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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];
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);
2077 /* Simulated annealing */
2078 CCTYPE("SIMULATED ANNEALING");
2079 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
2080 STYPE ("annealing", is->anneal, nullptr);
2081 CTYPE ("Number of time points to use for specifying annealing in each group");
2082 STYPE ("annealing-npoints", is->anneal_npoints, nullptr);
2083 CTYPE ("List of times at the annealing points for each group");
2084 STYPE ("annealing-time", is->anneal_time, nullptr);
2085 CTYPE ("Temp. at each annealing point, for each group.");
2086 STYPE ("annealing-temp", is->anneal_temp, nullptr);
2089 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
2090 EETYPE("gen-vel", opts->bGenVel, yesno_names);
2091 RTYPE ("gen-temp", opts->tempi, 300.0);
2092 ITYPE ("gen-seed", opts->seed, -1);
2095 CCTYPE ("OPTIONS FOR BONDS");
2096 EETYPE("constraints", opts->nshake, constraints);
2097 CTYPE ("Type of constraint algorithm");
2098 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
2099 CTYPE ("Do not constrain the start configuration");
2100 EETYPE("continuation", ir->bContinuation, yesno_names);
2101 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
2102 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
2103 CTYPE ("Relative tolerance of shake");
2104 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
2105 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
2106 ITYPE ("lincs-order", ir->nProjOrder, 4);
2107 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
2108 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
2109 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
2110 ITYPE ("lincs-iter", ir->nLincsIter, 1);
2111 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
2112 CTYPE ("rotates over more degrees than");
2113 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
2114 CTYPE ("Convert harmonic bonds to morse potentials");
2115 EETYPE("morse", opts->bMorse, yesno_names);
2117 /* Energy group exclusions */
2118 CCTYPE ("ENERGY GROUP EXCLUSIONS");
2119 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
2120 STYPE ("energygrp-excl", is->egpexcl, nullptr);
2124 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2125 ITYPE ("nwall", ir->nwall, 0);
2126 EETYPE("wall-type", ir->wall_type, ewt_names);
2127 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
2128 STYPE ("wall-atomtype", is->wall_atomtype, nullptr);
2129 STYPE ("wall-density", is->wall_density, nullptr);
2130 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
2133 CCTYPE("COM PULLING");
2134 EETYPE("pull", ir->bPull, yesno_names);
2138 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, wi);
2141 /* Enforced rotation */
2142 CCTYPE("ENFORCED ROTATION");
2143 CTYPE("Enforced rotation: No or Yes");
2144 EETYPE("rotation", ir->bRot, yesno_names);
2148 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2151 /* Interactive MD */
2153 CCTYPE("Group to display and/or manipulate in interactive MD session");
2154 STYPE ("IMD-group", is->imd_grp, nullptr);
2155 if (is->imd_grp[0] != '\0')
2162 CCTYPE("NMR refinement stuff");
2163 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2164 EETYPE("disre", ir->eDisre, edisre_names);
2165 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2166 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2167 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2168 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2169 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2170 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2171 CTYPE ("Output frequency for pair distances to energy file");
2172 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2173 CTYPE ("Orientation restraints: No or Yes");
2174 EETYPE("orire", opts->bOrire, yesno_names);
2175 CTYPE ("Orientation restraints force constant and tau for time averaging");
2176 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2177 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2178 STYPE ("orire-fitgrp", is->orirefitgrp, nullptr);
2179 CTYPE ("Output frequency for trace(SD) and S to energy file");
2180 ITYPE ("nstorireout", ir->nstorireout, 100);
2182 /* free energy variables */
2183 CCTYPE ("Free energy variables");
2184 EETYPE("free-energy", ir->efep, efep_names);
2185 STYPE ("couple-moltype", is->couple_moltype, nullptr);
2186 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2187 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2188 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2190 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2192 it was not entered */
2193 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2194 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2195 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2196 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], nullptr);
2197 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], nullptr);
2198 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], nullptr);
2199 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], nullptr);
2200 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], nullptr);
2201 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], nullptr);
2202 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], nullptr);
2203 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2204 STYPE ("init-lambda-weights", is->lambda_weights, nullptr);
2205 EETYPE("dhdl-print-energy", fep->edHdLPrintEnergy, edHdLPrintEnergy_names);
2206 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2207 ITYPE ("sc-power", fep->sc_power, 1);
2208 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2209 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2210 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2211 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2212 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2213 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2214 separate_dhdl_file_names);
2215 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2216 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2217 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2219 /* Non-equilibrium MD stuff */
2220 CCTYPE("Non-equilibrium MD stuff");
2221 STYPE ("acc-grps", is->accgrps, nullptr);
2222 STYPE ("accelerate", is->acc, nullptr);
2223 STYPE ("freezegrps", is->freeze, nullptr);
2224 STYPE ("freezedim", is->frdim, nullptr);
2225 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2226 STYPE ("deform", is->deform, nullptr);
2228 /* simulated tempering variables */
2229 CCTYPE("simulated tempering variables");
2230 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2231 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2232 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2233 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2235 /* expanded ensemble variables */
2236 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2238 read_expandedparams(&ninp, &inp, expand, wi);
2241 /* Electric fields */
2243 gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(ninp, inp);
2244 gmx::KeyValueTreeTransformer transform;
2245 transform.rules()->addRule()
2246 .keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
2247 mdModules->initMdpTransform(transform.rules());
2248 for (const auto &path : transform.mappedPaths())
2250 GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
2251 mark_einp_set(ninp, inp, path[0].c_str());
2253 MdpErrorHandler errorHandler(wi);
2255 = transform.transform(convertedValues, &errorHandler);
2256 ir->params = new gmx::KeyValueTreeObject(result.object());
2257 mdModules->adjustInputrecBasedOnModules(ir);
2258 errorHandler.setBackMapping(result.backMapping());
2259 mdModules->assignOptionsToModules(*ir->params, &errorHandler);
2262 /* Ion/water position swapping ("computational electrophysiology") */
2263 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2264 CTYPE("Swap positions along direction: no, X, Y, Z");
2265 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2266 if (ir->eSwapCoords != eswapNO)
2273 CTYPE("Swap attempt frequency");
2274 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2275 CTYPE("Number of ion types to be controlled");
2276 ITYPE("iontypes", nIonTypes, 1);
2279 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2281 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2282 snew(ir->swap->grp, ir->swap->ngrp);
2283 for (i = 0; i < ir->swap->ngrp; i++)
2285 snew(ir->swap->grp[i].molname, STRLEN);
2287 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2288 STYPE("split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
2289 STYPE("split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
2290 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2291 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2292 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2294 CTYPE("Name of solvent molecules");
2295 STYPE("solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
2297 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2298 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2299 CTYPE("however, if correctly defined, the permeation events are recorded per channel");
2300 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2301 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2302 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2303 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2304 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2305 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2307 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2308 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2310 CTYPE("Names of the ion types that can be exchanged with solvent molecules,");
2311 CTYPE("and the requested number of ions of this type in compartments A and B");
2312 CTYPE("-1 means fix the numbers as found in step 0");
2313 for (i = 0; i < nIonTypes; i++)
2315 int ig = eSwapFixedGrpNR + i;
2317 sprintf(buf, "iontype%d-name", i);
2318 STYPE(buf, ir->swap->grp[ig].molname, nullptr);
2319 sprintf(buf, "iontype%d-in-A", i);
2320 ITYPE(buf, ir->swap->grp[ig].nmolReq[0], -1);
2321 sprintf(buf, "iontype%d-in-B", i);
2322 ITYPE(buf, ir->swap->grp[ig].nmolReq[1], -1);
2325 CTYPE("By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2326 CTYPE("at maximum distance (= bulk concentration) to the split group layers. However,");
2327 CTYPE("an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0");
2328 CTYPE("towards one of the compartment-partitioning layers (at +/- 1.0).");
2329 RTYPE("bulk-offsetA", ir->swap->bulkOffset[0], 0.0);
2330 RTYPE("bulk-offsetB", ir->swap->bulkOffset[1], 0.0);
2331 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2332 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0) )
2334 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2337 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2338 RTYPE("threshold", ir->swap->threshold, 1.0);
2341 /* AdResS is no longer supported, but we need mdrun to be able to refuse to run old AdResS .tpr files */
2342 EETYPE("adress", ir->bAdress, yesno_names);
2344 /* User defined thingies */
2345 CCTYPE ("User defined thingies");
2346 STYPE ("user1-grps", is->user1, nullptr);
2347 STYPE ("user2-grps", is->user2, nullptr);
2348 ITYPE ("userint1", ir->userint1, 0);
2349 ITYPE ("userint2", ir->userint2, 0);
2350 ITYPE ("userint3", ir->userint3, 0);
2351 ITYPE ("userint4", ir->userint4, 0);
2352 RTYPE ("userreal1", ir->userreal1, 0);
2353 RTYPE ("userreal2", ir->userreal2, 0);
2354 RTYPE ("userreal3", ir->userreal3, 0);
2355 RTYPE ("userreal4", ir->userreal4, 0);
2359 gmx::TextOutputFile stream(mdparout);
2360 write_inpfile(&stream, mdparout, ninp, inp, FALSE, writeMdpHeader, wi);
2362 // Transform module data into a flat key-value tree for output.
2363 gmx::KeyValueTreeBuilder builder;
2364 gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
2365 mdModules->buildMdpOutput(&builderObject);
2367 gmx::TextWriter writer(&stream);
2368 writeKeyValueTreeAsMdp(&writer, builder.build());
2373 for (i = 0; (i < ninp); i++)
2376 sfree(inp[i].value);
2380 /* Process options if necessary */
2381 for (m = 0; m < 2; m++)
2383 for (i = 0; i < 2*DIM; i++)
2392 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2394 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 1)");
2396 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2398 case epctSEMIISOTROPIC:
2399 case epctSURFACETENSION:
2400 if (sscanf(dumstr[m], "%lf%lf", &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2402 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 2)");
2404 dumdub[m][YY] = dumdub[m][XX];
2406 case epctANISOTROPIC:
2407 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2408 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2409 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2411 warning_error(wi, "Pressure coupling incorrect number of values (I need exactly 6)");
2415 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2416 epcoupltype_names[ir->epct]);
2420 clear_mat(ir->ref_p);
2421 clear_mat(ir->compress);
2422 for (i = 0; i < DIM; i++)
2424 ir->ref_p[i][i] = dumdub[1][i];
2425 ir->compress[i][i] = dumdub[0][i];
2427 if (ir->epct == epctANISOTROPIC)
2429 ir->ref_p[XX][YY] = dumdub[1][3];
2430 ir->ref_p[XX][ZZ] = dumdub[1][4];
2431 ir->ref_p[YY][ZZ] = dumdub[1][5];
2432 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2434 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2436 ir->compress[XX][YY] = dumdub[0][3];
2437 ir->compress[XX][ZZ] = dumdub[0][4];
2438 ir->compress[YY][ZZ] = dumdub[0][5];
2439 for (i = 0; i < DIM; i++)
2441 for (m = 0; m < i; m++)
2443 ir->ref_p[i][m] = ir->ref_p[m][i];
2444 ir->compress[i][m] = ir->compress[m][i];
2449 if (ir->comm_mode == ecmNO)
2454 opts->couple_moltype = nullptr;
2455 if (strlen(is->couple_moltype) > 0)
2457 if (ir->efep != efepNO)
2459 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2460 if (opts->couple_lam0 == opts->couple_lam1)
2462 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2464 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2465 opts->couple_lam1 == ecouplamNONE))
2467 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2472 warning_note(wi, "Free energy is turned off, so we will not decouple the molecule listed in your input.");
2475 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2476 if (ir->efep != efepNO)
2478 if (fep->delta_lambda > 0)
2480 ir->efep = efepSLOWGROWTH;
2484 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2486 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2487 warning_note(wi, "Old option for dhdl-print-energy given: "
2488 "changing \"yes\" to \"total\"\n");
2491 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2493 /* always print out the energy to dhdl if we are doing
2494 expanded ensemble, since we need the total energy for
2495 analysis if the temperature is changing. In some
2496 conditions one may only want the potential energy, so
2497 we will allow that if the appropriate mdp setting has
2498 been enabled. Otherwise, total it is:
2500 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2503 if ((ir->efep != efepNO) || ir->bSimTemp)
2505 ir->bExpanded = FALSE;
2506 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2508 ir->bExpanded = TRUE;
2510 do_fep_params(ir, is->fep_lambda, is->lambda_weights, wi);
2511 if (ir->bSimTemp) /* done after fep params */
2513 do_simtemp_params(ir);
2516 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2517 * setup and not on the old way of specifying the free-energy setup,
2518 * we should check for using soft-core when not needed, since that
2519 * can complicate the sampling significantly.
2520 * Note that we only check for the automated coupling setup.
2521 * If the (advanced) user does FEP through manual topology changes,
2522 * this check will not be triggered.
2524 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 &&
2525 ir->fepvals->sc_alpha != 0 &&
2526 (couple_lambda_has_vdw_on(opts->couple_lam0) &&
2527 couple_lambda_has_vdw_on(opts->couple_lam1)))
2529 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.");
2534 ir->fepvals->n_lambda = 0;
2537 /* WALL PARAMETERS */
2539 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2541 /* ORIENTATION RESTRAINT PARAMETERS */
2543 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, nullptr) != 1)
2545 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2548 /* DEFORMATION PARAMETERS */
2550 clear_mat(ir->deform);
2551 for (i = 0; i < 6; i++)
2556 double gmx_unused canary;
2557 int ndeform = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf %lf",
2558 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2559 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]), &canary);
2561 if (strlen(is->deform) > 0 && ndeform != 6)
2563 warning_error(wi, gmx::formatString("Cannot parse exactly 6 box deformation velocities from string '%s'", is->deform).c_str());
2565 for (i = 0; i < 3; i++)
2567 ir->deform[i][i] = dumdub[0][i];
2569 ir->deform[YY][XX] = dumdub[0][3];
2570 ir->deform[ZZ][XX] = dumdub[0][4];
2571 ir->deform[ZZ][YY] = dumdub[0][5];
2572 if (ir->epc != epcNO)
2574 for (i = 0; i < 3; i++)
2576 for (j = 0; j <= i; j++)
2578 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2580 warning_error(wi, "A box element has deform set and compressibility > 0");
2584 for (i = 0; i < 3; i++)
2586 for (j = 0; j < i; j++)
2588 if (ir->deform[i][j] != 0)
2590 for (m = j; m < DIM; m++)
2592 if (ir->compress[m][j] != 0)
2594 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.");
2595 warning(wi, warn_buf);
2603 /* Ion/water position swapping checks */
2604 if (ir->eSwapCoords != eswapNO)
2606 if (ir->swap->nstswap < 1)
2608 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2610 if (ir->swap->nAverage < 1)
2612 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2614 if (ir->swap->threshold < 1.0)
2616 warning_error(wi, "Ion count threshold must be at least 1.\n");
2624 static int search_QMstring(const char *s, int ng, const char *gn[])
2626 /* same as normal search_string, but this one searches QM strings */
2629 for (i = 0; (i < ng); i++)
2631 if (gmx_strcasecmp(s, gn[i]) == 0)
2637 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2641 } /* search_QMstring */
2643 /* We would like gn to be const as well, but C doesn't allow this */
2644 /* TODO this is utility functionality (search for the index of a
2645 string in a collection), so should be refactored and located more
2647 int search_string(const char *s, int ng, char *gn[])
2651 for (i = 0; (i < ng); i++)
2653 if (gmx_strcasecmp(s, gn[i]) == 0)
2660 "Group %s referenced in the .mdp file was not found in the index file.\n"
2661 "Group names must match either [moleculetype] names or custom index group\n"
2662 "names, in which case you must supply an index file to the '-n' option\n"
2669 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2670 t_blocka *block, char *gnames[],
2671 int gtype, int restnm,
2672 int grptp, gmx_bool bVerbose,
2675 unsigned short *cbuf;
2676 t_grps *grps = &(groups->grps[gtype]);
2677 int i, j, gid, aj, ognr, ntot = 0;
2680 char warn_buf[STRLEN];
2684 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2687 title = gtypes[gtype];
2690 /* Mark all id's as not set */
2691 for (i = 0; (i < natoms); i++)
2696 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2697 for (i = 0; (i < ng); i++)
2699 /* Lookup the group name in the block structure */
2700 gid = search_string(ptrs[i], block->nr, gnames);
2701 if ((grptp != egrptpONE) || (i == 0))
2703 grps->nm_ind[grps->nr++] = gid;
2707 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2710 /* Now go over the atoms in the group */
2711 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2716 /* Range checking */
2717 if ((aj < 0) || (aj >= natoms))
2719 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2721 /* Lookup up the old group number */
2725 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2726 aj+1, title, ognr+1, i+1);
2730 /* Store the group number in buffer */
2731 if (grptp == egrptpONE)
2744 /* Now check whether we have done all atoms */
2748 if (grptp == egrptpALL)
2750 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2751 natoms-ntot, title);
2753 else if (grptp == egrptpPART)
2755 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2756 natoms-ntot, title);
2757 warning_note(wi, warn_buf);
2759 /* Assign all atoms currently unassigned to a rest group */
2760 for (j = 0; (j < natoms); j++)
2762 if (cbuf[j] == NOGID)
2768 if (grptp != egrptpPART)
2773 "Making dummy/rest group for %s containing %d elements\n",
2774 title, natoms-ntot);
2776 /* Add group name "rest" */
2777 grps->nm_ind[grps->nr] = restnm;
2779 /* Assign the rest name to all atoms not currently assigned to a group */
2780 for (j = 0; (j < natoms); j++)
2782 if (cbuf[j] == NOGID)
2791 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2793 /* All atoms are part of one (or no) group, no index required */
2794 groups->ngrpnr[gtype] = 0;
2795 groups->grpnr[gtype] = nullptr;
2799 groups->ngrpnr[gtype] = natoms;
2800 snew(groups->grpnr[gtype], natoms);
2801 for (j = 0; (j < natoms); j++)
2803 groups->grpnr[gtype][j] = cbuf[j];
2809 return (bRest && grptp == egrptpPART);
2812 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2815 gmx_groups_t *groups;
2816 pull_params_t *pull;
2817 int natoms, ai, aj, i, j, d, g, imin, jmin;
2819 int *nrdf2, *na_vcm, na_tot;
2820 double *nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
2822 gmx_mtop_atomloop_all_t aloop;
2823 int mb, mol, ftype, as;
2824 gmx_molblock_t *molb;
2825 gmx_moltype_t *molt;
2828 * First calc 3xnr-atoms for each group
2829 * then subtract half a degree of freedom for each constraint
2831 * Only atoms and nuclei contribute to the degrees of freedom...
2836 groups = &mtop->groups;
2837 natoms = mtop->natoms;
2839 /* Allocate one more for a possible rest group */
2840 /* We need to sum degrees of freedom into doubles,
2841 * since floats give too low nrdf's above 3 million atoms.
2843 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2844 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2845 snew(dof_vcm, groups->grps[egcVCM].nr+1);
2846 snew(na_vcm, groups->grps[egcVCM].nr+1);
2847 snew(nrdf_vcm_sub, groups->grps[egcVCM].nr+1);
2849 for (i = 0; i < groups->grps[egcTC].nr; i++)
2853 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2856 clear_ivec(dof_vcm[i]);
2858 nrdf_vcm_sub[i] = 0;
2861 snew(nrdf2, natoms);
2862 aloop = gmx_mtop_atomloop_all_init(mtop);
2864 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2867 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2869 g = ggrpnr(groups, egcFREEZE, i);
2870 for (d = 0; d < DIM; d++)
2872 if (opts->nFreeze[g][d] == 0)
2874 /* Add one DOF for particle i (counted as 2*1) */
2876 /* VCM group i has dim d as a DOF */
2877 dof_vcm[ggrpnr(groups, egcVCM, i)][d] = 1;
2880 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2881 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2886 for (mb = 0; mb < mtop->nmolblock; mb++)
2888 molb = &mtop->molblock[mb];
2889 molt = &mtop->moltype[molb->type];
2890 atom = molt->atoms.atom;
2891 for (mol = 0; mol < molb->nmol; mol++)
2893 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2895 ia = molt->ilist[ftype].iatoms;
2896 for (i = 0; i < molt->ilist[ftype].nr; )
2898 /* Subtract degrees of freedom for the constraints,
2899 * if the particles still have degrees of freedom left.
2900 * If one of the particles is a vsite or a shell, then all
2901 * constraint motion will go there, but since they do not
2902 * contribute to the constraints the degrees of freedom do not
2907 if (((atom[ia[1]].ptype == eptNucleus) ||
2908 (atom[ia[1]].ptype == eptAtom)) &&
2909 ((atom[ia[2]].ptype == eptNucleus) ||
2910 (atom[ia[2]].ptype == eptAtom)))
2928 imin = std::min(imin, nrdf2[ai]);
2929 jmin = std::min(jmin, nrdf2[aj]);
2932 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2933 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2934 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2935 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2937 ia += interaction_function[ftype].nratoms+1;
2938 i += interaction_function[ftype].nratoms+1;
2941 ia = molt->ilist[F_SETTLE].iatoms;
2942 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2944 /* Subtract 1 dof from every atom in the SETTLE */
2945 for (j = 0; j < 3; j++)
2948 imin = std::min(2, nrdf2[ai]);
2950 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2951 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2956 as += molt->atoms.nr;
2962 /* Correct nrdf for the COM constraints.
2963 * We correct using the TC and VCM group of the first atom
2964 * in the reference and pull group. If atoms in one pull group
2965 * belong to different TC or VCM groups it is anyhow difficult
2966 * to determine the optimal nrdf assignment.
2970 for (i = 0; i < pull->ncoord; i++)
2972 if (pull->coord[i].eType != epullCONSTRAINT)
2979 for (j = 0; j < 2; j++)
2981 const t_pull_group *pgrp;
2983 pgrp = &pull->group[pull->coord[i].group[j]];
2987 /* Subtract 1/2 dof from each group */
2989 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2990 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2991 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2993 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)]]);
2998 /* We need to subtract the whole DOF from group j=1 */
3005 if (ir->nstcomm != 0)
3009 /* We remove COM motion up to dim ndof_com() */
3010 ndim_rm_vcm = ndof_com(ir);
3012 /* Subtract ndim_rm_vcm (or less with frozen dimensions) from
3013 * the number of degrees of freedom in each vcm group when COM
3014 * translation is removed and 6 when rotation is removed as well.
3016 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
3018 switch (ir->comm_mode)
3021 case ecmLINEAR_ACCELERATION_CORRECTION:
3022 nrdf_vcm_sub[j] = 0;
3023 for (d = 0; d < ndim_rm_vcm; d++)
3032 nrdf_vcm_sub[j] = 6;
3035 gmx_incons("Checking comm_mode");
3039 for (i = 0; i < groups->grps[egcTC].nr; i++)
3041 /* Count the number of atoms of TC group i for every VCM group */
3042 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
3047 for (ai = 0; ai < natoms; ai++)
3049 if (ggrpnr(groups, egcTC, ai) == i)
3051 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
3055 /* Correct for VCM removal according to the fraction of each VCM
3056 * group present in this TC group.
3058 nrdf_uc = nrdf_tc[i];
3061 fprintf(debug, "T-group[%d] nrdf_uc = %g\n", i, nrdf_uc);
3064 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
3066 if (nrdf_vcm[j] > nrdf_vcm_sub[j])
3068 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
3069 (nrdf_vcm[j] - nrdf_vcm_sub[j])/nrdf_vcm[j];
3073 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
3074 j, nrdf_vcm[j], nrdf_tc[i]);
3079 for (i = 0; (i < groups->grps[egcTC].nr); i++)
3081 opts->nrdf[i] = nrdf_tc[i];
3082 if (opts->nrdf[i] < 0)
3087 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
3088 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
3096 sfree(nrdf_vcm_sub);
3099 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
3100 const char *option, const char *val, int flag)
3102 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3103 * But since this is much larger than STRLEN, such a line can not be parsed.
3104 * The real maximum is the number of names that fit in a string: STRLEN/2.
3106 #define EGP_MAX (STRLEN/2)
3107 int nelem, i, j, k, nr;
3108 char *names[EGP_MAX];
3112 gnames = groups->grpname;
3114 nelem = str_nelem(val, EGP_MAX, names);
3117 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3119 nr = groups->grps[egcENER].nr;
3121 for (i = 0; i < nelem/2; i++)
3125 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
3131 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3132 names[2*i], option);
3136 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
3142 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3143 names[2*i+1], option);
3145 if ((j < nr) && (k < nr))
3147 ir->opts.egp_flags[nr*j+k] |= flag;
3148 ir->opts.egp_flags[nr*k+j] |= flag;
3157 static void make_swap_groups(
3162 int ig = -1, i = 0, gind;
3166 /* Just a quick check here, more thorough checks are in mdrun */
3167 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3169 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3172 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3173 for (ig = 0; ig < swap->ngrp; ig++)
3175 swapg = &swap->grp[ig];
3176 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3177 swapg->nat = grps->index[gind+1] - grps->index[gind];
3181 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3182 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap",
3183 swap->grp[ig].molname, swapg->nat);
3184 snew(swapg->ind, swapg->nat);
3185 for (i = 0; i < swapg->nat; i++)
3187 swapg->ind[i] = grps->a[grps->index[gind]+i];
3192 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3198 static void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3203 ig = search_string(IMDgname, grps->nr, gnames);
3204 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3206 if (IMDgroup->nat > 0)
3208 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3209 IMDgname, IMDgroup->nat);
3210 snew(IMDgroup->ind, IMDgroup->nat);
3211 for (i = 0; i < IMDgroup->nat; i++)
3213 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3219 void do_index(const char* mdparin, const char *ndx,
3226 gmx_groups_t *groups;
3230 char warnbuf[STRLEN], **gnames;
3231 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3234 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3235 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3236 int i, j, k, restnm;
3237 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3238 int nQMmethod, nQMbasis, nQMg;
3239 char warn_buf[STRLEN];
3244 fprintf(stderr, "processing index file...\n");
3249 snew(grps->index, 1);
3251 atoms_all = gmx_mtop_global_atoms(mtop);
3252 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3253 done_atom(&atoms_all);
3257 grps = init_index(ndx, &gnames);
3260 groups = &mtop->groups;
3261 natoms = mtop->natoms;
3262 symtab = &mtop->symtab;
3264 snew(groups->grpname, grps->nr+1);
3266 for (i = 0; (i < grps->nr); i++)
3268 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3270 groups->grpname[i] = put_symtab(symtab, "rest");
3272 srenew(gnames, grps->nr+1);
3273 gnames[restnm] = *(groups->grpname[i]);
3274 groups->ngrpname = grps->nr+1;
3276 set_warning_line(wi, mdparin, -1);
3278 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3279 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3280 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3281 if ((ntau_t != ntcg) || (nref_t != ntcg))
3283 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3284 "%d tau-t values", ntcg, nref_t, ntau_t);
3287 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3288 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3289 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3290 nr = groups->grps[egcTC].nr;
3292 snew(ir->opts.nrdf, nr);
3293 snew(ir->opts.tau_t, nr);
3294 snew(ir->opts.ref_t, nr);
3295 if (ir->eI == eiBD && ir->bd_fric == 0)
3297 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3304 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3308 for (i = 0; (i < nr); i++)
3310 ir->opts.tau_t[i] = strtod(ptr1[i], &endptr);
3313 warning_error(wi, "Invalid value for mdp option tau-t. tau-t should only consist of real numbers separated by spaces.");
3315 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3317 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3318 warning_error(wi, warn_buf);
3321 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3323 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.");
3326 if (ir->opts.tau_t[i] >= 0)
3328 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3331 if (ir->etc != etcNO && ir->nsttcouple == -1)
3333 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3338 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3340 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");
3342 if (ir->epc == epcMTTK)
3344 if (ir->etc != etcNOSEHOOVER)
3346 gmx_fatal(FARGS, "Cannot do MTTK pressure coupling without Nose-Hoover temperature control");
3350 if (ir->nstpcouple != ir->nsttcouple)
3352 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3353 ir->nstpcouple = ir->nsttcouple = mincouple;
3354 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);
3355 warning_note(wi, warn_buf);
3360 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3361 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3363 if (ETC_ANDERSEN(ir->etc))
3365 if (ir->nsttcouple != 1)
3368 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");
3369 warning_note(wi, warn_buf);
3372 nstcmin = tcouple_min_integration_steps(ir->etc);
3375 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin - 10*GMX_REAL_EPS)
3377 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3378 ETCOUPLTYPE(ir->etc),
3380 ir->nsttcouple*ir->delta_t);
3381 warning(wi, warn_buf);
3384 for (i = 0; (i < nr); i++)
3386 ir->opts.ref_t[i] = strtod(ptr2[i], &endptr);
3389 warning_error(wi, "Invalid value for mdp option ref-t. ref-t should only consist of real numbers separated by spaces.");
3391 if (ir->opts.ref_t[i] < 0)
3393 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3396 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3397 if we are in this conditional) if mc_temp is negative */
3398 if (ir->expandedvals->mc_temp < 0)
3400 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3404 /* Simulated annealing for each group. There are nr groups */
3405 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3406 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3410 if (nSA > 0 && nSA != nr)
3412 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3416 snew(ir->opts.annealing, nr);
3417 snew(ir->opts.anneal_npoints, nr);
3418 snew(ir->opts.anneal_time, nr);
3419 snew(ir->opts.anneal_temp, nr);
3420 for (i = 0; i < nr; i++)
3422 ir->opts.annealing[i] = eannNO;
3423 ir->opts.anneal_npoints[i] = 0;
3424 ir->opts.anneal_time[i] = nullptr;
3425 ir->opts.anneal_temp[i] = nullptr;
3430 for (i = 0; i < nr; i++)
3432 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3434 ir->opts.annealing[i] = eannNO;
3436 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3438 ir->opts.annealing[i] = eannSINGLE;
3441 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3443 ir->opts.annealing[i] = eannPERIODIC;
3449 /* Read the other fields too */
3450 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3451 if (nSA_points != nSA)
3453 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3455 for (k = 0, i = 0; i < nr; i++)
3457 ir->opts.anneal_npoints[i] = strtol(ptr1[i], &endptr, 10);
3460 warning_error(wi, "Invalid value for mdp option annealing-npoints. annealing should only consist of integers separated by spaces.");
3462 if (ir->opts.anneal_npoints[i] == 1)
3464 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3466 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3467 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3468 k += ir->opts.anneal_npoints[i];
3471 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3474 gmx_fatal(FARGS, "Found %d annealing-time values, wanted %d\n", nSA_time, k);
3476 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3479 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3482 for (i = 0, k = 0; i < nr; i++)
3485 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3487 ir->opts.anneal_time[i][j] = strtod(ptr1[k], &endptr);
3490 warning_error(wi, "Invalid value for mdp option anneal-time. anneal-time should only consist of real numbers separated by spaces.");
3492 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], &endptr);
3495 warning_error(wi, "Invalid value for anneal-temp. anneal-temp should only consist of real numbers separated by spaces.");
3499 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3501 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3507 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3509 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3510 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3513 if (ir->opts.anneal_temp[i][j] < 0)
3515 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3520 /* Print out some summary information, to make sure we got it right */
3521 for (i = 0, k = 0; i < nr; i++)
3523 if (ir->opts.annealing[i] != eannNO)
3525 j = groups->grps[egcTC].nm_ind[i];
3526 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3527 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3528 ir->opts.anneal_npoints[i]);
3529 fprintf(stderr, "Time (ps) Temperature (K)\n");
3530 /* All terms except the last one */
3531 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3533 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3536 /* Finally the last one */
3537 j = ir->opts.anneal_npoints[i]-1;
3538 if (ir->opts.annealing[i] == eannSINGLE)
3540 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3544 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3545 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3547 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3558 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3560 make_pull_coords(ir->pull);
3565 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3568 if (ir->eSwapCoords != eswapNO)
3570 make_swap_groups(ir->swap, grps, gnames);
3573 /* Make indices for IMD session */
3576 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3579 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3580 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3581 if (nacg*DIM != nacc)
3583 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3586 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3587 restnm, egrptpALL_GENREST, bVerbose, wi);
3588 nr = groups->grps[egcACC].nr;
3589 snew(ir->opts.acc, nr);
3590 ir->opts.ngacc = nr;
3592 for (i = k = 0; (i < nacg); i++)
3594 for (j = 0; (j < DIM); j++, k++)
3596 ir->opts.acc[i][j] = strtod(ptr1[k], &endptr);
3599 warning_error(wi, "Invalid value for mdp option accelerate. accelerate should only consist of real numbers separated by spaces.");
3603 for (; (i < nr); i++)
3605 for (j = 0; (j < DIM); j++)
3607 ir->opts.acc[i][j] = 0;
3611 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3612 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3613 if (nfrdim != DIM*nfreeze)
3615 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3618 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3619 restnm, egrptpALL_GENREST, bVerbose, wi);
3620 nr = groups->grps[egcFREEZE].nr;
3621 ir->opts.ngfrz = nr;
3622 snew(ir->opts.nFreeze, nr);
3623 for (i = k = 0; (i < nfreeze); i++)
3625 for (j = 0; (j < DIM); j++, k++)
3627 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3628 if (!ir->opts.nFreeze[i][j])
3630 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3632 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3633 "(not %s)", ptr1[k]);
3634 warning(wi, warn_buf);
3639 for (; (i < nr); i++)
3641 for (j = 0; (j < DIM); j++)
3643 ir->opts.nFreeze[i][j] = 0;
3647 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3648 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3649 restnm, egrptpALL_GENREST, bVerbose, wi);
3650 add_wall_energrps(groups, ir->nwall, symtab);
3651 ir->opts.ngener = groups->grps[egcENER].nr;
3652 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3654 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3655 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3658 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3659 "This may lead to artifacts.\n"
3660 "In most cases one should use one group for the whole system.");
3663 /* Now we have filled the freeze struct, so we can calculate NRDF */
3664 calc_nrdf(mtop, ir, gnames);
3666 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3667 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3668 restnm, egrptpALL_GENREST, bVerbose, wi);
3669 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3670 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3671 restnm, egrptpALL_GENREST, bVerbose, wi);
3672 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3673 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3674 restnm, egrptpONE, bVerbose, wi);
3675 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3676 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3677 restnm, egrptpALL_GENREST, bVerbose, wi);
3679 /* QMMM input processing */
3680 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3681 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3682 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3683 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3685 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3686 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3688 /* group rest, if any, is always MM! */
3689 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3690 restnm, egrptpALL_GENREST, bVerbose, wi);
3691 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3692 ir->opts.ngQM = nQMg;
3693 snew(ir->opts.QMmethod, nr);
3694 snew(ir->opts.QMbasis, nr);
3695 for (i = 0; i < nr; i++)
3697 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3698 * converted to the corresponding enum in names.c
3700 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3702 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3706 str_nelem(is->QMmult, MAXPTR, ptr1);
3707 str_nelem(is->QMcharge, MAXPTR, ptr2);
3708 str_nelem(is->bSH, MAXPTR, ptr3);
3709 snew(ir->opts.QMmult, nr);
3710 snew(ir->opts.QMcharge, nr);
3711 snew(ir->opts.bSH, nr);
3713 for (i = 0; i < nr; i++)
3715 ir->opts.QMmult[i] = strtol(ptr1[i], &endptr, 10);
3718 warning_error(wi, "Invalid value for mdp option QMmult. QMmult should only consist of integers separated by spaces.");
3720 ir->opts.QMcharge[i] = strtol(ptr2[i], &endptr, 10);
3723 warning_error(wi, "Invalid value for mdp option QMcharge. QMcharge should only consist of integers separated by spaces.");
3725 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3728 str_nelem(is->CASelectrons, MAXPTR, ptr1);
3729 str_nelem(is->CASorbitals, MAXPTR, ptr2);
3730 snew(ir->opts.CASelectrons, nr);
3731 snew(ir->opts.CASorbitals, nr);
3732 for (i = 0; i < nr; i++)
3734 ir->opts.CASelectrons[i] = strtol(ptr1[i], &endptr, 10);
3737 warning_error(wi, "Invalid value for mdp option CASelectrons. CASelectrons should only consist of integers separated by spaces.");
3739 ir->opts.CASorbitals[i] = strtol(ptr2[i], &endptr, 10);
3742 warning_error(wi, "Invalid value for mdp option CASorbitals. CASorbitals should only consist of integers separated by spaces.");
3746 str_nelem(is->SAon, MAXPTR, ptr1);
3747 str_nelem(is->SAoff, MAXPTR, ptr2);
3748 str_nelem(is->SAsteps, MAXPTR, ptr3);
3749 snew(ir->opts.SAon, nr);
3750 snew(ir->opts.SAoff, nr);
3751 snew(ir->opts.SAsteps, nr);
3753 for (i = 0; i < nr; i++)
3755 ir->opts.SAon[i] = strtod(ptr1[i], &endptr);
3758 warning_error(wi, "Invalid value for mdp option SAon. SAon should only consist of real numbers separated by spaces.");
3760 ir->opts.SAoff[i] = strtod(ptr2[i], &endptr);
3763 warning_error(wi, "Invalid value for mdp option SAoff. SAoff should only consist of real numbers separated by spaces.");
3765 ir->opts.SAsteps[i] = strtol(ptr3[i], &endptr, 10);
3768 warning_error(wi, "Invalid value for mdp option SAsteps. SAsteps should only consist of integers separated by spaces.");
3771 /* end of QMMM input */
3775 for (i = 0; (i < egcNR); i++)
3777 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3778 for (j = 0; (j < groups->grps[i].nr); j++)
3780 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3782 fprintf(stderr, "\n");
3786 nr = groups->grps[egcENER].nr;
3787 snew(ir->opts.egp_flags, nr*nr);
3789 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3790 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3792 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3794 if (bExcl && EEL_FULL(ir->coulombtype))
3796 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3799 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3800 if (bTable && !(ir->vdwtype == evdwUSER) &&
3801 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3802 !(ir->coulombtype == eelPMEUSERSWITCH))
3804 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3807 for (i = 0; (i < grps->nr); i++)
3819 static void check_disre(gmx_mtop_t *mtop)
3821 gmx_ffparams_t *ffparams;
3822 t_functype *functype;
3824 int i, ndouble, ftype;
3825 int label, old_label;
3827 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3829 ffparams = &mtop->ffparams;
3830 functype = ffparams->functype;
3831 ip = ffparams->iparams;
3834 for (i = 0; i < ffparams->ntypes; i++)
3836 ftype = functype[i];
3837 if (ftype == F_DISRES)
3839 label = ip[i].disres.label;
3840 if (label == old_label)
3842 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3850 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3851 "probably the parameters for multiple pairs in one restraint "
3852 "are not identical\n", ndouble);
3857 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3858 gmx_bool posres_only,
3862 gmx_mtop_ilistloop_t iloop;
3872 for (d = 0; d < DIM; d++)
3874 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3876 /* Check for freeze groups */
3877 for (g = 0; g < ir->opts.ngfrz; g++)
3879 for (d = 0; d < DIM; d++)
3881 if (ir->opts.nFreeze[g][d] != 0)
3889 /* Check for position restraints */
3890 iloop = gmx_mtop_ilistloop_init(sys);
3891 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3894 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3896 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3898 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3899 for (d = 0; d < DIM; d++)
3901 if (pr->posres.fcA[d] != 0)
3907 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3909 /* Check for flat-bottom posres */
3910 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3911 if (pr->fbposres.k != 0)
3913 switch (pr->fbposres.geom)
3915 case efbposresSPHERE:
3916 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3918 case efbposresCYLINDERX:
3919 AbsRef[YY] = AbsRef[ZZ] = 1;
3921 case efbposresCYLINDERY:
3922 AbsRef[XX] = AbsRef[ZZ] = 1;
3924 case efbposresCYLINDER:
3925 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3926 case efbposresCYLINDERZ:
3927 AbsRef[XX] = AbsRef[YY] = 1;
3929 case efbposresX: /* d=XX */
3930 case efbposresY: /* d=YY */
3931 case efbposresZ: /* d=ZZ */
3932 d = pr->fbposres.geom - efbposresX;
3936 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3937 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3945 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3949 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3950 gmx_bool *bC6ParametersWorkWithGeometricRules,
3951 gmx_bool *bC6ParametersWorkWithLBRules,
3952 gmx_bool *bLBRulesPossible)
3954 int ntypes, tpi, tpj;
3957 double c6i, c6j, c12i, c12j;
3958 double c6, c6_geometric, c6_LB;
3959 double sigmai, sigmaj, epsi, epsj;
3960 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3963 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3964 * force-field floating point parameters.
3967 ptr = getenv("GMX_LJCOMB_TOL");
3971 double gmx_unused canary;
3973 if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
3975 gmx_fatal(FARGS, "Could not parse a single floating-point number from GMX_LJCOMB_TOL (%s)", ptr);
3980 *bC6ParametersWorkWithLBRules = TRUE;
3981 *bC6ParametersWorkWithGeometricRules = TRUE;
3982 bCanDoLBRules = TRUE;
3983 ntypes = mtop->ffparams.atnr;
3984 snew(typecount, ntypes);
3985 gmx_mtop_count_atomtypes(mtop, state, typecount);
3986 *bLBRulesPossible = TRUE;
3987 for (tpi = 0; tpi < ntypes; ++tpi)
3989 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3990 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3991 for (tpj = tpi; tpj < ntypes; ++tpj)
3993 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3994 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3995 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3996 c6_geometric = std::sqrt(c6i * c6j);
3997 if (!gmx_numzero(c6_geometric))
3999 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
4001 sigmai = gmx::sixthroot(c12i / c6i);
4002 sigmaj = gmx::sixthroot(c12j / c6j);
4003 epsi = c6i * c6i /(4.0 * c12i);
4004 epsj = c6j * c6j /(4.0 * c12j);
4005 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
4009 *bLBRulesPossible = FALSE;
4010 c6_LB = c6_geometric;
4012 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
4015 if (FALSE == bCanDoLBRules)
4017 *bC6ParametersWorkWithLBRules = FALSE;
4020 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
4022 if (FALSE == bCanDoGeometricRules)
4024 *bC6ParametersWorkWithGeometricRules = FALSE;
4032 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
4035 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4037 check_combination_rule_differences(mtop, 0,
4038 &bC6ParametersWorkWithGeometricRules,
4039 &bC6ParametersWorkWithLBRules,
4041 if (ir->ljpme_combination_rule == eljpmeLB)
4043 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
4045 warning(wi, "You are using arithmetic-geometric combination rules "
4046 "in LJ-PME, but your non-bonded C6 parameters do not "
4047 "follow these rules.");
4052 if (FALSE == bC6ParametersWorkWithGeometricRules)
4054 if (ir->eDispCorr != edispcNO)
4056 warning_note(wi, "You are using geometric combination rules in "
4057 "LJ-PME, but your non-bonded C6 parameters do "
4058 "not follow these rules. "
4059 "This will introduce very small errors in the forces and energies in "
4060 "your simulations. Dispersion correction will correct total energy "
4061 "and/or pressure for isotropic systems, but not forces or surface tensions.");
4065 warning_note(wi, "You are using geometric combination rules in "
4066 "LJ-PME, but your non-bonded C6 parameters do "
4067 "not follow these rules. "
4068 "This will introduce very small errors in the forces and energies in "
4069 "your simulations. If your system is homogeneous, consider using dispersion correction "
4070 "for the total energy and pressure.");
4076 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
4079 char err_buf[STRLEN];
4081 gmx_bool bCharge, bAcc;
4084 gmx_mtop_atomloop_block_t aloopb;
4085 gmx_mtop_atomloop_all_t aloop;
4087 char warn_buf[STRLEN];
4089 set_warning_line(wi, mdparin, -1);
4091 if (ir->cutoff_scheme == ecutsVERLET &&
4092 ir->verletbuf_tol > 0 &&
4094 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
4095 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4097 /* Check if a too small Verlet buffer might potentially
4098 * cause more drift than the thermostat can couple off.
4100 /* Temperature error fraction for warning and suggestion */
4101 const real T_error_warn = 0.002;
4102 const real T_error_suggest = 0.001;
4103 /* For safety: 2 DOF per atom (typical with constraints) */
4104 const real nrdf_at = 2;
4105 real T, tau, max_T_error;
4110 for (i = 0; i < ir->opts.ngtc; i++)
4112 T = std::max(T, ir->opts.ref_t[i]);
4113 tau = std::max(tau, ir->opts.tau_t[i]);
4117 /* This is a worst case estimate of the temperature error,
4118 * assuming perfect buffer estimation and no cancelation
4119 * of errors. The factor 0.5 is because energy distributes
4120 * equally over Ekin and Epot.
4122 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4123 if (max_T_error > T_error_warn)
4125 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.",
4126 ir->verletbuf_tol, T, tau,
4128 100*T_error_suggest,
4129 ir->verletbuf_tol*T_error_suggest/max_T_error);
4130 warning(wi, warn_buf);
4135 if (ETC_ANDERSEN(ir->etc))
4139 for (i = 0; i < ir->opts.ngtc; i++)
4141 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4142 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4143 sprintf(err_buf, "all tau_t must be positive using Andersen temperature control, tau_t[%d]=%10.6f",
4144 i, ir->opts.tau_t[i]);
4145 CHECK(ir->opts.tau_t[i] < 0);
4148 if (ir->etc == etcANDERSENMASSIVE && ir->comm_mode != ecmNO)
4150 for (i = 0; i < ir->opts.ngtc; i++)
4152 int nsteps = static_cast<int>(ir->opts.tau_t[i]/ir->delta_t + 0.5);
4153 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);
4154 CHECK(nsteps % ir->nstcomm != 0);
4159 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4160 ir->comm_mode == ecmNO &&
4161 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4162 !ETC_ANDERSEN(ir->etc))
4164 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");
4167 /* Check for pressure coupling with absolute position restraints */
4168 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4170 absolute_reference(ir, sys, TRUE, AbsRef);
4172 for (m = 0; m < DIM; m++)
4174 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4176 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4184 aloopb = gmx_mtop_atomloop_block_init(sys);
4186 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4188 if (atom->q != 0 || atom->qB != 0)
4196 if (EEL_FULL(ir->coulombtype))
4199 "You are using full electrostatics treatment %s for a system without charges.\n"
4200 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4201 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4202 warning(wi, err_buf);
4207 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4210 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4211 "You might want to consider using %s electrostatics.\n",
4213 warning_note(wi, err_buf);
4217 /* Check if combination rules used in LJ-PME are the same as in the force field */
4218 if (EVDW_PME(ir->vdwtype))
4220 check_combination_rules(ir, sys, wi);
4223 /* Generalized reaction field */
4224 if (ir->opts.ngtc == 0)
4226 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4228 CHECK(ir->coulombtype == eelGRF);
4232 sprintf(err_buf, "When using coulombtype = %s"
4233 " ref-t for temperature coupling should be > 0",
4235 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4239 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4241 for (m = 0; (m < DIM); m++)
4243 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4252 snew(mgrp, sys->groups.grps[egcACC].nr);
4253 aloop = gmx_mtop_atomloop_all_init(sys);
4255 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4257 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4260 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4262 for (m = 0; (m < DIM); m++)
4264 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4268 for (m = 0; (m < DIM); m++)
4270 if (fabs(acc[m]) > 1e-6)
4272 const char *dim[DIM] = { "X", "Y", "Z" };
4274 "Net Acceleration in %s direction, will %s be corrected\n",
4275 dim[m], ir->nstcomm != 0 ? "" : "not");
4276 if (ir->nstcomm != 0 && m < ndof_com(ir))
4279 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4281 ir->opts.acc[i][m] -= acc[m];
4289 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4290 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4292 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4300 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4302 if (ir->pull->coord[i].group[0] == 0 ||
4303 ir->pull->coord[i].group[1] == 0)
4305 absolute_reference(ir, sys, FALSE, AbsRef);
4306 for (m = 0; m < DIM; m++)
4308 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4310 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.");
4318 for (i = 0; i < 3; i++)
4320 for (m = 0; m <= i; m++)
4322 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4323 ir->deform[i][m] != 0)
4325 for (c = 0; c < ir->pull->ncoord; c++)
4327 if (ir->pull->coord[c].eGeom == epullgDIRPBC &&
4328 ir->pull->coord[c].vec[m] != 0)
4330 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->coord[c].eGeom), 'x'+m);
4341 void double_check(t_inputrec *ir, matrix box,
4342 gmx_bool bHasNormalConstraints,
4343 gmx_bool bHasAnyConstraints,
4347 char warn_buf[STRLEN];
4350 ptr = check_box(ir->ePBC, box);
4353 warning_error(wi, ptr);
4356 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4358 if (ir->shake_tol <= 0.0)
4360 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4362 warning_error(wi, warn_buf);
4366 if ( (ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4368 /* If we have Lincs constraints: */
4369 if (ir->eI == eiMD && ir->etc == etcNO &&
4370 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4372 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4373 warning_note(wi, warn_buf);
4376 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4378 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4379 warning_note(wi, warn_buf);
4381 if (ir->epc == epcMTTK)
4383 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4387 if (bHasAnyConstraints && ir->epc == epcMTTK)
4389 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4392 if (ir->LincsWarnAngle > 90.0)
4394 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4395 warning(wi, warn_buf);
4396 ir->LincsWarnAngle = 90.0;
4399 if (ir->ePBC != epbcNONE)
4401 if (ir->nstlist == 0)
4403 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4405 if (ir->ns_type == ensGRID)
4407 if (gmx::square(ir->rlist) >= max_cutoff2(ir->ePBC, box))
4409 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");
4410 warning_error(wi, warn_buf);
4415 min_size = std::min(box[XX][XX], std::min(box[YY][YY], box[ZZ][ZZ]));
4416 if (2*ir->rlist >= min_size)
4418 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4419 warning_error(wi, warn_buf);
4422 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4429 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4433 real rvdw1, rvdw2, rcoul1, rcoul2;
4434 char warn_buf[STRLEN];
4436 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4440 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4445 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4451 if (rvdw1 + rvdw2 > ir->rlist ||
4452 rcoul1 + rcoul2 > ir->rlist)
4455 "The sum of the two largest charge group radii (%f) "
4456 "is larger than rlist (%f)\n",
4457 std::max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4458 warning(wi, warn_buf);
4462 /* Here we do not use the zero at cut-off macro,
4463 * since user defined interactions might purposely
4464 * not be zero at the cut-off.
4466 if (ir_vdw_is_zero_at_cutoff(ir) &&
4467 rvdw1 + rvdw2 > ir->rlist - ir->rvdw)
4469 sprintf(warn_buf, "The sum of the two largest charge group "
4470 "radii (%f) is larger than rlist (%f) - rvdw (%f).\n"
4471 "With exact cut-offs, better performance can be "
4472 "obtained with cutoff-scheme = %s, because it "
4473 "does not use charge groups at all.",
4475 ir->rlist, ir->rvdw,
4476 ecutscheme_names[ecutsVERLET]);
4479 warning(wi, warn_buf);
4483 warning_note(wi, warn_buf);
4486 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4487 rcoul1 + rcoul2 > ir->rlist - ir->rcoulomb)
4489 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than rlist (%f) - rcoulomb (%f).\n"
4490 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4492 ir->rlist, ir->rcoulomb,
4493 ecutscheme_names[ecutsVERLET]);
4496 warning(wi, warn_buf);
4500 warning_note(wi, warn_buf);