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45 #include "gromacs/utility/smalloc.h"
49 #include "gmx_fatal.h"
53 #include "gromacs/utility/cstringutil.h"
62 #include "mtop_util.h"
63 #include "chargegroup.h"
65 #include "calc_verletbuf.h"
70 /* Resource parameters
71 * Do not change any of these until you read the instruction
72 * in readinp.h. Some cpp's do not take spaces after the backslash
73 * (like the c-shell), which will give you a very weird compiler
77 typedef struct t_inputrec_strings
79 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN],
80 acc[STRLEN], accgrps[STRLEN], freeze[STRLEN], frdim[STRLEN],
81 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
82 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
83 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN],
85 char fep_lambda[efptNR][STRLEN];
86 char lambda_weights[STRLEN];
89 char anneal[STRLEN], anneal_npoints[STRLEN],
90 anneal_time[STRLEN], anneal_temp[STRLEN];
91 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
92 bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
93 SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
94 char efield_x[STRLEN], efield_xt[STRLEN], efield_y[STRLEN],
95 efield_yt[STRLEN], efield_z[STRLEN], efield_zt[STRLEN];
97 } gmx_inputrec_strings;
99 static gmx_inputrec_strings *is = NULL;
101 void init_inputrec_strings()
105 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.");
110 void done_inputrec_strings()
116 static char swapgrp[STRLEN], splitgrp0[STRLEN], splitgrp1[STRLEN], solgrp[STRLEN];
119 egrptpALL, /* All particles have to be a member of a group. */
120 egrptpALL_GENREST, /* A rest group with name is generated for particles *
121 * that are not part of any group. */
122 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
123 * for the rest group. */
124 egrptpONE /* Merge all selected groups into one group, *
125 * make a rest group for the remaining particles. */
128 static const char *constraints[eshNR+1] = {
129 "none", "h-bonds", "all-bonds", "h-angles", "all-angles", NULL
132 static const char *couple_lam[ecouplamNR+1] = {
133 "vdw-q", "vdw", "q", "none", NULL
136 void init_ir(t_inputrec *ir, t_gromppopts *opts)
138 snew(opts->include, STRLEN);
139 snew(opts->define, STRLEN);
140 snew(ir->fepvals, 1);
141 snew(ir->expandedvals, 1);
142 snew(ir->simtempvals, 1);
145 static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
150 for (i = 0; i < ntemps; i++)
152 /* simple linear scaling -- allows more control */
153 if (simtemp->eSimTempScale == esimtempLINEAR)
155 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*temperature_lambdas[i];
157 else if (simtemp->eSimTempScale == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
159 simtemp->temperatures[i] = simtemp->simtemp_low * pow(simtemp->simtemp_high/simtemp->simtemp_low, (1.0*i)/(ntemps-1));
161 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
163 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*((exp(temperature_lambdas[i])-1)/(exp(1.0)-1));
168 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
169 gmx_fatal(FARGS, errorstr);
176 static void _low_check(gmx_bool b, char *s, warninp_t wi)
180 warning_error(wi, s);
184 static void check_nst(const char *desc_nst, int nst,
185 const char *desc_p, int *p,
190 if (*p > 0 && *p % nst != 0)
192 /* Round up to the next multiple of nst */
193 *p = ((*p)/nst + 1)*nst;
194 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n",
195 desc_p, desc_nst, desc_p, *p);
200 static gmx_bool ir_NVE(const t_inputrec *ir)
202 return ((ir->eI == eiMD || EI_VV(ir->eI)) && ir->etc == etcNO);
205 static int lcd(int n1, int n2)
210 for (i = 2; (i <= n1 && i <= n2); i++)
212 if (n1 % i == 0 && n2 % i == 0)
221 static void process_interaction_modifier(const t_inputrec *ir, int *eintmod)
223 if (*eintmod == eintmodPOTSHIFT_VERLET)
225 if (ir->cutoff_scheme == ecutsVERLET)
227 *eintmod = eintmodPOTSHIFT;
231 *eintmod = eintmodNONE;
236 void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
238 /* Check internal consistency.
239 * NOTE: index groups are not set here yet, don't check things
240 * like temperature coupling group options here, but in triple_check
243 /* Strange macro: first one fills the err_buf, and then one can check
244 * the condition, which will print the message and increase the error
247 #define CHECK(b) _low_check(b, err_buf, wi)
248 char err_buf[256], warn_buf[STRLEN];
254 t_lambda *fep = ir->fepvals;
255 t_expanded *expand = ir->expandedvals;
257 set_warning_line(wi, mdparin, -1);
259 /* BASIC CUT-OFF STUFF */
260 if (ir->rcoulomb < 0)
262 warning_error(wi, "rcoulomb should be >= 0");
266 warning_error(wi, "rvdw should be >= 0");
269 !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
271 warning_error(wi, "rlist should be >= 0");
274 process_interaction_modifier(ir, &ir->coulomb_modifier);
275 process_interaction_modifier(ir, &ir->vdw_modifier);
277 if (ir->cutoff_scheme == ecutsGROUP)
280 "The group cutoff scheme is deprecated in Gromacs 5.0 and will be removed in a future "
281 "release when all interaction forms are supported for the verlet scheme. The verlet "
282 "scheme already scales better, and it is compatible with GPUs and other accelerators.");
284 /* BASIC CUT-OFF STUFF */
285 if (ir->rlist == 0 ||
286 !((ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > ir->rlist) ||
287 (ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > ir->rlist)))
289 /* No switched potential and/or no twin-range:
290 * we can set the long-range cut-off to the maximum of the other cut-offs.
292 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
294 else if (ir->rlistlong < 0)
296 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
297 sprintf(warn_buf, "rlistlong was not set, setting it to %g (no buffer)",
299 warning(wi, warn_buf);
301 if (ir->rlistlong == 0 && ir->ePBC != epbcNONE)
303 warning_error(wi, "Can not have an infinite cut-off with PBC");
305 if (ir->rlistlong > 0 && (ir->rlist == 0 || ir->rlistlong < ir->rlist))
307 warning_error(wi, "rlistlong can not be shorter than rlist");
309 if (IR_TWINRANGE(*ir) && ir->nstlist <= 0)
311 warning_error(wi, "Can not have nstlist<=0 with twin-range interactions");
315 if (ir->rlistlong == ir->rlist)
319 else if (ir->rlistlong > ir->rlist && ir->nstcalclr == 0)
321 warning_error(wi, "With different cutoffs for electrostatics and VdW, nstcalclr must be -1 or a positive number");
324 if (ir->cutoff_scheme == ecutsVERLET)
328 /* Normal Verlet type neighbor-list, currently only limited feature support */
329 if (inputrec2nboundeddim(ir) < 3)
331 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
333 if (ir->rcoulomb != ir->rvdw)
335 warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported");
337 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
339 if (ir->vdw_modifier == eintmodNONE ||
340 ir->vdw_modifier == eintmodPOTSHIFT)
342 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
344 sprintf(warn_buf, "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], evdw_names[evdwCUT], eintmod_names[ir->vdw_modifier]);
345 warning_note(wi, warn_buf);
347 ir->vdwtype = evdwCUT;
351 sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
352 warning_error(wi, warn_buf);
356 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
358 warning_error(wi, "With Verlet lists only cut-off and PME LJ interactions are supported");
360 if (!(ir->coulombtype == eelCUT ||
361 (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC) ||
362 EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
364 warning_error(wi, "With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
366 if (!(ir->coulomb_modifier == eintmodNONE ||
367 ir->coulomb_modifier == eintmodPOTSHIFT))
369 sprintf(warn_buf, "coulomb_modifier=%s is not supported with the Verlet cut-off scheme", eintmod_names[ir->coulomb_modifier]);
370 warning_error(wi, warn_buf);
373 if (ir->implicit_solvent != eisNO)
375 warning_error(wi, "Implicit solvent is not (yet) supported with the with Verlet lists.");
378 if (ir->nstlist <= 0)
380 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
383 if (ir->nstlist < 10)
385 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.");
388 rc_max = max(ir->rvdw, ir->rcoulomb);
390 if (ir->verletbuf_tol <= 0)
392 if (ir->verletbuf_tol == 0)
394 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
397 if (ir->rlist < rc_max)
399 warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
402 if (ir->rlist == rc_max && ir->nstlist > 1)
404 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.");
409 if (ir->rlist > rc_max)
411 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.");
414 if (ir->nstlist == 1)
416 /* No buffer required */
421 if (EI_DYNAMICS(ir->eI))
423 if (inputrec2nboundeddim(ir) < 3)
425 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.");
427 /* Set rlist temporarily so we can continue processing */
432 /* Set the buffer to 5% of the cut-off */
433 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
438 /* No twin-range calculations with Verlet lists */
439 ir->rlistlong = ir->rlist;
442 if (ir->nstcalclr == -1)
444 /* if rlist=rlistlong, this will later be changed to nstcalclr=0 */
445 ir->nstcalclr = ir->nstlist;
447 else if (ir->nstcalclr > 0)
449 if (ir->nstlist > 0 && (ir->nstlist % ir->nstcalclr != 0))
451 warning_error(wi, "nstlist must be evenly divisible by nstcalclr. Use nstcalclr = -1 to automatically follow nstlist");
454 else if (ir->nstcalclr < -1)
456 warning_error(wi, "nstcalclr must be a positive number (divisor of nstcalclr), or -1 to follow nstlist.");
459 if (EEL_PME(ir->coulombtype) && ir->rcoulomb > ir->rvdw && ir->nstcalclr > 1)
461 warning_error(wi, "When used with PME, the long-range component of twin-range interactions must be updated every step (nstcalclr)");
464 /* GENERAL INTEGRATOR STUFF */
465 if (!(ir->eI == eiMD || EI_VV(ir->eI)))
469 if (ir->eI == eiVVAK)
471 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]);
472 warning_note(wi, warn_buf);
474 if (!EI_DYNAMICS(ir->eI))
478 if (EI_DYNAMICS(ir->eI))
480 if (ir->nstcalcenergy < 0)
482 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
483 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
485 /* nstcalcenergy larger than nstener does not make sense.
486 * We ideally want nstcalcenergy=nstener.
490 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
494 ir->nstcalcenergy = ir->nstenergy;
498 else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
499 (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
500 (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
503 const char *nsten = "nstenergy";
504 const char *nstdh = "nstdhdl";
505 const char *min_name = nsten;
506 int min_nst = ir->nstenergy;
508 /* find the smallest of ( nstenergy, nstdhdl ) */
509 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
510 (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
512 min_nst = ir->fepvals->nstdhdl;
515 /* If the user sets nstenergy small, we should respect that */
517 "Setting nstcalcenergy (%d) equal to %s (%d)",
518 ir->nstcalcenergy, min_name, min_nst);
519 warning_note(wi, warn_buf);
520 ir->nstcalcenergy = min_nst;
523 if (ir->epc != epcNO)
525 if (ir->nstpcouple < 0)
527 ir->nstpcouple = ir_optimal_nstpcouple(ir);
530 if (IR_TWINRANGE(*ir))
532 check_nst("nstlist", ir->nstlist,
533 "nstcalcenergy", &ir->nstcalcenergy, wi);
534 if (ir->epc != epcNO)
536 check_nst("nstlist", ir->nstlist,
537 "nstpcouple", &ir->nstpcouple, wi);
541 if (ir->nstcalcenergy > 0)
543 if (ir->efep != efepNO)
545 /* nstdhdl should be a multiple of nstcalcenergy */
546 check_nst("nstcalcenergy", ir->nstcalcenergy,
547 "nstdhdl", &ir->fepvals->nstdhdl, wi);
548 /* nstexpanded should be a multiple of nstcalcenergy */
549 check_nst("nstcalcenergy", ir->nstcalcenergy,
550 "nstexpanded", &ir->expandedvals->nstexpanded, wi);
552 /* for storing exact averages nstenergy should be
553 * a multiple of nstcalcenergy
555 check_nst("nstcalcenergy", ir->nstcalcenergy,
556 "nstenergy", &ir->nstenergy, wi);
560 if (ir->nsteps == 0 && !ir->bContinuation)
562 warning_note(wi, "For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates.");
566 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
567 ir->bContinuation && ir->ld_seed != -1)
569 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)");
575 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
576 CHECK(ir->ePBC != epbcXYZ);
577 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
578 CHECK(ir->ns_type != ensGRID);
579 sprintf(err_buf, "with TPI nstlist should be larger than zero");
580 CHECK(ir->nstlist <= 0);
581 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
582 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
583 sprintf(err_buf, "TPI does not work (yet) with the Verlet cut-off scheme");
584 CHECK(ir->cutoff_scheme == ecutsVERLET);
588 if ( (opts->nshake > 0) && (opts->bMorse) )
591 "Using morse bond-potentials while constraining bonds is useless");
592 warning(wi, warn_buf);
595 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
596 ir->bContinuation && ir->ld_seed != -1)
598 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)");
600 /* verify simulated tempering options */
604 gmx_bool bAllTempZero = TRUE;
605 for (i = 0; i < fep->n_lambda; i++)
607 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]);
608 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
609 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
611 bAllTempZero = FALSE;
614 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
615 CHECK(bAllTempZero == TRUE);
617 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
618 CHECK(ir->eI != eiVV);
620 /* check compatability of the temperature coupling with simulated tempering */
622 if (ir->etc == etcNOSEHOOVER)
624 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
625 warning_note(wi, warn_buf);
628 /* check that the temperatures make sense */
630 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);
631 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
633 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
634 CHECK(ir->simtempvals->simtemp_high <= 0);
636 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
637 CHECK(ir->simtempvals->simtemp_low <= 0);
640 /* verify free energy options */
642 if (ir->efep != efepNO)
645 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
647 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
649 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
650 (int)fep->sc_r_power);
651 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
653 sprintf(err_buf, "Can't use postive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
654 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
656 sprintf(err_buf, "Can't use postive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
657 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
659 sprintf(err_buf, "Can only use expanded ensemble with md-vv for now; should be supported for other integrators in 5.0");
660 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
662 sprintf(err_buf, "Free-energy not implemented for Ewald");
663 CHECK(ir->coulombtype == eelEWALD);
665 /* check validty of lambda inputs */
666 if (fep->n_lambda == 0)
668 /* Clear output in case of no states:*/
669 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
670 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
674 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
675 CHECK((fep->init_fep_state >= fep->n_lambda));
678 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
679 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
681 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",
682 fep->init_lambda, fep->init_fep_state);
683 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
687 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
691 for (i = 0; i < efptNR; i++)
693 if (fep->separate_dvdl[i])
698 if (n_lambda_terms > 1)
700 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.");
701 warning(wi, warn_buf);
704 if (n_lambda_terms < 2 && fep->n_lambda > 0)
707 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
711 for (j = 0; j < efptNR; j++)
713 for (i = 0; i < fep->n_lambda; i++)
715 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]);
716 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
720 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
722 for (i = 0; i < fep->n_lambda; i++)
724 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],
725 fep->all_lambda[efptCOUL][i]);
726 CHECK((fep->sc_alpha > 0) &&
727 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
728 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
729 ((fep->all_lambda[efptVDW][i] > 0.0) &&
730 (fep->all_lambda[efptVDW][i] < 1.0))));
734 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
736 real sigma, lambda, r_sc;
739 /* Maximum estimate for A and B charges equal with lambda power 1 */
741 r_sc = pow(lambda*fep->sc_alpha*pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
742 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.",
744 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
745 warning_note(wi, warn_buf);
748 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
749 be treated differently, but that's the next step */
751 for (i = 0; i < efptNR; i++)
753 for (j = 0; j < fep->n_lambda; j++)
755 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
756 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
761 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
764 expand = ir->expandedvals;
766 /* checking equilibration of weights inputs for validity */
768 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
769 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
770 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
772 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
773 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
774 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
776 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
777 expand->equil_steps, elmceq_names[elmceqSTEPS]);
778 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
780 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
781 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
782 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
784 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
785 expand->equil_ratio, elmceq_names[elmceqRATIO]);
786 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
788 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
789 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
790 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
792 sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
793 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
794 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
796 sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
797 expand->equil_steps, elmceq_names[elmceqSTEPS]);
798 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
800 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
801 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
802 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
804 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
805 expand->equil_ratio, elmceq_names[elmceqRATIO]);
806 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
808 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
809 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
810 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
812 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
813 CHECK((expand->lmc_repeats <= 0));
814 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
815 CHECK((expand->minvarmin <= 0));
816 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
817 CHECK((expand->c_range < 0));
818 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
819 fep->init_fep_state, expand->lmc_forced_nstart);
820 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
821 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
822 CHECK((expand->lmc_forced_nstart < 0));
823 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
824 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
826 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
827 CHECK((expand->init_wl_delta < 0));
828 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
829 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
830 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
831 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
833 /* if there is no temperature control, we need to specify an MC temperature */
834 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
835 if (expand->nstTij > 0)
837 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
838 expand->nstTij, ir->nstlog);
839 CHECK((mod(expand->nstTij, ir->nstlog) != 0));
844 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
845 CHECK(ir->nwall && ir->ePBC != epbcXY);
848 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
850 if (ir->ePBC == epbcNONE)
852 if (ir->epc != epcNO)
854 warning(wi, "Turning off pressure coupling for vacuum system");
860 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
861 epbc_names[ir->ePBC]);
862 CHECK(ir->epc != epcNO);
864 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
865 CHECK(EEL_FULL(ir->coulombtype));
867 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
868 epbc_names[ir->ePBC]);
869 CHECK(ir->eDispCorr != edispcNO);
872 if (ir->rlist == 0.0)
874 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
875 "with coulombtype = %s or coulombtype = %s\n"
876 "without periodic boundary conditions (pbc = %s) and\n"
877 "rcoulomb and rvdw set to zero",
878 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
879 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
880 (ir->ePBC != epbcNONE) ||
881 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
885 warning_error(wi, "Can not have heuristic neighborlist updates without cut-off");
889 warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
894 if (ir->nstcomm == 0)
896 ir->comm_mode = ecmNO;
898 if (ir->comm_mode != ecmNO)
902 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");
903 ir->nstcomm = abs(ir->nstcomm);
906 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
908 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
909 ir->nstcomm = ir->nstcalcenergy;
912 if (ir->comm_mode == ecmANGULAR)
914 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
915 CHECK(ir->bPeriodicMols);
916 if (ir->ePBC != epbcNONE)
918 warning(wi, "Removing the rotation around the center of mass in a periodic system (this is not a problem when you have only one molecule).");
923 if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
925 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.");
928 sprintf(err_buf, "Twin-range neighbour searching (NS) with simple NS"
929 " algorithm not implemented");
930 CHECK(((ir->rcoulomb > ir->rlist) || (ir->rvdw > ir->rlist))
931 && (ir->ns_type == ensSIMPLE));
933 /* TEMPERATURE COUPLING */
934 if (ir->etc == etcYES)
936 ir->etc = etcBERENDSEN;
937 warning_note(wi, "Old option for temperature coupling given: "
938 "changing \"yes\" to \"Berendsen\"\n");
941 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
943 if (ir->opts.nhchainlength < 1)
945 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
946 ir->opts.nhchainlength = 1;
947 warning(wi, warn_buf);
950 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
952 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
953 ir->opts.nhchainlength = 1;
958 ir->opts.nhchainlength = 0;
961 if (ir->eI == eiVVAK)
963 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
965 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
968 if (ETC_ANDERSEN(ir->etc))
970 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
971 CHECK(!(EI_VV(ir->eI)));
973 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
975 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]);
976 warning_note(wi, warn_buf);
979 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]);
980 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
983 if (ir->etc == etcBERENDSEN)
985 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
986 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
987 warning_note(wi, warn_buf);
990 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
991 && ir->epc == epcBERENDSEN)
993 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
994 "true ensemble for the thermostat");
995 warning(wi, warn_buf);
998 /* PRESSURE COUPLING */
999 if (ir->epc == epcISOTROPIC)
1001 ir->epc = epcBERENDSEN;
1002 warning_note(wi, "Old option for pressure coupling given: "
1003 "changing \"Isotropic\" to \"Berendsen\"\n");
1006 if (ir->epc != epcNO)
1008 dt_pcoupl = ir->nstpcouple*ir->delta_t;
1010 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1011 CHECK(ir->tau_p <= 0);
1013 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10*GMX_REAL_EPS)
1015 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
1016 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1017 warning(wi, warn_buf);
1020 sprintf(err_buf, "compressibility must be > 0 when using pressure"
1021 " coupling %s\n", EPCOUPLTYPE(ir->epc));
1022 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
1023 ir->compress[ZZ][ZZ] < 0 ||
1024 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
1025 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
1027 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1030 "You are generating velocities so I am assuming you "
1031 "are equilibrating a system. You are using "
1032 "%s pressure coupling, but this can be "
1033 "unstable for equilibration. If your system crashes, try "
1034 "equilibrating first with Berendsen pressure coupling. If "
1035 "you are not equilibrating the system, you can probably "
1036 "ignore this warning.",
1037 epcoupl_names[ir->epc]);
1038 warning(wi, warn_buf);
1044 if (ir->epc > epcNO)
1046 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1048 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.");
1054 if (ir->epc == epcMTTK)
1056 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1060 /* ELECTROSTATICS */
1061 /* More checks are in triple check (grompp.c) */
1063 if (ir->coulombtype == eelSWITCH)
1065 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1066 "artifacts, advice: use coulombtype = %s",
1067 eel_names[ir->coulombtype],
1068 eel_names[eelRF_ZERO]);
1069 warning(wi, warn_buf);
1072 if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
1074 sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
1075 warning_note(wi, warn_buf);
1078 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1080 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);
1081 warning(wi, warn_buf);
1082 ir->epsilon_rf = ir->epsilon_r;
1083 ir->epsilon_r = 1.0;
1086 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == NULL)
1088 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1089 CHECK(ir->epsilon_r < 0);
1092 if (EEL_RF(ir->coulombtype))
1094 /* reaction field (at the cut-off) */
1096 if (ir->coulombtype == eelRF_ZERO)
1098 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1099 eel_names[ir->coulombtype]);
1100 CHECK(ir->epsilon_rf != 0);
1101 ir->epsilon_rf = 0.0;
1104 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1105 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1106 (ir->epsilon_r == 0));
1107 if (ir->epsilon_rf == ir->epsilon_r)
1109 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1110 eel_names[ir->coulombtype]);
1111 warning(wi, warn_buf);
1114 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1115 * means the interaction is zero outside rcoulomb, but it helps to
1116 * provide accurate energy conservation.
1118 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1120 if (ir_coulomb_switched(ir))
1123 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1124 eel_names[ir->coulombtype]);
1125 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1128 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1130 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1132 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1133 eel_names[ir->coulombtype]);
1134 CHECK(ir->rlist > ir->rcoulomb);
1138 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1141 "Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier.");
1142 CHECK( ir->coulomb_modifier != eintmodNONE);
1144 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1147 "Explicit switch/shift vdw interactions cannot be used in combination with a secondary vdw-modifier.");
1148 CHECK( ir->vdw_modifier != eintmodNONE);
1151 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1152 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1155 "The switch/shift interaction settings are just for compatibility; you will get better "
1156 "performance from applying potential modifiers to your interactions!\n");
1157 warning_note(wi, warn_buf);
1160 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1162 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1164 real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
1165 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.",
1166 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1167 warning(wi, warn_buf);
1171 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1173 if (ir->rvdw_switch == 0)
1175 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.");
1176 warning(wi, warn_buf);
1180 if (EEL_FULL(ir->coulombtype))
1182 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1183 ir->coulombtype == eelPMEUSERSWITCH)
1185 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1186 eel_names[ir->coulombtype]);
1187 CHECK(ir->rcoulomb > ir->rlist);
1189 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1191 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1194 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
1195 "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
1196 "a potential modifier.", eel_names[ir->coulombtype]);
1197 if (ir->nstcalclr == 1)
1199 CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
1203 CHECK(ir->rcoulomb != ir->rlist);
1209 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1211 if (ir->pme_order < 3)
1213 warning_error(wi, "pme-order can not be smaller than 3");
1217 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1219 if (ir->ewald_geometry == eewg3D)
1221 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1222 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1223 warning(wi, warn_buf);
1225 /* This check avoids extra pbc coding for exclusion corrections */
1226 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1227 CHECK(ir->wall_ewald_zfac < 2);
1229 if ((ir->ewald_geometry == eewg3DC) && (ir->ePBC != epbcXY) &&
1230 EEL_FULL(ir->coulombtype))
1232 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1233 eel_names[ir->coulombtype], eewg_names[eewg3DC], epbc_names[epbcXY]);
1234 warning(wi, warn_buf);
1236 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1238 if (ir->cutoff_scheme == ecutsVERLET)
1240 sprintf(warn_buf, "Since molecules/charge groups are broken using the Verlet scheme, you can not use a dipole correction to the %s electrostatics.",
1241 eel_names[ir->coulombtype]);
1242 warning(wi, warn_buf);
1246 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",
1247 eel_names[ir->coulombtype]);
1248 warning_note(wi, warn_buf);
1252 if (ir_vdw_switched(ir))
1254 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1255 CHECK(ir->rvdw_switch >= ir->rvdw);
1257 if (ir->rvdw_switch < 0.5*ir->rvdw)
1259 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.",
1260 ir->rvdw_switch, ir->rvdw);
1261 warning_note(wi, warn_buf);
1264 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1266 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1268 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1269 CHECK(ir->rlist > ir->rvdw);
1273 if (ir->vdwtype == evdwPME)
1275 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1277 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s a\
1279 evdw_names[ir->vdwtype],
1280 eintmod_names[eintmodPOTSHIFT],
1281 eintmod_names[eintmodNONE]);
1285 if (ir->cutoff_scheme == ecutsGROUP)
1287 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1288 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)) &&
1291 warning_note(wi, "With exact cut-offs, rlist should be "
1292 "larger than rcoulomb and rvdw, so that there "
1293 "is a buffer region for particle motion "
1294 "between neighborsearch steps");
1297 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlistlong <= ir->rcoulomb)
1299 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
1300 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1301 warning_note(wi, warn_buf);
1303 if (ir_vdw_switched(ir) && (ir->rlistlong <= ir->rvdw))
1305 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
1306 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1307 warning_note(wi, warn_buf);
1311 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1313 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.");
1316 if (ir->nstlist == -1)
1318 sprintf(err_buf, "With nstlist=-1 rvdw and rcoulomb should be smaller than rlist to account for diffusion and possibly charge-group radii");
1319 CHECK(ir->rvdw >= ir->rlist || ir->rcoulomb >= ir->rlist);
1321 sprintf(err_buf, "nstlist can not be smaller than -1");
1322 CHECK(ir->nstlist < -1);
1324 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1327 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1330 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1332 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1335 /* ENERGY CONSERVATION */
1336 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1338 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1340 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1341 evdw_names[evdwSHIFT]);
1342 warning_note(wi, warn_buf);
1344 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1346 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1347 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1348 warning_note(wi, warn_buf);
1352 if (EI_VV(ir->eI) && IR_TWINRANGE(*ir) && ir->nstlist > 1)
1354 sprintf(warn_buf, "Twin-range multiple time stepping does not work with integrator %s.", ei_names[ir->eI]);
1355 warning_error(wi, warn_buf);
1358 /* IMPLICIT SOLVENT */
1359 if (ir->coulombtype == eelGB_NOTUSED)
1361 sprintf(warn_buf, "Invalid option %s for coulombtype",
1362 eel_names[ir->coulombtype]);
1363 warning_error(wi, warn_buf);
1366 if (ir->sa_algorithm == esaSTILL)
1368 sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
1369 CHECK(ir->sa_algorithm == esaSTILL);
1372 if (ir->implicit_solvent == eisGBSA)
1374 sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
1375 CHECK(ir->rgbradii != ir->rlist);
1377 if (ir->coulombtype != eelCUT)
1379 sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
1380 CHECK(ir->coulombtype != eelCUT);
1382 if (ir->vdwtype != evdwCUT)
1384 sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
1385 CHECK(ir->vdwtype != evdwCUT);
1387 if (ir->nstgbradii < 1)
1389 sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
1390 warning_note(wi, warn_buf);
1393 if (ir->sa_algorithm == esaNO)
1395 sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
1396 warning_note(wi, warn_buf);
1398 if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
1400 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");
1401 warning_note(wi, warn_buf);
1403 if (ir->gb_algorithm == egbSTILL)
1405 ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
1409 ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
1412 if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
1414 sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
1415 CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
1422 if (ir->cutoff_scheme != ecutsGROUP)
1424 warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
1428 warning_error(wi, "AdresS simulation supports only stochastic dynamics");
1430 if (ir->epc != epcNO)
1432 warning_error(wi, "AdresS simulation does not support pressure coupling");
1434 if (EEL_FULL(ir->coulombtype))
1436 warning_error(wi, "AdresS simulation does not support long-range electrostatics");
1441 /* count the number of text elemets separated by whitespace in a string.
1442 str = the input string
1443 maxptr = the maximum number of allowed elements
1444 ptr = the output array of pointers to the first character of each element
1445 returns: the number of elements. */
1446 int str_nelem(const char *str, int maxptr, char *ptr[])
1451 copy0 = strdup(str);
1454 while (*copy != '\0')
1458 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1466 while ((*copy != '\0') && !isspace(*copy))
1485 /* interpret a number of doubles from a string and put them in an array,
1486 after allocating space for them.
1487 str = the input string
1488 n = the (pre-allocated) number of doubles read
1489 r = the output array of doubles. */
1490 static void parse_n_real(char *str, int *n, real **r)
1495 *n = str_nelem(str, MAXPTR, ptr);
1498 for (i = 0; i < *n; i++)
1500 (*r)[i] = strtod(ptr[i], NULL);
1504 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
1507 int i, j, max_n_lambda, nweights, nfep[efptNR];
1508 t_lambda *fep = ir->fepvals;
1509 t_expanded *expand = ir->expandedvals;
1510 real **count_fep_lambdas;
1511 gmx_bool bOneLambda = TRUE;
1513 snew(count_fep_lambdas, efptNR);
1515 /* FEP input processing */
1516 /* first, identify the number of lambda values for each type.
1517 All that are nonzero must have the same number */
1519 for (i = 0; i < efptNR; i++)
1521 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
1524 /* now, determine the number of components. All must be either zero, or equal. */
1527 for (i = 0; i < efptNR; i++)
1529 if (nfep[i] > max_n_lambda)
1531 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1532 must have the same number if its not zero.*/
1537 for (i = 0; i < efptNR; i++)
1541 ir->fepvals->separate_dvdl[i] = FALSE;
1543 else if (nfep[i] == max_n_lambda)
1545 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1546 respect to the temperature currently */
1548 ir->fepvals->separate_dvdl[i] = TRUE;
1553 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1554 nfep[i], efpt_names[i], max_n_lambda);
1557 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1558 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1560 /* the number of lambdas is the number we've read in, which is either zero
1561 or the same for all */
1562 fep->n_lambda = max_n_lambda;
1564 /* allocate space for the array of lambda values */
1565 snew(fep->all_lambda, efptNR);
1566 /* if init_lambda is defined, we need to set lambda */
1567 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1569 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1571 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1572 for (i = 0; i < efptNR; i++)
1574 snew(fep->all_lambda[i], fep->n_lambda);
1575 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1578 for (j = 0; j < fep->n_lambda; j++)
1580 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1582 sfree(count_fep_lambdas[i]);
1585 sfree(count_fep_lambdas);
1587 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1588 bookkeeping -- for now, init_lambda */
1590 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1592 for (i = 0; i < fep->n_lambda; i++)
1594 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1598 /* check to see if only a single component lambda is defined, and soft core is defined.
1599 In this case, turn on coulomb soft core */
1601 if (max_n_lambda == 0)
1607 for (i = 0; i < efptNR; i++)
1609 if ((nfep[i] != 0) && (i != efptFEP))
1615 if ((bOneLambda) && (fep->sc_alpha > 0))
1617 fep->bScCoul = TRUE;
1620 /* Fill in the others with the efptFEP if they are not explicitly
1621 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1622 they are all zero. */
1624 for (i = 0; i < efptNR; i++)
1626 if ((nfep[i] == 0) && (i != efptFEP))
1628 for (j = 0; j < fep->n_lambda; j++)
1630 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1636 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1637 if (fep->sc_r_power == 48)
1639 if (fep->sc_alpha > 0.1)
1641 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1645 expand = ir->expandedvals;
1646 /* now read in the weights */
1647 parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
1650 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1652 else if (nweights != fep->n_lambda)
1654 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1655 nweights, fep->n_lambda);
1657 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1659 expand->nstexpanded = fep->nstdhdl;
1660 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1662 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1664 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1665 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1666 2*tau_t just to be careful so it's not to frequent */
1671 static void do_simtemp_params(t_inputrec *ir)
1674 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1675 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1680 static void do_wall_params(t_inputrec *ir,
1681 char *wall_atomtype, char *wall_density,
1685 char *names[MAXPTR];
1688 opts->wall_atomtype[0] = NULL;
1689 opts->wall_atomtype[1] = NULL;
1691 ir->wall_atomtype[0] = -1;
1692 ir->wall_atomtype[1] = -1;
1693 ir->wall_density[0] = 0;
1694 ir->wall_density[1] = 0;
1698 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1699 if (nstr != ir->nwall)
1701 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1704 for (i = 0; i < ir->nwall; i++)
1706 opts->wall_atomtype[i] = strdup(names[i]);
1709 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1711 nstr = str_nelem(wall_density, MAXPTR, names);
1712 if (nstr != ir->nwall)
1714 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1716 for (i = 0; i < ir->nwall; i++)
1718 sscanf(names[i], "%lf", &dbl);
1721 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1723 ir->wall_density[i] = dbl;
1729 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1737 srenew(groups->grpname, groups->ngrpname+nwall);
1738 grps = &(groups->grps[egcENER]);
1739 srenew(grps->nm_ind, grps->nr+nwall);
1740 for (i = 0; i < nwall; i++)
1742 sprintf(str, "wall%d", i);
1743 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1744 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1749 void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1750 t_expanded *expand, warninp_t wi)
1752 int ninp, nerror = 0;
1758 /* read expanded ensemble parameters */
1759 CCTYPE ("expanded ensemble variables");
1760 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1761 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1762 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1763 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1764 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1765 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1766 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1767 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1768 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1769 CCTYPE("Seed for Monte Carlo in lambda space");
1770 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1771 RTYPE ("mc-temperature", expand->mc_temp, -1);
1772 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1773 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1774 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1775 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1776 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1777 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1778 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1779 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1780 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1781 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1782 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
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 CTYPE("Pull type: no, umbrella, constraint or constant-force");
2098 EETYPE("pull", ir->ePull, epull_names);
2099 if (ir->ePull != epullNO)
2102 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
2105 /* Enforced rotation */
2106 CCTYPE("ENFORCED ROTATION");
2107 CTYPE("Enforced rotation: No or Yes");
2108 EETYPE("rotation", ir->bRot, yesno_names);
2112 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2115 /* Interactive MD */
2117 CCTYPE("Group to display and/or manipulate in interactive MD session");
2118 STYPE ("IMD-group", is->imd_grp, NULL);
2119 if (is->imd_grp[0] != '\0')
2126 CCTYPE("NMR refinement stuff");
2127 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2128 EETYPE("disre", ir->eDisre, edisre_names);
2129 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2130 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2131 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2132 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2133 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2134 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2135 CTYPE ("Output frequency for pair distances to energy file");
2136 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2137 CTYPE ("Orientation restraints: No or Yes");
2138 EETYPE("orire", opts->bOrire, yesno_names);
2139 CTYPE ("Orientation restraints force constant and tau for time averaging");
2140 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2141 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2142 STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
2143 CTYPE ("Output frequency for trace(SD) and S to energy file");
2144 ITYPE ("nstorireout", ir->nstorireout, 100);
2146 /* free energy variables */
2147 CCTYPE ("Free energy variables");
2148 EETYPE("free-energy", ir->efep, efep_names);
2149 STYPE ("couple-moltype", is->couple_moltype, NULL);
2150 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2151 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2152 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2154 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2156 it was not entered */
2157 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2158 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2159 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2160 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
2161 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
2162 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
2163 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
2164 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
2165 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
2166 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
2167 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2168 STYPE ("init-lambda-weights", is->lambda_weights, NULL);
2169 EETYPE("dhdl-print-energy", fep->edHdLPrintEnergy, edHdLPrintEnergy_names);
2170 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2171 ITYPE ("sc-power", fep->sc_power, 1);
2172 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2173 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2174 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2175 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2176 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2177 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2178 separate_dhdl_file_names);
2179 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2180 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2181 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2183 /* Non-equilibrium MD stuff */
2184 CCTYPE("Non-equilibrium MD stuff");
2185 STYPE ("acc-grps", is->accgrps, NULL);
2186 STYPE ("accelerate", is->acc, NULL);
2187 STYPE ("freezegrps", is->freeze, NULL);
2188 STYPE ("freezedim", is->frdim, NULL);
2189 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2190 STYPE ("deform", is->deform, NULL);
2192 /* simulated tempering variables */
2193 CCTYPE("simulated tempering variables");
2194 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2195 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2196 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2197 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2199 /* expanded ensemble variables */
2200 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2202 read_expandedparams(&ninp, &inp, expand, wi);
2205 /* Electric fields */
2206 CCTYPE("Electric fields");
2207 CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
2208 CTYPE ("and a phase angle (real)");
2209 STYPE ("E-x", is->efield_x, NULL);
2210 STYPE ("E-xt", is->efield_xt, NULL);
2211 STYPE ("E-y", is->efield_y, NULL);
2212 STYPE ("E-yt", is->efield_yt, NULL);
2213 STYPE ("E-z", is->efield_z, NULL);
2214 STYPE ("E-zt", is->efield_zt, NULL);
2216 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2217 CTYPE("Swap positions along direction: no, X, Y, Z");
2218 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2219 if (ir->eSwapCoords != eswapNO)
2222 CTYPE("Swap attempt frequency");
2223 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2224 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2225 STYPE("split-group0", splitgrp0, NULL);
2226 STYPE("split-group1", splitgrp1, NULL);
2227 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2228 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2229 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2231 CTYPE("Group name of ions that can be exchanged with solvent molecules");
2232 STYPE("swap-group", swapgrp, NULL);
2233 CTYPE("Group name of solvent molecules");
2234 STYPE("solvent-group", solgrp, NULL);
2236 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2237 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2238 CTYPE("however, if correctly defined, the ion permeation events are counted per channel");
2239 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2240 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2241 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2242 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2243 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2244 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2246 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2247 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2248 CTYPE("Requested number of anions and cations for each of the two compartments");
2249 CTYPE("-1 means fix the numbers as found in time step 0");
2250 ITYPE("anionsA", ir->swap->nanions[0], -1);
2251 ITYPE("cationsA", ir->swap->ncations[0], -1);
2252 ITYPE("anionsB", ir->swap->nanions[1], -1);
2253 ITYPE("cationsB", ir->swap->ncations[1], -1);
2254 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2255 RTYPE("threshold", ir->swap->threshold, 1.0);
2258 /* AdResS defined thingies */
2259 CCTYPE ("AdResS parameters");
2260 EETYPE("adress", ir->bAdress, yesno_names);
2263 snew(ir->adress, 1);
2264 read_adressparams(&ninp, &inp, ir->adress, wi);
2267 /* User defined thingies */
2268 CCTYPE ("User defined thingies");
2269 STYPE ("user1-grps", is->user1, NULL);
2270 STYPE ("user2-grps", is->user2, NULL);
2271 ITYPE ("userint1", ir->userint1, 0);
2272 ITYPE ("userint2", ir->userint2, 0);
2273 ITYPE ("userint3", ir->userint3, 0);
2274 ITYPE ("userint4", ir->userint4, 0);
2275 RTYPE ("userreal1", ir->userreal1, 0);
2276 RTYPE ("userreal2", ir->userreal2, 0);
2277 RTYPE ("userreal3", ir->userreal3, 0);
2278 RTYPE ("userreal4", ir->userreal4, 0);
2281 write_inpfile(mdparout, ninp, inp, FALSE, wi);
2282 for (i = 0; (i < ninp); i++)
2285 sfree(inp[i].value);
2289 /* Process options if necessary */
2290 for (m = 0; m < 2; m++)
2292 for (i = 0; i < 2*DIM; i++)
2301 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2303 warning_error(wi, "Pressure coupling not enough values (I need 1)");
2305 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2307 case epctSEMIISOTROPIC:
2308 case epctSURFACETENSION:
2309 if (sscanf(dumstr[m], "%lf%lf",
2310 &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2312 warning_error(wi, "Pressure coupling not enough values (I need 2)");
2314 dumdub[m][YY] = dumdub[m][XX];
2316 case epctANISOTROPIC:
2317 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2318 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2319 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2321 warning_error(wi, "Pressure coupling not enough values (I need 6)");
2325 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2326 epcoupltype_names[ir->epct]);
2330 clear_mat(ir->ref_p);
2331 clear_mat(ir->compress);
2332 for (i = 0; i < DIM; i++)
2334 ir->ref_p[i][i] = dumdub[1][i];
2335 ir->compress[i][i] = dumdub[0][i];
2337 if (ir->epct == epctANISOTROPIC)
2339 ir->ref_p[XX][YY] = dumdub[1][3];
2340 ir->ref_p[XX][ZZ] = dumdub[1][4];
2341 ir->ref_p[YY][ZZ] = dumdub[1][5];
2342 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2344 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2346 ir->compress[XX][YY] = dumdub[0][3];
2347 ir->compress[XX][ZZ] = dumdub[0][4];
2348 ir->compress[YY][ZZ] = dumdub[0][5];
2349 for (i = 0; i < DIM; i++)
2351 for (m = 0; m < i; m++)
2353 ir->ref_p[i][m] = ir->ref_p[m][i];
2354 ir->compress[i][m] = ir->compress[m][i];
2359 if (ir->comm_mode == ecmNO)
2364 opts->couple_moltype = NULL;
2365 if (strlen(is->couple_moltype) > 0)
2367 if (ir->efep != efepNO)
2369 opts->couple_moltype = strdup(is->couple_moltype);
2370 if (opts->couple_lam0 == opts->couple_lam1)
2372 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2374 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2375 opts->couple_lam1 == ecouplamNONE))
2377 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2382 warning_note(wi, "Free energy is turned off, so we will not decouple the molecule listed in your input.");
2385 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2386 if (ir->efep != efepNO)
2388 if (fep->delta_lambda > 0)
2390 ir->efep = efepSLOWGROWTH;
2394 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2396 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2397 warning_note(wi, "Old option for dhdl-print-energy given: "
2398 "changing \"yes\" to \"total\"\n");
2401 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2403 /* always print out the energy to dhdl if we are doing
2404 expanded ensemble, since we need the total energy for
2405 analysis if the temperature is changing. In some
2406 conditions one may only want the potential energy, so
2407 we will allow that if the appropriate mdp setting has
2408 been enabled. Otherwise, total it is:
2410 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2413 if ((ir->efep != efepNO) || ir->bSimTemp)
2415 ir->bExpanded = FALSE;
2416 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2418 ir->bExpanded = TRUE;
2420 do_fep_params(ir, is->fep_lambda, is->lambda_weights);
2421 if (ir->bSimTemp) /* done after fep params */
2423 do_simtemp_params(ir);
2428 ir->fepvals->n_lambda = 0;
2431 /* WALL PARAMETERS */
2433 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2435 /* ORIENTATION RESTRAINT PARAMETERS */
2437 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
2439 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2442 /* DEFORMATION PARAMETERS */
2444 clear_mat(ir->deform);
2445 for (i = 0; i < 6; i++)
2449 m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
2450 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2451 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2452 for (i = 0; i < 3; i++)
2454 ir->deform[i][i] = dumdub[0][i];
2456 ir->deform[YY][XX] = dumdub[0][3];
2457 ir->deform[ZZ][XX] = dumdub[0][4];
2458 ir->deform[ZZ][YY] = dumdub[0][5];
2459 if (ir->epc != epcNO)
2461 for (i = 0; i < 3; i++)
2463 for (j = 0; j <= i; j++)
2465 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2467 warning_error(wi, "A box element has deform set and compressibility > 0");
2471 for (i = 0; i < 3; i++)
2473 for (j = 0; j < i; j++)
2475 if (ir->deform[i][j] != 0)
2477 for (m = j; m < DIM; m++)
2479 if (ir->compress[m][j] != 0)
2481 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.");
2482 warning(wi, warn_buf);
2490 /* Ion/water position swapping checks */
2491 if (ir->eSwapCoords != eswapNO)
2493 if (ir->swap->nstswap < 1)
2495 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2497 if (ir->swap->nAverage < 1)
2499 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2501 if (ir->swap->threshold < 1.0)
2503 warning_error(wi, "Ion count threshold must be at least 1.\n");
2511 static int search_QMstring(const char *s, int ng, const char *gn[])
2513 /* same as normal search_string, but this one searches QM strings */
2516 for (i = 0; (i < ng); i++)
2518 if (gmx_strcasecmp(s, gn[i]) == 0)
2524 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2528 } /* search_QMstring */
2530 /* We would like gn to be const as well, but C doesn't allow this */
2531 int search_string(const char *s, int ng, char *gn[])
2535 for (i = 0; (i < ng); i++)
2537 if (gmx_strcasecmp(s, gn[i]) == 0)
2544 "Group %s referenced in the .mdp file was not found in the index file.\n"
2545 "Group names must match either [moleculetype] names or custom index group\n"
2546 "names, in which case you must supply an index file to the '-n' option\n"
2553 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2554 t_blocka *block, char *gnames[],
2555 int gtype, int restnm,
2556 int grptp, gmx_bool bVerbose,
2559 unsigned short *cbuf;
2560 t_grps *grps = &(groups->grps[gtype]);
2561 int i, j, gid, aj, ognr, ntot = 0;
2564 char warn_buf[STRLEN];
2568 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2571 title = gtypes[gtype];
2574 /* Mark all id's as not set */
2575 for (i = 0; (i < natoms); i++)
2580 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2581 for (i = 0; (i < ng); i++)
2583 /* Lookup the group name in the block structure */
2584 gid = search_string(ptrs[i], block->nr, gnames);
2585 if ((grptp != egrptpONE) || (i == 0))
2587 grps->nm_ind[grps->nr++] = gid;
2591 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2594 /* Now go over the atoms in the group */
2595 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2600 /* Range checking */
2601 if ((aj < 0) || (aj >= natoms))
2603 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2605 /* Lookup up the old group number */
2609 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2610 aj+1, title, ognr+1, i+1);
2614 /* Store the group number in buffer */
2615 if (grptp == egrptpONE)
2628 /* Now check whether we have done all atoms */
2632 if (grptp == egrptpALL)
2634 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2635 natoms-ntot, title);
2637 else if (grptp == egrptpPART)
2639 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2640 natoms-ntot, title);
2641 warning_note(wi, warn_buf);
2643 /* Assign all atoms currently unassigned to a rest group */
2644 for (j = 0; (j < natoms); j++)
2646 if (cbuf[j] == NOGID)
2652 if (grptp != egrptpPART)
2657 "Making dummy/rest group for %s containing %d elements\n",
2658 title, natoms-ntot);
2660 /* Add group name "rest" */
2661 grps->nm_ind[grps->nr] = restnm;
2663 /* Assign the rest name to all atoms not currently assigned to a group */
2664 for (j = 0; (j < natoms); j++)
2666 if (cbuf[j] == NOGID)
2675 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2677 /* All atoms are part of one (or no) group, no index required */
2678 groups->ngrpnr[gtype] = 0;
2679 groups->grpnr[gtype] = NULL;
2683 groups->ngrpnr[gtype] = natoms;
2684 snew(groups->grpnr[gtype], natoms);
2685 for (j = 0; (j < natoms); j++)
2687 groups->grpnr[gtype][j] = cbuf[j];
2693 return (bRest && grptp == egrptpPART);
2696 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2699 gmx_groups_t *groups;
2701 int natoms, ai, aj, i, j, d, g, imin, jmin;
2703 int *nrdf2, *na_vcm, na_tot;
2704 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2705 gmx_mtop_atomloop_all_t aloop;
2707 int mb, mol, ftype, as;
2708 gmx_molblock_t *molb;
2709 gmx_moltype_t *molt;
2712 * First calc 3xnr-atoms for each group
2713 * then subtract half a degree of freedom for each constraint
2715 * Only atoms and nuclei contribute to the degrees of freedom...
2720 groups = &mtop->groups;
2721 natoms = mtop->natoms;
2723 /* Allocate one more for a possible rest group */
2724 /* We need to sum degrees of freedom into doubles,
2725 * since floats give too low nrdf's above 3 million atoms.
2727 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2728 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2729 snew(na_vcm, groups->grps[egcVCM].nr+1);
2731 for (i = 0; i < groups->grps[egcTC].nr; i++)
2735 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2740 snew(nrdf2, natoms);
2741 aloop = gmx_mtop_atomloop_all_init(mtop);
2742 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2745 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2747 g = ggrpnr(groups, egcFREEZE, i);
2748 /* Double count nrdf for particle i */
2749 for (d = 0; d < DIM; d++)
2751 if (opts->nFreeze[g][d] == 0)
2756 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2757 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2762 for (mb = 0; mb < mtop->nmolblock; mb++)
2764 molb = &mtop->molblock[mb];
2765 molt = &mtop->moltype[molb->type];
2766 atom = molt->atoms.atom;
2767 for (mol = 0; mol < molb->nmol; mol++)
2769 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2771 ia = molt->ilist[ftype].iatoms;
2772 for (i = 0; i < molt->ilist[ftype].nr; )
2774 /* Subtract degrees of freedom for the constraints,
2775 * if the particles still have degrees of freedom left.
2776 * If one of the particles is a vsite or a shell, then all
2777 * constraint motion will go there, but since they do not
2778 * contribute to the constraints the degrees of freedom do not
2783 if (((atom[ia[1]].ptype == eptNucleus) ||
2784 (atom[ia[1]].ptype == eptAtom)) &&
2785 ((atom[ia[2]].ptype == eptNucleus) ||
2786 (atom[ia[2]].ptype == eptAtom)))
2804 imin = min(imin, nrdf2[ai]);
2805 jmin = min(jmin, nrdf2[aj]);
2808 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2809 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2810 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2811 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2813 ia += interaction_function[ftype].nratoms+1;
2814 i += interaction_function[ftype].nratoms+1;
2817 ia = molt->ilist[F_SETTLE].iatoms;
2818 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2820 /* Subtract 1 dof from every atom in the SETTLE */
2821 for (j = 0; j < 3; j++)
2824 imin = min(2, nrdf2[ai]);
2826 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2827 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2832 as += molt->atoms.nr;
2836 if (ir->ePull == epullCONSTRAINT)
2838 /* Correct nrdf for the COM constraints.
2839 * We correct using the TC and VCM group of the first atom
2840 * in the reference and pull group. If atoms in one pull group
2841 * belong to different TC or VCM groups it is anyhow difficult
2842 * to determine the optimal nrdf assignment.
2846 for (i = 0; i < pull->ncoord; i++)
2850 for (j = 0; j < 2; j++)
2852 const t_pull_group *pgrp;
2854 pgrp = &pull->group[pull->coord[i].group[j]];
2858 /* Subtract 1/2 dof from each group */
2860 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2861 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2862 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2864 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)]]);
2869 /* We need to subtract the whole DOF from group j=1 */
2876 if (ir->nstcomm != 0)
2878 /* Subtract 3 from the number of degrees of freedom in each vcm group
2879 * when com translation is removed and 6 when rotation is removed
2882 switch (ir->comm_mode)
2885 n_sub = ndof_com(ir);
2892 gmx_incons("Checking comm_mode");
2895 for (i = 0; i < groups->grps[egcTC].nr; i++)
2897 /* Count the number of atoms of TC group i for every VCM group */
2898 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2903 for (ai = 0; ai < natoms; ai++)
2905 if (ggrpnr(groups, egcTC, ai) == i)
2907 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2911 /* Correct for VCM removal according to the fraction of each VCM
2912 * group present in this TC group.
2914 nrdf_uc = nrdf_tc[i];
2917 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2921 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2923 if (nrdf_vcm[j] > n_sub)
2925 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2926 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2930 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2931 j, nrdf_vcm[j], nrdf_tc[i]);
2936 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2938 opts->nrdf[i] = nrdf_tc[i];
2939 if (opts->nrdf[i] < 0)
2944 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2945 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
2954 static void decode_cos(char *s, t_cosines *cosine)
2957 char format[STRLEN], f1[STRLEN];
2969 sscanf(t, "%d", &(cosine->n));
2976 snew(cosine->a, cosine->n);
2977 snew(cosine->phi, cosine->n);
2979 sprintf(format, "%%*d");
2980 for (i = 0; (i < cosine->n); i++)
2983 strcat(f1, "%lf%lf");
2984 if (sscanf(t, f1, &a, &phi) < 2)
2986 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
2989 cosine->phi[i] = phi;
2990 strcat(format, "%*lf%*lf");
2997 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
2998 const char *option, const char *val, int flag)
3000 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3001 * But since this is much larger than STRLEN, such a line can not be parsed.
3002 * The real maximum is the number of names that fit in a string: STRLEN/2.
3004 #define EGP_MAX (STRLEN/2)
3005 int nelem, i, j, k, nr;
3006 char *names[EGP_MAX];
3010 gnames = groups->grpname;
3012 nelem = str_nelem(val, EGP_MAX, names);
3015 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3017 nr = groups->grps[egcENER].nr;
3019 for (i = 0; i < nelem/2; i++)
3023 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
3029 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3030 names[2*i], option);
3034 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
3040 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3041 names[2*i+1], option);
3043 if ((j < nr) && (k < nr))
3045 ir->opts.egp_flags[nr*j+k] |= flag;
3046 ir->opts.egp_flags[nr*k+j] |= flag;
3055 static void make_swap_groups(
3064 int ig = -1, i = 0, j;
3068 /* Just a quick check here, more thorough checks are in mdrun */
3069 if (strcmp(splitg0name, splitg1name) == 0)
3071 gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
3074 /* First get the swap group index atoms */
3075 ig = search_string(swapgname, grps->nr, gnames);
3076 swap->nat = grps->index[ig+1] - grps->index[ig];
3079 fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
3080 snew(swap->ind, swap->nat);
3081 for (i = 0; i < swap->nat; i++)
3083 swap->ind[i] = grps->a[grps->index[ig]+i];
3088 gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
3091 /* Now do so for the split groups */
3092 for (j = 0; j < 2; j++)
3096 splitg = splitg0name;
3100 splitg = splitg1name;
3103 ig = search_string(splitg, grps->nr, gnames);
3104 swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
3105 if (swap->nat_split[j] > 0)
3107 fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
3108 j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
3109 snew(swap->ind_split[j], swap->nat_split[j]);
3110 for (i = 0; i < swap->nat_split[j]; i++)
3112 swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
3117 gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
3121 /* Now get the solvent group index atoms */
3122 ig = search_string(solgname, grps->nr, gnames);
3123 swap->nat_sol = grps->index[ig+1] - grps->index[ig];
3124 if (swap->nat_sol > 0)
3126 fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
3127 snew(swap->ind_sol, swap->nat_sol);
3128 for (i = 0; i < swap->nat_sol; i++)
3130 swap->ind_sol[i] = grps->a[grps->index[ig]+i];
3135 gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
3140 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3145 ig = search_string(IMDgname, grps->nr, gnames);
3146 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3148 if (IMDgroup->nat > 0)
3150 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3151 IMDgname, IMDgroup->nat);
3152 snew(IMDgroup->ind, IMDgroup->nat);
3153 for (i = 0; i < IMDgroup->nat; i++)
3155 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3161 void do_index(const char* mdparin, const char *ndx,
3164 t_inputrec *ir, rvec *v,
3168 gmx_groups_t *groups;
3172 char warnbuf[STRLEN], **gnames;
3173 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3176 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3177 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3178 int i, j, k, restnm;
3180 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3181 int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
3182 nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
3183 char warn_buf[STRLEN];
3187 fprintf(stderr, "processing index file...\n");
3193 snew(grps->index, 1);
3195 atoms_all = gmx_mtop_global_atoms(mtop);
3196 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3197 free_t_atoms(&atoms_all, FALSE);
3201 grps = init_index(ndx, &gnames);
3204 groups = &mtop->groups;
3205 natoms = mtop->natoms;
3206 symtab = &mtop->symtab;
3208 snew(groups->grpname, grps->nr+1);
3210 for (i = 0; (i < grps->nr); i++)
3212 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3214 groups->grpname[i] = put_symtab(symtab, "rest");
3216 srenew(gnames, grps->nr+1);
3217 gnames[restnm] = *(groups->grpname[i]);
3218 groups->ngrpname = grps->nr+1;
3220 set_warning_line(wi, mdparin, -1);
3222 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3223 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3224 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3225 if ((ntau_t != ntcg) || (nref_t != ntcg))
3227 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3228 "%d tau-t values", ntcg, nref_t, ntau_t);
3231 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3232 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3233 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3234 nr = groups->grps[egcTC].nr;
3236 snew(ir->opts.nrdf, nr);
3237 snew(ir->opts.tau_t, nr);
3238 snew(ir->opts.ref_t, nr);
3239 if (ir->eI == eiBD && ir->bd_fric == 0)
3241 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3248 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3252 for (i = 0; (i < nr); i++)
3254 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
3255 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
3257 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3258 warning_error(wi, warn_buf);
3261 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3263 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.");
3266 if (ir->opts.tau_t[i] >= 0)
3268 tau_min = min(tau_min, ir->opts.tau_t[i]);
3271 if (ir->etc != etcNO && ir->nsttcouple == -1)
3273 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3278 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3280 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");
3282 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
3284 if (ir->nstpcouple != ir->nsttcouple)
3286 int mincouple = min(ir->nstpcouple, ir->nsttcouple);
3287 ir->nstpcouple = ir->nsttcouple = mincouple;
3288 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);
3289 warning_note(wi, warn_buf);
3293 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3294 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3296 if (ETC_ANDERSEN(ir->etc))
3298 if (ir->nsttcouple != 1)
3301 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");
3302 warning_note(wi, warn_buf);
3305 nstcmin = tcouple_min_integration_steps(ir->etc);
3308 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin - 10*GMX_REAL_EPS)
3310 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3311 ETCOUPLTYPE(ir->etc),
3313 ir->nsttcouple*ir->delta_t);
3314 warning(wi, warn_buf);
3317 for (i = 0; (i < nr); i++)
3319 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
3320 if (ir->opts.ref_t[i] < 0)
3322 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3325 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3326 if we are in this conditional) if mc_temp is negative */
3327 if (ir->expandedvals->mc_temp < 0)
3329 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3333 /* Simulated annealing for each group. There are nr groups */
3334 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3335 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3339 if (nSA > 0 && nSA != nr)
3341 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3345 snew(ir->opts.annealing, nr);
3346 snew(ir->opts.anneal_npoints, nr);
3347 snew(ir->opts.anneal_time, nr);
3348 snew(ir->opts.anneal_temp, nr);
3349 for (i = 0; i < nr; i++)
3351 ir->opts.annealing[i] = eannNO;
3352 ir->opts.anneal_npoints[i] = 0;
3353 ir->opts.anneal_time[i] = NULL;
3354 ir->opts.anneal_temp[i] = NULL;
3359 for (i = 0; i < nr; i++)
3361 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3363 ir->opts.annealing[i] = eannNO;
3365 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3367 ir->opts.annealing[i] = eannSINGLE;
3370 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3372 ir->opts.annealing[i] = eannPERIODIC;
3378 /* Read the other fields too */
3379 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3380 if (nSA_points != nSA)
3382 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3384 for (k = 0, i = 0; i < nr; i++)
3386 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3387 if (ir->opts.anneal_npoints[i] == 1)
3389 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3391 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3392 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3393 k += ir->opts.anneal_npoints[i];
3396 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3399 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3401 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3404 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3407 for (i = 0, k = 0; i < nr; i++)
3410 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3412 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3413 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3416 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3418 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3424 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3426 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3427 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3430 if (ir->opts.anneal_temp[i][j] < 0)
3432 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3437 /* Print out some summary information, to make sure we got it right */
3438 for (i = 0, k = 0; i < nr; i++)
3440 if (ir->opts.annealing[i] != eannNO)
3442 j = groups->grps[egcTC].nm_ind[i];
3443 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3444 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3445 ir->opts.anneal_npoints[i]);
3446 fprintf(stderr, "Time (ps) Temperature (K)\n");
3447 /* All terms except the last one */
3448 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3450 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3453 /* Finally the last one */
3454 j = ir->opts.anneal_npoints[i]-1;
3455 if (ir->opts.annealing[i] == eannSINGLE)
3457 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3461 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3462 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3464 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3473 if (ir->ePull != epullNO)
3475 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3477 make_pull_coords(ir->pull);
3482 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3485 if (ir->eSwapCoords != eswapNO)
3487 make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
3490 /* Make indices for IMD session */
3493 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3496 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3497 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3498 if (nacg*DIM != nacc)
3500 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3503 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3504 restnm, egrptpALL_GENREST, bVerbose, wi);
3505 nr = groups->grps[egcACC].nr;
3506 snew(ir->opts.acc, nr);
3507 ir->opts.ngacc = nr;
3509 for (i = k = 0; (i < nacg); i++)
3511 for (j = 0; (j < DIM); j++, k++)
3513 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3516 for (; (i < nr); i++)
3518 for (j = 0; (j < DIM); j++)
3520 ir->opts.acc[i][j] = 0;
3524 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3525 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3526 if (nfrdim != DIM*nfreeze)
3528 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3531 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3532 restnm, egrptpALL_GENREST, bVerbose, wi);
3533 nr = groups->grps[egcFREEZE].nr;
3534 ir->opts.ngfrz = nr;
3535 snew(ir->opts.nFreeze, nr);
3536 for (i = k = 0; (i < nfreeze); i++)
3538 for (j = 0; (j < DIM); j++, k++)
3540 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3541 if (!ir->opts.nFreeze[i][j])
3543 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3545 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3546 "(not %s)", ptr1[k]);
3547 warning(wi, warn_buf);
3552 for (; (i < nr); i++)
3554 for (j = 0; (j < DIM); j++)
3556 ir->opts.nFreeze[i][j] = 0;
3560 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3561 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3562 restnm, egrptpALL_GENREST, bVerbose, wi);
3563 add_wall_energrps(groups, ir->nwall, symtab);
3564 ir->opts.ngener = groups->grps[egcENER].nr;
3565 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3567 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3568 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3571 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3572 "This may lead to artifacts.\n"
3573 "In most cases one should use one group for the whole system.");
3576 /* Now we have filled the freeze struct, so we can calculate NRDF */
3577 calc_nrdf(mtop, ir, gnames);
3583 /* Must check per group! */
3584 for (i = 0; (i < ir->opts.ngtc); i++)
3586 ntot += ir->opts.nrdf[i];
3588 if (ntot != (DIM*natoms))
3590 fac = sqrt(ntot/(DIM*natoms));
3593 fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
3594 "and removal of center of mass motion\n", fac);
3596 for (i = 0; (i < natoms); i++)
3598 svmul(fac, v[i], v[i]);
3603 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3604 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3605 restnm, egrptpALL_GENREST, bVerbose, wi);
3606 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3607 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3608 restnm, egrptpALL_GENREST, bVerbose, wi);
3609 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3610 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3611 restnm, egrptpONE, bVerbose, wi);
3612 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3613 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3614 restnm, egrptpALL_GENREST, bVerbose, wi);
3616 /* QMMM input processing */
3617 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3618 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3619 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3620 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3622 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3623 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3625 /* group rest, if any, is always MM! */
3626 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3627 restnm, egrptpALL_GENREST, bVerbose, wi);
3628 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3629 ir->opts.ngQM = nQMg;
3630 snew(ir->opts.QMmethod, nr);
3631 snew(ir->opts.QMbasis, nr);
3632 for (i = 0; i < nr; i++)
3634 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3635 * converted to the corresponding enum in names.c
3637 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3639 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3643 nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
3644 nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
3645 nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
3646 snew(ir->opts.QMmult, nr);
3647 snew(ir->opts.QMcharge, nr);
3648 snew(ir->opts.bSH, nr);
3650 for (i = 0; i < nr; i++)
3652 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3653 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3654 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3657 nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
3658 nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
3659 snew(ir->opts.CASelectrons, nr);
3660 snew(ir->opts.CASorbitals, nr);
3661 for (i = 0; i < nr; i++)
3663 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3664 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3666 /* special optimization options */
3668 nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
3669 nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
3670 snew(ir->opts.bOPT, nr);
3671 snew(ir->opts.bTS, nr);
3672 for (i = 0; i < nr; i++)
3674 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3675 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3677 nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
3678 nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
3679 nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
3680 snew(ir->opts.SAon, nr);
3681 snew(ir->opts.SAoff, nr);
3682 snew(ir->opts.SAsteps, nr);
3684 for (i = 0; i < nr; i++)
3686 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3687 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3688 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3690 /* end of QMMM input */
3694 for (i = 0; (i < egcNR); i++)
3696 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3697 for (j = 0; (j < groups->grps[i].nr); j++)
3699 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3701 fprintf(stderr, "\n");
3705 nr = groups->grps[egcENER].nr;
3706 snew(ir->opts.egp_flags, nr*nr);
3708 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3709 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3711 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3713 if (bExcl && EEL_FULL(ir->coulombtype))
3715 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3718 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3719 if (bTable && !(ir->vdwtype == evdwUSER) &&
3720 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3721 !(ir->coulombtype == eelPMEUSERSWITCH))
3723 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3726 decode_cos(is->efield_x, &(ir->ex[XX]));
3727 decode_cos(is->efield_xt, &(ir->et[XX]));
3728 decode_cos(is->efield_y, &(ir->ex[YY]));
3729 decode_cos(is->efield_yt, &(ir->et[YY]));
3730 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3731 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3735 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3738 for (i = 0; (i < grps->nr); i++)
3750 static void check_disre(gmx_mtop_t *mtop)
3752 gmx_ffparams_t *ffparams;
3753 t_functype *functype;
3755 int i, ndouble, ftype;
3756 int label, old_label;
3758 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3760 ffparams = &mtop->ffparams;
3761 functype = ffparams->functype;
3762 ip = ffparams->iparams;
3765 for (i = 0; i < ffparams->ntypes; i++)
3767 ftype = functype[i];
3768 if (ftype == F_DISRES)
3770 label = ip[i].disres.label;
3771 if (label == old_label)
3773 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3781 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3782 "probably the parameters for multiple pairs in one restraint "
3783 "are not identical\n", ndouble);
3788 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3789 gmx_bool posres_only,
3793 gmx_mtop_ilistloop_t iloop;
3803 for (d = 0; d < DIM; d++)
3805 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3807 /* Check for freeze groups */
3808 for (g = 0; g < ir->opts.ngfrz; g++)
3810 for (d = 0; d < DIM; d++)
3812 if (ir->opts.nFreeze[g][d] != 0)
3820 /* Check for position restraints */
3821 iloop = gmx_mtop_ilistloop_init(sys);
3822 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3825 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3827 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3829 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3830 for (d = 0; d < DIM; d++)
3832 if (pr->posres.fcA[d] != 0)
3838 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3840 /* Check for flat-bottom posres */
3841 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3842 if (pr->fbposres.k != 0)
3844 switch (pr->fbposres.geom)
3846 case efbposresSPHERE:
3847 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3849 case efbposresCYLINDER:
3850 AbsRef[XX] = AbsRef[YY] = 1;
3852 case efbposresX: /* d=XX */
3853 case efbposresY: /* d=YY */
3854 case efbposresZ: /* d=ZZ */
3855 d = pr->fbposres.geom - efbposresX;
3859 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3860 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3868 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3872 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3873 gmx_bool *bC6ParametersWorkWithGeometricRules,
3874 gmx_bool *bC6ParametersWorkWithLBRules,
3875 gmx_bool *bLBRulesPossible)
3877 int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
3880 double geometricdiff, LBdiff;
3881 double c6i, c6j, c12i, c12j;
3882 double c6, c6_geometric, c6_LB;
3883 double sigmai, sigmaj, epsi, epsj;
3884 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3887 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3888 * force-field floating point parameters.
3891 ptr = getenv("GMX_LJCOMB_TOL");
3896 sscanf(ptr, "%lf", &dbl);
3900 *bC6ParametersWorkWithLBRules = TRUE;
3901 *bC6ParametersWorkWithGeometricRules = TRUE;
3902 bCanDoLBRules = TRUE;
3903 bCanDoGeometricRules = TRUE;
3904 ntypes = mtop->ffparams.atnr;
3905 snew(typecount, ntypes);
3906 gmx_mtop_count_atomtypes(mtop, state, typecount);
3907 geometricdiff = LBdiff = 0.0;
3908 *bLBRulesPossible = TRUE;
3909 for (tpi = 0; tpi < ntypes; ++tpi)
3911 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3912 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3913 for (tpj = tpi; tpj < ntypes; ++tpj)
3915 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3916 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3917 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3918 c6_geometric = sqrt(c6i * c6j);
3919 if (!gmx_numzero(c6_geometric))
3921 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3923 sigmai = pow(c12i / c6i, 1.0/6.0);
3924 sigmaj = pow(c12j / c6j, 1.0/6.0);
3925 epsi = c6i * c6i /(4.0 * c12i);
3926 epsj = c6j * c6j /(4.0 * c12j);
3927 c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
3931 *bLBRulesPossible = FALSE;
3932 c6_LB = c6_geometric;
3934 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3937 if (FALSE == bCanDoLBRules)
3939 *bC6ParametersWorkWithLBRules = FALSE;
3942 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3944 if (FALSE == bCanDoGeometricRules)
3946 *bC6ParametersWorkWithGeometricRules = FALSE;
3954 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3958 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3960 check_combination_rule_differences(mtop, 0,
3961 &bC6ParametersWorkWithGeometricRules,
3962 &bC6ParametersWorkWithLBRules,
3964 if (ir->ljpme_combination_rule == eljpmeLB)
3966 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
3968 warning(wi, "You are using arithmetic-geometric combination rules "
3969 "in LJ-PME, but your non-bonded C6 parameters do not "
3970 "follow these rules.");
3975 if (FALSE == bC6ParametersWorkWithGeometricRules)
3977 if (ir->eDispCorr != edispcNO)
3979 warning_note(wi, "You are using geometric combination rules in "
3980 "LJ-PME, but your non-bonded C6 parameters do "
3981 "not follow these rules. "
3982 "This will introduce very small errors in the forces and energies in "
3983 "your simulations. Dispersion correction will correct total energy "
3984 "and/or pressure for isotropic systems, but not forces or surface tensions.");
3988 warning_note(wi, "You are using geometric combination rules in "
3989 "LJ-PME, but your non-bonded C6 parameters do "
3990 "not follow these rules. "
3991 "This will introduce very small errors in the forces and energies in "
3992 "your simulations. If your system is homogeneous, consider using dispersion correction "
3993 "for the total energy and pressure.");
3999 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
4002 char err_buf[STRLEN];
4003 int i, m, c, nmol, npct;
4004 gmx_bool bCharge, bAcc;
4005 real gdt_max, *mgrp, mt;
4007 gmx_mtop_atomloop_block_t aloopb;
4008 gmx_mtop_atomloop_all_t aloop;
4011 char warn_buf[STRLEN];
4013 set_warning_line(wi, mdparin, -1);
4015 if (ir->cutoff_scheme == ecutsVERLET &&
4016 ir->verletbuf_tol > 0 &&
4018 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
4019 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4021 /* Check if a too small Verlet buffer might potentially
4022 * cause more drift than the thermostat can couple off.
4024 /* Temperature error fraction for warning and suggestion */
4025 const real T_error_warn = 0.002;
4026 const real T_error_suggest = 0.001;
4027 /* For safety: 2 DOF per atom (typical with constraints) */
4028 const real nrdf_at = 2;
4029 real T, tau, max_T_error;
4034 for (i = 0; i < ir->opts.ngtc; i++)
4036 T = max(T, ir->opts.ref_t[i]);
4037 tau = max(tau, ir->opts.tau_t[i]);
4041 /* This is a worst case estimate of the temperature error,
4042 * assuming perfect buffer estimation and no cancelation
4043 * of errors. The factor 0.5 is because energy distributes
4044 * equally over Ekin and Epot.
4046 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4047 if (max_T_error > T_error_warn)
4049 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.",
4050 ir->verletbuf_tol, T, tau,
4052 100*T_error_suggest,
4053 ir->verletbuf_tol*T_error_suggest/max_T_error);
4054 warning(wi, warn_buf);
4059 if (ETC_ANDERSEN(ir->etc))
4063 for (i = 0; i < ir->opts.ngtc; i++)
4065 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4066 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4067 sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
4068 i, ir->opts.tau_t[i]);
4069 CHECK(ir->opts.tau_t[i] < 0);
4072 for (i = 0; i < ir->opts.ngtc; i++)
4074 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
4075 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);
4076 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
4080 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4081 ir->comm_mode == ecmNO &&
4082 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4083 !ETC_ANDERSEN(ir->etc))
4085 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");
4088 /* Check for pressure coupling with absolute position restraints */
4089 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4091 absolute_reference(ir, sys, TRUE, AbsRef);
4093 for (m = 0; m < DIM; m++)
4095 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4097 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4105 aloopb = gmx_mtop_atomloop_block_init(sys);
4106 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4108 if (atom->q != 0 || atom->qB != 0)
4116 if (EEL_FULL(ir->coulombtype))
4119 "You are using full electrostatics treatment %s for a system without charges.\n"
4120 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4121 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4122 warning(wi, err_buf);
4127 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4130 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4131 "You might want to consider using %s electrostatics.\n",
4133 warning_note(wi, err_buf);
4137 /* Check if combination rules used in LJ-PME are the same as in the force field */
4138 if (EVDW_PME(ir->vdwtype))
4140 check_combination_rules(ir, sys, wi);
4143 /* Generalized reaction field */
4144 if (ir->opts.ngtc == 0)
4146 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4148 CHECK(ir->coulombtype == eelGRF);
4152 sprintf(err_buf, "When using coulombtype = %s"
4153 " ref-t for temperature coupling should be > 0",
4155 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4158 if (ir->eI == eiSD2)
4160 sprintf(warn_buf, "The stochastic dynamics integrator %s is deprecated, since\n"
4161 "it is slower than integrator %s and is slightly less accurate\n"
4162 "with constraints. Use the %s integrator.",
4163 ei_names[ir->eI], ei_names[eiSD1], ei_names[eiSD1]);
4164 warning_note(wi, warn_buf);
4168 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4170 for (m = 0; (m < DIM); m++)
4172 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4181 snew(mgrp, sys->groups.grps[egcACC].nr);
4182 aloop = gmx_mtop_atomloop_all_init(sys);
4183 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4185 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4188 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4190 for (m = 0; (m < DIM); m++)
4192 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4196 for (m = 0; (m < DIM); m++)
4198 if (fabs(acc[m]) > 1e-6)
4200 const char *dim[DIM] = { "X", "Y", "Z" };
4202 "Net Acceleration in %s direction, will %s be corrected\n",
4203 dim[m], ir->nstcomm != 0 ? "" : "not");
4204 if (ir->nstcomm != 0 && m < ndof_com(ir))
4207 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4209 ir->opts.acc[i][m] -= acc[m];
4217 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4218 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4220 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4223 if (ir->ePull != epullNO)
4225 gmx_bool bPullAbsoluteRef;
4227 bPullAbsoluteRef = FALSE;
4228 for (i = 0; i < ir->pull->ncoord; i++)
4230 bPullAbsoluteRef = bPullAbsoluteRef ||
4231 ir->pull->coord[i].group[0] == 0 ||
4232 ir->pull->coord[i].group[1] == 0;
4234 if (bPullAbsoluteRef)
4236 absolute_reference(ir, sys, FALSE, AbsRef);
4237 for (m = 0; m < DIM; m++)
4239 if (ir->pull->dim[m] && !AbsRef[m])
4241 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.");
4247 if (ir->pull->eGeom == epullgDIRPBC)
4249 for (i = 0; i < 3; i++)
4251 for (m = 0; m <= i; m++)
4253 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4254 ir->deform[i][m] != 0)
4256 for (c = 0; c < ir->pull->ncoord; c++)
4258 if (ir->pull->coord[c].vec[m] != 0)
4260 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->eGeom), 'x'+m);
4272 void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr, warninp_t wi)
4276 char warn_buf[STRLEN];
4279 ptr = check_box(ir->ePBC, box);
4282 warning_error(wi, ptr);
4285 if (bConstr && ir->eConstrAlg == econtSHAKE)
4287 if (ir->shake_tol <= 0.0)
4289 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4291 warning_error(wi, warn_buf);
4294 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
4296 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
4297 if (ir->epc == epcNO)
4299 warning(wi, warn_buf);
4303 warning_error(wi, warn_buf);
4308 if ( (ir->eConstrAlg == econtLINCS) && bConstr)
4310 /* If we have Lincs constraints: */
4311 if (ir->eI == eiMD && ir->etc == etcNO &&
4312 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4314 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4315 warning_note(wi, warn_buf);
4318 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4320 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4321 warning_note(wi, warn_buf);
4323 if (ir->epc == epcMTTK)
4325 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4329 if (bConstr && ir->epc == epcMTTK)
4331 warning_note(wi, "MTTK with constraints is deprecated, and will be removed in GROMACS 5.1");
4334 if (ir->LincsWarnAngle > 90.0)
4336 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4337 warning(wi, warn_buf);
4338 ir->LincsWarnAngle = 90.0;
4341 if (ir->ePBC != epbcNONE)
4343 if (ir->nstlist == 0)
4345 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4347 bTWIN = (ir->rlistlong > ir->rlist);
4348 if (ir->ns_type == ensGRID)
4350 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
4352 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",
4353 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
4354 warning_error(wi, warn_buf);
4359 min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
4360 if (2*ir->rlistlong >= min_size)
4362 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4363 warning_error(wi, warn_buf);
4366 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4373 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4377 real rvdw1, rvdw2, rcoul1, rcoul2;
4378 char warn_buf[STRLEN];
4380 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4384 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4389 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4395 if (rvdw1 + rvdw2 > ir->rlist ||
4396 rcoul1 + rcoul2 > ir->rlist)
4399 "The sum of the two largest charge group radii (%f) "
4400 "is larger than rlist (%f)\n",
4401 max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4402 warning(wi, warn_buf);
4406 /* Here we do not use the zero at cut-off macro,
4407 * since user defined interactions might purposely
4408 * not be zero at the cut-off.
4410 if (ir_vdw_is_zero_at_cutoff(ir) &&
4411 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
4413 sprintf(warn_buf, "The sum of the two largest charge group "
4414 "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
4415 "With exact cut-offs, better performance can be "
4416 "obtained with cutoff-scheme = %s, because it "
4417 "does not use charge groups at all.",
4419 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4420 ir->rlistlong, ir->rvdw,
4421 ecutscheme_names[ecutsVERLET]);
4424 warning(wi, warn_buf);
4428 warning_note(wi, warn_buf);
4431 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4432 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
4434 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
4435 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4437 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4438 ir->rlistlong, ir->rcoulomb,
4439 ecutscheme_names[ecutsVERLET]);
4442 warning(wi, warn_buf);
4446 warning_note(wi, warn_buf);