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50 #include "gromacs/fileio/readinp.h"
51 #include "gromacs/fileio/warninp.h"
52 #include "gromacs/gmxlib/chargegroup.h"
53 #include "gromacs/gmxlib/network.h"
54 #include "gromacs/gmxpreprocess/keyvaluetreemdpwriter.h"
55 #include "gromacs/gmxpreprocess/toputil.h"
56 #include "gromacs/math/functions.h"
57 #include "gromacs/math/units.h"
58 #include "gromacs/math/vec.h"
59 #include "gromacs/mdlib/calc_verletbuf.h"
60 #include "gromacs/mdrunutility/mdmodules.h"
61 #include "gromacs/mdtypes/inputrec.h"
62 #include "gromacs/mdtypes/md_enums.h"
63 #include "gromacs/mdtypes/pull-params.h"
64 #include "gromacs/options/options.h"
65 #include "gromacs/options/treesupport.h"
66 #include "gromacs/pbcutil/pbc.h"
67 #include "gromacs/topology/block.h"
68 #include "gromacs/topology/ifunc.h"
69 #include "gromacs/topology/index.h"
70 #include "gromacs/topology/mtop_util.h"
71 #include "gromacs/topology/symtab.h"
72 #include "gromacs/topology/topology.h"
73 #include "gromacs/utility/cstringutil.h"
74 #include "gromacs/utility/exceptions.h"
75 #include "gromacs/utility/fatalerror.h"
76 #include "gromacs/utility/filestream.h"
77 #include "gromacs/utility/gmxassert.h"
78 #include "gromacs/utility/ikeyvaluetreeerror.h"
79 #include "gromacs/utility/keyvaluetree.h"
80 #include "gromacs/utility/keyvaluetreebuilder.h"
81 #include "gromacs/utility/keyvaluetreetransform.h"
82 #include "gromacs/utility/smalloc.h"
83 #include "gromacs/utility/stringcompare.h"
84 #include "gromacs/utility/stringutil.h"
85 #include "gromacs/utility/textwriter.h"
90 /* Resource parameters
91 * Do not change any of these until you read the instruction
92 * in readinp.h. Some cpp's do not take spaces after the backslash
93 * (like the c-shell), which will give you a very weird compiler
97 typedef struct t_inputrec_strings
99 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN],
100 acc[STRLEN], accgrps[STRLEN], freeze[STRLEN], frdim[STRLEN],
101 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
102 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
103 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN],
105 char fep_lambda[efptNR][STRLEN];
106 char lambda_weights[STRLEN];
109 char anneal[STRLEN], anneal_npoints[STRLEN],
110 anneal_time[STRLEN], anneal_temp[STRLEN];
111 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
112 bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
113 SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
115 } gmx_inputrec_strings;
117 static gmx_inputrec_strings *is = nullptr;
119 void init_inputrec_strings()
123 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.");
128 void done_inputrec_strings()
136 egrptpALL, /* All particles have to be a member of a group. */
137 egrptpALL_GENREST, /* A rest group with name is generated for particles *
138 * that are not part of any group. */
139 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
140 * for the rest group. */
141 egrptpONE /* Merge all selected groups into one group, *
142 * make a rest group for the remaining particles. */
145 static const char *constraints[eshNR+1] = {
146 "none", "h-bonds", "all-bonds", "h-angles", "all-angles", nullptr
149 static const char *couple_lam[ecouplamNR+1] = {
150 "vdw-q", "vdw", "q", "none", nullptr
153 static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
158 for (i = 0; i < ntemps; i++)
160 /* simple linear scaling -- allows more control */
161 if (simtemp->eSimTempScale == esimtempLINEAR)
163 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*temperature_lambdas[i];
165 else if (simtemp->eSimTempScale == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
167 simtemp->temperatures[i] = simtemp->simtemp_low * std::pow(simtemp->simtemp_high/simtemp->simtemp_low, static_cast<real>((1.0*i)/(ntemps-1)));
169 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
171 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*(std::expm1(temperature_lambdas[i])/std::expm1(1.0));
176 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
177 gmx_fatal(FARGS, errorstr);
184 static void _low_check(gmx_bool b, const char *s, warninp_t wi)
188 warning_error(wi, s);
192 static void check_nst(const char *desc_nst, int nst,
193 const char *desc_p, int *p,
198 if (*p > 0 && *p % nst != 0)
200 /* Round up to the next multiple of nst */
201 *p = ((*p)/nst + 1)*nst;
202 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n",
203 desc_p, desc_nst, desc_p, *p);
208 static gmx_bool ir_NVE(const t_inputrec *ir)
210 return (EI_MD(ir->eI) && ir->etc == etcNO);
213 static int lcd(int n1, int n2)
218 for (i = 2; (i <= n1 && i <= n2); i++)
220 if (n1 % i == 0 && n2 % i == 0)
229 static void process_interaction_modifier(const t_inputrec *ir, int *eintmod)
231 if (*eintmod == eintmodPOTSHIFT_VERLET)
233 if (ir->cutoff_scheme == ecutsVERLET)
235 *eintmod = eintmodPOTSHIFT;
239 *eintmod = eintmodNONE;
244 void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
246 /* Check internal consistency.
247 * NOTE: index groups are not set here yet, don't check things
248 * like temperature coupling group options here, but in triple_check
251 /* Strange macro: first one fills the err_buf, and then one can check
252 * the condition, which will print the message and increase the error
255 #define CHECK(b) _low_check(b, err_buf, wi)
256 char err_buf[256], warn_buf[STRLEN];
259 t_lambda *fep = ir->fepvals;
260 t_expanded *expand = ir->expandedvals;
262 set_warning_line(wi, mdparin, -1);
264 if (ir->coulombtype == eelRF_NEC_UNSUPPORTED)
266 sprintf(warn_buf, "%s electrostatics is no longer supported",
267 eel_names[eelRF_NEC_UNSUPPORTED]);
268 warning_error(wi, warn_buf);
271 /* BASIC CUT-OFF STUFF */
272 if (ir->rcoulomb < 0)
274 warning_error(wi, "rcoulomb should be >= 0");
278 warning_error(wi, "rvdw should be >= 0");
281 !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
283 warning_error(wi, "rlist should be >= 0");
285 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.)");
286 CHECK(ir->nstlist < 0);
288 process_interaction_modifier(ir, &ir->coulomb_modifier);
289 process_interaction_modifier(ir, &ir->vdw_modifier);
291 if (ir->cutoff_scheme == ecutsGROUP)
294 "The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future "
295 "release when all interaction forms are supported for the verlet scheme. The verlet "
296 "scheme already scales better, and it is compatible with GPUs and other accelerators.");
298 if (ir->rlist > 0 && ir->rlist < ir->rcoulomb)
300 gmx_fatal(FARGS, "rcoulomb must not be greater than rlist (twin-range schemes are not supported)");
302 if (ir->rlist > 0 && ir->rlist < ir->rvdw)
304 gmx_fatal(FARGS, "rvdw must not be greater than rlist (twin-range schemes are not supported)");
307 if (ir->rlist == 0 && ir->ePBC != epbcNONE)
309 warning_error(wi, "Can not have an infinite cut-off with PBC");
313 if (ir->cutoff_scheme == ecutsVERLET)
317 /* Normal Verlet type neighbor-list, currently only limited feature support */
318 if (inputrec2nboundeddim(ir) < 3)
320 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
323 // We don't (yet) have general Verlet kernels for rcoulomb!=rvdw
324 if (ir->rcoulomb != ir->rvdw)
326 // Since we have PME coulomb + LJ cut-off kernels with rcoulomb>rvdw
327 // for PME load balancing, we can support this exception.
328 bool bUsesPmeTwinRangeKernel = (EEL_PME_EWALD(ir->coulombtype) &&
329 ir->vdwtype == evdwCUT &&
330 ir->rcoulomb > ir->rvdw);
331 if (!bUsesPmeTwinRangeKernel)
333 warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported (except for rcoulomb>rvdw with PME electrostatics)");
337 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
339 if (ir->vdw_modifier == eintmodNONE ||
340 ir->vdw_modifier == eintmodPOTSHIFT)
342 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
344 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]);
345 warning_note(wi, warn_buf);
347 ir->vdwtype = evdwCUT;
351 sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
352 warning_error(wi, warn_buf);
356 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
358 warning_error(wi, "With Verlet lists only cut-off and PME LJ interactions are supported");
360 if (!(ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype) ||
361 EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
363 warning_error(wi, "With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
365 if (!(ir->coulomb_modifier == eintmodNONE ||
366 ir->coulomb_modifier == eintmodPOTSHIFT))
368 sprintf(warn_buf, "coulomb_modifier=%s is not supported with the Verlet cut-off scheme", eintmod_names[ir->coulomb_modifier]);
369 warning_error(wi, warn_buf);
372 if (ir->implicit_solvent != eisNO)
374 warning_error(wi, "Implicit solvent is not (yet) supported with the with Verlet lists.");
377 if (ir->nstlist <= 0)
379 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
382 if (ir->nstlist < 10)
384 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.");
387 rc_max = std::max(ir->rvdw, ir->rcoulomb);
389 if (ir->verletbuf_tol <= 0)
391 if (ir->verletbuf_tol == 0)
393 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
396 if (ir->rlist < rc_max)
398 warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
401 if (ir->rlist == rc_max && ir->nstlist > 1)
403 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.");
408 if (ir->rlist > rc_max)
410 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.");
413 if (ir->nstlist == 1)
415 /* No buffer required */
420 if (EI_DYNAMICS(ir->eI))
422 if (inputrec2nboundeddim(ir) < 3)
424 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.");
426 /* Set rlist temporarily so we can continue processing */
431 /* Set the buffer to 5% of the cut-off */
432 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
438 /* GENERAL INTEGRATOR STUFF */
441 if (ir->etc != etcNO)
443 if (EI_RANDOM(ir->eI))
445 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]);
449 sprintf(warn_buf, "Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
451 warning_note(wi, warn_buf);
455 if (ir->eI == eiVVAK)
457 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]);
458 warning_note(wi, warn_buf);
460 if (!EI_DYNAMICS(ir->eI))
462 if (ir->epc != epcNO)
464 sprintf(warn_buf, "Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.", epcoupl_names[ir->epc], ei_names[ir->eI]);
465 warning_note(wi, warn_buf);
469 if (EI_DYNAMICS(ir->eI))
471 if (ir->nstcalcenergy < 0)
473 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
474 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
476 /* nstcalcenergy larger than nstener does not make sense.
477 * We ideally want nstcalcenergy=nstener.
481 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
485 ir->nstcalcenergy = ir->nstenergy;
489 else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
490 (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
491 (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
494 const char *nsten = "nstenergy";
495 const char *nstdh = "nstdhdl";
496 const char *min_name = nsten;
497 int min_nst = ir->nstenergy;
499 /* find the smallest of ( nstenergy, nstdhdl ) */
500 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
501 (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
503 min_nst = ir->fepvals->nstdhdl;
506 /* If the user sets nstenergy small, we should respect that */
508 "Setting nstcalcenergy (%d) equal to %s (%d)",
509 ir->nstcalcenergy, min_name, min_nst);
510 warning_note(wi, warn_buf);
511 ir->nstcalcenergy = min_nst;
514 if (ir->epc != epcNO)
516 if (ir->nstpcouple < 0)
518 ir->nstpcouple = ir_optimal_nstpcouple(ir);
522 if (ir->nstcalcenergy > 0)
524 if (ir->efep != efepNO)
526 /* nstdhdl should be a multiple of nstcalcenergy */
527 check_nst("nstcalcenergy", ir->nstcalcenergy,
528 "nstdhdl", &ir->fepvals->nstdhdl, wi);
529 /* nstexpanded should be a multiple of nstcalcenergy */
530 check_nst("nstcalcenergy", ir->nstcalcenergy,
531 "nstexpanded", &ir->expandedvals->nstexpanded, wi);
533 /* for storing exact averages nstenergy should be
534 * a multiple of nstcalcenergy
536 check_nst("nstcalcenergy", ir->nstcalcenergy,
537 "nstenergy", &ir->nstenergy, wi);
541 if (ir->nsteps == 0 && !ir->bContinuation)
543 warning_note(wi, "For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates.");
547 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
548 ir->bContinuation && ir->ld_seed != -1)
550 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)");
556 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
557 CHECK(ir->ePBC != epbcXYZ);
558 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
559 CHECK(ir->ns_type != ensGRID);
560 sprintf(err_buf, "with TPI nstlist should be larger than zero");
561 CHECK(ir->nstlist <= 0);
562 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
563 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
564 sprintf(err_buf, "TPI does not work (yet) with the Verlet cut-off scheme");
565 CHECK(ir->cutoff_scheme == ecutsVERLET);
569 if ( (opts->nshake > 0) && (opts->bMorse) )
572 "Using morse bond-potentials while constraining bonds is useless");
573 warning(wi, warn_buf);
576 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
577 ir->bContinuation && ir->ld_seed != -1)
579 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)");
581 /* verify simulated tempering options */
585 gmx_bool bAllTempZero = TRUE;
586 for (i = 0; i < fep->n_lambda; i++)
588 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]);
589 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
590 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
592 bAllTempZero = FALSE;
595 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
596 CHECK(bAllTempZero == TRUE);
598 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
599 CHECK(ir->eI != eiVV);
601 /* check compatability of the temperature coupling with simulated tempering */
603 if (ir->etc == etcNOSEHOOVER)
605 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
606 warning_note(wi, warn_buf);
609 /* check that the temperatures make sense */
611 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);
612 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
614 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
615 CHECK(ir->simtempvals->simtemp_high <= 0);
617 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
618 CHECK(ir->simtempvals->simtemp_low <= 0);
621 /* verify free energy options */
623 if (ir->efep != efepNO)
626 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
628 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
630 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
631 (int)fep->sc_r_power);
632 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
634 sprintf(err_buf, "Can't use positive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
635 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
637 sprintf(err_buf, "Can't use positive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
638 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
640 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
641 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
643 sprintf(err_buf, "Free-energy not implemented for Ewald");
644 CHECK(ir->coulombtype == eelEWALD);
646 /* check validty of lambda inputs */
647 if (fep->n_lambda == 0)
649 /* Clear output in case of no states:*/
650 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
651 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
655 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
656 CHECK((fep->init_fep_state >= fep->n_lambda));
659 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
660 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
662 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",
663 fep->init_lambda, fep->init_fep_state);
664 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
668 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
672 for (i = 0; i < efptNR; i++)
674 if (fep->separate_dvdl[i])
679 if (n_lambda_terms > 1)
681 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.");
682 warning(wi, warn_buf);
685 if (n_lambda_terms < 2 && fep->n_lambda > 0)
688 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
692 for (j = 0; j < efptNR; j++)
694 for (i = 0; i < fep->n_lambda; i++)
696 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]);
697 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
701 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
703 for (i = 0; i < fep->n_lambda; i++)
705 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],
706 fep->all_lambda[efptCOUL][i]);
707 CHECK((fep->sc_alpha > 0) &&
708 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
709 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
710 ((fep->all_lambda[efptVDW][i] > 0.0) &&
711 (fep->all_lambda[efptVDW][i] < 1.0))));
715 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
717 real sigma, lambda, r_sc;
720 /* Maximum estimate for A and B charges equal with lambda power 1 */
722 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);
723 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.",
725 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
726 warning_note(wi, warn_buf);
729 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
730 be treated differently, but that's the next step */
732 for (i = 0; i < efptNR; i++)
734 for (j = 0; j < fep->n_lambda; j++)
736 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
737 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
742 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
746 /* checking equilibration of weights inputs for validity */
748 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
749 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
750 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
752 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
753 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
754 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
756 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
757 expand->equil_steps, elmceq_names[elmceqSTEPS]);
758 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
760 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
761 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
762 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
764 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
765 expand->equil_ratio, elmceq_names[elmceqRATIO]);
766 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
768 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
769 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
770 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
772 sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
773 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
774 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
776 sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
777 expand->equil_steps, elmceq_names[elmceqSTEPS]);
778 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
780 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
781 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
782 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
784 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
785 expand->equil_ratio, elmceq_names[elmceqRATIO]);
786 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
788 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
789 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
790 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
792 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
793 CHECK((expand->lmc_repeats <= 0));
794 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
795 CHECK((expand->minvarmin <= 0));
796 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
797 CHECK((expand->c_range < 0));
798 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
799 fep->init_fep_state, expand->lmc_forced_nstart);
800 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
801 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
802 CHECK((expand->lmc_forced_nstart < 0));
803 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
804 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
806 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
807 CHECK((expand->init_wl_delta < 0));
808 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
809 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
810 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
811 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
813 /* if there is no temperature control, we need to specify an MC temperature */
814 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
815 if (expand->nstTij > 0)
817 sprintf(err_buf, "nstlog must be non-zero");
818 CHECK(ir->nstlog == 0);
819 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
820 expand->nstTij, ir->nstlog);
821 CHECK((expand->nstTij % ir->nstlog) != 0);
826 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
827 CHECK(ir->nwall && ir->ePBC != epbcXY);
830 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
832 if (ir->ePBC == epbcNONE)
834 if (ir->epc != epcNO)
836 warning(wi, "Turning off pressure coupling for vacuum system");
842 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
843 epbc_names[ir->ePBC]);
844 CHECK(ir->epc != epcNO);
846 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
847 CHECK(EEL_FULL(ir->coulombtype));
849 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
850 epbc_names[ir->ePBC]);
851 CHECK(ir->eDispCorr != edispcNO);
854 if (ir->rlist == 0.0)
856 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
857 "with coulombtype = %s or coulombtype = %s\n"
858 "without periodic boundary conditions (pbc = %s) and\n"
859 "rcoulomb and rvdw set to zero",
860 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
861 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
862 (ir->ePBC != epbcNONE) ||
863 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
867 warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
872 if (ir->nstcomm == 0)
874 ir->comm_mode = ecmNO;
876 if (ir->comm_mode != ecmNO)
880 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");
881 ir->nstcomm = abs(ir->nstcomm);
884 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
886 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
887 ir->nstcomm = ir->nstcalcenergy;
890 if (ir->comm_mode == ecmANGULAR)
892 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
893 CHECK(ir->bPeriodicMols);
894 if (ir->ePBC != epbcNONE)
896 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.");
901 if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
903 warning_note(wi, "Tumbling and or flying ice-cubes: We are not removing rotation around center of mass in a non-periodic system. You should probably set comm_mode = ANGULAR.");
906 /* TEMPERATURE COUPLING */
907 if (ir->etc == etcYES)
909 ir->etc = etcBERENDSEN;
910 warning_note(wi, "Old option for temperature coupling given: "
911 "changing \"yes\" to \"Berendsen\"\n");
914 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
916 if (ir->opts.nhchainlength < 1)
918 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
919 ir->opts.nhchainlength = 1;
920 warning(wi, warn_buf);
923 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
925 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
926 ir->opts.nhchainlength = 1;
931 ir->opts.nhchainlength = 0;
934 if (ir->eI == eiVVAK)
936 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
938 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
941 if (ETC_ANDERSEN(ir->etc))
943 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
944 CHECK(!(EI_VV(ir->eI)));
946 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
948 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]);
949 warning_note(wi, warn_buf);
952 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]);
953 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
956 if (ir->etc == etcBERENDSEN)
958 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
959 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
960 warning_note(wi, warn_buf);
963 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
964 && ir->epc == epcBERENDSEN)
966 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
967 "true ensemble for the thermostat");
968 warning(wi, warn_buf);
971 /* PRESSURE COUPLING */
972 if (ir->epc == epcISOTROPIC)
974 ir->epc = epcBERENDSEN;
975 warning_note(wi, "Old option for pressure coupling given: "
976 "changing \"Isotropic\" to \"Berendsen\"\n");
979 if (ir->epc != epcNO)
981 dt_pcoupl = ir->nstpcouple*ir->delta_t;
983 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
984 CHECK(ir->tau_p <= 0);
986 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10*GMX_REAL_EPS)
988 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
989 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
990 warning(wi, warn_buf);
993 sprintf(err_buf, "compressibility must be > 0 when using pressure"
994 " coupling %s\n", EPCOUPLTYPE(ir->epc));
995 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
996 ir->compress[ZZ][ZZ] < 0 ||
997 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
998 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
1000 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1003 "You are generating velocities so I am assuming you "
1004 "are equilibrating a system. You are using "
1005 "%s pressure coupling, but this can be "
1006 "unstable for equilibration. If your system crashes, try "
1007 "equilibrating first with Berendsen pressure coupling. If "
1008 "you are not equilibrating the system, you can probably "
1009 "ignore this warning.",
1010 epcoupl_names[ir->epc]);
1011 warning(wi, warn_buf);
1017 if (ir->epc > epcNO)
1019 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1021 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.");
1027 if (ir->epc == epcMTTK)
1029 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1033 /* ELECTROSTATICS */
1034 /* More checks are in triple check (grompp.c) */
1036 if (ir->coulombtype == eelSWITCH)
1038 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1039 "artifacts, advice: use coulombtype = %s",
1040 eel_names[ir->coulombtype],
1041 eel_names[eelRF_ZERO]);
1042 warning(wi, warn_buf);
1045 if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
1047 sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
1048 warning_note(wi, warn_buf);
1051 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1053 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);
1054 warning(wi, warn_buf);
1055 ir->epsilon_rf = ir->epsilon_r;
1056 ir->epsilon_r = 1.0;
1059 if (ir->epsilon_r == 0)
1062 "It is pointless to use long-range or Generalized Born electrostatics with infinite relative permittivity."
1063 "Since you are effectively turning of electrostatics, a plain cutoff will be much faster.");
1064 CHECK(EEL_FULL(ir->coulombtype) || ir->implicit_solvent == eisGBSA);
1067 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
1069 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1070 CHECK(ir->epsilon_r < 0);
1073 if (EEL_RF(ir->coulombtype))
1075 /* reaction field (at the cut-off) */
1077 if (ir->coulombtype == eelRF_ZERO && ir->epsilon_rf != 0)
1079 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1080 eel_names[ir->coulombtype]);
1081 warning(wi, warn_buf);
1082 ir->epsilon_rf = 0.0;
1085 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1086 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1087 (ir->epsilon_r == 0));
1088 if (ir->epsilon_rf == ir->epsilon_r)
1090 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1091 eel_names[ir->coulombtype]);
1092 warning(wi, warn_buf);
1095 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1096 * means the interaction is zero outside rcoulomb, but it helps to
1097 * provide accurate energy conservation.
1099 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1101 if (ir_coulomb_switched(ir))
1104 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1105 eel_names[ir->coulombtype]);
1106 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1109 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1111 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1113 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1114 eel_names[ir->coulombtype]);
1115 CHECK(ir->rlist > ir->rcoulomb);
1119 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1122 "Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier.");
1123 CHECK( ir->coulomb_modifier != eintmodNONE);
1125 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1128 "Explicit switch/shift vdw interactions cannot be used in combination with a secondary vdw-modifier.");
1129 CHECK( ir->vdw_modifier != eintmodNONE);
1132 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1133 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1136 "The switch/shift interaction settings are just for compatibility; you will get better "
1137 "performance from applying potential modifiers to your interactions!\n");
1138 warning_note(wi, warn_buf);
1141 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1143 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1145 real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
1146 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.",
1147 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1148 warning(wi, warn_buf);
1152 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1154 if (ir->rvdw_switch == 0)
1156 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.");
1157 warning(wi, warn_buf);
1161 if (EEL_FULL(ir->coulombtype))
1163 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1164 ir->coulombtype == eelPMEUSERSWITCH)
1166 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1167 eel_names[ir->coulombtype]);
1168 CHECK(ir->rcoulomb > ir->rlist);
1170 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1172 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1175 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist.\n"
1176 "For optimal energy conservation,consider using\n"
1177 "a potential modifier.", eel_names[ir->coulombtype]);
1178 CHECK(ir->rcoulomb != ir->rlist);
1183 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1185 // TODO: Move these checks into the ewald module with the options class
1187 int orderMax = (ir->coulombtype == eelP3M_AD ? 8 : 12);
1189 if (ir->pme_order < orderMin || ir->pme_order > orderMax)
1191 sprintf(warn_buf, "With coulombtype = %s, you should have %d <= pme-order <= %d", eel_names[ir->coulombtype], orderMin, orderMax);
1192 warning_error(wi, warn_buf);
1196 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1198 if (ir->ewald_geometry == eewg3D)
1200 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1201 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1202 warning(wi, warn_buf);
1204 /* This check avoids extra pbc coding for exclusion corrections */
1205 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1206 CHECK(ir->wall_ewald_zfac < 2);
1208 if ((ir->ewald_geometry == eewg3DC) && (ir->ePBC != epbcXY) &&
1209 EEL_FULL(ir->coulombtype))
1211 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1212 eel_names[ir->coulombtype], eewg_names[eewg3DC], epbc_names[epbcXY]);
1213 warning(wi, warn_buf);
1215 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1217 if (ir->cutoff_scheme == ecutsVERLET)
1219 sprintf(warn_buf, "Since molecules/charge groups are broken using the Verlet scheme, you can not use a dipole correction to the %s electrostatics.",
1220 eel_names[ir->coulombtype]);
1221 warning(wi, warn_buf);
1225 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",
1226 eel_names[ir->coulombtype]);
1227 warning_note(wi, warn_buf);
1231 if (ir_vdw_switched(ir))
1233 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1234 CHECK(ir->rvdw_switch >= ir->rvdw);
1236 if (ir->rvdw_switch < 0.5*ir->rvdw)
1238 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.",
1239 ir->rvdw_switch, ir->rvdw);
1240 warning_note(wi, warn_buf);
1243 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1245 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1247 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1248 CHECK(ir->rlist > ir->rvdw);
1252 if (ir->vdwtype == evdwPME)
1254 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1256 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s and %s",
1257 evdw_names[ir->vdwtype],
1258 eintmod_names[eintmodPOTSHIFT],
1259 eintmod_names[eintmodNONE]);
1260 warning_error(wi, err_buf);
1264 if (ir->cutoff_scheme == ecutsGROUP)
1266 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1267 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)))
1269 warning_note(wi, "With exact cut-offs, rlist should be "
1270 "larger than rcoulomb and rvdw, so that there "
1271 "is a buffer region for particle motion "
1272 "between neighborsearch steps");
1275 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlist <= ir->rcoulomb)
1277 sprintf(warn_buf, "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb.");
1278 warning_note(wi, warn_buf);
1280 if (ir_vdw_switched(ir) && (ir->rlist <= ir->rvdw))
1282 sprintf(warn_buf, "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw.");
1283 warning_note(wi, warn_buf);
1287 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1289 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.");
1292 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1295 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1298 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1300 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1303 /* ENERGY CONSERVATION */
1304 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1306 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1308 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1309 evdw_names[evdwSHIFT]);
1310 warning_note(wi, warn_buf);
1312 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1314 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1315 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1316 warning_note(wi, warn_buf);
1320 /* IMPLICIT SOLVENT */
1321 if (ir->coulombtype == eelGB_NOTUSED)
1323 sprintf(warn_buf, "Invalid option %s for coulombtype",
1324 eel_names[ir->coulombtype]);
1325 warning_error(wi, warn_buf);
1328 if (ir->sa_algorithm == esaSTILL)
1330 sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
1331 CHECK(ir->sa_algorithm == esaSTILL);
1334 if (ir->implicit_solvent == eisGBSA)
1336 sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
1337 CHECK(ir->rgbradii != ir->rlist);
1339 if (ir->coulombtype != eelCUT)
1341 sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
1342 CHECK(ir->coulombtype != eelCUT);
1344 if (ir->vdwtype != evdwCUT)
1346 sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
1347 CHECK(ir->vdwtype != evdwCUT);
1349 if (ir->nstgbradii < 1)
1351 sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
1352 warning_note(wi, warn_buf);
1355 if (ir->sa_algorithm == esaNO)
1357 sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
1358 warning_note(wi, warn_buf);
1360 if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
1362 sprintf(warn_buf, "Value of sa_surface_tension is < 0. Changing it to 2.05016 or 2.25936 kJ/nm^2/mol for Still and HCT/OBC respectively\n");
1363 warning_note(wi, warn_buf);
1365 if (ir->gb_algorithm == egbSTILL)
1367 ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
1371 ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
1374 if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
1376 sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
1377 CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
1384 if (ir->cutoff_scheme != ecutsGROUP)
1386 warning_error(wi, "QMMM is currently only supported with cutoff-scheme=group");
1388 if (!EI_DYNAMICS(ir->eI))
1391 sprintf(buf, "QMMM is only supported with dynamics, not with integrator %s", ei_names[ir->eI]);
1392 warning_error(wi, buf);
1398 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1402 /* count the number of text elemets separated by whitespace in a string.
1403 str = the input string
1404 maxptr = the maximum number of allowed elements
1405 ptr = the output array of pointers to the first character of each element
1406 returns: the number of elements. */
1407 int str_nelem(const char *str, int maxptr, char *ptr[])
1412 copy0 = gmx_strdup(str);
1415 while (*copy != '\0')
1419 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1427 while ((*copy != '\0') && !isspace(*copy))
1446 /* interpret a number of doubles from a string and put them in an array,
1447 after allocating space for them.
1448 str = the input string
1449 n = the (pre-allocated) number of doubles read
1450 r = the output array of doubles. */
1451 static void parse_n_real(char *str, int *n, real **r, warninp_t wi)
1456 char warn_buf[STRLEN];
1458 *n = str_nelem(str, MAXPTR, ptr);
1461 for (i = 0; i < *n; i++)
1463 (*r)[i] = strtod(ptr[i], &endptr);
1466 sprintf(warn_buf, "Invalid value %s in string in mdp file. Expected a real number.", ptr[i]);
1467 warning_error(wi, warn_buf);
1472 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
1475 int i, j, max_n_lambda, nweights, nfep[efptNR];
1476 t_lambda *fep = ir->fepvals;
1477 t_expanded *expand = ir->expandedvals;
1478 real **count_fep_lambdas;
1479 gmx_bool bOneLambda = TRUE;
1481 snew(count_fep_lambdas, efptNR);
1483 /* FEP input processing */
1484 /* first, identify the number of lambda values for each type.
1485 All that are nonzero must have the same number */
1487 for (i = 0; i < efptNR; i++)
1489 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
1492 /* now, determine the number of components. All must be either zero, or equal. */
1495 for (i = 0; i < efptNR; i++)
1497 if (nfep[i] > max_n_lambda)
1499 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1500 must have the same number if its not zero.*/
1505 for (i = 0; i < efptNR; i++)
1509 ir->fepvals->separate_dvdl[i] = FALSE;
1511 else if (nfep[i] == max_n_lambda)
1513 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1514 respect to the temperature currently */
1516 ir->fepvals->separate_dvdl[i] = TRUE;
1521 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1522 nfep[i], efpt_names[i], max_n_lambda);
1525 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1526 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1528 /* the number of lambdas is the number we've read in, which is either zero
1529 or the same for all */
1530 fep->n_lambda = max_n_lambda;
1532 /* allocate space for the array of lambda values */
1533 snew(fep->all_lambda, efptNR);
1534 /* if init_lambda is defined, we need to set lambda */
1535 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1537 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1539 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1540 for (i = 0; i < efptNR; i++)
1542 snew(fep->all_lambda[i], fep->n_lambda);
1543 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1546 for (j = 0; j < fep->n_lambda; j++)
1548 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1550 sfree(count_fep_lambdas[i]);
1553 sfree(count_fep_lambdas);
1555 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1556 bookkeeping -- for now, init_lambda */
1558 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1560 for (i = 0; i < fep->n_lambda; i++)
1562 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1566 /* check to see if only a single component lambda is defined, and soft core is defined.
1567 In this case, turn on coulomb soft core */
1569 if (max_n_lambda == 0)
1575 for (i = 0; i < efptNR; i++)
1577 if ((nfep[i] != 0) && (i != efptFEP))
1583 if ((bOneLambda) && (fep->sc_alpha > 0))
1585 fep->bScCoul = TRUE;
1588 /* Fill in the others with the efptFEP if they are not explicitly
1589 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1590 they are all zero. */
1592 for (i = 0; i < efptNR; i++)
1594 if ((nfep[i] == 0) && (i != efptFEP))
1596 for (j = 0; j < fep->n_lambda; j++)
1598 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1604 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1605 if (fep->sc_r_power == 48)
1607 if (fep->sc_alpha > 0.1)
1609 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1613 /* now read in the weights */
1614 parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
1617 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1619 else if (nweights != fep->n_lambda)
1621 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1622 nweights, fep->n_lambda);
1624 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1626 expand->nstexpanded = fep->nstdhdl;
1627 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1629 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1631 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1632 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1633 2*tau_t just to be careful so it's not to frequent */
1638 static void do_simtemp_params(t_inputrec *ir)
1641 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1642 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1647 static void do_wall_params(t_inputrec *ir,
1648 char *wall_atomtype, char *wall_density,
1652 char *names[MAXPTR];
1655 opts->wall_atomtype[0] = nullptr;
1656 opts->wall_atomtype[1] = nullptr;
1658 ir->wall_atomtype[0] = -1;
1659 ir->wall_atomtype[1] = -1;
1660 ir->wall_density[0] = 0;
1661 ir->wall_density[1] = 0;
1665 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1666 if (nstr != ir->nwall)
1668 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1671 for (i = 0; i < ir->nwall; i++)
1673 opts->wall_atomtype[i] = gmx_strdup(names[i]);
1676 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1678 nstr = str_nelem(wall_density, MAXPTR, names);
1679 if (nstr != ir->nwall)
1681 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1683 for (i = 0; i < ir->nwall; i++)
1685 if (sscanf(names[i], "%lf", &dbl) != 1)
1687 gmx_fatal(FARGS, "Could not parse wall-density value from string '%s'", names[i]);
1691 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1693 ir->wall_density[i] = dbl;
1699 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1707 srenew(groups->grpname, groups->ngrpname+nwall);
1708 grps = &(groups->grps[egcENER]);
1709 srenew(grps->nm_ind, grps->nr+nwall);
1710 for (i = 0; i < nwall; i++)
1712 sprintf(str, "wall%d", i);
1713 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1714 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1719 static void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1720 t_expanded *expand, warninp_t wi)
1728 /* read expanded ensemble parameters */
1729 CCTYPE ("expanded ensemble variables");
1730 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1731 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1732 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1733 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1734 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1735 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1736 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1737 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1738 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1739 CCTYPE("Seed for Monte Carlo in lambda space");
1740 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1741 RTYPE ("mc-temperature", expand->mc_temp, -1);
1742 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1743 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1744 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1745 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1746 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1747 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1748 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1749 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1750 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1751 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1752 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
1760 /*! \brief Return whether an end state with the given coupling-lambda
1761 * value describes fully-interacting VDW.
1763 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1764 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1766 static gmx_bool couple_lambda_has_vdw_on(int couple_lambda_value)
1768 return (couple_lambda_value == ecouplamVDW ||
1769 couple_lambda_value == ecouplamVDWQ);
1775 class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
1778 explicit MdpErrorHandler(warninp_t wi)
1779 : wi_(wi), mapping_(nullptr)
1783 void setBackMapping(const gmx::IKeyValueTreeBackMapping &mapping)
1785 mapping_ = &mapping;
1788 virtual bool onError(gmx::UserInputError *ex, const gmx::KeyValueTreePath &context)
1790 ex->prependContext(gmx::formatString("Error in mdp option \"%s\":",
1791 getOptionName(context).c_str()));
1792 std::string message = gmx::formatExceptionMessageToString(*ex);
1793 warning_error(wi_, message.c_str());
1798 std::string getOptionName(const gmx::KeyValueTreePath &context)
1800 if (mapping_ != nullptr)
1802 gmx::KeyValueTreePath path = mapping_->originalPath(context);
1803 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
1806 GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
1811 const gmx::IKeyValueTreeBackMapping *mapping_;
1816 void get_ir(const char *mdparin, const char *mdparout,
1817 gmx::MDModules *mdModules, t_inputrec *ir, t_gromppopts *opts,
1818 WriteMdpHeader writeMdpHeader, warninp_t wi)
1821 double dumdub[2][6];
1825 char warn_buf[STRLEN];
1826 t_lambda *fep = ir->fepvals;
1827 t_expanded *expand = ir->expandedvals;
1829 init_inputrec_strings();
1830 gmx::TextInputFile stream(mdparin);
1831 inp = read_inpfile(&stream, mdparin, &ninp, wi);
1833 snew(dumstr[0], STRLEN);
1834 snew(dumstr[1], STRLEN);
1836 if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
1839 "%s did not specify a value for the .mdp option "
1840 "\"cutoff-scheme\". Probably it was first intended for use "
1841 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1842 "introduced, but the group scheme was still the default. "
1843 "The default is now the Verlet scheme, so you will observe "
1844 "different behaviour.", mdparin);
1845 warning_note(wi, warn_buf);
1848 /* ignore the following deprecated commands */
1851 REM_TYPE("domain-decomposition");
1852 REM_TYPE("andersen-seed");
1854 REM_TYPE("dihre-fc");
1855 REM_TYPE("dihre-tau");
1856 REM_TYPE("nstdihreout");
1857 REM_TYPE("nstcheckpoint");
1858 REM_TYPE("optimize-fft");
1859 REM_TYPE("adress_type");
1860 REM_TYPE("adress_const_wf");
1861 REM_TYPE("adress_ex_width");
1862 REM_TYPE("adress_hy_width");
1863 REM_TYPE("adress_ex_forcecap");
1864 REM_TYPE("adress_interface_correction");
1865 REM_TYPE("adress_site");
1866 REM_TYPE("adress_reference_coords");
1867 REM_TYPE("adress_tf_grp_names");
1868 REM_TYPE("adress_cg_grp_names");
1869 REM_TYPE("adress_do_hybridpairs");
1870 REM_TYPE("rlistlong");
1871 REM_TYPE("nstcalclr");
1872 REM_TYPE("pull-print-com2");
1874 /* replace the following commands with the clearer new versions*/
1875 REPL_TYPE("unconstrained-start", "continuation");
1876 REPL_TYPE("foreign-lambda", "fep-lambdas");
1877 REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
1878 REPL_TYPE("nstxtcout", "nstxout-compressed");
1879 REPL_TYPE("xtc-grps", "compressed-x-grps");
1880 REPL_TYPE("xtc-precision", "compressed-x-precision");
1881 REPL_TYPE("pull-print-com1", "pull-print-com");
1883 CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
1884 CTYPE ("Preprocessor information: use cpp syntax.");
1885 CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
1886 STYPE ("include", opts->include, nullptr);
1887 CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1888 STYPE ("define", opts->define, nullptr);
1890 CCTYPE ("RUN CONTROL PARAMETERS");
1891 EETYPE("integrator", ir->eI, ei_names);
1892 CTYPE ("Start time and timestep in ps");
1893 RTYPE ("tinit", ir->init_t, 0.0);
1894 RTYPE ("dt", ir->delta_t, 0.001);
1895 STEPTYPE ("nsteps", ir->nsteps, 0);
1896 CTYPE ("For exact run continuation or redoing part of a run");
1897 STEPTYPE ("init-step", ir->init_step, 0);
1898 CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
1899 ITYPE ("simulation-part", ir->simulation_part, 1);
1900 CTYPE ("mode for center of mass motion removal");
1901 EETYPE("comm-mode", ir->comm_mode, ecm_names);
1902 CTYPE ("number of steps for center of mass motion removal");
1903 ITYPE ("nstcomm", ir->nstcomm, 100);
1904 CTYPE ("group(s) for center of mass motion removal");
1905 STYPE ("comm-grps", is->vcm, nullptr);
1907 CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
1908 CTYPE ("Friction coefficient (amu/ps) and random seed");
1909 RTYPE ("bd-fric", ir->bd_fric, 0.0);
1910 STEPTYPE ("ld-seed", ir->ld_seed, -1);
1913 CCTYPE ("ENERGY MINIMIZATION OPTIONS");
1914 CTYPE ("Force tolerance and initial step-size");
1915 RTYPE ("emtol", ir->em_tol, 10.0);
1916 RTYPE ("emstep", ir->em_stepsize, 0.01);
1917 CTYPE ("Max number of iterations in relax-shells");
1918 ITYPE ("niter", ir->niter, 20);
1919 CTYPE ("Step size (ps^2) for minimization of flexible constraints");
1920 RTYPE ("fcstep", ir->fc_stepsize, 0);
1921 CTYPE ("Frequency of steepest descents steps when doing CG");
1922 ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
1923 ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
1925 CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
1926 RTYPE ("rtpi", ir->rtpi, 0.05);
1928 /* Output options */
1929 CCTYPE ("OUTPUT CONTROL OPTIONS");
1930 CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
1931 ITYPE ("nstxout", ir->nstxout, 0);
1932 ITYPE ("nstvout", ir->nstvout, 0);
1933 ITYPE ("nstfout", ir->nstfout, 0);
1934 CTYPE ("Output frequency for energies to log file and energy file");
1935 ITYPE ("nstlog", ir->nstlog, 1000);
1936 ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
1937 ITYPE ("nstenergy", ir->nstenergy, 1000);
1938 CTYPE ("Output frequency and precision for .xtc file");
1939 ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
1940 RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
1941 CTYPE ("This selects the subset of atoms for the compressed");
1942 CTYPE ("trajectory file. You can select multiple groups. By");
1943 CTYPE ("default, all atoms will be written.");
1944 STYPE ("compressed-x-grps", is->x_compressed_groups, nullptr);
1945 CTYPE ("Selection of energy groups");
1946 STYPE ("energygrps", is->energy, nullptr);
1948 /* Neighbor searching */
1949 CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
1950 CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1951 EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
1952 CTYPE ("nblist update frequency");
1953 ITYPE ("nstlist", ir->nstlist, 10);
1954 CTYPE ("ns algorithm (simple or grid)");
1955 EETYPE("ns-type", ir->ns_type, ens_names);
1956 CTYPE ("Periodic boundary conditions: xyz, no, xy");
1957 EETYPE("pbc", ir->ePBC, epbc_names);
1958 EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
1959 CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1960 CTYPE ("a value of -1 means: use rlist");
1961 RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
1962 CTYPE ("nblist cut-off");
1963 RTYPE ("rlist", ir->rlist, 1.0);
1964 CTYPE ("long-range cut-off for switched potentials");
1966 /* Electrostatics */
1967 CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
1968 CTYPE ("Method for doing electrostatics");
1969 EETYPE("coulombtype", ir->coulombtype, eel_names);
1970 EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
1971 CTYPE ("cut-off lengths");
1972 RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
1973 RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
1974 CTYPE ("Relative dielectric constant for the medium and the reaction field");
1975 RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
1976 RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
1977 CTYPE ("Method for doing Van der Waals");
1978 EETYPE("vdw-type", ir->vdwtype, evdw_names);
1979 EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
1980 CTYPE ("cut-off lengths");
1981 RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
1982 RTYPE ("rvdw", ir->rvdw, 1.0);
1983 CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
1984 EETYPE("DispCorr", ir->eDispCorr, edispc_names);
1985 CTYPE ("Extension of the potential lookup tables beyond the cut-off");
1986 RTYPE ("table-extension", ir->tabext, 1.0);
1987 CTYPE ("Separate tables between energy group pairs");
1988 STYPE ("energygrp-table", is->egptable, nullptr);
1989 CTYPE ("Spacing for the PME/PPPM FFT grid");
1990 RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
1991 CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
1992 ITYPE ("fourier-nx", ir->nkx, 0);
1993 ITYPE ("fourier-ny", ir->nky, 0);
1994 ITYPE ("fourier-nz", ir->nkz, 0);
1995 CTYPE ("EWALD/PME/PPPM parameters");
1996 ITYPE ("pme-order", ir->pme_order, 4);
1997 RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
1998 RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
1999 EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
2000 EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
2001 RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
2003 CCTYPE("IMPLICIT SOLVENT ALGORITHM");
2004 EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
2006 CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
2007 CTYPE ("Algorithm for calculating Born radii");
2008 EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
2009 CTYPE ("Frequency of calculating the Born radii inside rlist");
2010 ITYPE ("nstgbradii", ir->nstgbradii, 1);
2011 CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
2012 CTYPE ("between rlist and rgbradii is updated every nstlist steps");
2013 RTYPE ("rgbradii", ir->rgbradii, 1.0);
2014 CTYPE ("Dielectric coefficient of the implicit solvent");
2015 RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
2016 CTYPE ("Salt concentration in M for Generalized Born models");
2017 RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
2018 CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
2019 RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
2020 RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
2021 RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
2022 RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
2023 EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
2024 CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
2025 CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
2026 RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
2028 /* Coupling stuff */
2029 CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
2030 CTYPE ("Temperature coupling");
2031 EETYPE("tcoupl", ir->etc, etcoupl_names);
2032 ITYPE ("nsttcouple", ir->nsttcouple, -1);
2033 ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
2034 EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
2035 CTYPE ("Groups to couple separately");
2036 STYPE ("tc-grps", is->tcgrps, nullptr);
2037 CTYPE ("Time constant (ps) and reference temperature (K)");
2038 STYPE ("tau-t", is->tau_t, nullptr);
2039 STYPE ("ref-t", is->ref_t, nullptr);
2040 CTYPE ("pressure coupling");
2041 EETYPE("pcoupl", ir->epc, epcoupl_names);
2042 EETYPE("pcoupltype", ir->epct, epcoupltype_names);
2043 ITYPE ("nstpcouple", ir->nstpcouple, -1);
2044 CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
2045 RTYPE ("tau-p", ir->tau_p, 1.0);
2046 STYPE ("compressibility", dumstr[0], nullptr);
2047 STYPE ("ref-p", dumstr[1], nullptr);
2048 CTYPE ("Scaling of reference coordinates, No, All or COM");
2049 EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
2052 CCTYPE ("OPTIONS FOR QMMM calculations");
2053 EETYPE("QMMM", ir->bQMMM, yesno_names);
2054 CTYPE ("Groups treated Quantum Mechanically");
2055 STYPE ("QMMM-grps", is->QMMM, nullptr);
2056 CTYPE ("QM method");
2057 STYPE("QMmethod", is->QMmethod, nullptr);
2058 CTYPE ("QMMM scheme");
2059 EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
2060 CTYPE ("QM basisset");
2061 STYPE("QMbasis", is->QMbasis, nullptr);
2062 CTYPE ("QM charge");
2063 STYPE ("QMcharge", is->QMcharge, nullptr);
2064 CTYPE ("QM multiplicity");
2065 STYPE ("QMmult", is->QMmult, nullptr);
2066 CTYPE ("Surface Hopping");
2067 STYPE ("SH", is->bSH, nullptr);
2068 CTYPE ("CAS space options");
2069 STYPE ("CASorbitals", is->CASorbitals, nullptr);
2070 STYPE ("CASelectrons", is->CASelectrons, nullptr);
2071 STYPE ("SAon", is->SAon, nullptr);
2072 STYPE ("SAoff", is->SAoff, nullptr);
2073 STYPE ("SAsteps", is->SAsteps, nullptr);
2074 CTYPE ("Scale factor for MM charges");
2075 RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
2076 CTYPE ("Optimization of QM subsystem");
2077 STYPE ("bOPT", is->bOPT, nullptr);
2078 STYPE ("bTS", is->bTS, nullptr);
2080 /* Simulated annealing */
2081 CCTYPE("SIMULATED ANNEALING");
2082 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
2083 STYPE ("annealing", is->anneal, nullptr);
2084 CTYPE ("Number of time points to use for specifying annealing in each group");
2085 STYPE ("annealing-npoints", is->anneal_npoints, nullptr);
2086 CTYPE ("List of times at the annealing points for each group");
2087 STYPE ("annealing-time", is->anneal_time, nullptr);
2088 CTYPE ("Temp. at each annealing point, for each group.");
2089 STYPE ("annealing-temp", is->anneal_temp, nullptr);
2092 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
2093 EETYPE("gen-vel", opts->bGenVel, yesno_names);
2094 RTYPE ("gen-temp", opts->tempi, 300.0);
2095 ITYPE ("gen-seed", opts->seed, -1);
2098 CCTYPE ("OPTIONS FOR BONDS");
2099 EETYPE("constraints", opts->nshake, constraints);
2100 CTYPE ("Type of constraint algorithm");
2101 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
2102 CTYPE ("Do not constrain the start configuration");
2103 EETYPE("continuation", ir->bContinuation, yesno_names);
2104 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
2105 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
2106 CTYPE ("Relative tolerance of shake");
2107 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
2108 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
2109 ITYPE ("lincs-order", ir->nProjOrder, 4);
2110 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
2111 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
2112 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
2113 ITYPE ("lincs-iter", ir->nLincsIter, 1);
2114 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
2115 CTYPE ("rotates over more degrees than");
2116 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
2117 CTYPE ("Convert harmonic bonds to morse potentials");
2118 EETYPE("morse", opts->bMorse, yesno_names);
2120 /* Energy group exclusions */
2121 CCTYPE ("ENERGY GROUP EXCLUSIONS");
2122 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
2123 STYPE ("energygrp-excl", is->egpexcl, nullptr);
2127 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2128 ITYPE ("nwall", ir->nwall, 0);
2129 EETYPE("wall-type", ir->wall_type, ewt_names);
2130 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
2131 STYPE ("wall-atomtype", is->wall_atomtype, nullptr);
2132 STYPE ("wall-density", is->wall_density, nullptr);
2133 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
2136 CCTYPE("COM PULLING");
2137 EETYPE("pull", ir->bPull, yesno_names);
2141 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, wi);
2144 /* Enforced rotation */
2145 CCTYPE("ENFORCED ROTATION");
2146 CTYPE("Enforced rotation: No or Yes");
2147 EETYPE("rotation", ir->bRot, yesno_names);
2151 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2154 /* Interactive MD */
2156 CCTYPE("Group to display and/or manipulate in interactive MD session");
2157 STYPE ("IMD-group", is->imd_grp, nullptr);
2158 if (is->imd_grp[0] != '\0')
2165 CCTYPE("NMR refinement stuff");
2166 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2167 EETYPE("disre", ir->eDisre, edisre_names);
2168 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2169 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2170 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2171 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2172 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2173 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2174 CTYPE ("Output frequency for pair distances to energy file");
2175 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2176 CTYPE ("Orientation restraints: No or Yes");
2177 EETYPE("orire", opts->bOrire, yesno_names);
2178 CTYPE ("Orientation restraints force constant and tau for time averaging");
2179 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2180 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2181 STYPE ("orire-fitgrp", is->orirefitgrp, nullptr);
2182 CTYPE ("Output frequency for trace(SD) and S to energy file");
2183 ITYPE ("nstorireout", ir->nstorireout, 100);
2185 /* free energy variables */
2186 CCTYPE ("Free energy variables");
2187 EETYPE("free-energy", ir->efep, efep_names);
2188 STYPE ("couple-moltype", is->couple_moltype, nullptr);
2189 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2190 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2191 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2193 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2195 it was not entered */
2196 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2197 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2198 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2199 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], nullptr);
2200 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], nullptr);
2201 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], nullptr);
2202 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], nullptr);
2203 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], nullptr);
2204 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], nullptr);
2205 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], nullptr);
2206 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2207 STYPE ("init-lambda-weights", is->lambda_weights, nullptr);
2208 EETYPE("dhdl-print-energy", fep->edHdLPrintEnergy, edHdLPrintEnergy_names);
2209 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2210 ITYPE ("sc-power", fep->sc_power, 1);
2211 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2212 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2213 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2214 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2215 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2216 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2217 separate_dhdl_file_names);
2218 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2219 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2220 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2222 /* Non-equilibrium MD stuff */
2223 CCTYPE("Non-equilibrium MD stuff");
2224 STYPE ("acc-grps", is->accgrps, nullptr);
2225 STYPE ("accelerate", is->acc, nullptr);
2226 STYPE ("freezegrps", is->freeze, nullptr);
2227 STYPE ("freezedim", is->frdim, nullptr);
2228 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2229 STYPE ("deform", is->deform, nullptr);
2231 /* simulated tempering variables */
2232 CCTYPE("simulated tempering variables");
2233 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2234 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2235 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2236 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2238 /* expanded ensemble variables */
2239 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2241 read_expandedparams(&ninp, &inp, expand, wi);
2244 /* Electric fields */
2246 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(ninp, inp);
2247 gmx::KeyValueTreeTransformer transform;
2248 transform.rules()->addRule()
2249 .keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2250 mdModules->initMdpTransform(transform.rules());
2251 for (const auto &path : transform.mappedPaths())
2253 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2254 mark_einp_set(ninp, inp, path[0].c_str());
2256 MdpErrorHandler errorHandler(wi);
2258 = transform.transform(convertedValues, &errorHandler);
2259 ir->params = new gmx::KeyValueTreeObject(result.object());
2260 mdModules->adjustInputrecBasedOnModules(ir);
2261 errorHandler.setBackMapping(result.backMapping());
2262 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2265 /* Ion/water position swapping ("computational electrophysiology") */
2266 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2267 CTYPE("Swap positions along direction: no, X, Y, Z");
2268 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2269 if (ir->eSwapCoords != eswapNO)
2276 CTYPE("Swap attempt frequency");
2277 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2278 CTYPE("Number of ion types to be controlled");
2279 ITYPE("iontypes", nIonTypes, 1);
2282 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2284 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2285 snew(ir->swap->grp, ir->swap->ngrp);
2286 for (i = 0; i < ir->swap->ngrp; i++)
2288 snew(ir->swap->grp[i].molname, STRLEN);
2290 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2291 STYPE("split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2292 STYPE("split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2293 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2294 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2295 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2297 CTYPE("Name of solvent molecules");
2298 STYPE("solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2300 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2301 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2302 CTYPE("however, if correctly defined, the permeation events are recorded per channel");
2303 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2304 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2305 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2306 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2307 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2308 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2310 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2311 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2313 CTYPE("Names of the ion types that can be exchanged with solvent molecules,");
2314 CTYPE("and the requested number of ions of this type in compartments A and B");
2315 CTYPE("-1 means fix the numbers as found in step 0");
2316 for (i = 0; i < nIonTypes; i++)
2318 int ig = eSwapFixedGrpNR + i;
2320 sprintf(buf, "iontype%d-name", i);
2321 STYPE(buf, ir->swap->grp[ig].molname, nullptr);
2322 sprintf(buf, "iontype%d-in-A", i);
2323 ITYPE(buf, ir->swap->grp[ig].nmolReq[0], -1);
2324 sprintf(buf, "iontype%d-in-B", i);
2325 ITYPE(buf, ir->swap->grp[ig].nmolReq[1], -1);
2328 CTYPE("By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2329 CTYPE("at maximum distance (= bulk concentration) to the split group layers. However,");
2330 CTYPE("an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0");
2331 CTYPE("towards one of the compartment-partitioning layers (at +/- 1.0).");
2332 RTYPE("bulk-offsetA", ir->swap->bulkOffset[0], 0.0);
2333 RTYPE("bulk-offsetB", ir->swap->bulkOffset[1], 0.0);
2334 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2335 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0) )
2337 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2340 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2341 RTYPE("threshold", ir->swap->threshold, 1.0);
2344 /* AdResS is no longer supported, but we need mdrun to be able to refuse to run old AdResS .tpr files */
2345 EETYPE("adress", ir->bAdress, yesno_names);
2347 /* User defined thingies */
2348 CCTYPE ("User defined thingies");
2349 STYPE ("user1-grps", is->user1, nullptr);
2350 STYPE ("user2-grps", is->user2, nullptr);
2351 ITYPE ("userint1", ir->userint1, 0);
2352 ITYPE ("userint2", ir->userint2, 0);
2353 ITYPE ("userint3", ir->userint3, 0);
2354 ITYPE ("userint4", ir->userint4, 0);
2355 RTYPE ("userreal1", ir->userreal1, 0);
2356 RTYPE ("userreal2", ir->userreal2, 0);
2357 RTYPE ("userreal3", ir->userreal3, 0);
2358 RTYPE ("userreal4", ir->userreal4, 0);
2362 gmx::TextOutputFile stream(mdparout);
2363 write_inpfile(&stream, mdparout, ninp, inp, FALSE, writeMdpHeader, wi);
2365 // Transform module data into a flat key-value tree for output.
2366 gmx::KeyValueTreeBuilder builder;
2367 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2368 mdModules->buildMdpOutput(&builderObject);
2370 gmx::TextWriter writer(&stream);
2371 writeKeyValueTreeAsMdp(&writer, builder.build());
2376 for (i = 0; (i < ninp); i++)
2379 sfree(inp[i].value);
2383 /* Process options if necessary */
2384 for (m = 0; m < 2; m++)
2386 for (i = 0; i < 2*DIM; i++)
2395 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2397 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 1)");
2399 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2401 case epctSEMIISOTROPIC:
2402 case epctSURFACETENSION:
2403 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2405 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 2)");
2407 dumdub[m][YY] = dumdub[m][XX];
2409 case epctANISOTROPIC:
2410 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2411 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2412 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2414 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 6)");
2418 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2419 epcoupltype_names[ir->epct]);
2423 clear_mat(ir->ref_p);
2424 clear_mat(ir->compress);
2425 for (i = 0; i < DIM; i++)
2427 ir->ref_p[i][i] = dumdub[1][i];
2428 ir->compress[i][i] = dumdub[0][i];
2430 if (ir->epct == epctANISOTROPIC)
2432 ir->ref_p[XX][YY] = dumdub[1][3];
2433 ir->ref_p[XX][ZZ] = dumdub[1][4];
2434 ir->ref_p[YY][ZZ] = dumdub[1][5];
2435 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2437 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2439 ir->compress[XX][YY] = dumdub[0][3];
2440 ir->compress[XX][ZZ] = dumdub[0][4];
2441 ir->compress[YY][ZZ] = dumdub[0][5];
2442 for (i = 0; i < DIM; i++)
2444 for (m = 0; m < i; m++)
2446 ir->ref_p[i][m] = ir->ref_p[m][i];
2447 ir->compress[i][m] = ir->compress[m][i];
2452 if (ir->comm_mode == ecmNO)
2457 opts->couple_moltype = nullptr;
2458 if (strlen(is->couple_moltype) > 0)
2460 if (ir->efep != efepNO)
2462 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2463 if (opts->couple_lam0 == opts->couple_lam1)
2465 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2467 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2468 opts->couple_lam1 == ecouplamNONE))
2470 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2475 warning_note(wi, "Free energy is turned off, so we will not decouple the molecule listed in your input.");
2478 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2479 if (ir->efep != efepNO)
2481 if (fep->delta_lambda > 0)
2483 ir->efep = efepSLOWGROWTH;
2487 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2489 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2490 warning_note(wi, "Old option for dhdl-print-energy given: "
2491 "changing \"yes\" to \"total\"\n");
2494 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2496 /* always print out the energy to dhdl if we are doing
2497 expanded ensemble, since we need the total energy for
2498 analysis if the temperature is changing. In some
2499 conditions one may only want the potential energy, so
2500 we will allow that if the appropriate mdp setting has
2501 been enabled. Otherwise, total it is:
2503 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2506 if ((ir->efep != efepNO) || ir->bSimTemp)
2508 ir->bExpanded = FALSE;
2509 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2511 ir->bExpanded = TRUE;
2513 do_fep_params(ir, is->fep_lambda, is->lambda_weights, wi);
2514 if (ir->bSimTemp) /* done after fep params */
2516 do_simtemp_params(ir);
2519 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2520 * setup and not on the old way of specifying the free-energy setup,
2521 * we should check for using soft-core when not needed, since that
2522 * can complicate the sampling significantly.
2523 * Note that we only check for the automated coupling setup.
2524 * If the (advanced) user does FEP through manual topology changes,
2525 * this check will not be triggered.
2527 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 &&
2528 ir->fepvals->sc_alpha != 0 &&
2529 (couple_lambda_has_vdw_on(opts->couple_lam0) &&
2530 couple_lambda_has_vdw_on(opts->couple_lam1)))
2532 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.");
2537 ir->fepvals->n_lambda = 0;
2540 /* WALL PARAMETERS */
2542 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2544 /* ORIENTATION RESTRAINT PARAMETERS */
2546 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, nullptr) != 1)
2548 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2551 /* DEFORMATION PARAMETERS */
2553 clear_mat(ir->deform);
2554 for (i = 0; i < 6; i++)
2559 double gmx_unused canary;
2560 int ndeform = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf %lf",
2561 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2562 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]), &canary);
2564 if (strlen(is->deform) > 0 && ndeform != 6)
2566 warning_error(wi, gmx::formatString("Cannot parse exactly 6 box deformation velocities from string '%s'", is->deform).c_str());
2568 for (i = 0; i < 3; i++)
2570 ir->deform[i][i] = dumdub[0][i];
2572 ir->deform[YY][XX] = dumdub[0][3];
2573 ir->deform[ZZ][XX] = dumdub[0][4];
2574 ir->deform[ZZ][YY] = dumdub[0][5];
2575 if (ir->epc != epcNO)
2577 for (i = 0; i < 3; i++)
2579 for (j = 0; j <= i; j++)
2581 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2583 warning_error(wi, "A box element has deform set and compressibility > 0");
2587 for (i = 0; i < 3; i++)
2589 for (j = 0; j < i; j++)
2591 if (ir->deform[i][j] != 0)
2593 for (m = j; m < DIM; m++)
2595 if (ir->compress[m][j] != 0)
2597 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.");
2598 warning(wi, warn_buf);
2606 /* Ion/water position swapping checks */
2607 if (ir->eSwapCoords != eswapNO)
2609 if (ir->swap->nstswap < 1)
2611 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2613 if (ir->swap->nAverage < 1)
2615 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2617 if (ir->swap->threshold < 1.0)
2619 warning_error(wi, "Ion count threshold must be at least 1.\n");
2627 static int search_QMstring(const char *s, int ng, const char *gn[])
2629 /* same as normal search_string, but this one searches QM strings */
2632 for (i = 0; (i < ng); i++)
2634 if (gmx_strcasecmp(s, gn[i]) == 0)
2640 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2644 } /* search_QMstring */
2646 /* We would like gn to be const as well, but C doesn't allow this */
2647 /* TODO this is utility functionality (search for the index of a
2648 string in a collection), so should be refactored and located more
2650 int search_string(const char *s, int ng, char *gn[])
2654 for (i = 0; (i < ng); i++)
2656 if (gmx_strcasecmp(s, gn[i]) == 0)
2663 "Group %s referenced in the .mdp file was not found in the index file.\n"
2664 "Group names must match either [moleculetype] names or custom index group\n"
2665 "names, in which case you must supply an index file to the '-n' option\n"
2672 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2673 t_blocka *block, char *gnames[],
2674 int gtype, int restnm,
2675 int grptp, gmx_bool bVerbose,
2678 unsigned short *cbuf;
2679 t_grps *grps = &(groups->grps[gtype]);
2680 int i, j, gid, aj, ognr, ntot = 0;
2683 char warn_buf[STRLEN];
2687 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2690 title = gtypes[gtype];
2693 /* Mark all id's as not set */
2694 for (i = 0; (i < natoms); i++)
2699 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2700 for (i = 0; (i < ng); i++)
2702 /* Lookup the group name in the block structure */
2703 gid = search_string(ptrs[i], block->nr, gnames);
2704 if ((grptp != egrptpONE) || (i == 0))
2706 grps->nm_ind[grps->nr++] = gid;
2710 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2713 /* Now go over the atoms in the group */
2714 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2719 /* Range checking */
2720 if ((aj < 0) || (aj >= natoms))
2722 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2724 /* Lookup up the old group number */
2728 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2729 aj+1, title, ognr+1, i+1);
2733 /* Store the group number in buffer */
2734 if (grptp == egrptpONE)
2747 /* Now check whether we have done all atoms */
2751 if (grptp == egrptpALL)
2753 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2754 natoms-ntot, title);
2756 else if (grptp == egrptpPART)
2758 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2759 natoms-ntot, title);
2760 warning_note(wi, warn_buf);
2762 /* Assign all atoms currently unassigned to a rest group */
2763 for (j = 0; (j < natoms); j++)
2765 if (cbuf[j] == NOGID)
2771 if (grptp != egrptpPART)
2776 "Making dummy/rest group for %s containing %d elements\n",
2777 title, natoms-ntot);
2779 /* Add group name "rest" */
2780 grps->nm_ind[grps->nr] = restnm;
2782 /* Assign the rest name to all atoms not currently assigned to a group */
2783 for (j = 0; (j < natoms); j++)
2785 if (cbuf[j] == NOGID)
2794 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2796 /* All atoms are part of one (or no) group, no index required */
2797 groups->ngrpnr[gtype] = 0;
2798 groups->grpnr[gtype] = nullptr;
2802 groups->ngrpnr[gtype] = natoms;
2803 snew(groups->grpnr[gtype], natoms);
2804 for (j = 0; (j < natoms); j++)
2806 groups->grpnr[gtype][j] = cbuf[j];
2812 return (bRest && grptp == egrptpPART);
2815 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2818 gmx_groups_t *groups;
2819 pull_params_t *pull;
2820 int natoms, ai, aj, i, j, d, g, imin, jmin;
2822 int *nrdf2, *na_vcm, na_tot;
2823 double *nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2825 gmx_mtop_atomloop_all_t aloop;
2826 int mb, mol, ftype, as;
2827 gmx_molblock_t *molb;
2828 gmx_moltype_t *molt;
2831 * First calc 3xnr-atoms for each group
2832 * then subtract half a degree of freedom for each constraint
2834 * Only atoms and nuclei contribute to the degrees of freedom...
2839 groups = &mtop->groups;
2840 natoms = mtop->natoms;
2842 /* Allocate one more for a possible rest group */
2843 /* We need to sum degrees of freedom into doubles,
2844 * since floats give too low nrdf's above 3 million atoms.
2846 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2847 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2848 snew(dof_vcm, groups->grps[egcVCM].nr+1);
2849 snew(na_vcm, groups->grps[egcVCM].nr+1);
2850 snew(nrdf_vcm_sub, groups->grps[egcVCM].nr+1);
2852 for (i = 0; i < groups->grps[egcTC].nr; i++)
2856 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2859 clear_ivec(dof_vcm[i]);
2861 nrdf_vcm_sub[i] = 0;
2864 snew(nrdf2, natoms);
2865 aloop = gmx_mtop_atomloop_all_init(mtop);
2867 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2870 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2872 g = ggrpnr(groups, egcFREEZE, i);
2873 for (d = 0; d < DIM; d++)
2875 if (opts->nFreeze[g][d] == 0)
2877 /* Add one DOF for particle i (counted as 2*1) */
2879 /* VCM group i has dim d as a DOF */
2880 dof_vcm[ggrpnr(groups, egcVCM, i)][d] = 1;
2883 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2884 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2889 for (mb = 0; mb < mtop->nmolblock; mb++)
2891 molb = &mtop->molblock[mb];
2892 molt = &mtop->moltype[molb->type];
2893 atom = molt->atoms.atom;
2894 for (mol = 0; mol < molb->nmol; mol++)
2896 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2898 ia = molt->ilist[ftype].iatoms;
2899 for (i = 0; i < molt->ilist[ftype].nr; )
2901 /* Subtract degrees of freedom for the constraints,
2902 * if the particles still have degrees of freedom left.
2903 * If one of the particles is a vsite or a shell, then all
2904 * constraint motion will go there, but since they do not
2905 * contribute to the constraints the degrees of freedom do not
2910 if (((atom[ia[1]].ptype == eptNucleus) ||
2911 (atom[ia[1]].ptype == eptAtom)) &&
2912 ((atom[ia[2]].ptype == eptNucleus) ||
2913 (atom[ia[2]].ptype == eptAtom)))
2931 imin = std::min(imin, nrdf2[ai]);
2932 jmin = std::min(jmin, nrdf2[aj]);
2935 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2936 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2937 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2938 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2940 ia += interaction_function[ftype].nratoms+1;
2941 i += interaction_function[ftype].nratoms+1;
2944 ia = molt->ilist[F_SETTLE].iatoms;
2945 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2947 /* Subtract 1 dof from every atom in the SETTLE */
2948 for (j = 0; j < 3; j++)
2951 imin = std::min(2, nrdf2[ai]);
2953 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2954 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2959 as += molt->atoms.nr;
2965 /* Correct nrdf for the COM constraints.
2966 * We correct using the TC and VCM group of the first atom
2967 * in the reference and pull group. If atoms in one pull group
2968 * belong to different TC or VCM groups it is anyhow difficult
2969 * to determine the optimal nrdf assignment.
2973 for (i = 0; i < pull->ncoord; i++)
2975 if (pull->coord[i].eType != epullCONSTRAINT)
2982 for (j = 0; j < 2; j++)
2984 const t_pull_group *pgrp;
2986 pgrp = &pull->group[pull->coord[i].group[j]];
2990 /* Subtract 1/2 dof from each group */
2992 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2993 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2994 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2996 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)]]);
3001 /* We need to subtract the whole DOF from group j=1 */
3008 if (ir->nstcomm != 0)
3012 /* We remove COM motion up to dim ndof_com() */
3013 ndim_rm_vcm = ndof_com(ir);
3015 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3016 * the number of degrees of freedom in each vcm group when COM
3017 * translation is removed and 6 when rotation is removed as well.
3019 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
3021 switch (ir->comm_mode)
3024 nrdf_vcm_sub[j] = 0;
3025 for (d = 0; d < ndim_rm_vcm; d++)
3034 nrdf_vcm_sub[j] = 6;
3037 gmx_incons("Checking comm_mode");
3041 for (i = 0; i < groups->grps[egcTC].nr; i++)
3043 /* Count the number of atoms of TC group i for every VCM group */
3044 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
3049 for (ai = 0; ai < natoms; ai++)
3051 if (ggrpnr(groups, egcTC, ai) == i)
3053 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
3057 /* Correct for VCM removal according to the fraction of each VCM
3058 * group present in this TC group.
3060 nrdf_uc = nrdf_tc[i];
3063 fprintf(debug, "T-group[%d] nrdf_uc = %g\n", i, nrdf_uc);
3066 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
3068 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3070 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
3071 (nrdf_vcm[j] - nrdf_vcm_sub[j])/nrdf_vcm[j];
3075 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
3076 j, nrdf_vcm[j], nrdf_tc[i]);
3081 for (i = 0; (i < groups->grps[egcTC].nr); i++)
3083 opts->nrdf[i] = nrdf_tc[i];
3084 if (opts->nrdf[i] < 0)
3089 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3090 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
3098 sfree(nrdf_vcm_sub);
3101 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
3102 const char *option, const char *val, int flag)
3104 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3105 * But since this is much larger than STRLEN, such a line can not be parsed.
3106 * The real maximum is the number of names that fit in a string: STRLEN/2.
3108 #define EGP_MAX (STRLEN/2)
3109 int nelem, i, j, k, nr;
3110 char *names[EGP_MAX];
3114 gnames = groups->grpname;
3116 nelem = str_nelem(val, EGP_MAX, names);
3119 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3121 nr = groups->grps[egcENER].nr;
3123 for (i = 0; i < nelem/2; i++)
3127 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
3133 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3134 names[2*i], option);
3138 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
3144 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3145 names[2*i+1], option);
3147 if ((j < nr) && (k < nr))
3149 ir->opts.egp_flags[nr*j+k] |= flag;
3150 ir->opts.egp_flags[nr*k+j] |= flag;
3159 static void make_swap_groups(
3164 int ig = -1, i = 0, gind;
3168 /* Just a quick check here, more thorough checks are in mdrun */
3169 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3171 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3174 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3175 for (ig = 0; ig < swap->ngrp; ig++)
3177 swapg = &swap->grp[ig];
3178 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3179 swapg->nat = grps->index[gind+1] - grps->index[gind];
3183 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3184 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap",
3185 swap->grp[ig].molname, swapg->nat);
3186 snew(swapg->ind, swapg->nat);
3187 for (i = 0; i < swapg->nat; i++)
3189 swapg->ind[i] = grps->a[grps->index[gind]+i];
3194 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3200 static void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3205 ig = search_string(IMDgname, grps->nr, gnames);
3206 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3208 if (IMDgroup->nat > 0)
3210 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3211 IMDgname, IMDgroup->nat);
3212 snew(IMDgroup->ind, IMDgroup->nat);
3213 for (i = 0; i < IMDgroup->nat; i++)
3215 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3221 void do_index(const char* mdparin, const char *ndx,
3228 gmx_groups_t *groups;
3232 char warnbuf[STRLEN], **gnames;
3233 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3236 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3237 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3238 int i, j, k, restnm;
3239 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3240 int nQMmethod, nQMbasis, nQMg;
3241 char warn_buf[STRLEN];
3246 fprintf(stderr, "processing index file...\n");
3251 snew(grps->index, 1);
3253 atoms_all = gmx_mtop_global_atoms(mtop);
3254 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3255 done_atom(&atoms_all);
3259 grps = init_index(ndx, &gnames);
3262 groups = &mtop->groups;
3263 natoms = mtop->natoms;
3264 symtab = &mtop->symtab;
3266 snew(groups->grpname, grps->nr+1);
3268 for (i = 0; (i < grps->nr); i++)
3270 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3272 groups->grpname[i] = put_symtab(symtab, "rest");
3274 srenew(gnames, grps->nr+1);
3275 gnames[restnm] = *(groups->grpname[i]);
3276 groups->ngrpname = grps->nr+1;
3278 set_warning_line(wi, mdparin, -1);
3280 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3281 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3282 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3283 if ((ntau_t != ntcg) || (nref_t != ntcg))
3285 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3286 "%d tau-t values", ntcg, nref_t, ntau_t);
3289 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3290 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3291 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3292 nr = groups->grps[egcTC].nr;
3294 snew(ir->opts.nrdf, nr);
3295 snew(ir->opts.tau_t, nr);
3296 snew(ir->opts.ref_t, nr);
3297 if (ir->eI == eiBD && ir->bd_fric == 0)
3299 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3306 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3310 for (i = 0; (i < nr); i++)
3312 ir->opts.tau_t[i] = strtod(ptr1[i], &endptr);
3315 warning_error(wi, "Invalid value for mdp option tau-t. tau-t should only consist of real numbers separated by spaces.");
3317 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3319 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3320 warning_error(wi, warn_buf);
3323 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3325 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.");
3328 if (ir->opts.tau_t[i] >= 0)
3330 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3333 if (ir->etc != etcNO && ir->nsttcouple == -1)
3335 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3340 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3342 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");
3344 if (ir->epc == epcMTTK)
3346 if (ir->etc != etcNOSEHOOVER)
3348 gmx_fatal(FARGS, "Cannot do MTTK pressure coupling without Nose-Hoover temperature control");
3352 if (ir->nstpcouple != ir->nsttcouple)
3354 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3355 ir->nstpcouple = ir->nsttcouple = mincouple;
3356 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);
3357 warning_note(wi, warn_buf);
3362 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3363 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3365 if (ETC_ANDERSEN(ir->etc))
3367 if (ir->nsttcouple != 1)
3370 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");
3371 warning_note(wi, warn_buf);
3374 nstcmin = tcouple_min_integration_steps(ir->etc);
3377 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin - 10*GMX_REAL_EPS)
3379 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3380 ETCOUPLTYPE(ir->etc),
3382 ir->nsttcouple*ir->delta_t);
3383 warning(wi, warn_buf);
3386 for (i = 0; (i < nr); i++)
3388 ir->opts.ref_t[i] = strtod(ptr2[i], &endptr);
3391 warning_error(wi, "Invalid value for mdp option ref-t. ref-t should only consist of real numbers separated by spaces.");
3393 if (ir->opts.ref_t[i] < 0)
3395 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3398 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3399 if we are in this conditional) if mc_temp is negative */
3400 if (ir->expandedvals->mc_temp < 0)
3402 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3406 /* Simulated annealing for each group. There are nr groups */
3407 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3408 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3412 if (nSA > 0 && nSA != nr)
3414 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3418 snew(ir->opts.annealing, nr);
3419 snew(ir->opts.anneal_npoints, nr);
3420 snew(ir->opts.anneal_time, nr);
3421 snew(ir->opts.anneal_temp, nr);
3422 for (i = 0; i < nr; i++)
3424 ir->opts.annealing[i] = eannNO;
3425 ir->opts.anneal_npoints[i] = 0;
3426 ir->opts.anneal_time[i] = nullptr;
3427 ir->opts.anneal_temp[i] = nullptr;
3432 for (i = 0; i < nr; i++)
3434 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3436 ir->opts.annealing[i] = eannNO;
3438 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3440 ir->opts.annealing[i] = eannSINGLE;
3443 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3445 ir->opts.annealing[i] = eannPERIODIC;
3451 /* Read the other fields too */
3452 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3453 if (nSA_points != nSA)
3455 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3457 for (k = 0, i = 0; i < nr; i++)
3459 ir->opts.anneal_npoints[i] = strtol(ptr1[i], &endptr, 10);
3462 warning_error(wi, "Invalid value for mdp option annealing-npoints. annealing should only consist of integers separated by spaces.");
3464 if (ir->opts.anneal_npoints[i] == 1)
3466 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3468 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3469 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3470 k += ir->opts.anneal_npoints[i];
3473 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3476 gmx_fatal(FARGS, "Found %d annealing-time values, wanted %d\n", nSA_time, k);
3478 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3481 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3484 for (i = 0, k = 0; i < nr; i++)
3487 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3489 ir->opts.anneal_time[i][j] = strtod(ptr1[k], &endptr);
3492 warning_error(wi, "Invalid value for mdp option anneal-time. anneal-time should only consist of real numbers separated by spaces.");
3494 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], &endptr);
3497 warning_error(wi, "Invalid value for anneal-temp. anneal-temp should only consist of real numbers separated by spaces.");
3501 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3503 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3509 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3511 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3512 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3515 if (ir->opts.anneal_temp[i][j] < 0)
3517 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3522 /* Print out some summary information, to make sure we got it right */
3523 for (i = 0, k = 0; i < nr; i++)
3525 if (ir->opts.annealing[i] != eannNO)
3527 j = groups->grps[egcTC].nm_ind[i];
3528 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3529 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3530 ir->opts.anneal_npoints[i]);
3531 fprintf(stderr, "Time (ps) Temperature (K)\n");
3532 /* All terms except the last one */
3533 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3535 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3538 /* Finally the last one */
3539 j = ir->opts.anneal_npoints[i]-1;
3540 if (ir->opts.annealing[i] == eannSINGLE)
3542 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3546 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3547 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3549 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3560 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3562 make_pull_coords(ir->pull);
3567 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3570 if (ir->eSwapCoords != eswapNO)
3572 make_swap_groups(ir->swap, grps, gnames);
3575 /* Make indices for IMD session */
3578 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3581 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3582 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3583 if (nacg*DIM != nacc)
3585 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3588 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3589 restnm, egrptpALL_GENREST, bVerbose, wi);
3590 nr = groups->grps[egcACC].nr;
3591 snew(ir->opts.acc, nr);
3592 ir->opts.ngacc = nr;
3594 for (i = k = 0; (i < nacg); i++)
3596 for (j = 0; (j < DIM); j++, k++)
3598 ir->opts.acc[i][j] = strtod(ptr1[k], &endptr);
3601 warning_error(wi, "Invalid value for mdp option accelerate. accelerate should only consist of real numbers separated by spaces.");
3605 for (; (i < nr); i++)
3607 for (j = 0; (j < DIM); j++)
3609 ir->opts.acc[i][j] = 0;
3613 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3614 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3615 if (nfrdim != DIM*nfreeze)
3617 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3620 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3621 restnm, egrptpALL_GENREST, bVerbose, wi);
3622 nr = groups->grps[egcFREEZE].nr;
3623 ir->opts.ngfrz = nr;
3624 snew(ir->opts.nFreeze, nr);
3625 for (i = k = 0; (i < nfreeze); i++)
3627 for (j = 0; (j < DIM); j++, k++)
3629 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3630 if (!ir->opts.nFreeze[i][j])
3632 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3634 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3635 "(not %s)", ptr1[k]);
3636 warning(wi, warn_buf);
3641 for (; (i < nr); i++)
3643 for (j = 0; (j < DIM); j++)
3645 ir->opts.nFreeze[i][j] = 0;
3649 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3650 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3651 restnm, egrptpALL_GENREST, bVerbose, wi);
3652 add_wall_energrps(groups, ir->nwall, symtab);
3653 ir->opts.ngener = groups->grps[egcENER].nr;
3654 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3656 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3657 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3660 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3661 "This may lead to artifacts.\n"
3662 "In most cases one should use one group for the whole system.");
3665 /* Now we have filled the freeze struct, so we can calculate NRDF */
3666 calc_nrdf(mtop, ir, gnames);
3668 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3669 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3670 restnm, egrptpALL_GENREST, bVerbose, wi);
3671 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3672 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3673 restnm, egrptpALL_GENREST, bVerbose, wi);
3674 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3675 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3676 restnm, egrptpONE, bVerbose, wi);
3677 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3678 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3679 restnm, egrptpALL_GENREST, bVerbose, wi);
3681 /* QMMM input processing */
3682 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3683 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3684 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3685 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3687 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3688 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3690 /* group rest, if any, is always MM! */
3691 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3692 restnm, egrptpALL_GENREST, bVerbose, wi);
3693 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3694 ir->opts.ngQM = nQMg;
3695 snew(ir->opts.QMmethod, nr);
3696 snew(ir->opts.QMbasis, nr);
3697 for (i = 0; i < nr; i++)
3699 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3700 * converted to the corresponding enum in names.c
3702 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3704 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3708 str_nelem(is->QMmult, MAXPTR, ptr1);
3709 str_nelem(is->QMcharge, MAXPTR, ptr2);
3710 str_nelem(is->bSH, MAXPTR, ptr3);
3711 snew(ir->opts.QMmult, nr);
3712 snew(ir->opts.QMcharge, nr);
3713 snew(ir->opts.bSH, nr);
3715 for (i = 0; i < nr; i++)
3717 ir->opts.QMmult[i] = strtol(ptr1[i], &endptr, 10);
3720 warning_error(wi, "Invalid value for mdp option QMmult. QMmult should only consist of integers separated by spaces.");
3722 ir->opts.QMcharge[i] = strtol(ptr2[i], &endptr, 10);
3725 warning_error(wi, "Invalid value for mdp option QMcharge. QMcharge should only consist of integers separated by spaces.");
3727 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3730 str_nelem(is->CASelectrons, MAXPTR, ptr1);
3731 str_nelem(is->CASorbitals, MAXPTR, ptr2);
3732 snew(ir->opts.CASelectrons, nr);
3733 snew(ir->opts.CASorbitals, nr);
3734 for (i = 0; i < nr; i++)
3736 ir->opts.CASelectrons[i] = strtol(ptr1[i], &endptr, 10);
3739 warning_error(wi, "Invalid value for mdp option CASelectrons. CASelectrons should only consist of integers separated by spaces.");
3741 ir->opts.CASorbitals[i] = strtol(ptr2[i], &endptr, 10);
3744 warning_error(wi, "Invalid value for mdp option CASorbitals. CASorbitals should only consist of integers separated by spaces.");
3747 /* special optimization options */
3749 str_nelem(is->bOPT, MAXPTR, ptr1);
3750 str_nelem(is->bTS, MAXPTR, ptr2);
3751 snew(ir->opts.bOPT, nr);
3752 snew(ir->opts.bTS, nr);
3753 for (i = 0; i < nr; i++)
3755 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3756 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3758 str_nelem(is->SAon, MAXPTR, ptr1);
3759 str_nelem(is->SAoff, MAXPTR, ptr2);
3760 str_nelem(is->SAsteps, MAXPTR, ptr3);
3761 snew(ir->opts.SAon, nr);
3762 snew(ir->opts.SAoff, nr);
3763 snew(ir->opts.SAsteps, nr);
3765 for (i = 0; i < nr; i++)
3767 ir->opts.SAon[i] = strtod(ptr1[i], &endptr);
3770 warning_error(wi, "Invalid value for mdp option SAon. SAon should only consist of real numbers separated by spaces.");
3772 ir->opts.SAoff[i] = strtod(ptr2[i], &endptr);
3775 warning_error(wi, "Invalid value for mdp option SAoff. SAoff should only consist of real numbers separated by spaces.");
3777 ir->opts.SAsteps[i] = strtol(ptr3[i], &endptr, 10);
3780 warning_error(wi, "Invalid value for mdp option SAsteps. SAsteps should only consist of integers separated by spaces.");
3783 /* end of QMMM input */
3787 for (i = 0; (i < egcNR); i++)
3789 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3790 for (j = 0; (j < groups->grps[i].nr); j++)
3792 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3794 fprintf(stderr, "\n");
3798 nr = groups->grps[egcENER].nr;
3799 snew(ir->opts.egp_flags, nr*nr);
3801 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3802 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3804 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3806 if (bExcl && EEL_FULL(ir->coulombtype))
3808 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3811 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3812 if (bTable && !(ir->vdwtype == evdwUSER) &&
3813 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3814 !(ir->coulombtype == eelPMEUSERSWITCH))
3816 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3819 for (i = 0; (i < grps->nr); i++)
3831 static void check_disre(gmx_mtop_t *mtop)
3833 gmx_ffparams_t *ffparams;
3834 t_functype *functype;
3836 int i, ndouble, ftype;
3837 int label, old_label;
3839 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3841 ffparams = &mtop->ffparams;
3842 functype = ffparams->functype;
3843 ip = ffparams->iparams;
3846 for (i = 0; i < ffparams->ntypes; i++)
3848 ftype = functype[i];
3849 if (ftype == F_DISRES)
3851 label = ip[i].disres.label;
3852 if (label == old_label)
3854 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3862 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3863 "probably the parameters for multiple pairs in one restraint "
3864 "are not identical\n", ndouble);
3869 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3870 gmx_bool posres_only,
3874 gmx_mtop_ilistloop_t iloop;
3884 for (d = 0; d < DIM; d++)
3886 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3888 /* Check for freeze groups */
3889 for (g = 0; g < ir->opts.ngfrz; g++)
3891 for (d = 0; d < DIM; d++)
3893 if (ir->opts.nFreeze[g][d] != 0)
3901 /* Check for position restraints */
3902 iloop = gmx_mtop_ilistloop_init(sys);
3903 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3906 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3908 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3910 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3911 for (d = 0; d < DIM; d++)
3913 if (pr->posres.fcA[d] != 0)
3919 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3921 /* Check for flat-bottom posres */
3922 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3923 if (pr->fbposres.k != 0)
3925 switch (pr->fbposres.geom)
3927 case efbposresSPHERE:
3928 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3930 case efbposresCYLINDERX:
3931 AbsRef[YY] = AbsRef[ZZ] = 1;
3933 case efbposresCYLINDERY:
3934 AbsRef[XX] = AbsRef[ZZ] = 1;
3936 case efbposresCYLINDER:
3937 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3938 case efbposresCYLINDERZ:
3939 AbsRef[XX] = AbsRef[YY] = 1;
3941 case efbposresX: /* d=XX */
3942 case efbposresY: /* d=YY */
3943 case efbposresZ: /* d=ZZ */
3944 d = pr->fbposres.geom - efbposresX;
3948 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3949 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3957 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3961 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3962 gmx_bool *bC6ParametersWorkWithGeometricRules,
3963 gmx_bool *bC6ParametersWorkWithLBRules,
3964 gmx_bool *bLBRulesPossible)
3966 int ntypes, tpi, tpj;
3969 double c6i, c6j, c12i, c12j;
3970 double c6, c6_geometric, c6_LB;
3971 double sigmai, sigmaj, epsi, epsj;
3972 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3975 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3976 * force-field floating point parameters.
3979 ptr = getenv("GMX_LJCOMB_TOL");
3983 double gmx_unused canary;
3985 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
3987 gmx_fatal(FARGS, "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
3992 *bC6ParametersWorkWithLBRules = TRUE;
3993 *bC6ParametersWorkWithGeometricRules = TRUE;
3994 bCanDoLBRules = TRUE;
3995 ntypes = mtop->ffparams.atnr;
3996 snew(typecount, ntypes);
3997 gmx_mtop_count_atomtypes(mtop, state, typecount);
3998 *bLBRulesPossible = TRUE;
3999 for (tpi = 0; tpi < ntypes; ++tpi)
4001 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
4002 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
4003 for (tpj = tpi; tpj < ntypes; ++tpj)
4005 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
4006 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
4007 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
4008 c6_geometric = std::sqrt(c6i * c6j);
4009 if (!gmx_numzero(c6_geometric))
4011 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4013 sigmai = gmx::sixthroot(c12i / c6i);
4014 sigmaj = gmx::sixthroot(c12j / c6j);
4015 epsi = c6i * c6i /(4.0 * c12i);
4016 epsj = c6j * c6j /(4.0 * c12j);
4017 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4021 *bLBRulesPossible = FALSE;
4022 c6_LB = c6_geometric;
4024 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4027 if (FALSE == bCanDoLBRules)
4029 *bC6ParametersWorkWithLBRules = FALSE;
4032 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4034 if (FALSE == bCanDoGeometricRules)
4036 *bC6ParametersWorkWithGeometricRules = FALSE;
4044 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
4047 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4049 check_combination_rule_differences(mtop, 0,
4050 &bC6ParametersWorkWithGeometricRules,
4051 &bC6ParametersWorkWithLBRules,
4053 if (ir->ljpme_combination_rule == eljpmeLB)
4055 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
4057 warning(wi, "You are using arithmetic-geometric combination rules "
4058 "in LJ-PME, but your non-bonded C6 parameters do not "
4059 "follow these rules.");
4064 if (FALSE == bC6ParametersWorkWithGeometricRules)
4066 if (ir->eDispCorr != edispcNO)
4068 warning_note(wi, "You are using geometric combination rules in "
4069 "LJ-PME, but your non-bonded C6 parameters do "
4070 "not follow these rules. "
4071 "This will introduce very small errors in the forces and energies in "
4072 "your simulations. Dispersion correction will correct total energy "
4073 "and/or pressure for isotropic systems, but not forces or surface tensions.");
4077 warning_note(wi, "You are using geometric combination rules in "
4078 "LJ-PME, but your non-bonded C6 parameters do "
4079 "not follow these rules. "
4080 "This will introduce very small errors in the forces and energies in "
4081 "your simulations. If your system is homogeneous, consider using dispersion correction "
4082 "for the total energy and pressure.");
4088 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
4091 char err_buf[STRLEN];
4093 gmx_bool bCharge, bAcc;
4096 gmx_mtop_atomloop_block_t aloopb;
4097 gmx_mtop_atomloop_all_t aloop;
4099 char warn_buf[STRLEN];
4101 set_warning_line(wi, mdparin, -1);
4103 if (ir->cutoff_scheme == ecutsVERLET &&
4104 ir->verletbuf_tol > 0 &&
4106 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
4107 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4109 /* Check if a too small Verlet buffer might potentially
4110 * cause more drift than the thermostat can couple off.
4112 /* Temperature error fraction for warning and suggestion */
4113 const real T_error_warn = 0.002;
4114 const real T_error_suggest = 0.001;
4115 /* For safety: 2 DOF per atom (typical with constraints) */
4116 const real nrdf_at = 2;
4117 real T, tau, max_T_error;
4122 for (i = 0; i < ir->opts.ngtc; i++)
4124 T = std::max(T, ir->opts.ref_t[i]);
4125 tau = std::max(tau, ir->opts.tau_t[i]);
4129 /* This is a worst case estimate of the temperature error,
4130 * assuming perfect buffer estimation and no cancelation
4131 * of errors. The factor 0.5 is because energy distributes
4132 * equally over Ekin and Epot.
4134 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4135 if (max_T_error > T_error_warn)
4137 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.",
4138 ir->verletbuf_tol, T, tau,
4140 100*T_error_suggest,
4141 ir->verletbuf_tol*T_error_suggest/max_T_error);
4142 warning(wi, warn_buf);
4147 if (ETC_ANDERSEN(ir->etc))
4151 for (i = 0; i < ir->opts.ngtc; i++)
4153 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4154 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4155 sprintf(err_buf, "all tau_t must be positive using Andersen temperature control, tau_t[%d]=%10.6f",
4156 i, ir->opts.tau_t[i]);
4157 CHECK(ir->opts.tau_t[i] < 0);
4160 for (i = 0; i < ir->opts.ngtc; i++)
4162 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
4163 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);
4164 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
4168 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4169 ir->comm_mode == ecmNO &&
4170 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4171 !ETC_ANDERSEN(ir->etc))
4173 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");
4176 /* Check for pressure coupling with absolute position restraints */
4177 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4179 absolute_reference(ir, sys, TRUE, AbsRef);
4181 for (m = 0; m < DIM; m++)
4183 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4185 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4193 aloopb = gmx_mtop_atomloop_block_init(sys);
4195 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4197 if (atom->q != 0 || atom->qB != 0)
4205 if (EEL_FULL(ir->coulombtype))
4208 "You are using full electrostatics treatment %s for a system without charges.\n"
4209 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4210 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4211 warning(wi, err_buf);
4216 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4219 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4220 "You might want to consider using %s electrostatics.\n",
4222 warning_note(wi, err_buf);
4226 /* Check if combination rules used in LJ-PME are the same as in the force field */
4227 if (EVDW_PME(ir->vdwtype))
4229 check_combination_rules(ir, sys, wi);
4232 /* Generalized reaction field */
4233 if (ir->opts.ngtc == 0)
4235 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4237 CHECK(ir->coulombtype == eelGRF);
4241 sprintf(err_buf, "When using coulombtype = %s"
4242 " ref-t for temperature coupling should be > 0",
4244 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4248 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4250 for (m = 0; (m < DIM); m++)
4252 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4261 snew(mgrp, sys->groups.grps[egcACC].nr);
4262 aloop = gmx_mtop_atomloop_all_init(sys);
4264 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4266 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4269 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4271 for (m = 0; (m < DIM); m++)
4273 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4277 for (m = 0; (m < DIM); m++)
4279 if (fabs(acc[m]) > 1e-6)
4281 const char *dim[DIM] = { "X", "Y", "Z" };
4283 "Net Acceleration in %s direction, will %s be corrected\n",
4284 dim[m], ir->nstcomm != 0 ? "" : "not");
4285 if (ir->nstcomm != 0 && m < ndof_com(ir))
4288 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4290 ir->opts.acc[i][m] -= acc[m];
4298 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4299 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4301 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4309 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4311 if (ir->pull->coord[i].group[0] == 0 ||
4312 ir->pull->coord[i].group[1] == 0)
4314 absolute_reference(ir, sys, FALSE, AbsRef);
4315 for (m = 0; m < DIM; m++)
4317 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4319 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.");
4327 for (i = 0; i < 3; i++)
4329 for (m = 0; m <= i; m++)
4331 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4332 ir->deform[i][m] != 0)
4334 for (c = 0; c < ir->pull->ncoord; c++)
4336 if (ir->pull->coord[c].eGeom == epullgDIRPBC &&
4337 ir->pull->coord[c].vec[m] != 0)
4339 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->coord[c].eGeom), 'x'+m);
4350 void double_check(t_inputrec *ir, matrix box,
4351 gmx_bool bHasNormalConstraints,
4352 gmx_bool bHasAnyConstraints,
4356 char warn_buf[STRLEN];
4359 ptr = check_box(ir->ePBC, box);
4362 warning_error(wi, ptr);
4365 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4367 if (ir->shake_tol <= 0.0)
4369 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4371 warning_error(wi, warn_buf);
4375 if ( (ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4377 /* If we have Lincs constraints: */
4378 if (ir->eI == eiMD && ir->etc == etcNO &&
4379 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4381 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4382 warning_note(wi, warn_buf);
4385 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4387 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4388 warning_note(wi, warn_buf);
4390 if (ir->epc == epcMTTK)
4392 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4396 if (bHasAnyConstraints && ir->epc == epcMTTK)
4398 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4401 if (ir->LincsWarnAngle > 90.0)
4403 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4404 warning(wi, warn_buf);
4405 ir->LincsWarnAngle = 90.0;
4408 if (ir->ePBC != epbcNONE)
4410 if (ir->nstlist == 0)
4412 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4414 if (ir->ns_type == ensGRID)
4416 if (gmx::square(ir->rlist) >= max_cutoff2(ir->ePBC, box))
4418 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");
4419 warning_error(wi, warn_buf);
4424 min_size = std::min(box[XX][XX], std::min(box[YY][YY], box[ZZ][ZZ]));
4425 if (2*ir->rlist >= min_size)
4427 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4428 warning_error(wi, warn_buf);
4431 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4438 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4442 real rvdw1, rvdw2, rcoul1, rcoul2;
4443 char warn_buf[STRLEN];
4445 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4449 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4454 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4460 if (rvdw1 + rvdw2 > ir->rlist ||
4461 rcoul1 + rcoul2 > ir->rlist)
4464 "The sum of the two largest charge group radii (%f) "
4465 "is larger than rlist (%f)\n",
4466 std::max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4467 warning(wi, warn_buf);
4471 /* Here we do not use the zero at cut-off macro,
4472 * since user defined interactions might purposely
4473 * not be zero at the cut-off.
4475 if (ir_vdw_is_zero_at_cutoff(ir) &&
4476 rvdw1 + rvdw2 > ir->rlist - ir->rvdw)
4478 sprintf(warn_buf, "The sum of the two largest charge group "
4479 "radii (%f) is larger than rlist (%f) - rvdw (%f).\n"
4480 "With exact cut-offs, better performance can be "
4481 "obtained with cutoff-scheme = %s, because it "
4482 "does not use charge groups at all.",
4484 ir->rlist, ir->rvdw,
4485 ecutscheme_names[ecutsVERLET]);
4488 warning(wi, warn_buf);
4492 warning_note(wi, warn_buf);
4495 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4496 rcoul1 + rcoul2 > ir->rlist - ir->rcoulomb)
4498 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than rlist (%f) - rcoulomb (%f).\n"
4499 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4501 ir->rlist, ir->rcoulomb,
4502 ecutscheme_names[ecutsVERLET]);
4505 warning(wi, warn_buf);
4509 warning_note(wi, warn_buf);