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45 #include "gromacs/gmxpreprocess/toputil.h"
46 #include "gromacs/legacyheaders/chargegroup.h"
47 #include "gromacs/legacyheaders/inputrec.h"
48 #include "gromacs/legacyheaders/macros.h"
49 #include "gromacs/legacyheaders/names.h"
50 #include "gromacs/legacyheaders/network.h"
51 #include "gromacs/legacyheaders/readinp.h"
52 #include "gromacs/legacyheaders/typedefs.h"
53 #include "gromacs/legacyheaders/warninp.h"
54 #include "gromacs/math/units.h"
55 #include "gromacs/math/vec.h"
56 #include "gromacs/mdlib/calc_verletbuf.h"
57 #include "gromacs/pbcutil/pbc.h"
58 #include "gromacs/topology/block.h"
59 #include "gromacs/topology/index.h"
60 #include "gromacs/topology/mtop_util.h"
61 #include "gromacs/topology/symtab.h"
62 #include "gromacs/utility/cstringutil.h"
63 #include "gromacs/utility/fatalerror.h"
64 #include "gromacs/utility/smalloc.h"
69 /* Resource parameters
70 * Do not change any of these until you read the instruction
71 * in readinp.h. Some cpp's do not take spaces after the backslash
72 * (like the c-shell), which will give you a very weird compiler
76 typedef struct t_inputrec_strings
78 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN],
79 acc[STRLEN], accgrps[STRLEN], freeze[STRLEN], frdim[STRLEN],
80 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
81 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
82 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN],
84 char fep_lambda[efptNR][STRLEN];
85 char lambda_weights[STRLEN];
88 char anneal[STRLEN], anneal_npoints[STRLEN],
89 anneal_time[STRLEN], anneal_temp[STRLEN];
90 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
91 bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
92 SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
93 char efield_x[STRLEN], efield_xt[STRLEN], efield_y[STRLEN],
94 efield_yt[STRLEN], efield_z[STRLEN], efield_zt[STRLEN];
96 } gmx_inputrec_strings;
98 static gmx_inputrec_strings *is = NULL;
100 void init_inputrec_strings()
104 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.");
109 void done_inputrec_strings()
115 static char swapgrp[STRLEN], splitgrp0[STRLEN], splitgrp1[STRLEN], solgrp[STRLEN];
118 egrptpALL, /* All particles have to be a member of a group. */
119 egrptpALL_GENREST, /* A rest group with name is generated for particles *
120 * that are not part of any group. */
121 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
122 * for the rest group. */
123 egrptpONE /* Merge all selected groups into one group, *
124 * make a rest group for the remaining particles. */
127 static const char *constraints[eshNR+1] = {
128 "none", "h-bonds", "all-bonds", "h-angles", "all-angles", NULL
131 static const char *couple_lam[ecouplamNR+1] = {
132 "vdw-q", "vdw", "q", "none", NULL
135 void init_ir(t_inputrec *ir, t_gromppopts *opts)
137 snew(opts->include, STRLEN);
138 snew(opts->define, STRLEN);
139 snew(ir->fepvals, 1);
140 snew(ir->expandedvals, 1);
141 snew(ir->simtempvals, 1);
144 static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
149 for (i = 0; i < ntemps; i++)
151 /* simple linear scaling -- allows more control */
152 if (simtemp->eSimTempScale == esimtempLINEAR)
154 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*temperature_lambdas[i];
156 else if (simtemp->eSimTempScale == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
158 simtemp->temperatures[i] = simtemp->simtemp_low * pow(simtemp->simtemp_high/simtemp->simtemp_low, (1.0*i)/(ntemps-1));
160 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
162 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*(gmx_expm1(temperature_lambdas[i])/gmx_expm1(1.0));
167 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
168 gmx_fatal(FARGS, errorstr);
175 static void _low_check(gmx_bool b, char *s, warninp_t wi)
179 warning_error(wi, s);
183 static void check_nst(const char *desc_nst, int nst,
184 const char *desc_p, int *p,
189 if (*p > 0 && *p % nst != 0)
191 /* Round up to the next multiple of nst */
192 *p = ((*p)/nst + 1)*nst;
193 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n",
194 desc_p, desc_nst, desc_p, *p);
199 static gmx_bool ir_NVE(const t_inputrec *ir)
201 return ((ir->eI == eiMD || EI_VV(ir->eI)) && ir->etc == etcNO);
204 static int lcd(int n1, int n2)
209 for (i = 2; (i <= n1 && i <= n2); i++)
211 if (n1 % i == 0 && n2 % i == 0)
220 static void process_interaction_modifier(const t_inputrec *ir, int *eintmod)
222 if (*eintmod == eintmodPOTSHIFT_VERLET)
224 if (ir->cutoff_scheme == ecutsVERLET)
226 *eintmod = eintmodPOTSHIFT;
230 *eintmod = eintmodNONE;
235 void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
237 /* Check internal consistency.
238 * NOTE: index groups are not set here yet, don't check things
239 * like temperature coupling group options here, but in triple_check
242 /* Strange macro: first one fills the err_buf, and then one can check
243 * the condition, which will print the message and increase the error
246 #define CHECK(b) _low_check(b, err_buf, wi)
247 char err_buf[256], warn_buf[STRLEN];
253 t_lambda *fep = ir->fepvals;
254 t_expanded *expand = ir->expandedvals;
256 set_warning_line(wi, mdparin, -1);
258 /* BASIC CUT-OFF STUFF */
259 if (ir->rcoulomb < 0)
261 warning_error(wi, "rcoulomb should be >= 0");
265 warning_error(wi, "rvdw should be >= 0");
268 !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
270 warning_error(wi, "rlist should be >= 0");
272 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.)");
273 CHECK(ir->nstlist < 0);
275 process_interaction_modifier(ir, &ir->coulomb_modifier);
276 process_interaction_modifier(ir, &ir->vdw_modifier);
278 if (ir->cutoff_scheme == ecutsGROUP)
281 "The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future "
282 "release when all interaction forms are supported for the verlet scheme. The verlet "
283 "scheme already scales better, and it is compatible with GPUs and other accelerators.");
285 /* BASIC CUT-OFF STUFF */
286 if (ir->rlist == 0 ||
287 !((ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > ir->rlist) ||
288 (ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > ir->rlist)))
290 /* No switched potential and/or no twin-range:
291 * we can set the long-range cut-off to the maximum of the other cut-offs.
293 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
295 else if (ir->rlistlong < 0)
297 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
298 sprintf(warn_buf, "rlistlong was not set, setting it to %g (no buffer)",
300 warning(wi, warn_buf);
302 if (ir->rlistlong == 0 && ir->ePBC != epbcNONE)
304 warning_error(wi, "Can not have an infinite cut-off with PBC");
306 if (ir->rlistlong > 0 && (ir->rlist == 0 || ir->rlistlong < ir->rlist))
308 warning_error(wi, "rlistlong can not be shorter than rlist");
310 if (IR_TWINRANGE(*ir) && ir->nstlist == 0)
312 warning_error(wi, "Can not have nstlist == 0 with twin-range interactions");
316 if (ir->rlistlong == ir->rlist)
320 else if (ir->rlistlong > ir->rlist && ir->nstcalclr == 0)
322 warning_error(wi, "With different cutoffs for electrostatics and VdW, nstcalclr must be -1 or a positive number");
325 if (ir->cutoff_scheme == ecutsVERLET)
329 /* Normal Verlet type neighbor-list, currently only limited feature support */
330 if (inputrec2nboundeddim(ir) < 3)
332 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
334 if (ir->rcoulomb != ir->rvdw)
336 warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported");
338 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
340 if (ir->vdw_modifier == eintmodNONE ||
341 ir->vdw_modifier == eintmodPOTSHIFT)
343 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
345 sprintf(warn_buf, "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], evdw_names[evdwCUT], eintmod_names[ir->vdw_modifier]);
346 warning_note(wi, warn_buf);
348 ir->vdwtype = evdwCUT;
352 sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
353 warning_error(wi, warn_buf);
357 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
359 warning_error(wi, "With Verlet lists only cut-off and PME LJ interactions are supported");
361 if (!(ir->coulombtype == eelCUT ||
362 (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC) ||
363 EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
365 warning_error(wi, "With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
367 if (!(ir->coulomb_modifier == eintmodNONE ||
368 ir->coulomb_modifier == eintmodPOTSHIFT))
370 sprintf(warn_buf, "coulomb_modifier=%s is not supported with the Verlet cut-off scheme", eintmod_names[ir->coulomb_modifier]);
371 warning_error(wi, warn_buf);
374 if (ir->implicit_solvent != eisNO)
376 warning_error(wi, "Implicit solvent is not (yet) supported with the with Verlet lists.");
379 if (ir->nstlist <= 0)
381 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
384 if (ir->nstlist < 10)
386 warning_note(wi, "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation.");
389 rc_max = max(ir->rvdw, ir->rcoulomb);
391 if (ir->verletbuf_tol <= 0)
393 if (ir->verletbuf_tol == 0)
395 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
398 if (ir->rlist < rc_max)
400 warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
403 if (ir->rlist == rc_max && ir->nstlist > 1)
405 warning_note(wi, "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet buffer. The cluster pair list does have a buffering effect, but choosing a larger rlist might be necessary for good energy conservation.");
410 if (ir->rlist > rc_max)
412 warning_note(wi, "You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance.");
415 if (ir->nstlist == 1)
417 /* No buffer required */
422 if (EI_DYNAMICS(ir->eI))
424 if (inputrec2nboundeddim(ir) < 3)
426 warning_error(wi, "The box volume is required for calculating rlist from the energy drift with verlet-buffer-tolerance > 0. You are using at least one unbounded dimension, so no volume can be computed. Either use a finite box, or set rlist yourself together with verlet-buffer-tolerance = -1.");
428 /* Set rlist temporarily so we can continue processing */
433 /* Set the buffer to 5% of the cut-off */
434 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
439 /* No twin-range calculations with Verlet lists */
440 ir->rlistlong = ir->rlist;
443 if (ir->nstcalclr == -1)
445 /* if rlist=rlistlong, this will later be changed to nstcalclr=0 */
446 ir->nstcalclr = ir->nstlist;
448 else if (ir->nstcalclr > 0)
450 if (ir->nstlist > 0 && (ir->nstlist % ir->nstcalclr != 0))
452 warning_error(wi, "nstlist must be evenly divisible by nstcalclr. Use nstcalclr = -1 to automatically follow nstlist");
455 else if (ir->nstcalclr < -1)
457 warning_error(wi, "nstcalclr must be a positive number (divisor of nstcalclr), or -1 to follow nstlist.");
460 if (EEL_PME(ir->coulombtype) && ir->rcoulomb > ir->rlist && ir->nstcalclr > 1)
462 warning_error(wi, "When used with PME, the long-range component of twin-range interactions must be updated every step (nstcalclr)");
465 /* GENERAL INTEGRATOR STUFF */
466 if (!(ir->eI == eiMD || EI_VV(ir->eI)))
470 if (ir->eI == eiVVAK)
472 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]);
473 warning_note(wi, warn_buf);
475 if (!EI_DYNAMICS(ir->eI))
479 if (EI_DYNAMICS(ir->eI))
481 if (ir->nstcalcenergy < 0)
483 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
484 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
486 /* nstcalcenergy larger than nstener does not make sense.
487 * We ideally want nstcalcenergy=nstener.
491 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
495 ir->nstcalcenergy = ir->nstenergy;
499 else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
500 (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
501 (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
504 const char *nsten = "nstenergy";
505 const char *nstdh = "nstdhdl";
506 const char *min_name = nsten;
507 int min_nst = ir->nstenergy;
509 /* find the smallest of ( nstenergy, nstdhdl ) */
510 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
511 (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
513 min_nst = ir->fepvals->nstdhdl;
516 /* If the user sets nstenergy small, we should respect that */
518 "Setting nstcalcenergy (%d) equal to %s (%d)",
519 ir->nstcalcenergy, min_name, min_nst);
520 warning_note(wi, warn_buf);
521 ir->nstcalcenergy = min_nst;
524 if (ir->epc != epcNO)
526 if (ir->nstpcouple < 0)
528 ir->nstpcouple = ir_optimal_nstpcouple(ir);
531 if (IR_TWINRANGE(*ir))
533 check_nst("nstlist", ir->nstlist,
534 "nstcalcenergy", &ir->nstcalcenergy, wi);
535 if (ir->epc != epcNO)
537 check_nst("nstlist", ir->nstlist,
538 "nstpcouple", &ir->nstpcouple, wi);
542 if (ir->nstcalcenergy > 0)
544 if (ir->efep != efepNO)
546 /* nstdhdl should be a multiple of nstcalcenergy */
547 check_nst("nstcalcenergy", ir->nstcalcenergy,
548 "nstdhdl", &ir->fepvals->nstdhdl, wi);
549 /* nstexpanded should be a multiple of nstcalcenergy */
550 check_nst("nstcalcenergy", ir->nstcalcenergy,
551 "nstexpanded", &ir->expandedvals->nstexpanded, wi);
553 /* for storing exact averages nstenergy should be
554 * a multiple of nstcalcenergy
556 check_nst("nstcalcenergy", ir->nstcalcenergy,
557 "nstenergy", &ir->nstenergy, wi);
561 if (ir->nsteps == 0 && !ir->bContinuation)
563 warning_note(wi, "For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates.");
567 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
568 ir->bContinuation && ir->ld_seed != -1)
570 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)");
576 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
577 CHECK(ir->ePBC != epbcXYZ);
578 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
579 CHECK(ir->ns_type != ensGRID);
580 sprintf(err_buf, "with TPI nstlist should be larger than zero");
581 CHECK(ir->nstlist <= 0);
582 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
583 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
584 sprintf(err_buf, "TPI does not work (yet) with the Verlet cut-off scheme");
585 CHECK(ir->cutoff_scheme == ecutsVERLET);
589 if ( (opts->nshake > 0) && (opts->bMorse) )
592 "Using morse bond-potentials while constraining bonds is useless");
593 warning(wi, warn_buf);
596 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
597 ir->bContinuation && ir->ld_seed != -1)
599 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)");
601 /* verify simulated tempering options */
605 gmx_bool bAllTempZero = TRUE;
606 for (i = 0; i < fep->n_lambda; i++)
608 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]);
609 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
610 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
612 bAllTempZero = FALSE;
615 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
616 CHECK(bAllTempZero == TRUE);
618 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
619 CHECK(ir->eI != eiVV);
621 /* check compatability of the temperature coupling with simulated tempering */
623 if (ir->etc == etcNOSEHOOVER)
625 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
626 warning_note(wi, warn_buf);
629 /* check that the temperatures make sense */
631 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);
632 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
634 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
635 CHECK(ir->simtempvals->simtemp_high <= 0);
637 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
638 CHECK(ir->simtempvals->simtemp_low <= 0);
641 /* verify free energy options */
643 if (ir->efep != efepNO)
646 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
648 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
650 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
651 (int)fep->sc_r_power);
652 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
654 sprintf(err_buf, "Can't use postive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
655 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
657 sprintf(err_buf, "Can't use postive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
658 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
660 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
661 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
663 sprintf(err_buf, "Free-energy not implemented for Ewald");
664 CHECK(ir->coulombtype == eelEWALD);
666 /* check validty of lambda inputs */
667 if (fep->n_lambda == 0)
669 /* Clear output in case of no states:*/
670 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
671 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
675 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
676 CHECK((fep->init_fep_state >= fep->n_lambda));
679 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
680 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
682 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",
683 fep->init_lambda, fep->init_fep_state);
684 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
688 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
692 for (i = 0; i < efptNR; i++)
694 if (fep->separate_dvdl[i])
699 if (n_lambda_terms > 1)
701 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.");
702 warning(wi, warn_buf);
705 if (n_lambda_terms < 2 && fep->n_lambda > 0)
708 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
712 for (j = 0; j < efptNR; j++)
714 for (i = 0; i < fep->n_lambda; i++)
716 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]);
717 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
721 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
723 for (i = 0; i < fep->n_lambda; i++)
725 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],
726 fep->all_lambda[efptCOUL][i]);
727 CHECK((fep->sc_alpha > 0) &&
728 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
729 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
730 ((fep->all_lambda[efptVDW][i] > 0.0) &&
731 (fep->all_lambda[efptVDW][i] < 1.0))));
735 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
737 real sigma, lambda, r_sc;
740 /* Maximum estimate for A and B charges equal with lambda power 1 */
742 r_sc = pow(lambda*fep->sc_alpha*pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
743 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.",
745 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
746 warning_note(wi, warn_buf);
749 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
750 be treated differently, but that's the next step */
752 for (i = 0; i < efptNR; i++)
754 for (j = 0; j < fep->n_lambda; j++)
756 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
757 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
762 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
765 expand = ir->expandedvals;
767 /* checking equilibration of weights inputs for validity */
769 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
770 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
771 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
773 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
774 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
775 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
777 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
778 expand->equil_steps, elmceq_names[elmceqSTEPS]);
779 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
781 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
782 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
783 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
785 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
786 expand->equil_ratio, elmceq_names[elmceqRATIO]);
787 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
789 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
790 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
791 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
793 sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
794 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
795 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
797 sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
798 expand->equil_steps, elmceq_names[elmceqSTEPS]);
799 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
801 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
802 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
803 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
805 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
806 expand->equil_ratio, elmceq_names[elmceqRATIO]);
807 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
809 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
810 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
811 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
813 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
814 CHECK((expand->lmc_repeats <= 0));
815 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
816 CHECK((expand->minvarmin <= 0));
817 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
818 CHECK((expand->c_range < 0));
819 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
820 fep->init_fep_state, expand->lmc_forced_nstart);
821 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
822 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
823 CHECK((expand->lmc_forced_nstart < 0));
824 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
825 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
827 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
828 CHECK((expand->init_wl_delta < 0));
829 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
830 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
831 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
832 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
834 /* if there is no temperature control, we need to specify an MC temperature */
835 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
836 if (expand->nstTij > 0)
838 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
839 expand->nstTij, ir->nstlog);
840 CHECK((mod(expand->nstTij, ir->nstlog) != 0));
845 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
846 CHECK(ir->nwall && ir->ePBC != epbcXY);
849 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
851 if (ir->ePBC == epbcNONE)
853 if (ir->epc != epcNO)
855 warning(wi, "Turning off pressure coupling for vacuum system");
861 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
862 epbc_names[ir->ePBC]);
863 CHECK(ir->epc != epcNO);
865 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
866 CHECK(EEL_FULL(ir->coulombtype));
868 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
869 epbc_names[ir->ePBC]);
870 CHECK(ir->eDispCorr != edispcNO);
873 if (ir->rlist == 0.0)
875 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
876 "with coulombtype = %s or coulombtype = %s\n"
877 "without periodic boundary conditions (pbc = %s) and\n"
878 "rcoulomb and rvdw set to zero",
879 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
880 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
881 (ir->ePBC != epbcNONE) ||
882 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
886 warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
891 if (ir->nstcomm == 0)
893 ir->comm_mode = ecmNO;
895 if (ir->comm_mode != ecmNO)
899 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");
900 ir->nstcomm = abs(ir->nstcomm);
903 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
905 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
906 ir->nstcomm = ir->nstcalcenergy;
909 if (ir->comm_mode == ecmANGULAR)
911 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
912 CHECK(ir->bPeriodicMols);
913 if (ir->ePBC != epbcNONE)
915 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.");
920 if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
922 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.");
925 sprintf(err_buf, "Twin-range neighbour searching (NS) with simple NS"
926 " algorithm not implemented");
927 CHECK(((ir->rcoulomb > ir->rlist) || (ir->rvdw > ir->rlist))
928 && (ir->ns_type == ensSIMPLE));
930 /* TEMPERATURE COUPLING */
931 if (ir->etc == etcYES)
933 ir->etc = etcBERENDSEN;
934 warning_note(wi, "Old option for temperature coupling given: "
935 "changing \"yes\" to \"Berendsen\"\n");
938 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
940 if (ir->opts.nhchainlength < 1)
942 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
943 ir->opts.nhchainlength = 1;
944 warning(wi, warn_buf);
947 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
949 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
950 ir->opts.nhchainlength = 1;
955 ir->opts.nhchainlength = 0;
958 if (ir->eI == eiVVAK)
960 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
962 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
965 if (ETC_ANDERSEN(ir->etc))
967 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
968 CHECK(!(EI_VV(ir->eI)));
970 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
972 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]);
973 warning_note(wi, warn_buf);
976 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]);
977 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
980 if (ir->etc == etcBERENDSEN)
982 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
983 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
984 warning_note(wi, warn_buf);
987 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
988 && ir->epc == epcBERENDSEN)
990 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
991 "true ensemble for the thermostat");
992 warning(wi, warn_buf);
995 /* PRESSURE COUPLING */
996 if (ir->epc == epcISOTROPIC)
998 ir->epc = epcBERENDSEN;
999 warning_note(wi, "Old option for pressure coupling given: "
1000 "changing \"Isotropic\" to \"Berendsen\"\n");
1003 if (ir->epc != epcNO)
1005 dt_pcoupl = ir->nstpcouple*ir->delta_t;
1007 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1008 CHECK(ir->tau_p <= 0);
1010 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10*GMX_REAL_EPS)
1012 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
1013 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1014 warning(wi, warn_buf);
1017 sprintf(err_buf, "compressibility must be > 0 when using pressure"
1018 " coupling %s\n", EPCOUPLTYPE(ir->epc));
1019 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
1020 ir->compress[ZZ][ZZ] < 0 ||
1021 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
1022 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
1024 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1027 "You are generating velocities so I am assuming you "
1028 "are equilibrating a system. You are using "
1029 "%s pressure coupling, but this can be "
1030 "unstable for equilibration. If your system crashes, try "
1031 "equilibrating first with Berendsen pressure coupling. If "
1032 "you are not equilibrating the system, you can probably "
1033 "ignore this warning.",
1034 epcoupl_names[ir->epc]);
1035 warning(wi, warn_buf);
1041 if (ir->epc > epcNO)
1043 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1045 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.");
1051 if (ir->epc == epcMTTK)
1053 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1057 /* ELECTROSTATICS */
1058 /* More checks are in triple check (grompp.c) */
1060 if (ir->coulombtype == eelSWITCH)
1062 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1063 "artifacts, advice: use coulombtype = %s",
1064 eel_names[ir->coulombtype],
1065 eel_names[eelRF_ZERO]);
1066 warning(wi, warn_buf);
1069 if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
1071 sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
1072 warning_note(wi, warn_buf);
1075 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1077 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);
1078 warning(wi, warn_buf);
1079 ir->epsilon_rf = ir->epsilon_r;
1080 ir->epsilon_r = 1.0;
1083 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == NULL)
1085 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1086 CHECK(ir->epsilon_r < 0);
1089 if (EEL_RF(ir->coulombtype))
1091 /* reaction field (at the cut-off) */
1093 if (ir->coulombtype == eelRF_ZERO)
1095 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1096 eel_names[ir->coulombtype]);
1097 CHECK(ir->epsilon_rf != 0);
1098 ir->epsilon_rf = 0.0;
1101 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1102 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1103 (ir->epsilon_r == 0));
1104 if (ir->epsilon_rf == ir->epsilon_r)
1106 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1107 eel_names[ir->coulombtype]);
1108 warning(wi, warn_buf);
1111 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1112 * means the interaction is zero outside rcoulomb, but it helps to
1113 * provide accurate energy conservation.
1115 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1117 if (ir_coulomb_switched(ir))
1120 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1121 eel_names[ir->coulombtype]);
1122 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1125 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1127 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1129 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1130 eel_names[ir->coulombtype]);
1131 CHECK(ir->rlist > ir->rcoulomb);
1135 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1138 "Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier.");
1139 CHECK( ir->coulomb_modifier != eintmodNONE);
1141 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1144 "Explicit switch/shift vdw interactions cannot be used in combination with a secondary vdw-modifier.");
1145 CHECK( ir->vdw_modifier != eintmodNONE);
1148 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1149 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1152 "The switch/shift interaction settings are just for compatibility; you will get better "
1153 "performance from applying potential modifiers to your interactions!\n");
1154 warning_note(wi, warn_buf);
1157 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1159 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1161 real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
1162 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.",
1163 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1164 warning(wi, warn_buf);
1168 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1170 if (ir->rvdw_switch == 0)
1172 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.");
1173 warning(wi, warn_buf);
1177 if (EEL_FULL(ir->coulombtype))
1179 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1180 ir->coulombtype == eelPMEUSERSWITCH)
1182 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1183 eel_names[ir->coulombtype]);
1184 CHECK(ir->rcoulomb > ir->rlist);
1186 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1188 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1191 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
1192 "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
1193 "a potential modifier.", eel_names[ir->coulombtype]);
1194 if (ir->nstcalclr == 1)
1196 CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
1200 CHECK(ir->rcoulomb != ir->rlist);
1206 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1208 if (ir->pme_order < 3)
1210 warning_error(wi, "pme-order can not be smaller than 3");
1214 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1216 if (ir->ewald_geometry == eewg3D)
1218 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1219 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1220 warning(wi, warn_buf);
1222 /* This check avoids extra pbc coding for exclusion corrections */
1223 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1224 CHECK(ir->wall_ewald_zfac < 2);
1226 if ((ir->ewald_geometry == eewg3DC) && (ir->ePBC != epbcXY) &&
1227 EEL_FULL(ir->coulombtype))
1229 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1230 eel_names[ir->coulombtype], eewg_names[eewg3DC], epbc_names[epbcXY]);
1231 warning(wi, warn_buf);
1233 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1235 if (ir->cutoff_scheme == ecutsVERLET)
1237 sprintf(warn_buf, "Since molecules/charge groups are broken using the Verlet scheme, you can not use a dipole correction to the %s electrostatics.",
1238 eel_names[ir->coulombtype]);
1239 warning(wi, warn_buf);
1243 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",
1244 eel_names[ir->coulombtype]);
1245 warning_note(wi, warn_buf);
1249 if (ir_vdw_switched(ir))
1251 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1252 CHECK(ir->rvdw_switch >= ir->rvdw);
1254 if (ir->rvdw_switch < 0.5*ir->rvdw)
1256 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.",
1257 ir->rvdw_switch, ir->rvdw);
1258 warning_note(wi, warn_buf);
1261 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1263 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1265 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1266 CHECK(ir->rlist > ir->rvdw);
1270 if (ir->vdwtype == evdwPME)
1272 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1274 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s a\
1276 evdw_names[ir->vdwtype],
1277 eintmod_names[eintmodPOTSHIFT],
1278 eintmod_names[eintmodNONE]);
1282 if (ir->cutoff_scheme == ecutsGROUP)
1284 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1285 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)))
1287 warning_note(wi, "With exact cut-offs, rlist should be "
1288 "larger than rcoulomb and rvdw, so that there "
1289 "is a buffer region for particle motion "
1290 "between neighborsearch steps");
1293 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlistlong <= ir->rcoulomb)
1295 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
1296 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1297 warning_note(wi, warn_buf);
1299 if (ir_vdw_switched(ir) && (ir->rlistlong <= ir->rvdw))
1301 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
1302 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1303 warning_note(wi, warn_buf);
1307 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1309 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.");
1312 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1315 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1318 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1320 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1323 /* ENERGY CONSERVATION */
1324 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1326 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1328 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1329 evdw_names[evdwSHIFT]);
1330 warning_note(wi, warn_buf);
1332 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1334 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1335 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1336 warning_note(wi, warn_buf);
1340 if (EI_VV(ir->eI) && IR_TWINRANGE(*ir) && ir->nstlist > 1)
1342 sprintf(warn_buf, "Twin-range multiple time stepping does not work with integrator %s.", ei_names[ir->eI]);
1343 warning_error(wi, warn_buf);
1346 /* IMPLICIT SOLVENT */
1347 if (ir->coulombtype == eelGB_NOTUSED)
1349 sprintf(warn_buf, "Invalid option %s for coulombtype",
1350 eel_names[ir->coulombtype]);
1351 warning_error(wi, warn_buf);
1354 if (ir->sa_algorithm == esaSTILL)
1356 sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
1357 CHECK(ir->sa_algorithm == esaSTILL);
1360 if (ir->implicit_solvent == eisGBSA)
1362 sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
1363 CHECK(ir->rgbradii != ir->rlist);
1365 if (ir->coulombtype != eelCUT)
1367 sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
1368 CHECK(ir->coulombtype != eelCUT);
1370 if (ir->vdwtype != evdwCUT)
1372 sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
1373 CHECK(ir->vdwtype != evdwCUT);
1375 if (ir->nstgbradii < 1)
1377 sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
1378 warning_note(wi, warn_buf);
1381 if (ir->sa_algorithm == esaNO)
1383 sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
1384 warning_note(wi, warn_buf);
1386 if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
1388 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");
1389 warning_note(wi, warn_buf);
1391 if (ir->gb_algorithm == egbSTILL)
1393 ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
1397 ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
1400 if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
1402 sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
1403 CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
1410 if (ir->cutoff_scheme != ecutsGROUP)
1412 warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
1416 warning_error(wi, "AdresS simulation supports only stochastic dynamics");
1418 if (ir->epc != epcNO)
1420 warning_error(wi, "AdresS simulation does not support pressure coupling");
1422 if (EEL_FULL(ir->coulombtype))
1424 warning_error(wi, "AdresS simulation does not support long-range electrostatics");
1429 /* count the number of text elemets separated by whitespace in a string.
1430 str = the input string
1431 maxptr = the maximum number of allowed elements
1432 ptr = the output array of pointers to the first character of each element
1433 returns: the number of elements. */
1434 int str_nelem(const char *str, int maxptr, char *ptr[])
1439 copy0 = gmx_strdup(str);
1442 while (*copy != '\0')
1446 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1454 while ((*copy != '\0') && !isspace(*copy))
1473 /* interpret a number of doubles from a string and put them in an array,
1474 after allocating space for them.
1475 str = the input string
1476 n = the (pre-allocated) number of doubles read
1477 r = the output array of doubles. */
1478 static void parse_n_real(char *str, int *n, real **r)
1483 *n = str_nelem(str, MAXPTR, ptr);
1486 for (i = 0; i < *n; i++)
1488 (*r)[i] = strtod(ptr[i], NULL);
1492 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
1495 int i, j, max_n_lambda, nweights, nfep[efptNR];
1496 t_lambda *fep = ir->fepvals;
1497 t_expanded *expand = ir->expandedvals;
1498 real **count_fep_lambdas;
1499 gmx_bool bOneLambda = TRUE;
1501 snew(count_fep_lambdas, efptNR);
1503 /* FEP input processing */
1504 /* first, identify the number of lambda values for each type.
1505 All that are nonzero must have the same number */
1507 for (i = 0; i < efptNR; i++)
1509 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
1512 /* now, determine the number of components. All must be either zero, or equal. */
1515 for (i = 0; i < efptNR; i++)
1517 if (nfep[i] > max_n_lambda)
1519 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1520 must have the same number if its not zero.*/
1525 for (i = 0; i < efptNR; i++)
1529 ir->fepvals->separate_dvdl[i] = FALSE;
1531 else if (nfep[i] == max_n_lambda)
1533 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1534 respect to the temperature currently */
1536 ir->fepvals->separate_dvdl[i] = TRUE;
1541 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1542 nfep[i], efpt_names[i], max_n_lambda);
1545 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1546 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1548 /* the number of lambdas is the number we've read in, which is either zero
1549 or the same for all */
1550 fep->n_lambda = max_n_lambda;
1552 /* allocate space for the array of lambda values */
1553 snew(fep->all_lambda, efptNR);
1554 /* if init_lambda is defined, we need to set lambda */
1555 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1557 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1559 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1560 for (i = 0; i < efptNR; i++)
1562 snew(fep->all_lambda[i], fep->n_lambda);
1563 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1566 for (j = 0; j < fep->n_lambda; j++)
1568 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1570 sfree(count_fep_lambdas[i]);
1573 sfree(count_fep_lambdas);
1575 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1576 bookkeeping -- for now, init_lambda */
1578 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1580 for (i = 0; i < fep->n_lambda; i++)
1582 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1586 /* check to see if only a single component lambda is defined, and soft core is defined.
1587 In this case, turn on coulomb soft core */
1589 if (max_n_lambda == 0)
1595 for (i = 0; i < efptNR; i++)
1597 if ((nfep[i] != 0) && (i != efptFEP))
1603 if ((bOneLambda) && (fep->sc_alpha > 0))
1605 fep->bScCoul = TRUE;
1608 /* Fill in the others with the efptFEP if they are not explicitly
1609 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1610 they are all zero. */
1612 for (i = 0; i < efptNR; i++)
1614 if ((nfep[i] == 0) && (i != efptFEP))
1616 for (j = 0; j < fep->n_lambda; j++)
1618 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1624 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1625 if (fep->sc_r_power == 48)
1627 if (fep->sc_alpha > 0.1)
1629 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1633 expand = ir->expandedvals;
1634 /* now read in the weights */
1635 parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
1638 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1640 else if (nweights != fep->n_lambda)
1642 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1643 nweights, fep->n_lambda);
1645 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1647 expand->nstexpanded = fep->nstdhdl;
1648 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1650 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1652 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1653 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1654 2*tau_t just to be careful so it's not to frequent */
1659 static void do_simtemp_params(t_inputrec *ir)
1662 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1663 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1668 static void do_wall_params(t_inputrec *ir,
1669 char *wall_atomtype, char *wall_density,
1673 char *names[MAXPTR];
1676 opts->wall_atomtype[0] = NULL;
1677 opts->wall_atomtype[1] = NULL;
1679 ir->wall_atomtype[0] = -1;
1680 ir->wall_atomtype[1] = -1;
1681 ir->wall_density[0] = 0;
1682 ir->wall_density[1] = 0;
1686 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1687 if (nstr != ir->nwall)
1689 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1692 for (i = 0; i < ir->nwall; i++)
1694 opts->wall_atomtype[i] = gmx_strdup(names[i]);
1697 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1699 nstr = str_nelem(wall_density, MAXPTR, names);
1700 if (nstr != ir->nwall)
1702 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1704 for (i = 0; i < ir->nwall; i++)
1706 sscanf(names[i], "%lf", &dbl);
1709 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1711 ir->wall_density[i] = dbl;
1717 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1725 srenew(groups->grpname, groups->ngrpname+nwall);
1726 grps = &(groups->grps[egcENER]);
1727 srenew(grps->nm_ind, grps->nr+nwall);
1728 for (i = 0; i < nwall; i++)
1730 sprintf(str, "wall%d", i);
1731 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1732 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1737 void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1738 t_expanded *expand, warninp_t wi)
1740 int ninp, nerror = 0;
1746 /* read expanded ensemble parameters */
1747 CCTYPE ("expanded ensemble variables");
1748 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1749 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1750 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1751 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1752 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1753 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1754 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1755 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1756 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1757 CCTYPE("Seed for Monte Carlo in lambda space");
1758 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1759 RTYPE ("mc-temperature", expand->mc_temp, -1);
1760 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1761 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1762 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1763 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1764 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1765 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1766 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1767 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1768 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1769 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1770 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
1778 /*! \brief Return whether an end state with the given coupling-lambda
1779 * value describes fully-interacting VDW.
1781 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1782 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1784 static gmx_bool couple_lambda_has_vdw_on(int couple_lambda_value)
1786 return (couple_lambda_value == ecouplamVDW ||
1787 couple_lambda_value == ecouplamVDWQ);
1790 void get_ir(const char *mdparin, const char *mdparout,
1791 t_inputrec *ir, t_gromppopts *opts,
1795 double dumdub[2][6];
1799 char warn_buf[STRLEN];
1800 t_lambda *fep = ir->fepvals;
1801 t_expanded *expand = ir->expandedvals;
1803 init_inputrec_strings();
1804 inp = read_inpfile(mdparin, &ninp, wi);
1806 snew(dumstr[0], STRLEN);
1807 snew(dumstr[1], STRLEN);
1809 if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
1812 "%s did not specify a value for the .mdp option "
1813 "\"cutoff-scheme\". Probably it was first intended for use "
1814 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1815 "introduced, but the group scheme was still the default. "
1816 "The default is now the Verlet scheme, so you will observe "
1817 "different behaviour.", mdparin);
1818 warning_note(wi, warn_buf);
1821 /* ignore the following deprecated commands */
1824 REM_TYPE("domain-decomposition");
1825 REM_TYPE("andersen-seed");
1827 REM_TYPE("dihre-fc");
1828 REM_TYPE("dihre-tau");
1829 REM_TYPE("nstdihreout");
1830 REM_TYPE("nstcheckpoint");
1831 REM_TYPE("optimize-fft");
1833 /* replace the following commands with the clearer new versions*/
1834 REPL_TYPE("unconstrained-start", "continuation");
1835 REPL_TYPE("foreign-lambda", "fep-lambdas");
1836 REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
1837 REPL_TYPE("nstxtcout", "nstxout-compressed");
1838 REPL_TYPE("xtc-grps", "compressed-x-grps");
1839 REPL_TYPE("xtc-precision", "compressed-x-precision");
1841 CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
1842 CTYPE ("Preprocessor information: use cpp syntax.");
1843 CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
1844 STYPE ("include", opts->include, NULL);
1845 CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1846 STYPE ("define", opts->define, NULL);
1848 CCTYPE ("RUN CONTROL PARAMETERS");
1849 EETYPE("integrator", ir->eI, ei_names);
1850 CTYPE ("Start time and timestep in ps");
1851 RTYPE ("tinit", ir->init_t, 0.0);
1852 RTYPE ("dt", ir->delta_t, 0.001);
1853 STEPTYPE ("nsteps", ir->nsteps, 0);
1854 CTYPE ("For exact run continuation or redoing part of a run");
1855 STEPTYPE ("init-step", ir->init_step, 0);
1856 CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
1857 ITYPE ("simulation-part", ir->simulation_part, 1);
1858 CTYPE ("mode for center of mass motion removal");
1859 EETYPE("comm-mode", ir->comm_mode, ecm_names);
1860 CTYPE ("number of steps for center of mass motion removal");
1861 ITYPE ("nstcomm", ir->nstcomm, 100);
1862 CTYPE ("group(s) for center of mass motion removal");
1863 STYPE ("comm-grps", is->vcm, NULL);
1865 CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
1866 CTYPE ("Friction coefficient (amu/ps) and random seed");
1867 RTYPE ("bd-fric", ir->bd_fric, 0.0);
1868 STEPTYPE ("ld-seed", ir->ld_seed, -1);
1871 CCTYPE ("ENERGY MINIMIZATION OPTIONS");
1872 CTYPE ("Force tolerance and initial step-size");
1873 RTYPE ("emtol", ir->em_tol, 10.0);
1874 RTYPE ("emstep", ir->em_stepsize, 0.01);
1875 CTYPE ("Max number of iterations in relax-shells");
1876 ITYPE ("niter", ir->niter, 20);
1877 CTYPE ("Step size (ps^2) for minimization of flexible constraints");
1878 RTYPE ("fcstep", ir->fc_stepsize, 0);
1879 CTYPE ("Frequency of steepest descents steps when doing CG");
1880 ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
1881 ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
1883 CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
1884 RTYPE ("rtpi", ir->rtpi, 0.05);
1886 /* Output options */
1887 CCTYPE ("OUTPUT CONTROL OPTIONS");
1888 CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
1889 ITYPE ("nstxout", ir->nstxout, 0);
1890 ITYPE ("nstvout", ir->nstvout, 0);
1891 ITYPE ("nstfout", ir->nstfout, 0);
1892 CTYPE ("Output frequency for energies to log file and energy file");
1893 ITYPE ("nstlog", ir->nstlog, 1000);
1894 ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
1895 ITYPE ("nstenergy", ir->nstenergy, 1000);
1896 CTYPE ("Output frequency and precision for .xtc file");
1897 ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
1898 RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
1899 CTYPE ("This selects the subset of atoms for the compressed");
1900 CTYPE ("trajectory file. You can select multiple groups. By");
1901 CTYPE ("default, all atoms will be written.");
1902 STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
1903 CTYPE ("Selection of energy groups");
1904 STYPE ("energygrps", is->energy, NULL);
1906 /* Neighbor searching */
1907 CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
1908 CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1909 EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
1910 CTYPE ("nblist update frequency");
1911 ITYPE ("nstlist", ir->nstlist, 10);
1912 CTYPE ("ns algorithm (simple or grid)");
1913 EETYPE("ns-type", ir->ns_type, ens_names);
1914 CTYPE ("Periodic boundary conditions: xyz, no, xy");
1915 EETYPE("pbc", ir->ePBC, epbc_names);
1916 EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
1917 CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1918 CTYPE ("a value of -1 means: use rlist");
1919 RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
1920 CTYPE ("nblist cut-off");
1921 RTYPE ("rlist", ir->rlist, 1.0);
1922 CTYPE ("long-range cut-off for switched potentials");
1923 RTYPE ("rlistlong", ir->rlistlong, -1);
1924 ITYPE ("nstcalclr", ir->nstcalclr, -1);
1926 /* Electrostatics */
1927 CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
1928 CTYPE ("Method for doing electrostatics");
1929 EETYPE("coulombtype", ir->coulombtype, eel_names);
1930 EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
1931 CTYPE ("cut-off lengths");
1932 RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
1933 RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
1934 CTYPE ("Relative dielectric constant for the medium and the reaction field");
1935 RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
1936 RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
1937 CTYPE ("Method for doing Van der Waals");
1938 EETYPE("vdw-type", ir->vdwtype, evdw_names);
1939 EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
1940 CTYPE ("cut-off lengths");
1941 RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
1942 RTYPE ("rvdw", ir->rvdw, 1.0);
1943 CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
1944 EETYPE("DispCorr", ir->eDispCorr, edispc_names);
1945 CTYPE ("Extension of the potential lookup tables beyond the cut-off");
1946 RTYPE ("table-extension", ir->tabext, 1.0);
1947 CTYPE ("Separate tables between energy group pairs");
1948 STYPE ("energygrp-table", is->egptable, NULL);
1949 CTYPE ("Spacing for the PME/PPPM FFT grid");
1950 RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
1951 CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
1952 ITYPE ("fourier-nx", ir->nkx, 0);
1953 ITYPE ("fourier-ny", ir->nky, 0);
1954 ITYPE ("fourier-nz", ir->nkz, 0);
1955 CTYPE ("EWALD/PME/PPPM parameters");
1956 ITYPE ("pme-order", ir->pme_order, 4);
1957 RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
1958 RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
1959 EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
1960 EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
1961 RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
1963 CCTYPE("IMPLICIT SOLVENT ALGORITHM");
1964 EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
1966 CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
1967 CTYPE ("Algorithm for calculating Born radii");
1968 EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
1969 CTYPE ("Frequency of calculating the Born radii inside rlist");
1970 ITYPE ("nstgbradii", ir->nstgbradii, 1);
1971 CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
1972 CTYPE ("between rlist and rgbradii is updated every nstlist steps");
1973 RTYPE ("rgbradii", ir->rgbradii, 1.0);
1974 CTYPE ("Dielectric coefficient of the implicit solvent");
1975 RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
1976 CTYPE ("Salt concentration in M for Generalized Born models");
1977 RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
1978 CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
1979 RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
1980 RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
1981 RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
1982 RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
1983 EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
1984 CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
1985 CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
1986 RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
1988 /* Coupling stuff */
1989 CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
1990 CTYPE ("Temperature coupling");
1991 EETYPE("tcoupl", ir->etc, etcoupl_names);
1992 ITYPE ("nsttcouple", ir->nsttcouple, -1);
1993 ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
1994 EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
1995 CTYPE ("Groups to couple separately");
1996 STYPE ("tc-grps", is->tcgrps, NULL);
1997 CTYPE ("Time constant (ps) and reference temperature (K)");
1998 STYPE ("tau-t", is->tau_t, NULL);
1999 STYPE ("ref-t", is->ref_t, NULL);
2000 CTYPE ("pressure coupling");
2001 EETYPE("pcoupl", ir->epc, epcoupl_names);
2002 EETYPE("pcoupltype", ir->epct, epcoupltype_names);
2003 ITYPE ("nstpcouple", ir->nstpcouple, -1);
2004 CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
2005 RTYPE ("tau-p", ir->tau_p, 1.0);
2006 STYPE ("compressibility", dumstr[0], NULL);
2007 STYPE ("ref-p", dumstr[1], NULL);
2008 CTYPE ("Scaling of reference coordinates, No, All or COM");
2009 EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
2012 CCTYPE ("OPTIONS FOR QMMM calculations");
2013 EETYPE("QMMM", ir->bQMMM, yesno_names);
2014 CTYPE ("Groups treated Quantum Mechanically");
2015 STYPE ("QMMM-grps", is->QMMM, NULL);
2016 CTYPE ("QM method");
2017 STYPE("QMmethod", is->QMmethod, NULL);
2018 CTYPE ("QMMM scheme");
2019 EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
2020 CTYPE ("QM basisset");
2021 STYPE("QMbasis", is->QMbasis, NULL);
2022 CTYPE ("QM charge");
2023 STYPE ("QMcharge", is->QMcharge, NULL);
2024 CTYPE ("QM multiplicity");
2025 STYPE ("QMmult", is->QMmult, NULL);
2026 CTYPE ("Surface Hopping");
2027 STYPE ("SH", is->bSH, NULL);
2028 CTYPE ("CAS space options");
2029 STYPE ("CASorbitals", is->CASorbitals, NULL);
2030 STYPE ("CASelectrons", is->CASelectrons, NULL);
2031 STYPE ("SAon", is->SAon, NULL);
2032 STYPE ("SAoff", is->SAoff, NULL);
2033 STYPE ("SAsteps", is->SAsteps, NULL);
2034 CTYPE ("Scale factor for MM charges");
2035 RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
2036 CTYPE ("Optimization of QM subsystem");
2037 STYPE ("bOPT", is->bOPT, NULL);
2038 STYPE ("bTS", is->bTS, NULL);
2040 /* Simulated annealing */
2041 CCTYPE("SIMULATED ANNEALING");
2042 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
2043 STYPE ("annealing", is->anneal, NULL);
2044 CTYPE ("Number of time points to use for specifying annealing in each group");
2045 STYPE ("annealing-npoints", is->anneal_npoints, NULL);
2046 CTYPE ("List of times at the annealing points for each group");
2047 STYPE ("annealing-time", is->anneal_time, NULL);
2048 CTYPE ("Temp. at each annealing point, for each group.");
2049 STYPE ("annealing-temp", is->anneal_temp, NULL);
2052 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
2053 EETYPE("gen-vel", opts->bGenVel, yesno_names);
2054 RTYPE ("gen-temp", opts->tempi, 300.0);
2055 ITYPE ("gen-seed", opts->seed, -1);
2058 CCTYPE ("OPTIONS FOR BONDS");
2059 EETYPE("constraints", opts->nshake, constraints);
2060 CTYPE ("Type of constraint algorithm");
2061 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
2062 CTYPE ("Do not constrain the start configuration");
2063 EETYPE("continuation", ir->bContinuation, yesno_names);
2064 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
2065 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
2066 CTYPE ("Relative tolerance of shake");
2067 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
2068 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
2069 ITYPE ("lincs-order", ir->nProjOrder, 4);
2070 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
2071 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
2072 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
2073 ITYPE ("lincs-iter", ir->nLincsIter, 1);
2074 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
2075 CTYPE ("rotates over more degrees than");
2076 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
2077 CTYPE ("Convert harmonic bonds to morse potentials");
2078 EETYPE("morse", opts->bMorse, yesno_names);
2080 /* Energy group exclusions */
2081 CCTYPE ("ENERGY GROUP EXCLUSIONS");
2082 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
2083 STYPE ("energygrp-excl", is->egpexcl, NULL);
2087 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2088 ITYPE ("nwall", ir->nwall, 0);
2089 EETYPE("wall-type", ir->wall_type, ewt_names);
2090 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
2091 STYPE ("wall-atomtype", is->wall_atomtype, NULL);
2092 STYPE ("wall-density", is->wall_density, NULL);
2093 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
2096 CCTYPE("COM PULLING");
2097 EETYPE("pull", ir->bPull, yesno_names);
2101 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, wi);
2104 /* Enforced rotation */
2105 CCTYPE("ENFORCED ROTATION");
2106 CTYPE("Enforced rotation: No or Yes");
2107 EETYPE("rotation", ir->bRot, yesno_names);
2111 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2114 /* Interactive MD */
2116 CCTYPE("Group to display and/or manipulate in interactive MD session");
2117 STYPE ("IMD-group", is->imd_grp, NULL);
2118 if (is->imd_grp[0] != '\0')
2125 CCTYPE("NMR refinement stuff");
2126 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2127 EETYPE("disre", ir->eDisre, edisre_names);
2128 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2129 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2130 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2131 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2132 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2133 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2134 CTYPE ("Output frequency for pair distances to energy file");
2135 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2136 CTYPE ("Orientation restraints: No or Yes");
2137 EETYPE("orire", opts->bOrire, yesno_names);
2138 CTYPE ("Orientation restraints force constant and tau for time averaging");
2139 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2140 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2141 STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
2142 CTYPE ("Output frequency for trace(SD) and S to energy file");
2143 ITYPE ("nstorireout", ir->nstorireout, 100);
2145 /* free energy variables */
2146 CCTYPE ("Free energy variables");
2147 EETYPE("free-energy", ir->efep, efep_names);
2148 STYPE ("couple-moltype", is->couple_moltype, NULL);
2149 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2150 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2151 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2153 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2155 it was not entered */
2156 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2157 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2158 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2159 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
2160 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
2161 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
2162 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
2163 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
2164 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
2165 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
2166 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2167 STYPE ("init-lambda-weights", is->lambda_weights, NULL);
2168 EETYPE("dhdl-print-energy", fep->edHdLPrintEnergy, edHdLPrintEnergy_names);
2169 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2170 ITYPE ("sc-power", fep->sc_power, 1);
2171 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2172 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2173 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2174 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2175 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2176 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2177 separate_dhdl_file_names);
2178 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2179 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2180 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2182 /* Non-equilibrium MD stuff */
2183 CCTYPE("Non-equilibrium MD stuff");
2184 STYPE ("acc-grps", is->accgrps, NULL);
2185 STYPE ("accelerate", is->acc, NULL);
2186 STYPE ("freezegrps", is->freeze, NULL);
2187 STYPE ("freezedim", is->frdim, NULL);
2188 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2189 STYPE ("deform", is->deform, NULL);
2191 /* simulated tempering variables */
2192 CCTYPE("simulated tempering variables");
2193 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2194 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2195 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2196 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2198 /* expanded ensemble variables */
2199 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2201 read_expandedparams(&ninp, &inp, expand, wi);
2204 /* Electric fields */
2205 CCTYPE("Electric fields");
2206 CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
2207 CTYPE ("and a phase angle (real)");
2208 STYPE ("E-x", is->efield_x, NULL);
2209 CTYPE ("Time dependent (pulsed) electric field. Format is omega, time for pulse");
2210 CTYPE ("peak, and sigma (width) for pulse. Sigma = 0 removes pulse, leaving");
2211 CTYPE ("the field to be a cosine function.");
2212 STYPE ("E-xt", is->efield_xt, NULL);
2213 STYPE ("E-y", is->efield_y, NULL);
2214 STYPE ("E-yt", is->efield_yt, NULL);
2215 STYPE ("E-z", is->efield_z, NULL);
2216 STYPE ("E-zt", is->efield_zt, NULL);
2218 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2219 CTYPE("Swap positions along direction: no, X, Y, Z");
2220 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2221 if (ir->eSwapCoords != eswapNO)
2224 CTYPE("Swap attempt frequency");
2225 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2226 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2227 STYPE("split-group0", splitgrp0, NULL);
2228 STYPE("split-group1", splitgrp1, NULL);
2229 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2230 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2231 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2233 CTYPE("Group name of ions that can be exchanged with solvent molecules");
2234 STYPE("swap-group", swapgrp, NULL);
2235 CTYPE("Group name of solvent molecules");
2236 STYPE("solvent-group", solgrp, NULL);
2238 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2239 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2240 CTYPE("however, if correctly defined, the ion permeation events are counted per channel");
2241 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2242 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2243 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2244 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2245 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2246 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2248 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2249 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2250 CTYPE("Requested number of anions and cations for each of the two compartments");
2251 CTYPE("-1 means fix the numbers as found in time step 0");
2252 ITYPE("anionsA", ir->swap->nanions[0], -1);
2253 ITYPE("cationsA", ir->swap->ncations[0], -1);
2254 ITYPE("anionsB", ir->swap->nanions[1], -1);
2255 ITYPE("cationsB", ir->swap->ncations[1], -1);
2256 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2257 RTYPE("threshold", ir->swap->threshold, 1.0);
2260 /* AdResS defined thingies */
2261 CCTYPE ("AdResS parameters");
2262 EETYPE("adress", ir->bAdress, yesno_names);
2265 snew(ir->adress, 1);
2266 read_adressparams(&ninp, &inp, ir->adress, wi);
2269 /* User defined thingies */
2270 CCTYPE ("User defined thingies");
2271 STYPE ("user1-grps", is->user1, NULL);
2272 STYPE ("user2-grps", is->user2, NULL);
2273 ITYPE ("userint1", ir->userint1, 0);
2274 ITYPE ("userint2", ir->userint2, 0);
2275 ITYPE ("userint3", ir->userint3, 0);
2276 ITYPE ("userint4", ir->userint4, 0);
2277 RTYPE ("userreal1", ir->userreal1, 0);
2278 RTYPE ("userreal2", ir->userreal2, 0);
2279 RTYPE ("userreal3", ir->userreal3, 0);
2280 RTYPE ("userreal4", ir->userreal4, 0);
2283 write_inpfile(mdparout, ninp, inp, FALSE, wi);
2284 for (i = 0; (i < ninp); i++)
2287 sfree(inp[i].value);
2291 /* Process options if necessary */
2292 for (m = 0; m < 2; m++)
2294 for (i = 0; i < 2*DIM; i++)
2303 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2305 warning_error(wi, "Pressure coupling not enough values (I need 1)");
2307 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2309 case epctSEMIISOTROPIC:
2310 case epctSURFACETENSION:
2311 if (sscanf(dumstr[m], "%lf%lf",
2312 &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2314 warning_error(wi, "Pressure coupling not enough values (I need 2)");
2316 dumdub[m][YY] = dumdub[m][XX];
2318 case epctANISOTROPIC:
2319 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2320 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2321 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2323 warning_error(wi, "Pressure coupling not enough values (I need 6)");
2327 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2328 epcoupltype_names[ir->epct]);
2332 clear_mat(ir->ref_p);
2333 clear_mat(ir->compress);
2334 for (i = 0; i < DIM; i++)
2336 ir->ref_p[i][i] = dumdub[1][i];
2337 ir->compress[i][i] = dumdub[0][i];
2339 if (ir->epct == epctANISOTROPIC)
2341 ir->ref_p[XX][YY] = dumdub[1][3];
2342 ir->ref_p[XX][ZZ] = dumdub[1][4];
2343 ir->ref_p[YY][ZZ] = dumdub[1][5];
2344 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2346 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2348 ir->compress[XX][YY] = dumdub[0][3];
2349 ir->compress[XX][ZZ] = dumdub[0][4];
2350 ir->compress[YY][ZZ] = dumdub[0][5];
2351 for (i = 0; i < DIM; i++)
2353 for (m = 0; m < i; m++)
2355 ir->ref_p[i][m] = ir->ref_p[m][i];
2356 ir->compress[i][m] = ir->compress[m][i];
2361 if (ir->comm_mode == ecmNO)
2366 opts->couple_moltype = NULL;
2367 if (strlen(is->couple_moltype) > 0)
2369 if (ir->efep != efepNO)
2371 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2372 if (opts->couple_lam0 == opts->couple_lam1)
2374 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2376 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2377 opts->couple_lam1 == ecouplamNONE))
2379 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2384 warning_note(wi, "Free energy is turned off, so we will not decouple the molecule listed in your input.");
2387 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2388 if (ir->efep != efepNO)
2390 if (fep->delta_lambda > 0)
2392 ir->efep = efepSLOWGROWTH;
2396 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2398 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2399 warning_note(wi, "Old option for dhdl-print-energy given: "
2400 "changing \"yes\" to \"total\"\n");
2403 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2405 /* always print out the energy to dhdl if we are doing
2406 expanded ensemble, since we need the total energy for
2407 analysis if the temperature is changing. In some
2408 conditions one may only want the potential energy, so
2409 we will allow that if the appropriate mdp setting has
2410 been enabled. Otherwise, total it is:
2412 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2415 if ((ir->efep != efepNO) || ir->bSimTemp)
2417 ir->bExpanded = FALSE;
2418 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2420 ir->bExpanded = TRUE;
2422 do_fep_params(ir, is->fep_lambda, is->lambda_weights);
2423 if (ir->bSimTemp) /* done after fep params */
2425 do_simtemp_params(ir);
2428 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2429 * setup and not on the old way of specifying the free-energy setup,
2430 * we should check for using soft-core when not needed, since that
2431 * can complicate the sampling significantly.
2432 * Note that we only check for the automated coupling setup.
2433 * If the (advanced) user does FEP through manual topology changes,
2434 * this check will not be triggered.
2436 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 &&
2437 ir->fepvals->sc_alpha != 0 &&
2438 (couple_lambda_has_vdw_on(opts->couple_lam0) &&
2439 couple_lambda_has_vdw_on(opts->couple_lam1)))
2441 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.");
2446 ir->fepvals->n_lambda = 0;
2449 /* WALL PARAMETERS */
2451 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2453 /* ORIENTATION RESTRAINT PARAMETERS */
2455 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
2457 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2460 /* DEFORMATION PARAMETERS */
2462 clear_mat(ir->deform);
2463 for (i = 0; i < 6; i++)
2467 m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
2468 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2469 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2470 for (i = 0; i < 3; i++)
2472 ir->deform[i][i] = dumdub[0][i];
2474 ir->deform[YY][XX] = dumdub[0][3];
2475 ir->deform[ZZ][XX] = dumdub[0][4];
2476 ir->deform[ZZ][YY] = dumdub[0][5];
2477 if (ir->epc != epcNO)
2479 for (i = 0; i < 3; i++)
2481 for (j = 0; j <= i; j++)
2483 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2485 warning_error(wi, "A box element has deform set and compressibility > 0");
2489 for (i = 0; i < 3; i++)
2491 for (j = 0; j < i; j++)
2493 if (ir->deform[i][j] != 0)
2495 for (m = j; m < DIM; m++)
2497 if (ir->compress[m][j] != 0)
2499 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.");
2500 warning(wi, warn_buf);
2508 /* Ion/water position swapping checks */
2509 if (ir->eSwapCoords != eswapNO)
2511 if (ir->swap->nstswap < 1)
2513 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2515 if (ir->swap->nAverage < 1)
2517 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2519 if (ir->swap->threshold < 1.0)
2521 warning_error(wi, "Ion count threshold must be at least 1.\n");
2529 static int search_QMstring(const char *s, int ng, const char *gn[])
2531 /* same as normal search_string, but this one searches QM strings */
2534 for (i = 0; (i < ng); i++)
2536 if (gmx_strcasecmp(s, gn[i]) == 0)
2542 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2546 } /* search_QMstring */
2548 /* We would like gn to be const as well, but C doesn't allow this */
2549 /* TODO this is utility functionality (search for the index of a
2550 string in a collection), so should be refactored and located more
2552 int search_string(const char *s, int ng, char *gn[])
2556 for (i = 0; (i < ng); i++)
2558 if (gmx_strcasecmp(s, gn[i]) == 0)
2565 "Group %s referenced in the .mdp file was not found in the index file.\n"
2566 "Group names must match either [moleculetype] names or custom index group\n"
2567 "names, in which case you must supply an index file to the '-n' option\n"
2574 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2575 t_blocka *block, char *gnames[],
2576 int gtype, int restnm,
2577 int grptp, gmx_bool bVerbose,
2580 unsigned short *cbuf;
2581 t_grps *grps = &(groups->grps[gtype]);
2582 int i, j, gid, aj, ognr, ntot = 0;
2585 char warn_buf[STRLEN];
2589 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2592 title = gtypes[gtype];
2595 /* Mark all id's as not set */
2596 for (i = 0; (i < natoms); i++)
2601 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2602 for (i = 0; (i < ng); i++)
2604 /* Lookup the group name in the block structure */
2605 gid = search_string(ptrs[i], block->nr, gnames);
2606 if ((grptp != egrptpONE) || (i == 0))
2608 grps->nm_ind[grps->nr++] = gid;
2612 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2615 /* Now go over the atoms in the group */
2616 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2621 /* Range checking */
2622 if ((aj < 0) || (aj >= natoms))
2624 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2626 /* Lookup up the old group number */
2630 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2631 aj+1, title, ognr+1, i+1);
2635 /* Store the group number in buffer */
2636 if (grptp == egrptpONE)
2649 /* Now check whether we have done all atoms */
2653 if (grptp == egrptpALL)
2655 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2656 natoms-ntot, title);
2658 else if (grptp == egrptpPART)
2660 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2661 natoms-ntot, title);
2662 warning_note(wi, warn_buf);
2664 /* Assign all atoms currently unassigned to a rest group */
2665 for (j = 0; (j < natoms); j++)
2667 if (cbuf[j] == NOGID)
2673 if (grptp != egrptpPART)
2678 "Making dummy/rest group for %s containing %d elements\n",
2679 title, natoms-ntot);
2681 /* Add group name "rest" */
2682 grps->nm_ind[grps->nr] = restnm;
2684 /* Assign the rest name to all atoms not currently assigned to a group */
2685 for (j = 0; (j < natoms); j++)
2687 if (cbuf[j] == NOGID)
2696 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2698 /* All atoms are part of one (or no) group, no index required */
2699 groups->ngrpnr[gtype] = 0;
2700 groups->grpnr[gtype] = NULL;
2704 groups->ngrpnr[gtype] = natoms;
2705 snew(groups->grpnr[gtype], natoms);
2706 for (j = 0; (j < natoms); j++)
2708 groups->grpnr[gtype][j] = cbuf[j];
2714 return (bRest && grptp == egrptpPART);
2717 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2720 gmx_groups_t *groups;
2721 pull_params_t *pull;
2722 int natoms, ai, aj, i, j, d, g, imin, jmin;
2724 int *nrdf2, *na_vcm, na_tot;
2725 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2726 gmx_mtop_atomloop_all_t aloop;
2728 int mb, mol, ftype, as;
2729 gmx_molblock_t *molb;
2730 gmx_moltype_t *molt;
2733 * First calc 3xnr-atoms for each group
2734 * then subtract half a degree of freedom for each constraint
2736 * Only atoms and nuclei contribute to the degrees of freedom...
2741 groups = &mtop->groups;
2742 natoms = mtop->natoms;
2744 /* Allocate one more for a possible rest group */
2745 /* We need to sum degrees of freedom into doubles,
2746 * since floats give too low nrdf's above 3 million atoms.
2748 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2749 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2750 snew(na_vcm, groups->grps[egcVCM].nr+1);
2752 for (i = 0; i < groups->grps[egcTC].nr; i++)
2756 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2761 snew(nrdf2, natoms);
2762 aloop = gmx_mtop_atomloop_all_init(mtop);
2763 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2766 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2768 g = ggrpnr(groups, egcFREEZE, i);
2769 /* Double count nrdf for particle i */
2770 for (d = 0; d < DIM; d++)
2772 if (opts->nFreeze[g][d] == 0)
2777 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2778 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2783 for (mb = 0; mb < mtop->nmolblock; mb++)
2785 molb = &mtop->molblock[mb];
2786 molt = &mtop->moltype[molb->type];
2787 atom = molt->atoms.atom;
2788 for (mol = 0; mol < molb->nmol; mol++)
2790 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2792 ia = molt->ilist[ftype].iatoms;
2793 for (i = 0; i < molt->ilist[ftype].nr; )
2795 /* Subtract degrees of freedom for the constraints,
2796 * if the particles still have degrees of freedom left.
2797 * If one of the particles is a vsite or a shell, then all
2798 * constraint motion will go there, but since they do not
2799 * contribute to the constraints the degrees of freedom do not
2804 if (((atom[ia[1]].ptype == eptNucleus) ||
2805 (atom[ia[1]].ptype == eptAtom)) &&
2806 ((atom[ia[2]].ptype == eptNucleus) ||
2807 (atom[ia[2]].ptype == eptAtom)))
2825 imin = min(imin, nrdf2[ai]);
2826 jmin = min(jmin, nrdf2[aj]);
2829 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2830 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2831 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2832 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2834 ia += interaction_function[ftype].nratoms+1;
2835 i += interaction_function[ftype].nratoms+1;
2838 ia = molt->ilist[F_SETTLE].iatoms;
2839 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2841 /* Subtract 1 dof from every atom in the SETTLE */
2842 for (j = 0; j < 3; j++)
2845 imin = min(2, nrdf2[ai]);
2847 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2848 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2853 as += molt->atoms.nr;
2859 /* Correct nrdf for the COM constraints.
2860 * We correct using the TC and VCM group of the first atom
2861 * in the reference and pull group. If atoms in one pull group
2862 * belong to different TC or VCM groups it is anyhow difficult
2863 * to determine the optimal nrdf assignment.
2867 for (i = 0; i < pull->ncoord; i++)
2869 if (pull->coord[i].eType != epullCONSTRAINT)
2876 for (j = 0; j < 2; j++)
2878 const t_pull_group *pgrp;
2880 pgrp = &pull->group[pull->coord[i].group[j]];
2884 /* Subtract 1/2 dof from each group */
2886 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2887 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2888 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2890 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)]]);
2895 /* We need to subtract the whole DOF from group j=1 */
2902 if (ir->nstcomm != 0)
2904 /* Subtract 3 from the number of degrees of freedom in each vcm group
2905 * when com translation is removed and 6 when rotation is removed
2908 switch (ir->comm_mode)
2911 n_sub = ndof_com(ir);
2918 gmx_incons("Checking comm_mode");
2921 for (i = 0; i < groups->grps[egcTC].nr; i++)
2923 /* Count the number of atoms of TC group i for every VCM group */
2924 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2929 for (ai = 0; ai < natoms; ai++)
2931 if (ggrpnr(groups, egcTC, ai) == i)
2933 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2937 /* Correct for VCM removal according to the fraction of each VCM
2938 * group present in this TC group.
2940 nrdf_uc = nrdf_tc[i];
2943 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2947 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2949 if (nrdf_vcm[j] > n_sub)
2951 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2952 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2956 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2957 j, nrdf_vcm[j], nrdf_tc[i]);
2962 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2964 opts->nrdf[i] = nrdf_tc[i];
2965 if (opts->nrdf[i] < 0)
2970 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2971 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
2980 static void decode_cos(char *s, t_cosines *cosine)
2983 char format[STRLEN], f1[STRLEN];
2995 sscanf(t, "%d", &(cosine->n));
3002 snew(cosine->a, cosine->n);
3003 snew(cosine->phi, cosine->n);
3005 sprintf(format, "%%*d");
3006 for (i = 0; (i < cosine->n); i++)
3009 strcat(f1, "%lf%lf");
3010 if (sscanf(t, f1, &a, &phi) < 2)
3012 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
3015 cosine->phi[i] = phi;
3016 strcat(format, "%*lf%*lf");
3023 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
3024 const char *option, const char *val, int flag)
3026 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3027 * But since this is much larger than STRLEN, such a line can not be parsed.
3028 * The real maximum is the number of names that fit in a string: STRLEN/2.
3030 #define EGP_MAX (STRLEN/2)
3031 int nelem, i, j, k, nr;
3032 char *names[EGP_MAX];
3036 gnames = groups->grpname;
3038 nelem = str_nelem(val, EGP_MAX, names);
3041 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3043 nr = groups->grps[egcENER].nr;
3045 for (i = 0; i < nelem/2; i++)
3049 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
3055 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3056 names[2*i], option);
3060 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
3066 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3067 names[2*i+1], option);
3069 if ((j < nr) && (k < nr))
3071 ir->opts.egp_flags[nr*j+k] |= flag;
3072 ir->opts.egp_flags[nr*k+j] |= flag;
3081 static void make_swap_groups(
3090 int ig = -1, i = 0, j;
3094 /* Just a quick check here, more thorough checks are in mdrun */
3095 if (strcmp(splitg0name, splitg1name) == 0)
3097 gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
3100 /* First get the swap group index atoms */
3101 ig = search_string(swapgname, grps->nr, gnames);
3102 swap->nat = grps->index[ig+1] - grps->index[ig];
3105 fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
3106 snew(swap->ind, swap->nat);
3107 for (i = 0; i < swap->nat; i++)
3109 swap->ind[i] = grps->a[grps->index[ig]+i];
3114 gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
3117 /* Now do so for the split groups */
3118 for (j = 0; j < 2; j++)
3122 splitg = splitg0name;
3126 splitg = splitg1name;
3129 ig = search_string(splitg, grps->nr, gnames);
3130 swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
3131 if (swap->nat_split[j] > 0)
3133 fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
3134 j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
3135 snew(swap->ind_split[j], swap->nat_split[j]);
3136 for (i = 0; i < swap->nat_split[j]; i++)
3138 swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
3143 gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
3147 /* Now get the solvent group index atoms */
3148 ig = search_string(solgname, grps->nr, gnames);
3149 swap->nat_sol = grps->index[ig+1] - grps->index[ig];
3150 if (swap->nat_sol > 0)
3152 fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
3153 snew(swap->ind_sol, swap->nat_sol);
3154 for (i = 0; i < swap->nat_sol; i++)
3156 swap->ind_sol[i] = grps->a[grps->index[ig]+i];
3161 gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
3166 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3171 ig = search_string(IMDgname, grps->nr, gnames);
3172 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3174 if (IMDgroup->nat > 0)
3176 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3177 IMDgname, IMDgroup->nat);
3178 snew(IMDgroup->ind, IMDgroup->nat);
3179 for (i = 0; i < IMDgroup->nat; i++)
3181 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3187 void do_index(const char* mdparin, const char *ndx,
3190 t_inputrec *ir, rvec *v,
3194 gmx_groups_t *groups;
3198 char warnbuf[STRLEN], **gnames;
3199 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3202 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3203 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3204 int i, j, k, restnm;
3206 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3207 int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
3208 nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
3209 char warn_buf[STRLEN];
3213 fprintf(stderr, "processing index file...\n");
3219 snew(grps->index, 1);
3221 atoms_all = gmx_mtop_global_atoms(mtop);
3222 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3223 free_t_atoms(&atoms_all, FALSE);
3227 grps = init_index(ndx, &gnames);
3230 groups = &mtop->groups;
3231 natoms = mtop->natoms;
3232 symtab = &mtop->symtab;
3234 snew(groups->grpname, grps->nr+1);
3236 for (i = 0; (i < grps->nr); i++)
3238 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3240 groups->grpname[i] = put_symtab(symtab, "rest");
3242 srenew(gnames, grps->nr+1);
3243 gnames[restnm] = *(groups->grpname[i]);
3244 groups->ngrpname = grps->nr+1;
3246 set_warning_line(wi, mdparin, -1);
3248 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3249 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3250 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3251 if ((ntau_t != ntcg) || (nref_t != ntcg))
3253 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3254 "%d tau-t values", ntcg, nref_t, ntau_t);
3257 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3258 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3259 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3260 nr = groups->grps[egcTC].nr;
3262 snew(ir->opts.nrdf, nr);
3263 snew(ir->opts.tau_t, nr);
3264 snew(ir->opts.ref_t, nr);
3265 if (ir->eI == eiBD && ir->bd_fric == 0)
3267 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3274 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3278 for (i = 0; (i < nr); i++)
3280 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
3281 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
3283 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3284 warning_error(wi, warn_buf);
3287 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3289 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.");
3292 if (ir->opts.tau_t[i] >= 0)
3294 tau_min = min(tau_min, ir->opts.tau_t[i]);
3297 if (ir->etc != etcNO && ir->nsttcouple == -1)
3299 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3304 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3306 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");
3308 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
3310 if (ir->nstpcouple != ir->nsttcouple)
3312 int mincouple = min(ir->nstpcouple, ir->nsttcouple);
3313 ir->nstpcouple = ir->nsttcouple = mincouple;
3314 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);
3315 warning_note(wi, warn_buf);
3319 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3320 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3322 if (ETC_ANDERSEN(ir->etc))
3324 if (ir->nsttcouple != 1)
3327 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");
3328 warning_note(wi, warn_buf);
3331 nstcmin = tcouple_min_integration_steps(ir->etc);
3334 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin - 10*GMX_REAL_EPS)
3336 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3337 ETCOUPLTYPE(ir->etc),
3339 ir->nsttcouple*ir->delta_t);
3340 warning(wi, warn_buf);
3343 for (i = 0; (i < nr); i++)
3345 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
3346 if (ir->opts.ref_t[i] < 0)
3348 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3351 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3352 if we are in this conditional) if mc_temp is negative */
3353 if (ir->expandedvals->mc_temp < 0)
3355 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3359 /* Simulated annealing for each group. There are nr groups */
3360 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3361 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3365 if (nSA > 0 && nSA != nr)
3367 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3371 snew(ir->opts.annealing, nr);
3372 snew(ir->opts.anneal_npoints, nr);
3373 snew(ir->opts.anneal_time, nr);
3374 snew(ir->opts.anneal_temp, nr);
3375 for (i = 0; i < nr; i++)
3377 ir->opts.annealing[i] = eannNO;
3378 ir->opts.anneal_npoints[i] = 0;
3379 ir->opts.anneal_time[i] = NULL;
3380 ir->opts.anneal_temp[i] = NULL;
3385 for (i = 0; i < nr; i++)
3387 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3389 ir->opts.annealing[i] = eannNO;
3391 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3393 ir->opts.annealing[i] = eannSINGLE;
3396 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3398 ir->opts.annealing[i] = eannPERIODIC;
3404 /* Read the other fields too */
3405 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3406 if (nSA_points != nSA)
3408 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3410 for (k = 0, i = 0; i < nr; i++)
3412 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3413 if (ir->opts.anneal_npoints[i] == 1)
3415 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3417 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3418 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3419 k += ir->opts.anneal_npoints[i];
3422 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3425 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3427 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3430 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3433 for (i = 0, k = 0; i < nr; i++)
3436 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3438 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3439 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3442 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3444 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3450 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3452 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3453 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3456 if (ir->opts.anneal_temp[i][j] < 0)
3458 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3463 /* Print out some summary information, to make sure we got it right */
3464 for (i = 0, k = 0; i < nr; i++)
3466 if (ir->opts.annealing[i] != eannNO)
3468 j = groups->grps[egcTC].nm_ind[i];
3469 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3470 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3471 ir->opts.anneal_npoints[i]);
3472 fprintf(stderr, "Time (ps) Temperature (K)\n");
3473 /* All terms except the last one */
3474 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3476 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3479 /* Finally the last one */
3480 j = ir->opts.anneal_npoints[i]-1;
3481 if (ir->opts.annealing[i] == eannSINGLE)
3483 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3487 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3488 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3490 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3501 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3503 make_pull_coords(ir->pull);
3508 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3511 if (ir->eSwapCoords != eswapNO)
3513 make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
3516 /* Make indices for IMD session */
3519 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3522 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3523 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3524 if (nacg*DIM != nacc)
3526 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3529 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3530 restnm, egrptpALL_GENREST, bVerbose, wi);
3531 nr = groups->grps[egcACC].nr;
3532 snew(ir->opts.acc, nr);
3533 ir->opts.ngacc = nr;
3535 for (i = k = 0; (i < nacg); i++)
3537 for (j = 0; (j < DIM); j++, k++)
3539 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3542 for (; (i < nr); i++)
3544 for (j = 0; (j < DIM); j++)
3546 ir->opts.acc[i][j] = 0;
3550 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3551 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3552 if (nfrdim != DIM*nfreeze)
3554 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3557 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3558 restnm, egrptpALL_GENREST, bVerbose, wi);
3559 nr = groups->grps[egcFREEZE].nr;
3560 ir->opts.ngfrz = nr;
3561 snew(ir->opts.nFreeze, nr);
3562 for (i = k = 0; (i < nfreeze); i++)
3564 for (j = 0; (j < DIM); j++, k++)
3566 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3567 if (!ir->opts.nFreeze[i][j])
3569 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3571 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3572 "(not %s)", ptr1[k]);
3573 warning(wi, warn_buf);
3578 for (; (i < nr); i++)
3580 for (j = 0; (j < DIM); j++)
3582 ir->opts.nFreeze[i][j] = 0;
3586 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3587 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3588 restnm, egrptpALL_GENREST, bVerbose, wi);
3589 add_wall_energrps(groups, ir->nwall, symtab);
3590 ir->opts.ngener = groups->grps[egcENER].nr;
3591 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3593 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3594 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3597 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3598 "This may lead to artifacts.\n"
3599 "In most cases one should use one group for the whole system.");
3602 /* Now we have filled the freeze struct, so we can calculate NRDF */
3603 calc_nrdf(mtop, ir, gnames);
3609 /* Must check per group! */
3610 for (i = 0; (i < ir->opts.ngtc); i++)
3612 ntot += ir->opts.nrdf[i];
3614 if (ntot != (DIM*natoms))
3616 fac = sqrt(ntot/(DIM*natoms));
3619 fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
3620 "and removal of center of mass motion\n", fac);
3622 for (i = 0; (i < natoms); i++)
3624 svmul(fac, v[i], v[i]);
3629 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3630 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3631 restnm, egrptpALL_GENREST, bVerbose, wi);
3632 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3633 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3634 restnm, egrptpALL_GENREST, bVerbose, wi);
3635 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3636 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3637 restnm, egrptpONE, bVerbose, wi);
3638 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3639 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3640 restnm, egrptpALL_GENREST, bVerbose, wi);
3642 /* QMMM input processing */
3643 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3644 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3645 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3646 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3648 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3649 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3651 /* group rest, if any, is always MM! */
3652 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3653 restnm, egrptpALL_GENREST, bVerbose, wi);
3654 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3655 ir->opts.ngQM = nQMg;
3656 snew(ir->opts.QMmethod, nr);
3657 snew(ir->opts.QMbasis, nr);
3658 for (i = 0; i < nr; i++)
3660 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3661 * converted to the corresponding enum in names.c
3663 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3665 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3669 nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
3670 nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
3671 nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
3672 snew(ir->opts.QMmult, nr);
3673 snew(ir->opts.QMcharge, nr);
3674 snew(ir->opts.bSH, nr);
3676 for (i = 0; i < nr; i++)
3678 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3679 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3680 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3683 nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
3684 nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
3685 snew(ir->opts.CASelectrons, nr);
3686 snew(ir->opts.CASorbitals, nr);
3687 for (i = 0; i < nr; i++)
3689 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3690 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3692 /* special optimization options */
3694 nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
3695 nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
3696 snew(ir->opts.bOPT, nr);
3697 snew(ir->opts.bTS, nr);
3698 for (i = 0; i < nr; i++)
3700 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3701 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3703 nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
3704 nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
3705 nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
3706 snew(ir->opts.SAon, nr);
3707 snew(ir->opts.SAoff, nr);
3708 snew(ir->opts.SAsteps, nr);
3710 for (i = 0; i < nr; i++)
3712 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3713 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3714 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3716 /* end of QMMM input */
3720 for (i = 0; (i < egcNR); i++)
3722 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3723 for (j = 0; (j < groups->grps[i].nr); j++)
3725 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3727 fprintf(stderr, "\n");
3731 nr = groups->grps[egcENER].nr;
3732 snew(ir->opts.egp_flags, nr*nr);
3734 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3735 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3737 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3739 if (bExcl && EEL_FULL(ir->coulombtype))
3741 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3744 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3745 if (bTable && !(ir->vdwtype == evdwUSER) &&
3746 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3747 !(ir->coulombtype == eelPMEUSERSWITCH))
3749 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3752 decode_cos(is->efield_x, &(ir->ex[XX]));
3753 decode_cos(is->efield_xt, &(ir->et[XX]));
3754 decode_cos(is->efield_y, &(ir->ex[YY]));
3755 decode_cos(is->efield_yt, &(ir->et[YY]));
3756 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3757 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3761 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3764 for (i = 0; (i < grps->nr); i++)
3776 static void check_disre(gmx_mtop_t *mtop)
3778 gmx_ffparams_t *ffparams;
3779 t_functype *functype;
3781 int i, ndouble, ftype;
3782 int label, old_label;
3784 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3786 ffparams = &mtop->ffparams;
3787 functype = ffparams->functype;
3788 ip = ffparams->iparams;
3791 for (i = 0; i < ffparams->ntypes; i++)
3793 ftype = functype[i];
3794 if (ftype == F_DISRES)
3796 label = ip[i].disres.label;
3797 if (label == old_label)
3799 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3807 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3808 "probably the parameters for multiple pairs in one restraint "
3809 "are not identical\n", ndouble);
3814 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3815 gmx_bool posres_only,
3819 gmx_mtop_ilistloop_t iloop;
3829 for (d = 0; d < DIM; d++)
3831 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3833 /* Check for freeze groups */
3834 for (g = 0; g < ir->opts.ngfrz; g++)
3836 for (d = 0; d < DIM; d++)
3838 if (ir->opts.nFreeze[g][d] != 0)
3846 /* Check for position restraints */
3847 iloop = gmx_mtop_ilistloop_init(sys);
3848 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3851 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3853 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3855 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3856 for (d = 0; d < DIM; d++)
3858 if (pr->posres.fcA[d] != 0)
3864 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3866 /* Check for flat-bottom posres */
3867 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3868 if (pr->fbposres.k != 0)
3870 switch (pr->fbposres.geom)
3872 case efbposresSPHERE:
3873 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3875 case efbposresCYLINDERX:
3876 AbsRef[YY] = AbsRef[ZZ] = 1;
3878 case efbposresCYLINDERY:
3879 AbsRef[XX] = AbsRef[ZZ] = 1;
3881 case efbposresCYLINDER:
3882 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3883 case efbposresCYLINDERZ:
3884 AbsRef[XX] = AbsRef[YY] = 1;
3886 case efbposresX: /* d=XX */
3887 case efbposresY: /* d=YY */
3888 case efbposresZ: /* d=ZZ */
3889 d = pr->fbposres.geom - efbposresX;
3893 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3894 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3902 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3906 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3907 gmx_bool *bC6ParametersWorkWithGeometricRules,
3908 gmx_bool *bC6ParametersWorkWithLBRules,
3909 gmx_bool *bLBRulesPossible)
3911 int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
3914 double geometricdiff, LBdiff;
3915 double c6i, c6j, c12i, c12j;
3916 double c6, c6_geometric, c6_LB;
3917 double sigmai, sigmaj, epsi, epsj;
3918 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3921 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3922 * force-field floating point parameters.
3925 ptr = getenv("GMX_LJCOMB_TOL");
3930 sscanf(ptr, "%lf", &dbl);
3934 *bC6ParametersWorkWithLBRules = TRUE;
3935 *bC6ParametersWorkWithGeometricRules = TRUE;
3936 bCanDoLBRules = TRUE;
3937 bCanDoGeometricRules = TRUE;
3938 ntypes = mtop->ffparams.atnr;
3939 snew(typecount, ntypes);
3940 gmx_mtop_count_atomtypes(mtop, state, typecount);
3941 geometricdiff = LBdiff = 0.0;
3942 *bLBRulesPossible = TRUE;
3943 for (tpi = 0; tpi < ntypes; ++tpi)
3945 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3946 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3947 for (tpj = tpi; tpj < ntypes; ++tpj)
3949 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3950 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3951 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3952 c6_geometric = sqrt(c6i * c6j);
3953 if (!gmx_numzero(c6_geometric))
3955 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3957 sigmai = pow(c12i / c6i, 1.0/6.0);
3958 sigmaj = pow(c12j / c6j, 1.0/6.0);
3959 epsi = c6i * c6i /(4.0 * c12i);
3960 epsj = c6j * c6j /(4.0 * c12j);
3961 c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
3965 *bLBRulesPossible = FALSE;
3966 c6_LB = c6_geometric;
3968 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3971 if (FALSE == bCanDoLBRules)
3973 *bC6ParametersWorkWithLBRules = FALSE;
3976 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3978 if (FALSE == bCanDoGeometricRules)
3980 *bC6ParametersWorkWithGeometricRules = FALSE;
3988 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3992 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3994 check_combination_rule_differences(mtop, 0,
3995 &bC6ParametersWorkWithGeometricRules,
3996 &bC6ParametersWorkWithLBRules,
3998 if (ir->ljpme_combination_rule == eljpmeLB)
4000 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
4002 warning(wi, "You are using arithmetic-geometric combination rules "
4003 "in LJ-PME, but your non-bonded C6 parameters do not "
4004 "follow these rules.");
4009 if (FALSE == bC6ParametersWorkWithGeometricRules)
4011 if (ir->eDispCorr != edispcNO)
4013 warning_note(wi, "You are using geometric combination rules in "
4014 "LJ-PME, but your non-bonded C6 parameters do "
4015 "not follow these rules. "
4016 "This will introduce very small errors in the forces and energies in "
4017 "your simulations. Dispersion correction will correct total energy "
4018 "and/or pressure for isotropic systems, but not forces or surface tensions.");
4022 warning_note(wi, "You are using geometric combination rules in "
4023 "LJ-PME, but your non-bonded C6 parameters do "
4024 "not follow these rules. "
4025 "This will introduce very small errors in the forces and energies in "
4026 "your simulations. If your system is homogeneous, consider using dispersion correction "
4027 "for the total energy and pressure.");
4033 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
4036 char err_buf[STRLEN];
4037 int i, m, c, nmol, npct;
4038 gmx_bool bCharge, bAcc;
4039 real gdt_max, *mgrp, mt;
4041 gmx_mtop_atomloop_block_t aloopb;
4042 gmx_mtop_atomloop_all_t aloop;
4045 char warn_buf[STRLEN];
4047 set_warning_line(wi, mdparin, -1);
4049 if (ir->cutoff_scheme == ecutsVERLET &&
4050 ir->verletbuf_tol > 0 &&
4052 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
4053 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4055 /* Check if a too small Verlet buffer might potentially
4056 * cause more drift than the thermostat can couple off.
4058 /* Temperature error fraction for warning and suggestion */
4059 const real T_error_warn = 0.002;
4060 const real T_error_suggest = 0.001;
4061 /* For safety: 2 DOF per atom (typical with constraints) */
4062 const real nrdf_at = 2;
4063 real T, tau, max_T_error;
4068 for (i = 0; i < ir->opts.ngtc; i++)
4070 T = max(T, ir->opts.ref_t[i]);
4071 tau = max(tau, ir->opts.tau_t[i]);
4075 /* This is a worst case estimate of the temperature error,
4076 * assuming perfect buffer estimation and no cancelation
4077 * of errors. The factor 0.5 is because energy distributes
4078 * equally over Ekin and Epot.
4080 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4081 if (max_T_error > T_error_warn)
4083 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.",
4084 ir->verletbuf_tol, T, tau,
4086 100*T_error_suggest,
4087 ir->verletbuf_tol*T_error_suggest/max_T_error);
4088 warning(wi, warn_buf);
4093 if (ETC_ANDERSEN(ir->etc))
4097 for (i = 0; i < ir->opts.ngtc; i++)
4099 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4100 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4101 sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
4102 i, ir->opts.tau_t[i]);
4103 CHECK(ir->opts.tau_t[i] < 0);
4106 for (i = 0; i < ir->opts.ngtc; i++)
4108 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
4109 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);
4110 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
4114 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4115 ir->comm_mode == ecmNO &&
4116 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4117 !ETC_ANDERSEN(ir->etc))
4119 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");
4122 /* Check for pressure coupling with absolute position restraints */
4123 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4125 absolute_reference(ir, sys, TRUE, AbsRef);
4127 for (m = 0; m < DIM; m++)
4129 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4131 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4139 aloopb = gmx_mtop_atomloop_block_init(sys);
4140 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4142 if (atom->q != 0 || atom->qB != 0)
4150 if (EEL_FULL(ir->coulombtype))
4153 "You are using full electrostatics treatment %s for a system without charges.\n"
4154 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4155 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4156 warning(wi, err_buf);
4161 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4164 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4165 "You might want to consider using %s electrostatics.\n",
4167 warning_note(wi, err_buf);
4171 /* Check if combination rules used in LJ-PME are the same as in the force field */
4172 if (EVDW_PME(ir->vdwtype))
4174 check_combination_rules(ir, sys, wi);
4177 /* Generalized reaction field */
4178 if (ir->opts.ngtc == 0)
4180 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4182 CHECK(ir->coulombtype == eelGRF);
4186 sprintf(err_buf, "When using coulombtype = %s"
4187 " ref-t for temperature coupling should be > 0",
4189 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4192 if (ir->eI == eiSD2)
4194 sprintf(warn_buf, "The stochastic dynamics integrator %s is deprecated, since\n"
4195 "it is slower than integrator %s and is slightly less accurate\n"
4196 "with constraints. Use the %s integrator.",
4197 ei_names[ir->eI], ei_names[eiSD1], ei_names[eiSD1]);
4198 warning_note(wi, warn_buf);
4202 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4204 for (m = 0; (m < DIM); m++)
4206 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4215 snew(mgrp, sys->groups.grps[egcACC].nr);
4216 aloop = gmx_mtop_atomloop_all_init(sys);
4217 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4219 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4222 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4224 for (m = 0; (m < DIM); m++)
4226 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4230 for (m = 0; (m < DIM); m++)
4232 if (fabs(acc[m]) > 1e-6)
4234 const char *dim[DIM] = { "X", "Y", "Z" };
4236 "Net Acceleration in %s direction, will %s be corrected\n",
4237 dim[m], ir->nstcomm != 0 ? "" : "not");
4238 if (ir->nstcomm != 0 && m < ndof_com(ir))
4241 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4243 ir->opts.acc[i][m] -= acc[m];
4251 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4252 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4254 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4262 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4264 if (ir->pull->coord[i].group[0] == 0 ||
4265 ir->pull->coord[i].group[1] == 0)
4267 absolute_reference(ir, sys, FALSE, AbsRef);
4268 for (m = 0; m < DIM; m++)
4270 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4272 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.");
4280 for (i = 0; i < 3; i++)
4282 for (m = 0; m <= i; m++)
4284 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4285 ir->deform[i][m] != 0)
4287 for (c = 0; c < ir->pull->ncoord; c++)
4289 if (ir->pull->coord[c].eGeom == epullgDIRPBC &&
4290 ir->pull->coord[c].vec[m] != 0)
4292 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->coord[c].eGeom), 'x'+m);
4303 void double_check(t_inputrec *ir, matrix box,
4304 gmx_bool bHasNormalConstraints,
4305 gmx_bool bHasAnyConstraints,
4310 char warn_buf[STRLEN];
4313 ptr = check_box(ir->ePBC, box);
4316 warning_error(wi, ptr);
4319 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4321 if (ir->shake_tol <= 0.0)
4323 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4325 warning_error(wi, warn_buf);
4328 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
4330 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
4331 if (ir->epc == epcNO)
4333 warning(wi, warn_buf);
4337 warning_error(wi, warn_buf);
4342 if ( (ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4344 /* If we have Lincs constraints: */
4345 if (ir->eI == eiMD && ir->etc == etcNO &&
4346 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4348 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4349 warning_note(wi, warn_buf);
4352 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4354 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4355 warning_note(wi, warn_buf);
4357 if (ir->epc == epcMTTK)
4359 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4363 if (bHasAnyConstraints && ir->epc == epcMTTK)
4365 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4368 if (ir->LincsWarnAngle > 90.0)
4370 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4371 warning(wi, warn_buf);
4372 ir->LincsWarnAngle = 90.0;
4375 if (ir->ePBC != epbcNONE)
4377 if (ir->nstlist == 0)
4379 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4381 bTWIN = (ir->rlistlong > ir->rlist);
4382 if (ir->ns_type == ensGRID)
4384 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
4386 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",
4387 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
4388 warning_error(wi, warn_buf);
4393 min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
4394 if (2*ir->rlistlong >= min_size)
4396 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4397 warning_error(wi, warn_buf);
4400 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4407 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4411 real rvdw1, rvdw2, rcoul1, rcoul2;
4412 char warn_buf[STRLEN];
4414 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4418 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4423 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4429 if (rvdw1 + rvdw2 > ir->rlist ||
4430 rcoul1 + rcoul2 > ir->rlist)
4433 "The sum of the two largest charge group radii (%f) "
4434 "is larger than rlist (%f)\n",
4435 max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4436 warning(wi, warn_buf);
4440 /* Here we do not use the zero at cut-off macro,
4441 * since user defined interactions might purposely
4442 * not be zero at the cut-off.
4444 if (ir_vdw_is_zero_at_cutoff(ir) &&
4445 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
4447 sprintf(warn_buf, "The sum of the two largest charge group "
4448 "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
4449 "With exact cut-offs, better performance can be "
4450 "obtained with cutoff-scheme = %s, because it "
4451 "does not use charge groups at all.",
4453 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4454 ir->rlistlong, ir->rvdw,
4455 ecutscheme_names[ecutsVERLET]);
4458 warning(wi, warn_buf);
4462 warning_note(wi, warn_buf);
4465 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4466 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
4468 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
4469 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4471 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4472 ir->rlistlong, ir->rcoulomb,
4473 ecutscheme_names[ecutsVERLET]);
4476 warning(wi, warn_buf);
4480 warning_note(wi, warn_buf);