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49 #include "gromacs/gmxpreprocess/toputil.h"
50 #include "gromacs/legacyheaders/chargegroup.h"
51 #include "gromacs/legacyheaders/inputrec.h"
52 #include "gromacs/legacyheaders/macros.h"
53 #include "gromacs/legacyheaders/names.h"
54 #include "gromacs/legacyheaders/network.h"
55 #include "gromacs/legacyheaders/readinp.h"
56 #include "gromacs/legacyheaders/typedefs.h"
57 #include "gromacs/legacyheaders/warninp.h"
58 #include "gromacs/math/units.h"
59 #include "gromacs/math/vec.h"
60 #include "gromacs/mdlib/calc_verletbuf.h"
61 #include "gromacs/pbcutil/pbc.h"
62 #include "gromacs/topology/block.h"
63 #include "gromacs/topology/index.h"
64 #include "gromacs/topology/mtop_util.h"
65 #include "gromacs/topology/symtab.h"
66 #include "gromacs/utility/cstringutil.h"
67 #include "gromacs/utility/fatalerror.h"
68 #include "gromacs/utility/smalloc.h"
73 /* Resource parameters
74 * Do not change any of these until you read the instruction
75 * in readinp.h. Some cpp's do not take spaces after the backslash
76 * (like the c-shell), which will give you a very weird compiler
80 typedef struct t_inputrec_strings
82 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN],
83 acc[STRLEN], accgrps[STRLEN], freeze[STRLEN], frdim[STRLEN],
84 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
85 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
86 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN],
88 char fep_lambda[efptNR][STRLEN];
89 char lambda_weights[STRLEN];
92 char anneal[STRLEN], anneal_npoints[STRLEN],
93 anneal_time[STRLEN], anneal_temp[STRLEN];
94 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
95 bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
96 SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
97 char efield_x[STRLEN], efield_xt[STRLEN], efield_y[STRLEN],
98 efield_yt[STRLEN], efield_z[STRLEN], efield_zt[STRLEN];
100 } gmx_inputrec_strings;
102 static gmx_inputrec_strings *is = NULL;
104 void init_inputrec_strings()
108 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.");
113 void done_inputrec_strings()
119 static char swapgrp[STRLEN], splitgrp0[STRLEN], splitgrp1[STRLEN], solgrp[STRLEN];
122 egrptpALL, /* All particles have to be a member of a group. */
123 egrptpALL_GENREST, /* A rest group with name is generated for particles *
124 * that are not part of any group. */
125 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
126 * for the rest group. */
127 egrptpONE /* Merge all selected groups into one group, *
128 * make a rest group for the remaining particles. */
131 static const char *constraints[eshNR+1] = {
132 "none", "h-bonds", "all-bonds", "h-angles", "all-angles", NULL
135 static const char *couple_lam[ecouplamNR+1] = {
136 "vdw-q", "vdw", "q", "none", NULL
139 void init_ir(t_inputrec *ir, t_gromppopts *opts)
141 snew(opts->include, STRLEN);
142 snew(opts->define, STRLEN);
143 snew(ir->fepvals, 1);
144 snew(ir->expandedvals, 1);
145 snew(ir->simtempvals, 1);
148 static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
153 for (i = 0; i < ntemps; i++)
155 /* simple linear scaling -- allows more control */
156 if (simtemp->eSimTempScale == esimtempLINEAR)
158 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*temperature_lambdas[i];
160 else if (simtemp->eSimTempScale == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
162 simtemp->temperatures[i] = simtemp->simtemp_low * std::pow(simtemp->simtemp_high/simtemp->simtemp_low, static_cast<real>((1.0*i)/(ntemps-1)));
164 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
166 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*(gmx_expm1(temperature_lambdas[i])/gmx_expm1(1.0));
171 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
172 gmx_fatal(FARGS, errorstr);
179 static void _low_check(gmx_bool b, const char *s, warninp_t wi)
183 warning_error(wi, s);
187 static void check_nst(const char *desc_nst, int nst,
188 const char *desc_p, int *p,
193 if (*p > 0 && *p % nst != 0)
195 /* Round up to the next multiple of nst */
196 *p = ((*p)/nst + 1)*nst;
197 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n",
198 desc_p, desc_nst, desc_p, *p);
203 static gmx_bool ir_NVE(const t_inputrec *ir)
205 return ((ir->eI == eiMD || EI_VV(ir->eI)) && ir->etc == etcNO);
208 static int lcd(int n1, int n2)
213 for (i = 2; (i <= n1 && i <= n2); i++)
215 if (n1 % i == 0 && n2 % i == 0)
224 static void process_interaction_modifier(const t_inputrec *ir, int *eintmod)
226 if (*eintmod == eintmodPOTSHIFT_VERLET)
228 if (ir->cutoff_scheme == ecutsVERLET)
230 *eintmod = eintmodPOTSHIFT;
234 *eintmod = eintmodNONE;
239 void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
241 /* Check internal consistency.
242 * NOTE: index groups are not set here yet, don't check things
243 * like temperature coupling group options here, but in triple_check
246 /* Strange macro: first one fills the err_buf, and then one can check
247 * the condition, which will print the message and increase the error
250 #define CHECK(b) _low_check(b, err_buf, wi)
251 char err_buf[256], warn_buf[STRLEN];
254 t_lambda *fep = ir->fepvals;
255 t_expanded *expand = ir->expandedvals;
257 set_warning_line(wi, mdparin, -1);
259 /* BASIC CUT-OFF STUFF */
260 if (ir->rcoulomb < 0)
262 warning_error(wi, "rcoulomb should be >= 0");
266 warning_error(wi, "rvdw should be >= 0");
269 !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
271 warning_error(wi, "rlist should be >= 0");
273 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.)");
274 CHECK(ir->nstlist < 0);
276 process_interaction_modifier(ir, &ir->coulomb_modifier);
277 process_interaction_modifier(ir, &ir->vdw_modifier);
279 if (ir->cutoff_scheme == ecutsGROUP)
282 "The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future "
283 "release when all interaction forms are supported for the verlet scheme. The verlet "
284 "scheme already scales better, and it is compatible with GPUs and other accelerators.");
286 /* BASIC CUT-OFF STUFF */
287 if (ir->rlist == 0 ||
288 !((ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > ir->rlist) ||
289 (ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > ir->rlist)))
291 /* No switched potential and/or no twin-range:
292 * we can set the long-range cut-off to the maximum of the other cut-offs.
294 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
296 else if (ir->rlistlong < 0)
298 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
299 sprintf(warn_buf, "rlistlong was not set, setting it to %g (no buffer)",
301 warning(wi, warn_buf);
303 if (ir->rlistlong == 0 && ir->ePBC != epbcNONE)
305 warning_error(wi, "Can not have an infinite cut-off with PBC");
307 if (ir->rlistlong > 0 && (ir->rlist == 0 || ir->rlistlong < ir->rlist))
309 warning_error(wi, "rlistlong can not be shorter than rlist");
311 if (IR_TWINRANGE(*ir) && ir->nstlist == 0)
313 warning_error(wi, "Can not have nstlist == 0 with twin-range interactions");
317 if (ir->rlistlong == ir->rlist)
321 else if (ir->rlistlong > ir->rlist && ir->nstcalclr == 0)
323 warning_error(wi, "With different cutoffs for electrostatics and VdW, nstcalclr must be -1 or a positive number");
326 if (ir->cutoff_scheme == ecutsVERLET)
330 /* Normal Verlet type neighbor-list, currently only limited feature support */
331 if (inputrec2nboundeddim(ir) < 3)
333 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
335 if (ir->rcoulomb != ir->rvdw)
337 warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported");
339 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
341 if (ir->vdw_modifier == eintmodNONE ||
342 ir->vdw_modifier == eintmodPOTSHIFT)
344 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
346 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]);
347 warning_note(wi, warn_buf);
349 ir->vdwtype = evdwCUT;
353 sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
354 warning_error(wi, warn_buf);
358 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
360 warning_error(wi, "With Verlet lists only cut-off and PME LJ interactions are supported");
362 if (!(ir->coulombtype == eelCUT ||
363 (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC) ||
364 EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
366 warning_error(wi, "With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
368 if (!(ir->coulomb_modifier == eintmodNONE ||
369 ir->coulomb_modifier == eintmodPOTSHIFT))
371 sprintf(warn_buf, "coulomb_modifier=%s is not supported with the Verlet cut-off scheme", eintmod_names[ir->coulomb_modifier]);
372 warning_error(wi, warn_buf);
375 if (ir->implicit_solvent != eisNO)
377 warning_error(wi, "Implicit solvent is not (yet) supported with the with Verlet lists.");
380 if (ir->nstlist <= 0)
382 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
385 if (ir->nstlist < 10)
387 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.");
390 rc_max = std::max(ir->rvdw, ir->rcoulomb);
392 if (ir->verletbuf_tol <= 0)
394 if (ir->verletbuf_tol == 0)
396 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
399 if (ir->rlist < rc_max)
401 warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
404 if (ir->rlist == rc_max && ir->nstlist > 1)
406 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.");
411 if (ir->rlist > rc_max)
413 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.");
416 if (ir->nstlist == 1)
418 /* No buffer required */
423 if (EI_DYNAMICS(ir->eI))
425 if (inputrec2nboundeddim(ir) < 3)
427 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.");
429 /* Set rlist temporarily so we can continue processing */
434 /* Set the buffer to 5% of the cut-off */
435 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
440 /* No twin-range calculations with Verlet lists */
441 ir->rlistlong = ir->rlist;
444 if (ir->nstcalclr == -1)
446 /* if rlist=rlistlong, this will later be changed to nstcalclr=0 */
447 ir->nstcalclr = ir->nstlist;
449 else if (ir->nstcalclr > 0)
451 if (ir->nstlist > 0 && (ir->nstlist % ir->nstcalclr != 0))
453 warning_error(wi, "nstlist must be evenly divisible by nstcalclr. Use nstcalclr = -1 to automatically follow nstlist");
456 else if (ir->nstcalclr < -1)
458 warning_error(wi, "nstcalclr must be a positive number (divisor of nstcalclr), or -1 to follow nstlist.");
461 if (EEL_PME(ir->coulombtype) && ir->rcoulomb > ir->rlist && ir->nstcalclr > 1)
463 warning_error(wi, "When used with PME, the long-range component of twin-range interactions must be updated every step (nstcalclr)");
466 /* GENERAL INTEGRATOR STUFF */
467 if (!(ir->eI == eiMD || EI_VV(ir->eI)))
471 if (ir->eI == eiVVAK)
473 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]);
474 warning_note(wi, warn_buf);
476 if (!EI_DYNAMICS(ir->eI))
480 if (EI_DYNAMICS(ir->eI))
482 if (ir->nstcalcenergy < 0)
484 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
485 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
487 /* nstcalcenergy larger than nstener does not make sense.
488 * We ideally want nstcalcenergy=nstener.
492 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
496 ir->nstcalcenergy = ir->nstenergy;
500 else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
501 (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
502 (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
505 const char *nsten = "nstenergy";
506 const char *nstdh = "nstdhdl";
507 const char *min_name = nsten;
508 int min_nst = ir->nstenergy;
510 /* find the smallest of ( nstenergy, nstdhdl ) */
511 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
512 (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
514 min_nst = ir->fepvals->nstdhdl;
517 /* If the user sets nstenergy small, we should respect that */
519 "Setting nstcalcenergy (%d) equal to %s (%d)",
520 ir->nstcalcenergy, min_name, min_nst);
521 warning_note(wi, warn_buf);
522 ir->nstcalcenergy = min_nst;
525 if (ir->epc != epcNO)
527 if (ir->nstpcouple < 0)
529 ir->nstpcouple = ir_optimal_nstpcouple(ir);
532 if (IR_TWINRANGE(*ir))
534 check_nst("nstcalclr", ir->nstcalclr,
535 "nstcalcenergy", &ir->nstcalcenergy, wi);
536 if (ir->epc != epcNO)
538 check_nst("nstlist", ir->nstlist,
539 "nstpcouple", &ir->nstpcouple, wi);
543 if (ir->nstcalcenergy > 0)
545 if (ir->efep != efepNO)
547 /* nstdhdl should be a multiple of nstcalcenergy */
548 check_nst("nstcalcenergy", ir->nstcalcenergy,
549 "nstdhdl", &ir->fepvals->nstdhdl, wi);
550 /* nstexpanded should be a multiple of nstcalcenergy */
551 check_nst("nstcalcenergy", ir->nstcalcenergy,
552 "nstexpanded", &ir->expandedvals->nstexpanded, wi);
554 /* for storing exact averages nstenergy should be
555 * a multiple of nstcalcenergy
557 check_nst("nstcalcenergy", ir->nstcalcenergy,
558 "nstenergy", &ir->nstenergy, wi);
562 if (ir->nsteps == 0 && !ir->bContinuation)
564 warning_note(wi, "For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates.");
568 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
569 ir->bContinuation && ir->ld_seed != -1)
571 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)");
577 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
578 CHECK(ir->ePBC != epbcXYZ);
579 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
580 CHECK(ir->ns_type != ensGRID);
581 sprintf(err_buf, "with TPI nstlist should be larger than zero");
582 CHECK(ir->nstlist <= 0);
583 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
584 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
585 sprintf(err_buf, "TPI does not work (yet) with the Verlet cut-off scheme");
586 CHECK(ir->cutoff_scheme == ecutsVERLET);
590 if ( (opts->nshake > 0) && (opts->bMorse) )
593 "Using morse bond-potentials while constraining bonds is useless");
594 warning(wi, warn_buf);
597 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
598 ir->bContinuation && ir->ld_seed != -1)
600 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)");
602 /* verify simulated tempering options */
606 gmx_bool bAllTempZero = TRUE;
607 for (i = 0; i < fep->n_lambda; i++)
609 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]);
610 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
611 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
613 bAllTempZero = FALSE;
616 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
617 CHECK(bAllTempZero == TRUE);
619 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
620 CHECK(ir->eI != eiVV);
622 /* check compatability of the temperature coupling with simulated tempering */
624 if (ir->etc == etcNOSEHOOVER)
626 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
627 warning_note(wi, warn_buf);
630 /* check that the temperatures make sense */
632 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);
633 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
635 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
636 CHECK(ir->simtempvals->simtemp_high <= 0);
638 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
639 CHECK(ir->simtempvals->simtemp_low <= 0);
642 /* verify free energy options */
644 if (ir->efep != efepNO)
647 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
649 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
651 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
652 (int)fep->sc_r_power);
653 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
655 sprintf(err_buf, "Can't use postive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
656 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
658 sprintf(err_buf, "Can't use postive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
659 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
661 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
662 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
664 sprintf(err_buf, "Free-energy not implemented for Ewald");
665 CHECK(ir->coulombtype == eelEWALD);
667 /* check validty of lambda inputs */
668 if (fep->n_lambda == 0)
670 /* Clear output in case of no states:*/
671 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
672 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
676 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
677 CHECK((fep->init_fep_state >= fep->n_lambda));
680 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
681 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
683 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",
684 fep->init_lambda, fep->init_fep_state);
685 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
689 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
693 for (i = 0; i < efptNR; i++)
695 if (fep->separate_dvdl[i])
700 if (n_lambda_terms > 1)
702 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.");
703 warning(wi, warn_buf);
706 if (n_lambda_terms < 2 && fep->n_lambda > 0)
709 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
713 for (j = 0; j < efptNR; j++)
715 for (i = 0; i < fep->n_lambda; i++)
717 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]);
718 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
722 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
724 for (i = 0; i < fep->n_lambda; i++)
726 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],
727 fep->all_lambda[efptCOUL][i]);
728 CHECK((fep->sc_alpha > 0) &&
729 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
730 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
731 ((fep->all_lambda[efptVDW][i] > 0.0) &&
732 (fep->all_lambda[efptVDW][i] < 1.0))));
736 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
738 real sigma, lambda, r_sc;
741 /* Maximum estimate for A and B charges equal with lambda power 1 */
743 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);
744 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.",
746 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
747 warning_note(wi, warn_buf);
750 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
751 be treated differently, but that's the next step */
753 for (i = 0; i < efptNR; i++)
755 for (j = 0; j < fep->n_lambda; j++)
757 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
758 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
762 if (IR_TWINRANGE(*ir))
764 sprintf(err_buf, "nstdhdl must be divisible by nstcalclr");
765 CHECK(ir->fepvals->nstdhdl > 0 &&
766 ir->fepvals->nstdhdl % ir->nstcalclr != 0);
768 if (ir->efep == efepEXPANDED)
770 sprintf(err_buf, "nstexpanded must be divisible by nstcalclr");
771 CHECK(ir->expandedvals->nstexpanded % ir->nstcalclr != 0);
776 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
780 /* checking equilibration of weights inputs for validity */
782 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
783 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
784 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
786 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
787 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
788 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
790 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
791 expand->equil_steps, elmceq_names[elmceqSTEPS]);
792 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
794 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
795 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
796 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
798 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
799 expand->equil_ratio, elmceq_names[elmceqRATIO]);
800 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
802 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
803 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
804 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
806 sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
807 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
808 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
810 sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
811 expand->equil_steps, elmceq_names[elmceqSTEPS]);
812 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
814 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
815 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
816 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
818 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
819 expand->equil_ratio, elmceq_names[elmceqRATIO]);
820 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
822 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
823 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
824 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
826 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
827 CHECK((expand->lmc_repeats <= 0));
828 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
829 CHECK((expand->minvarmin <= 0));
830 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
831 CHECK((expand->c_range < 0));
832 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
833 fep->init_fep_state, expand->lmc_forced_nstart);
834 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
835 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
836 CHECK((expand->lmc_forced_nstart < 0));
837 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
838 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
840 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
841 CHECK((expand->init_wl_delta < 0));
842 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
843 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
844 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
845 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
847 /* if there is no temperature control, we need to specify an MC temperature */
848 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
849 if (expand->nstTij > 0)
851 sprintf(err_buf, "nstlog must be non-zero");
852 CHECK(ir->nstlog != 0);
853 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
854 expand->nstTij, ir->nstlog);
855 CHECK((expand->nstTij % ir->nstlog) != 0);
860 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
861 CHECK(ir->nwall && ir->ePBC != epbcXY);
864 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
866 if (ir->ePBC == epbcNONE)
868 if (ir->epc != epcNO)
870 warning(wi, "Turning off pressure coupling for vacuum system");
876 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
877 epbc_names[ir->ePBC]);
878 CHECK(ir->epc != epcNO);
880 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
881 CHECK(EEL_FULL(ir->coulombtype));
883 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
884 epbc_names[ir->ePBC]);
885 CHECK(ir->eDispCorr != edispcNO);
888 if (ir->rlist == 0.0)
890 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
891 "with coulombtype = %s or coulombtype = %s\n"
892 "without periodic boundary conditions (pbc = %s) and\n"
893 "rcoulomb and rvdw set to zero",
894 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
895 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
896 (ir->ePBC != epbcNONE) ||
897 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
901 warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
906 if (ir->nstcomm == 0)
908 ir->comm_mode = ecmNO;
910 if (ir->comm_mode != ecmNO)
914 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");
915 ir->nstcomm = abs(ir->nstcomm);
918 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
920 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
921 ir->nstcomm = ir->nstcalcenergy;
924 if (ir->comm_mode == ecmANGULAR)
926 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
927 CHECK(ir->bPeriodicMols);
928 if (ir->ePBC != epbcNONE)
930 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.");
935 if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
937 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.");
940 sprintf(err_buf, "Twin-range neighbour searching (NS) with simple NS"
941 " algorithm not implemented");
942 CHECK(((ir->rcoulomb > ir->rlist) || (ir->rvdw > ir->rlist))
943 && (ir->ns_type == ensSIMPLE));
945 /* TEMPERATURE COUPLING */
946 if (ir->etc == etcYES)
948 ir->etc = etcBERENDSEN;
949 warning_note(wi, "Old option for temperature coupling given: "
950 "changing \"yes\" to \"Berendsen\"\n");
953 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
955 if (ir->opts.nhchainlength < 1)
957 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
958 ir->opts.nhchainlength = 1;
959 warning(wi, warn_buf);
962 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
964 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
965 ir->opts.nhchainlength = 1;
970 ir->opts.nhchainlength = 0;
973 if (ir->eI == eiVVAK)
975 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
977 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
980 if (ETC_ANDERSEN(ir->etc))
982 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
983 CHECK(!(EI_VV(ir->eI)));
985 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
987 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]);
988 warning_note(wi, warn_buf);
991 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]);
992 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
995 if (ir->etc == etcBERENDSEN)
997 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
998 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
999 warning_note(wi, warn_buf);
1002 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
1003 && ir->epc == epcBERENDSEN)
1005 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
1006 "true ensemble for the thermostat");
1007 warning(wi, warn_buf);
1010 /* PRESSURE COUPLING */
1011 if (ir->epc == epcISOTROPIC)
1013 ir->epc = epcBERENDSEN;
1014 warning_note(wi, "Old option for pressure coupling given: "
1015 "changing \"Isotropic\" to \"Berendsen\"\n");
1018 if (ir->epc != epcNO)
1020 dt_pcoupl = ir->nstpcouple*ir->delta_t;
1022 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1023 CHECK(ir->tau_p <= 0);
1025 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10*GMX_REAL_EPS)
1027 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
1028 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1029 warning(wi, warn_buf);
1032 sprintf(err_buf, "compressibility must be > 0 when using pressure"
1033 " coupling %s\n", EPCOUPLTYPE(ir->epc));
1034 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
1035 ir->compress[ZZ][ZZ] < 0 ||
1036 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
1037 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
1039 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1042 "You are generating velocities so I am assuming you "
1043 "are equilibrating a system. You are using "
1044 "%s pressure coupling, but this can be "
1045 "unstable for equilibration. If your system crashes, try "
1046 "equilibrating first with Berendsen pressure coupling. If "
1047 "you are not equilibrating the system, you can probably "
1048 "ignore this warning.",
1049 epcoupl_names[ir->epc]);
1050 warning(wi, warn_buf);
1056 if (ir->epc > epcNO)
1058 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1060 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.");
1066 if (ir->epc == epcMTTK)
1068 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1072 /* ELECTROSTATICS */
1073 /* More checks are in triple check (grompp.c) */
1075 if (ir->coulombtype == eelSWITCH)
1077 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1078 "artifacts, advice: use coulombtype = %s",
1079 eel_names[ir->coulombtype],
1080 eel_names[eelRF_ZERO]);
1081 warning(wi, warn_buf);
1084 if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
1086 sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
1087 warning_note(wi, warn_buf);
1090 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1092 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);
1093 warning(wi, warn_buf);
1094 ir->epsilon_rf = ir->epsilon_r;
1095 ir->epsilon_r = 1.0;
1098 if (ir->epsilon_r == 0)
1101 "It is pointless to use long-range or Generalized Born electrostatics with infinite relative permittivity."
1102 "Since you are effectively turning of electrostatics, a plain cutoff will be much faster.");
1103 CHECK(EEL_FULL(ir->coulombtype) || ir->implicit_solvent == eisGBSA);
1106 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == NULL)
1108 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1109 CHECK(ir->epsilon_r < 0);
1112 if (EEL_RF(ir->coulombtype))
1114 /* reaction field (at the cut-off) */
1116 if (ir->coulombtype == eelRF_ZERO)
1118 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1119 eel_names[ir->coulombtype]);
1120 CHECK(ir->epsilon_rf != 0);
1121 ir->epsilon_rf = 0.0;
1124 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1125 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1126 (ir->epsilon_r == 0));
1127 if (ir->epsilon_rf == ir->epsilon_r)
1129 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1130 eel_names[ir->coulombtype]);
1131 warning(wi, warn_buf);
1134 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1135 * means the interaction is zero outside rcoulomb, but it helps to
1136 * provide accurate energy conservation.
1138 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1140 if (ir_coulomb_switched(ir))
1143 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1144 eel_names[ir->coulombtype]);
1145 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1148 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1150 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1152 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1153 eel_names[ir->coulombtype]);
1154 CHECK(ir->rlist > ir->rcoulomb);
1158 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1161 "Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier.");
1162 CHECK( ir->coulomb_modifier != eintmodNONE);
1164 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1167 "Explicit switch/shift vdw interactions cannot be used in combination with a secondary vdw-modifier.");
1168 CHECK( ir->vdw_modifier != eintmodNONE);
1171 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1172 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1175 "The switch/shift interaction settings are just for compatibility; you will get better "
1176 "performance from applying potential modifiers to your interactions!\n");
1177 warning_note(wi, warn_buf);
1180 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1182 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1184 real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
1185 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.",
1186 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1187 warning(wi, warn_buf);
1191 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1193 if (ir->rvdw_switch == 0)
1195 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.");
1196 warning(wi, warn_buf);
1200 if (EEL_FULL(ir->coulombtype))
1202 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1203 ir->coulombtype == eelPMEUSERSWITCH)
1205 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1206 eel_names[ir->coulombtype]);
1207 CHECK(ir->rcoulomb > ir->rlist);
1209 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1211 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1214 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
1215 "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
1216 "a potential modifier.", eel_names[ir->coulombtype]);
1217 if (ir->nstcalclr == 1)
1219 CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
1223 CHECK(ir->rcoulomb != ir->rlist);
1229 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1231 if (ir->pme_order < 3)
1233 warning_error(wi, "pme-order can not be smaller than 3");
1237 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1239 if (ir->ewald_geometry == eewg3D)
1241 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1242 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1243 warning(wi, warn_buf);
1245 /* This check avoids extra pbc coding for exclusion corrections */
1246 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1247 CHECK(ir->wall_ewald_zfac < 2);
1249 if ((ir->ewald_geometry == eewg3DC) && (ir->ePBC != epbcXY) &&
1250 EEL_FULL(ir->coulombtype))
1252 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1253 eel_names[ir->coulombtype], eewg_names[eewg3DC], epbc_names[epbcXY]);
1254 warning(wi, warn_buf);
1256 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1258 if (ir->cutoff_scheme == ecutsVERLET)
1260 sprintf(warn_buf, "Since molecules/charge groups are broken using the Verlet scheme, you can not use a dipole correction to the %s electrostatics.",
1261 eel_names[ir->coulombtype]);
1262 warning(wi, warn_buf);
1266 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",
1267 eel_names[ir->coulombtype]);
1268 warning_note(wi, warn_buf);
1272 if (ir_vdw_switched(ir))
1274 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1275 CHECK(ir->rvdw_switch >= ir->rvdw);
1277 if (ir->rvdw_switch < 0.5*ir->rvdw)
1279 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.",
1280 ir->rvdw_switch, ir->rvdw);
1281 warning_note(wi, warn_buf);
1284 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1286 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1288 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1289 CHECK(ir->rlist > ir->rvdw);
1293 if (ir->vdwtype == evdwPME)
1295 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1297 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s a\
1299 evdw_names[ir->vdwtype],
1300 eintmod_names[eintmodPOTSHIFT],
1301 eintmod_names[eintmodNONE]);
1305 if (ir->cutoff_scheme == ecutsGROUP)
1307 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1308 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)))
1310 warning_note(wi, "With exact cut-offs, rlist should be "
1311 "larger than rcoulomb and rvdw, so that there "
1312 "is a buffer region for particle motion "
1313 "between neighborsearch steps");
1316 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlistlong <= ir->rcoulomb)
1318 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
1319 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1320 warning_note(wi, warn_buf);
1322 if (ir_vdw_switched(ir) && (ir->rlistlong <= ir->rvdw))
1324 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
1325 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1326 warning_note(wi, warn_buf);
1330 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1332 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.");
1335 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1338 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1341 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1343 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1346 /* ENERGY CONSERVATION */
1347 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1349 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1351 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1352 evdw_names[evdwSHIFT]);
1353 warning_note(wi, warn_buf);
1355 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1357 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1358 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1359 warning_note(wi, warn_buf);
1363 if (EI_VV(ir->eI) && IR_TWINRANGE(*ir) && ir->nstlist > 1)
1365 sprintf(warn_buf, "Twin-range multiple time stepping does not work with integrator %s.", ei_names[ir->eI]);
1366 warning_error(wi, warn_buf);
1369 /* IMPLICIT SOLVENT */
1370 if (ir->coulombtype == eelGB_NOTUSED)
1372 sprintf(warn_buf, "Invalid option %s for coulombtype",
1373 eel_names[ir->coulombtype]);
1374 warning_error(wi, warn_buf);
1377 if (ir->sa_algorithm == esaSTILL)
1379 sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
1380 CHECK(ir->sa_algorithm == esaSTILL);
1383 if (ir->implicit_solvent == eisGBSA)
1385 sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
1386 CHECK(ir->rgbradii != ir->rlist);
1388 if (ir->coulombtype != eelCUT)
1390 sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
1391 CHECK(ir->coulombtype != eelCUT);
1393 if (ir->vdwtype != evdwCUT)
1395 sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
1396 CHECK(ir->vdwtype != evdwCUT);
1398 if (ir->nstgbradii < 1)
1400 sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
1401 warning_note(wi, warn_buf);
1404 if (ir->sa_algorithm == esaNO)
1406 sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
1407 warning_note(wi, warn_buf);
1409 if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
1411 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");
1412 warning_note(wi, warn_buf);
1414 if (ir->gb_algorithm == egbSTILL)
1416 ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
1420 ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
1423 if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
1425 sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
1426 CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
1433 if (ir->cutoff_scheme != ecutsGROUP)
1435 warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
1439 warning_error(wi, "AdresS simulation supports only stochastic dynamics");
1441 if (ir->epc != epcNO)
1443 warning_error(wi, "AdresS simulation does not support pressure coupling");
1445 if (EEL_FULL(ir->coulombtype))
1447 warning_error(wi, "AdresS simulation does not support long-range electrostatics");
1452 /* count the number of text elemets separated by whitespace in a string.
1453 str = the input string
1454 maxptr = the maximum number of allowed elements
1455 ptr = the output array of pointers to the first character of each element
1456 returns: the number of elements. */
1457 int str_nelem(const char *str, int maxptr, char *ptr[])
1462 copy0 = gmx_strdup(str);
1465 while (*copy != '\0')
1469 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1477 while ((*copy != '\0') && !isspace(*copy))
1496 /* interpret a number of doubles from a string and put them in an array,
1497 after allocating space for them.
1498 str = the input string
1499 n = the (pre-allocated) number of doubles read
1500 r = the output array of doubles. */
1501 static void parse_n_real(char *str, int *n, real **r)
1506 *n = str_nelem(str, MAXPTR, ptr);
1509 for (i = 0; i < *n; i++)
1511 (*r)[i] = strtod(ptr[i], NULL);
1515 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
1518 int i, j, max_n_lambda, nweights, nfep[efptNR];
1519 t_lambda *fep = ir->fepvals;
1520 t_expanded *expand = ir->expandedvals;
1521 real **count_fep_lambdas;
1522 gmx_bool bOneLambda = TRUE;
1524 snew(count_fep_lambdas, efptNR);
1526 /* FEP input processing */
1527 /* first, identify the number of lambda values for each type.
1528 All that are nonzero must have the same number */
1530 for (i = 0; i < efptNR; i++)
1532 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
1535 /* now, determine the number of components. All must be either zero, or equal. */
1538 for (i = 0; i < efptNR; i++)
1540 if (nfep[i] > max_n_lambda)
1542 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1543 must have the same number if its not zero.*/
1548 for (i = 0; i < efptNR; i++)
1552 ir->fepvals->separate_dvdl[i] = FALSE;
1554 else if (nfep[i] == max_n_lambda)
1556 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1557 respect to the temperature currently */
1559 ir->fepvals->separate_dvdl[i] = TRUE;
1564 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1565 nfep[i], efpt_names[i], max_n_lambda);
1568 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1569 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1571 /* the number of lambdas is the number we've read in, which is either zero
1572 or the same for all */
1573 fep->n_lambda = max_n_lambda;
1575 /* allocate space for the array of lambda values */
1576 snew(fep->all_lambda, efptNR);
1577 /* if init_lambda is defined, we need to set lambda */
1578 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1580 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1582 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1583 for (i = 0; i < efptNR; i++)
1585 snew(fep->all_lambda[i], fep->n_lambda);
1586 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1589 for (j = 0; j < fep->n_lambda; j++)
1591 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1593 sfree(count_fep_lambdas[i]);
1596 sfree(count_fep_lambdas);
1598 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1599 bookkeeping -- for now, init_lambda */
1601 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1603 for (i = 0; i < fep->n_lambda; i++)
1605 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1609 /* check to see if only a single component lambda is defined, and soft core is defined.
1610 In this case, turn on coulomb soft core */
1612 if (max_n_lambda == 0)
1618 for (i = 0; i < efptNR; i++)
1620 if ((nfep[i] != 0) && (i != efptFEP))
1626 if ((bOneLambda) && (fep->sc_alpha > 0))
1628 fep->bScCoul = TRUE;
1631 /* Fill in the others with the efptFEP if they are not explicitly
1632 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1633 they are all zero. */
1635 for (i = 0; i < efptNR; i++)
1637 if ((nfep[i] == 0) && (i != efptFEP))
1639 for (j = 0; j < fep->n_lambda; j++)
1641 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1647 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1648 if (fep->sc_r_power == 48)
1650 if (fep->sc_alpha > 0.1)
1652 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1656 /* now read in the weights */
1657 parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
1660 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1662 else if (nweights != fep->n_lambda)
1664 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1665 nweights, fep->n_lambda);
1667 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1669 expand->nstexpanded = fep->nstdhdl;
1670 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1672 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1674 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1675 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1676 2*tau_t just to be careful so it's not to frequent */
1681 static void do_simtemp_params(t_inputrec *ir)
1684 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1685 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1690 static void do_wall_params(t_inputrec *ir,
1691 char *wall_atomtype, char *wall_density,
1695 char *names[MAXPTR];
1698 opts->wall_atomtype[0] = NULL;
1699 opts->wall_atomtype[1] = NULL;
1701 ir->wall_atomtype[0] = -1;
1702 ir->wall_atomtype[1] = -1;
1703 ir->wall_density[0] = 0;
1704 ir->wall_density[1] = 0;
1708 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1709 if (nstr != ir->nwall)
1711 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1714 for (i = 0; i < ir->nwall; i++)
1716 opts->wall_atomtype[i] = gmx_strdup(names[i]);
1719 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1721 nstr = str_nelem(wall_density, MAXPTR, names);
1722 if (nstr != ir->nwall)
1724 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1726 for (i = 0; i < ir->nwall; i++)
1728 sscanf(names[i], "%lf", &dbl);
1731 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1733 ir->wall_density[i] = dbl;
1739 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1747 srenew(groups->grpname, groups->ngrpname+nwall);
1748 grps = &(groups->grps[egcENER]);
1749 srenew(grps->nm_ind, grps->nr+nwall);
1750 for (i = 0; i < nwall; i++)
1752 sprintf(str, "wall%d", i);
1753 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1754 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1759 void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1760 t_expanded *expand, warninp_t wi)
1768 /* read expanded ensemble parameters */
1769 CCTYPE ("expanded ensemble variables");
1770 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1771 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1772 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1773 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1774 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1775 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1776 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1777 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1778 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1779 CCTYPE("Seed for Monte Carlo in lambda space");
1780 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1781 RTYPE ("mc-temperature", expand->mc_temp, -1);
1782 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1783 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1784 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1785 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1786 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1787 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1788 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1789 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1790 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1791 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1792 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
1800 /*! \brief Return whether an end state with the given coupling-lambda
1801 * value describes fully-interacting VDW.
1803 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1804 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1806 static gmx_bool couple_lambda_has_vdw_on(int couple_lambda_value)
1808 return (couple_lambda_value == ecouplamVDW ||
1809 couple_lambda_value == ecouplamVDWQ);
1812 void get_ir(const char *mdparin, const char *mdparout,
1813 t_inputrec *ir, t_gromppopts *opts,
1817 double dumdub[2][6];
1821 char warn_buf[STRLEN];
1822 t_lambda *fep = ir->fepvals;
1823 t_expanded *expand = ir->expandedvals;
1825 init_inputrec_strings();
1826 inp = read_inpfile(mdparin, &ninp, wi);
1828 snew(dumstr[0], STRLEN);
1829 snew(dumstr[1], STRLEN);
1831 if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
1834 "%s did not specify a value for the .mdp option "
1835 "\"cutoff-scheme\". Probably it was first intended for use "
1836 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1837 "introduced, but the group scheme was still the default. "
1838 "The default is now the Verlet scheme, so you will observe "
1839 "different behaviour.", mdparin);
1840 warning_note(wi, warn_buf);
1843 /* ignore the following deprecated commands */
1846 REM_TYPE("domain-decomposition");
1847 REM_TYPE("andersen-seed");
1849 REM_TYPE("dihre-fc");
1850 REM_TYPE("dihre-tau");
1851 REM_TYPE("nstdihreout");
1852 REM_TYPE("nstcheckpoint");
1853 REM_TYPE("optimize-fft");
1855 /* replace the following commands with the clearer new versions*/
1856 REPL_TYPE("unconstrained-start", "continuation");
1857 REPL_TYPE("foreign-lambda", "fep-lambdas");
1858 REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
1859 REPL_TYPE("nstxtcout", "nstxout-compressed");
1860 REPL_TYPE("xtc-grps", "compressed-x-grps");
1861 REPL_TYPE("xtc-precision", "compressed-x-precision");
1863 CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
1864 CTYPE ("Preprocessor information: use cpp syntax.");
1865 CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
1866 STYPE ("include", opts->include, NULL);
1867 CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1868 STYPE ("define", opts->define, NULL);
1870 CCTYPE ("RUN CONTROL PARAMETERS");
1871 EETYPE("integrator", ir->eI, ei_names);
1872 CTYPE ("Start time and timestep in ps");
1873 RTYPE ("tinit", ir->init_t, 0.0);
1874 RTYPE ("dt", ir->delta_t, 0.001);
1875 STEPTYPE ("nsteps", ir->nsteps, 0);
1876 CTYPE ("For exact run continuation or redoing part of a run");
1877 STEPTYPE ("init-step", ir->init_step, 0);
1878 CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
1879 ITYPE ("simulation-part", ir->simulation_part, 1);
1880 CTYPE ("mode for center of mass motion removal");
1881 EETYPE("comm-mode", ir->comm_mode, ecm_names);
1882 CTYPE ("number of steps for center of mass motion removal");
1883 ITYPE ("nstcomm", ir->nstcomm, 100);
1884 CTYPE ("group(s) for center of mass motion removal");
1885 STYPE ("comm-grps", is->vcm, NULL);
1887 CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
1888 CTYPE ("Friction coefficient (amu/ps) and random seed");
1889 RTYPE ("bd-fric", ir->bd_fric, 0.0);
1890 STEPTYPE ("ld-seed", ir->ld_seed, -1);
1893 CCTYPE ("ENERGY MINIMIZATION OPTIONS");
1894 CTYPE ("Force tolerance and initial step-size");
1895 RTYPE ("emtol", ir->em_tol, 10.0);
1896 RTYPE ("emstep", ir->em_stepsize, 0.01);
1897 CTYPE ("Max number of iterations in relax-shells");
1898 ITYPE ("niter", ir->niter, 20);
1899 CTYPE ("Step size (ps^2) for minimization of flexible constraints");
1900 RTYPE ("fcstep", ir->fc_stepsize, 0);
1901 CTYPE ("Frequency of steepest descents steps when doing CG");
1902 ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
1903 ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
1905 CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
1906 RTYPE ("rtpi", ir->rtpi, 0.05);
1908 /* Output options */
1909 CCTYPE ("OUTPUT CONTROL OPTIONS");
1910 CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
1911 ITYPE ("nstxout", ir->nstxout, 0);
1912 ITYPE ("nstvout", ir->nstvout, 0);
1913 ITYPE ("nstfout", ir->nstfout, 0);
1914 CTYPE ("Output frequency for energies to log file and energy file");
1915 ITYPE ("nstlog", ir->nstlog, 1000);
1916 ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
1917 ITYPE ("nstenergy", ir->nstenergy, 1000);
1918 CTYPE ("Output frequency and precision for .xtc file");
1919 ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
1920 RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
1921 CTYPE ("This selects the subset of atoms for the compressed");
1922 CTYPE ("trajectory file. You can select multiple groups. By");
1923 CTYPE ("default, all atoms will be written.");
1924 STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
1925 CTYPE ("Selection of energy groups");
1926 STYPE ("energygrps", is->energy, NULL);
1928 /* Neighbor searching */
1929 CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
1930 CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1931 EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
1932 CTYPE ("nblist update frequency");
1933 ITYPE ("nstlist", ir->nstlist, 10);
1934 CTYPE ("ns algorithm (simple or grid)");
1935 EETYPE("ns-type", ir->ns_type, ens_names);
1936 CTYPE ("Periodic boundary conditions: xyz, no, xy");
1937 EETYPE("pbc", ir->ePBC, epbc_names);
1938 EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
1939 CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1940 CTYPE ("a value of -1 means: use rlist");
1941 RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
1942 CTYPE ("nblist cut-off");
1943 RTYPE ("rlist", ir->rlist, 1.0);
1944 CTYPE ("long-range cut-off for switched potentials");
1945 RTYPE ("rlistlong", ir->rlistlong, -1);
1946 ITYPE ("nstcalclr", ir->nstcalclr, -1);
1948 /* Electrostatics */
1949 CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
1950 CTYPE ("Method for doing electrostatics");
1951 EETYPE("coulombtype", ir->coulombtype, eel_names);
1952 EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
1953 CTYPE ("cut-off lengths");
1954 RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
1955 RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
1956 CTYPE ("Relative dielectric constant for the medium and the reaction field");
1957 RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
1958 RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
1959 CTYPE ("Method for doing Van der Waals");
1960 EETYPE("vdw-type", ir->vdwtype, evdw_names);
1961 EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
1962 CTYPE ("cut-off lengths");
1963 RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
1964 RTYPE ("rvdw", ir->rvdw, 1.0);
1965 CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
1966 EETYPE("DispCorr", ir->eDispCorr, edispc_names);
1967 CTYPE ("Extension of the potential lookup tables beyond the cut-off");
1968 RTYPE ("table-extension", ir->tabext, 1.0);
1969 CTYPE ("Separate tables between energy group pairs");
1970 STYPE ("energygrp-table", is->egptable, NULL);
1971 CTYPE ("Spacing for the PME/PPPM FFT grid");
1972 RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
1973 CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
1974 ITYPE ("fourier-nx", ir->nkx, 0);
1975 ITYPE ("fourier-ny", ir->nky, 0);
1976 ITYPE ("fourier-nz", ir->nkz, 0);
1977 CTYPE ("EWALD/PME/PPPM parameters");
1978 ITYPE ("pme-order", ir->pme_order, 4);
1979 RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
1980 RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
1981 EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
1982 EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
1983 RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
1985 CCTYPE("IMPLICIT SOLVENT ALGORITHM");
1986 EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
1988 CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
1989 CTYPE ("Algorithm for calculating Born radii");
1990 EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
1991 CTYPE ("Frequency of calculating the Born radii inside rlist");
1992 ITYPE ("nstgbradii", ir->nstgbradii, 1);
1993 CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
1994 CTYPE ("between rlist and rgbradii is updated every nstlist steps");
1995 RTYPE ("rgbradii", ir->rgbradii, 1.0);
1996 CTYPE ("Dielectric coefficient of the implicit solvent");
1997 RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
1998 CTYPE ("Salt concentration in M for Generalized Born models");
1999 RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
2000 CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
2001 RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
2002 RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
2003 RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
2004 RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
2005 EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
2006 CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
2007 CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
2008 RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
2010 /* Coupling stuff */
2011 CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
2012 CTYPE ("Temperature coupling");
2013 EETYPE("tcoupl", ir->etc, etcoupl_names);
2014 ITYPE ("nsttcouple", ir->nsttcouple, -1);
2015 ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
2016 EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
2017 CTYPE ("Groups to couple separately");
2018 STYPE ("tc-grps", is->tcgrps, NULL);
2019 CTYPE ("Time constant (ps) and reference temperature (K)");
2020 STYPE ("tau-t", is->tau_t, NULL);
2021 STYPE ("ref-t", is->ref_t, NULL);
2022 CTYPE ("pressure coupling");
2023 EETYPE("pcoupl", ir->epc, epcoupl_names);
2024 EETYPE("pcoupltype", ir->epct, epcoupltype_names);
2025 ITYPE ("nstpcouple", ir->nstpcouple, -1);
2026 CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
2027 RTYPE ("tau-p", ir->tau_p, 1.0);
2028 STYPE ("compressibility", dumstr[0], NULL);
2029 STYPE ("ref-p", dumstr[1], NULL);
2030 CTYPE ("Scaling of reference coordinates, No, All or COM");
2031 EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
2034 CCTYPE ("OPTIONS FOR QMMM calculations");
2035 EETYPE("QMMM", ir->bQMMM, yesno_names);
2036 CTYPE ("Groups treated Quantum Mechanically");
2037 STYPE ("QMMM-grps", is->QMMM, NULL);
2038 CTYPE ("QM method");
2039 STYPE("QMmethod", is->QMmethod, NULL);
2040 CTYPE ("QMMM scheme");
2041 EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
2042 CTYPE ("QM basisset");
2043 STYPE("QMbasis", is->QMbasis, NULL);
2044 CTYPE ("QM charge");
2045 STYPE ("QMcharge", is->QMcharge, NULL);
2046 CTYPE ("QM multiplicity");
2047 STYPE ("QMmult", is->QMmult, NULL);
2048 CTYPE ("Surface Hopping");
2049 STYPE ("SH", is->bSH, NULL);
2050 CTYPE ("CAS space options");
2051 STYPE ("CASorbitals", is->CASorbitals, NULL);
2052 STYPE ("CASelectrons", is->CASelectrons, NULL);
2053 STYPE ("SAon", is->SAon, NULL);
2054 STYPE ("SAoff", is->SAoff, NULL);
2055 STYPE ("SAsteps", is->SAsteps, NULL);
2056 CTYPE ("Scale factor for MM charges");
2057 RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
2058 CTYPE ("Optimization of QM subsystem");
2059 STYPE ("bOPT", is->bOPT, NULL);
2060 STYPE ("bTS", is->bTS, NULL);
2062 /* Simulated annealing */
2063 CCTYPE("SIMULATED ANNEALING");
2064 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
2065 STYPE ("annealing", is->anneal, NULL);
2066 CTYPE ("Number of time points to use for specifying annealing in each group");
2067 STYPE ("annealing-npoints", is->anneal_npoints, NULL);
2068 CTYPE ("List of times at the annealing points for each group");
2069 STYPE ("annealing-time", is->anneal_time, NULL);
2070 CTYPE ("Temp. at each annealing point, for each group.");
2071 STYPE ("annealing-temp", is->anneal_temp, NULL);
2074 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
2075 EETYPE("gen-vel", opts->bGenVel, yesno_names);
2076 RTYPE ("gen-temp", opts->tempi, 300.0);
2077 ITYPE ("gen-seed", opts->seed, -1);
2080 CCTYPE ("OPTIONS FOR BONDS");
2081 EETYPE("constraints", opts->nshake, constraints);
2082 CTYPE ("Type of constraint algorithm");
2083 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
2084 CTYPE ("Do not constrain the start configuration");
2085 EETYPE("continuation", ir->bContinuation, yesno_names);
2086 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
2087 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
2088 CTYPE ("Relative tolerance of shake");
2089 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
2090 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
2091 ITYPE ("lincs-order", ir->nProjOrder, 4);
2092 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
2093 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
2094 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
2095 ITYPE ("lincs-iter", ir->nLincsIter, 1);
2096 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
2097 CTYPE ("rotates over more degrees than");
2098 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
2099 CTYPE ("Convert harmonic bonds to morse potentials");
2100 EETYPE("morse", opts->bMorse, yesno_names);
2102 /* Energy group exclusions */
2103 CCTYPE ("ENERGY GROUP EXCLUSIONS");
2104 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
2105 STYPE ("energygrp-excl", is->egpexcl, NULL);
2109 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2110 ITYPE ("nwall", ir->nwall, 0);
2111 EETYPE("wall-type", ir->wall_type, ewt_names);
2112 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
2113 STYPE ("wall-atomtype", is->wall_atomtype, NULL);
2114 STYPE ("wall-density", is->wall_density, NULL);
2115 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
2118 CCTYPE("COM PULLING");
2119 EETYPE("pull", ir->bPull, yesno_names);
2123 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, wi);
2126 /* Enforced rotation */
2127 CCTYPE("ENFORCED ROTATION");
2128 CTYPE("Enforced rotation: No or Yes");
2129 EETYPE("rotation", ir->bRot, yesno_names);
2133 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2136 /* Interactive MD */
2138 CCTYPE("Group to display and/or manipulate in interactive MD session");
2139 STYPE ("IMD-group", is->imd_grp, NULL);
2140 if (is->imd_grp[0] != '\0')
2147 CCTYPE("NMR refinement stuff");
2148 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2149 EETYPE("disre", ir->eDisre, edisre_names);
2150 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2151 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2152 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2153 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2154 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2155 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2156 CTYPE ("Output frequency for pair distances to energy file");
2157 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2158 CTYPE ("Orientation restraints: No or Yes");
2159 EETYPE("orire", opts->bOrire, yesno_names);
2160 CTYPE ("Orientation restraints force constant and tau for time averaging");
2161 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2162 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2163 STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
2164 CTYPE ("Output frequency for trace(SD) and S to energy file");
2165 ITYPE ("nstorireout", ir->nstorireout, 100);
2167 /* free energy variables */
2168 CCTYPE ("Free energy variables");
2169 EETYPE("free-energy", ir->efep, efep_names);
2170 STYPE ("couple-moltype", is->couple_moltype, NULL);
2171 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2172 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2173 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2175 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2177 it was not entered */
2178 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2179 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2180 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2181 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
2182 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
2183 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
2184 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
2185 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
2186 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
2187 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
2188 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2189 STYPE ("init-lambda-weights", is->lambda_weights, NULL);
2190 EETYPE("dhdl-print-energy", fep->edHdLPrintEnergy, edHdLPrintEnergy_names);
2191 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2192 ITYPE ("sc-power", fep->sc_power, 1);
2193 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2194 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2195 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2196 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2197 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2198 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2199 separate_dhdl_file_names);
2200 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2201 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2202 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2204 /* Non-equilibrium MD stuff */
2205 CCTYPE("Non-equilibrium MD stuff");
2206 STYPE ("acc-grps", is->accgrps, NULL);
2207 STYPE ("accelerate", is->acc, NULL);
2208 STYPE ("freezegrps", is->freeze, NULL);
2209 STYPE ("freezedim", is->frdim, NULL);
2210 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2211 STYPE ("deform", is->deform, NULL);
2213 /* simulated tempering variables */
2214 CCTYPE("simulated tempering variables");
2215 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2216 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2217 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2218 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2220 /* expanded ensemble variables */
2221 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2223 read_expandedparams(&ninp, &inp, expand, wi);
2226 /* Electric fields */
2227 CCTYPE("Electric fields");
2228 CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
2229 CTYPE ("and a phase angle (real)");
2230 STYPE ("E-x", is->efield_x, NULL);
2231 CTYPE ("Time dependent (pulsed) electric field. Format is omega, time for pulse");
2232 CTYPE ("peak, and sigma (width) for pulse. Sigma = 0 removes pulse, leaving");
2233 CTYPE ("the field to be a cosine function.");
2234 STYPE ("E-xt", is->efield_xt, NULL);
2235 STYPE ("E-y", is->efield_y, NULL);
2236 STYPE ("E-yt", is->efield_yt, NULL);
2237 STYPE ("E-z", is->efield_z, NULL);
2238 STYPE ("E-zt", is->efield_zt, NULL);
2240 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2241 CTYPE("Swap positions along direction: no, X, Y, Z");
2242 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2243 if (ir->eSwapCoords != eswapNO)
2246 CTYPE("Swap attempt frequency");
2247 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2248 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2249 STYPE("split-group0", splitgrp0, NULL);
2250 STYPE("split-group1", splitgrp1, NULL);
2251 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2252 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2253 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2255 CTYPE("Group name of ions that can be exchanged with solvent molecules");
2256 STYPE("swap-group", swapgrp, NULL);
2257 CTYPE("Group name of solvent molecules");
2258 STYPE("solvent-group", solgrp, NULL);
2260 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2261 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2262 CTYPE("however, if correctly defined, the ion permeation events are counted per channel");
2263 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2264 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2265 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2266 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2267 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2268 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2270 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2271 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2272 CTYPE("Requested number of anions and cations for each of the two compartments");
2273 CTYPE("-1 means fix the numbers as found in time step 0");
2274 ITYPE("anionsA", ir->swap->nanions[0], -1);
2275 ITYPE("cationsA", ir->swap->ncations[0], -1);
2276 ITYPE("anionsB", ir->swap->nanions[1], -1);
2277 ITYPE("cationsB", ir->swap->ncations[1], -1);
2278 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2279 RTYPE("threshold", ir->swap->threshold, 1.0);
2282 /* AdResS defined thingies */
2283 CCTYPE ("AdResS parameters");
2284 EETYPE("adress", ir->bAdress, yesno_names);
2287 snew(ir->adress, 1);
2288 read_adressparams(&ninp, &inp, ir->adress, wi);
2291 /* User defined thingies */
2292 CCTYPE ("User defined thingies");
2293 STYPE ("user1-grps", is->user1, NULL);
2294 STYPE ("user2-grps", is->user2, NULL);
2295 ITYPE ("userint1", ir->userint1, 0);
2296 ITYPE ("userint2", ir->userint2, 0);
2297 ITYPE ("userint3", ir->userint3, 0);
2298 ITYPE ("userint4", ir->userint4, 0);
2299 RTYPE ("userreal1", ir->userreal1, 0);
2300 RTYPE ("userreal2", ir->userreal2, 0);
2301 RTYPE ("userreal3", ir->userreal3, 0);
2302 RTYPE ("userreal4", ir->userreal4, 0);
2305 write_inpfile(mdparout, ninp, inp, FALSE, wi);
2306 for (i = 0; (i < ninp); i++)
2309 sfree(inp[i].value);
2313 /* Process options if necessary */
2314 for (m = 0; m < 2; m++)
2316 for (i = 0; i < 2*DIM; i++)
2325 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2327 warning_error(wi, "Pressure coupling not enough values (I need 1)");
2329 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2331 case epctSEMIISOTROPIC:
2332 case epctSURFACETENSION:
2333 if (sscanf(dumstr[m], "%lf%lf",
2334 &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2336 warning_error(wi, "Pressure coupling not enough values (I need 2)");
2338 dumdub[m][YY] = dumdub[m][XX];
2340 case epctANISOTROPIC:
2341 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2342 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2343 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2345 warning_error(wi, "Pressure coupling not enough values (I need 6)");
2349 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2350 epcoupltype_names[ir->epct]);
2354 clear_mat(ir->ref_p);
2355 clear_mat(ir->compress);
2356 for (i = 0; i < DIM; i++)
2358 ir->ref_p[i][i] = dumdub[1][i];
2359 ir->compress[i][i] = dumdub[0][i];
2361 if (ir->epct == epctANISOTROPIC)
2363 ir->ref_p[XX][YY] = dumdub[1][3];
2364 ir->ref_p[XX][ZZ] = dumdub[1][4];
2365 ir->ref_p[YY][ZZ] = dumdub[1][5];
2366 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2368 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2370 ir->compress[XX][YY] = dumdub[0][3];
2371 ir->compress[XX][ZZ] = dumdub[0][4];
2372 ir->compress[YY][ZZ] = dumdub[0][5];
2373 for (i = 0; i < DIM; i++)
2375 for (m = 0; m < i; m++)
2377 ir->ref_p[i][m] = ir->ref_p[m][i];
2378 ir->compress[i][m] = ir->compress[m][i];
2383 if (ir->comm_mode == ecmNO)
2388 opts->couple_moltype = NULL;
2389 if (strlen(is->couple_moltype) > 0)
2391 if (ir->efep != efepNO)
2393 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2394 if (opts->couple_lam0 == opts->couple_lam1)
2396 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2398 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2399 opts->couple_lam1 == ecouplamNONE))
2401 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2406 warning_note(wi, "Free energy is turned off, so we will not decouple the molecule listed in your input.");
2409 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2410 if (ir->efep != efepNO)
2412 if (fep->delta_lambda > 0)
2414 ir->efep = efepSLOWGROWTH;
2418 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2420 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2421 warning_note(wi, "Old option for dhdl-print-energy given: "
2422 "changing \"yes\" to \"total\"\n");
2425 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2427 /* always print out the energy to dhdl if we are doing
2428 expanded ensemble, since we need the total energy for
2429 analysis if the temperature is changing. In some
2430 conditions one may only want the potential energy, so
2431 we will allow that if the appropriate mdp setting has
2432 been enabled. Otherwise, total it is:
2434 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2437 if ((ir->efep != efepNO) || ir->bSimTemp)
2439 ir->bExpanded = FALSE;
2440 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2442 ir->bExpanded = TRUE;
2444 do_fep_params(ir, is->fep_lambda, is->lambda_weights);
2445 if (ir->bSimTemp) /* done after fep params */
2447 do_simtemp_params(ir);
2450 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2451 * setup and not on the old way of specifying the free-energy setup,
2452 * we should check for using soft-core when not needed, since that
2453 * can complicate the sampling significantly.
2454 * Note that we only check for the automated coupling setup.
2455 * If the (advanced) user does FEP through manual topology changes,
2456 * this check will not be triggered.
2458 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 &&
2459 ir->fepvals->sc_alpha != 0 &&
2460 (couple_lambda_has_vdw_on(opts->couple_lam0) &&
2461 couple_lambda_has_vdw_on(opts->couple_lam1)))
2463 warning(wi, "You are using soft-core interactions while the Van der Waals interactions are not decoupled (note that the sc-coul option is only active when using lambda states). Although this will not lead to errors, you will need much more sampling than without soft-core interactions. Consider using sc-alpha=0.");
2468 ir->fepvals->n_lambda = 0;
2471 /* WALL PARAMETERS */
2473 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2475 /* ORIENTATION RESTRAINT PARAMETERS */
2477 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
2479 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2482 /* DEFORMATION PARAMETERS */
2484 clear_mat(ir->deform);
2485 for (i = 0; i < 6; i++)
2489 sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
2490 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2491 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2492 for (i = 0; i < 3; i++)
2494 ir->deform[i][i] = dumdub[0][i];
2496 ir->deform[YY][XX] = dumdub[0][3];
2497 ir->deform[ZZ][XX] = dumdub[0][4];
2498 ir->deform[ZZ][YY] = dumdub[0][5];
2499 if (ir->epc != epcNO)
2501 for (i = 0; i < 3; i++)
2503 for (j = 0; j <= i; j++)
2505 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2507 warning_error(wi, "A box element has deform set and compressibility > 0");
2511 for (i = 0; i < 3; i++)
2513 for (j = 0; j < i; j++)
2515 if (ir->deform[i][j] != 0)
2517 for (m = j; m < DIM; m++)
2519 if (ir->compress[m][j] != 0)
2521 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.");
2522 warning(wi, warn_buf);
2530 /* Ion/water position swapping checks */
2531 if (ir->eSwapCoords != eswapNO)
2533 if (ir->swap->nstswap < 1)
2535 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2537 if (ir->swap->nAverage < 1)
2539 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2541 if (ir->swap->threshold < 1.0)
2543 warning_error(wi, "Ion count threshold must be at least 1.\n");
2551 static int search_QMstring(const char *s, int ng, const char *gn[])
2553 /* same as normal search_string, but this one searches QM strings */
2556 for (i = 0; (i < ng); i++)
2558 if (gmx_strcasecmp(s, gn[i]) == 0)
2564 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2568 } /* search_QMstring */
2570 /* We would like gn to be const as well, but C doesn't allow this */
2571 /* TODO this is utility functionality (search for the index of a
2572 string in a collection), so should be refactored and located more
2574 int search_string(const char *s, int ng, char *gn[])
2578 for (i = 0; (i < ng); i++)
2580 if (gmx_strcasecmp(s, gn[i]) == 0)
2587 "Group %s referenced in the .mdp file was not found in the index file.\n"
2588 "Group names must match either [moleculetype] names or custom index group\n"
2589 "names, in which case you must supply an index file to the '-n' option\n"
2596 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2597 t_blocka *block, char *gnames[],
2598 int gtype, int restnm,
2599 int grptp, gmx_bool bVerbose,
2602 unsigned short *cbuf;
2603 t_grps *grps = &(groups->grps[gtype]);
2604 int i, j, gid, aj, ognr, ntot = 0;
2607 char warn_buf[STRLEN];
2611 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2614 title = gtypes[gtype];
2617 /* Mark all id's as not set */
2618 for (i = 0; (i < natoms); i++)
2623 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2624 for (i = 0; (i < ng); i++)
2626 /* Lookup the group name in the block structure */
2627 gid = search_string(ptrs[i], block->nr, gnames);
2628 if ((grptp != egrptpONE) || (i == 0))
2630 grps->nm_ind[grps->nr++] = gid;
2634 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2637 /* Now go over the atoms in the group */
2638 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2643 /* Range checking */
2644 if ((aj < 0) || (aj >= natoms))
2646 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2648 /* Lookup up the old group number */
2652 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2653 aj+1, title, ognr+1, i+1);
2657 /* Store the group number in buffer */
2658 if (grptp == egrptpONE)
2671 /* Now check whether we have done all atoms */
2675 if (grptp == egrptpALL)
2677 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2678 natoms-ntot, title);
2680 else if (grptp == egrptpPART)
2682 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2683 natoms-ntot, title);
2684 warning_note(wi, warn_buf);
2686 /* Assign all atoms currently unassigned to a rest group */
2687 for (j = 0; (j < natoms); j++)
2689 if (cbuf[j] == NOGID)
2695 if (grptp != egrptpPART)
2700 "Making dummy/rest group for %s containing %d elements\n",
2701 title, natoms-ntot);
2703 /* Add group name "rest" */
2704 grps->nm_ind[grps->nr] = restnm;
2706 /* Assign the rest name to all atoms not currently assigned to a group */
2707 for (j = 0; (j < natoms); j++)
2709 if (cbuf[j] == NOGID)
2718 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2720 /* All atoms are part of one (or no) group, no index required */
2721 groups->ngrpnr[gtype] = 0;
2722 groups->grpnr[gtype] = NULL;
2726 groups->ngrpnr[gtype] = natoms;
2727 snew(groups->grpnr[gtype], natoms);
2728 for (j = 0; (j < natoms); j++)
2730 groups->grpnr[gtype][j] = cbuf[j];
2736 return (bRest && grptp == egrptpPART);
2739 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2742 gmx_groups_t *groups;
2743 pull_params_t *pull;
2744 int natoms, ai, aj, i, j, d, g, imin, jmin;
2746 int *nrdf2, *na_vcm, na_tot;
2747 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2748 gmx_mtop_atomloop_all_t aloop;
2750 int mb, mol, ftype, as;
2751 gmx_molblock_t *molb;
2752 gmx_moltype_t *molt;
2755 * First calc 3xnr-atoms for each group
2756 * then subtract half a degree of freedom for each constraint
2758 * Only atoms and nuclei contribute to the degrees of freedom...
2763 groups = &mtop->groups;
2764 natoms = mtop->natoms;
2766 /* Allocate one more for a possible rest group */
2767 /* We need to sum degrees of freedom into doubles,
2768 * since floats give too low nrdf's above 3 million atoms.
2770 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2771 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2772 snew(na_vcm, groups->grps[egcVCM].nr+1);
2774 for (i = 0; i < groups->grps[egcTC].nr; i++)
2778 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2783 snew(nrdf2, natoms);
2784 aloop = gmx_mtop_atomloop_all_init(mtop);
2785 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2788 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2790 g = ggrpnr(groups, egcFREEZE, i);
2791 /* Double count nrdf for particle i */
2792 for (d = 0; d < DIM; d++)
2794 if (opts->nFreeze[g][d] == 0)
2799 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2800 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2805 for (mb = 0; mb < mtop->nmolblock; mb++)
2807 molb = &mtop->molblock[mb];
2808 molt = &mtop->moltype[molb->type];
2809 atom = molt->atoms.atom;
2810 for (mol = 0; mol < molb->nmol; mol++)
2812 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2814 ia = molt->ilist[ftype].iatoms;
2815 for (i = 0; i < molt->ilist[ftype].nr; )
2817 /* Subtract degrees of freedom for the constraints,
2818 * if the particles still have degrees of freedom left.
2819 * If one of the particles is a vsite or a shell, then all
2820 * constraint motion will go there, but since they do not
2821 * contribute to the constraints the degrees of freedom do not
2826 if (((atom[ia[1]].ptype == eptNucleus) ||
2827 (atom[ia[1]].ptype == eptAtom)) &&
2828 ((atom[ia[2]].ptype == eptNucleus) ||
2829 (atom[ia[2]].ptype == eptAtom)))
2847 imin = std::min(imin, nrdf2[ai]);
2848 jmin = std::min(jmin, nrdf2[aj]);
2851 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2852 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2853 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2854 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2856 ia += interaction_function[ftype].nratoms+1;
2857 i += interaction_function[ftype].nratoms+1;
2860 ia = molt->ilist[F_SETTLE].iatoms;
2861 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2863 /* Subtract 1 dof from every atom in the SETTLE */
2864 for (j = 0; j < 3; j++)
2867 imin = std::min(2, nrdf2[ai]);
2869 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2870 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2875 as += molt->atoms.nr;
2881 /* Correct nrdf for the COM constraints.
2882 * We correct using the TC and VCM group of the first atom
2883 * in the reference and pull group. If atoms in one pull group
2884 * belong to different TC or VCM groups it is anyhow difficult
2885 * to determine the optimal nrdf assignment.
2889 for (i = 0; i < pull->ncoord; i++)
2891 if (pull->coord[i].eType != epullCONSTRAINT)
2898 for (j = 0; j < 2; j++)
2900 const t_pull_group *pgrp;
2902 pgrp = &pull->group[pull->coord[i].group[j]];
2906 /* Subtract 1/2 dof from each group */
2908 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2909 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2910 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2912 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)]]);
2917 /* We need to subtract the whole DOF from group j=1 */
2924 if (ir->nstcomm != 0)
2926 /* Subtract 3 from the number of degrees of freedom in each vcm group
2927 * when com translation is removed and 6 when rotation is removed
2930 switch (ir->comm_mode)
2933 n_sub = ndof_com(ir);
2939 gmx_incons("Checking comm_mode");
2942 for (i = 0; i < groups->grps[egcTC].nr; i++)
2944 /* Count the number of atoms of TC group i for every VCM group */
2945 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2950 for (ai = 0; ai < natoms; ai++)
2952 if (ggrpnr(groups, egcTC, ai) == i)
2954 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2958 /* Correct for VCM removal according to the fraction of each VCM
2959 * group present in this TC group.
2961 nrdf_uc = nrdf_tc[i];
2964 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2968 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2970 if (nrdf_vcm[j] > n_sub)
2972 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2973 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2977 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2978 j, nrdf_vcm[j], nrdf_tc[i]);
2983 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2985 opts->nrdf[i] = nrdf_tc[i];
2986 if (opts->nrdf[i] < 0)
2991 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2992 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
3001 static void decode_cos(char *s, t_cosines *cosine)
3004 char format[STRLEN], f1[STRLEN];
3016 sscanf(t, "%d", &(cosine->n));
3023 snew(cosine->a, cosine->n);
3024 snew(cosine->phi, cosine->n);
3026 sprintf(format, "%%*d");
3027 for (i = 0; (i < cosine->n); i++)
3030 strcat(f1, "%lf%lf");
3031 if (sscanf(t, f1, &a, &phi) < 2)
3033 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
3036 cosine->phi[i] = phi;
3037 strcat(format, "%*lf%*lf");
3044 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
3045 const char *option, const char *val, int flag)
3047 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3048 * But since this is much larger than STRLEN, such a line can not be parsed.
3049 * The real maximum is the number of names that fit in a string: STRLEN/2.
3051 #define EGP_MAX (STRLEN/2)
3052 int nelem, i, j, k, nr;
3053 char *names[EGP_MAX];
3057 gnames = groups->grpname;
3059 nelem = str_nelem(val, EGP_MAX, names);
3062 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3064 nr = groups->grps[egcENER].nr;
3066 for (i = 0; i < nelem/2; i++)
3070 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
3076 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3077 names[2*i], option);
3081 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
3087 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3088 names[2*i+1], option);
3090 if ((j < nr) && (k < nr))
3092 ir->opts.egp_flags[nr*j+k] |= flag;
3093 ir->opts.egp_flags[nr*k+j] |= flag;
3102 static void make_swap_groups(
3111 int ig = -1, i = 0, j;
3115 /* Just a quick check here, more thorough checks are in mdrun */
3116 if (strcmp(splitg0name, splitg1name) == 0)
3118 gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
3121 /* First get the swap group index atoms */
3122 ig = search_string(swapgname, grps->nr, gnames);
3123 swap->nat = grps->index[ig+1] - grps->index[ig];
3126 fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
3127 snew(swap->ind, swap->nat);
3128 for (i = 0; i < swap->nat; i++)
3130 swap->ind[i] = grps->a[grps->index[ig]+i];
3135 gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
3138 /* Now do so for the split groups */
3139 for (j = 0; j < 2; j++)
3143 splitg = splitg0name;
3147 splitg = splitg1name;
3150 ig = search_string(splitg, grps->nr, gnames);
3151 swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
3152 if (swap->nat_split[j] > 0)
3154 fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
3155 j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
3156 snew(swap->ind_split[j], swap->nat_split[j]);
3157 for (i = 0; i < swap->nat_split[j]; i++)
3159 swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
3164 gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
3168 /* Now get the solvent group index atoms */
3169 ig = search_string(solgname, grps->nr, gnames);
3170 swap->nat_sol = grps->index[ig+1] - grps->index[ig];
3171 if (swap->nat_sol > 0)
3173 fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
3174 snew(swap->ind_sol, swap->nat_sol);
3175 for (i = 0; i < swap->nat_sol; i++)
3177 swap->ind_sol[i] = grps->a[grps->index[ig]+i];
3182 gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
3187 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3192 ig = search_string(IMDgname, grps->nr, gnames);
3193 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3195 if (IMDgroup->nat > 0)
3197 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3198 IMDgname, IMDgroup->nat);
3199 snew(IMDgroup->ind, IMDgroup->nat);
3200 for (i = 0; i < IMDgroup->nat; i++)
3202 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3208 void do_index(const char* mdparin, const char *ndx,
3215 gmx_groups_t *groups;
3219 char warnbuf[STRLEN], **gnames;
3220 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3223 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3224 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3225 int i, j, k, restnm;
3226 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3227 int nQMmethod, nQMbasis, nQMg;
3228 char warn_buf[STRLEN];
3232 fprintf(stderr, "processing index file...\n");
3238 snew(grps->index, 1);
3240 atoms_all = gmx_mtop_global_atoms(mtop);
3241 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3242 free_t_atoms(&atoms_all, FALSE);
3246 grps = init_index(ndx, &gnames);
3249 groups = &mtop->groups;
3250 natoms = mtop->natoms;
3251 symtab = &mtop->symtab;
3253 snew(groups->grpname, grps->nr+1);
3255 for (i = 0; (i < grps->nr); i++)
3257 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3259 groups->grpname[i] = put_symtab(symtab, "rest");
3261 srenew(gnames, grps->nr+1);
3262 gnames[restnm] = *(groups->grpname[i]);
3263 groups->ngrpname = grps->nr+1;
3265 set_warning_line(wi, mdparin, -1);
3267 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3268 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3269 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3270 if ((ntau_t != ntcg) || (nref_t != ntcg))
3272 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3273 "%d tau-t values", ntcg, nref_t, ntau_t);
3276 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3277 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3278 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3279 nr = groups->grps[egcTC].nr;
3281 snew(ir->opts.nrdf, nr);
3282 snew(ir->opts.tau_t, nr);
3283 snew(ir->opts.ref_t, nr);
3284 if (ir->eI == eiBD && ir->bd_fric == 0)
3286 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3293 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3297 for (i = 0; (i < nr); i++)
3299 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
3300 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
3302 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3303 warning_error(wi, warn_buf);
3306 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3308 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.");
3311 if (ir->opts.tau_t[i] >= 0)
3313 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3316 if (ir->etc != etcNO && ir->nsttcouple == -1)
3318 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3323 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3325 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");
3327 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
3329 if (ir->nstpcouple != ir->nsttcouple)
3331 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3332 ir->nstpcouple = ir->nsttcouple = mincouple;
3333 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);
3334 warning_note(wi, warn_buf);
3338 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3339 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3341 if (ETC_ANDERSEN(ir->etc))
3343 if (ir->nsttcouple != 1)
3346 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");
3347 warning_note(wi, warn_buf);
3350 nstcmin = tcouple_min_integration_steps(ir->etc);
3353 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin - 10*GMX_REAL_EPS)
3355 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3356 ETCOUPLTYPE(ir->etc),
3358 ir->nsttcouple*ir->delta_t);
3359 warning(wi, warn_buf);
3362 for (i = 0; (i < nr); i++)
3364 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
3365 if (ir->opts.ref_t[i] < 0)
3367 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3370 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3371 if we are in this conditional) if mc_temp is negative */
3372 if (ir->expandedvals->mc_temp < 0)
3374 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3378 /* Simulated annealing for each group. There are nr groups */
3379 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3380 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3384 if (nSA > 0 && nSA != nr)
3386 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3390 snew(ir->opts.annealing, nr);
3391 snew(ir->opts.anneal_npoints, nr);
3392 snew(ir->opts.anneal_time, nr);
3393 snew(ir->opts.anneal_temp, nr);
3394 for (i = 0; i < nr; i++)
3396 ir->opts.annealing[i] = eannNO;
3397 ir->opts.anneal_npoints[i] = 0;
3398 ir->opts.anneal_time[i] = NULL;
3399 ir->opts.anneal_temp[i] = NULL;
3404 for (i = 0; i < nr; i++)
3406 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3408 ir->opts.annealing[i] = eannNO;
3410 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3412 ir->opts.annealing[i] = eannSINGLE;
3415 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3417 ir->opts.annealing[i] = eannPERIODIC;
3423 /* Read the other fields too */
3424 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3425 if (nSA_points != nSA)
3427 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3429 for (k = 0, i = 0; i < nr; i++)
3431 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3432 if (ir->opts.anneal_npoints[i] == 1)
3434 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3436 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3437 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3438 k += ir->opts.anneal_npoints[i];
3441 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3444 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3446 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3449 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3452 for (i = 0, k = 0; i < nr; i++)
3455 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3457 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3458 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3461 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3463 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3469 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3471 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3472 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3475 if (ir->opts.anneal_temp[i][j] < 0)
3477 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3482 /* Print out some summary information, to make sure we got it right */
3483 for (i = 0, k = 0; i < nr; i++)
3485 if (ir->opts.annealing[i] != eannNO)
3487 j = groups->grps[egcTC].nm_ind[i];
3488 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3489 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3490 ir->opts.anneal_npoints[i]);
3491 fprintf(stderr, "Time (ps) Temperature (K)\n");
3492 /* All terms except the last one */
3493 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3495 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3498 /* Finally the last one */
3499 j = ir->opts.anneal_npoints[i]-1;
3500 if (ir->opts.annealing[i] == eannSINGLE)
3502 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3506 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3507 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3509 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3520 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3522 make_pull_coords(ir->pull);
3527 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3530 if (ir->eSwapCoords != eswapNO)
3532 make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
3535 /* Make indices for IMD session */
3538 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3541 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3542 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3543 if (nacg*DIM != nacc)
3545 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3548 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3549 restnm, egrptpALL_GENREST, bVerbose, wi);
3550 nr = groups->grps[egcACC].nr;
3551 snew(ir->opts.acc, nr);
3552 ir->opts.ngacc = nr;
3554 for (i = k = 0; (i < nacg); i++)
3556 for (j = 0; (j < DIM); j++, k++)
3558 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3561 for (; (i < nr); i++)
3563 for (j = 0; (j < DIM); j++)
3565 ir->opts.acc[i][j] = 0;
3569 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3570 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3571 if (nfrdim != DIM*nfreeze)
3573 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3576 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3577 restnm, egrptpALL_GENREST, bVerbose, wi);
3578 nr = groups->grps[egcFREEZE].nr;
3579 ir->opts.ngfrz = nr;
3580 snew(ir->opts.nFreeze, nr);
3581 for (i = k = 0; (i < nfreeze); i++)
3583 for (j = 0; (j < DIM); j++, k++)
3585 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3586 if (!ir->opts.nFreeze[i][j])
3588 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3590 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3591 "(not %s)", ptr1[k]);
3592 warning(wi, warn_buf);
3597 for (; (i < nr); i++)
3599 for (j = 0; (j < DIM); j++)
3601 ir->opts.nFreeze[i][j] = 0;
3605 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3606 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3607 restnm, egrptpALL_GENREST, bVerbose, wi);
3608 add_wall_energrps(groups, ir->nwall, symtab);
3609 ir->opts.ngener = groups->grps[egcENER].nr;
3610 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3612 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3613 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3616 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3617 "This may lead to artifacts.\n"
3618 "In most cases one should use one group for the whole system.");
3621 /* Now we have filled the freeze struct, so we can calculate NRDF */
3622 calc_nrdf(mtop, ir, gnames);
3624 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3625 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3626 restnm, egrptpALL_GENREST, bVerbose, wi);
3627 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3628 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3629 restnm, egrptpALL_GENREST, bVerbose, wi);
3630 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3631 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3632 restnm, egrptpONE, bVerbose, wi);
3633 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3634 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3635 restnm, egrptpALL_GENREST, bVerbose, wi);
3637 /* QMMM input processing */
3638 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3639 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3640 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3641 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3643 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3644 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3646 /* group rest, if any, is always MM! */
3647 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3648 restnm, egrptpALL_GENREST, bVerbose, wi);
3649 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3650 ir->opts.ngQM = nQMg;
3651 snew(ir->opts.QMmethod, nr);
3652 snew(ir->opts.QMbasis, nr);
3653 for (i = 0; i < nr; i++)
3655 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3656 * converted to the corresponding enum in names.c
3658 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3660 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3664 str_nelem(is->QMmult, MAXPTR, ptr1);
3665 str_nelem(is->QMcharge, MAXPTR, ptr2);
3666 str_nelem(is->bSH, MAXPTR, ptr3);
3667 snew(ir->opts.QMmult, nr);
3668 snew(ir->opts.QMcharge, nr);
3669 snew(ir->opts.bSH, nr);
3671 for (i = 0; i < nr; i++)
3673 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3674 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3675 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3678 str_nelem(is->CASelectrons, MAXPTR, ptr1);
3679 str_nelem(is->CASorbitals, MAXPTR, ptr2);
3680 snew(ir->opts.CASelectrons, nr);
3681 snew(ir->opts.CASorbitals, nr);
3682 for (i = 0; i < nr; i++)
3684 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3685 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3687 /* special optimization options */
3689 str_nelem(is->bOPT, MAXPTR, ptr1);
3690 str_nelem(is->bTS, MAXPTR, ptr2);
3691 snew(ir->opts.bOPT, nr);
3692 snew(ir->opts.bTS, nr);
3693 for (i = 0; i < nr; i++)
3695 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3696 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3698 str_nelem(is->SAon, MAXPTR, ptr1);
3699 str_nelem(is->SAoff, MAXPTR, ptr2);
3700 str_nelem(is->SAsteps, MAXPTR, ptr3);
3701 snew(ir->opts.SAon, nr);
3702 snew(ir->opts.SAoff, nr);
3703 snew(ir->opts.SAsteps, nr);
3705 for (i = 0; i < nr; i++)
3707 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3708 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3709 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3711 /* end of QMMM input */
3715 for (i = 0; (i < egcNR); i++)
3717 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3718 for (j = 0; (j < groups->grps[i].nr); j++)
3720 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3722 fprintf(stderr, "\n");
3726 nr = groups->grps[egcENER].nr;
3727 snew(ir->opts.egp_flags, nr*nr);
3729 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3730 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3732 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3734 if (bExcl && EEL_FULL(ir->coulombtype))
3736 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3739 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3740 if (bTable && !(ir->vdwtype == evdwUSER) &&
3741 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3742 !(ir->coulombtype == eelPMEUSERSWITCH))
3744 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3747 decode_cos(is->efield_x, &(ir->ex[XX]));
3748 decode_cos(is->efield_xt, &(ir->et[XX]));
3749 decode_cos(is->efield_y, &(ir->ex[YY]));
3750 decode_cos(is->efield_yt, &(ir->et[YY]));
3751 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3752 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3756 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3759 for (i = 0; (i < grps->nr); i++)
3771 static void check_disre(gmx_mtop_t *mtop)
3773 gmx_ffparams_t *ffparams;
3774 t_functype *functype;
3776 int i, ndouble, ftype;
3777 int label, old_label;
3779 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3781 ffparams = &mtop->ffparams;
3782 functype = ffparams->functype;
3783 ip = ffparams->iparams;
3786 for (i = 0; i < ffparams->ntypes; i++)
3788 ftype = functype[i];
3789 if (ftype == F_DISRES)
3791 label = ip[i].disres.label;
3792 if (label == old_label)
3794 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3802 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3803 "probably the parameters for multiple pairs in one restraint "
3804 "are not identical\n", ndouble);
3809 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3810 gmx_bool posres_only,
3814 gmx_mtop_ilistloop_t iloop;
3824 for (d = 0; d < DIM; d++)
3826 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3828 /* Check for freeze groups */
3829 for (g = 0; g < ir->opts.ngfrz; g++)
3831 for (d = 0; d < DIM; d++)
3833 if (ir->opts.nFreeze[g][d] != 0)
3841 /* Check for position restraints */
3842 iloop = gmx_mtop_ilistloop_init(sys);
3843 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3846 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3848 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3850 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3851 for (d = 0; d < DIM; d++)
3853 if (pr->posres.fcA[d] != 0)
3859 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3861 /* Check for flat-bottom posres */
3862 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3863 if (pr->fbposres.k != 0)
3865 switch (pr->fbposres.geom)
3867 case efbposresSPHERE:
3868 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3870 case efbposresCYLINDERX:
3871 AbsRef[YY] = AbsRef[ZZ] = 1;
3873 case efbposresCYLINDERY:
3874 AbsRef[XX] = AbsRef[ZZ] = 1;
3876 case efbposresCYLINDER:
3877 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3878 case efbposresCYLINDERZ:
3879 AbsRef[XX] = AbsRef[YY] = 1;
3881 case efbposresX: /* d=XX */
3882 case efbposresY: /* d=YY */
3883 case efbposresZ: /* d=ZZ */
3884 d = pr->fbposres.geom - efbposresX;
3888 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3889 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3897 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3901 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3902 gmx_bool *bC6ParametersWorkWithGeometricRules,
3903 gmx_bool *bC6ParametersWorkWithLBRules,
3904 gmx_bool *bLBRulesPossible)
3906 int ntypes, tpi, tpj;
3909 double c6i, c6j, c12i, c12j;
3910 double c6, c6_geometric, c6_LB;
3911 double sigmai, sigmaj, epsi, epsj;
3912 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3915 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3916 * force-field floating point parameters.
3919 ptr = getenv("GMX_LJCOMB_TOL");
3924 sscanf(ptr, "%lf", &dbl);
3928 *bC6ParametersWorkWithLBRules = TRUE;
3929 *bC6ParametersWorkWithGeometricRules = TRUE;
3930 bCanDoLBRules = TRUE;
3931 ntypes = mtop->ffparams.atnr;
3932 snew(typecount, ntypes);
3933 gmx_mtop_count_atomtypes(mtop, state, typecount);
3934 *bLBRulesPossible = TRUE;
3935 for (tpi = 0; tpi < ntypes; ++tpi)
3937 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3938 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3939 for (tpj = tpi; tpj < ntypes; ++tpj)
3941 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3942 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3943 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3944 c6_geometric = std::sqrt(c6i * c6j);
3945 if (!gmx_numzero(c6_geometric))
3947 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3949 sigmai = std::pow(c12i / c6i, 1.0/6.0);
3950 sigmaj = std::pow(c12j / c6j, 1.0/6.0);
3951 epsi = c6i * c6i /(4.0 * c12i);
3952 epsj = c6j * c6j /(4.0 * c12j);
3953 c6_LB = 4.0 * std::pow(epsi * epsj, 1.0/2.0) * std::pow(0.5 * (sigmai + sigmaj), 6);
3957 *bLBRulesPossible = FALSE;
3958 c6_LB = c6_geometric;
3960 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3963 if (FALSE == bCanDoLBRules)
3965 *bC6ParametersWorkWithLBRules = FALSE;
3968 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3970 if (FALSE == bCanDoGeometricRules)
3972 *bC6ParametersWorkWithGeometricRules = FALSE;
3980 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3983 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3985 check_combination_rule_differences(mtop, 0,
3986 &bC6ParametersWorkWithGeometricRules,
3987 &bC6ParametersWorkWithLBRules,
3989 if (ir->ljpme_combination_rule == eljpmeLB)
3991 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
3993 warning(wi, "You are using arithmetic-geometric combination rules "
3994 "in LJ-PME, but your non-bonded C6 parameters do not "
3995 "follow these rules.");
4000 if (FALSE == bC6ParametersWorkWithGeometricRules)
4002 if (ir->eDispCorr != edispcNO)
4004 warning_note(wi, "You are using geometric combination rules in "
4005 "LJ-PME, but your non-bonded C6 parameters do "
4006 "not follow these rules. "
4007 "This will introduce very small errors in the forces and energies in "
4008 "your simulations. Dispersion correction will correct total energy "
4009 "and/or pressure for isotropic systems, but not forces or surface tensions.");
4013 warning_note(wi, "You are using geometric combination rules in "
4014 "LJ-PME, but your non-bonded C6 parameters do "
4015 "not follow these rules. "
4016 "This will introduce very small errors in the forces and energies in "
4017 "your simulations. If your system is homogeneous, consider using dispersion correction "
4018 "for the total energy and pressure.");
4024 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
4027 char err_buf[STRLEN];
4029 gmx_bool bCharge, bAcc;
4032 gmx_mtop_atomloop_block_t aloopb;
4033 gmx_mtop_atomloop_all_t aloop;
4036 char warn_buf[STRLEN];
4038 set_warning_line(wi, mdparin, -1);
4040 if (ir->cutoff_scheme == ecutsVERLET &&
4041 ir->verletbuf_tol > 0 &&
4043 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
4044 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4046 /* Check if a too small Verlet buffer might potentially
4047 * cause more drift than the thermostat can couple off.
4049 /* Temperature error fraction for warning and suggestion */
4050 const real T_error_warn = 0.002;
4051 const real T_error_suggest = 0.001;
4052 /* For safety: 2 DOF per atom (typical with constraints) */
4053 const real nrdf_at = 2;
4054 real T, tau, max_T_error;
4059 for (i = 0; i < ir->opts.ngtc; i++)
4061 T = std::max(T, ir->opts.ref_t[i]);
4062 tau = std::max(tau, ir->opts.tau_t[i]);
4066 /* This is a worst case estimate of the temperature error,
4067 * assuming perfect buffer estimation and no cancelation
4068 * of errors. The factor 0.5 is because energy distributes
4069 * equally over Ekin and Epot.
4071 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4072 if (max_T_error > T_error_warn)
4074 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.",
4075 ir->verletbuf_tol, T, tau,
4077 100*T_error_suggest,
4078 ir->verletbuf_tol*T_error_suggest/max_T_error);
4079 warning(wi, warn_buf);
4084 if (ETC_ANDERSEN(ir->etc))
4088 for (i = 0; i < ir->opts.ngtc; i++)
4090 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4091 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4092 sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
4093 i, ir->opts.tau_t[i]);
4094 CHECK(ir->opts.tau_t[i] < 0);
4097 for (i = 0; i < ir->opts.ngtc; i++)
4099 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
4100 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);
4101 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
4105 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4106 ir->comm_mode == ecmNO &&
4107 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4108 !ETC_ANDERSEN(ir->etc))
4110 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");
4113 /* Check for pressure coupling with absolute position restraints */
4114 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4116 absolute_reference(ir, sys, TRUE, AbsRef);
4118 for (m = 0; m < DIM; m++)
4120 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4122 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4130 aloopb = gmx_mtop_atomloop_block_init(sys);
4131 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4133 if (atom->q != 0 || atom->qB != 0)
4141 if (EEL_FULL(ir->coulombtype))
4144 "You are using full electrostatics treatment %s for a system without charges.\n"
4145 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4146 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4147 warning(wi, err_buf);
4152 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4155 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4156 "You might want to consider using %s electrostatics.\n",
4158 warning_note(wi, err_buf);
4162 /* Check if combination rules used in LJ-PME are the same as in the force field */
4163 if (EVDW_PME(ir->vdwtype))
4165 check_combination_rules(ir, sys, wi);
4168 /* Generalized reaction field */
4169 if (ir->opts.ngtc == 0)
4171 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4173 CHECK(ir->coulombtype == eelGRF);
4177 sprintf(err_buf, "When using coulombtype = %s"
4178 " ref-t for temperature coupling should be > 0",
4180 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4183 if (ir->eI == eiSD2)
4185 sprintf(warn_buf, "The stochastic dynamics integrator %s is deprecated, since\n"
4186 "it is slower than integrator %s and is slightly less accurate\n"
4187 "with constraints. Use the %s integrator.",
4188 ei_names[ir->eI], ei_names[eiSD1], ei_names[eiSD1]);
4189 warning_note(wi, warn_buf);
4193 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4195 for (m = 0; (m < DIM); m++)
4197 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4206 snew(mgrp, sys->groups.grps[egcACC].nr);
4207 aloop = gmx_mtop_atomloop_all_init(sys);
4208 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4210 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4213 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4215 for (m = 0; (m < DIM); m++)
4217 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4221 for (m = 0; (m < DIM); m++)
4223 if (fabs(acc[m]) > 1e-6)
4225 const char *dim[DIM] = { "X", "Y", "Z" };
4227 "Net Acceleration in %s direction, will %s be corrected\n",
4228 dim[m], ir->nstcomm != 0 ? "" : "not");
4229 if (ir->nstcomm != 0 && m < ndof_com(ir))
4232 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4234 ir->opts.acc[i][m] -= acc[m];
4242 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4243 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4245 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4253 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4255 if (ir->pull->coord[i].group[0] == 0 ||
4256 ir->pull->coord[i].group[1] == 0)
4258 absolute_reference(ir, sys, FALSE, AbsRef);
4259 for (m = 0; m < DIM; m++)
4261 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4263 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.");
4271 for (i = 0; i < 3; i++)
4273 for (m = 0; m <= i; m++)
4275 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4276 ir->deform[i][m] != 0)
4278 for (c = 0; c < ir->pull->ncoord; c++)
4280 if (ir->pull->coord[c].eGeom == epullgDIRPBC &&
4281 ir->pull->coord[c].vec[m] != 0)
4283 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->coord[c].eGeom), 'x'+m);
4294 void double_check(t_inputrec *ir, matrix box,
4295 gmx_bool bHasNormalConstraints,
4296 gmx_bool bHasAnyConstraints,
4301 char warn_buf[STRLEN];
4304 ptr = check_box(ir->ePBC, box);
4307 warning_error(wi, ptr);
4310 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4312 if (ir->shake_tol <= 0.0)
4314 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4316 warning_error(wi, warn_buf);
4319 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
4321 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
4322 if (ir->epc == epcNO)
4324 warning(wi, warn_buf);
4328 warning_error(wi, warn_buf);
4333 if ( (ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4335 /* If we have Lincs constraints: */
4336 if (ir->eI == eiMD && ir->etc == etcNO &&
4337 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4339 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4340 warning_note(wi, warn_buf);
4343 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4345 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4346 warning_note(wi, warn_buf);
4348 if (ir->epc == epcMTTK)
4350 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4354 if (bHasAnyConstraints && ir->epc == epcMTTK)
4356 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4359 if (ir->LincsWarnAngle > 90.0)
4361 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4362 warning(wi, warn_buf);
4363 ir->LincsWarnAngle = 90.0;
4366 if (ir->ePBC != epbcNONE)
4368 if (ir->nstlist == 0)
4370 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4372 bTWIN = (ir->rlistlong > ir->rlist);
4373 if (ir->ns_type == ensGRID)
4375 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
4377 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 %s.\n",
4378 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
4379 warning_error(wi, warn_buf);
4384 min_size = std::min(box[XX][XX], std::min(box[YY][YY], box[ZZ][ZZ]));
4385 if (2*ir->rlistlong >= min_size)
4387 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4388 warning_error(wi, warn_buf);
4391 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4398 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4402 real rvdw1, rvdw2, rcoul1, rcoul2;
4403 char warn_buf[STRLEN];
4405 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4409 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4414 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4420 if (rvdw1 + rvdw2 > ir->rlist ||
4421 rcoul1 + rcoul2 > ir->rlist)
4424 "The sum of the two largest charge group radii (%f) "
4425 "is larger than rlist (%f)\n",
4426 std::max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4427 warning(wi, warn_buf);
4431 /* Here we do not use the zero at cut-off macro,
4432 * since user defined interactions might purposely
4433 * not be zero at the cut-off.
4435 if (ir_vdw_is_zero_at_cutoff(ir) &&
4436 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
4438 sprintf(warn_buf, "The sum of the two largest charge group "
4439 "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
4440 "With exact cut-offs, better performance can be "
4441 "obtained with cutoff-scheme = %s, because it "
4442 "does not use charge groups at all.",
4444 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4445 ir->rlistlong, ir->rvdw,
4446 ecutscheme_names[ecutsVERLET]);
4449 warning(wi, warn_buf);
4453 warning_note(wi, warn_buf);
4456 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4457 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
4459 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
4460 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4462 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4463 ir->rlistlong, ir->rcoulomb,
4464 ecutscheme_names[ecutsVERLET]);
4467 warning(wi, warn_buf);
4471 warning_note(wi, warn_buf);