&inp, "RUN CONTROL PARAMETERS");
1836 ir->eI = get_eeenum(&inp, "integrator", ei_names, wi);
1837 printStringNoNewline(&inp, "Start time and timestep in ps");
1838 ir->init_t = get_ereal(&inp, "tinit", 0.0, wi);
1839 ir->delta_t = get_ereal(&inp, "dt", 0.001, wi);
1840 ir->nsteps = get_eint64(&inp, "nsteps", 0, wi);
1841 printStringNoNewline(&inp, "For exact run continuation or redoing part of a run");
1842 ir->init_step = get_eint64(&inp, "init-step", 0, wi);
1843 printStringNoNewline(&inp, "Part index is updated automatically on checkpointing (keeps files separate)");
1844 ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
1845 printStringNoNewline(&inp, "mode for center of mass motion removal");
1846 ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
1847 printStringNoNewline(&inp, "number of steps for center of mass motion removal");
1848 ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
1849 printStringNoNewline(&inp, "group(s) for center of mass motion removal");
1850 setStringEntry(&inp, "comm-grps", is->vcm, nullptr);
1852 printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
1853 printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
1854 ir->bd_fric = get_ereal(&inp, "bd-fric", 0.0, wi);
1855 ir->ld_seed = get_eint64(&inp, "ld-seed", -1, wi);
1858 printStringNewline(&inp, "ENERGY MINIMIZATION OPTIONS");
1859 printStringNoNewline(&inp, "Force tolerance and initial step-size");
1860 ir->em_tol = get_ereal(&inp, "emtol", 10.0, wi);
1861 ir->em_stepsize = get_ereal(&inp, "emstep", 0.01, wi);
1862 printStringNoNewline(&inp, "Max number of iterations in relax-shells");
1863 ir->niter = get_eint(&inp, "niter", 20, wi);
1864 printStringNoNewline(&inp, "Step size (ps^2) for minimization of flexible constraints");
1865 ir->fc_stepsize = get_ereal(&inp, "fcstep", 0, wi);
1866 printStringNoNewline(&inp, "Frequency of steepest descents steps when doing CG");
1867 ir->nstcgsteep = get_eint(&inp, "nstcgsteep", 1000, wi);
1868 ir->nbfgscorr = get_eint(&inp, "nbfgscorr", 10, wi);
1870 printStringNewline(&inp, "TEST PARTICLE INSERTION OPTIONS");
1871 ir->rtpi = get_ereal(&inp, "rtpi", 0.05, wi);
1873 /* Output options */
1874 printStringNewline(&inp, "OUTPUT CONTROL OPTIONS");
1875 printStringNoNewline(&inp, "Output frequency for coords (x), velocities (v) and forces (f)");
1876 ir->nstxout = get_eint(&inp, "nstxout", 0, wi);
1877 ir->nstvout = get_eint(&inp, "nstvout", 0, wi);
1878 ir->nstfout = get_eint(&inp, "nstfout", 0, wi);
1879 printStringNoNewline(&inp, "Output frequency for energies to log file and energy file");
1880 ir->nstlog = get_eint(&inp, "nstlog", 1000, wi);
1881 ir->nstcalcenergy = get_eint(&inp, "nstcalcenergy", 100, wi);
1882 ir->nstenergy = get_eint(&inp, "nstenergy", 1000, wi);
1883 printStringNoNewline(&inp, "Output frequency and precision for .xtc file");
1884 ir->nstxout_compressed = get_eint(&inp, "nstxout-compressed", 0, wi);
1885 ir->x_compression_precision = get_ereal(&inp, "compressed-x-precision", 1000.0, wi);
1886 printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
1887 printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
1888 printStringNoNewline(&inp, "default, all atoms will be written.");
1889 setStringEntry(&inp, "compressed-x-grps", is->x_compressed_groups, nullptr);
1890 printStringNoNewline(&inp, "Selection of energy groups");
1891 setStringEntry(&inp, "energygrps", is->energy, nullptr);
1893 /* Neighbor searching */
1894 printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
1895 printStringNoNewline(&inp, "cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1896 ir->cutoff_scheme = get_eeenum(&inp, "cutoff-scheme", ecutscheme_names, wi);
1897 printStringNoNewline(&inp, "nblist update frequency");
1898 ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
1899 printStringNoNewline(&inp, "ns algorithm (simple or grid)");
1900 ir->ns_type = get_eeenum(&inp, "ns-type", ens_names, wi);
1901 printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
1902 ir->ePBC = get_eeenum(&inp, "pbc", epbc_names, wi);
1903 ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi);
1904 printStringNoNewline(&inp, "Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1905 printStringNoNewline(&inp, "a value of -1 means: use rlist");
1906 ir->verletbuf_tol = get_ereal(&inp, "verlet-buffer-tolerance", 0.005, wi);
1907 printStringNoNewline(&inp, "nblist cut-off");
1908 ir->rlist = get_ereal(&inp, "rlist", 1.0, wi);
1909 printStringNoNewline(&inp, "long-range cut-off for switched potentials");
1911 /* Electrostatics */
1912 printStringNewline(&inp, "OPTIONS FOR ELECTROSTATICS AND VDW");
1913 printStringNoNewline(&inp, "Method for doing electrostatics");
1914 ir->coulombtype = get_eeenum(&inp, "coulombtype", eel_names, wi);
1915 ir->coulomb_modifier = get_eeenum(&inp, "coulomb-modifier", eintmod_names, wi);
1916 printStringNoNewline(&inp, "cut-off lengths");
1917 ir->rcoulomb_switch = get_ereal(&inp, "rcoulomb-switch", 0.0, wi);
1918 ir->rcoulomb = get_ereal(&inp, "rcoulomb", 1.0, wi);
1919 printStringNoNewline(&inp, "Relative dielectric constant for the medium and the reaction field");
1920 ir->epsilon_r = get_ereal(&inp, "epsilon-r", 1.0, wi);
1921 ir->epsilon_rf = get_ereal(&inp, "epsilon-rf", 0.0, wi);
1922 printStringNoNewline(&inp, "Method for doing Van der Waals");
1923 ir->vdwtype = get_eeenum(&inp, "vdw-type", evdw_names, wi);
1924 ir->vdw_modifier = get_eeenum(&inp, "vdw-modifier", eintmod_names, wi);
1925 printStringNoNewline(&inp, "cut-off lengths");
1926 ir->rvdw_switch = get_ereal(&inp, "rvdw-switch", 0.0, wi);
1927 ir->rvdw = get_ereal(&inp, "rvdw", 1.0, wi);
1928 printStringNoNewline(&inp, "Apply long range dispersion corrections for Energy and Pressure");
1929 ir->eDispCorr = get_eeenum(&inp, "DispCorr", edispc_names, wi);
1930 printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
1931 ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
1932 printStringNoNewline(&inp, "Separate tables between energy group pairs");
1933 setStringEntry(&inp, "energygrp-table", is->egptable, nullptr);
1934 printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
1935 ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
1936 printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
1937 ir->nkx = get_eint(&inp, "fourier-nx", 0, wi);
1938 ir->nky = get_eint(&inp, "fourier-ny", 0, wi);
1939 ir->nkz = get_eint(&inp, "fourier-nz", 0, wi);
1940 printStringNoNewline(&inp, "EWALD/PME/PPPM parameters");
1941 ir->pme_order = get_eint(&inp, "pme-order", 4, wi);
1942 ir->ewald_rtol = get_ereal(&inp, "ewald-rtol", 0.00001, wi);
1943 ir->ewald_rtol_lj = get_ereal(&inp, "ewald-rtol-lj", 0.001, wi);
1944 ir->ljpme_combination_rule = get_eeenum(&inp, "lj-pme-comb-rule", eljpme_names, wi);
1945 ir->ewald_geometry = get_eeenum(&inp, "ewald-geometry", eewg_names, wi);
1946 ir->epsilon_surface = get_ereal(&inp, "epsilon-surface", 0.0, wi);
1948 /* Implicit solvation is no longer supported, but we need grompp
1949 to be able to refuse old .mdp files that would have built a tpr
1950 to run it. Thus, only "no" is accepted. */
1951 ir->implicit_solvent = get_eeenum(&inp, "implicit-solvent", no_names, wi);
1953 /* Coupling stuff */
1954 printStringNewline(&inp, "OPTIONS FOR WEAK COUPLING ALGORITHMS");
1955 printStringNoNewline(&inp, "Temperature coupling");
1956 ir->etc = get_eeenum(&inp, "tcoupl", etcoupl_names, wi);
1957 ir->nsttcouple = get_eint(&inp, "nsttcouple", -1, wi);
1958 ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
1959 ir->bPrintNHChains = get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi);
1960 printStringNoNewline(&inp, "Groups to couple separately");
1961 setStringEntry(&inp, "tc-grps", is->tcgrps, nullptr);
1962 printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
1963 setStringEntry(&inp, "tau-t", is->tau_t, nullptr);
1964 setStringEntry(&inp, "ref-t", is->ref_t, nullptr);
1965 printStringNoNewline(&inp, "pressure coupling");
1966 ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
1967 ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
1968 ir->nstpcouple = get_eint(&inp, "nstpcouple", -1, wi);
1969 printStringNoNewline(&inp, "Time constant (ps), compressibility (1/bar) and reference P (bar)");
1970 ir->tau_p = get_ereal(&inp, "tau-p", 1.0, wi);
1971 setStringEntry(&inp, "compressibility", dumstr[0], nullptr);
1972 setStringEntry(&inp, "ref-p", dumstr[1], nullptr);
1973 printStringNoNewline(&inp, "Scaling of reference coordinates, No, All or COM");
1974 ir->refcoord_scaling = get_eeenum(&inp, "refcoord-scaling", erefscaling_names, wi);
1977 printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
1978 ir->bQMMM = get_eeenum(&inp, "QMMM", yesno_names, wi);
1979 printStringNoNewline(&inp, "Groups treated Quantum Mechanically");
1980 setStringEntry(&inp, "QMMM-grps", is->QMMM, nullptr);
1981 printStringNoNewline(&inp, "QM method");
1982 setStringEntry(&inp, "QMmethod", is->QMmethod, nullptr);
1983 printStringNoNewline(&inp, "QMMM scheme");
1984 ir->QMMMscheme = get_eeenum(&inp, "QMMMscheme", eQMMMscheme_names, wi);
1985 printStringNoNewline(&inp, "QM basisset");
1986 setStringEntry(&inp, "QMbasis", is->QMbasis, nullptr);
1987 printStringNoNewline(&inp, "QM charge");
1988 setStringEntry(&inp, "QMcharge", is->QMcharge, nullptr);
1989 printStringNoNewline(&inp, "QM multiplicity");
1990 setStringEntry(&inp, "QMmult", is->QMmult, nullptr);
1991 printStringNoNewline(&inp, "Surface Hopping");
1992 setStringEntry(&inp, "SH", is->bSH, nullptr);
1993 printStringNoNewline(&inp, "CAS space options");
1994 setStringEntry(&inp, "CASorbitals", is->CASorbitals, nullptr);
1995 setStringEntry(&inp, "CASelectrons", is->CASelectrons, nullptr);
1996 setStringEntry(&inp, "SAon", is->SAon, nullptr);
1997 setStringEntry(&inp, "SAoff", is->SAoff, nullptr);
1998 setStringEntry(&inp, "SAsteps", is->SAsteps, nullptr);
1999 printStringNoNewline(&inp, "Scale factor for MM charges");
2000 ir->scalefactor = get_ereal(&inp, "MMChargeScaleFactor", 1.0, wi);
2002 /* Simulated annealing */
2003 printStringNewline(&inp, "SIMULATED ANNEALING");
2004 printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
2005 setStringEntry(&inp, "annealing", is->anneal, nullptr);
2006 printStringNoNewline(&inp, "Number of time points to use for specifying annealing in each group");
2007 setStringEntry(&inp, "annealing-npoints", is->anneal_npoints, nullptr);
2008 printStringNoNewline(&inp, "List of times at the annealing points for each group");
2009 setStringEntry(&inp, "annealing-time", is->anneal_time, nullptr);
2010 printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
2011 setStringEntry(&inp, "annealing-temp", is->anneal_temp, nullptr);
2014 printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
2015 opts->bGenVel = get_eeenum(&inp, "gen-vel", yesno_names, wi);
2016 opts->tempi = get_ereal(&inp, "gen-temp", 300.0, wi);
2017 opts->seed = get_eint(&inp, "gen-seed", -1, wi);
2020 printStringNewline(&inp, "OPTIONS FOR BONDS");
2021 opts->nshake = get_eeenum(&inp, "constraints", constraints, wi);
2022 printStringNoNewline(&inp, "Type of constraint algorithm");
2023 ir->eConstrAlg = get_eeenum(&inp, "constraint-algorithm", econstr_names, wi);
2024 printStringNoNewline(&inp, "Do not constrain the start configuration");
2025 ir->bContinuation = get_eeenum(&inp, "continuation", yesno_names, wi);
2026 printStringNoNewline(&inp, "Use successive overrelaxation to reduce the number of shake iterations");
2027 ir->bShakeSOR = get_eeenum(&inp, "Shake-SOR", yesno_names, wi);
2028 printStringNoNewline(&inp, "Relative tolerance of shake");
2029 ir->shake_tol = get_ereal(&inp, "shake-tol", 0.0001, wi);
2030 printStringNoNewline(&inp, "Highest order in the expansion of the constraint coupling matrix");
2031 ir->nProjOrder = get_eint(&inp, "lincs-order", 4, wi);
2032 printStringNoNewline(&inp, "Number of iterations in the final step of LINCS. 1 is fine for");
2033 printStringNoNewline(&inp, "normal simulations, but use 2 to conserve energy in NVE runs.");
2034 printStringNoNewline(&inp, "For energy minimization with constraints it should be 4 to 8.");
2035 ir->nLincsIter = get_eint(&inp, "lincs-iter", 1, wi);
2036 printStringNoNewline(&inp, "Lincs will write a warning to the stderr if in one step a bond");
2037 printStringNoNewline(&inp, "rotates over more degrees than");
2038 ir->LincsWarnAngle = get_ereal(&inp, "lincs-warnangle", 30.0, wi);
2039 printStringNoNewline(&inp, "Convert harmonic bonds to morse potentials");
2040 opts->bMorse = get_eeenum(&inp, "morse", yesno_names, wi);
2042 /* Energy group exclusions */
2043 printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
2044 printStringNoNewline(&inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
2045 setStringEntry(&inp, "energygrp-excl", is->egpexcl, nullptr);
2048 printStringNewline(&inp, "WALLS");
2049 printStringNoNewline(&inp, "Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2050 ir->nwall = get_eint(&inp, "nwall", 0, wi);
2051 ir->wall_type = get_eeenum(&inp, "wall-type", ewt_names, wi);
2052 ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
2053 setStringEntry(&inp, "wall-atomtype", is->wall_atomtype, nullptr);
2054 setStringEntry(&inp, "wall-density", is->wall_density, nullptr);
2055 ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
2058 printStringNewline(&inp, "COM PULLING");
2059 ir->bPull = get_eeenum(&inp, "pull", yesno_names, wi);
2063 is->pull_grp = read_pullparams(&inp, ir->pull, wi);
2067 NOTE: needs COM pulling input */
2068 printStringNewline(&inp, "AWH biasing");
2069 ir->bDoAwh = get_eeenum(&inp, "awh", yesno_names, wi);
2074 ir->awhParams = gmx::readAndCheckAwhParams(&inp, ir, wi);
2078 gmx_fatal(FARGS, "AWH biasing is only compatible with COM pulling turned on");
2082 /* Enforced rotation */
2083 printStringNewline(&inp, "ENFORCED ROTATION");
2084 printStringNoNewline(&inp, "Enforced rotation: No or Yes");
2085 ir->bRot = get_eeenum(&inp, "rotation", yesno_names, wi);
2089 is->rot_grp = read_rotparams(&inp, ir->rot, wi);
2092 /* Interactive MD */
2094 printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
2095 setStringEntry(&inp, "IMD-group", is->imd_grp, nullptr);
2096 if (is->imd_grp[0] != '\0')
2103 printStringNewline(&inp, "NMR refinement stuff");
2104 printStringNoNewline(&inp, "Distance restraints type: No, Simple or Ensemble");
2105 ir->eDisre = get_eeenum(&inp, "disre", edisre_names, wi);
2106 printStringNoNewline(&inp, "Force weighting of pairs in one distance restraint: Conservative or Equal");
2107 ir->eDisreWeighting = get_eeenum(&inp, "disre-weighting", edisreweighting_names, wi);
2108 printStringNoNewline(&inp, "Use sqrt of the time averaged times the instantaneous violation");
2109 ir->bDisreMixed = get_eeenum(&inp, "disre-mixed", yesno_names, wi);
2110 ir->dr_fc = get_ereal(&inp, "disre-fc", 1000.0, wi);
2111 ir->dr_tau = get_ereal(&inp, "disre-tau", 0.0, wi);
2112 printStringNoNewline(&inp, "Output frequency for pair distances to energy file");
2113 ir->nstdisreout = get_eint(&inp, "nstdisreout", 100, wi);
2114 printStringNoNewline(&inp, "Orientation restraints: No or Yes");
2115 opts->bOrire = get_eeenum(&inp, "orire", yesno_names, wi);
2116 printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
2117 ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
2118 ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
2119 setStringEntry(&inp, "orire-fitgrp", is->orirefitgrp, nullptr);
2120 printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
2121 ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
2123 /* free energy variables */
2124 printStringNewline(&inp, "Free energy variables");
2125 ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
2126 setStringEntry(&inp, "couple-moltype", is->couple_moltype, nullptr);
2127 opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
2128 opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
2129 opts->bCoupleIntra = get_eeenum(&inp, "couple-intramol", yesno_names, wi);
2131 fep->init_lambda = get_ereal(&inp, "init-lambda", -1, wi); /* start with -1 so
2133 it was not entered */
2134 fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
2135 fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
2136 fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
2137 setStringEntry(&inp, "fep-lambdas", is->fep_lambda[efptFEP], nullptr);
2138 setStringEntry(&inp, "mass-lambdas", is->fep_lambda[efptMASS], nullptr);
2139 setStringEntry(&inp, "coul-lambdas", is->fep_lambda[efptCOUL], nullptr);
2140 setStringEntry(&inp, "vdw-lambdas", is->fep_lambda[efptVDW], nullptr);
2141 setStringEntry(&inp, "bonded-lambdas", is->fep_lambda[efptBONDED], nullptr);
2142 setStringEntry(&inp, "restraint-lambdas", is->fep_lambda[efptRESTRAINT], nullptr);
2143 setStringEntry(&inp, "temperature-lambdas", is->fep_lambda[efptTEMPERATURE], nullptr);
2144 fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
2145 setStringEntry(&inp, "init-lambda-weights", is->lambda_weights, nullptr);
2146 fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
2147 fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
2148 fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
2149 fep->sc_r_power = get_ereal(&inp, "sc-r-power", 6.0, wi);
2150 fep->sc_sigma = get_ereal(&inp, "sc-sigma", 0.3, wi);
2151 fep->bScCoul = get_eeenum(&inp, "sc-coul", yesno_names, wi);
2152 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2153 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2154 fep->separate_dhdl_file = get_eeenum(&inp, "separate-dhdl-file", separate_dhdl_file_names, wi);
2155 fep->dhdl_derivatives = get_eeenum(&inp, "dhdl-derivatives", dhdl_derivatives_names, wi);
2156 fep->dh_hist_size = get_eint(&inp, "dh_hist_size", 0, wi);
2157 fep->dh_hist_spacing = get_ereal(&inp, "dh_hist_spacing", 0.1, wi);
2159 /* Non-equilibrium MD stuff */
2160 printStringNewline(&inp, "Non-equilibrium MD stuff");
2161 setStringEntry(&inp, "acc-grps", is->accgrps, nullptr);
2162 setStringEntry(&inp, "accelerate", is->acc, nullptr);
2163 setStringEntry(&inp, "freezegrps", is->freeze, nullptr);
2164 setStringEntry(&inp, "freezedim", is->frdim, nullptr);
2165 ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
2166 setStringEntry(&inp, "deform", is->deform, nullptr);
2168 /* simulated tempering variables */
2169 printStringNewline(&inp, "simulated tempering variables");
2170 ir->bSimTemp = get_eeenum(&inp, "simulated-tempering", yesno_names, wi);
2171 ir->simtempvals->eSimTempScale = get_eeenum(&inp, "simulated-tempering-scaling", esimtemp_names, wi);
2172 ir->simtempvals->simtemp_low = get_ereal(&inp, "sim-temp-low", 300.0, wi);
2173 ir->simtempvals->simtemp_high = get_ereal(&inp, "sim-temp-high", 300.0, wi);
2175 /* expanded ensemble variables */
2176 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2178 read_expandedparams(&inp, expand, wi);
2181 /* Electric fields */
2183 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(inp);
2184 gmx::KeyValueTreeTransformer transform;
2185 transform.rules()->addRule()
2186 .keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2187 mdModules->initMdpTransform(transform.rules());
2188 for (const auto &path : transform.mappedPaths())
2190 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2191 mark_einp_set(inp, path[0].c_str());
2193 MdpErrorHandler errorHandler(wi);
2195 = transform.transform(convertedValues, &errorHandler);
2196 ir->params = new gmx::KeyValueTreeObject(result.object());
2197 mdModules->adjustInputrecBasedOnModules(ir);
2198 errorHandler.setBackMapping(result.backMapping());
2199 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2202 /* Ion/water position swapping ("computational electrophysiology") */
2203 printStringNewline(&inp, "Ion/water position swapping for computational electrophysiology setups");
2204 printStringNoNewline(&inp, "Swap positions along direction: no, X, Y, Z");
2205 ir->eSwapCoords = get_eeenum(&inp, "swapcoords", eSwapTypes_names, wi);
2206 if (ir->eSwapCoords != eswapNO)
2213 printStringNoNewline(&inp, "Swap attempt frequency");
2214 ir->swap->nstswap = get_eint(&inp, "swap-frequency", 1, wi);
2215 printStringNoNewline(&inp, "Number of ion types to be controlled");
2216 nIonTypes = get_eint(&inp, "iontypes", 1, wi);
2219 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2221 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2222 snew(ir->swap->grp, ir->swap->ngrp);
2223 for (i = 0; i < ir->swap->ngrp; i++)
2225 snew(ir->swap->grp[i].molname, STRLEN);
2227 printStringNoNewline(&inp, "Two index groups that contain the compartment-partitioning atoms");
2228 setStringEntry(&inp, "split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2229 setStringEntry(&inp, "split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2230 printStringNoNewline(&inp, "Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2231 ir->swap->massw_split[0] = get_eeenum(&inp, "massw-split0", yesno_names, wi);
2232 ir->swap->massw_split[1] = get_eeenum(&inp, "massw-split1", yesno_names, wi);
2234 printStringNoNewline(&inp, "Name of solvent molecules");
2235 setStringEntry(&inp, "solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2237 printStringNoNewline(&inp, "Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2238 printStringNoNewline(&inp, "Note that the split cylinder settings do not have an influence on the swapping protocol,");
2239 printStringNoNewline(&inp, "however, if correctly defined, the permeation events are recorded per channel");
2240 ir->swap->cyl0r = get_ereal(&inp, "cyl0-r", 2.0, wi);
2241 ir->swap->cyl0u = get_ereal(&inp, "cyl0-up", 1.0, wi);
2242 ir->swap->cyl0l = get_ereal(&inp, "cyl0-down", 1.0, wi);
2243 ir->swap->cyl1r = get_ereal(&inp, "cyl1-r", 2.0, wi);
2244 ir->swap->cyl1u = get_ereal(&inp, "cyl1-up", 1.0, wi);
2245 ir->swap->cyl1l = get_ereal(&inp, "cyl1-down", 1.0, wi);
2247 printStringNoNewline(&inp, "Average the number of ions per compartment over these many swap attempt steps");
2248 ir->swap->nAverage = get_eint(&inp, "coupl-steps", 10, wi);
2250 printStringNoNewline(&inp, "Names of the ion types that can be exchanged with solvent molecules,");
2251 printStringNoNewline(&inp, "and the requested number of ions of this type in compartments A and B");
2252 printStringNoNewline(&inp, "-1 means fix the numbers as found in step 0");
2253 for (i = 0; i < nIonTypes; i++)
2255 int ig = eSwapFixedGrpNR + i;
2257 sprintf(buf, "iontype%d-name", i);
2258 setStringEntry(&inp, buf, ir->swap->grp[ig].molname, nullptr);
2259 sprintf(buf, "iontype%d-in-A", i);
2260 ir->swap->grp[ig].nmolReq[0] = get_eint(&inp, buf, -1, wi);
2261 sprintf(buf, "iontype%d-in-B", i);
2262 ir->swap->grp[ig].nmolReq[1] = get_eint(&inp, buf, -1, wi);
2265 printStringNoNewline(&inp, "By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2266 printStringNoNewline(&inp, "at maximum distance (= bulk concentration) to the split group layers. However,");
2267 printStringNoNewline(&inp, "an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0");
2268 printStringNoNewline(&inp, "towards one of the compartment-partitioning layers (at +/- 1.0).");
2269 ir->swap->bulkOffset[0] = get_ereal(&inp, "bulk-offsetA", 0.0, wi);
2270 ir->swap->bulkOffset[1] = get_ereal(&inp, "bulk-offsetB", 0.0, wi);
2271 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2272 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0) )
2274 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2277 printStringNoNewline(&inp, "Start to swap ions if threshold difference to requested count is reached");
2278 ir->swap->threshold = get_ereal(&inp, "threshold", 1.0, wi);
2281 /* AdResS is no longer supported, but we need grompp to be able to
2282 refuse to process old .mdp files that used it. */
2283 ir->bAdress = get_eeenum(&inp, "adress", no_names, wi);
2285 /* User defined thingies */
2286 printStringNewline(&inp, "User defined thingies");
2287 setStringEntry(&inp, "user1-grps", is->user1, nullptr);
2288 setStringEntry(&inp, "user2-grps", is->user2, nullptr);
2289 ir->userint1 = get_eint(&inp, "userint1", 0, wi);
2290 ir->userint2 = get_eint(&inp, "userint2", 0, wi);
2291 ir->userint3 = get_eint(&inp, "userint3", 0, wi);
2292 ir->userint4 = get_eint(&inp, "userint4", 0, wi);
2293 ir->userreal1 = get_ereal(&inp, "userreal1", 0, wi);
2294 ir->userreal2 = get_ereal(&inp, "userreal2", 0, wi);
2295 ir->userreal3 = get_ereal(&inp, "userreal3", 0, wi);
2296 ir->userreal4 = get_ereal(&inp, "userreal4", 0, wi);
2300 gmx::TextOutputFile stream(mdparout);
2301 write_inpfile(&stream, mdparout, &inp, FALSE, writeMdpHeader, wi);
2303 // Transform module data into a flat key-value tree for output.
2304 gmx::KeyValueTreeBuilder builder;
2305 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2306 mdModules->buildMdpOutput(&builderObject);
2308 gmx::TextWriter writer(&stream);
2309 writeKeyValueTreeAsMdp(&writer, builder.build());
2314 /* Process options if necessary */
2315 for (m = 0; m < 2; m++)
2317 for (i = 0; i < 2*DIM; i++)
2326 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2328 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 1)");
2330 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2332 case epctSEMIISOTROPIC:
2333 case epctSURFACETENSION:
2334 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2336 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 2)");
2338 dumdub[m][YY] = dumdub[m][XX];
2340 case epctANISOTROPIC:
2341 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2342 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2343 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2345 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 6)");
2349 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2350 epcoupltype_names[ir->epct]);
2354 clear_mat(ir->ref_p);
2355 clear_mat(ir->compress);
2356 for (i = 0; i < DIM; i++)
2358 ir->ref_p[i][i] = dumdub[1][i];
2359 ir->compress[i][i] = dumdub[0][i];
2361 if (ir->epct == epctANISOTROPIC)
2363 ir->ref_p[XX][YY] = dumdub[1][3];
2364 ir->ref_p[XX][ZZ] = dumdub[1][4];
2365 ir->ref_p[YY][ZZ] = dumdub[1][5];
2366 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2368 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2370 ir->compress[XX][YY] = dumdub[0][3];
2371 ir->compress[XX][ZZ] = dumdub[0][4];
2372 ir->compress[YY][ZZ] = dumdub[0][5];
2373 for (i = 0; i < DIM; i++)
2375 for (m = 0; m < i; m++)
2377 ir->ref_p[i][m] = ir->ref_p[m][i];
2378 ir->compress[i][m] = ir->compress[m][i];
2383 if (ir->comm_mode == ecmNO)
2388 opts->couple_moltype = nullptr;
2389 if (strlen(is->couple_moltype) > 0)
2391 if (ir->efep != efepNO)
2393 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2394 if (opts->couple_lam0 == opts->couple_lam1)
2396 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2398 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2399 opts->couple_lam1 == ecouplamNONE))
2401 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2406 warning_note(wi, "Free energy is turned off, so we will not decouple the molecule listed in your input.");
2409 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2410 if (ir->efep != efepNO)
2412 if (fep->delta_lambda > 0)
2414 ir->efep = efepSLOWGROWTH;
2418 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2420 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2421 warning_note(wi, "Old option for dhdl-print-energy given: "
2422 "changing \"yes\" to \"total\"\n");
2425 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2427 /* always print out the energy to dhdl if we are doing
2428 expanded ensemble, since we need the total energy for
2429 analysis if the temperature is changing. In some
2430 conditions one may only want the potential energy, so
2431 we will allow that if the appropriate mdp setting has
2432 been enabled. Otherwise, total it is:
2434 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2437 if ((ir->efep != efepNO) || ir->bSimTemp)
2439 ir->bExpanded = FALSE;
2440 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2442 ir->bExpanded = TRUE;
2444 do_fep_params(ir, is->fep_lambda, is->lambda_weights, wi);
2445 if (ir->bSimTemp) /* done after fep params */
2447 do_simtemp_params(ir);
2450 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2451 * setup and not on the old way of specifying the free-energy setup,
2452 * we should check for using soft-core when not needed, since that
2453 * can complicate the sampling significantly.
2454 * Note that we only check for the automated coupling setup.
2455 * If the (advanced) user does FEP through manual topology changes,
2456 * this check will not be triggered.
2458 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 &&
2459 ir->fepvals->sc_alpha != 0 &&
2460 (couple_lambda_has_vdw_on(opts->couple_lam0) &&
2461 couple_lambda_has_vdw_on(opts->couple_lam1)))
2463 warning(wi, "You are using soft-core interactions while the Van der Waals interactions are not decoupled (note that the sc-coul option is only active when using lambda states). Although this will not lead to errors, you will need much more sampling than without soft-core interactions. Consider using sc-alpha=0.");
2468 ir->fepvals->n_lambda = 0;
2471 /* WALL PARAMETERS */
2473 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2475 /* ORIENTATION RESTRAINT PARAMETERS */
2477 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, nullptr) != 1)
2479 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2482 /* DEFORMATION PARAMETERS */
2484 clear_mat(ir->deform);
2485 for (i = 0; i < 6; i++)
2490 double gmx_unused canary;
2491 int ndeform = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf %lf",
2492 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2493 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]), &canary);
2495 if (strlen(is->deform) > 0 && ndeform != 6)
2497 warning_error(wi, gmx::formatString("Cannot parse exactly 6 box deformation velocities from string '%s'", is->deform).c_str());
2499 for (i = 0; i < 3; i++)
2501 ir->deform[i][i] = dumdub[0][i];
2503 ir->deform[YY][XX] = dumdub[0][3];
2504 ir->deform[ZZ][XX] = dumdub[0][4];
2505 ir->deform[ZZ][YY] = dumdub[0][5];
2506 if (ir->epc != epcNO)
2508 for (i = 0; i < 3; i++)
2510 for (j = 0; j <= i; j++)
2512 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2514 warning_error(wi, "A box element has deform set and compressibility > 0");
2518 for (i = 0; i < 3; i++)
2520 for (j = 0; j < i; j++)
2522 if (ir->deform[i][j] != 0)
2524 for (m = j; m < DIM; m++)
2526 if (ir->compress[m][j] != 0)
2528 sprintf(warn_buf, "An off-diagonal box element has deform set while compressibility > 0 for the same component of another box vector, this might lead to spurious periodicity effects.");
2529 warning(wi, warn_buf);
2537 /* Ion/water position swapping checks */
2538 if (ir->eSwapCoords != eswapNO)
2540 if (ir->swap->nstswap < 1)
2542 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2544 if (ir->swap->nAverage < 1)
2546 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2548 if (ir->swap->threshold < 1.0)
2550 warning_error(wi, "Ion count threshold must be at least 1.\n");
2558 static int search_QMstring(const char *s, int ng, const char *gn[])
2560 /* same as normal search_string, but this one searches QM strings */
2563 for (i = 0; (i < ng); i++)
2565 if (gmx_strcasecmp(s, gn[i]) == 0)
2571 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2572 } /* search_QMstring */
2574 /* We would like gn to be const as well, but C doesn't allow this */
2575 /* TODO this is utility functionality (search for the index of a
2576 string in a collection), so should be refactored and located more
2578 int search_string(const char *s, int ng, char *gn[])
2582 for (i = 0; (i < ng); i++)
2584 if (gmx_strcasecmp(s, gn[i]) == 0)
2591 "Group %s referenced in the .mdp file was not found in the index file.\n"
2592 "Group names must match either [moleculetype] names or custom index group\n"
2593 "names, in which case you must supply an index file to the '-n' option\n"
2598 static bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2599 t_blocka *block, char *gnames[],
2600 int gtype, int restnm,
2601 int grptp, bool bVerbose,
2604 unsigned short *cbuf;
2605 t_grps *grps = &(groups->grps[gtype]);
2606 int i, j, gid, aj, ognr, ntot = 0;
2609 char warn_buf[STRLEN];
2611 title = gtypes[gtype];
2614 /* Mark all id's as not set */
2615 for (i = 0; (i < natoms); i++)
2620 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2621 for (i = 0; (i < ng); i++)
2623 /* Lookup the group name in the block structure */
2624 gid = search_string(ptrs[i], block->nr, gnames);
2625 if ((grptp != egrptpONE) || (i == 0))
2627 grps->nm_ind[grps->nr++] = gid;
2630 /* Now go over the atoms in the group */
2631 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2636 /* Range checking */
2637 if ((aj < 0) || (aj >= natoms))
2639 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2641 /* Lookup up the old group number */
2645 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2646 aj+1, title, ognr+1, i+1);
2650 /* Store the group number in buffer */
2651 if (grptp == egrptpONE)
2664 /* Now check whether we have done all atoms */
2668 if (grptp == egrptpALL)
2670 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2671 natoms-ntot, title);
2673 else if (grptp == egrptpPART)
2675 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2676 natoms-ntot, title);
2677 warning_note(wi, warn_buf);
2679 /* Assign all atoms currently unassigned to a rest group */
2680 for (j = 0; (j < natoms); j++)
2682 if (cbuf[j] == NOGID)
2688 if (grptp != egrptpPART)
2693 "Making dummy/rest group for %s containing %d elements\n",
2694 title, natoms-ntot);
2696 /* Add group name "rest" */
2697 grps->nm_ind[grps->nr] = restnm;
2699 /* Assign the rest name to all atoms not currently assigned to a group */
2700 for (j = 0; (j < natoms); j++)
2702 if (cbuf[j] == NOGID)
2711 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2713 /* All atoms are part of one (or no) group, no index required */
2714 groups->ngrpnr[gtype] = 0;
2715 groups->grpnr[gtype] = nullptr;
2719 groups->ngrpnr[gtype] = natoms;
2720 snew(groups->grpnr[gtype], natoms);
2721 for (j = 0; (j < natoms); j++)
2723 groups->grpnr[gtype][j] = cbuf[j];
2729 return (bRest && grptp == egrptpPART);
2732 static void calc_nrdf(const gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2735 const gmx_groups_t *groups;
2736 pull_params_t *pull;
2737 int natoms, ai, aj, i, j, d, g, imin, jmin;
2739 int *nrdf2, *na_vcm, na_tot;
2740 double *nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2742 gmx_mtop_atomloop_all_t aloop;
2746 * First calc 3xnr-atoms for each group
2747 * then subtract half a degree of freedom for each constraint
2749 * Only atoms and nuclei contribute to the degrees of freedom...
2754 groups = &mtop->groups;
2755 natoms = mtop->natoms;
2757 /* Allocate one more for a possible rest group */
2758 /* We need to sum degrees of freedom into doubles,
2759 * since floats give too low nrdf's above 3 million atoms.
2761 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2762 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2763 snew(dof_vcm, groups->grps[egcVCM].nr+1);
2764 snew(na_vcm, groups->grps[egcVCM].nr+1);
2765 snew(nrdf_vcm_sub, groups->grps[egcVCM].nr+1);
2767 for (i = 0; i < groups->grps[egcTC].nr; i++)
2771 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2774 clear_ivec(dof_vcm[i]);
2776 nrdf_vcm_sub[i] = 0;
2779 snew(nrdf2, natoms);
2780 aloop = gmx_mtop_atomloop_all_init(mtop);
2782 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2785 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2787 g = ggrpnr(groups, egcFREEZE, i);
2788 for (d = 0; d < DIM; d++)
2790 if (opts->nFreeze[g][d] == 0)
2792 /* Add one DOF for particle i (counted as 2*1) */
2794 /* VCM group i has dim d as a DOF */
2795 dof_vcm[ggrpnr(groups, egcVCM, i)][d] = 1;
2798 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2799 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2804 for (const gmx_molblock_t &molb : mtop->molblock)
2806 const gmx_moltype_t &molt = mtop->moltype[molb.type];
2807 atom = molt.atoms.atom;
2808 for (mol = 0; mol < molb.nmol; mol++)
2810 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2812 ia = molt.ilist[ftype].iatoms;
2813 for (i = 0; i < molt.ilist[ftype].nr; )
2815 /* Subtract degrees of freedom for the constraints,
2816 * if the particles still have degrees of freedom left.
2817 * If one of the particles is a vsite or a shell, then all
2818 * constraint motion will go there, but since they do not
2819 * contribute to the constraints the degrees of freedom do not
2824 if (((atom[ia[1]].ptype == eptNucleus) ||
2825 (atom[ia[1]].ptype == eptAtom)) &&
2826 ((atom[ia[2]].ptype == eptNucleus) ||
2827 (atom[ia[2]].ptype == eptAtom)))
2845 imin = std::min(imin, nrdf2[ai]);
2846 jmin = std::min(jmin, nrdf2[aj]);
2849 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2850 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2851 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2852 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2854 ia += interaction_function[ftype].nratoms+1;
2855 i += interaction_function[ftype].nratoms+1;
2858 ia = molt.ilist[F_SETTLE].iatoms;
2859 for (i = 0; i < molt.ilist[F_SETTLE].nr; )
2861 /* Subtract 1 dof from every atom in the SETTLE */
2862 for (j = 0; j < 3; j++)
2865 imin = std::min(2, nrdf2[ai]);
2867 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2868 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2873 as += molt.atoms.nr;
2879 /* Correct nrdf for the COM constraints.
2880 * We correct using the TC and VCM group of the first atom
2881 * in the reference and pull group. If atoms in one pull group
2882 * belong to different TC or VCM groups it is anyhow difficult
2883 * to determine the optimal nrdf assignment.
2887 for (i = 0; i < pull->ncoord; i++)
2889 if (pull->coord[i].eType != epullCONSTRAINT)
2896 for (j = 0; j < 2; j++)
2898 const t_pull_group *pgrp;
2900 pgrp = &pull->group[pull->coord[i].group[j]];
2904 /* Subtract 1/2 dof from each group */
2906 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2907 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2908 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2910 gmx_fatal(FARGS, "Center of mass pulling constraints caused the number of degrees of freedom for temperature coupling group %s to be negative", gnames[groups->grps[egcTC].nm_ind[ggrpnr(groups, egcTC, ai)]]);
2915 /* We need to subtract the whole DOF from group j=1 */
2922 if (ir->nstcomm != 0)
2926 /* We remove COM motion up to dim ndof_com() */
2927 ndim_rm_vcm = ndof_com(ir);
2929 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
2930 * the number of degrees of freedom in each vcm group when COM
2931 * translation is removed and 6 when rotation is removed as well.
2933 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2935 switch (ir->comm_mode)
2938 case ecmLINEAR_ACCELERATION_CORRECTION:
2939 nrdf_vcm_sub[j] = 0;
2940 for (d = 0; d < ndim_rm_vcm; d++)
2949 nrdf_vcm_sub[j] = 6;
2952 gmx_incons("Checking comm_mode");
2956 for (i = 0; i < groups->grps[egcTC].nr; i++)
2958 /* Count the number of atoms of TC group i for every VCM group */
2959 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2964 for (ai = 0; ai < natoms; ai++)
2966 if (ggrpnr(groups, egcTC, ai) == i)
2968 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2972 /* Correct for VCM removal according to the fraction of each VCM
2973 * group present in this TC group.
2975 nrdf_uc = nrdf_tc[i];
2977 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2979 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
2981 nrdf_tc[i] += nrdf_uc*(static_cast<double>(na_vcm[j])/static_cast<double>(na_tot))*
2982 (nrdf_vcm[j] - nrdf_vcm_sub[j])/nrdf_vcm[j];
2987 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2989 opts->nrdf[i] = nrdf_tc[i];
2990 if (opts->nrdf[i] < 0)
2995 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2996 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
3004 sfree(nrdf_vcm_sub);
3007 static bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
3008 const char *option, const char *val, int flag)
3010 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3011 * But since this is much larger than STRLEN, such a line can not be parsed.
3012 * The real maximum is the number of names that fit in a string: STRLEN/2.
3014 #define EGP_MAX (STRLEN/2)
3015 int nelem, i, j, k, nr;
3016 char *names[EGP_MAX];
3020 gnames = groups->grpname;
3022 nelem = str_nelem(val, EGP_MAX, names);
3025 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3027 nr = groups->grps[egcENER].nr;
3029 for (i = 0; i < nelem/2; i++)
3033 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
3039 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3040 names[2*i], option);
3044 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
3050 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3051 names[2*i+1], option);
3053 if ((j < nr) && (k < nr))
3055 ir->opts.egp_flags[nr*j+k] |= flag;
3056 ir->opts.egp_flags[nr*k+j] |= flag;
3065 static void make_swap_groups(
3070 int ig = -1, i = 0, gind;
3074 /* Just a quick check here, more thorough checks are in mdrun */
3075 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3077 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3080 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3081 for (ig = 0; ig < swap->ngrp; ig++)
3083 swapg = &swap->grp[ig];
3084 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3085 swapg->nat = grps->index[gind+1] - grps->index[gind];
3089 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3090 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap",
3091 swap->grp[ig].molname, swapg->nat);
3092 snew(swapg->ind, swapg->nat);
3093 for (i = 0; i < swapg->nat; i++)
3095 swapg->ind[i] = grps->a[grps->index[gind]+i];
3100 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3106 static void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3111 ig = search_string(IMDgname, grps->nr, gnames);
3112 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3114 if (IMDgroup->nat > 0)
3116 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3117 IMDgname, IMDgroup->nat);
3118 snew(IMDgroup->ind, IMDgroup->nat);
3119 for (i = 0; i < IMDgroup->nat; i++)
3121 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3127 void do_index(const char* mdparin, const char *ndx,
3134 gmx_groups_t *groups;
3138 char warnbuf[STRLEN], **gnames;
3139 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3142 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3143 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3144 int i, j, k, restnm;
3145 bool bExcl, bTable, bAnneal, bRest;
3146 int nQMmethod, nQMbasis, nQMg;
3147 char warn_buf[STRLEN];
3152 fprintf(stderr, "processing index file...\n");
3157 snew(grps->index, 1);
3159 atoms_all = gmx_mtop_global_atoms(mtop);
3160 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3161 done_atom(&atoms_all);
3165 grps = init_index(ndx, &gnames);
3168 groups = &mtop->groups;
3169 natoms = mtop->natoms;
3170 symtab = &mtop->symtab;
3172 snew(groups->grpname, grps->nr+1);
3174 for (i = 0; (i < grps->nr); i++)
3176 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3178 groups->grpname[i] = put_symtab(symtab, "rest");
3180 srenew(gnames, grps->nr+1);
3181 gnames[restnm] = *(groups->grpname[i]);
3182 groups->ngrpname = grps->nr+1;
3184 set_warning_line(wi, mdparin, -1);
3186 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3187 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3188 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3189 if ((ntau_t != ntcg) || (nref_t != ntcg))
3191 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3192 "%d tau-t values", ntcg, nref_t, ntau_t);
3195 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3196 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3197 restnm, useReferenceTemperature ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3198 nr = groups->grps[egcTC].nr;
3200 snew(ir->opts.nrdf, nr);
3201 snew(ir->opts.tau_t, nr);
3202 snew(ir->opts.ref_t, nr);
3203 if (ir->eI == eiBD && ir->bd_fric == 0)
3205 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3208 if (useReferenceTemperature)
3212 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3216 for (i = 0; (i < nr); i++)
3218 ir->opts.tau_t[i] = strtod(ptr1[i], &endptr);
3221 warning_error(wi, "Invalid value for mdp option tau-t. tau-t should only consist of real numbers separated by spaces.");
3223 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3225 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3226 warning_error(wi, warn_buf);
3229 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3231 warning_note(wi, "tau-t = -1 is the value to signal that a group should not have temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3234 if (ir->opts.tau_t[i] >= 0)
3236 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3239 if (ir->etc != etcNO && ir->nsttcouple == -1)
3241 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3246 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3248 gmx_fatal(FARGS, "Cannot do Nose-Hoover temperature with Berendsen pressure control with md-vv; use either vrescale temperature with berendsen pressure or Nose-Hoover temperature with MTTK pressure");
3250 if (ir->epc == epcMTTK)
3252 if (ir->etc != etcNOSEHOOVER)
3254 gmx_fatal(FARGS, "Cannot do MTTK pressure coupling without Nose-Hoover temperature control");
3258 if (ir->nstpcouple != ir->nsttcouple)
3260 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3261 ir->nstpcouple = ir->nsttcouple = mincouple;
3262 sprintf(warn_buf, "for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple) = %d", mincouple);
3263 warning_note(wi, warn_buf);
3268 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3269 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3271 if (ETC_ANDERSEN(ir->etc))
3273 if (ir->nsttcouple != 1)
3276 sprintf(warn_buf, "Andersen temperature control methods assume nsttcouple = 1; there is no need for larger nsttcouple > 1, since no global parameters are computed. nsttcouple has been reset to 1");
3277 warning_note(wi, warn_buf);
3280 nstcmin = tcouple_min_integration_steps(ir->etc);
3283 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin - 10*GMX_REAL_EPS)
3285 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3286 ETCOUPLTYPE(ir->etc),
3288 ir->nsttcouple*ir->delta_t);
3289 warning(wi, warn_buf);
3292 for (i = 0; (i < nr); i++)
3294 ir->opts.ref_t[i] = strtod(ptr2[i], &endptr);
3297 warning_error(wi, "Invalid value for mdp option ref-t. ref-t should only consist of real numbers separated by spaces.");
3299 if (ir->opts.ref_t[i] < 0)
3301 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3304 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3305 if we are in this conditional) if mc_temp is negative */
3306 if (ir->expandedvals->mc_temp < 0)
3308 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3312 /* Simulated annealing for each group. There are nr groups */
3313 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3314 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3318 if (nSA > 0 && nSA != nr)
3320 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3324 snew(ir->opts.annealing, nr);
3325 snew(ir->opts.anneal_npoints, nr);
3326 snew(ir->opts.anneal_time, nr);
3327 snew(ir->opts.anneal_temp, nr);
3328 for (i = 0; i < nr; i++)
3330 ir->opts.annealing[i] = eannNO;
3331 ir->opts.anneal_npoints[i] = 0;
3332 ir->opts.anneal_time[i] = nullptr;
3333 ir->opts.anneal_temp[i] = nullptr;
3338 for (i = 0; i < nr; i++)
3340 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3342 ir->opts.annealing[i] = eannNO;
3344 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3346 ir->opts.annealing[i] = eannSINGLE;
3349 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3351 ir->opts.annealing[i] = eannPERIODIC;
3357 /* Read the other fields too */
3358 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3359 if (nSA_points != nSA)
3361 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3363 for (k = 0, i = 0; i < nr; i++)
3365 ir->opts.anneal_npoints[i] = strtol(ptr1[i], &endptr, 10);
3368 warning_error(wi, "Invalid value for mdp option annealing-npoints. annealing should only consist of integers separated by spaces.");
3370 if (ir->opts.anneal_npoints[i] == 1)
3372 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3374 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3375 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3376 k += ir->opts.anneal_npoints[i];
3379 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3382 gmx_fatal(FARGS, "Found %d annealing-time values, wanted %d\n", nSA_time, k);
3384 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3387 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3390 for (i = 0, k = 0; i < nr; i++)
3393 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3395 ir->opts.anneal_time[i][j] = strtod(ptr1[k], &endptr);
3398 warning_error(wi, "Invalid value for mdp option anneal-time. anneal-time should only consist of real numbers separated by spaces.");
3400 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], &endptr);
3403 warning_error(wi, "Invalid value for anneal-temp. anneal-temp should only consist of real numbers separated by spaces.");
3407 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3409 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3415 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3417 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3418 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3421 if (ir->opts.anneal_temp[i][j] < 0)
3423 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3428 /* Print out some summary information, to make sure we got it right */
3429 for (i = 0, k = 0; i < nr; i++)
3431 if (ir->opts.annealing[i] != eannNO)
3433 j = groups->grps[egcTC].nm_ind[i];
3434 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3435 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3436 ir->opts.anneal_npoints[i]);
3437 fprintf(stderr, "Time (ps) Temperature (K)\n");
3438 /* All terms except the last one */
3439 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3441 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3444 /* Finally the last one */
3445 j = ir->opts.anneal_npoints[i]-1;
3446 if (ir->opts.annealing[i] == eannSINGLE)
3448 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3452 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3453 if (std::fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3455 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3466 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3468 make_pull_coords(ir->pull);
3473 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3476 if (ir->eSwapCoords != eswapNO)
3478 make_swap_groups(ir->swap, grps, gnames);
3481 /* Make indices for IMD session */
3484 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3487 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3488 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3489 if (nacg*DIM != nacc)
3491 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3494 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3495 restnm, egrptpALL_GENREST, bVerbose, wi);
3496 nr = groups->grps[egcACC].nr;
3497 snew(ir->opts.acc, nr);
3498 ir->opts.ngacc = nr;
3500 for (i = k = 0; (i < nacg); i++)
3502 for (j = 0; (j < DIM); j++, k++)
3504 ir->opts.acc[i][j] = strtod(ptr1[k], &endptr);
3507 warning_error(wi, "Invalid value for mdp option accelerate. accelerate should only consist of real numbers separated by spaces.");
3511 for (; (i < nr); i++)
3513 for (j = 0; (j < DIM); j++)
3515 ir->opts.acc[i][j] = 0;
3519 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3520 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3521 if (nfrdim != DIM*nfreeze)
3523 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3526 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3527 restnm, egrptpALL_GENREST, bVerbose, wi);
3528 nr = groups->grps[egcFREEZE].nr;
3529 ir->opts.ngfrz = nr;
3530 snew(ir->opts.nFreeze, nr);
3531 for (i = k = 0; (i < nfreeze); i++)
3533 for (j = 0; (j < DIM); j++, k++)
3535 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3536 if (!ir->opts.nFreeze[i][j])
3538 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3540 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3541 "(not %s)", ptr1[k]);
3542 warning(wi, warn_buf);
3547 for (; (i < nr); i++)
3549 for (j = 0; (j < DIM); j++)
3551 ir->opts.nFreeze[i][j] = 0;
3555 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3556 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3557 restnm, egrptpALL_GENREST, bVerbose, wi);
3558 add_wall_energrps(groups, ir->nwall, symtab);
3559 ir->opts.ngener = groups->grps[egcENER].nr;
3560 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3562 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3563 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3566 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3567 "This may lead to artifacts.\n"
3568 "In most cases one should use one group for the whole system.");
3571 /* Now we have filled the freeze struct, so we can calculate NRDF */
3572 calc_nrdf(mtop, ir, gnames);
3574 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3575 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3576 restnm, egrptpALL_GENREST, bVerbose, wi);
3577 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3578 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3579 restnm, egrptpALL_GENREST, bVerbose, wi);
3580 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3581 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3582 restnm, egrptpONE, bVerbose, wi);
3583 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3584 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3585 restnm, egrptpALL_GENREST, bVerbose, wi);
3587 /* QMMM input processing */
3588 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3589 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3590 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3591 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3593 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3594 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3596 /* group rest, if any, is always MM! */
3597 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3598 restnm, egrptpALL_GENREST, bVerbose, wi);
3599 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3600 ir->opts.ngQM = nQMg;
3601 snew(ir->opts.QMmethod, nr);
3602 snew(ir->opts.QMbasis, nr);
3603 for (i = 0; i < nr; i++)
3605 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3606 * converted to the corresponding enum in names.c
3608 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3610 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3614 str_nelem(is->QMmult, MAXPTR, ptr1);
3615 str_nelem(is->QMcharge, MAXPTR, ptr2);
3616 str_nelem(is->bSH, MAXPTR, ptr3);
3617 snew(ir->opts.QMmult, nr);
3618 snew(ir->opts.QMcharge, nr);
3619 snew(ir->opts.bSH, nr);
3621 for (i = 0; i < nr; i++)
3623 ir->opts.QMmult[i] = strtol(ptr1[i], &endptr, 10);
3626 warning_error(wi, "Invalid value for mdp option QMmult. QMmult should only consist of integers separated by spaces.");
3628 ir->opts.QMcharge[i] = strtol(ptr2[i], &endptr, 10);
3631 warning_error(wi, "Invalid value for mdp option QMcharge. QMcharge should only consist of integers separated by spaces.");
3633 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3636 str_nelem(is->CASelectrons, MAXPTR, ptr1);
3637 str_nelem(is->CASorbitals, MAXPTR, ptr2);
3638 snew(ir->opts.CASelectrons, nr);
3639 snew(ir->opts.CASorbitals, nr);
3640 for (i = 0; i < nr; i++)
3642 ir->opts.CASelectrons[i] = strtol(ptr1[i], &endptr, 10);
3645 warning_error(wi, "Invalid value for mdp option CASelectrons. CASelectrons should only consist of integers separated by spaces.");
3647 ir->opts.CASorbitals[i] = strtol(ptr2[i], &endptr, 10);
3650 warning_error(wi, "Invalid value for mdp option CASorbitals. CASorbitals should only consist of integers separated by spaces.");
3654 str_nelem(is->SAon, MAXPTR, ptr1);
3655 str_nelem(is->SAoff, MAXPTR, ptr2);
3656 str_nelem(is->SAsteps, MAXPTR, ptr3);
3657 snew(ir->opts.SAon, nr);
3658 snew(ir->opts.SAoff, nr);
3659 snew(ir->opts.SAsteps, nr);
3661 for (i = 0; i < nr; i++)
3663 ir->opts.SAon[i] = strtod(ptr1[i], &endptr);
3666 warning_error(wi, "Invalid value for mdp option SAon. SAon should only consist of real numbers separated by spaces.");
3668 ir->opts.SAoff[i] = strtod(ptr2[i], &endptr);
3671 warning_error(wi, "Invalid value for mdp option SAoff. SAoff should only consist of real numbers separated by spaces.");
3673 ir->opts.SAsteps[i] = strtol(ptr3[i], &endptr, 10);
3676 warning_error(wi, "Invalid value for mdp option SAsteps. SAsteps should only consist of integers separated by spaces.");
3679 /* end of QMMM input */
3683 for (i = 0; (i < egcNR); i++)
3685 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3686 for (j = 0; (j < groups->grps[i].nr); j++)
3688 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3690 fprintf(stderr, "\n");
3694 nr = groups->grps[egcENER].nr;
3695 snew(ir->opts.egp_flags, nr*nr);
3697 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3698 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3700 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3702 if (bExcl && EEL_FULL(ir->coulombtype))
3704 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3707 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3708 if (bTable && !(ir->vdwtype == evdwUSER) &&
3709 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3710 !(ir->coulombtype == eelPMEUSERSWITCH))
3712 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3715 for (i = 0; (i < grps->nr); i++)
3727 static void check_disre(gmx_mtop_t *mtop)
3729 gmx_ffparams_t *ffparams;
3730 t_functype *functype;
3732 int i, ndouble, ftype;
3733 int label, old_label;
3735 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3737 ffparams = &mtop->ffparams;
3738 functype = ffparams->functype;
3739 ip = ffparams->iparams;
3742 for (i = 0; i < ffparams->ntypes; i++)
3744 ftype = functype[i];
3745 if (ftype == F_DISRES)
3747 label = ip[i].disres.label;
3748 if (label == old_label)
3750 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3758 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3759 "probably the parameters for multiple pairs in one restraint "
3760 "are not identical\n", ndouble);
3765 static bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3770 gmx_mtop_ilistloop_t iloop;
3771 const t_ilist *ilist;
3780 for (d = 0; d < DIM; d++)
3782 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3784 /* Check for freeze groups */
3785 for (g = 0; g < ir->opts.ngfrz; g++)
3787 for (d = 0; d < DIM; d++)
3789 if (ir->opts.nFreeze[g][d] != 0)
3797 /* Check for position restraints */
3798 iloop = gmx_mtop_ilistloop_init(sys);
3799 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3802 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3804 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3806 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3807 for (d = 0; d < DIM; d++)
3809 if (pr->posres.fcA[d] != 0)
3815 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3817 /* Check for flat-bottom posres */
3818 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3819 if (pr->fbposres.k != 0)
3821 switch (pr->fbposres.geom)
3823 case efbposresSPHERE:
3824 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3826 case efbposresCYLINDERX:
3827 AbsRef[YY] = AbsRef[ZZ] = 1;
3829 case efbposresCYLINDERY:
3830 AbsRef[XX] = AbsRef[ZZ] = 1;
3832 case efbposresCYLINDER:
3833 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3834 case efbposresCYLINDERZ:
3835 AbsRef[XX] = AbsRef[YY] = 1;
3837 case efbposresX: /* d=XX */
3838 case efbposresY: /* d=YY */
3839 case efbposresZ: /* d=ZZ */
3840 d = pr->fbposres.geom - efbposresX;
3844 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3845 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3853 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3857 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3858 bool *bC6ParametersWorkWithGeometricRules,
3859 bool *bC6ParametersWorkWithLBRules,
3860 bool *bLBRulesPossible)
3862 int ntypes, tpi, tpj;
3865 double c6i, c6j, c12i, c12j;
3866 double c6, c6_geometric, c6_LB;
3867 double sigmai, sigmaj, epsi, epsj;
3868 bool bCanDoLBRules, bCanDoGeometricRules;
3871 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3872 * force-field floating point parameters.
3875 ptr = getenv("GMX_LJCOMB_TOL");
3879 double gmx_unused canary;
3881 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
3883 gmx_fatal(FARGS, "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
3888 *bC6ParametersWorkWithLBRules = TRUE;
3889 *bC6ParametersWorkWithGeometricRules = TRUE;
3890 bCanDoLBRules = TRUE;
3891 ntypes = mtop->ffparams.atnr;
3892 snew(typecount, ntypes);
3893 gmx_mtop_count_atomtypes(mtop, state, typecount);
3894 *bLBRulesPossible = TRUE;
3895 for (tpi = 0; tpi < ntypes; ++tpi)
3897 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3898 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3899 for (tpj = tpi; tpj < ntypes; ++tpj)
3901 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3902 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3903 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3904 c6_geometric = std::sqrt(c6i * c6j);
3905 if (!gmx_numzero(c6_geometric))
3907 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3909 sigmai = gmx::sixthroot(c12i / c6i);
3910 sigmaj = gmx::sixthroot(c12j / c6j);
3911 epsi = c6i * c6i /(4.0 * c12i);
3912 epsj = c6j * c6j /(4.0 * c12j);
3913 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
3917 *bLBRulesPossible = FALSE;
3918 c6_LB = c6_geometric;
3920 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3923 if (FALSE == bCanDoLBRules)
3925 *bC6ParametersWorkWithLBRules = FALSE;
3928 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3930 if (FALSE == bCanDoGeometricRules)
3932 *bC6ParametersWorkWithGeometricRules = FALSE;
3940 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3943 bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3945 check_combination_rule_differences(mtop, 0,
3946 &bC6ParametersWorkWithGeometricRules,
3947 &bC6ParametersWorkWithLBRules,
3949 if (ir->ljpme_combination_rule == eljpmeLB)
3951 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
3953 warning(wi, "You are using arithmetic-geometric combination rules "
3954 "in LJ-PME, but your non-bonded C6 parameters do not "
3955 "follow these rules.");
3960 if (FALSE == bC6ParametersWorkWithGeometricRules)
3962 if (ir->eDispCorr != edispcNO)
3964 warning_note(wi, "You are using geometric combination rules in "
3965 "LJ-PME, but your non-bonded C6 parameters do "
3966 "not follow these rules. "
3967 "This will introduce very small errors in the forces and energies in "
3968 "your simulations. Dispersion correction will correct total energy "
3969 "and/or pressure for isotropic systems, but not forces or surface tensions.");
3973 warning_note(wi, "You are using geometric combination rules in "
3974 "LJ-PME, but your non-bonded C6 parameters do "
3975 "not follow these rules. "
3976 "This will introduce very small errors in the forces and energies in "
3977 "your simulations. If your system is homogeneous, consider using dispersion correction "
3978 "for the total energy and pressure.");
3984 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
3987 char err_buf[STRLEN];
3992 gmx_mtop_atomloop_block_t aloopb;
3993 gmx_mtop_atomloop_all_t aloop;
3995 char warn_buf[STRLEN];
3997 set_warning_line(wi, mdparin, -1);
3999 if (ir->cutoff_scheme == ecutsVERLET &&
4000 ir->verletbuf_tol > 0 &&
4002 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
4003 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4005 /* Check if a too small Verlet buffer might potentially
4006 * cause more drift than the thermostat can couple off.
4008 /* Temperature error fraction for warning and suggestion */
4009 const real T_error_warn = 0.002;
4010 const real T_error_suggest = 0.001;
4011 /* For safety: 2 DOF per atom (typical with constraints) */
4012 const real nrdf_at = 2;
4013 real T, tau, max_T_error;
4018 for (i = 0; i < ir->opts.ngtc; i++)
4020 T = std::max(T, ir->opts.ref_t[i]);
4021 tau = std::max(tau, ir->opts.tau_t[i]);
4025 /* This is a worst case estimate of the temperature error,
4026 * assuming perfect buffer estimation and no cancelation
4027 * of errors. The factor 0.5 is because energy distributes
4028 * equally over Ekin and Epot.
4030 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4031 if (max_T_error > T_error_warn)
4033 sprintf(warn_buf, "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to %.0e or decrease tau_t.",
4034 ir->verletbuf_tol, T, tau,
4036 100*T_error_suggest,
4037 ir->verletbuf_tol*T_error_suggest/max_T_error);
4038 warning(wi, warn_buf);
4043 if (ETC_ANDERSEN(ir->etc))
4047 for (i = 0; i < ir->opts.ngtc; i++)
4049 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4050 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4051 sprintf(err_buf, "all tau_t must be positive using Andersen temperature control, tau_t[%d]=%10.6f",
4052 i, ir->opts.tau_t[i]);
4053 CHECK(ir->opts.tau_t[i] < 0);
4056 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4058 for (i = 0; i < ir->opts.ngtc; i++)
4060 int nsteps = static_cast<int>(ir->opts.tau_t[i]/ir->delta_t + 0.5);
4061 sprintf(err_buf, "tau_t/delta_t for group %d for temperature control method %s must be a multiple of nstcomm (%d), as velocities of atoms in coupled groups are randomized every time step. The input tau_t (%8.3f) leads to %d steps per randomization", i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
4062 CHECK(nsteps % ir->nstcomm != 0);
4067 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4068 ir->comm_mode == ecmNO &&
4069 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4070 !ETC_ANDERSEN(ir->etc))
4072 warning(wi, "You are not using center of mass motion removal (mdp option comm-mode), numerical rounding errors can lead to build up of kinetic energy of the center of mass");
4075 /* Check for pressure coupling with absolute position restraints */
4076 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4078 absolute_reference(ir, sys, TRUE, AbsRef);
4080 for (m = 0; m < DIM; m++)
4082 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4084 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4092 aloopb = gmx_mtop_atomloop_block_init(sys);
4094 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4096 if (atom->q != 0 || atom->qB != 0)
4104 if (EEL_FULL(ir->coulombtype))
4107 "You are using full electrostatics treatment %s for a system without charges.\n"
4108 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4109 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4110 warning(wi, err_buf);
4115 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
4118 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4119 "You might want to consider using %s electrostatics.\n",
4121 warning_note(wi, err_buf);
4125 /* Check if combination rules used in LJ-PME are the same as in the force field */
4126 if (EVDW_PME(ir->vdwtype))
4128 check_combination_rules(ir, sys, wi);
4131 /* Generalized reaction field */
4132 if (ir->opts.ngtc == 0)
4134 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4136 CHECK(ir->coulombtype == eelGRF);
4140 sprintf(err_buf, "When using coulombtype = %s"
4141 " ref-t for temperature coupling should be > 0",
4143 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4147 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4149 for (m = 0; (m < DIM); m++)
4151 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4160 snew(mgrp, sys->groups.grps[egcACC].nr);
4161 aloop = gmx_mtop_atomloop_all_init(sys);
4163 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4165 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4168 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4170 for (m = 0; (m < DIM); m++)
4172 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4176 for (m = 0; (m < DIM); m++)
4178 if (fabs(acc[m]) > 1e-6)
4180 const char *dim[DIM] = { "X", "Y", "Z" };
4182 "Net Acceleration in %s direction, will %s be corrected\n",
4183 dim[m], ir->nstcomm != 0 ? "" : "not");
4184 if (ir->nstcomm != 0 && m < ndof_com(ir))
4187 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4189 ir->opts.acc[i][m] -= acc[m];
4197 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4198 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4200 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4208 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4210 if (ir->pull->coord[i].group[0] == 0 ||
4211 ir->pull->coord[i].group[1] == 0)
4213 absolute_reference(ir, sys, FALSE, AbsRef);
4214 for (m = 0; m < DIM; m++)
4216 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4218 warning(wi, "You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts.");
4226 for (i = 0; i < 3; i++)
4228 for (m = 0; m <= i; m++)
4230 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4231 ir->deform[i][m] != 0)
4233 for (c = 0; c < ir->pull->ncoord; c++)
4235 if (ir->pull->coord[c].eGeom == epullgDIRPBC &&
4236 ir->pull->coord[c].vec[m] != 0)
4238 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->coord[c].eGeom), 'x'+m);
4249 void double_check(t_inputrec *ir, matrix box,
4250 bool bHasNormalConstraints,
4251 bool bHasAnyConstraints,
4255 char warn_buf[STRLEN];
4258 ptr = check_box(ir->ePBC, box);
4261 warning_error(wi, ptr);
4264 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4266 if (ir->shake_tol <= 0.0)
4268 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4270 warning_error(wi, warn_buf);
4274 if ( (ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4276 /* If we have Lincs constraints: */
4277 if (ir->eI == eiMD && ir->etc == etcNO &&
4278 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4280 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4281 warning_note(wi, warn_buf);
4284 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4286 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4287 warning_note(wi, warn_buf);
4289 if (ir->epc == epcMTTK)
4291 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4295 if (bHasAnyConstraints && ir->epc == epcMTTK)
4297 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4300 if (ir->LincsWarnAngle > 90.0)
4302 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4303 warning(wi, warn_buf);
4304 ir->LincsWarnAngle = 90.0;
4307 if (ir->ePBC != epbcNONE)
4309 if (ir->nstlist == 0)
4311 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4313 if (ir->ns_type == ensGRID)
4315 if (gmx::square(ir->rlist) >= max_cutoff2(ir->ePBC, box))
4317 sprintf(warn_buf, "ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist.\n");
4318 warning_error(wi, warn_buf);
4323 min_size = std::min(box[XX][XX], std::min(box[YY][YY], box[ZZ][ZZ]));
4324 if (2*ir->rlist >= min_size)
4326 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4327 warning_error(wi, warn_buf);
4330 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4337 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4341 real rvdw1, rvdw2, rcoul1, rcoul2;
4342 char warn_buf[STRLEN];
4344 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4348 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4353 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4359 if (rvdw1 + rvdw2 > ir->rlist ||
4360 rcoul1 + rcoul2 > ir->rlist)
4363 "The sum of the two largest charge group radii (%f) "
4364 "is larger than rlist (%f)\n",
4365 std::max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4366 warning(wi, warn_buf);
4370 /* Here we do not use the zero at cut-off macro,
4371 * since user defined interactions might purposely
4372 * not be zero at the cut-off.
4374 if (ir_vdw_is_zero_at_cutoff(ir) &&
4375 rvdw1 + rvdw2 > ir->rlist - ir->rvdw)
4377 sprintf(warn_buf, "The sum of the two largest charge group "
4378 "radii (%f) is larger than rlist (%f) - rvdw (%f).\n"
4379 "With exact cut-offs, better performance can be "
4380 "obtained with cutoff-scheme = %s, because it "
4381 "does not use charge groups at all.",
4383 ir->rlist, ir->rvdw,
4384 ecutscheme_names[ecutsVERLET]);
4387 warning(wi, warn_buf);
4391 warning_note(wi, warn_buf);
4394 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4395 rcoul1 + rcoul2 > ir->rlist - ir->rcoulomb)
4397 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than rlist (%f) - rcoulomb (%f).\n"
4398 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4400 ir->rlist, ir->rcoulomb,
4401 ecutscheme_names[ecutsVERLET]);
4404 warning(wi, warn_buf);
4408 warning_note(wi, warn_buf);