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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, errorstr);
185 static void _low_check(gmx_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 gmx_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 gmx_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 (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 gmx_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] = (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*(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]);
1594 static void do_wall_params(t_inputrec *ir,
1595 char *wall_atomtype, char *wall_density,
1599 char *names[MAXPTR];
1602 opts->wall_atomtype[0] = nullptr;
1603 opts->wall_atomtype[1] = nullptr;
1605 ir->wall_atomtype[0] = -1;
1606 ir->wall_atomtype[1] = -1;
1607 ir->wall_density[0] = 0;
1608 ir->wall_density[1] = 0;
1612 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1613 if (nstr != ir->nwall)
1615 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1618 for (i = 0; i < ir->nwall; i++)
1620 opts->wall_atomtype[i] = gmx_strdup(names[i]);
1623 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1625 nstr = str_nelem(wall_density, MAXPTR, names);
1626 if (nstr != ir->nwall)
1628 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1630 for (i = 0; i < ir->nwall; i++)
1632 if (sscanf(names[i], "%lf", &dbl) != 1)
1634 gmx_fatal(FARGS, "Could not parse wall-density value from string '%s'", names[i]);
1638 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1640 ir->wall_density[i] = dbl;
1646 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1654 srenew(groups->grpname, groups->ngrpname+nwall);
1655 grps = &(groups->grps[egcENER]);
1656 srenew(grps->nm_ind, grps->nr+nwall);
1657 for (i = 0; i < nwall; i++)
1659 sprintf(str, "wall%d", i);
1660 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1661 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1666 static void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1667 t_expanded *expand, warninp_t wi)
1675 /* read expanded ensemble parameters */
1676 CCTYPE ("expanded ensemble variables");
1677 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1678 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1679 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1680 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1681 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1682 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1683 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1684 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1685 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1686 CCTYPE("Seed for Monte Carlo in lambda space");
1687 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1688 RTYPE ("mc-temperature", expand->mc_temp, -1);
1689 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1690 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1691 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1692 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1693 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1694 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1695 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1696 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1697 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1698 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1699 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
1707 /*! \brief Return whether an end state with the given coupling-lambda
1708 * value describes fully-interacting VDW.
1710 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1711 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1713 static gmx_bool couple_lambda_has_vdw_on(int couple_lambda_value)
1715 return (couple_lambda_value == ecouplamVDW ||
1716 couple_lambda_value == ecouplamVDWQ);
1722 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1725 explicit MdpErrorHandler(warninp_t wi)
1726 : wi_(wi), mapping_(nullptr)
1730 void setBackMapping(const gmx::IKeyValueTreeBackMapping &mapping)
1732 mapping_ = &mapping;
1735 virtual bool onError(gmx::UserInputError *ex, const gmx::KeyValueTreePath &context)
1737 ex->prependContext(gmx::formatString("Error in mdp option \"%s\":",
1738 getOptionName(context).c_str()));
1739 std::string message = gmx::formatExceptionMessageToString(*ex);
1740 warning_error(wi_, message.c_str());
1745 std::string getOptionName(const gmx::KeyValueTreePath &context)
1747 if (mapping_ != nullptr)
1749 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1750 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1753 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1758 const gmx::IKeyValueTreeBackMapping *mapping_;
1763 void get_ir(const char *mdparin, const char *mdparout,
1764 gmx::MDModules *mdModules, t_inputrec *ir, t_gromppopts *opts,
1765 WriteMdpHeader writeMdpHeader, warninp_t wi)
1768 double dumdub[2][6];
1772 char warn_buf[STRLEN];
1773 t_lambda *fep = ir->fepvals;
1774 t_expanded *expand = ir->expandedvals;
1776 const char *no_names[] = { "no", nullptr };
1778 init_inputrec_strings();
1779 gmx::TextInputFile stream(mdparin);
1780 inp = read_inpfile(&stream, mdparin, &ninp, wi);
1782 snew(dumstr[0], STRLEN);
1783 snew(dumstr[1], STRLEN);
1785 if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
1788 "%s did not specify a value for the .mdp option "
1789 "\"cutoff-scheme\". Probably it was first intended for use "
1790 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1791 "introduced, but the group scheme was still the default. "
1792 "The default is now the Verlet scheme, so you will observe "
1793 "different behaviour.", mdparin);
1794 warning_note(wi, warn_buf);
1797 /* ignore the following deprecated commands */
1800 REM_TYPE("domain-decomposition");
1801 REM_TYPE("andersen-seed");
1803 REM_TYPE("dihre-fc");
1804 REM_TYPE("dihre-tau");
1805 REM_TYPE("nstdihreout");
1806 REM_TYPE("nstcheckpoint");
1807 REM_TYPE("optimize-fft");
1808 REM_TYPE("adress_type");
1809 REM_TYPE("adress_const_wf");
1810 REM_TYPE("adress_ex_width");
1811 REM_TYPE("adress_hy_width");
1812 REM_TYPE("adress_ex_forcecap");
1813 REM_TYPE("adress_interface_correction");
1814 REM_TYPE("adress_site");
1815 REM_TYPE("adress_reference_coords");
1816 REM_TYPE("adress_tf_grp_names");
1817 REM_TYPE("adress_cg_grp_names");
1818 REM_TYPE("adress_do_hybridpairs");
1819 REM_TYPE("rlistlong");
1820 REM_TYPE("nstcalclr");
1821 REM_TYPE("pull-print-com2");
1822 REM_TYPE("gb-algorithm");
1823 REM_TYPE("nstgbradii");
1824 REM_TYPE("rgbradii");
1825 REM_TYPE("gb-epsilon-solvent");
1826 REM_TYPE("gb-saltconc");
1827 REM_TYPE("gb-obc-alpha");
1828 REM_TYPE("gb-obc-beta");
1829 REM_TYPE("gb-obc-gamma");
1830 REM_TYPE("gb-dielectric-offset");
1831 REM_TYPE("sa-algorithm");
1832 REM_TYPE("sa-surface-tension");
1834 /* replace the following commands with the clearer new versions*/
1835 REPL_TYPE("unconstrained-start", "continuation");
1836 REPL_TYPE("foreign-lambda", "fep-lambdas");
1837 REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
1838 REPL_TYPE("nstxtcout", "nstxout-compressed");
1839 REPL_TYPE("xtc-grps", "compressed-x-grps");
1840 REPL_TYPE("xtc-precision", "compressed-x-precision");
1841 REPL_TYPE("pull-print-com1", "pull-print-com");
1843 CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
1844 CTYPE ("Preprocessor information: use cpp syntax.");
1845 CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
1846 STYPE ("include", opts->include, nullptr);
1847 CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1848 STYPE ("define", opts->define, nullptr);
1850 CCTYPE ("RUN CONTROL PARAMETERS");
1851 EETYPE("integrator", ir->eI, ei_names);
1852 CTYPE ("Start time and timestep in ps");
1853 RTYPE ("tinit", ir->init_t, 0.0);
1854 RTYPE ("dt", ir->delta_t, 0.001);
1855 STEPTYPE ("nsteps", ir->nsteps, 0);
1856 CTYPE ("For exact run continuation or redoing part of a run");
1857 STEPTYPE ("init-step", ir->init_step, 0);
1858 CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
1859 ITYPE ("simulation-part", ir->simulation_part, 1);
1860 CTYPE ("mode for center of mass motion removal");
1861 EETYPE("comm-mode", ir->comm_mode, ecm_names);
1862 CTYPE ("number of steps for center of mass motion removal");
1863 ITYPE ("nstcomm", ir->nstcomm, 100);
1864 CTYPE ("group(s) for center of mass motion removal");
1865 STYPE ("comm-grps", is->vcm, nullptr);
1867 CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
1868 CTYPE ("Friction coefficient (amu/ps) and random seed");
1869 RTYPE ("bd-fric", ir->bd_fric, 0.0);
1870 STEPTYPE ("ld-seed", ir->ld_seed, -1);
1873 CCTYPE ("ENERGY MINIMIZATION OPTIONS");
1874 CTYPE ("Force tolerance and initial step-size");
1875 RTYPE ("emtol", ir->em_tol, 10.0);
1876 RTYPE ("emstep", ir->em_stepsize, 0.01);
1877 CTYPE ("Max number of iterations in relax-shells");
1878 ITYPE ("niter", ir->niter, 20);
1879 CTYPE ("Step size (ps^2) for minimization of flexible constraints");
1880 RTYPE ("fcstep", ir->fc_stepsize, 0);
1881 CTYPE ("Frequency of steepest descents steps when doing CG");
1882 ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
1883 ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
1885 CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
1886 RTYPE ("rtpi", ir->rtpi, 0.05);
1888 /* Output options */
1889 CCTYPE ("OUTPUT CONTROL OPTIONS");
1890 CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
1891 ITYPE ("nstxout", ir->nstxout, 0);
1892 ITYPE ("nstvout", ir->nstvout, 0);
1893 ITYPE ("nstfout", ir->nstfout, 0);
1894 CTYPE ("Output frequency for energies to log file and energy file");
1895 ITYPE ("nstlog", ir->nstlog, 1000);
1896 ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
1897 ITYPE ("nstenergy", ir->nstenergy, 1000);
1898 CTYPE ("Output frequency and precision for .xtc file");
1899 ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
1900 RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
1901 CTYPE ("This selects the subset of atoms for the compressed");
1902 CTYPE ("trajectory file. You can select multiple groups. By");
1903 CTYPE ("default, all atoms will be written.");
1904 STYPE ("compressed-x-grps", is->x_compressed_groups, nullptr);
1905 CTYPE ("Selection of energy groups");
1906 STYPE ("energygrps", is->energy, nullptr);
1908 /* Neighbor searching */
1909 CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
1910 CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1911 EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
1912 CTYPE ("nblist update frequency");
1913 ITYPE ("nstlist", ir->nstlist, 10);
1914 CTYPE ("ns algorithm (simple or grid)");
1915 EETYPE("ns-type", ir->ns_type, ens_names);
1916 CTYPE ("Periodic boundary conditions: xyz, no, xy");
1917 EETYPE("pbc", ir->ePBC, epbc_names);
1918 EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
1919 CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1920 CTYPE ("a value of -1 means: use rlist");
1921 RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
1922 CTYPE ("nblist cut-off");
1923 RTYPE ("rlist", ir->rlist, 1.0);
1924 CTYPE ("long-range cut-off for switched potentials");
1926 /* Electrostatics */
1927 CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
1928 CTYPE ("Method for doing electrostatics");
1929 EETYPE("coulombtype", ir->coulombtype, eel_names);
1930 EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
1931 CTYPE ("cut-off lengths");
1932 RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
1933 RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
1934 CTYPE ("Relative dielectric constant for the medium and the reaction field");
1935 RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
1936 RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
1937 CTYPE ("Method for doing Van der Waals");
1938 EETYPE("vdw-type", ir->vdwtype, evdw_names);
1939 EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
1940 CTYPE ("cut-off lengths");
1941 RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
1942 RTYPE ("rvdw", ir->rvdw, 1.0);
1943 CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
1944 EETYPE("DispCorr", ir->eDispCorr, edispc_names);
1945 CTYPE ("Extension of the potential lookup tables beyond the cut-off");
1946 RTYPE ("table-extension", ir->tabext, 1.0);
1947 CTYPE ("Separate tables between energy group pairs");
1948 STYPE ("energygrp-table", is->egptable, nullptr);
1949 CTYPE ("Spacing for the PME/PPPM FFT grid");
1950 RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
1951 CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
1952 ITYPE ("fourier-nx", ir->nkx, 0);
1953 ITYPE ("fourier-ny", ir->nky, 0);
1954 ITYPE ("fourier-nz", ir->nkz, 0);
1955 CTYPE ("EWALD/PME/PPPM parameters");
1956 ITYPE ("pme-order", ir->pme_order, 4);
1957 RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
1958 RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
1959 EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
1960 EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
1961 RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
1963 /* Implicit solvation is no longer supported, but we need grompp
1964 to be able to refuse old .mdp files that would have built a tpr
1965 to run it. Thus, only "no" is accepted. */
1966 EETYPE("implicit-solvent", ir->implicit_solvent, no_names);
1968 /* Coupling stuff */
1969 CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
1970 CTYPE ("Temperature coupling");
1971 EETYPE("tcoupl", ir->etc, etcoupl_names);
1972 ITYPE ("nsttcouple", ir->nsttcouple, -1);
1973 ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
1974 EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
1975 CTYPE ("Groups to couple separately");
1976 STYPE ("tc-grps", is->tcgrps, nullptr);
1977 CTYPE ("Time constant (ps) and reference temperature (K)");
1978 STYPE ("tau-t", is->tau_t, nullptr);
1979 STYPE ("ref-t", is->ref_t, nullptr);
1980 CTYPE ("pressure coupling");
1981 EETYPE("pcoupl", ir->epc, epcoupl_names);
1982 EETYPE("pcoupltype", ir->epct, epcoupltype_names);
1983 ITYPE ("nstpcouple", ir->nstpcouple, -1);
1984 CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
1985 RTYPE ("tau-p", ir->tau_p, 1.0);
1986 STYPE ("compressibility", dumstr[0], nullptr);
1987 STYPE ("ref-p", dumstr[1], nullptr);
1988 CTYPE ("Scaling of reference coordinates, No, All or COM");
1989 EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
1992 CCTYPE ("OPTIONS FOR QMMM calculations");
1993 EETYPE("QMMM", ir->bQMMM, yesno_names);
1994 CTYPE ("Groups treated Quantum Mechanically");
1995 STYPE ("QMMM-grps", is->QMMM, nullptr);
1996 CTYPE ("QM method");
1997 STYPE("QMmethod", is->QMmethod, nullptr);
1998 CTYPE ("QMMM scheme");
1999 EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
2000 CTYPE ("QM basisset");
2001 STYPE("QMbasis", is->QMbasis, nullptr);
2002 CTYPE ("QM charge");
2003 STYPE ("QMcharge", is->QMcharge, nullptr);
2004 CTYPE ("QM multiplicity");
2005 STYPE ("QMmult", is->QMmult, nullptr);
2006 CTYPE ("Surface Hopping");
2007 STYPE ("SH", is->bSH, nullptr);
2008 CTYPE ("CAS space options");
2009 STYPE ("CASorbitals", is->CASorbitals, nullptr);
2010 STYPE ("CASelectrons", is->CASelectrons, nullptr);
2011 STYPE ("SAon", is->SAon, nullptr);
2012 STYPE ("SAoff", is->SAoff, nullptr);
2013 STYPE ("SAsteps", is->SAsteps, nullptr);
2014 CTYPE ("Scale factor for MM charges");
2015 RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
2017 /* Simulated annealing */
2018 CCTYPE("SIMULATED ANNEALING");
2019 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
2020 STYPE ("annealing", is->anneal, nullptr);
2021 CTYPE ("Number of time points to use for specifying annealing in each group");
2022 STYPE ("annealing-npoints", is->anneal_npoints, nullptr);
2023 CTYPE ("List of times at the annealing points for each group");
2024 STYPE ("annealing-time", is->anneal_time, nullptr);
2025 CTYPE ("Temp. at each annealing point, for each group.");
2026 STYPE ("annealing-temp", is->anneal_temp, nullptr);
2029 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
2030 EETYPE("gen-vel", opts->bGenVel, yesno_names);
2031 RTYPE ("gen-temp", opts->tempi, 300.0);
2032 ITYPE ("gen-seed", opts->seed, -1);
2035 CCTYPE ("OPTIONS FOR BONDS");
2036 EETYPE("constraints", opts->nshake, constraints);
2037 CTYPE ("Type of constraint algorithm");
2038 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
2039 CTYPE ("Do not constrain the start configuration");
2040 EETYPE("continuation", ir->bContinuation, yesno_names);
2041 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
2042 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
2043 CTYPE ("Relative tolerance of shake");
2044 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
2045 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
2046 ITYPE ("lincs-order", ir->nProjOrder, 4);
2047 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
2048 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
2049 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
2050 ITYPE ("lincs-iter", ir->nLincsIter, 1);
2051 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
2052 CTYPE ("rotates over more degrees than");
2053 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
2054 CTYPE ("Convert harmonic bonds to morse potentials");
2055 EETYPE("morse", opts->bMorse, yesno_names);
2057 /* Energy group exclusions */
2058 CCTYPE ("ENERGY GROUP EXCLUSIONS");
2059 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
2060 STYPE ("energygrp-excl", is->egpexcl, nullptr);
2064 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2065 ITYPE ("nwall", ir->nwall, 0);
2066 EETYPE("wall-type", ir->wall_type, ewt_names);
2067 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
2068 STYPE ("wall-atomtype", is->wall_atomtype, nullptr);
2069 STYPE ("wall-density", is->wall_density, nullptr);
2070 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
2073 CCTYPE("COM PULLING");
2074 EETYPE("pull", ir->bPull, yesno_names);
2078 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, wi);
2082 NOTE: needs COM pulling input */
2083 CCTYPE("AWH biasing");
2084 EETYPE("awh", ir->bDoAwh, yesno_names);
2089 ir->awhParams = gmx::readAndCheckAwhParams(&ninp, &inp, ir, wi);
2093 gmx_fatal(FARGS, "AWH biasing is only compatible with COM pulling turned on");
2097 /* Enforced rotation */
2098 CCTYPE("ENFORCED ROTATION");
2099 CTYPE("Enforced rotation: No or Yes");
2100 EETYPE("rotation", ir->bRot, yesno_names);
2104 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2107 /* Interactive MD */
2109 CCTYPE("Group to display and/or manipulate in interactive MD session");
2110 STYPE ("IMD-group", is->imd_grp, nullptr);
2111 if (is->imd_grp[0] != '\0')
2118 CCTYPE("NMR refinement stuff");
2119 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2120 EETYPE("disre", ir->eDisre, edisre_names);
2121 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2122 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2123 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2124 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2125 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2126 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2127 CTYPE ("Output frequency for pair distances to energy file");
2128 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2129 CTYPE ("Orientation restraints: No or Yes");
2130 EETYPE("orire", opts->bOrire, yesno_names);
2131 CTYPE ("Orientation restraints force constant and tau for time averaging");
2132 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2133 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2134 STYPE ("orire-fitgrp", is->orirefitgrp, nullptr);
2135 CTYPE ("Output frequency for trace(SD) and S to energy file");
2136 ITYPE ("nstorireout", ir->nstorireout, 100);
2138 /* free energy variables */
2139 CCTYPE ("Free energy variables");
2140 EETYPE("free-energy", ir->efep, efep_names);
2141 STYPE ("couple-moltype", is->couple_moltype, nullptr);
2142 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2143 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2144 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2146 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2148 it was not entered */
2149 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2150 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2151 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2152 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], nullptr);
2153 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], nullptr);
2154 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], nullptr);
2155 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], nullptr);
2156 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], nullptr);
2157 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], nullptr);
2158 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], nullptr);
2159 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2160 STYPE ("init-lambda-weights", is->lambda_weights, nullptr);
2161 EETYPE("dhdl-print-energy", fep->edHdLPrintEnergy, edHdLPrintEnergy_names);
2162 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2163 ITYPE ("sc-power", fep->sc_power, 1);
2164 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2165 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2166 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2167 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2168 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2169 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2170 separate_dhdl_file_names);
2171 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2172 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2173 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2175 /* Non-equilibrium MD stuff */
2176 CCTYPE("Non-equilibrium MD stuff");
2177 STYPE ("acc-grps", is->accgrps, nullptr);
2178 STYPE ("accelerate", is->acc, nullptr);
2179 STYPE ("freezegrps", is->freeze, nullptr);
2180 STYPE ("freezedim", is->frdim, nullptr);
2181 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2182 STYPE ("deform", is->deform, nullptr);
2184 /* simulated tempering variables */
2185 CCTYPE("simulated tempering variables");
2186 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2187 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2188 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2189 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2191 /* expanded ensemble variables */
2192 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2194 read_expandedparams(&ninp, &inp, expand, wi);
2197 /* Electric fields */
2199 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(ninp, inp);
2200 gmx::KeyValueTreeTransformer transform;
2201 transform.rules()->addRule()
2202 .keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2203 mdModules->initMdpTransform(transform.rules());
2204 for (const auto &path : transform.mappedPaths())
2206 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2207 mark_einp_set(ninp, inp, path[0].c_str());
2209 MdpErrorHandler errorHandler(wi);
2211 = transform.transform(convertedValues, &errorHandler);
2212 ir->params = new gmx::KeyValueTreeObject(result.object());
2213 mdModules->adjustInputrecBasedOnModules(ir);
2214 errorHandler.setBackMapping(result.backMapping());
2215 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2218 /* Ion/water position swapping ("computational electrophysiology") */
2219 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2220 CTYPE("Swap positions along direction: no, X, Y, Z");
2221 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2222 if (ir->eSwapCoords != eswapNO)
2229 CTYPE("Swap attempt frequency");
2230 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2231 CTYPE("Number of ion types to be controlled");
2232 ITYPE("iontypes", nIonTypes, 1);
2235 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2237 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2238 snew(ir->swap->grp, ir->swap->ngrp);
2239 for (i = 0; i < ir->swap->ngrp; i++)
2241 snew(ir->swap->grp[i].molname, STRLEN);
2243 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2244 STYPE("split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2245 STYPE("split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2246 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2247 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2248 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2250 CTYPE("Name of solvent molecules");
2251 STYPE("solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2253 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2254 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2255 CTYPE("however, if correctly defined, the permeation events are recorded per channel");
2256 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2257 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2258 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2259 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2260 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2261 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2263 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2264 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2266 CTYPE("Names of the ion types that can be exchanged with solvent molecules,");
2267 CTYPE("and the requested number of ions of this type in compartments A and B");
2268 CTYPE("-1 means fix the numbers as found in step 0");
2269 for (i = 0; i < nIonTypes; i++)
2271 int ig = eSwapFixedGrpNR + i;
2273 sprintf(buf, "iontype%d-name", i);
2274 STYPE(buf, ir->swap->grp[ig].molname, nullptr);
2275 sprintf(buf, "iontype%d-in-A", i);
2276 ITYPE(buf, ir->swap->grp[ig].nmolReq[0], -1);
2277 sprintf(buf, "iontype%d-in-B", i);
2278 ITYPE(buf, ir->swap->grp[ig].nmolReq[1], -1);
2281 CTYPE("By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2282 CTYPE("at maximum distance (= bulk concentration) to the split group layers. However,");
2283 CTYPE("an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0");
2284 CTYPE("towards one of the compartment-partitioning layers (at +/- 1.0).");
2285 RTYPE("bulk-offsetA", ir->swap->bulkOffset[0], 0.0);
2286 RTYPE("bulk-offsetB", ir->swap->bulkOffset[1], 0.0);
2287 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2288 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0) )
2290 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2293 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2294 RTYPE("threshold", ir->swap->threshold, 1.0);
2297 /* AdResS is no longer supported, but we need grompp to be able to
2298 refuse to process old .mdp files that used it. */
2299 EETYPE("adress", ir->bAdress, no_names);
2301 /* User defined thingies */
2302 CCTYPE ("User defined thingies");
2303 STYPE ("user1-grps", is->user1, nullptr);
2304 STYPE ("user2-grps", is->user2, nullptr);
2305 ITYPE ("userint1", ir->userint1, 0);
2306 ITYPE ("userint2", ir->userint2, 0);
2307 ITYPE ("userint3", ir->userint3, 0);
2308 ITYPE ("userint4", ir->userint4, 0);
2309 RTYPE ("userreal1", ir->userreal1, 0);
2310 RTYPE ("userreal2", ir->userreal2, 0);
2311 RTYPE ("userreal3", ir->userreal3, 0);
2312 RTYPE ("userreal4", ir->userreal4, 0);
2316 gmx::TextOutputFile stream(mdparout);
2317 write_inpfile(&stream, mdparout, ninp, inp, FALSE, writeMdpHeader, wi);
2319 // Transform module data into a flat key-value tree for output.
2320 gmx::KeyValueTreeBuilder builder;
2321 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2322 mdModules->buildMdpOutput(&builderObject);
2324 gmx::TextWriter writer(&stream);
2325 writeKeyValueTreeAsMdp(&writer, builder.build());
2330 for (i = 0; (i < ninp); i++)
2333 sfree(inp[i].value);
2337 /* Process options if necessary */
2338 for (m = 0; m < 2; m++)
2340 for (i = 0; i < 2*DIM; i++)
2349 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2351 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 1)");
2353 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2355 case epctSEMIISOTROPIC:
2356 case epctSURFACETENSION:
2357 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2359 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 2)");
2361 dumdub[m][YY] = dumdub[m][XX];
2363 case epctANISOTROPIC:
2364 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2365 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2366 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2368 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 6)");
2372 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2373 epcoupltype_names[ir->epct]);
2377 clear_mat(ir->ref_p);
2378 clear_mat(ir->compress);
2379 for (i = 0; i < DIM; i++)
2381 ir->ref_p[i][i] = dumdub[1][i];
2382 ir->compress[i][i] = dumdub[0][i];
2384 if (ir->epct == epctANISOTROPIC)
2386 ir->ref_p[XX][YY] = dumdub[1][3];
2387 ir->ref_p[XX][ZZ] = dumdub[1][4];
2388 ir->ref_p[YY][ZZ] = dumdub[1][5];
2389 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2391 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2393 ir->compress[XX][YY] = dumdub[0][3];
2394 ir->compress[XX][ZZ] = dumdub[0][4];
2395 ir->compress[YY][ZZ] = dumdub[0][5];
2396 for (i = 0; i < DIM; i++)
2398 for (m = 0; m < i; m++)
2400 ir->ref_p[i][m] = ir->ref_p[m][i];
2401 ir->compress[i][m] = ir->compress[m][i];
2406 if (ir->comm_mode == ecmNO)
2411 opts->couple_moltype = nullptr;
2412 if (strlen(is->couple_moltype) > 0)
2414 if (ir->efep != efepNO)
2416 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2417 if (opts->couple_lam0 == opts->couple_lam1)
2419 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2421 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2422 opts->couple_lam1 == ecouplamNONE))
2424 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2429 warning_note(wi, "Free energy is turned off, so we will not decouple the molecule listed in your input.");
2432 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2433 if (ir->efep != efepNO)
2435 if (fep->delta_lambda > 0)
2437 ir->efep = efepSLOWGROWTH;
2441 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2443 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2444 warning_note(wi, "Old option for dhdl-print-energy given: "
2445 "changing \"yes\" to \"total\"\n");
2448 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2450 /* always print out the energy to dhdl if we are doing
2451 expanded ensemble, since we need the total energy for
2452 analysis if the temperature is changing. In some
2453 conditions one may only want the potential energy, so
2454 we will allow that if the appropriate mdp setting has
2455 been enabled. Otherwise, total it is:
2457 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2460 if ((ir->efep != efepNO) || ir->bSimTemp)
2462 ir->bExpanded = FALSE;
2463 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2465 ir->bExpanded = TRUE;
2467 do_fep_params(ir, is->fep_lambda, is->lambda_weights, wi);
2468 if (ir->bSimTemp) /* done after fep params */
2470 do_simtemp_params(ir);
2473 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2474 * setup and not on the old way of specifying the free-energy setup,
2475 * we should check for using soft-core when not needed, since that
2476 * can complicate the sampling significantly.
2477 * Note that we only check for the automated coupling setup.
2478 * If the (advanced) user does FEP through manual topology changes,
2479 * this check will not be triggered.
2481 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 &&
2482 ir->fepvals->sc_alpha != 0 &&
2483 (couple_lambda_has_vdw_on(opts->couple_lam0) &&
2484 couple_lambda_has_vdw_on(opts->couple_lam1)))
2486 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.");
2491 ir->fepvals->n_lambda = 0;
2494 /* WALL PARAMETERS */
2496 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2498 /* ORIENTATION RESTRAINT PARAMETERS */
2500 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, nullptr) != 1)
2502 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2505 /* DEFORMATION PARAMETERS */
2507 clear_mat(ir->deform);
2508 for (i = 0; i < 6; i++)
2513 double gmx_unused canary;
2514 int ndeform = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf %lf",
2515 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2516 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]), &canary);
2518 if (strlen(is->deform) > 0 && ndeform != 6)
2520 warning_error(wi, gmx::formatString("Cannot parse exactly 6 box deformation velocities from string '%s'", is->deform).c_str());
2522 for (i = 0; i < 3; i++)
2524 ir->deform[i][i] = dumdub[0][i];
2526 ir->deform[YY][XX] = dumdub[0][3];
2527 ir->deform[ZZ][XX] = dumdub[0][4];
2528 ir->deform[ZZ][YY] = dumdub[0][5];
2529 if (ir->epc != epcNO)
2531 for (i = 0; i < 3; i++)
2533 for (j = 0; j <= i; j++)
2535 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2537 warning_error(wi, "A box element has deform set and compressibility > 0");
2541 for (i = 0; i < 3; i++)
2543 for (j = 0; j < i; j++)
2545 if (ir->deform[i][j] != 0)
2547 for (m = j; m < DIM; m++)
2549 if (ir->compress[m][j] != 0)
2551 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.");
2552 warning(wi, warn_buf);
2560 /* Ion/water position swapping checks */
2561 if (ir->eSwapCoords != eswapNO)
2563 if (ir->swap->nstswap < 1)
2565 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2567 if (ir->swap->nAverage < 1)
2569 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2571 if (ir->swap->threshold < 1.0)
2573 warning_error(wi, "Ion count threshold must be at least 1.\n");
2581 static int search_QMstring(const char *s, int ng, const char *gn[])
2583 /* same as normal search_string, but this one searches QM strings */
2586 for (i = 0; (i < ng); i++)
2588 if (gmx_strcasecmp(s, gn[i]) == 0)
2594 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2598 } /* search_QMstring */
2600 /* We would like gn to be const as well, but C doesn't allow this */
2601 /* TODO this is utility functionality (search for the index of a
2602 string in a collection), so should be refactored and located more
2604 int search_string(const char *s, int ng, char *gn[])
2608 for (i = 0; (i < ng); i++)
2610 if (gmx_strcasecmp(s, gn[i]) == 0)
2617 "Group %s referenced in the .mdp file was not found in the index file.\n"
2618 "Group names must match either [moleculetype] names or custom index group\n"
2619 "names, in which case you must supply an index file to the '-n' option\n"
2626 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2627 t_blocka *block, char *gnames[],
2628 int gtype, int restnm,
2629 int grptp, gmx_bool bVerbose,
2632 unsigned short *cbuf;
2633 t_grps *grps = &(groups->grps[gtype]);
2634 int i, j, gid, aj, ognr, ntot = 0;
2637 char warn_buf[STRLEN];
2641 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2644 title = gtypes[gtype];
2647 /* Mark all id's as not set */
2648 for (i = 0; (i < natoms); i++)
2653 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2654 for (i = 0; (i < ng); i++)
2656 /* Lookup the group name in the block structure */
2657 gid = search_string(ptrs[i], block->nr, gnames);
2658 if ((grptp != egrptpONE) || (i == 0))
2660 grps->nm_ind[grps->nr++] = gid;
2664 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2667 /* Now go over the atoms in the group */
2668 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2673 /* Range checking */
2674 if ((aj < 0) || (aj >= natoms))
2676 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2678 /* Lookup up the old group number */
2682 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2683 aj+1, title, ognr+1, i+1);
2687 /* Store the group number in buffer */
2688 if (grptp == egrptpONE)
2701 /* Now check whether we have done all atoms */
2705 if (grptp == egrptpALL)
2707 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2708 natoms-ntot, title);
2710 else if (grptp == egrptpPART)
2712 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2713 natoms-ntot, title);
2714 warning_note(wi, warn_buf);
2716 /* Assign all atoms currently unassigned to a rest group */
2717 for (j = 0; (j < natoms); j++)
2719 if (cbuf[j] == NOGID)
2725 if (grptp != egrptpPART)
2730 "Making dummy/rest group for %s containing %d elements\n",
2731 title, natoms-ntot);
2733 /* Add group name "rest" */
2734 grps->nm_ind[grps->nr] = restnm;
2736 /* Assign the rest name to all atoms not currently assigned to a group */
2737 for (j = 0; (j < natoms); j++)
2739 if (cbuf[j] == NOGID)
2748 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2750 /* All atoms are part of one (or no) group, no index required */
2751 groups->ngrpnr[gtype] = 0;
2752 groups->grpnr[gtype] = nullptr;
2756 groups->ngrpnr[gtype] = natoms;
2757 snew(groups->grpnr[gtype], natoms);
2758 for (j = 0; (j < natoms); j++)
2760 groups->grpnr[gtype][j] = cbuf[j];
2766 return (bRest && grptp == egrptpPART);
2769 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2772 gmx_groups_t *groups;
2773 pull_params_t *pull;
2774 int natoms, ai, aj, i, j, d, g, imin, jmin;
2776 int *nrdf2, *na_vcm, na_tot;
2777 double *nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2779 gmx_mtop_atomloop_all_t aloop;
2780 int mb, mol, ftype, as;
2781 gmx_molblock_t *molb;
2782 gmx_moltype_t *molt;
2785 * First calc 3xnr-atoms for each group
2786 * then subtract half a degree of freedom for each constraint
2788 * Only atoms and nuclei contribute to the degrees of freedom...
2793 groups = &mtop->groups;
2794 natoms = mtop->natoms;
2796 /* Allocate one more for a possible rest group */
2797 /* We need to sum degrees of freedom into doubles,
2798 * since floats give too low nrdf's above 3 million atoms.
2800 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2801 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2802 snew(dof_vcm, groups->grps[egcVCM].nr+1);
2803 snew(na_vcm, groups->grps[egcVCM].nr+1);
2804 snew(nrdf_vcm_sub, groups->grps[egcVCM].nr+1);
2806 for (i = 0; i < groups->grps[egcTC].nr; i++)
2810 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2813 clear_ivec(dof_vcm[i]);
2815 nrdf_vcm_sub[i] = 0;
2818 snew(nrdf2, natoms);
2819 aloop = gmx_mtop_atomloop_all_init(mtop);
2821 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2824 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2826 g = ggrpnr(groups, egcFREEZE, i);
2827 for (d = 0; d < DIM; d++)
2829 if (opts->nFreeze[g][d] == 0)
2831 /* Add one DOF for particle i (counted as 2*1) */
2833 /* VCM group i has dim d as a DOF */
2834 dof_vcm[ggrpnr(groups, egcVCM, i)][d] = 1;
2837 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2838 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2843 for (mb = 0; mb < mtop->nmolblock; mb++)
2845 molb = &mtop->molblock[mb];
2846 molt = &mtop->moltype[molb->type];
2847 atom = molt->atoms.atom;
2848 for (mol = 0; mol < molb->nmol; mol++)
2850 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2852 ia = molt->ilist[ftype].iatoms;
2853 for (i = 0; i < molt->ilist[ftype].nr; )
2855 /* Subtract degrees of freedom for the constraints,
2856 * if the particles still have degrees of freedom left.
2857 * If one of the particles is a vsite or a shell, then all
2858 * constraint motion will go there, but since they do not
2859 * contribute to the constraints the degrees of freedom do not
2864 if (((atom[ia[1]].ptype == eptNucleus) ||
2865 (atom[ia[1]].ptype == eptAtom)) &&
2866 ((atom[ia[2]].ptype == eptNucleus) ||
2867 (atom[ia[2]].ptype == eptAtom)))
2885 imin = std::min(imin, nrdf2[ai]);
2886 jmin = std::min(jmin, nrdf2[aj]);
2889 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2890 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2891 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2892 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2894 ia += interaction_function[ftype].nratoms+1;
2895 i += interaction_function[ftype].nratoms+1;
2898 ia = molt->ilist[F_SETTLE].iatoms;
2899 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2901 /* Subtract 1 dof from every atom in the SETTLE */
2902 for (j = 0; j < 3; j++)
2905 imin = std::min(2, nrdf2[ai]);
2907 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2908 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2913 as += molt->atoms.nr;
2919 /* Correct nrdf for the COM constraints.
2920 * We correct using the TC and VCM group of the first atom
2921 * in the reference and pull group. If atoms in one pull group
2922 * belong to different TC or VCM groups it is anyhow difficult
2923 * to determine the optimal nrdf assignment.
2927 for (i = 0; i < pull->ncoord; i++)
2929 if (pull->coord[i].eType != epullCONSTRAINT)
2936 for (j = 0; j < 2; j++)
2938 const t_pull_group *pgrp;
2940 pgrp = &pull->group[pull->coord[i].group[j]];
2944 /* Subtract 1/2 dof from each group */
2946 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2947 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2948 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2950 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)]]);
2955 /* We need to subtract the whole DOF from group j=1 */
2962 if (ir->nstcomm != 0)
2966 /* We remove COM motion up to dim ndof_com() */
2967 ndim_rm_vcm = ndof_com(ir);
2969 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
2970 * the number of degrees of freedom in each vcm group when COM
2971 * translation is removed and 6 when rotation is removed as well.
2973 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2975 switch (ir->comm_mode)
2978 case ecmLINEAR_ACCELERATION_CORRECTION:
2979 nrdf_vcm_sub[j] = 0;
2980 for (d = 0; d < ndim_rm_vcm; d++)
2989 nrdf_vcm_sub[j] = 6;
2992 gmx_incons("Checking comm_mode");
2996 for (i = 0; i < groups->grps[egcTC].nr; i++)
2998 /* Count the number of atoms of TC group i for every VCM group */
2999 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
3004 for (ai = 0; ai < natoms; ai++)
3006 if (ggrpnr(groups, egcTC, ai) == i)
3008 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
3012 /* Correct for VCM removal according to the fraction of each VCM
3013 * group present in this TC group.
3015 nrdf_uc = nrdf_tc[i];
3018 fprintf(debug, "T-group[%d] nrdf_uc = %g\n", i, nrdf_uc);
3021 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
3023 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3025 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
3026 (nrdf_vcm[j] - nrdf_vcm_sub[j])/nrdf_vcm[j];
3030 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
3031 j, nrdf_vcm[j], nrdf_tc[i]);
3036 for (i = 0; (i < groups->grps[egcTC].nr); i++)
3038 opts->nrdf[i] = nrdf_tc[i];
3039 if (opts->nrdf[i] < 0)
3044 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3045 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
3053 sfree(nrdf_vcm_sub);
3056 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
3057 const char *option, const char *val, int flag)
3059 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3060 * But since this is much larger than STRLEN, such a line can not be parsed.
3061 * The real maximum is the number of names that fit in a string: STRLEN/2.
3063 #define EGP_MAX (STRLEN/2)
3064 int nelem, i, j, k, nr;
3065 char *names[EGP_MAX];
3069 gnames = groups->grpname;
3071 nelem = str_nelem(val, EGP_MAX, names);
3074 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3076 nr = groups->grps[egcENER].nr;
3078 for (i = 0; i < nelem/2; i++)
3082 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
3088 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3089 names[2*i], option);
3093 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
3099 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3100 names[2*i+1], option);
3102 if ((j < nr) && (k < nr))
3104 ir->opts.egp_flags[nr*j+k] |= flag;
3105 ir->opts.egp_flags[nr*k+j] |= flag;
3114 static void make_swap_groups(
3119 int ig = -1, i = 0, gind;
3123 /* Just a quick check here, more thorough checks are in mdrun */
3124 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3126 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3129 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3130 for (ig = 0; ig < swap->ngrp; ig++)
3132 swapg = &swap->grp[ig];
3133 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3134 swapg->nat = grps->index[gind+1] - grps->index[gind];
3138 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3139 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap",
3140 swap->grp[ig].molname, swapg->nat);
3141 snew(swapg->ind, swapg->nat);
3142 for (i = 0; i < swapg->nat; i++)
3144 swapg->ind[i] = grps->a[grps->index[gind]+i];
3149 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3155 static void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3160 ig = search_string(IMDgname, grps->nr, gnames);
3161 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3163 if (IMDgroup->nat > 0)
3165 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3166 IMDgname, IMDgroup->nat);
3167 snew(IMDgroup->ind, IMDgroup->nat);
3168 for (i = 0; i < IMDgroup->nat; i++)
3170 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3176 void do_index(const char* mdparin, const char *ndx,
3183 gmx_groups_t *groups;
3187 char warnbuf[STRLEN], **gnames;
3188 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3191 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3192 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3193 int i, j, k, restnm;
3194 gmx_bool bExcl, bTable, bAnneal, bRest;
3195 int nQMmethod, nQMbasis, nQMg;
3196 char warn_buf[STRLEN];
3201 fprintf(stderr, "processing index file...\n");
3206 snew(grps->index, 1);
3208 atoms_all = gmx_mtop_global_atoms(mtop);
3209 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3210 done_atom(&atoms_all);
3214 grps = init_index(ndx, &gnames);
3217 groups = &mtop->groups;
3218 natoms = mtop->natoms;
3219 symtab = &mtop->symtab;
3221 snew(groups->grpname, grps->nr+1);
3223 for (i = 0; (i < grps->nr); i++)
3225 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3227 groups->grpname[i] = put_symtab(symtab, "rest");
3229 srenew(gnames, grps->nr+1);
3230 gnames[restnm] = *(groups->grpname[i]);
3231 groups->ngrpname = grps->nr+1;
3233 set_warning_line(wi, mdparin, -1);
3235 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3236 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3237 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3238 if ((ntau_t != ntcg) || (nref_t != ntcg))
3240 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3241 "%d tau-t values", ntcg, nref_t, ntau_t);
3244 const bool useReferenceTemperature = integratorHasReferenceTemperature(ir);
3245 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3246 restnm, useReferenceTemperature ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3247 nr = groups->grps[egcTC].nr;
3249 snew(ir->opts.nrdf, nr);
3250 snew(ir->opts.tau_t, nr);
3251 snew(ir->opts.ref_t, nr);
3252 if (ir->eI == eiBD && ir->bd_fric == 0)
3254 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3257 if (useReferenceTemperature)
3261 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3265 for (i = 0; (i < nr); i++)
3267 ir->opts.tau_t[i] = strtod(ptr1[i], &endptr);
3270 warning_error(wi, "Invalid value for mdp option tau-t. tau-t should only consist of real numbers separated by spaces.");
3272 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3274 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3275 warning_error(wi, warn_buf);
3278 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3280 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.");
3283 if (ir->opts.tau_t[i] >= 0)
3285 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3288 if (ir->etc != etcNO && ir->nsttcouple == -1)
3290 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3295 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3297 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");
3299 if (ir->epc == epcMTTK)
3301 if (ir->etc != etcNOSEHOOVER)
3303 gmx_fatal(FARGS, "Cannot do MTTK pressure coupling without Nose-Hoover temperature control");
3307 if (ir->nstpcouple != ir->nsttcouple)
3309 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3310 ir->nstpcouple = ir->nsttcouple = mincouple;
3311 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);
3312 warning_note(wi, warn_buf);
3317 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3318 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3320 if (ETC_ANDERSEN(ir->etc))
3322 if (ir->nsttcouple != 1)
3325 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");
3326 warning_note(wi, warn_buf);
3329 nstcmin = tcouple_min_integration_steps(ir->etc);
3332 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin - 10*GMX_REAL_EPS)
3334 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3335 ETCOUPLTYPE(ir->etc),
3337 ir->nsttcouple*ir->delta_t);
3338 warning(wi, warn_buf);
3341 for (i = 0; (i < nr); i++)
3343 ir->opts.ref_t[i] = strtod(ptr2[i], &endptr);
3346 warning_error(wi, "Invalid value for mdp option ref-t. ref-t should only consist of real numbers separated by spaces.");
3348 if (ir->opts.ref_t[i] < 0)
3350 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3353 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3354 if we are in this conditional) if mc_temp is negative */
3355 if (ir->expandedvals->mc_temp < 0)
3357 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3361 /* Simulated annealing for each group. There are nr groups */
3362 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3363 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3367 if (nSA > 0 && nSA != nr)
3369 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3373 snew(ir->opts.annealing, nr);
3374 snew(ir->opts.anneal_npoints, nr);
3375 snew(ir->opts.anneal_time, nr);
3376 snew(ir->opts.anneal_temp, nr);
3377 for (i = 0; i < nr; i++)
3379 ir->opts.annealing[i] = eannNO;
3380 ir->opts.anneal_npoints[i] = 0;
3381 ir->opts.anneal_time[i] = nullptr;
3382 ir->opts.anneal_temp[i] = nullptr;
3387 for (i = 0; i < nr; i++)
3389 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3391 ir->opts.annealing[i] = eannNO;
3393 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3395 ir->opts.annealing[i] = eannSINGLE;
3398 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3400 ir->opts.annealing[i] = eannPERIODIC;
3406 /* Read the other fields too */
3407 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3408 if (nSA_points != nSA)
3410 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3412 for (k = 0, i = 0; i < nr; i++)
3414 ir->opts.anneal_npoints[i] = strtol(ptr1[i], &endptr, 10);
3417 warning_error(wi, "Invalid value for mdp option annealing-npoints. annealing should only consist of integers separated by spaces.");
3419 if (ir->opts.anneal_npoints[i] == 1)
3421 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3423 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3424 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3425 k += ir->opts.anneal_npoints[i];
3428 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3431 gmx_fatal(FARGS, "Found %d annealing-time values, wanted %d\n", nSA_time, k);
3433 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3436 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3439 for (i = 0, k = 0; i < nr; i++)
3442 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3444 ir->opts.anneal_time[i][j] = strtod(ptr1[k], &endptr);
3447 warning_error(wi, "Invalid value for mdp option anneal-time. anneal-time should only consist of real numbers separated by spaces.");
3449 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], &endptr);
3452 warning_error(wi, "Invalid value for anneal-temp. anneal-temp should only consist of real numbers separated by spaces.");
3456 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3458 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3464 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3466 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3467 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3470 if (ir->opts.anneal_temp[i][j] < 0)
3472 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3477 /* Print out some summary information, to make sure we got it right */
3478 for (i = 0, k = 0; i < nr; i++)
3480 if (ir->opts.annealing[i] != eannNO)
3482 j = groups->grps[egcTC].nm_ind[i];
3483 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3484 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3485 ir->opts.anneal_npoints[i]);
3486 fprintf(stderr, "Time (ps) Temperature (K)\n");
3487 /* All terms except the last one */
3488 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3490 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3493 /* Finally the last one */
3494 j = ir->opts.anneal_npoints[i]-1;
3495 if (ir->opts.annealing[i] == eannSINGLE)
3497 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3501 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3502 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3504 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3515 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3517 make_pull_coords(ir->pull);
3522 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3525 if (ir->eSwapCoords != eswapNO)
3527 make_swap_groups(ir->swap, grps, gnames);
3530 /* Make indices for IMD session */
3533 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3536 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3537 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3538 if (nacg*DIM != nacc)
3540 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3543 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3544 restnm, egrptpALL_GENREST, bVerbose, wi);
3545 nr = groups->grps[egcACC].nr;
3546 snew(ir->opts.acc, nr);
3547 ir->opts.ngacc = nr;
3549 for (i = k = 0; (i < nacg); i++)
3551 for (j = 0; (j < DIM); j++, k++)
3553 ir->opts.acc[i][j] = strtod(ptr1[k], &endptr);
3556 warning_error(wi, "Invalid value for mdp option accelerate. accelerate should only consist of real numbers separated by spaces.");
3560 for (; (i < nr); i++)
3562 for (j = 0; (j < DIM); j++)
3564 ir->opts.acc[i][j] = 0;
3568 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3569 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3570 if (nfrdim != DIM*nfreeze)
3572 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3575 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3576 restnm, egrptpALL_GENREST, bVerbose, wi);
3577 nr = groups->grps[egcFREEZE].nr;
3578 ir->opts.ngfrz = nr;
3579 snew(ir->opts.nFreeze, nr);
3580 for (i = k = 0; (i < nfreeze); i++)
3582 for (j = 0; (j < DIM); j++, k++)
3584 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3585 if (!ir->opts.nFreeze[i][j])
3587 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3589 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3590 "(not %s)", ptr1[k]);
3591 warning(wi, warn_buf);
3596 for (; (i < nr); i++)
3598 for (j = 0; (j < DIM); j++)
3600 ir->opts.nFreeze[i][j] = 0;
3604 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3605 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3606 restnm, egrptpALL_GENREST, bVerbose, wi);
3607 add_wall_energrps(groups, ir->nwall, symtab);
3608 ir->opts.ngener = groups->grps[egcENER].nr;
3609 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3611 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3612 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3615 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3616 "This may lead to artifacts.\n"
3617 "In most cases one should use one group for the whole system.");
3620 /* Now we have filled the freeze struct, so we can calculate NRDF */
3621 calc_nrdf(mtop, ir, gnames);
3623 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3624 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3625 restnm, egrptpALL_GENREST, bVerbose, wi);
3626 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3627 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3628 restnm, egrptpALL_GENREST, bVerbose, wi);
3629 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3630 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3631 restnm, egrptpONE, bVerbose, wi);
3632 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3633 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3634 restnm, egrptpALL_GENREST, bVerbose, wi);
3636 /* QMMM input processing */
3637 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3638 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3639 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3640 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3642 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3643 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3645 /* group rest, if any, is always MM! */
3646 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3647 restnm, egrptpALL_GENREST, bVerbose, wi);
3648 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3649 ir->opts.ngQM = nQMg;
3650 snew(ir->opts.QMmethod, nr);
3651 snew(ir->opts.QMbasis, nr);
3652 for (i = 0; i < nr; i++)
3654 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3655 * converted to the corresponding enum in names.c
3657 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3659 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3663 str_nelem(is->QMmult, MAXPTR, ptr1);
3664 str_nelem(is->QMcharge, MAXPTR, ptr2);
3665 str_nelem(is->bSH, MAXPTR, ptr3);
3666 snew(ir->opts.QMmult, nr);
3667 snew(ir->opts.QMcharge, nr);
3668 snew(ir->opts.bSH, nr);
3670 for (i = 0; i < nr; i++)
3672 ir->opts.QMmult[i] = strtol(ptr1[i], &endptr, 10);
3675 warning_error(wi, "Invalid value for mdp option QMmult. QMmult should only consist of integers separated by spaces.");
3677 ir->opts.QMcharge[i] = strtol(ptr2[i], &endptr, 10);
3680 warning_error(wi, "Invalid value for mdp option QMcharge. QMcharge should only consist of integers separated by spaces.");
3682 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3685 str_nelem(is->CASelectrons, MAXPTR, ptr1);
3686 str_nelem(is->CASorbitals, MAXPTR, ptr2);
3687 snew(ir->opts.CASelectrons, nr);
3688 snew(ir->opts.CASorbitals, nr);
3689 for (i = 0; i < nr; i++)
3691 ir->opts.CASelectrons[i] = strtol(ptr1[i], &endptr, 10);
3694 warning_error(wi, "Invalid value for mdp option CASelectrons. CASelectrons should only consist of integers separated by spaces.");
3696 ir->opts.CASorbitals[i] = strtol(ptr2[i], &endptr, 10);
3699 warning_error(wi, "Invalid value for mdp option CASorbitals. CASorbitals should only consist of integers separated by spaces.");
3703 str_nelem(is->SAon, MAXPTR, ptr1);
3704 str_nelem(is->SAoff, MAXPTR, ptr2);
3705 str_nelem(is->SAsteps, MAXPTR, ptr3);
3706 snew(ir->opts.SAon, nr);
3707 snew(ir->opts.SAoff, nr);
3708 snew(ir->opts.SAsteps, nr);
3710 for (i = 0; i < nr; i++)
3712 ir->opts.SAon[i] = strtod(ptr1[i], &endptr);
3715 warning_error(wi, "Invalid value for mdp option SAon. SAon should only consist of real numbers separated by spaces.");
3717 ir->opts.SAoff[i] = strtod(ptr2[i], &endptr);
3720 warning_error(wi, "Invalid value for mdp option SAoff. SAoff should only consist of real numbers separated by spaces.");
3722 ir->opts.SAsteps[i] = strtol(ptr3[i], &endptr, 10);
3725 warning_error(wi, "Invalid value for mdp option SAsteps. SAsteps should only consist of integers separated by spaces.");
3728 /* end of QMMM input */
3732 for (i = 0; (i < egcNR); i++)
3734 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3735 for (j = 0; (j < groups->grps[i].nr); j++)
3737 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3739 fprintf(stderr, "\n");
3743 nr = groups->grps[egcENER].nr;
3744 snew(ir->opts.egp_flags, nr*nr);
3746 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3747 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3749 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3751 if (bExcl && EEL_FULL(ir->coulombtype))
3753 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3756 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3757 if (bTable && !(ir->vdwtype == evdwUSER) &&
3758 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3759 !(ir->coulombtype == eelPMEUSERSWITCH))
3761 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3764 for (i = 0; (i < grps->nr); i++)
3776 static void check_disre(gmx_mtop_t *mtop)
3778 gmx_ffparams_t *ffparams;
3779 t_functype *functype;
3781 int i, ndouble, ftype;
3782 int label, old_label;
3784 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3786 ffparams = &mtop->ffparams;
3787 functype = ffparams->functype;
3788 ip = ffparams->iparams;
3791 for (i = 0; i < ffparams->ntypes; i++)
3793 ftype = functype[i];
3794 if (ftype == F_DISRES)
3796 label = ip[i].disres.label;
3797 if (label == old_label)
3799 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3807 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3808 "probably the parameters for multiple pairs in one restraint "
3809 "are not identical\n", ndouble);
3814 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3815 gmx_bool posres_only,
3819 gmx_mtop_ilistloop_t iloop;
3829 for (d = 0; d < DIM; d++)
3831 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3833 /* Check for freeze groups */
3834 for (g = 0; g < ir->opts.ngfrz; g++)
3836 for (d = 0; d < DIM; d++)
3838 if (ir->opts.nFreeze[g][d] != 0)
3846 /* Check for position restraints */
3847 iloop = gmx_mtop_ilistloop_init(sys);
3848 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3851 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3853 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3855 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3856 for (d = 0; d < DIM; d++)
3858 if (pr->posres.fcA[d] != 0)
3864 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3866 /* Check for flat-bottom posres */
3867 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3868 if (pr->fbposres.k != 0)
3870 switch (pr->fbposres.geom)
3872 case efbposresSPHERE:
3873 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3875 case efbposresCYLINDERX:
3876 AbsRef[YY] = AbsRef[ZZ] = 1;
3878 case efbposresCYLINDERY:
3879 AbsRef[XX] = AbsRef[ZZ] = 1;
3881 case efbposresCYLINDER:
3882 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3883 case efbposresCYLINDERZ:
3884 AbsRef[XX] = AbsRef[YY] = 1;
3886 case efbposresX: /* d=XX */
3887 case efbposresY: /* d=YY */
3888 case efbposresZ: /* d=ZZ */
3889 d = pr->fbposres.geom - efbposresX;
3893 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3894 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3902 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3906 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3907 gmx_bool *bC6ParametersWorkWithGeometricRules,
3908 gmx_bool *bC6ParametersWorkWithLBRules,
3909 gmx_bool *bLBRulesPossible)
3911 int ntypes, tpi, tpj;
3914 double c6i, c6j, c12i, c12j;
3915 double c6, c6_geometric, c6_LB;
3916 double sigmai, sigmaj, epsi, epsj;
3917 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3920 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3921 * force-field floating point parameters.
3924 ptr = getenv("GMX_LJCOMB_TOL");
3928 double gmx_unused canary;
3930 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
3932 gmx_fatal(FARGS, "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
3937 *bC6ParametersWorkWithLBRules = TRUE;
3938 *bC6ParametersWorkWithGeometricRules = TRUE;
3939 bCanDoLBRules = TRUE;
3940 ntypes = mtop->ffparams.atnr;
3941 snew(typecount, ntypes);
3942 gmx_mtop_count_atomtypes(mtop, state, typecount);
3943 *bLBRulesPossible = TRUE;
3944 for (tpi = 0; tpi < ntypes; ++tpi)
3946 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3947 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3948 for (tpj = tpi; tpj < ntypes; ++tpj)
3950 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3951 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3952 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3953 c6_geometric = std::sqrt(c6i * c6j);
3954 if (!gmx_numzero(c6_geometric))
3956 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3958 sigmai = gmx::sixthroot(c12i / c6i);
3959 sigmaj = gmx::sixthroot(c12j / c6j);
3960 epsi = c6i * c6i /(4.0 * c12i);
3961 epsj = c6j * c6j /(4.0 * c12j);
3962 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
3966 *bLBRulesPossible = FALSE;
3967 c6_LB = c6_geometric;
3969 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3972 if (FALSE == bCanDoLBRules)
3974 *bC6ParametersWorkWithLBRules = FALSE;
3977 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3979 if (FALSE == bCanDoGeometricRules)
3981 *bC6ParametersWorkWithGeometricRules = FALSE;
3989 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3992 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3994 check_combination_rule_differences(mtop, 0,
3995 &bC6ParametersWorkWithGeometricRules,
3996 &bC6ParametersWorkWithLBRules,
3998 if (ir->ljpme_combination_rule == eljpmeLB)
4000 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
4002 warning(wi, "You are using arithmetic-geometric combination rules "
4003 "in LJ-PME, but your non-bonded C6 parameters do not "
4004 "follow these rules.");
4009 if (FALSE == bC6ParametersWorkWithGeometricRules)
4011 if (ir->eDispCorr != edispcNO)
4013 warning_note(wi, "You are using geometric combination rules in "
4014 "LJ-PME, but your non-bonded C6 parameters do "
4015 "not follow these rules. "
4016 "This will introduce very small errors in the forces and energies in "
4017 "your simulations. Dispersion correction will correct total energy "
4018 "and/or pressure for isotropic systems, but not forces or surface tensions.");
4022 warning_note(wi, "You are using geometric combination rules in "
4023 "LJ-PME, but your non-bonded C6 parameters do "
4024 "not follow these rules. "
4025 "This will introduce very small errors in the forces and energies in "
4026 "your simulations. If your system is homogeneous, consider using dispersion correction "
4027 "for the total energy and pressure.");
4033 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
4036 char err_buf[STRLEN];
4038 gmx_bool bCharge, bAcc;
4041 gmx_mtop_atomloop_block_t aloopb;
4042 gmx_mtop_atomloop_all_t aloop;
4044 char warn_buf[STRLEN];
4046 set_warning_line(wi, mdparin, -1);
4048 if (ir->cutoff_scheme == ecutsVERLET &&
4049 ir->verletbuf_tol > 0 &&
4051 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
4052 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4054 /* Check if a too small Verlet buffer might potentially
4055 * cause more drift than the thermostat can couple off.
4057 /* Temperature error fraction for warning and suggestion */
4058 const real T_error_warn = 0.002;
4059 const real T_error_suggest = 0.001;
4060 /* For safety: 2 DOF per atom (typical with constraints) */
4061 const real nrdf_at = 2;
4062 real T, tau, max_T_error;
4067 for (i = 0; i < ir->opts.ngtc; i++)
4069 T = std::max(T, ir->opts.ref_t[i]);
4070 tau = std::max(tau, ir->opts.tau_t[i]);
4074 /* This is a worst case estimate of the temperature error,
4075 * assuming perfect buffer estimation and no cancelation
4076 * of errors. The factor 0.5 is because energy distributes
4077 * equally over Ekin and Epot.
4079 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4080 if (max_T_error > T_error_warn)
4082 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.",
4083 ir->verletbuf_tol, T, tau,
4085 100*T_error_suggest,
4086 ir->verletbuf_tol*T_error_suggest/max_T_error);
4087 warning(wi, warn_buf);
4092 if (ETC_ANDERSEN(ir->etc))
4096 for (i = 0; i < ir->opts.ngtc; i++)
4098 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4099 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4100 sprintf(err_buf, "all tau_t must be positive using Andersen temperature control, tau_t[%d]=%10.6f",
4101 i, ir->opts.tau_t[i]);
4102 CHECK(ir->opts.tau_t[i] < 0);
4105 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4107 for (i = 0; i < ir->opts.ngtc; i++)
4109 int nsteps = static_cast<int>(ir->opts.tau_t[i]/ir->delta_t + 0.5);
4110 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);
4111 CHECK(nsteps % ir->nstcomm != 0);
4116 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4117 ir->comm_mode == ecmNO &&
4118 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4119 !ETC_ANDERSEN(ir->etc))
4121 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");
4124 /* Check for pressure coupling with absolute position restraints */
4125 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4127 absolute_reference(ir, sys, TRUE, AbsRef);
4129 for (m = 0; m < DIM; m++)
4131 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4133 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4141 aloopb = gmx_mtop_atomloop_block_init(sys);
4143 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4145 if (atom->q != 0 || atom->qB != 0)
4153 if (EEL_FULL(ir->coulombtype))
4156 "You are using full electrostatics treatment %s for a system without charges.\n"
4157 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4158 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4159 warning(wi, err_buf);
4164 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
4167 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4168 "You might want to consider using %s electrostatics.\n",
4170 warning_note(wi, err_buf);
4174 /* Check if combination rules used in LJ-PME are the same as in the force field */
4175 if (EVDW_PME(ir->vdwtype))
4177 check_combination_rules(ir, sys, wi);
4180 /* Generalized reaction field */
4181 if (ir->opts.ngtc == 0)
4183 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4185 CHECK(ir->coulombtype == eelGRF);
4189 sprintf(err_buf, "When using coulombtype = %s"
4190 " ref-t for temperature coupling should be > 0",
4192 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4196 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4198 for (m = 0; (m < DIM); m++)
4200 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4209 snew(mgrp, sys->groups.grps[egcACC].nr);
4210 aloop = gmx_mtop_atomloop_all_init(sys);
4212 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4214 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4217 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4219 for (m = 0; (m < DIM); m++)
4221 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4225 for (m = 0; (m < DIM); m++)
4227 if (fabs(acc[m]) > 1e-6)
4229 const char *dim[DIM] = { "X", "Y", "Z" };
4231 "Net Acceleration in %s direction, will %s be corrected\n",
4232 dim[m], ir->nstcomm != 0 ? "" : "not");
4233 if (ir->nstcomm != 0 && m < ndof_com(ir))
4236 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4238 ir->opts.acc[i][m] -= acc[m];
4246 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4247 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4249 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4257 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4259 if (ir->pull->coord[i].group[0] == 0 ||
4260 ir->pull->coord[i].group[1] == 0)
4262 absolute_reference(ir, sys, FALSE, AbsRef);
4263 for (m = 0; m < DIM; m++)
4265 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4267 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.");
4275 for (i = 0; i < 3; i++)
4277 for (m = 0; m <= i; m++)
4279 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4280 ir->deform[i][m] != 0)
4282 for (c = 0; c < ir->pull->ncoord; c++)
4284 if (ir->pull->coord[c].eGeom == epullgDIRPBC &&
4285 ir->pull->coord[c].vec[m] != 0)
4287 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->coord[c].eGeom), 'x'+m);
4298 void double_check(t_inputrec *ir, matrix box,
4299 gmx_bool bHasNormalConstraints,
4300 gmx_bool bHasAnyConstraints,
4304 char warn_buf[STRLEN];
4307 ptr = check_box(ir->ePBC, box);
4310 warning_error(wi, ptr);
4313 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4315 if (ir->shake_tol <= 0.0)
4317 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4319 warning_error(wi, warn_buf);
4323 if ( (ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4325 /* If we have Lincs constraints: */
4326 if (ir->eI == eiMD && ir->etc == etcNO &&
4327 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4329 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4330 warning_note(wi, warn_buf);
4333 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4335 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4336 warning_note(wi, warn_buf);
4338 if (ir->epc == epcMTTK)
4340 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4344 if (bHasAnyConstraints && ir->epc == epcMTTK)
4346 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4349 if (ir->LincsWarnAngle > 90.0)
4351 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4352 warning(wi, warn_buf);
4353 ir->LincsWarnAngle = 90.0;
4356 if (ir->ePBC != epbcNONE)
4358 if (ir->nstlist == 0)
4360 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4362 if (ir->ns_type == ensGRID)
4364 if (gmx::square(ir->rlist) >= max_cutoff2(ir->ePBC, box))
4366 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");
4367 warning_error(wi, warn_buf);
4372 min_size = std::min(box[XX][XX], std::min(box[YY][YY], box[ZZ][ZZ]));
4373 if (2*ir->rlist >= min_size)
4375 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4376 warning_error(wi, warn_buf);
4379 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4386 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4390 real rvdw1, rvdw2, rcoul1, rcoul2;
4391 char warn_buf[STRLEN];
4393 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4397 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4402 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4408 if (rvdw1 + rvdw2 > ir->rlist ||
4409 rcoul1 + rcoul2 > ir->rlist)
4412 "The sum of the two largest charge group radii (%f) "
4413 "is larger than rlist (%f)\n",
4414 std::max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4415 warning(wi, warn_buf);
4419 /* Here we do not use the zero at cut-off macro,
4420 * since user defined interactions might purposely
4421 * not be zero at the cut-off.
4423 if (ir_vdw_is_zero_at_cutoff(ir) &&
4424 rvdw1 + rvdw2 > ir->rlist - ir->rvdw)
4426 sprintf(warn_buf, "The sum of the two largest charge group "
4427 "radii (%f) is larger than rlist (%f) - rvdw (%f).\n"
4428 "With exact cut-offs, better performance can be "
4429 "obtained with cutoff-scheme = %s, because it "
4430 "does not use charge groups at all.",
4432 ir->rlist, ir->rvdw,
4433 ecutscheme_names[ecutsVERLET]);
4436 warning(wi, warn_buf);
4440 warning_note(wi, warn_buf);
4443 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4444 rcoul1 + rcoul2 > ir->rlist - ir->rcoulomb)
4446 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than rlist (%f) - rcoulomb (%f).\n"
4447 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4449 ir->rlist, ir->rcoulomb,
4450 ecutscheme_names[ecutsVERLET]);
4453 warning(wi, warn_buf);
4457 warning_note(wi, warn_buf);