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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->nstlist <= 0)
375 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
378 if (ir->nstlist < 10)
380 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.");
383 rc_max = max(ir->rvdw, ir->rcoulomb);
385 if (ir->verletbuf_tol <= 0)
387 if (ir->verletbuf_tol == 0)
389 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
392 if (ir->rlist < rc_max)
394 warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
397 if (ir->rlist == rc_max && ir->nstlist > 1)
399 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.");
404 if (ir->rlist > rc_max)
406 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.");
409 if (ir->nstlist == 1)
411 /* No buffer required */
416 if (EI_DYNAMICS(ir->eI))
418 if (inputrec2nboundeddim(ir) < 3)
420 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.");
422 /* Set rlist temporarily so we can continue processing */
427 /* Set the buffer to 5% of the cut-off */
428 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
433 /* No twin-range calculations with Verlet lists */
434 ir->rlistlong = ir->rlist;
437 if (ir->nstcalclr == -1)
439 /* if rlist=rlistlong, this will later be changed to nstcalclr=0 */
440 ir->nstcalclr = ir->nstlist;
442 else if (ir->nstcalclr > 0)
444 if (ir->nstlist > 0 && (ir->nstlist % ir->nstcalclr != 0))
446 warning_error(wi, "nstlist must be evenly divisible by nstcalclr. Use nstcalclr = -1 to automatically follow nstlist");
449 else if (ir->nstcalclr < -1)
451 warning_error(wi, "nstcalclr must be a positive number (divisor of nstcalclr), or -1 to follow nstlist.");
454 if (EEL_PME(ir->coulombtype) && ir->rcoulomb > ir->rvdw && ir->nstcalclr > 1)
456 warning_error(wi, "When used with PME, the long-range component of twin-range interactions must be updated every step (nstcalclr)");
459 /* GENERAL INTEGRATOR STUFF */
460 if (!(ir->eI == eiMD || EI_VV(ir->eI)))
464 if (ir->eI == eiVVAK)
466 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]);
467 warning_note(wi, warn_buf);
469 if (!EI_DYNAMICS(ir->eI))
473 if (EI_DYNAMICS(ir->eI))
475 if (ir->nstcalcenergy < 0)
477 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
478 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
480 /* nstcalcenergy larger than nstener does not make sense.
481 * We ideally want nstcalcenergy=nstener.
485 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
489 ir->nstcalcenergy = ir->nstenergy;
493 else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
494 (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
495 (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
498 const char *nsten = "nstenergy";
499 const char *nstdh = "nstdhdl";
500 const char *min_name = nsten;
501 int min_nst = ir->nstenergy;
503 /* find the smallest of ( nstenergy, nstdhdl ) */
504 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
505 (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
507 min_nst = ir->fepvals->nstdhdl;
510 /* If the user sets nstenergy small, we should respect that */
512 "Setting nstcalcenergy (%d) equal to %s (%d)",
513 ir->nstcalcenergy, min_name, min_nst);
514 warning_note(wi, warn_buf);
515 ir->nstcalcenergy = min_nst;
518 if (ir->epc != epcNO)
520 if (ir->nstpcouple < 0)
522 ir->nstpcouple = ir_optimal_nstpcouple(ir);
525 if (IR_TWINRANGE(*ir))
527 check_nst("nstlist", ir->nstlist,
528 "nstcalcenergy", &ir->nstcalcenergy, wi);
529 if (ir->epc != epcNO)
531 check_nst("nstlist", ir->nstlist,
532 "nstpcouple", &ir->nstpcouple, wi);
536 if (ir->nstcalcenergy > 0)
538 if (ir->efep != efepNO)
540 /* nstdhdl should be a multiple of nstcalcenergy */
541 check_nst("nstcalcenergy", ir->nstcalcenergy,
542 "nstdhdl", &ir->fepvals->nstdhdl, wi);
543 /* nstexpanded should be a multiple of nstcalcenergy */
544 check_nst("nstcalcenergy", ir->nstcalcenergy,
545 "nstexpanded", &ir->expandedvals->nstexpanded, wi);
547 /* for storing exact averages nstenergy should be
548 * a multiple of nstcalcenergy
550 check_nst("nstcalcenergy", ir->nstcalcenergy,
551 "nstenergy", &ir->nstenergy, wi);
556 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
557 ir->bContinuation && ir->ld_seed != -1)
559 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)");
565 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
566 CHECK(ir->ePBC != epbcXYZ);
567 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
568 CHECK(ir->ns_type != ensGRID);
569 sprintf(err_buf, "with TPI nstlist should be larger than zero");
570 CHECK(ir->nstlist <= 0);
571 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
572 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
576 if ( (opts->nshake > 0) && (opts->bMorse) )
579 "Using morse bond-potentials while constraining bonds is useless");
580 warning(wi, warn_buf);
583 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
584 ir->bContinuation && ir->ld_seed != -1)
586 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)");
588 /* verify simulated tempering options */
592 gmx_bool bAllTempZero = TRUE;
593 for (i = 0; i < fep->n_lambda; i++)
595 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]);
596 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
597 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
599 bAllTempZero = FALSE;
602 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
603 CHECK(bAllTempZero == TRUE);
605 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
606 CHECK(ir->eI != eiVV);
608 /* check compatability of the temperature coupling with simulated tempering */
610 if (ir->etc == etcNOSEHOOVER)
612 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
613 warning_note(wi, warn_buf);
616 /* check that the temperatures make sense */
618 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);
619 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
621 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
622 CHECK(ir->simtempvals->simtemp_high <= 0);
624 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
625 CHECK(ir->simtempvals->simtemp_low <= 0);
628 /* verify free energy options */
630 if (ir->efep != efepNO)
633 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
635 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
637 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
638 (int)fep->sc_r_power);
639 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
641 sprintf(err_buf, "Can't use postive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
642 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
644 sprintf(err_buf, "Can't use postive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
645 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
647 sprintf(err_buf, "Can only use expanded ensemble with md-vv for now; should be supported for other integrators in 5.0");
648 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
650 sprintf(err_buf, "Free-energy not implemented for Ewald");
651 CHECK(ir->coulombtype == eelEWALD);
653 /* check validty of lambda inputs */
654 if (fep->n_lambda == 0)
656 /* Clear output in case of no states:*/
657 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
658 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
662 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
663 CHECK((fep->init_fep_state >= fep->n_lambda));
666 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
667 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
669 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",
670 fep->init_lambda, fep->init_fep_state);
671 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
675 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
679 for (i = 0; i < efptNR; i++)
681 if (fep->separate_dvdl[i])
686 if (n_lambda_terms > 1)
688 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.");
689 warning(wi, warn_buf);
692 if (n_lambda_terms < 2 && fep->n_lambda > 0)
695 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
699 for (j = 0; j < efptNR; j++)
701 for (i = 0; i < fep->n_lambda; i++)
703 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]);
704 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
708 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
710 for (i = 0; i < fep->n_lambda; i++)
712 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],
713 fep->all_lambda[efptCOUL][i]);
714 CHECK((fep->sc_alpha > 0) &&
715 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
716 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
717 ((fep->all_lambda[efptVDW][i] > 0.0) &&
718 (fep->all_lambda[efptVDW][i] < 1.0))));
722 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
724 real sigma, lambda, r_sc;
727 /* Maximum estimate for A and B charges equal with lambda power 1 */
729 r_sc = pow(lambda*fep->sc_alpha*pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
730 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.",
732 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
733 warning_note(wi, warn_buf);
736 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
737 be treated differently, but that's the next step */
739 for (i = 0; i < efptNR; i++)
741 for (j = 0; j < fep->n_lambda; j++)
743 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
744 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
749 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
752 expand = ir->expandedvals;
754 /* checking equilibration of weights inputs for validity */
756 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
757 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
758 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
760 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
761 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
762 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
764 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
765 expand->equil_steps, elmceq_names[elmceqSTEPS]);
766 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
768 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
769 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
770 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
772 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
773 expand->equil_ratio, elmceq_names[elmceqRATIO]);
774 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
776 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
777 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
778 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
780 sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
781 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
782 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
784 sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
785 expand->equil_steps, elmceq_names[elmceqSTEPS]);
786 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
788 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
789 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
790 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
792 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
793 expand->equil_ratio, elmceq_names[elmceqRATIO]);
794 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
796 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
797 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
798 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
800 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
801 CHECK((expand->lmc_repeats <= 0));
802 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
803 CHECK((expand->minvarmin <= 0));
804 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
805 CHECK((expand->c_range < 0));
806 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
807 fep->init_fep_state, expand->lmc_forced_nstart);
808 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
809 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
810 CHECK((expand->lmc_forced_nstart < 0));
811 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
812 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
814 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
815 CHECK((expand->init_wl_delta < 0));
816 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
817 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
818 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
819 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
821 /* if there is no temperature control, we need to specify an MC temperature */
822 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
823 if (expand->nstTij > 0)
825 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
826 expand->nstTij, ir->nstlog);
827 CHECK((mod(expand->nstTij, ir->nstlog) != 0));
832 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
833 CHECK(ir->nwall && ir->ePBC != epbcXY);
836 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
838 if (ir->ePBC == epbcNONE)
840 if (ir->epc != epcNO)
842 warning(wi, "Turning off pressure coupling for vacuum system");
848 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
849 epbc_names[ir->ePBC]);
850 CHECK(ir->epc != epcNO);
852 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
853 CHECK(EEL_FULL(ir->coulombtype));
855 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
856 epbc_names[ir->ePBC]);
857 CHECK(ir->eDispCorr != edispcNO);
860 if (ir->rlist == 0.0)
862 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
863 "with coulombtype = %s or coulombtype = %s\n"
864 "without periodic boundary conditions (pbc = %s) and\n"
865 "rcoulomb and rvdw set to zero",
866 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
867 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
868 (ir->ePBC != epbcNONE) ||
869 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
873 warning_error(wi, "Can not have heuristic neighborlist updates without cut-off");
877 warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
882 if (ir->nstcomm == 0)
884 ir->comm_mode = ecmNO;
886 if (ir->comm_mode != ecmNO)
890 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");
891 ir->nstcomm = abs(ir->nstcomm);
894 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
896 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
897 ir->nstcomm = ir->nstcalcenergy;
900 if (ir->comm_mode == ecmANGULAR)
902 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
903 CHECK(ir->bPeriodicMols);
904 if (ir->ePBC != epbcNONE)
906 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).");
911 if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
913 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.");
916 sprintf(err_buf, "Twin-range neighbour searching (NS) with simple NS"
917 " algorithm not implemented");
918 CHECK(((ir->rcoulomb > ir->rlist) || (ir->rvdw > ir->rlist))
919 && (ir->ns_type == ensSIMPLE));
921 /* TEMPERATURE COUPLING */
922 if (ir->etc == etcYES)
924 ir->etc = etcBERENDSEN;
925 warning_note(wi, "Old option for temperature coupling given: "
926 "changing \"yes\" to \"Berendsen\"\n");
929 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
931 if (ir->opts.nhchainlength < 1)
933 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
934 ir->opts.nhchainlength = 1;
935 warning(wi, warn_buf);
938 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
940 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
941 ir->opts.nhchainlength = 1;
946 ir->opts.nhchainlength = 0;
949 if (ir->eI == eiVVAK)
951 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
953 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
956 if (ETC_ANDERSEN(ir->etc))
958 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
959 CHECK(!(EI_VV(ir->eI)));
961 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
963 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]);
964 warning_note(wi, warn_buf);
967 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]);
968 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
971 if (ir->etc == etcBERENDSEN)
973 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
974 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
975 warning_note(wi, warn_buf);
978 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
979 && ir->epc == epcBERENDSEN)
981 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
982 "true ensemble for the thermostat");
983 warning(wi, warn_buf);
986 /* PRESSURE COUPLING */
987 if (ir->epc == epcISOTROPIC)
989 ir->epc = epcBERENDSEN;
990 warning_note(wi, "Old option for pressure coupling given: "
991 "changing \"Isotropic\" to \"Berendsen\"\n");
994 if (ir->epc != epcNO)
996 dt_pcoupl = ir->nstpcouple*ir->delta_t;
998 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
999 CHECK(ir->tau_p <= 0);
1001 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc))
1003 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
1004 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1005 warning(wi, warn_buf);
1008 sprintf(err_buf, "compressibility must be > 0 when using pressure"
1009 " coupling %s\n", EPCOUPLTYPE(ir->epc));
1010 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
1011 ir->compress[ZZ][ZZ] < 0 ||
1012 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
1013 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
1015 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1018 "You are generating velocities so I am assuming you "
1019 "are equilibrating a system. You are using "
1020 "%s pressure coupling, but this can be "
1021 "unstable for equilibration. If your system crashes, try "
1022 "equilibrating first with Berendsen pressure coupling. If "
1023 "you are not equilibrating the system, you can probably "
1024 "ignore this warning.",
1025 epcoupl_names[ir->epc]);
1026 warning(wi, warn_buf);
1032 if (ir->epc > epcNO)
1034 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1036 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.");
1042 if (ir->epc == epcMTTK)
1044 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1048 /* ELECTROSTATICS */
1049 /* More checks are in triple check (grompp.c) */
1051 if (ir->coulombtype == eelSWITCH)
1053 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1054 "artifacts, advice: use coulombtype = %s",
1055 eel_names[ir->coulombtype],
1056 eel_names[eelRF_ZERO]);
1057 warning(wi, warn_buf);
1060 if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
1062 sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
1063 warning_note(wi, warn_buf);
1066 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1068 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);
1069 warning(wi, warn_buf);
1070 ir->epsilon_rf = ir->epsilon_r;
1071 ir->epsilon_r = 1.0;
1074 if (getenv("GALACTIC_DYNAMICS") == NULL)
1076 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1077 CHECK(ir->epsilon_r < 0);
1080 if (EEL_RF(ir->coulombtype))
1082 /* reaction field (at the cut-off) */
1084 if (ir->coulombtype == eelRF_ZERO)
1086 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1087 eel_names[ir->coulombtype]);
1088 CHECK(ir->epsilon_rf != 0);
1089 ir->epsilon_rf = 0.0;
1092 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1093 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1094 (ir->epsilon_r == 0));
1095 if (ir->epsilon_rf == ir->epsilon_r)
1097 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1098 eel_names[ir->coulombtype]);
1099 warning(wi, warn_buf);
1102 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1103 * means the interaction is zero outside rcoulomb, but it helps to
1104 * provide accurate energy conservation.
1106 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1108 if (ir_coulomb_switched(ir))
1111 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1112 eel_names[ir->coulombtype]);
1113 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1116 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1118 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1120 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1121 eel_names[ir->coulombtype]);
1122 CHECK(ir->rlist > ir->rcoulomb);
1126 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1127 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1130 "The switch/shift interaction settings are just for compatibility; you will get better "
1131 "performance from applying potential modifiers to your interactions!\n");
1132 warning_note(wi, warn_buf);
1135 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1137 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1139 real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
1140 sprintf(warn_buf, "The switching range for 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.",
1141 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1142 warning(wi, warn_buf);
1146 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1148 if (ir->rvdw_switch == 0)
1150 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.");
1151 warning(wi, warn_buf);
1155 if (EEL_FULL(ir->coulombtype))
1157 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1158 ir->coulombtype == eelPMEUSERSWITCH)
1160 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1161 eel_names[ir->coulombtype]);
1162 CHECK(ir->rcoulomb > ir->rlist);
1164 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1166 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1169 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
1170 "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
1171 "a potential modifier.", eel_names[ir->coulombtype]);
1172 if (ir->nstcalclr == 1)
1174 CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
1178 CHECK(ir->rcoulomb != ir->rlist);
1184 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1186 if (ir->pme_order < 3)
1188 warning_error(wi, "pme-order can not be smaller than 3");
1192 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1194 if (ir->ewald_geometry == eewg3D)
1196 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1197 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1198 warning(wi, warn_buf);
1200 /* This check avoids extra pbc coding for exclusion corrections */
1201 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1202 CHECK(ir->wall_ewald_zfac < 2);
1205 if (ir_vdw_switched(ir))
1207 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1208 CHECK(ir->rvdw_switch >= ir->rvdw);
1210 if (ir->rvdw_switch < 0.5*ir->rvdw)
1212 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.",
1213 ir->rvdw_switch, ir->rvdw);
1214 warning_note(wi, warn_buf);
1217 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1219 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1221 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1222 CHECK(ir->rlist > ir->rvdw);
1226 if (ir->vdwtype == evdwPME)
1228 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1230 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s a\
1232 evdw_names[ir->vdwtype],
1233 eintmod_names[eintmodPOTSHIFT],
1234 eintmod_names[eintmodNONE]);
1238 if (ir->cutoff_scheme == ecutsGROUP)
1240 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1241 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)) &&
1244 warning_note(wi, "With exact cut-offs, rlist should be "
1245 "larger than rcoulomb and rvdw, so that there "
1246 "is a buffer region for particle motion "
1247 "between neighborsearch steps");
1250 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlistlong <= ir->rcoulomb)
1252 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
1253 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1254 warning_note(wi, warn_buf);
1256 if (ir_vdw_switched(ir) && (ir->rlistlong <= ir->rvdw))
1258 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
1259 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1260 warning_note(wi, warn_buf);
1264 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1266 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.");
1269 if (ir->nstlist == -1)
1271 sprintf(err_buf, "With nstlist=-1 rvdw and rcoulomb should be smaller than rlist to account for diffusion and possibly charge-group radii");
1272 CHECK(ir->rvdw >= ir->rlist || ir->rcoulomb >= ir->rlist);
1274 sprintf(err_buf, "nstlist can not be smaller than -1");
1275 CHECK(ir->nstlist < -1);
1277 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1280 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1283 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1285 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1288 /* ENERGY CONSERVATION */
1289 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1291 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1293 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1294 evdw_names[evdwSHIFT]);
1295 warning_note(wi, warn_buf);
1297 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1299 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1300 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1301 warning_note(wi, warn_buf);
1305 /* IMPLICIT SOLVENT */
1306 if (ir->coulombtype == eelGB_NOTUSED)
1308 ir->coulombtype = eelCUT;
1309 ir->implicit_solvent = eisGBSA;
1310 fprintf(stderr, "Note: Old option for generalized born electrostatics given:\n"
1311 "Changing coulombtype from \"generalized-born\" to \"cut-off\" and instead\n"
1312 "setting implicit-solvent value to \"GBSA\" in input section.\n");
1315 if (ir->sa_algorithm == esaSTILL)
1317 sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
1318 CHECK(ir->sa_algorithm == esaSTILL);
1321 if (ir->implicit_solvent == eisGBSA)
1323 sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
1324 CHECK(ir->rgbradii != ir->rlist);
1326 if (ir->coulombtype != eelCUT)
1328 sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
1329 CHECK(ir->coulombtype != eelCUT);
1331 if (ir->vdwtype != evdwCUT)
1333 sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
1334 CHECK(ir->vdwtype != evdwCUT);
1336 if (ir->nstgbradii < 1)
1338 sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
1339 warning_note(wi, warn_buf);
1342 if (ir->sa_algorithm == esaNO)
1344 sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
1345 warning_note(wi, warn_buf);
1347 if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
1349 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");
1350 warning_note(wi, warn_buf);
1352 if (ir->gb_algorithm == egbSTILL)
1354 ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
1358 ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
1361 if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
1363 sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
1364 CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
1371 if (ir->cutoff_scheme != ecutsGROUP)
1373 warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
1377 warning_error(wi, "AdresS simulation supports only stochastic dynamics");
1379 if (ir->epc != epcNO)
1381 warning_error(wi, "AdresS simulation does not support pressure coupling");
1383 if (EEL_FULL(ir->coulombtype))
1385 warning_error(wi, "AdresS simulation does not support long-range electrostatics");
1390 /* count the number of text elemets separated by whitespace in a string.
1391 str = the input string
1392 maxptr = the maximum number of allowed elements
1393 ptr = the output array of pointers to the first character of each element
1394 returns: the number of elements. */
1395 int str_nelem(const char *str, int maxptr, char *ptr[])
1400 copy0 = strdup(str);
1403 while (*copy != '\0')
1407 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1415 while ((*copy != '\0') && !isspace(*copy))
1434 /* interpret a number of doubles from a string and put them in an array,
1435 after allocating space for them.
1436 str = the input string
1437 n = the (pre-allocated) number of doubles read
1438 r = the output array of doubles. */
1439 static void parse_n_real(char *str, int *n, real **r)
1444 *n = str_nelem(str, MAXPTR, ptr);
1447 for (i = 0; i < *n; i++)
1449 (*r)[i] = strtod(ptr[i], NULL);
1453 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
1456 int i, j, max_n_lambda, nweights, nfep[efptNR];
1457 t_lambda *fep = ir->fepvals;
1458 t_expanded *expand = ir->expandedvals;
1459 real **count_fep_lambdas;
1460 gmx_bool bOneLambda = TRUE;
1462 snew(count_fep_lambdas, efptNR);
1464 /* FEP input processing */
1465 /* first, identify the number of lambda values for each type.
1466 All that are nonzero must have the same number */
1468 for (i = 0; i < efptNR; i++)
1470 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
1473 /* now, determine the number of components. All must be either zero, or equal. */
1476 for (i = 0; i < efptNR; i++)
1478 if (nfep[i] > max_n_lambda)
1480 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1481 must have the same number if its not zero.*/
1486 for (i = 0; i < efptNR; i++)
1490 ir->fepvals->separate_dvdl[i] = FALSE;
1492 else if (nfep[i] == max_n_lambda)
1494 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1495 respect to the temperature currently */
1497 ir->fepvals->separate_dvdl[i] = TRUE;
1502 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1503 nfep[i], efpt_names[i], max_n_lambda);
1506 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1507 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1509 /* the number of lambdas is the number we've read in, which is either zero
1510 or the same for all */
1511 fep->n_lambda = max_n_lambda;
1513 /* allocate space for the array of lambda values */
1514 snew(fep->all_lambda, efptNR);
1515 /* if init_lambda is defined, we need to set lambda */
1516 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1518 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1520 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1521 for (i = 0; i < efptNR; i++)
1523 snew(fep->all_lambda[i], fep->n_lambda);
1524 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1527 for (j = 0; j < fep->n_lambda; j++)
1529 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1531 sfree(count_fep_lambdas[i]);
1534 sfree(count_fep_lambdas);
1536 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1537 bookkeeping -- for now, init_lambda */
1539 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1541 for (i = 0; i < fep->n_lambda; i++)
1543 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1547 /* check to see if only a single component lambda is defined, and soft core is defined.
1548 In this case, turn on coulomb soft core */
1550 if (max_n_lambda == 0)
1556 for (i = 0; i < efptNR; i++)
1558 if ((nfep[i] != 0) && (i != efptFEP))
1564 if ((bOneLambda) && (fep->sc_alpha > 0))
1566 fep->bScCoul = TRUE;
1569 /* Fill in the others with the efptFEP if they are not explicitly
1570 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1571 they are all zero. */
1573 for (i = 0; i < efptNR; i++)
1575 if ((nfep[i] == 0) && (i != efptFEP))
1577 for (j = 0; j < fep->n_lambda; j++)
1579 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1585 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1586 if (fep->sc_r_power == 48)
1588 if (fep->sc_alpha > 0.1)
1590 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1594 expand = ir->expandedvals;
1595 /* now read in the weights */
1596 parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
1599 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1601 else if (nweights != fep->n_lambda)
1603 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1604 nweights, fep->n_lambda);
1606 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1608 expand->nstexpanded = fep->nstdhdl;
1609 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1611 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1613 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1614 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1615 2*tau_t just to be careful so it's not to frequent */
1620 static void do_simtemp_params(t_inputrec *ir)
1623 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1624 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1629 static void do_wall_params(t_inputrec *ir,
1630 char *wall_atomtype, char *wall_density,
1634 char *names[MAXPTR];
1637 opts->wall_atomtype[0] = NULL;
1638 opts->wall_atomtype[1] = NULL;
1640 ir->wall_atomtype[0] = -1;
1641 ir->wall_atomtype[1] = -1;
1642 ir->wall_density[0] = 0;
1643 ir->wall_density[1] = 0;
1647 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1648 if (nstr != ir->nwall)
1650 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1653 for (i = 0; i < ir->nwall; i++)
1655 opts->wall_atomtype[i] = strdup(names[i]);
1658 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1660 nstr = str_nelem(wall_density, MAXPTR, names);
1661 if (nstr != ir->nwall)
1663 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1665 for (i = 0; i < ir->nwall; i++)
1667 sscanf(names[i], "%lf", &dbl);
1670 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1672 ir->wall_density[i] = dbl;
1678 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1686 srenew(groups->grpname, groups->ngrpname+nwall);
1687 grps = &(groups->grps[egcENER]);
1688 srenew(grps->nm_ind, grps->nr+nwall);
1689 for (i = 0; i < nwall; i++)
1691 sprintf(str, "wall%d", i);
1692 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1693 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1698 void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1699 t_expanded *expand, warninp_t wi)
1701 int ninp, nerror = 0;
1707 /* read expanded ensemble parameters */
1708 CCTYPE ("expanded ensemble variables");
1709 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1710 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1711 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1712 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1713 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1714 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1715 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1716 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1717 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1718 CCTYPE("Seed for Monte Carlo in lambda space");
1719 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1720 RTYPE ("mc-temperature", expand->mc_temp, -1);
1721 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1722 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1723 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1724 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1725 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1726 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1727 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1728 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1729 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1730 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1731 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
1739 void get_ir(const char *mdparin, const char *mdparout,
1740 t_inputrec *ir, t_gromppopts *opts,
1744 double dumdub[2][6];
1748 char warn_buf[STRLEN];
1749 t_lambda *fep = ir->fepvals;
1750 t_expanded *expand = ir->expandedvals;
1752 init_inputrec_strings();
1753 inp = read_inpfile(mdparin, &ninp, wi);
1755 snew(dumstr[0], STRLEN);
1756 snew(dumstr[1], STRLEN);
1758 if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
1761 "%s did not specify a value for the .mdp option "
1762 "\"cutoff-scheme\". Probably it was first intended for use "
1763 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1764 "introduced, but the group scheme was still the default. "
1765 "The default is now the Verlet scheme, so you will observe "
1766 "different behaviour.", mdparin);
1767 warning_note(wi, warn_buf);
1770 /* remove the following deprecated commands */
1773 REM_TYPE("domain-decomposition");
1774 REM_TYPE("andersen-seed");
1776 REM_TYPE("dihre-fc");
1777 REM_TYPE("dihre-tau");
1778 REM_TYPE("nstdihreout");
1779 REM_TYPE("nstcheckpoint");
1781 /* replace the following commands with the clearer new versions*/
1782 REPL_TYPE("unconstrained-start", "continuation");
1783 REPL_TYPE("foreign-lambda", "fep-lambdas");
1784 REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
1785 REPL_TYPE("nstxtcout", "nstxout-compressed");
1786 REPL_TYPE("xtc-grps", "compressed-x-grps");
1787 REPL_TYPE("xtc-precision", "compressed-x-precision");
1789 CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
1790 CTYPE ("Preprocessor information: use cpp syntax.");
1791 CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
1792 STYPE ("include", opts->include, NULL);
1793 CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1794 STYPE ("define", opts->define, NULL);
1796 CCTYPE ("RUN CONTROL PARAMETERS");
1797 EETYPE("integrator", ir->eI, ei_names);
1798 CTYPE ("Start time and timestep in ps");
1799 RTYPE ("tinit", ir->init_t, 0.0);
1800 RTYPE ("dt", ir->delta_t, 0.001);
1801 STEPTYPE ("nsteps", ir->nsteps, 0);
1802 CTYPE ("For exact run continuation or redoing part of a run");
1803 STEPTYPE ("init-step", ir->init_step, 0);
1804 CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
1805 ITYPE ("simulation-part", ir->simulation_part, 1);
1806 CTYPE ("mode for center of mass motion removal");
1807 EETYPE("comm-mode", ir->comm_mode, ecm_names);
1808 CTYPE ("number of steps for center of mass motion removal");
1809 ITYPE ("nstcomm", ir->nstcomm, 100);
1810 CTYPE ("group(s) for center of mass motion removal");
1811 STYPE ("comm-grps", is->vcm, NULL);
1813 CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
1814 CTYPE ("Friction coefficient (amu/ps) and random seed");
1815 RTYPE ("bd-fric", ir->bd_fric, 0.0);
1816 STEPTYPE ("ld-seed", ir->ld_seed, -1);
1819 CCTYPE ("ENERGY MINIMIZATION OPTIONS");
1820 CTYPE ("Force tolerance and initial step-size");
1821 RTYPE ("emtol", ir->em_tol, 10.0);
1822 RTYPE ("emstep", ir->em_stepsize, 0.01);
1823 CTYPE ("Max number of iterations in relax-shells");
1824 ITYPE ("niter", ir->niter, 20);
1825 CTYPE ("Step size (ps^2) for minimization of flexible constraints");
1826 RTYPE ("fcstep", ir->fc_stepsize, 0);
1827 CTYPE ("Frequency of steepest descents steps when doing CG");
1828 ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
1829 ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
1831 CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
1832 RTYPE ("rtpi", ir->rtpi, 0.05);
1834 /* Output options */
1835 CCTYPE ("OUTPUT CONTROL OPTIONS");
1836 CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
1837 ITYPE ("nstxout", ir->nstxout, 0);
1838 ITYPE ("nstvout", ir->nstvout, 0);
1839 ITYPE ("nstfout", ir->nstfout, 0);
1840 ir->nstcheckpoint = 1000;
1841 CTYPE ("Output frequency for energies to log file and energy file");
1842 ITYPE ("nstlog", ir->nstlog, 1000);
1843 ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
1844 ITYPE ("nstenergy", ir->nstenergy, 1000);
1845 CTYPE ("Output frequency and precision for .xtc file");
1846 ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
1847 RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
1848 CTYPE ("This selects the subset of atoms for the compressed");
1849 CTYPE ("trajectory file. You can select multiple groups. By");
1850 CTYPE ("default, all atoms will be written.");
1851 STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
1852 CTYPE ("Selection of energy groups");
1853 STYPE ("energygrps", is->energy, NULL);
1855 /* Neighbor searching */
1856 CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
1857 CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1858 EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
1859 CTYPE ("nblist update frequency");
1860 ITYPE ("nstlist", ir->nstlist, 10);
1861 CTYPE ("ns algorithm (simple or grid)");
1862 EETYPE("ns-type", ir->ns_type, ens_names);
1863 /* set ndelta to the optimal value of 2 */
1865 CTYPE ("Periodic boundary conditions: xyz, no, xy");
1866 EETYPE("pbc", ir->ePBC, epbc_names);
1867 EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
1868 CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1869 CTYPE ("a value of -1 means: use rlist");
1870 RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
1871 CTYPE ("nblist cut-off");
1872 RTYPE ("rlist", ir->rlist, 1.0);
1873 CTYPE ("long-range cut-off for switched potentials");
1874 RTYPE ("rlistlong", ir->rlistlong, -1);
1875 ITYPE ("nstcalclr", ir->nstcalclr, -1);
1877 /* Electrostatics */
1878 CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
1879 CTYPE ("Method for doing electrostatics");
1880 EETYPE("coulombtype", ir->coulombtype, eel_names);
1881 EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
1882 CTYPE ("cut-off lengths");
1883 RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
1884 RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
1885 CTYPE ("Relative dielectric constant for the medium and the reaction field");
1886 RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
1887 RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
1888 CTYPE ("Method for doing Van der Waals");
1889 EETYPE("vdw-type", ir->vdwtype, evdw_names);
1890 EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
1891 CTYPE ("cut-off lengths");
1892 RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
1893 RTYPE ("rvdw", ir->rvdw, 1.0);
1894 CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
1895 EETYPE("DispCorr", ir->eDispCorr, edispc_names);
1896 CTYPE ("Extension of the potential lookup tables beyond the cut-off");
1897 RTYPE ("table-extension", ir->tabext, 1.0);
1898 CTYPE ("Separate tables between energy group pairs");
1899 STYPE ("energygrp-table", is->egptable, NULL);
1900 CTYPE ("Spacing for the PME/PPPM FFT grid");
1901 RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
1902 CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
1903 ITYPE ("fourier-nx", ir->nkx, 0);
1904 ITYPE ("fourier-ny", ir->nky, 0);
1905 ITYPE ("fourier-nz", ir->nkz, 0);
1906 CTYPE ("EWALD/PME/PPPM parameters");
1907 ITYPE ("pme-order", ir->pme_order, 4);
1908 RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
1909 RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
1910 EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
1911 EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
1912 RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
1913 EETYPE("optimize-fft", ir->bOptFFT, yesno_names);
1915 CCTYPE("IMPLICIT SOLVENT ALGORITHM");
1916 EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
1918 CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
1919 CTYPE ("Algorithm for calculating Born radii");
1920 EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
1921 CTYPE ("Frequency of calculating the Born radii inside rlist");
1922 ITYPE ("nstgbradii", ir->nstgbradii, 1);
1923 CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
1924 CTYPE ("between rlist and rgbradii is updated every nstlist steps");
1925 RTYPE ("rgbradii", ir->rgbradii, 1.0);
1926 CTYPE ("Dielectric coefficient of the implicit solvent");
1927 RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
1928 CTYPE ("Salt concentration in M for Generalized Born models");
1929 RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
1930 CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
1931 RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
1932 RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
1933 RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
1934 RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
1935 EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
1936 CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
1937 CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
1938 RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
1940 /* Coupling stuff */
1941 CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
1942 CTYPE ("Temperature coupling");
1943 EETYPE("tcoupl", ir->etc, etcoupl_names);
1944 ITYPE ("nsttcouple", ir->nsttcouple, -1);
1945 ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
1946 EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
1947 CTYPE ("Groups to couple separately");
1948 STYPE ("tc-grps", is->tcgrps, NULL);
1949 CTYPE ("Time constant (ps) and reference temperature (K)");
1950 STYPE ("tau-t", is->tau_t, NULL);
1951 STYPE ("ref-t", is->ref_t, NULL);
1952 CTYPE ("pressure coupling");
1953 EETYPE("pcoupl", ir->epc, epcoupl_names);
1954 EETYPE("pcoupltype", ir->epct, epcoupltype_names);
1955 ITYPE ("nstpcouple", ir->nstpcouple, -1);
1956 CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
1957 RTYPE ("tau-p", ir->tau_p, 1.0);
1958 STYPE ("compressibility", dumstr[0], NULL);
1959 STYPE ("ref-p", dumstr[1], NULL);
1960 CTYPE ("Scaling of reference coordinates, No, All or COM");
1961 EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
1964 CCTYPE ("OPTIONS FOR QMMM calculations");
1965 EETYPE("QMMM", ir->bQMMM, yesno_names);
1966 CTYPE ("Groups treated Quantum Mechanically");
1967 STYPE ("QMMM-grps", is->QMMM, NULL);
1968 CTYPE ("QM method");
1969 STYPE("QMmethod", is->QMmethod, NULL);
1970 CTYPE ("QMMM scheme");
1971 EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
1972 CTYPE ("QM basisset");
1973 STYPE("QMbasis", is->QMbasis, NULL);
1974 CTYPE ("QM charge");
1975 STYPE ("QMcharge", is->QMcharge, NULL);
1976 CTYPE ("QM multiplicity");
1977 STYPE ("QMmult", is->QMmult, NULL);
1978 CTYPE ("Surface Hopping");
1979 STYPE ("SH", is->bSH, NULL);
1980 CTYPE ("CAS space options");
1981 STYPE ("CASorbitals", is->CASorbitals, NULL);
1982 STYPE ("CASelectrons", is->CASelectrons, NULL);
1983 STYPE ("SAon", is->SAon, NULL);
1984 STYPE ("SAoff", is->SAoff, NULL);
1985 STYPE ("SAsteps", is->SAsteps, NULL);
1986 CTYPE ("Scale factor for MM charges");
1987 RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
1988 CTYPE ("Optimization of QM subsystem");
1989 STYPE ("bOPT", is->bOPT, NULL);
1990 STYPE ("bTS", is->bTS, NULL);
1992 /* Simulated annealing */
1993 CCTYPE("SIMULATED ANNEALING");
1994 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
1995 STYPE ("annealing", is->anneal, NULL);
1996 CTYPE ("Number of time points to use for specifying annealing in each group");
1997 STYPE ("annealing-npoints", is->anneal_npoints, NULL);
1998 CTYPE ("List of times at the annealing points for each group");
1999 STYPE ("annealing-time", is->anneal_time, NULL);
2000 CTYPE ("Temp. at each annealing point, for each group.");
2001 STYPE ("annealing-temp", is->anneal_temp, NULL);
2004 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
2005 EETYPE("gen-vel", opts->bGenVel, yesno_names);
2006 RTYPE ("gen-temp", opts->tempi, 300.0);
2007 ITYPE ("gen-seed", opts->seed, -1);
2010 CCTYPE ("OPTIONS FOR BONDS");
2011 EETYPE("constraints", opts->nshake, constraints);
2012 CTYPE ("Type of constraint algorithm");
2013 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
2014 CTYPE ("Do not constrain the start configuration");
2015 EETYPE("continuation", ir->bContinuation, yesno_names);
2016 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
2017 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
2018 CTYPE ("Relative tolerance of shake");
2019 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
2020 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
2021 ITYPE ("lincs-order", ir->nProjOrder, 4);
2022 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
2023 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
2024 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
2025 ITYPE ("lincs-iter", ir->nLincsIter, 1);
2026 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
2027 CTYPE ("rotates over more degrees than");
2028 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
2029 CTYPE ("Convert harmonic bonds to morse potentials");
2030 EETYPE("morse", opts->bMorse, yesno_names);
2032 /* Energy group exclusions */
2033 CCTYPE ("ENERGY GROUP EXCLUSIONS");
2034 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
2035 STYPE ("energygrp-excl", is->egpexcl, NULL);
2039 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2040 ITYPE ("nwall", ir->nwall, 0);
2041 EETYPE("wall-type", ir->wall_type, ewt_names);
2042 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
2043 STYPE ("wall-atomtype", is->wall_atomtype, NULL);
2044 STYPE ("wall-density", is->wall_density, NULL);
2045 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
2048 CCTYPE("COM PULLING");
2049 CTYPE("Pull type: no, umbrella, constraint or constant-force");
2050 EETYPE("pull", ir->ePull, epull_names);
2051 if (ir->ePull != epullNO)
2054 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
2057 /* Enforced rotation */
2058 CCTYPE("ENFORCED ROTATION");
2059 CTYPE("Enforced rotation: No or Yes");
2060 EETYPE("rotation", ir->bRot, yesno_names);
2064 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2067 /* Interactive MD */
2069 CCTYPE("Group to display and/or manipulate in interactive MD session");
2070 STYPE ("IMD-group", is->imd_grp, NULL);
2071 if (is->imd_grp[0] != '\0')
2078 CCTYPE("NMR refinement stuff");
2079 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2080 EETYPE("disre", ir->eDisre, edisre_names);
2081 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2082 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2083 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2084 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2085 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2086 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2087 CTYPE ("Output frequency for pair distances to energy file");
2088 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2089 CTYPE ("Orientation restraints: No or Yes");
2090 EETYPE("orire", opts->bOrire, yesno_names);
2091 CTYPE ("Orientation restraints force constant and tau for time averaging");
2092 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2093 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2094 STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
2095 CTYPE ("Output frequency for trace(SD) and S to energy file");
2096 ITYPE ("nstorireout", ir->nstorireout, 100);
2098 /* free energy variables */
2099 CCTYPE ("Free energy variables");
2100 EETYPE("free-energy", ir->efep, efep_names);
2101 STYPE ("couple-moltype", is->couple_moltype, NULL);
2102 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2103 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2104 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2106 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2108 it was not entered */
2109 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2110 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2111 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2112 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
2113 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
2114 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
2115 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
2116 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
2117 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
2118 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
2119 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2120 STYPE ("init-lambda-weights", is->lambda_weights, NULL);
2121 EETYPE("dhdl-print-energy", fep->bPrintEnergy, yesno_names);
2122 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2123 ITYPE ("sc-power", fep->sc_power, 1);
2124 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2125 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2126 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2127 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2128 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2129 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2130 separate_dhdl_file_names);
2131 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2132 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2133 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2135 /* Non-equilibrium MD stuff */
2136 CCTYPE("Non-equilibrium MD stuff");
2137 STYPE ("acc-grps", is->accgrps, NULL);
2138 STYPE ("accelerate", is->acc, NULL);
2139 STYPE ("freezegrps", is->freeze, NULL);
2140 STYPE ("freezedim", is->frdim, NULL);
2141 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2142 STYPE ("deform", is->deform, NULL);
2144 /* simulated tempering variables */
2145 CCTYPE("simulated tempering variables");
2146 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2147 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2148 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2149 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2151 /* expanded ensemble variables */
2152 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2154 read_expandedparams(&ninp, &inp, expand, wi);
2157 /* Electric fields */
2158 CCTYPE("Electric fields");
2159 CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
2160 CTYPE ("and a phase angle (real)");
2161 STYPE ("E-x", is->efield_x, NULL);
2162 STYPE ("E-xt", is->efield_xt, NULL);
2163 STYPE ("E-y", is->efield_y, NULL);
2164 STYPE ("E-yt", is->efield_yt, NULL);
2165 STYPE ("E-z", is->efield_z, NULL);
2166 STYPE ("E-zt", is->efield_zt, NULL);
2168 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2169 CTYPE("Swap positions along direction: no, X, Y, Z");
2170 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2171 if (ir->eSwapCoords != eswapNO)
2174 CTYPE("Swap attempt frequency");
2175 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2176 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2177 STYPE("split-group0", splitgrp0, NULL);
2178 STYPE("split-group1", splitgrp1, NULL);
2179 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2180 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2181 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2183 CTYPE("Group name of ions that can be exchanged with solvent molecules");
2184 STYPE("swap-group", swapgrp, NULL);
2185 CTYPE("Group name of solvent molecules");
2186 STYPE("solvent-group", solgrp, NULL);
2188 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2189 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2190 CTYPE("however, if correctly defined, the ion permeation events are counted per channel");
2191 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2192 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2193 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2194 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2195 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2196 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2198 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2199 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2200 CTYPE("Requested number of anions and cations for each of the two compartments");
2201 CTYPE("-1 means fix the numbers as found in time step 0");
2202 ITYPE("anionsA", ir->swap->nanions[0], -1);
2203 ITYPE("cationsA", ir->swap->ncations[0], -1);
2204 ITYPE("anionsB", ir->swap->nanions[1], -1);
2205 ITYPE("cationsB", ir->swap->ncations[1], -1);
2206 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2207 RTYPE("threshold", ir->swap->threshold, 1.0);
2210 /* AdResS defined thingies */
2211 CCTYPE ("AdResS parameters");
2212 EETYPE("adress", ir->bAdress, yesno_names);
2215 snew(ir->adress, 1);
2216 read_adressparams(&ninp, &inp, ir->adress, wi);
2219 /* User defined thingies */
2220 CCTYPE ("User defined thingies");
2221 STYPE ("user1-grps", is->user1, NULL);
2222 STYPE ("user2-grps", is->user2, NULL);
2223 ITYPE ("userint1", ir->userint1, 0);
2224 ITYPE ("userint2", ir->userint2, 0);
2225 ITYPE ("userint3", ir->userint3, 0);
2226 ITYPE ("userint4", ir->userint4, 0);
2227 RTYPE ("userreal1", ir->userreal1, 0);
2228 RTYPE ("userreal2", ir->userreal2, 0);
2229 RTYPE ("userreal3", ir->userreal3, 0);
2230 RTYPE ("userreal4", ir->userreal4, 0);
2233 write_inpfile(mdparout, ninp, inp, FALSE, wi);
2234 for (i = 0; (i < ninp); i++)
2237 sfree(inp[i].value);
2241 /* Process options if necessary */
2242 for (m = 0; m < 2; m++)
2244 for (i = 0; i < 2*DIM; i++)
2253 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2255 warning_error(wi, "Pressure coupling not enough values (I need 1)");
2257 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2259 case epctSEMIISOTROPIC:
2260 case epctSURFACETENSION:
2261 if (sscanf(dumstr[m], "%lf%lf",
2262 &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2264 warning_error(wi, "Pressure coupling not enough values (I need 2)");
2266 dumdub[m][YY] = dumdub[m][XX];
2268 case epctANISOTROPIC:
2269 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2270 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2271 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2273 warning_error(wi, "Pressure coupling not enough values (I need 6)");
2277 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2278 epcoupltype_names[ir->epct]);
2282 clear_mat(ir->ref_p);
2283 clear_mat(ir->compress);
2284 for (i = 0; i < DIM; i++)
2286 ir->ref_p[i][i] = dumdub[1][i];
2287 ir->compress[i][i] = dumdub[0][i];
2289 if (ir->epct == epctANISOTROPIC)
2291 ir->ref_p[XX][YY] = dumdub[1][3];
2292 ir->ref_p[XX][ZZ] = dumdub[1][4];
2293 ir->ref_p[YY][ZZ] = dumdub[1][5];
2294 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2296 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2298 ir->compress[XX][YY] = dumdub[0][3];
2299 ir->compress[XX][ZZ] = dumdub[0][4];
2300 ir->compress[YY][ZZ] = dumdub[0][5];
2301 for (i = 0; i < DIM; i++)
2303 for (m = 0; m < i; m++)
2305 ir->ref_p[i][m] = ir->ref_p[m][i];
2306 ir->compress[i][m] = ir->compress[m][i];
2311 if (ir->comm_mode == ecmNO)
2316 opts->couple_moltype = NULL;
2317 if (strlen(is->couple_moltype) > 0)
2319 if (ir->efep != efepNO)
2321 opts->couple_moltype = strdup(is->couple_moltype);
2322 if (opts->couple_lam0 == opts->couple_lam1)
2324 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2326 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2327 opts->couple_lam1 == ecouplamNONE))
2329 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2334 warning(wi, "Can not couple a molecule with free_energy = no");
2337 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2338 if (ir->efep != efepNO)
2340 if (fep->delta_lambda > 0)
2342 ir->efep = efepSLOWGROWTH;
2348 fep->bPrintEnergy = TRUE;
2349 /* always print out the energy to dhdl if we are doing expanded ensemble, since we need the total energy
2350 if the temperature is changing. */
2353 if ((ir->efep != efepNO) || ir->bSimTemp)
2355 ir->bExpanded = FALSE;
2356 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2358 ir->bExpanded = TRUE;
2360 do_fep_params(ir, is->fep_lambda, is->lambda_weights);
2361 if (ir->bSimTemp) /* done after fep params */
2363 do_simtemp_params(ir);
2368 ir->fepvals->n_lambda = 0;
2371 /* WALL PARAMETERS */
2373 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2375 /* ORIENTATION RESTRAINT PARAMETERS */
2377 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
2379 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2382 /* DEFORMATION PARAMETERS */
2384 clear_mat(ir->deform);
2385 for (i = 0; i < 6; i++)
2389 m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
2390 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2391 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2392 for (i = 0; i < 3; i++)
2394 ir->deform[i][i] = dumdub[0][i];
2396 ir->deform[YY][XX] = dumdub[0][3];
2397 ir->deform[ZZ][XX] = dumdub[0][4];
2398 ir->deform[ZZ][YY] = dumdub[0][5];
2399 if (ir->epc != epcNO)
2401 for (i = 0; i < 3; i++)
2403 for (j = 0; j <= i; j++)
2405 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2407 warning_error(wi, "A box element has deform set and compressibility > 0");
2411 for (i = 0; i < 3; i++)
2413 for (j = 0; j < i; j++)
2415 if (ir->deform[i][j] != 0)
2417 for (m = j; m < DIM; m++)
2419 if (ir->compress[m][j] != 0)
2421 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.");
2422 warning(wi, warn_buf);
2430 /* Ion/water position swapping checks */
2431 if (ir->eSwapCoords != eswapNO)
2433 if (ir->swap->nstswap < 1)
2435 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2437 if (ir->swap->nAverage < 1)
2439 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2441 if (ir->swap->threshold < 1.0)
2443 warning_error(wi, "Ion count threshold must be at least 1.\n");
2451 static int search_QMstring(const char *s, int ng, const char *gn[])
2453 /* same as normal search_string, but this one searches QM strings */
2456 for (i = 0; (i < ng); i++)
2458 if (gmx_strcasecmp(s, gn[i]) == 0)
2464 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2468 } /* search_QMstring */
2470 /* We would like gn to be const as well, but C doesn't allow this */
2471 int search_string(const char *s, int ng, char *gn[])
2475 for (i = 0; (i < ng); i++)
2477 if (gmx_strcasecmp(s, gn[i]) == 0)
2484 "Group %s referenced in the .mdp file was not found in the index file.\n"
2485 "Group names must match either [moleculetype] names or custom index group\n"
2486 "names, in which case you must supply an index file to the '-n' option\n"
2493 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2494 t_blocka *block, char *gnames[],
2495 int gtype, int restnm,
2496 int grptp, gmx_bool bVerbose,
2499 unsigned short *cbuf;
2500 t_grps *grps = &(groups->grps[gtype]);
2501 int i, j, gid, aj, ognr, ntot = 0;
2504 char warn_buf[STRLEN];
2508 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2511 title = gtypes[gtype];
2514 /* Mark all id's as not set */
2515 for (i = 0; (i < natoms); i++)
2520 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2521 for (i = 0; (i < ng); i++)
2523 /* Lookup the group name in the block structure */
2524 gid = search_string(ptrs[i], block->nr, gnames);
2525 if ((grptp != egrptpONE) || (i == 0))
2527 grps->nm_ind[grps->nr++] = gid;
2531 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2534 /* Now go over the atoms in the group */
2535 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2540 /* Range checking */
2541 if ((aj < 0) || (aj >= natoms))
2543 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2545 /* Lookup up the old group number */
2549 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2550 aj+1, title, ognr+1, i+1);
2554 /* Store the group number in buffer */
2555 if (grptp == egrptpONE)
2568 /* Now check whether we have done all atoms */
2572 if (grptp == egrptpALL)
2574 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2575 natoms-ntot, title);
2577 else if (grptp == egrptpPART)
2579 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2580 natoms-ntot, title);
2581 warning_note(wi, warn_buf);
2583 /* Assign all atoms currently unassigned to a rest group */
2584 for (j = 0; (j < natoms); j++)
2586 if (cbuf[j] == NOGID)
2592 if (grptp != egrptpPART)
2597 "Making dummy/rest group for %s containing %d elements\n",
2598 title, natoms-ntot);
2600 /* Add group name "rest" */
2601 grps->nm_ind[grps->nr] = restnm;
2603 /* Assign the rest name to all atoms not currently assigned to a group */
2604 for (j = 0; (j < natoms); j++)
2606 if (cbuf[j] == NOGID)
2615 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2617 /* All atoms are part of one (or no) group, no index required */
2618 groups->ngrpnr[gtype] = 0;
2619 groups->grpnr[gtype] = NULL;
2623 groups->ngrpnr[gtype] = natoms;
2624 snew(groups->grpnr[gtype], natoms);
2625 for (j = 0; (j < natoms); j++)
2627 groups->grpnr[gtype][j] = cbuf[j];
2633 return (bRest && grptp == egrptpPART);
2636 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2639 gmx_groups_t *groups;
2641 int natoms, ai, aj, i, j, d, g, imin, jmin;
2643 int *nrdf2, *na_vcm, na_tot;
2644 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2645 gmx_mtop_atomloop_all_t aloop;
2647 int mb, mol, ftype, as;
2648 gmx_molblock_t *molb;
2649 gmx_moltype_t *molt;
2652 * First calc 3xnr-atoms for each group
2653 * then subtract half a degree of freedom for each constraint
2655 * Only atoms and nuclei contribute to the degrees of freedom...
2660 groups = &mtop->groups;
2661 natoms = mtop->natoms;
2663 /* Allocate one more for a possible rest group */
2664 /* We need to sum degrees of freedom into doubles,
2665 * since floats give too low nrdf's above 3 million atoms.
2667 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2668 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2669 snew(na_vcm, groups->grps[egcVCM].nr+1);
2671 for (i = 0; i < groups->grps[egcTC].nr; i++)
2675 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2680 snew(nrdf2, natoms);
2681 aloop = gmx_mtop_atomloop_all_init(mtop);
2682 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2685 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2687 g = ggrpnr(groups, egcFREEZE, i);
2688 /* Double count nrdf for particle i */
2689 for (d = 0; d < DIM; d++)
2691 if (opts->nFreeze[g][d] == 0)
2696 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2697 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2702 for (mb = 0; mb < mtop->nmolblock; mb++)
2704 molb = &mtop->molblock[mb];
2705 molt = &mtop->moltype[molb->type];
2706 atom = molt->atoms.atom;
2707 for (mol = 0; mol < molb->nmol; mol++)
2709 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2711 ia = molt->ilist[ftype].iatoms;
2712 for (i = 0; i < molt->ilist[ftype].nr; )
2714 /* Subtract degrees of freedom for the constraints,
2715 * if the particles still have degrees of freedom left.
2716 * If one of the particles is a vsite or a shell, then all
2717 * constraint motion will go there, but since they do not
2718 * contribute to the constraints the degrees of freedom do not
2723 if (((atom[ia[1]].ptype == eptNucleus) ||
2724 (atom[ia[1]].ptype == eptAtom)) &&
2725 ((atom[ia[2]].ptype == eptNucleus) ||
2726 (atom[ia[2]].ptype == eptAtom)))
2744 imin = min(imin, nrdf2[ai]);
2745 jmin = min(jmin, nrdf2[aj]);
2748 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2749 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2750 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2751 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2753 ia += interaction_function[ftype].nratoms+1;
2754 i += interaction_function[ftype].nratoms+1;
2757 ia = molt->ilist[F_SETTLE].iatoms;
2758 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2760 /* Subtract 1 dof from every atom in the SETTLE */
2761 for (j = 0; j < 3; j++)
2764 imin = min(2, nrdf2[ai]);
2766 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2767 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2772 as += molt->atoms.nr;
2776 if (ir->ePull == epullCONSTRAINT)
2778 /* Correct nrdf for the COM constraints.
2779 * We correct using the TC and VCM group of the first atom
2780 * in the reference and pull group. If atoms in one pull group
2781 * belong to different TC or VCM groups it is anyhow difficult
2782 * to determine the optimal nrdf assignment.
2786 for (i = 0; i < pull->ncoord; i++)
2790 for (j = 0; j < 2; j++)
2792 const t_pull_group *pgrp;
2794 pgrp = &pull->group[pull->coord[i].group[j]];
2798 /* Subtract 1/2 dof from each group */
2800 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2801 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2802 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2804 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)]]);
2809 /* We need to subtract the whole DOF from group j=1 */
2816 if (ir->nstcomm != 0)
2818 /* Subtract 3 from the number of degrees of freedom in each vcm group
2819 * when com translation is removed and 6 when rotation is removed
2822 switch (ir->comm_mode)
2825 n_sub = ndof_com(ir);
2832 gmx_incons("Checking comm_mode");
2835 for (i = 0; i < groups->grps[egcTC].nr; i++)
2837 /* Count the number of atoms of TC group i for every VCM group */
2838 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2843 for (ai = 0; ai < natoms; ai++)
2845 if (ggrpnr(groups, egcTC, ai) == i)
2847 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2851 /* Correct for VCM removal according to the fraction of each VCM
2852 * group present in this TC group.
2854 nrdf_uc = nrdf_tc[i];
2857 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2861 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2863 if (nrdf_vcm[j] > n_sub)
2865 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2866 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2870 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2871 j, nrdf_vcm[j], nrdf_tc[i]);
2876 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2878 opts->nrdf[i] = nrdf_tc[i];
2879 if (opts->nrdf[i] < 0)
2884 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2885 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
2894 static void decode_cos(char *s, t_cosines *cosine)
2897 char format[STRLEN], f1[STRLEN];
2909 sscanf(t, "%d", &(cosine->n));
2916 snew(cosine->a, cosine->n);
2917 snew(cosine->phi, cosine->n);
2919 sprintf(format, "%%*d");
2920 for (i = 0; (i < cosine->n); i++)
2923 strcat(f1, "%lf%lf");
2924 if (sscanf(t, f1, &a, &phi) < 2)
2926 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
2929 cosine->phi[i] = phi;
2930 strcat(format, "%*lf%*lf");
2937 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
2938 const char *option, const char *val, int flag)
2940 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
2941 * But since this is much larger than STRLEN, such a line can not be parsed.
2942 * The real maximum is the number of names that fit in a string: STRLEN/2.
2944 #define EGP_MAX (STRLEN/2)
2945 int nelem, i, j, k, nr;
2946 char *names[EGP_MAX];
2950 gnames = groups->grpname;
2952 nelem = str_nelem(val, EGP_MAX, names);
2955 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
2957 nr = groups->grps[egcENER].nr;
2959 for (i = 0; i < nelem/2; i++)
2963 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
2969 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
2970 names[2*i], option);
2974 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
2980 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
2981 names[2*i+1], option);
2983 if ((j < nr) && (k < nr))
2985 ir->opts.egp_flags[nr*j+k] |= flag;
2986 ir->opts.egp_flags[nr*k+j] |= flag;
2995 static void make_swap_groups(
3004 int ig = -1, i = 0, j;
3008 /* Just a quick check here, more thorough checks are in mdrun */
3009 if (strcmp(splitg0name, splitg1name) == 0)
3011 gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
3014 /* First get the swap group index atoms */
3015 ig = search_string(swapgname, grps->nr, gnames);
3016 swap->nat = grps->index[ig+1] - grps->index[ig];
3019 fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
3020 snew(swap->ind, swap->nat);
3021 for (i = 0; i < swap->nat; i++)
3023 swap->ind[i] = grps->a[grps->index[ig]+i];
3028 gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
3031 /* Now do so for the split groups */
3032 for (j = 0; j < 2; j++)
3036 splitg = splitg0name;
3040 splitg = splitg1name;
3043 ig = search_string(splitg, grps->nr, gnames);
3044 swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
3045 if (swap->nat_split[j] > 0)
3047 fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
3048 j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
3049 snew(swap->ind_split[j], swap->nat_split[j]);
3050 for (i = 0; i < swap->nat_split[j]; i++)
3052 swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
3057 gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
3061 /* Now get the solvent group index atoms */
3062 ig = search_string(solgname, grps->nr, gnames);
3063 swap->nat_sol = grps->index[ig+1] - grps->index[ig];
3064 if (swap->nat_sol > 0)
3066 fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
3067 snew(swap->ind_sol, swap->nat_sol);
3068 for (i = 0; i < swap->nat_sol; i++)
3070 swap->ind_sol[i] = grps->a[grps->index[ig]+i];
3075 gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
3080 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3085 ig = search_string(IMDgname, grps->nr, gnames);
3086 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3088 if (IMDgroup->nat > 0)
3090 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3091 IMDgname, IMDgroup->nat);
3092 snew(IMDgroup->ind, IMDgroup->nat);
3093 for (i = 0; i < IMDgroup->nat; i++)
3095 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3101 void do_index(const char* mdparin, const char *ndx,
3104 t_inputrec *ir, rvec *v,
3108 gmx_groups_t *groups;
3112 char warnbuf[STRLEN], **gnames;
3113 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3116 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3117 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3118 int i, j, k, restnm;
3120 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3121 int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
3122 nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
3123 char warn_buf[STRLEN];
3127 fprintf(stderr, "processing index file...\n");
3133 snew(grps->index, 1);
3135 atoms_all = gmx_mtop_global_atoms(mtop);
3136 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3137 free_t_atoms(&atoms_all, FALSE);
3141 grps = init_index(ndx, &gnames);
3144 groups = &mtop->groups;
3145 natoms = mtop->natoms;
3146 symtab = &mtop->symtab;
3148 snew(groups->grpname, grps->nr+1);
3150 for (i = 0; (i < grps->nr); i++)
3152 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3154 groups->grpname[i] = put_symtab(symtab, "rest");
3156 srenew(gnames, grps->nr+1);
3157 gnames[restnm] = *(groups->grpname[i]);
3158 groups->ngrpname = grps->nr+1;
3160 set_warning_line(wi, mdparin, -1);
3162 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3163 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3164 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3165 if ((ntau_t != ntcg) || (nref_t != ntcg))
3167 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3168 "%d tau-t values", ntcg, nref_t, ntau_t);
3171 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3172 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3173 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3174 nr = groups->grps[egcTC].nr;
3176 snew(ir->opts.nrdf, nr);
3177 snew(ir->opts.tau_t, nr);
3178 snew(ir->opts.ref_t, nr);
3179 if (ir->eI == eiBD && ir->bd_fric == 0)
3181 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3188 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3192 for (i = 0; (i < nr); i++)
3194 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
3195 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
3197 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3198 warning_error(wi, warn_buf);
3201 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3203 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.");
3206 if (ir->opts.tau_t[i] >= 0)
3208 tau_min = min(tau_min, ir->opts.tau_t[i]);
3211 if (ir->etc != etcNO && ir->nsttcouple == -1)
3213 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3218 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3220 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");
3222 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
3224 if (ir->nstpcouple != ir->nsttcouple)
3226 int mincouple = min(ir->nstpcouple, ir->nsttcouple);
3227 ir->nstpcouple = ir->nsttcouple = mincouple;
3228 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);
3229 warning_note(wi, warn_buf);
3233 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3234 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3236 if (ETC_ANDERSEN(ir->etc))
3238 if (ir->nsttcouple != 1)
3241 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");
3242 warning_note(wi, warn_buf);
3245 nstcmin = tcouple_min_integration_steps(ir->etc);
3248 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
3250 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3251 ETCOUPLTYPE(ir->etc),
3253 ir->nsttcouple*ir->delta_t);
3254 warning(wi, warn_buf);
3257 for (i = 0; (i < nr); i++)
3259 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
3260 if (ir->opts.ref_t[i] < 0)
3262 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3265 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3266 if we are in this conditional) if mc_temp is negative */
3267 if (ir->expandedvals->mc_temp < 0)
3269 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3273 /* Simulated annealing for each group. There are nr groups */
3274 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3275 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3279 if (nSA > 0 && nSA != nr)
3281 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3285 snew(ir->opts.annealing, nr);
3286 snew(ir->opts.anneal_npoints, nr);
3287 snew(ir->opts.anneal_time, nr);
3288 snew(ir->opts.anneal_temp, nr);
3289 for (i = 0; i < nr; i++)
3291 ir->opts.annealing[i] = eannNO;
3292 ir->opts.anneal_npoints[i] = 0;
3293 ir->opts.anneal_time[i] = NULL;
3294 ir->opts.anneal_temp[i] = NULL;
3299 for (i = 0; i < nr; i++)
3301 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3303 ir->opts.annealing[i] = eannNO;
3305 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3307 ir->opts.annealing[i] = eannSINGLE;
3310 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3312 ir->opts.annealing[i] = eannPERIODIC;
3318 /* Read the other fields too */
3319 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3320 if (nSA_points != nSA)
3322 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3324 for (k = 0, i = 0; i < nr; i++)
3326 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3327 if (ir->opts.anneal_npoints[i] == 1)
3329 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3331 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3332 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3333 k += ir->opts.anneal_npoints[i];
3336 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3339 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3341 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3344 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3347 for (i = 0, k = 0; i < nr; i++)
3350 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3352 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3353 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3356 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3358 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3364 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3366 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3367 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3370 if (ir->opts.anneal_temp[i][j] < 0)
3372 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3377 /* Print out some summary information, to make sure we got it right */
3378 for (i = 0, k = 0; i < nr; i++)
3380 if (ir->opts.annealing[i] != eannNO)
3382 j = groups->grps[egcTC].nm_ind[i];
3383 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3384 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3385 ir->opts.anneal_npoints[i]);
3386 fprintf(stderr, "Time (ps) Temperature (K)\n");
3387 /* All terms except the last one */
3388 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3390 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3393 /* Finally the last one */
3394 j = ir->opts.anneal_npoints[i]-1;
3395 if (ir->opts.annealing[i] == eannSINGLE)
3397 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3401 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3402 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3404 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3413 if (ir->ePull != epullNO)
3415 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3417 make_pull_coords(ir->pull);
3422 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3425 if (ir->eSwapCoords != eswapNO)
3427 make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
3430 /* Make indices for IMD session */
3433 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3436 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3437 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3438 if (nacg*DIM != nacc)
3440 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3443 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3444 restnm, egrptpALL_GENREST, bVerbose, wi);
3445 nr = groups->grps[egcACC].nr;
3446 snew(ir->opts.acc, nr);
3447 ir->opts.ngacc = nr;
3449 for (i = k = 0; (i < nacg); i++)
3451 for (j = 0; (j < DIM); j++, k++)
3453 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3456 for (; (i < nr); i++)
3458 for (j = 0; (j < DIM); j++)
3460 ir->opts.acc[i][j] = 0;
3464 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3465 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3466 if (nfrdim != DIM*nfreeze)
3468 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3471 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3472 restnm, egrptpALL_GENREST, bVerbose, wi);
3473 nr = groups->grps[egcFREEZE].nr;
3474 ir->opts.ngfrz = nr;
3475 snew(ir->opts.nFreeze, nr);
3476 for (i = k = 0; (i < nfreeze); i++)
3478 for (j = 0; (j < DIM); j++, k++)
3480 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3481 if (!ir->opts.nFreeze[i][j])
3483 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3485 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3486 "(not %s)", ptr1[k]);
3487 warning(wi, warn_buf);
3492 for (; (i < nr); i++)
3494 for (j = 0; (j < DIM); j++)
3496 ir->opts.nFreeze[i][j] = 0;
3500 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3501 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3502 restnm, egrptpALL_GENREST, bVerbose, wi);
3503 add_wall_energrps(groups, ir->nwall, symtab);
3504 ir->opts.ngener = groups->grps[egcENER].nr;
3505 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3507 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3508 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3511 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3512 "This may lead to artifacts.\n"
3513 "In most cases one should use one group for the whole system.");
3516 /* Now we have filled the freeze struct, so we can calculate NRDF */
3517 calc_nrdf(mtop, ir, gnames);
3523 /* Must check per group! */
3524 for (i = 0; (i < ir->opts.ngtc); i++)
3526 ntot += ir->opts.nrdf[i];
3528 if (ntot != (DIM*natoms))
3530 fac = sqrt(ntot/(DIM*natoms));
3533 fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
3534 "and removal of center of mass motion\n", fac);
3536 for (i = 0; (i < natoms); i++)
3538 svmul(fac, v[i], v[i]);
3543 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3544 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3545 restnm, egrptpALL_GENREST, bVerbose, wi);
3546 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3547 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3548 restnm, egrptpALL_GENREST, bVerbose, wi);
3549 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3550 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3551 restnm, egrptpONE, bVerbose, wi);
3552 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3553 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3554 restnm, egrptpALL_GENREST, bVerbose, wi);
3556 /* QMMM input processing */
3557 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3558 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3559 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3560 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3562 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3563 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3565 /* group rest, if any, is always MM! */
3566 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3567 restnm, egrptpALL_GENREST, bVerbose, wi);
3568 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3569 ir->opts.ngQM = nQMg;
3570 snew(ir->opts.QMmethod, nr);
3571 snew(ir->opts.QMbasis, nr);
3572 for (i = 0; i < nr; i++)
3574 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3575 * converted to the corresponding enum in names.c
3577 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3579 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3583 nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
3584 nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
3585 nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
3586 snew(ir->opts.QMmult, nr);
3587 snew(ir->opts.QMcharge, nr);
3588 snew(ir->opts.bSH, nr);
3590 for (i = 0; i < nr; i++)
3592 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3593 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3594 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3597 nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
3598 nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
3599 snew(ir->opts.CASelectrons, nr);
3600 snew(ir->opts.CASorbitals, nr);
3601 for (i = 0; i < nr; i++)
3603 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3604 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3606 /* special optimization options */
3608 nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
3609 nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
3610 snew(ir->opts.bOPT, nr);
3611 snew(ir->opts.bTS, nr);
3612 for (i = 0; i < nr; i++)
3614 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3615 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3617 nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
3618 nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
3619 nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
3620 snew(ir->opts.SAon, nr);
3621 snew(ir->opts.SAoff, nr);
3622 snew(ir->opts.SAsteps, nr);
3624 for (i = 0; i < nr; i++)
3626 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3627 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3628 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3630 /* end of QMMM input */
3634 for (i = 0; (i < egcNR); i++)
3636 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3637 for (j = 0; (j < groups->grps[i].nr); j++)
3639 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3641 fprintf(stderr, "\n");
3645 nr = groups->grps[egcENER].nr;
3646 snew(ir->opts.egp_flags, nr*nr);
3648 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3649 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3651 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3653 if (bExcl && EEL_FULL(ir->coulombtype))
3655 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3658 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3659 if (bTable && !(ir->vdwtype == evdwUSER) &&
3660 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3661 !(ir->coulombtype == eelPMEUSERSWITCH))
3663 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3666 decode_cos(is->efield_x, &(ir->ex[XX]));
3667 decode_cos(is->efield_xt, &(ir->et[XX]));
3668 decode_cos(is->efield_y, &(ir->ex[YY]));
3669 decode_cos(is->efield_yt, &(ir->et[YY]));
3670 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3671 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3675 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3678 for (i = 0; (i < grps->nr); i++)
3690 static void check_disre(gmx_mtop_t *mtop)
3692 gmx_ffparams_t *ffparams;
3693 t_functype *functype;
3695 int i, ndouble, ftype;
3696 int label, old_label;
3698 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3700 ffparams = &mtop->ffparams;
3701 functype = ffparams->functype;
3702 ip = ffparams->iparams;
3705 for (i = 0; i < ffparams->ntypes; i++)
3707 ftype = functype[i];
3708 if (ftype == F_DISRES)
3710 label = ip[i].disres.label;
3711 if (label == old_label)
3713 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3721 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3722 "probably the parameters for multiple pairs in one restraint "
3723 "are not identical\n", ndouble);
3728 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3729 gmx_bool posres_only,
3733 gmx_mtop_ilistloop_t iloop;
3743 for (d = 0; d < DIM; d++)
3745 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3747 /* Check for freeze groups */
3748 for (g = 0; g < ir->opts.ngfrz; g++)
3750 for (d = 0; d < DIM; d++)
3752 if (ir->opts.nFreeze[g][d] != 0)
3760 /* Check for position restraints */
3761 iloop = gmx_mtop_ilistloop_init(sys);
3762 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3765 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3767 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3769 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3770 for (d = 0; d < DIM; d++)
3772 if (pr->posres.fcA[d] != 0)
3778 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3780 /* Check for flat-bottom posres */
3781 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3782 if (pr->fbposres.k != 0)
3784 switch (pr->fbposres.geom)
3786 case efbposresSPHERE:
3787 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3789 case efbposresCYLINDER:
3790 AbsRef[XX] = AbsRef[YY] = 1;
3792 case efbposresX: /* d=XX */
3793 case efbposresY: /* d=YY */
3794 case efbposresZ: /* d=ZZ */
3795 d = pr->fbposres.geom - efbposresX;
3799 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3800 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3808 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3812 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3813 gmx_bool *bC6ParametersWorkWithGeometricRules,
3814 gmx_bool *bC6ParametersWorkWithLBRules,
3815 gmx_bool *bLBRulesPossible)
3817 int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
3820 double geometricdiff, LBdiff;
3821 double c6i, c6j, c12i, c12j;
3822 double c6, c6_geometric, c6_LB;
3823 double sigmai, sigmaj, epsi, epsj;
3824 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3827 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3828 * force-field floating point parameters.
3831 ptr = getenv("GMX_LJCOMB_TOL");
3836 sscanf(ptr, "%lf", &dbl);
3840 *bC6ParametersWorkWithLBRules = TRUE;
3841 *bC6ParametersWorkWithGeometricRules = TRUE;
3842 bCanDoLBRules = TRUE;
3843 bCanDoGeometricRules = TRUE;
3844 ntypes = mtop->ffparams.atnr;
3845 snew(typecount, ntypes);
3846 gmx_mtop_count_atomtypes(mtop, state, typecount);
3847 geometricdiff = LBdiff = 0.0;
3848 *bLBRulesPossible = TRUE;
3849 for (tpi = 0; tpi < ntypes; ++tpi)
3851 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3852 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3853 for (tpj = tpi; tpj < ntypes; ++tpj)
3855 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3856 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3857 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3858 c6_geometric = sqrt(c6i * c6j);
3859 if (!gmx_numzero(c6_geometric))
3861 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3863 sigmai = pow(c12i / c6i, 1.0/6.0);
3864 sigmaj = pow(c12j / c6j, 1.0/6.0);
3865 epsi = c6i * c6i /(4.0 * c12i);
3866 epsj = c6j * c6j /(4.0 * c12j);
3867 c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
3871 *bLBRulesPossible = FALSE;
3872 c6_LB = c6_geometric;
3874 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3877 if (FALSE == bCanDoLBRules)
3879 *bC6ParametersWorkWithLBRules = FALSE;
3882 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3884 if (FALSE == bCanDoGeometricRules)
3886 *bC6ParametersWorkWithGeometricRules = FALSE;
3894 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3898 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3900 check_combination_rule_differences(mtop, 0,
3901 &bC6ParametersWorkWithGeometricRules,
3902 &bC6ParametersWorkWithLBRules,
3904 if (ir->ljpme_combination_rule == eljpmeLB)
3906 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
3908 warning(wi, "You are using arithmetic-geometric combination rules "
3909 "in LJ-PME, but your non-bonded C6 parameters do not "
3910 "follow these rules.");
3915 if (FALSE == bC6ParametersWorkWithGeometricRules)
3917 if (ir->eDispCorr != edispcNO)
3919 warning_note(wi, "You are using geometric combination rules in "
3920 "LJ-PME, but your non-bonded C6 parameters do "
3921 "not follow these rules. "
3922 "This will introduce very small errors in the forces and energies in "
3923 "your simulations. Dispersion correction will correct total energy "
3924 "and/or pressure for isotropic systems, but not forces or surface tensions.");
3928 warning_note(wi, "You are using geometric combination rules in "
3929 "LJ-PME, but your non-bonded C6 parameters do "
3930 "not follow these rules. "
3931 "This will introduce very small errors in the forces and energies in "
3932 "your simulations. If your system is homogeneous, consider using dispersion correction "
3933 "for the total energy and pressure.");
3939 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
3942 char err_buf[STRLEN];
3943 int i, m, c, nmol, npct;
3944 gmx_bool bCharge, bAcc;
3945 real gdt_max, *mgrp, mt;
3947 gmx_mtop_atomloop_block_t aloopb;
3948 gmx_mtop_atomloop_all_t aloop;
3951 char warn_buf[STRLEN];
3953 set_warning_line(wi, mdparin, -1);
3955 if (ir->cutoff_scheme == ecutsVERLET &&
3956 ir->verletbuf_tol > 0 &&
3958 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
3959 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
3961 /* Check if a too small Verlet buffer might potentially
3962 * cause more drift than the thermostat can couple off.
3964 /* Temperature error fraction for warning and suggestion */
3965 const real T_error_warn = 0.002;
3966 const real T_error_suggest = 0.001;
3967 /* For safety: 2 DOF per atom (typical with constraints) */
3968 const real nrdf_at = 2;
3969 real T, tau, max_T_error;
3974 for (i = 0; i < ir->opts.ngtc; i++)
3976 T = max(T, ir->opts.ref_t[i]);
3977 tau = max(tau, ir->opts.tau_t[i]);
3981 /* This is a worst case estimate of the temperature error,
3982 * assuming perfect buffer estimation and no cancelation
3983 * of errors. The factor 0.5 is because energy distributes
3984 * equally over Ekin and Epot.
3986 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
3987 if (max_T_error > T_error_warn)
3989 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.",
3990 ir->verletbuf_tol, T, tau,
3992 100*T_error_suggest,
3993 ir->verletbuf_tol*T_error_suggest/max_T_error);
3994 warning(wi, warn_buf);
3999 if (ETC_ANDERSEN(ir->etc))
4003 for (i = 0; i < ir->opts.ngtc; i++)
4005 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4006 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4007 sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
4008 i, ir->opts.tau_t[i]);
4009 CHECK(ir->opts.tau_t[i] < 0);
4012 for (i = 0; i < ir->opts.ngtc; i++)
4014 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
4015 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);
4016 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
4020 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4021 ir->comm_mode == ecmNO &&
4022 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4023 !ETC_ANDERSEN(ir->etc))
4025 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");
4028 /* Check for pressure coupling with absolute position restraints */
4029 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4031 absolute_reference(ir, sys, TRUE, AbsRef);
4033 for (m = 0; m < DIM; m++)
4035 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4037 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4045 aloopb = gmx_mtop_atomloop_block_init(sys);
4046 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4048 if (atom->q != 0 || atom->qB != 0)
4056 if (EEL_FULL(ir->coulombtype))
4059 "You are using full electrostatics treatment %s for a system without charges.\n"
4060 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4061 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4062 warning(wi, err_buf);
4067 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4070 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4071 "You might want to consider using %s electrostatics.\n",
4073 warning_note(wi, err_buf);
4077 /* Check if combination rules used in LJ-PME are the same as in the force field */
4078 if (EVDW_PME(ir->vdwtype))
4080 check_combination_rules(ir, sys, wi);
4083 /* Generalized reaction field */
4084 if (ir->opts.ngtc == 0)
4086 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4088 CHECK(ir->coulombtype == eelGRF);
4092 sprintf(err_buf, "When using coulombtype = %s"
4093 " ref-t for temperature coupling should be > 0",
4095 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4098 if (ir->eI == eiSD1 &&
4099 (gmx_mtop_ftype_count(sys, F_CONSTR) > 0 ||
4100 gmx_mtop_ftype_count(sys, F_SETTLE) > 0))
4102 sprintf(warn_buf, "With constraints integrator %s is less accurate, consider using %s instead", ei_names[ir->eI], ei_names[eiSD2]);
4103 warning_note(wi, warn_buf);
4107 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4109 for (m = 0; (m < DIM); m++)
4111 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4120 snew(mgrp, sys->groups.grps[egcACC].nr);
4121 aloop = gmx_mtop_atomloop_all_init(sys);
4122 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4124 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4127 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4129 for (m = 0; (m < DIM); m++)
4131 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4135 for (m = 0; (m < DIM); m++)
4137 if (fabs(acc[m]) > 1e-6)
4139 const char *dim[DIM] = { "X", "Y", "Z" };
4141 "Net Acceleration in %s direction, will %s be corrected\n",
4142 dim[m], ir->nstcomm != 0 ? "" : "not");
4143 if (ir->nstcomm != 0 && m < ndof_com(ir))
4146 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4148 ir->opts.acc[i][m] -= acc[m];
4156 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4157 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4159 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4162 if (ir->ePull != epullNO)
4164 gmx_bool bPullAbsoluteRef;
4166 bPullAbsoluteRef = FALSE;
4167 for (i = 0; i < ir->pull->ncoord; i++)
4169 bPullAbsoluteRef = bPullAbsoluteRef ||
4170 ir->pull->coord[i].group[0] == 0 ||
4171 ir->pull->coord[i].group[1] == 0;
4173 if (bPullAbsoluteRef)
4175 absolute_reference(ir, sys, FALSE, AbsRef);
4176 for (m = 0; m < DIM; m++)
4178 if (ir->pull->dim[m] && !AbsRef[m])
4180 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.");
4186 if (ir->pull->eGeom == epullgDIRPBC)
4188 for (i = 0; i < 3; i++)
4190 for (m = 0; m <= i; m++)
4192 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4193 ir->deform[i][m] != 0)
4195 for (c = 0; c < ir->pull->ncoord; c++)
4197 if (ir->pull->coord[c].vec[m] != 0)
4199 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->eGeom), 'x'+m);
4211 void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr, warninp_t wi)
4215 char warn_buf[STRLEN];
4218 ptr = check_box(ir->ePBC, box);
4221 warning_error(wi, ptr);
4224 if (bConstr && ir->eConstrAlg == econtSHAKE)
4226 if (ir->shake_tol <= 0.0)
4228 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4230 warning_error(wi, warn_buf);
4233 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
4235 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
4236 if (ir->epc == epcNO)
4238 warning(wi, warn_buf);
4242 warning_error(wi, warn_buf);
4247 if ( (ir->eConstrAlg == econtLINCS) && bConstr)
4249 /* If we have Lincs constraints: */
4250 if (ir->eI == eiMD && ir->etc == etcNO &&
4251 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4253 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4254 warning_note(wi, warn_buf);
4257 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4259 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4260 warning_note(wi, warn_buf);
4262 if (ir->epc == epcMTTK)
4264 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4268 if (bConstr && ir->epc == epcMTTK)
4270 warning_note(wi, "MTTK with constraints is deprecated, and will be removed in GROMACS 5.1");
4273 if (ir->LincsWarnAngle > 90.0)
4275 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4276 warning(wi, warn_buf);
4277 ir->LincsWarnAngle = 90.0;
4280 if (ir->ePBC != epbcNONE)
4282 if (ir->nstlist == 0)
4284 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4286 bTWIN = (ir->rlistlong > ir->rlist);
4287 if (ir->ns_type == ensGRID)
4289 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
4291 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",
4292 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
4293 warning_error(wi, warn_buf);
4298 min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
4299 if (2*ir->rlistlong >= min_size)
4301 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4302 warning_error(wi, warn_buf);
4305 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4312 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4316 real rvdw1, rvdw2, rcoul1, rcoul2;
4317 char warn_buf[STRLEN];
4319 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4323 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4328 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4334 if (rvdw1 + rvdw2 > ir->rlist ||
4335 rcoul1 + rcoul2 > ir->rlist)
4338 "The sum of the two largest charge group radii (%f) "
4339 "is larger than rlist (%f)\n",
4340 max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4341 warning(wi, warn_buf);
4345 /* Here we do not use the zero at cut-off macro,
4346 * since user defined interactions might purposely
4347 * not be zero at the cut-off.
4349 if (ir_vdw_is_zero_at_cutoff(ir) &&
4350 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
4352 sprintf(warn_buf, "The sum of the two largest charge group "
4353 "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
4354 "With exact cut-offs, better performance can be "
4355 "obtained with cutoff-scheme = %s, because it "
4356 "does not use charge groups at all.",
4358 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4359 ir->rlistlong, ir->rvdw,
4360 ecutscheme_names[ecutsVERLET]);
4363 warning(wi, warn_buf);
4367 warning_note(wi, warn_buf);
4370 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4371 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
4373 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
4374 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4376 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4377 ir->rlistlong, ir->rcoulomb,
4378 ecutscheme_names[ecutsVERLET]);
4381 warning(wi, warn_buf);
4385 warning_note(wi, warn_buf);