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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);
555 if (ir->nsteps == 0 && !ir->bContinuation)
557 warning_note(wi, "For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates.");
561 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
562 ir->bContinuation && ir->ld_seed != -1)
564 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)");
570 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
571 CHECK(ir->ePBC != epbcXYZ);
572 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
573 CHECK(ir->ns_type != ensGRID);
574 sprintf(err_buf, "with TPI nstlist should be larger than zero");
575 CHECK(ir->nstlist <= 0);
576 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
577 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
581 if ( (opts->nshake > 0) && (opts->bMorse) )
584 "Using morse bond-potentials while constraining bonds is useless");
585 warning(wi, warn_buf);
588 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
589 ir->bContinuation && ir->ld_seed != -1)
591 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)");
593 /* verify simulated tempering options */
597 gmx_bool bAllTempZero = TRUE;
598 for (i = 0; i < fep->n_lambda; i++)
600 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]);
601 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
602 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
604 bAllTempZero = FALSE;
607 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
608 CHECK(bAllTempZero == TRUE);
610 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
611 CHECK(ir->eI != eiVV);
613 /* check compatability of the temperature coupling with simulated tempering */
615 if (ir->etc == etcNOSEHOOVER)
617 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
618 warning_note(wi, warn_buf);
621 /* check that the temperatures make sense */
623 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);
624 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
626 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
627 CHECK(ir->simtempvals->simtemp_high <= 0);
629 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
630 CHECK(ir->simtempvals->simtemp_low <= 0);
633 /* verify free energy options */
635 if (ir->efep != efepNO)
638 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
640 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
642 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
643 (int)fep->sc_r_power);
644 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
646 sprintf(err_buf, "Can't use postive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
647 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
649 sprintf(err_buf, "Can't use postive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
650 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
652 sprintf(err_buf, "Can only use expanded ensemble with md-vv for now; should be supported for other integrators in 5.0");
653 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
655 sprintf(err_buf, "Free-energy not implemented for Ewald");
656 CHECK(ir->coulombtype == eelEWALD);
658 /* check validty of lambda inputs */
659 if (fep->n_lambda == 0)
661 /* Clear output in case of no states:*/
662 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
663 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
667 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
668 CHECK((fep->init_fep_state >= fep->n_lambda));
671 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
672 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
674 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",
675 fep->init_lambda, fep->init_fep_state);
676 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
680 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
684 for (i = 0; i < efptNR; i++)
686 if (fep->separate_dvdl[i])
691 if (n_lambda_terms > 1)
693 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.");
694 warning(wi, warn_buf);
697 if (n_lambda_terms < 2 && fep->n_lambda > 0)
700 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
704 for (j = 0; j < efptNR; j++)
706 for (i = 0; i < fep->n_lambda; i++)
708 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]);
709 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
713 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
715 for (i = 0; i < fep->n_lambda; i++)
717 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],
718 fep->all_lambda[efptCOUL][i]);
719 CHECK((fep->sc_alpha > 0) &&
720 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
721 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
722 ((fep->all_lambda[efptVDW][i] > 0.0) &&
723 (fep->all_lambda[efptVDW][i] < 1.0))));
727 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
729 real sigma, lambda, r_sc;
732 /* Maximum estimate for A and B charges equal with lambda power 1 */
734 r_sc = pow(lambda*fep->sc_alpha*pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
735 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.",
737 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
738 warning_note(wi, warn_buf);
741 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
742 be treated differently, but that's the next step */
744 for (i = 0; i < efptNR; i++)
746 for (j = 0; j < fep->n_lambda; j++)
748 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
749 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
754 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
757 expand = ir->expandedvals;
759 /* checking equilibration of weights inputs for validity */
761 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
762 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
763 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
765 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
766 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
767 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
769 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
770 expand->equil_steps, elmceq_names[elmceqSTEPS]);
771 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
773 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
774 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
775 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
777 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
778 expand->equil_ratio, elmceq_names[elmceqRATIO]);
779 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
781 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
782 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
783 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
785 sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
786 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
787 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
789 sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
790 expand->equil_steps, elmceq_names[elmceqSTEPS]);
791 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
793 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
794 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
795 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
797 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
798 expand->equil_ratio, elmceq_names[elmceqRATIO]);
799 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
801 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
802 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
803 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
805 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
806 CHECK((expand->lmc_repeats <= 0));
807 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
808 CHECK((expand->minvarmin <= 0));
809 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
810 CHECK((expand->c_range < 0));
811 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
812 fep->init_fep_state, expand->lmc_forced_nstart);
813 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
814 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
815 CHECK((expand->lmc_forced_nstart < 0));
816 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
817 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
819 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
820 CHECK((expand->init_wl_delta < 0));
821 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
822 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
823 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
824 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
826 /* if there is no temperature control, we need to specify an MC temperature */
827 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
828 if (expand->nstTij > 0)
830 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
831 expand->nstTij, ir->nstlog);
832 CHECK((mod(expand->nstTij, ir->nstlog) != 0));
837 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
838 CHECK(ir->nwall && ir->ePBC != epbcXY);
841 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
843 if (ir->ePBC == epbcNONE)
845 if (ir->epc != epcNO)
847 warning(wi, "Turning off pressure coupling for vacuum system");
853 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
854 epbc_names[ir->ePBC]);
855 CHECK(ir->epc != epcNO);
857 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
858 CHECK(EEL_FULL(ir->coulombtype));
860 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
861 epbc_names[ir->ePBC]);
862 CHECK(ir->eDispCorr != edispcNO);
865 if (ir->rlist == 0.0)
867 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
868 "with coulombtype = %s or coulombtype = %s\n"
869 "without periodic boundary conditions (pbc = %s) and\n"
870 "rcoulomb and rvdw set to zero",
871 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
872 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
873 (ir->ePBC != epbcNONE) ||
874 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
878 warning_error(wi, "Can not have heuristic neighborlist updates without cut-off");
882 warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
887 if (ir->nstcomm == 0)
889 ir->comm_mode = ecmNO;
891 if (ir->comm_mode != ecmNO)
895 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");
896 ir->nstcomm = abs(ir->nstcomm);
899 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
901 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
902 ir->nstcomm = ir->nstcalcenergy;
905 if (ir->comm_mode == ecmANGULAR)
907 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
908 CHECK(ir->bPeriodicMols);
909 if (ir->ePBC != epbcNONE)
911 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).");
916 if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
918 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.");
921 sprintf(err_buf, "Twin-range neighbour searching (NS) with simple NS"
922 " algorithm not implemented");
923 CHECK(((ir->rcoulomb > ir->rlist) || (ir->rvdw > ir->rlist))
924 && (ir->ns_type == ensSIMPLE));
926 /* TEMPERATURE COUPLING */
927 if (ir->etc == etcYES)
929 ir->etc = etcBERENDSEN;
930 warning_note(wi, "Old option for temperature coupling given: "
931 "changing \"yes\" to \"Berendsen\"\n");
934 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
936 if (ir->opts.nhchainlength < 1)
938 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
939 ir->opts.nhchainlength = 1;
940 warning(wi, warn_buf);
943 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
945 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
946 ir->opts.nhchainlength = 1;
951 ir->opts.nhchainlength = 0;
954 if (ir->eI == eiVVAK)
956 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
958 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
961 if (ETC_ANDERSEN(ir->etc))
963 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
964 CHECK(!(EI_VV(ir->eI)));
966 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
968 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]);
969 warning_note(wi, warn_buf);
972 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]);
973 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
976 if (ir->etc == etcBERENDSEN)
978 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
979 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
980 warning_note(wi, warn_buf);
983 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
984 && ir->epc == epcBERENDSEN)
986 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
987 "true ensemble for the thermostat");
988 warning(wi, warn_buf);
991 /* PRESSURE COUPLING */
992 if (ir->epc == epcISOTROPIC)
994 ir->epc = epcBERENDSEN;
995 warning_note(wi, "Old option for pressure coupling given: "
996 "changing \"Isotropic\" to \"Berendsen\"\n");
999 if (ir->epc != epcNO)
1001 dt_pcoupl = ir->nstpcouple*ir->delta_t;
1003 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1004 CHECK(ir->tau_p <= 0);
1006 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc))
1008 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
1009 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1010 warning(wi, warn_buf);
1013 sprintf(err_buf, "compressibility must be > 0 when using pressure"
1014 " coupling %s\n", EPCOUPLTYPE(ir->epc));
1015 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
1016 ir->compress[ZZ][ZZ] < 0 ||
1017 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
1018 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
1020 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1023 "You are generating velocities so I am assuming you "
1024 "are equilibrating a system. You are using "
1025 "%s pressure coupling, but this can be "
1026 "unstable for equilibration. If your system crashes, try "
1027 "equilibrating first with Berendsen pressure coupling. If "
1028 "you are not equilibrating the system, you can probably "
1029 "ignore this warning.",
1030 epcoupl_names[ir->epc]);
1031 warning(wi, warn_buf);
1037 if (ir->epc > epcNO)
1039 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1041 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.");
1047 if (ir->epc == epcMTTK)
1049 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1053 /* ELECTROSTATICS */
1054 /* More checks are in triple check (grompp.c) */
1056 if (ir->coulombtype == eelSWITCH)
1058 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1059 "artifacts, advice: use coulombtype = %s",
1060 eel_names[ir->coulombtype],
1061 eel_names[eelRF_ZERO]);
1062 warning(wi, warn_buf);
1065 if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
1067 sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
1068 warning_note(wi, warn_buf);
1071 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1073 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);
1074 warning(wi, warn_buf);
1075 ir->epsilon_rf = ir->epsilon_r;
1076 ir->epsilon_r = 1.0;
1079 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == NULL)
1081 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1082 CHECK(ir->epsilon_r < 0);
1085 if (EEL_RF(ir->coulombtype))
1087 /* reaction field (at the cut-off) */
1089 if (ir->coulombtype == eelRF_ZERO)
1091 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1092 eel_names[ir->coulombtype]);
1093 CHECK(ir->epsilon_rf != 0);
1094 ir->epsilon_rf = 0.0;
1097 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1098 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1099 (ir->epsilon_r == 0));
1100 if (ir->epsilon_rf == ir->epsilon_r)
1102 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1103 eel_names[ir->coulombtype]);
1104 warning(wi, warn_buf);
1107 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1108 * means the interaction is zero outside rcoulomb, but it helps to
1109 * provide accurate energy conservation.
1111 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1113 if (ir_coulomb_switched(ir))
1116 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1117 eel_names[ir->coulombtype]);
1118 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1121 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1123 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1125 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1126 eel_names[ir->coulombtype]);
1127 CHECK(ir->rlist > ir->rcoulomb);
1131 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1132 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1135 "The switch/shift interaction settings are just for compatibility; you will get better "
1136 "performance from applying potential modifiers to your interactions!\n");
1137 warning_note(wi, warn_buf);
1140 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1142 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1144 real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
1145 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.",
1146 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1147 warning(wi, warn_buf);
1151 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1153 if (ir->rvdw_switch == 0)
1155 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.");
1156 warning(wi, warn_buf);
1160 if (EEL_FULL(ir->coulombtype))
1162 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1163 ir->coulombtype == eelPMEUSERSWITCH)
1165 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1166 eel_names[ir->coulombtype]);
1167 CHECK(ir->rcoulomb > ir->rlist);
1169 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1171 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1174 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
1175 "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
1176 "a potential modifier.", eel_names[ir->coulombtype]);
1177 if (ir->nstcalclr == 1)
1179 CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
1183 CHECK(ir->rcoulomb != ir->rlist);
1189 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1191 if (ir->pme_order < 3)
1193 warning_error(wi, "pme-order can not be smaller than 3");
1197 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1199 if (ir->ewald_geometry == eewg3D)
1201 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1202 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1203 warning(wi, warn_buf);
1205 /* This check avoids extra pbc coding for exclusion corrections */
1206 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1207 CHECK(ir->wall_ewald_zfac < 2);
1210 if (ir_vdw_switched(ir))
1212 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1213 CHECK(ir->rvdw_switch >= ir->rvdw);
1215 if (ir->rvdw_switch < 0.5*ir->rvdw)
1217 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.",
1218 ir->rvdw_switch, ir->rvdw);
1219 warning_note(wi, warn_buf);
1222 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1224 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1226 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1227 CHECK(ir->rlist > ir->rvdw);
1231 if (ir->vdwtype == evdwPME)
1233 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1235 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s a\
1237 evdw_names[ir->vdwtype],
1238 eintmod_names[eintmodPOTSHIFT],
1239 eintmod_names[eintmodNONE]);
1243 if (ir->cutoff_scheme == ecutsGROUP)
1245 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1246 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)) &&
1249 warning_note(wi, "With exact cut-offs, rlist should be "
1250 "larger than rcoulomb and rvdw, so that there "
1251 "is a buffer region for particle motion "
1252 "between neighborsearch steps");
1255 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlistlong <= ir->rcoulomb)
1257 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
1258 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1259 warning_note(wi, warn_buf);
1261 if (ir_vdw_switched(ir) && (ir->rlistlong <= ir->rvdw))
1263 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
1264 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1265 warning_note(wi, warn_buf);
1269 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1271 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.");
1274 if (ir->nstlist == -1)
1276 sprintf(err_buf, "With nstlist=-1 rvdw and rcoulomb should be smaller than rlist to account for diffusion and possibly charge-group radii");
1277 CHECK(ir->rvdw >= ir->rlist || ir->rcoulomb >= ir->rlist);
1279 sprintf(err_buf, "nstlist can not be smaller than -1");
1280 CHECK(ir->nstlist < -1);
1282 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1285 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1288 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1290 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1293 /* ENERGY CONSERVATION */
1294 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1296 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1298 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1299 evdw_names[evdwSHIFT]);
1300 warning_note(wi, warn_buf);
1302 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1304 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1305 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1306 warning_note(wi, warn_buf);
1310 if (EI_VV(ir->eI) && IR_TWINRANGE(*ir) && ir->nstlist > 1)
1312 sprintf(warn_buf, "Twin-range multiple time stepping does not work with integrator %s.", ei_names[ir->eI]);
1313 warning_error(wi, warn_buf);
1316 /* IMPLICIT SOLVENT */
1317 if (ir->coulombtype == eelGB_NOTUSED)
1319 ir->coulombtype = eelCUT;
1320 ir->implicit_solvent = eisGBSA;
1321 fprintf(stderr, "Note: Old option for generalized born electrostatics given:\n"
1322 "Changing coulombtype from \"generalized-born\" to \"cut-off\" and instead\n"
1323 "setting implicit-solvent value to \"GBSA\" in input section.\n");
1326 if (ir->sa_algorithm == esaSTILL)
1328 sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
1329 CHECK(ir->sa_algorithm == esaSTILL);
1332 if (ir->implicit_solvent == eisGBSA)
1334 sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
1335 CHECK(ir->rgbradii != ir->rlist);
1337 if (ir->coulombtype != eelCUT)
1339 sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
1340 CHECK(ir->coulombtype != eelCUT);
1342 if (ir->vdwtype != evdwCUT)
1344 sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
1345 CHECK(ir->vdwtype != evdwCUT);
1347 if (ir->nstgbradii < 1)
1349 sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
1350 warning_note(wi, warn_buf);
1353 if (ir->sa_algorithm == esaNO)
1355 sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
1356 warning_note(wi, warn_buf);
1358 if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
1360 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");
1361 warning_note(wi, warn_buf);
1363 if (ir->gb_algorithm == egbSTILL)
1365 ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
1369 ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
1372 if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
1374 sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
1375 CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
1382 if (ir->cutoff_scheme != ecutsGROUP)
1384 warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
1388 warning_error(wi, "AdresS simulation supports only stochastic dynamics");
1390 if (ir->epc != epcNO)
1392 warning_error(wi, "AdresS simulation does not support pressure coupling");
1394 if (EEL_FULL(ir->coulombtype))
1396 warning_error(wi, "AdresS simulation does not support long-range electrostatics");
1401 /* count the number of text elemets separated by whitespace in a string.
1402 str = the input string
1403 maxptr = the maximum number of allowed elements
1404 ptr = the output array of pointers to the first character of each element
1405 returns: the number of elements. */
1406 int str_nelem(const char *str, int maxptr, char *ptr[])
1411 copy0 = strdup(str);
1414 while (*copy != '\0')
1418 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1426 while ((*copy != '\0') && !isspace(*copy))
1445 /* interpret a number of doubles from a string and put them in an array,
1446 after allocating space for them.
1447 str = the input string
1448 n = the (pre-allocated) number of doubles read
1449 r = the output array of doubles. */
1450 static void parse_n_real(char *str, int *n, real **r)
1455 *n = str_nelem(str, MAXPTR, ptr);
1458 for (i = 0; i < *n; i++)
1460 (*r)[i] = strtod(ptr[i], NULL);
1464 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
1467 int i, j, max_n_lambda, nweights, nfep[efptNR];
1468 t_lambda *fep = ir->fepvals;
1469 t_expanded *expand = ir->expandedvals;
1470 real **count_fep_lambdas;
1471 gmx_bool bOneLambda = TRUE;
1473 snew(count_fep_lambdas, efptNR);
1475 /* FEP input processing */
1476 /* first, identify the number of lambda values for each type.
1477 All that are nonzero must have the same number */
1479 for (i = 0; i < efptNR; i++)
1481 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
1484 /* now, determine the number of components. All must be either zero, or equal. */
1487 for (i = 0; i < efptNR; i++)
1489 if (nfep[i] > max_n_lambda)
1491 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1492 must have the same number if its not zero.*/
1497 for (i = 0; i < efptNR; i++)
1501 ir->fepvals->separate_dvdl[i] = FALSE;
1503 else if (nfep[i] == max_n_lambda)
1505 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1506 respect to the temperature currently */
1508 ir->fepvals->separate_dvdl[i] = TRUE;
1513 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1514 nfep[i], efpt_names[i], max_n_lambda);
1517 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1518 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1520 /* the number of lambdas is the number we've read in, which is either zero
1521 or the same for all */
1522 fep->n_lambda = max_n_lambda;
1524 /* allocate space for the array of lambda values */
1525 snew(fep->all_lambda, efptNR);
1526 /* if init_lambda is defined, we need to set lambda */
1527 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1529 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1531 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1532 for (i = 0; i < efptNR; i++)
1534 snew(fep->all_lambda[i], fep->n_lambda);
1535 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1538 for (j = 0; j < fep->n_lambda; j++)
1540 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1542 sfree(count_fep_lambdas[i]);
1545 sfree(count_fep_lambdas);
1547 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1548 bookkeeping -- for now, init_lambda */
1550 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1552 for (i = 0; i < fep->n_lambda; i++)
1554 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1558 /* check to see if only a single component lambda is defined, and soft core is defined.
1559 In this case, turn on coulomb soft core */
1561 if (max_n_lambda == 0)
1567 for (i = 0; i < efptNR; i++)
1569 if ((nfep[i] != 0) && (i != efptFEP))
1575 if ((bOneLambda) && (fep->sc_alpha > 0))
1577 fep->bScCoul = TRUE;
1580 /* Fill in the others with the efptFEP if they are not explicitly
1581 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1582 they are all zero. */
1584 for (i = 0; i < efptNR; i++)
1586 if ((nfep[i] == 0) && (i != efptFEP))
1588 for (j = 0; j < fep->n_lambda; j++)
1590 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1596 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1597 if (fep->sc_r_power == 48)
1599 if (fep->sc_alpha > 0.1)
1601 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1605 expand = ir->expandedvals;
1606 /* now read in the weights */
1607 parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
1610 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1612 else if (nweights != fep->n_lambda)
1614 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1615 nweights, fep->n_lambda);
1617 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1619 expand->nstexpanded = fep->nstdhdl;
1620 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1622 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1624 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1625 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1626 2*tau_t just to be careful so it's not to frequent */
1631 static void do_simtemp_params(t_inputrec *ir)
1634 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1635 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1640 static void do_wall_params(t_inputrec *ir,
1641 char *wall_atomtype, char *wall_density,
1645 char *names[MAXPTR];
1648 opts->wall_atomtype[0] = NULL;
1649 opts->wall_atomtype[1] = NULL;
1651 ir->wall_atomtype[0] = -1;
1652 ir->wall_atomtype[1] = -1;
1653 ir->wall_density[0] = 0;
1654 ir->wall_density[1] = 0;
1658 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1659 if (nstr != ir->nwall)
1661 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1664 for (i = 0; i < ir->nwall; i++)
1666 opts->wall_atomtype[i] = strdup(names[i]);
1669 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1671 nstr = str_nelem(wall_density, MAXPTR, names);
1672 if (nstr != ir->nwall)
1674 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1676 for (i = 0; i < ir->nwall; i++)
1678 sscanf(names[i], "%lf", &dbl);
1681 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1683 ir->wall_density[i] = dbl;
1689 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1697 srenew(groups->grpname, groups->ngrpname+nwall);
1698 grps = &(groups->grps[egcENER]);
1699 srenew(grps->nm_ind, grps->nr+nwall);
1700 for (i = 0; i < nwall; i++)
1702 sprintf(str, "wall%d", i);
1703 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1704 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1709 void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1710 t_expanded *expand, warninp_t wi)
1712 int ninp, nerror = 0;
1718 /* read expanded ensemble parameters */
1719 CCTYPE ("expanded ensemble variables");
1720 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1721 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1722 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1723 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1724 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1725 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1726 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1727 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1728 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1729 CCTYPE("Seed for Monte Carlo in lambda space");
1730 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1731 RTYPE ("mc-temperature", expand->mc_temp, -1);
1732 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1733 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1734 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1735 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1736 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1737 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1738 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1739 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1740 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1741 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1742 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
1750 void get_ir(const char *mdparin, const char *mdparout,
1751 t_inputrec *ir, t_gromppopts *opts,
1755 double dumdub[2][6];
1759 char warn_buf[STRLEN];
1760 t_lambda *fep = ir->fepvals;
1761 t_expanded *expand = ir->expandedvals;
1763 init_inputrec_strings();
1764 inp = read_inpfile(mdparin, &ninp, wi);
1766 snew(dumstr[0], STRLEN);
1767 snew(dumstr[1], STRLEN);
1769 if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
1772 "%s did not specify a value for the .mdp option "
1773 "\"cutoff-scheme\". Probably it was first intended for use "
1774 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1775 "introduced, but the group scheme was still the default. "
1776 "The default is now the Verlet scheme, so you will observe "
1777 "different behaviour.", mdparin);
1778 warning_note(wi, warn_buf);
1781 /* ignore the following deprecated commands */
1784 REM_TYPE("domain-decomposition");
1785 REM_TYPE("andersen-seed");
1787 REM_TYPE("dihre-fc");
1788 REM_TYPE("dihre-tau");
1789 REM_TYPE("nstdihreout");
1790 REM_TYPE("nstcheckpoint");
1791 REM_TYPE("optimize-fft");
1793 /* replace the following commands with the clearer new versions*/
1794 REPL_TYPE("unconstrained-start", "continuation");
1795 REPL_TYPE("foreign-lambda", "fep-lambdas");
1796 REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
1797 REPL_TYPE("nstxtcout", "nstxout-compressed");
1798 REPL_TYPE("xtc-grps", "compressed-x-grps");
1799 REPL_TYPE("xtc-precision", "compressed-x-precision");
1801 CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
1802 CTYPE ("Preprocessor information: use cpp syntax.");
1803 CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
1804 STYPE ("include", opts->include, NULL);
1805 CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1806 STYPE ("define", opts->define, NULL);
1808 CCTYPE ("RUN CONTROL PARAMETERS");
1809 EETYPE("integrator", ir->eI, ei_names);
1810 CTYPE ("Start time and timestep in ps");
1811 RTYPE ("tinit", ir->init_t, 0.0);
1812 RTYPE ("dt", ir->delta_t, 0.001);
1813 STEPTYPE ("nsteps", ir->nsteps, 0);
1814 CTYPE ("For exact run continuation or redoing part of a run");
1815 STEPTYPE ("init-step", ir->init_step, 0);
1816 CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
1817 ITYPE ("simulation-part", ir->simulation_part, 1);
1818 CTYPE ("mode for center of mass motion removal");
1819 EETYPE("comm-mode", ir->comm_mode, ecm_names);
1820 CTYPE ("number of steps for center of mass motion removal");
1821 ITYPE ("nstcomm", ir->nstcomm, 100);
1822 CTYPE ("group(s) for center of mass motion removal");
1823 STYPE ("comm-grps", is->vcm, NULL);
1825 CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
1826 CTYPE ("Friction coefficient (amu/ps) and random seed");
1827 RTYPE ("bd-fric", ir->bd_fric, 0.0);
1828 STEPTYPE ("ld-seed", ir->ld_seed, -1);
1831 CCTYPE ("ENERGY MINIMIZATION OPTIONS");
1832 CTYPE ("Force tolerance and initial step-size");
1833 RTYPE ("emtol", ir->em_tol, 10.0);
1834 RTYPE ("emstep", ir->em_stepsize, 0.01);
1835 CTYPE ("Max number of iterations in relax-shells");
1836 ITYPE ("niter", ir->niter, 20);
1837 CTYPE ("Step size (ps^2) for minimization of flexible constraints");
1838 RTYPE ("fcstep", ir->fc_stepsize, 0);
1839 CTYPE ("Frequency of steepest descents steps when doing CG");
1840 ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
1841 ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
1843 CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
1844 RTYPE ("rtpi", ir->rtpi, 0.05);
1846 /* Output options */
1847 CCTYPE ("OUTPUT CONTROL OPTIONS");
1848 CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
1849 ITYPE ("nstxout", ir->nstxout, 0);
1850 ITYPE ("nstvout", ir->nstvout, 0);
1851 ITYPE ("nstfout", ir->nstfout, 0);
1852 CTYPE ("Output frequency for energies to log file and energy file");
1853 ITYPE ("nstlog", ir->nstlog, 1000);
1854 ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
1855 ITYPE ("nstenergy", ir->nstenergy, 1000);
1856 CTYPE ("Output frequency and precision for .xtc file");
1857 ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
1858 RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
1859 CTYPE ("This selects the subset of atoms for the compressed");
1860 CTYPE ("trajectory file. You can select multiple groups. By");
1861 CTYPE ("default, all atoms will be written.");
1862 STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
1863 CTYPE ("Selection of energy groups");
1864 STYPE ("energygrps", is->energy, NULL);
1866 /* Neighbor searching */
1867 CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
1868 CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1869 EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
1870 CTYPE ("nblist update frequency");
1871 ITYPE ("nstlist", ir->nstlist, 10);
1872 CTYPE ("ns algorithm (simple or grid)");
1873 EETYPE("ns-type", ir->ns_type, ens_names);
1874 CTYPE ("Periodic boundary conditions: xyz, no, xy");
1875 EETYPE("pbc", ir->ePBC, epbc_names);
1876 EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
1877 CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1878 CTYPE ("a value of -1 means: use rlist");
1879 RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
1880 CTYPE ("nblist cut-off");
1881 RTYPE ("rlist", ir->rlist, 1.0);
1882 CTYPE ("long-range cut-off for switched potentials");
1883 RTYPE ("rlistlong", ir->rlistlong, -1);
1884 ITYPE ("nstcalclr", ir->nstcalclr, -1);
1886 /* Electrostatics */
1887 CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
1888 CTYPE ("Method for doing electrostatics");
1889 EETYPE("coulombtype", ir->coulombtype, eel_names);
1890 EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
1891 CTYPE ("cut-off lengths");
1892 RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
1893 RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
1894 CTYPE ("Relative dielectric constant for the medium and the reaction field");
1895 RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
1896 RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
1897 CTYPE ("Method for doing Van der Waals");
1898 EETYPE("vdw-type", ir->vdwtype, evdw_names);
1899 EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
1900 CTYPE ("cut-off lengths");
1901 RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
1902 RTYPE ("rvdw", ir->rvdw, 1.0);
1903 CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
1904 EETYPE("DispCorr", ir->eDispCorr, edispc_names);
1905 CTYPE ("Extension of the potential lookup tables beyond the cut-off");
1906 RTYPE ("table-extension", ir->tabext, 1.0);
1907 CTYPE ("Separate tables between energy group pairs");
1908 STYPE ("energygrp-table", is->egptable, NULL);
1909 CTYPE ("Spacing for the PME/PPPM FFT grid");
1910 RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
1911 CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
1912 ITYPE ("fourier-nx", ir->nkx, 0);
1913 ITYPE ("fourier-ny", ir->nky, 0);
1914 ITYPE ("fourier-nz", ir->nkz, 0);
1915 CTYPE ("EWALD/PME/PPPM parameters");
1916 ITYPE ("pme-order", ir->pme_order, 4);
1917 RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
1918 RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
1919 EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
1920 EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
1921 RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
1923 CCTYPE("IMPLICIT SOLVENT ALGORITHM");
1924 EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
1926 CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
1927 CTYPE ("Algorithm for calculating Born radii");
1928 EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
1929 CTYPE ("Frequency of calculating the Born radii inside rlist");
1930 ITYPE ("nstgbradii", ir->nstgbradii, 1);
1931 CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
1932 CTYPE ("between rlist and rgbradii is updated every nstlist steps");
1933 RTYPE ("rgbradii", ir->rgbradii, 1.0);
1934 CTYPE ("Dielectric coefficient of the implicit solvent");
1935 RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
1936 CTYPE ("Salt concentration in M for Generalized Born models");
1937 RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
1938 CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
1939 RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
1940 RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
1941 RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
1942 RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
1943 EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
1944 CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
1945 CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
1946 RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
1948 /* Coupling stuff */
1949 CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
1950 CTYPE ("Temperature coupling");
1951 EETYPE("tcoupl", ir->etc, etcoupl_names);
1952 ITYPE ("nsttcouple", ir->nsttcouple, -1);
1953 ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
1954 EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
1955 CTYPE ("Groups to couple separately");
1956 STYPE ("tc-grps", is->tcgrps, NULL);
1957 CTYPE ("Time constant (ps) and reference temperature (K)");
1958 STYPE ("tau-t", is->tau_t, NULL);
1959 STYPE ("ref-t", is->ref_t, NULL);
1960 CTYPE ("pressure coupling");
1961 EETYPE("pcoupl", ir->epc, epcoupl_names);
1962 EETYPE("pcoupltype", ir->epct, epcoupltype_names);
1963 ITYPE ("nstpcouple", ir->nstpcouple, -1);
1964 CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
1965 RTYPE ("tau-p", ir->tau_p, 1.0);
1966 STYPE ("compressibility", dumstr[0], NULL);
1967 STYPE ("ref-p", dumstr[1], NULL);
1968 CTYPE ("Scaling of reference coordinates, No, All or COM");
1969 EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
1972 CCTYPE ("OPTIONS FOR QMMM calculations");
1973 EETYPE("QMMM", ir->bQMMM, yesno_names);
1974 CTYPE ("Groups treated Quantum Mechanically");
1975 STYPE ("QMMM-grps", is->QMMM, NULL);
1976 CTYPE ("QM method");
1977 STYPE("QMmethod", is->QMmethod, NULL);
1978 CTYPE ("QMMM scheme");
1979 EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
1980 CTYPE ("QM basisset");
1981 STYPE("QMbasis", is->QMbasis, NULL);
1982 CTYPE ("QM charge");
1983 STYPE ("QMcharge", is->QMcharge, NULL);
1984 CTYPE ("QM multiplicity");
1985 STYPE ("QMmult", is->QMmult, NULL);
1986 CTYPE ("Surface Hopping");
1987 STYPE ("SH", is->bSH, NULL);
1988 CTYPE ("CAS space options");
1989 STYPE ("CASorbitals", is->CASorbitals, NULL);
1990 STYPE ("CASelectrons", is->CASelectrons, NULL);
1991 STYPE ("SAon", is->SAon, NULL);
1992 STYPE ("SAoff", is->SAoff, NULL);
1993 STYPE ("SAsteps", is->SAsteps, NULL);
1994 CTYPE ("Scale factor for MM charges");
1995 RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
1996 CTYPE ("Optimization of QM subsystem");
1997 STYPE ("bOPT", is->bOPT, NULL);
1998 STYPE ("bTS", is->bTS, NULL);
2000 /* Simulated annealing */
2001 CCTYPE("SIMULATED ANNEALING");
2002 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
2003 STYPE ("annealing", is->anneal, NULL);
2004 CTYPE ("Number of time points to use for specifying annealing in each group");
2005 STYPE ("annealing-npoints", is->anneal_npoints, NULL);
2006 CTYPE ("List of times at the annealing points for each group");
2007 STYPE ("annealing-time", is->anneal_time, NULL);
2008 CTYPE ("Temp. at each annealing point, for each group.");
2009 STYPE ("annealing-temp", is->anneal_temp, NULL);
2012 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
2013 EETYPE("gen-vel", opts->bGenVel, yesno_names);
2014 RTYPE ("gen-temp", opts->tempi, 300.0);
2015 ITYPE ("gen-seed", opts->seed, -1);
2018 CCTYPE ("OPTIONS FOR BONDS");
2019 EETYPE("constraints", opts->nshake, constraints);
2020 CTYPE ("Type of constraint algorithm");
2021 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
2022 CTYPE ("Do not constrain the start configuration");
2023 EETYPE("continuation", ir->bContinuation, yesno_names);
2024 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
2025 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
2026 CTYPE ("Relative tolerance of shake");
2027 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
2028 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
2029 ITYPE ("lincs-order", ir->nProjOrder, 4);
2030 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
2031 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
2032 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
2033 ITYPE ("lincs-iter", ir->nLincsIter, 1);
2034 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
2035 CTYPE ("rotates over more degrees than");
2036 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
2037 CTYPE ("Convert harmonic bonds to morse potentials");
2038 EETYPE("morse", opts->bMorse, yesno_names);
2040 /* Energy group exclusions */
2041 CCTYPE ("ENERGY GROUP EXCLUSIONS");
2042 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
2043 STYPE ("energygrp-excl", is->egpexcl, NULL);
2047 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2048 ITYPE ("nwall", ir->nwall, 0);
2049 EETYPE("wall-type", ir->wall_type, ewt_names);
2050 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
2051 STYPE ("wall-atomtype", is->wall_atomtype, NULL);
2052 STYPE ("wall-density", is->wall_density, NULL);
2053 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
2056 CCTYPE("COM PULLING");
2057 CTYPE("Pull type: no, umbrella, constraint or constant-force");
2058 EETYPE("pull", ir->ePull, epull_names);
2059 if (ir->ePull != epullNO)
2062 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
2065 /* Enforced rotation */
2066 CCTYPE("ENFORCED ROTATION");
2067 CTYPE("Enforced rotation: No or Yes");
2068 EETYPE("rotation", ir->bRot, yesno_names);
2072 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2075 /* Interactive MD */
2077 CCTYPE("Group to display and/or manipulate in interactive MD session");
2078 STYPE ("IMD-group", is->imd_grp, NULL);
2079 if (is->imd_grp[0] != '\0')
2086 CCTYPE("NMR refinement stuff");
2087 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2088 EETYPE("disre", ir->eDisre, edisre_names);
2089 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2090 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2091 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2092 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2093 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2094 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2095 CTYPE ("Output frequency for pair distances to energy file");
2096 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2097 CTYPE ("Orientation restraints: No or Yes");
2098 EETYPE("orire", opts->bOrire, yesno_names);
2099 CTYPE ("Orientation restraints force constant and tau for time averaging");
2100 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2101 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2102 STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
2103 CTYPE ("Output frequency for trace(SD) and S to energy file");
2104 ITYPE ("nstorireout", ir->nstorireout, 100);
2106 /* free energy variables */
2107 CCTYPE ("Free energy variables");
2108 EETYPE("free-energy", ir->efep, efep_names);
2109 STYPE ("couple-moltype", is->couple_moltype, NULL);
2110 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2111 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2112 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2114 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2116 it was not entered */
2117 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2118 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2119 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2120 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
2121 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
2122 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
2123 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
2124 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
2125 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
2126 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
2127 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2128 STYPE ("init-lambda-weights", is->lambda_weights, NULL);
2129 EETYPE("dhdl-print-energy", fep->bPrintEnergy, yesno_names);
2130 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2131 ITYPE ("sc-power", fep->sc_power, 1);
2132 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2133 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2134 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2135 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2136 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2137 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2138 separate_dhdl_file_names);
2139 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2140 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2141 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2143 /* Non-equilibrium MD stuff */
2144 CCTYPE("Non-equilibrium MD stuff");
2145 STYPE ("acc-grps", is->accgrps, NULL);
2146 STYPE ("accelerate", is->acc, NULL);
2147 STYPE ("freezegrps", is->freeze, NULL);
2148 STYPE ("freezedim", is->frdim, NULL);
2149 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2150 STYPE ("deform", is->deform, NULL);
2152 /* simulated tempering variables */
2153 CCTYPE("simulated tempering variables");
2154 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2155 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2156 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2157 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2159 /* expanded ensemble variables */
2160 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2162 read_expandedparams(&ninp, &inp, expand, wi);
2165 /* Electric fields */
2166 CCTYPE("Electric fields");
2167 CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
2168 CTYPE ("and a phase angle (real)");
2169 STYPE ("E-x", is->efield_x, NULL);
2170 STYPE ("E-xt", is->efield_xt, NULL);
2171 STYPE ("E-y", is->efield_y, NULL);
2172 STYPE ("E-yt", is->efield_yt, NULL);
2173 STYPE ("E-z", is->efield_z, NULL);
2174 STYPE ("E-zt", is->efield_zt, NULL);
2176 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2177 CTYPE("Swap positions along direction: no, X, Y, Z");
2178 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2179 if (ir->eSwapCoords != eswapNO)
2182 CTYPE("Swap attempt frequency");
2183 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2184 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2185 STYPE("split-group0", splitgrp0, NULL);
2186 STYPE("split-group1", splitgrp1, NULL);
2187 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2188 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2189 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2191 CTYPE("Group name of ions that can be exchanged with solvent molecules");
2192 STYPE("swap-group", swapgrp, NULL);
2193 CTYPE("Group name of solvent molecules");
2194 STYPE("solvent-group", solgrp, NULL);
2196 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2197 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2198 CTYPE("however, if correctly defined, the ion permeation events are counted per channel");
2199 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2200 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2201 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2202 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2203 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2204 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2206 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2207 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2208 CTYPE("Requested number of anions and cations for each of the two compartments");
2209 CTYPE("-1 means fix the numbers as found in time step 0");
2210 ITYPE("anionsA", ir->swap->nanions[0], -1);
2211 ITYPE("cationsA", ir->swap->ncations[0], -1);
2212 ITYPE("anionsB", ir->swap->nanions[1], -1);
2213 ITYPE("cationsB", ir->swap->ncations[1], -1);
2214 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2215 RTYPE("threshold", ir->swap->threshold, 1.0);
2218 /* AdResS defined thingies */
2219 CCTYPE ("AdResS parameters");
2220 EETYPE("adress", ir->bAdress, yesno_names);
2223 snew(ir->adress, 1);
2224 read_adressparams(&ninp, &inp, ir->adress, wi);
2227 /* User defined thingies */
2228 CCTYPE ("User defined thingies");
2229 STYPE ("user1-grps", is->user1, NULL);
2230 STYPE ("user2-grps", is->user2, NULL);
2231 ITYPE ("userint1", ir->userint1, 0);
2232 ITYPE ("userint2", ir->userint2, 0);
2233 ITYPE ("userint3", ir->userint3, 0);
2234 ITYPE ("userint4", ir->userint4, 0);
2235 RTYPE ("userreal1", ir->userreal1, 0);
2236 RTYPE ("userreal2", ir->userreal2, 0);
2237 RTYPE ("userreal3", ir->userreal3, 0);
2238 RTYPE ("userreal4", ir->userreal4, 0);
2241 write_inpfile(mdparout, ninp, inp, FALSE, wi);
2242 for (i = 0; (i < ninp); i++)
2245 sfree(inp[i].value);
2249 /* Process options if necessary */
2250 for (m = 0; m < 2; m++)
2252 for (i = 0; i < 2*DIM; i++)
2261 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2263 warning_error(wi, "Pressure coupling not enough values (I need 1)");
2265 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2267 case epctSEMIISOTROPIC:
2268 case epctSURFACETENSION:
2269 if (sscanf(dumstr[m], "%lf%lf",
2270 &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2272 warning_error(wi, "Pressure coupling not enough values (I need 2)");
2274 dumdub[m][YY] = dumdub[m][XX];
2276 case epctANISOTROPIC:
2277 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2278 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2279 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2281 warning_error(wi, "Pressure coupling not enough values (I need 6)");
2285 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2286 epcoupltype_names[ir->epct]);
2290 clear_mat(ir->ref_p);
2291 clear_mat(ir->compress);
2292 for (i = 0; i < DIM; i++)
2294 ir->ref_p[i][i] = dumdub[1][i];
2295 ir->compress[i][i] = dumdub[0][i];
2297 if (ir->epct == epctANISOTROPIC)
2299 ir->ref_p[XX][YY] = dumdub[1][3];
2300 ir->ref_p[XX][ZZ] = dumdub[1][4];
2301 ir->ref_p[YY][ZZ] = dumdub[1][5];
2302 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2304 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2306 ir->compress[XX][YY] = dumdub[0][3];
2307 ir->compress[XX][ZZ] = dumdub[0][4];
2308 ir->compress[YY][ZZ] = dumdub[0][5];
2309 for (i = 0; i < DIM; i++)
2311 for (m = 0; m < i; m++)
2313 ir->ref_p[i][m] = ir->ref_p[m][i];
2314 ir->compress[i][m] = ir->compress[m][i];
2319 if (ir->comm_mode == ecmNO)
2324 opts->couple_moltype = NULL;
2325 if (strlen(is->couple_moltype) > 0)
2327 if (ir->efep != efepNO)
2329 opts->couple_moltype = strdup(is->couple_moltype);
2330 if (opts->couple_lam0 == opts->couple_lam1)
2332 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2334 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2335 opts->couple_lam1 == ecouplamNONE))
2337 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2342 warning(wi, "Can not couple a molecule with free_energy = no");
2345 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2346 if (ir->efep != efepNO)
2348 if (fep->delta_lambda > 0)
2350 ir->efep = efepSLOWGROWTH;
2356 fep->bPrintEnergy = TRUE;
2357 /* always print out the energy to dhdl if we are doing expanded ensemble, since we need the total energy
2358 if the temperature is changing. */
2361 if ((ir->efep != efepNO) || ir->bSimTemp)
2363 ir->bExpanded = FALSE;
2364 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2366 ir->bExpanded = TRUE;
2368 do_fep_params(ir, is->fep_lambda, is->lambda_weights);
2369 if (ir->bSimTemp) /* done after fep params */
2371 do_simtemp_params(ir);
2376 ir->fepvals->n_lambda = 0;
2379 /* WALL PARAMETERS */
2381 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2383 /* ORIENTATION RESTRAINT PARAMETERS */
2385 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
2387 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2390 /* DEFORMATION PARAMETERS */
2392 clear_mat(ir->deform);
2393 for (i = 0; i < 6; i++)
2397 m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
2398 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2399 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2400 for (i = 0; i < 3; i++)
2402 ir->deform[i][i] = dumdub[0][i];
2404 ir->deform[YY][XX] = dumdub[0][3];
2405 ir->deform[ZZ][XX] = dumdub[0][4];
2406 ir->deform[ZZ][YY] = dumdub[0][5];
2407 if (ir->epc != epcNO)
2409 for (i = 0; i < 3; i++)
2411 for (j = 0; j <= i; j++)
2413 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2415 warning_error(wi, "A box element has deform set and compressibility > 0");
2419 for (i = 0; i < 3; i++)
2421 for (j = 0; j < i; j++)
2423 if (ir->deform[i][j] != 0)
2425 for (m = j; m < DIM; m++)
2427 if (ir->compress[m][j] != 0)
2429 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.");
2430 warning(wi, warn_buf);
2438 /* Ion/water position swapping checks */
2439 if (ir->eSwapCoords != eswapNO)
2441 if (ir->swap->nstswap < 1)
2443 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2445 if (ir->swap->nAverage < 1)
2447 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2449 if (ir->swap->threshold < 1.0)
2451 warning_error(wi, "Ion count threshold must be at least 1.\n");
2459 static int search_QMstring(const char *s, int ng, const char *gn[])
2461 /* same as normal search_string, but this one searches QM strings */
2464 for (i = 0; (i < ng); i++)
2466 if (gmx_strcasecmp(s, gn[i]) == 0)
2472 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2476 } /* search_QMstring */
2478 /* We would like gn to be const as well, but C doesn't allow this */
2479 int search_string(const char *s, int ng, char *gn[])
2483 for (i = 0; (i < ng); i++)
2485 if (gmx_strcasecmp(s, gn[i]) == 0)
2492 "Group %s referenced in the .mdp file was not found in the index file.\n"
2493 "Group names must match either [moleculetype] names or custom index group\n"
2494 "names, in which case you must supply an index file to the '-n' option\n"
2501 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2502 t_blocka *block, char *gnames[],
2503 int gtype, int restnm,
2504 int grptp, gmx_bool bVerbose,
2507 unsigned short *cbuf;
2508 t_grps *grps = &(groups->grps[gtype]);
2509 int i, j, gid, aj, ognr, ntot = 0;
2512 char warn_buf[STRLEN];
2516 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2519 title = gtypes[gtype];
2522 /* Mark all id's as not set */
2523 for (i = 0; (i < natoms); i++)
2528 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2529 for (i = 0; (i < ng); i++)
2531 /* Lookup the group name in the block structure */
2532 gid = search_string(ptrs[i], block->nr, gnames);
2533 if ((grptp != egrptpONE) || (i == 0))
2535 grps->nm_ind[grps->nr++] = gid;
2539 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2542 /* Now go over the atoms in the group */
2543 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2548 /* Range checking */
2549 if ((aj < 0) || (aj >= natoms))
2551 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2553 /* Lookup up the old group number */
2557 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2558 aj+1, title, ognr+1, i+1);
2562 /* Store the group number in buffer */
2563 if (grptp == egrptpONE)
2576 /* Now check whether we have done all atoms */
2580 if (grptp == egrptpALL)
2582 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2583 natoms-ntot, title);
2585 else if (grptp == egrptpPART)
2587 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2588 natoms-ntot, title);
2589 warning_note(wi, warn_buf);
2591 /* Assign all atoms currently unassigned to a rest group */
2592 for (j = 0; (j < natoms); j++)
2594 if (cbuf[j] == NOGID)
2600 if (grptp != egrptpPART)
2605 "Making dummy/rest group for %s containing %d elements\n",
2606 title, natoms-ntot);
2608 /* Add group name "rest" */
2609 grps->nm_ind[grps->nr] = restnm;
2611 /* Assign the rest name to all atoms not currently assigned to a group */
2612 for (j = 0; (j < natoms); j++)
2614 if (cbuf[j] == NOGID)
2623 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2625 /* All atoms are part of one (or no) group, no index required */
2626 groups->ngrpnr[gtype] = 0;
2627 groups->grpnr[gtype] = NULL;
2631 groups->ngrpnr[gtype] = natoms;
2632 snew(groups->grpnr[gtype], natoms);
2633 for (j = 0; (j < natoms); j++)
2635 groups->grpnr[gtype][j] = cbuf[j];
2641 return (bRest && grptp == egrptpPART);
2644 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2647 gmx_groups_t *groups;
2649 int natoms, ai, aj, i, j, d, g, imin, jmin;
2651 int *nrdf2, *na_vcm, na_tot;
2652 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2653 gmx_mtop_atomloop_all_t aloop;
2655 int mb, mol, ftype, as;
2656 gmx_molblock_t *molb;
2657 gmx_moltype_t *molt;
2660 * First calc 3xnr-atoms for each group
2661 * then subtract half a degree of freedom for each constraint
2663 * Only atoms and nuclei contribute to the degrees of freedom...
2668 groups = &mtop->groups;
2669 natoms = mtop->natoms;
2671 /* Allocate one more for a possible rest group */
2672 /* We need to sum degrees of freedom into doubles,
2673 * since floats give too low nrdf's above 3 million atoms.
2675 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2676 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2677 snew(na_vcm, groups->grps[egcVCM].nr+1);
2679 for (i = 0; i < groups->grps[egcTC].nr; i++)
2683 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2688 snew(nrdf2, natoms);
2689 aloop = gmx_mtop_atomloop_all_init(mtop);
2690 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2693 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2695 g = ggrpnr(groups, egcFREEZE, i);
2696 /* Double count nrdf for particle i */
2697 for (d = 0; d < DIM; d++)
2699 if (opts->nFreeze[g][d] == 0)
2704 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2705 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2710 for (mb = 0; mb < mtop->nmolblock; mb++)
2712 molb = &mtop->molblock[mb];
2713 molt = &mtop->moltype[molb->type];
2714 atom = molt->atoms.atom;
2715 for (mol = 0; mol < molb->nmol; mol++)
2717 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2719 ia = molt->ilist[ftype].iatoms;
2720 for (i = 0; i < molt->ilist[ftype].nr; )
2722 /* Subtract degrees of freedom for the constraints,
2723 * if the particles still have degrees of freedom left.
2724 * If one of the particles is a vsite or a shell, then all
2725 * constraint motion will go there, but since they do not
2726 * contribute to the constraints the degrees of freedom do not
2731 if (((atom[ia[1]].ptype == eptNucleus) ||
2732 (atom[ia[1]].ptype == eptAtom)) &&
2733 ((atom[ia[2]].ptype == eptNucleus) ||
2734 (atom[ia[2]].ptype == eptAtom)))
2752 imin = min(imin, nrdf2[ai]);
2753 jmin = min(jmin, nrdf2[aj]);
2756 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2757 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2758 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2759 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2761 ia += interaction_function[ftype].nratoms+1;
2762 i += interaction_function[ftype].nratoms+1;
2765 ia = molt->ilist[F_SETTLE].iatoms;
2766 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2768 /* Subtract 1 dof from every atom in the SETTLE */
2769 for (j = 0; j < 3; j++)
2772 imin = min(2, nrdf2[ai]);
2774 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2775 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2780 as += molt->atoms.nr;
2784 if (ir->ePull == epullCONSTRAINT)
2786 /* Correct nrdf for the COM constraints.
2787 * We correct using the TC and VCM group of the first atom
2788 * in the reference and pull group. If atoms in one pull group
2789 * belong to different TC or VCM groups it is anyhow difficult
2790 * to determine the optimal nrdf assignment.
2794 for (i = 0; i < pull->ncoord; i++)
2798 for (j = 0; j < 2; j++)
2800 const t_pull_group *pgrp;
2802 pgrp = &pull->group[pull->coord[i].group[j]];
2806 /* Subtract 1/2 dof from each group */
2808 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2809 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2810 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2812 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)]]);
2817 /* We need to subtract the whole DOF from group j=1 */
2824 if (ir->nstcomm != 0)
2826 /* Subtract 3 from the number of degrees of freedom in each vcm group
2827 * when com translation is removed and 6 when rotation is removed
2830 switch (ir->comm_mode)
2833 n_sub = ndof_com(ir);
2840 gmx_incons("Checking comm_mode");
2843 for (i = 0; i < groups->grps[egcTC].nr; i++)
2845 /* Count the number of atoms of TC group i for every VCM group */
2846 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2851 for (ai = 0; ai < natoms; ai++)
2853 if (ggrpnr(groups, egcTC, ai) == i)
2855 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2859 /* Correct for VCM removal according to the fraction of each VCM
2860 * group present in this TC group.
2862 nrdf_uc = nrdf_tc[i];
2865 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2869 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2871 if (nrdf_vcm[j] > n_sub)
2873 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2874 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2878 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2879 j, nrdf_vcm[j], nrdf_tc[i]);
2884 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2886 opts->nrdf[i] = nrdf_tc[i];
2887 if (opts->nrdf[i] < 0)
2892 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2893 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
2902 static void decode_cos(char *s, t_cosines *cosine)
2905 char format[STRLEN], f1[STRLEN];
2917 sscanf(t, "%d", &(cosine->n));
2924 snew(cosine->a, cosine->n);
2925 snew(cosine->phi, cosine->n);
2927 sprintf(format, "%%*d");
2928 for (i = 0; (i < cosine->n); i++)
2931 strcat(f1, "%lf%lf");
2932 if (sscanf(t, f1, &a, &phi) < 2)
2934 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
2937 cosine->phi[i] = phi;
2938 strcat(format, "%*lf%*lf");
2945 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
2946 const char *option, const char *val, int flag)
2948 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
2949 * But since this is much larger than STRLEN, such a line can not be parsed.
2950 * The real maximum is the number of names that fit in a string: STRLEN/2.
2952 #define EGP_MAX (STRLEN/2)
2953 int nelem, i, j, k, nr;
2954 char *names[EGP_MAX];
2958 gnames = groups->grpname;
2960 nelem = str_nelem(val, EGP_MAX, names);
2963 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
2965 nr = groups->grps[egcENER].nr;
2967 for (i = 0; i < nelem/2; i++)
2971 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
2977 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
2978 names[2*i], option);
2982 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
2988 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
2989 names[2*i+1], option);
2991 if ((j < nr) && (k < nr))
2993 ir->opts.egp_flags[nr*j+k] |= flag;
2994 ir->opts.egp_flags[nr*k+j] |= flag;
3003 static void make_swap_groups(
3012 int ig = -1, i = 0, j;
3016 /* Just a quick check here, more thorough checks are in mdrun */
3017 if (strcmp(splitg0name, splitg1name) == 0)
3019 gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
3022 /* First get the swap group index atoms */
3023 ig = search_string(swapgname, grps->nr, gnames);
3024 swap->nat = grps->index[ig+1] - grps->index[ig];
3027 fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
3028 snew(swap->ind, swap->nat);
3029 for (i = 0; i < swap->nat; i++)
3031 swap->ind[i] = grps->a[grps->index[ig]+i];
3036 gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
3039 /* Now do so for the split groups */
3040 for (j = 0; j < 2; j++)
3044 splitg = splitg0name;
3048 splitg = splitg1name;
3051 ig = search_string(splitg, grps->nr, gnames);
3052 swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
3053 if (swap->nat_split[j] > 0)
3055 fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
3056 j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
3057 snew(swap->ind_split[j], swap->nat_split[j]);
3058 for (i = 0; i < swap->nat_split[j]; i++)
3060 swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
3065 gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
3069 /* Now get the solvent group index atoms */
3070 ig = search_string(solgname, grps->nr, gnames);
3071 swap->nat_sol = grps->index[ig+1] - grps->index[ig];
3072 if (swap->nat_sol > 0)
3074 fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
3075 snew(swap->ind_sol, swap->nat_sol);
3076 for (i = 0; i < swap->nat_sol; i++)
3078 swap->ind_sol[i] = grps->a[grps->index[ig]+i];
3083 gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
3088 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3093 ig = search_string(IMDgname, grps->nr, gnames);
3094 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3096 if (IMDgroup->nat > 0)
3098 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3099 IMDgname, IMDgroup->nat);
3100 snew(IMDgroup->ind, IMDgroup->nat);
3101 for (i = 0; i < IMDgroup->nat; i++)
3103 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3109 void do_index(const char* mdparin, const char *ndx,
3112 t_inputrec *ir, rvec *v,
3116 gmx_groups_t *groups;
3120 char warnbuf[STRLEN], **gnames;
3121 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3124 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3125 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3126 int i, j, k, restnm;
3128 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3129 int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
3130 nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
3131 char warn_buf[STRLEN];
3135 fprintf(stderr, "processing index file...\n");
3141 snew(grps->index, 1);
3143 atoms_all = gmx_mtop_global_atoms(mtop);
3144 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3145 free_t_atoms(&atoms_all, FALSE);
3149 grps = init_index(ndx, &gnames);
3152 groups = &mtop->groups;
3153 natoms = mtop->natoms;
3154 symtab = &mtop->symtab;
3156 snew(groups->grpname, grps->nr+1);
3158 for (i = 0; (i < grps->nr); i++)
3160 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3162 groups->grpname[i] = put_symtab(symtab, "rest");
3164 srenew(gnames, grps->nr+1);
3165 gnames[restnm] = *(groups->grpname[i]);
3166 groups->ngrpname = grps->nr+1;
3168 set_warning_line(wi, mdparin, -1);
3170 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3171 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3172 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3173 if ((ntau_t != ntcg) || (nref_t != ntcg))
3175 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3176 "%d tau-t values", ntcg, nref_t, ntau_t);
3179 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3180 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3181 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3182 nr = groups->grps[egcTC].nr;
3184 snew(ir->opts.nrdf, nr);
3185 snew(ir->opts.tau_t, nr);
3186 snew(ir->opts.ref_t, nr);
3187 if (ir->eI == eiBD && ir->bd_fric == 0)
3189 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3196 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3200 for (i = 0; (i < nr); i++)
3202 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
3203 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
3205 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3206 warning_error(wi, warn_buf);
3209 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3211 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.");
3214 if (ir->opts.tau_t[i] >= 0)
3216 tau_min = min(tau_min, ir->opts.tau_t[i]);
3219 if (ir->etc != etcNO && ir->nsttcouple == -1)
3221 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3226 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3228 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");
3230 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
3232 if (ir->nstpcouple != ir->nsttcouple)
3234 int mincouple = min(ir->nstpcouple, ir->nsttcouple);
3235 ir->nstpcouple = ir->nsttcouple = mincouple;
3236 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);
3237 warning_note(wi, warn_buf);
3241 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3242 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3244 if (ETC_ANDERSEN(ir->etc))
3246 if (ir->nsttcouple != 1)
3249 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");
3250 warning_note(wi, warn_buf);
3253 nstcmin = tcouple_min_integration_steps(ir->etc);
3256 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
3258 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3259 ETCOUPLTYPE(ir->etc),
3261 ir->nsttcouple*ir->delta_t);
3262 warning(wi, warn_buf);
3265 for (i = 0; (i < nr); i++)
3267 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
3268 if (ir->opts.ref_t[i] < 0)
3270 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3273 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3274 if we are in this conditional) if mc_temp is negative */
3275 if (ir->expandedvals->mc_temp < 0)
3277 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3281 /* Simulated annealing for each group. There are nr groups */
3282 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3283 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3287 if (nSA > 0 && nSA != nr)
3289 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3293 snew(ir->opts.annealing, nr);
3294 snew(ir->opts.anneal_npoints, nr);
3295 snew(ir->opts.anneal_time, nr);
3296 snew(ir->opts.anneal_temp, nr);
3297 for (i = 0; i < nr; i++)
3299 ir->opts.annealing[i] = eannNO;
3300 ir->opts.anneal_npoints[i] = 0;
3301 ir->opts.anneal_time[i] = NULL;
3302 ir->opts.anneal_temp[i] = NULL;
3307 for (i = 0; i < nr; i++)
3309 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3311 ir->opts.annealing[i] = eannNO;
3313 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3315 ir->opts.annealing[i] = eannSINGLE;
3318 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3320 ir->opts.annealing[i] = eannPERIODIC;
3326 /* Read the other fields too */
3327 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3328 if (nSA_points != nSA)
3330 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3332 for (k = 0, i = 0; i < nr; i++)
3334 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3335 if (ir->opts.anneal_npoints[i] == 1)
3337 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3339 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3340 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3341 k += ir->opts.anneal_npoints[i];
3344 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3347 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3349 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3352 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3355 for (i = 0, k = 0; i < nr; i++)
3358 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3360 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3361 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3364 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3366 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3372 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3374 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3375 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3378 if (ir->opts.anneal_temp[i][j] < 0)
3380 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3385 /* Print out some summary information, to make sure we got it right */
3386 for (i = 0, k = 0; i < nr; i++)
3388 if (ir->opts.annealing[i] != eannNO)
3390 j = groups->grps[egcTC].nm_ind[i];
3391 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3392 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3393 ir->opts.anneal_npoints[i]);
3394 fprintf(stderr, "Time (ps) Temperature (K)\n");
3395 /* All terms except the last one */
3396 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3398 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3401 /* Finally the last one */
3402 j = ir->opts.anneal_npoints[i]-1;
3403 if (ir->opts.annealing[i] == eannSINGLE)
3405 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3409 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3410 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3412 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3421 if (ir->ePull != epullNO)
3423 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3425 make_pull_coords(ir->pull);
3430 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3433 if (ir->eSwapCoords != eswapNO)
3435 make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
3438 /* Make indices for IMD session */
3441 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3444 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3445 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3446 if (nacg*DIM != nacc)
3448 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3451 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3452 restnm, egrptpALL_GENREST, bVerbose, wi);
3453 nr = groups->grps[egcACC].nr;
3454 snew(ir->opts.acc, nr);
3455 ir->opts.ngacc = nr;
3457 for (i = k = 0; (i < nacg); i++)
3459 for (j = 0; (j < DIM); j++, k++)
3461 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3464 for (; (i < nr); i++)
3466 for (j = 0; (j < DIM); j++)
3468 ir->opts.acc[i][j] = 0;
3472 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3473 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3474 if (nfrdim != DIM*nfreeze)
3476 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3479 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3480 restnm, egrptpALL_GENREST, bVerbose, wi);
3481 nr = groups->grps[egcFREEZE].nr;
3482 ir->opts.ngfrz = nr;
3483 snew(ir->opts.nFreeze, nr);
3484 for (i = k = 0; (i < nfreeze); i++)
3486 for (j = 0; (j < DIM); j++, k++)
3488 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3489 if (!ir->opts.nFreeze[i][j])
3491 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3493 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3494 "(not %s)", ptr1[k]);
3495 warning(wi, warn_buf);
3500 for (; (i < nr); i++)
3502 for (j = 0; (j < DIM); j++)
3504 ir->opts.nFreeze[i][j] = 0;
3508 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3509 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3510 restnm, egrptpALL_GENREST, bVerbose, wi);
3511 add_wall_energrps(groups, ir->nwall, symtab);
3512 ir->opts.ngener = groups->grps[egcENER].nr;
3513 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3515 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3516 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3519 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3520 "This may lead to artifacts.\n"
3521 "In most cases one should use one group for the whole system.");
3524 /* Now we have filled the freeze struct, so we can calculate NRDF */
3525 calc_nrdf(mtop, ir, gnames);
3531 /* Must check per group! */
3532 for (i = 0; (i < ir->opts.ngtc); i++)
3534 ntot += ir->opts.nrdf[i];
3536 if (ntot != (DIM*natoms))
3538 fac = sqrt(ntot/(DIM*natoms));
3541 fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
3542 "and removal of center of mass motion\n", fac);
3544 for (i = 0; (i < natoms); i++)
3546 svmul(fac, v[i], v[i]);
3551 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3552 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3553 restnm, egrptpALL_GENREST, bVerbose, wi);
3554 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3555 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3556 restnm, egrptpALL_GENREST, bVerbose, wi);
3557 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3558 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3559 restnm, egrptpONE, bVerbose, wi);
3560 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3561 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3562 restnm, egrptpALL_GENREST, bVerbose, wi);
3564 /* QMMM input processing */
3565 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3566 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3567 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3568 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3570 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3571 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3573 /* group rest, if any, is always MM! */
3574 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3575 restnm, egrptpALL_GENREST, bVerbose, wi);
3576 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3577 ir->opts.ngQM = nQMg;
3578 snew(ir->opts.QMmethod, nr);
3579 snew(ir->opts.QMbasis, nr);
3580 for (i = 0; i < nr; i++)
3582 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3583 * converted to the corresponding enum in names.c
3585 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3587 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3591 nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
3592 nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
3593 nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
3594 snew(ir->opts.QMmult, nr);
3595 snew(ir->opts.QMcharge, nr);
3596 snew(ir->opts.bSH, nr);
3598 for (i = 0; i < nr; i++)
3600 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3601 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3602 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3605 nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
3606 nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
3607 snew(ir->opts.CASelectrons, nr);
3608 snew(ir->opts.CASorbitals, nr);
3609 for (i = 0; i < nr; i++)
3611 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3612 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3614 /* special optimization options */
3616 nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
3617 nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
3618 snew(ir->opts.bOPT, nr);
3619 snew(ir->opts.bTS, nr);
3620 for (i = 0; i < nr; i++)
3622 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3623 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3625 nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
3626 nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
3627 nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
3628 snew(ir->opts.SAon, nr);
3629 snew(ir->opts.SAoff, nr);
3630 snew(ir->opts.SAsteps, nr);
3632 for (i = 0; i < nr; i++)
3634 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3635 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3636 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3638 /* end of QMMM input */
3642 for (i = 0; (i < egcNR); i++)
3644 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3645 for (j = 0; (j < groups->grps[i].nr); j++)
3647 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3649 fprintf(stderr, "\n");
3653 nr = groups->grps[egcENER].nr;
3654 snew(ir->opts.egp_flags, nr*nr);
3656 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3657 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3659 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3661 if (bExcl && EEL_FULL(ir->coulombtype))
3663 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3666 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3667 if (bTable && !(ir->vdwtype == evdwUSER) &&
3668 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3669 !(ir->coulombtype == eelPMEUSERSWITCH))
3671 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3674 decode_cos(is->efield_x, &(ir->ex[XX]));
3675 decode_cos(is->efield_xt, &(ir->et[XX]));
3676 decode_cos(is->efield_y, &(ir->ex[YY]));
3677 decode_cos(is->efield_yt, &(ir->et[YY]));
3678 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3679 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3683 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3686 for (i = 0; (i < grps->nr); i++)
3698 static void check_disre(gmx_mtop_t *mtop)
3700 gmx_ffparams_t *ffparams;
3701 t_functype *functype;
3703 int i, ndouble, ftype;
3704 int label, old_label;
3706 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3708 ffparams = &mtop->ffparams;
3709 functype = ffparams->functype;
3710 ip = ffparams->iparams;
3713 for (i = 0; i < ffparams->ntypes; i++)
3715 ftype = functype[i];
3716 if (ftype == F_DISRES)
3718 label = ip[i].disres.label;
3719 if (label == old_label)
3721 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3729 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3730 "probably the parameters for multiple pairs in one restraint "
3731 "are not identical\n", ndouble);
3736 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3737 gmx_bool posres_only,
3741 gmx_mtop_ilistloop_t iloop;
3751 for (d = 0; d < DIM; d++)
3753 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3755 /* Check for freeze groups */
3756 for (g = 0; g < ir->opts.ngfrz; g++)
3758 for (d = 0; d < DIM; d++)
3760 if (ir->opts.nFreeze[g][d] != 0)
3768 /* Check for position restraints */
3769 iloop = gmx_mtop_ilistloop_init(sys);
3770 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3773 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3775 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3777 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3778 for (d = 0; d < DIM; d++)
3780 if (pr->posres.fcA[d] != 0)
3786 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3788 /* Check for flat-bottom posres */
3789 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3790 if (pr->fbposres.k != 0)
3792 switch (pr->fbposres.geom)
3794 case efbposresSPHERE:
3795 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3797 case efbposresCYLINDER:
3798 AbsRef[XX] = AbsRef[YY] = 1;
3800 case efbposresX: /* d=XX */
3801 case efbposresY: /* d=YY */
3802 case efbposresZ: /* d=ZZ */
3803 d = pr->fbposres.geom - efbposresX;
3807 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3808 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3816 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3820 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3821 gmx_bool *bC6ParametersWorkWithGeometricRules,
3822 gmx_bool *bC6ParametersWorkWithLBRules,
3823 gmx_bool *bLBRulesPossible)
3825 int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
3828 double geometricdiff, LBdiff;
3829 double c6i, c6j, c12i, c12j;
3830 double c6, c6_geometric, c6_LB;
3831 double sigmai, sigmaj, epsi, epsj;
3832 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3835 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3836 * force-field floating point parameters.
3839 ptr = getenv("GMX_LJCOMB_TOL");
3844 sscanf(ptr, "%lf", &dbl);
3848 *bC6ParametersWorkWithLBRules = TRUE;
3849 *bC6ParametersWorkWithGeometricRules = TRUE;
3850 bCanDoLBRules = TRUE;
3851 bCanDoGeometricRules = TRUE;
3852 ntypes = mtop->ffparams.atnr;
3853 snew(typecount, ntypes);
3854 gmx_mtop_count_atomtypes(mtop, state, typecount);
3855 geometricdiff = LBdiff = 0.0;
3856 *bLBRulesPossible = TRUE;
3857 for (tpi = 0; tpi < ntypes; ++tpi)
3859 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3860 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3861 for (tpj = tpi; tpj < ntypes; ++tpj)
3863 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3864 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3865 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3866 c6_geometric = sqrt(c6i * c6j);
3867 if (!gmx_numzero(c6_geometric))
3869 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3871 sigmai = pow(c12i / c6i, 1.0/6.0);
3872 sigmaj = pow(c12j / c6j, 1.0/6.0);
3873 epsi = c6i * c6i /(4.0 * c12i);
3874 epsj = c6j * c6j /(4.0 * c12j);
3875 c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
3879 *bLBRulesPossible = FALSE;
3880 c6_LB = c6_geometric;
3882 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3885 if (FALSE == bCanDoLBRules)
3887 *bC6ParametersWorkWithLBRules = FALSE;
3890 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3892 if (FALSE == bCanDoGeometricRules)
3894 *bC6ParametersWorkWithGeometricRules = FALSE;
3902 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3906 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3908 check_combination_rule_differences(mtop, 0,
3909 &bC6ParametersWorkWithGeometricRules,
3910 &bC6ParametersWorkWithLBRules,
3912 if (ir->ljpme_combination_rule == eljpmeLB)
3914 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
3916 warning(wi, "You are using arithmetic-geometric combination rules "
3917 "in LJ-PME, but your non-bonded C6 parameters do not "
3918 "follow these rules.");
3923 if (FALSE == bC6ParametersWorkWithGeometricRules)
3925 if (ir->eDispCorr != edispcNO)
3927 warning_note(wi, "You are using geometric combination rules in "
3928 "LJ-PME, but your non-bonded C6 parameters do "
3929 "not follow these rules. "
3930 "This will introduce very small errors in the forces and energies in "
3931 "your simulations. Dispersion correction will correct total energy "
3932 "and/or pressure for isotropic systems, but not forces or surface tensions.");
3936 warning_note(wi, "You are using geometric combination rules in "
3937 "LJ-PME, but your non-bonded C6 parameters do "
3938 "not follow these rules. "
3939 "This will introduce very small errors in the forces and energies in "
3940 "your simulations. If your system is homogeneous, consider using dispersion correction "
3941 "for the total energy and pressure.");
3947 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
3950 char err_buf[STRLEN];
3951 int i, m, c, nmol, npct;
3952 gmx_bool bCharge, bAcc;
3953 real gdt_max, *mgrp, mt;
3955 gmx_mtop_atomloop_block_t aloopb;
3956 gmx_mtop_atomloop_all_t aloop;
3959 char warn_buf[STRLEN];
3961 set_warning_line(wi, mdparin, -1);
3963 if (ir->cutoff_scheme == ecutsVERLET &&
3964 ir->verletbuf_tol > 0 &&
3966 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
3967 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
3969 /* Check if a too small Verlet buffer might potentially
3970 * cause more drift than the thermostat can couple off.
3972 /* Temperature error fraction for warning and suggestion */
3973 const real T_error_warn = 0.002;
3974 const real T_error_suggest = 0.001;
3975 /* For safety: 2 DOF per atom (typical with constraints) */
3976 const real nrdf_at = 2;
3977 real T, tau, max_T_error;
3982 for (i = 0; i < ir->opts.ngtc; i++)
3984 T = max(T, ir->opts.ref_t[i]);
3985 tau = max(tau, ir->opts.tau_t[i]);
3989 /* This is a worst case estimate of the temperature error,
3990 * assuming perfect buffer estimation and no cancelation
3991 * of errors. The factor 0.5 is because energy distributes
3992 * equally over Ekin and Epot.
3994 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
3995 if (max_T_error > T_error_warn)
3997 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.",
3998 ir->verletbuf_tol, T, tau,
4000 100*T_error_suggest,
4001 ir->verletbuf_tol*T_error_suggest/max_T_error);
4002 warning(wi, warn_buf);
4007 if (ETC_ANDERSEN(ir->etc))
4011 for (i = 0; i < ir->opts.ngtc; i++)
4013 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4014 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4015 sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
4016 i, ir->opts.tau_t[i]);
4017 CHECK(ir->opts.tau_t[i] < 0);
4020 for (i = 0; i < ir->opts.ngtc; i++)
4022 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
4023 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);
4024 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
4028 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4029 ir->comm_mode == ecmNO &&
4030 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4031 !ETC_ANDERSEN(ir->etc))
4033 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");
4036 /* Check for pressure coupling with absolute position restraints */
4037 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4039 absolute_reference(ir, sys, TRUE, AbsRef);
4041 for (m = 0; m < DIM; m++)
4043 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4045 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4053 aloopb = gmx_mtop_atomloop_block_init(sys);
4054 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4056 if (atom->q != 0 || atom->qB != 0)
4064 if (EEL_FULL(ir->coulombtype))
4067 "You are using full electrostatics treatment %s for a system without charges.\n"
4068 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4069 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4070 warning(wi, err_buf);
4075 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4078 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4079 "You might want to consider using %s electrostatics.\n",
4081 warning_note(wi, err_buf);
4085 /* Check if combination rules used in LJ-PME are the same as in the force field */
4086 if (EVDW_PME(ir->vdwtype))
4088 check_combination_rules(ir, sys, wi);
4091 /* Generalized reaction field */
4092 if (ir->opts.ngtc == 0)
4094 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4096 CHECK(ir->coulombtype == eelGRF);
4100 sprintf(err_buf, "When using coulombtype = %s"
4101 " ref-t for temperature coupling should be > 0",
4103 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4106 if (ir->eI == eiSD1 &&
4107 (gmx_mtop_ftype_count(sys, F_CONSTR) > 0 ||
4108 gmx_mtop_ftype_count(sys, F_SETTLE) > 0))
4110 sprintf(warn_buf, "With constraints integrator %s is less accurate, consider using %s instead", ei_names[ir->eI], ei_names[eiSD2]);
4111 warning_note(wi, warn_buf);
4115 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4117 for (m = 0; (m < DIM); m++)
4119 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4128 snew(mgrp, sys->groups.grps[egcACC].nr);
4129 aloop = gmx_mtop_atomloop_all_init(sys);
4130 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4132 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4135 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4137 for (m = 0; (m < DIM); m++)
4139 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4143 for (m = 0; (m < DIM); m++)
4145 if (fabs(acc[m]) > 1e-6)
4147 const char *dim[DIM] = { "X", "Y", "Z" };
4149 "Net Acceleration in %s direction, will %s be corrected\n",
4150 dim[m], ir->nstcomm != 0 ? "" : "not");
4151 if (ir->nstcomm != 0 && m < ndof_com(ir))
4154 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4156 ir->opts.acc[i][m] -= acc[m];
4164 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4165 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4167 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4170 if (ir->ePull != epullNO)
4172 gmx_bool bPullAbsoluteRef;
4174 bPullAbsoluteRef = FALSE;
4175 for (i = 0; i < ir->pull->ncoord; i++)
4177 bPullAbsoluteRef = bPullAbsoluteRef ||
4178 ir->pull->coord[i].group[0] == 0 ||
4179 ir->pull->coord[i].group[1] == 0;
4181 if (bPullAbsoluteRef)
4183 absolute_reference(ir, sys, FALSE, AbsRef);
4184 for (m = 0; m < DIM; m++)
4186 if (ir->pull->dim[m] && !AbsRef[m])
4188 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.");
4194 if (ir->pull->eGeom == epullgDIRPBC)
4196 for (i = 0; i < 3; i++)
4198 for (m = 0; m <= i; m++)
4200 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4201 ir->deform[i][m] != 0)
4203 for (c = 0; c < ir->pull->ncoord; c++)
4205 if (ir->pull->coord[c].vec[m] != 0)
4207 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->eGeom), 'x'+m);
4219 void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr, warninp_t wi)
4223 char warn_buf[STRLEN];
4226 ptr = check_box(ir->ePBC, box);
4229 warning_error(wi, ptr);
4232 if (bConstr && ir->eConstrAlg == econtSHAKE)
4234 if (ir->shake_tol <= 0.0)
4236 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4238 warning_error(wi, warn_buf);
4241 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
4243 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
4244 if (ir->epc == epcNO)
4246 warning(wi, warn_buf);
4250 warning_error(wi, warn_buf);
4255 if ( (ir->eConstrAlg == econtLINCS) && bConstr)
4257 /* If we have Lincs constraints: */
4258 if (ir->eI == eiMD && ir->etc == etcNO &&
4259 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4261 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4262 warning_note(wi, warn_buf);
4265 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4267 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4268 warning_note(wi, warn_buf);
4270 if (ir->epc == epcMTTK)
4272 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4276 if (bConstr && ir->epc == epcMTTK)
4278 warning_note(wi, "MTTK with constraints is deprecated, and will be removed in GROMACS 5.1");
4281 if (ir->LincsWarnAngle > 90.0)
4283 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4284 warning(wi, warn_buf);
4285 ir->LincsWarnAngle = 90.0;
4288 if (ir->ePBC != epbcNONE)
4290 if (ir->nstlist == 0)
4292 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4294 bTWIN = (ir->rlistlong > ir->rlist);
4295 if (ir->ns_type == ensGRID)
4297 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
4299 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",
4300 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
4301 warning_error(wi, warn_buf);
4306 min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
4307 if (2*ir->rlistlong >= min_size)
4309 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4310 warning_error(wi, warn_buf);
4313 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4320 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4324 real rvdw1, rvdw2, rcoul1, rcoul2;
4325 char warn_buf[STRLEN];
4327 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4331 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4336 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4342 if (rvdw1 + rvdw2 > ir->rlist ||
4343 rcoul1 + rcoul2 > ir->rlist)
4346 "The sum of the two largest charge group radii (%f) "
4347 "is larger than rlist (%f)\n",
4348 max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4349 warning(wi, warn_buf);
4353 /* Here we do not use the zero at cut-off macro,
4354 * since user defined interactions might purposely
4355 * not be zero at the cut-off.
4357 if (ir_vdw_is_zero_at_cutoff(ir) &&
4358 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
4360 sprintf(warn_buf, "The sum of the two largest charge group "
4361 "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
4362 "With exact cut-offs, better performance can be "
4363 "obtained with cutoff-scheme = %s, because it "
4364 "does not use charge groups at all.",
4366 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4367 ir->rlistlong, ir->rvdw,
4368 ecutscheme_names[ecutsVERLET]);
4371 warning(wi, warn_buf);
4375 warning_note(wi, warn_buf);
4378 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4379 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
4381 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
4382 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4384 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4385 ir->rlistlong, ir->rcoulomb,
4386 ecutscheme_names[ecutsVERLET]);
4389 warning(wi, warn_buf);
4393 warning_note(wi, warn_buf);