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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)
1134 "Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier.");
1135 CHECK( ir->coulomb_modifier != eintmodNONE);
1137 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1140 "Explicit switch/shift vdw interactions cannot be used in combination with a secondary vdw-modifier.");
1141 CHECK( ir->vdw_modifier != eintmodNONE);
1144 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1145 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1148 "The switch/shift interaction settings are just for compatibility; you will get better "
1149 "performance from applying potential modifiers to your interactions!\n");
1150 warning_note(wi, warn_buf);
1153 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1155 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1157 real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
1158 sprintf(warn_buf, "The switching range should be 5%% or less (currently %.2f%% using a switching range of %4f-%4f) for accurate electrostatic energies, energy conservation will be good regardless, since ewald_rtol = %g.",
1159 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1160 warning(wi, warn_buf);
1164 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1166 if (ir->rvdw_switch == 0)
1168 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.");
1169 warning(wi, warn_buf);
1173 if (EEL_FULL(ir->coulombtype))
1175 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1176 ir->coulombtype == eelPMEUSERSWITCH)
1178 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1179 eel_names[ir->coulombtype]);
1180 CHECK(ir->rcoulomb > ir->rlist);
1182 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1184 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1187 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
1188 "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
1189 "a potential modifier.", eel_names[ir->coulombtype]);
1190 if (ir->nstcalclr == 1)
1192 CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
1196 CHECK(ir->rcoulomb != ir->rlist);
1202 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1204 if (ir->pme_order < 3)
1206 warning_error(wi, "pme-order can not be smaller than 3");
1210 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1212 if (ir->ewald_geometry == eewg3D)
1214 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1215 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1216 warning(wi, warn_buf);
1218 /* This check avoids extra pbc coding for exclusion corrections */
1219 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1220 CHECK(ir->wall_ewald_zfac < 2);
1223 if (ir_vdw_switched(ir))
1225 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1226 CHECK(ir->rvdw_switch >= ir->rvdw);
1228 if (ir->rvdw_switch < 0.5*ir->rvdw)
1230 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.",
1231 ir->rvdw_switch, ir->rvdw);
1232 warning_note(wi, warn_buf);
1235 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1237 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1239 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1240 CHECK(ir->rlist > ir->rvdw);
1244 if (ir->vdwtype == evdwPME)
1246 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1248 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s a\
1250 evdw_names[ir->vdwtype],
1251 eintmod_names[eintmodPOTSHIFT],
1252 eintmod_names[eintmodNONE]);
1256 if (ir->cutoff_scheme == ecutsGROUP)
1258 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1259 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)) &&
1262 warning_note(wi, "With exact cut-offs, rlist should be "
1263 "larger than rcoulomb and rvdw, so that there "
1264 "is a buffer region for particle motion "
1265 "between neighborsearch steps");
1268 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlistlong <= ir->rcoulomb)
1270 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
1271 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1272 warning_note(wi, warn_buf);
1274 if (ir_vdw_switched(ir) && (ir->rlistlong <= ir->rvdw))
1276 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
1277 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1278 warning_note(wi, warn_buf);
1282 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1284 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.");
1287 if (ir->nstlist == -1)
1289 sprintf(err_buf, "With nstlist=-1 rvdw and rcoulomb should be smaller than rlist to account for diffusion and possibly charge-group radii");
1290 CHECK(ir->rvdw >= ir->rlist || ir->rcoulomb >= ir->rlist);
1292 sprintf(err_buf, "nstlist can not be smaller than -1");
1293 CHECK(ir->nstlist < -1);
1295 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1298 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1301 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1303 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1306 /* ENERGY CONSERVATION */
1307 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1309 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1311 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1312 evdw_names[evdwSHIFT]);
1313 warning_note(wi, warn_buf);
1315 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1317 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1318 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1319 warning_note(wi, warn_buf);
1323 if (EI_VV(ir->eI) && IR_TWINRANGE(*ir) && ir->nstlist > 1)
1325 sprintf(warn_buf, "Twin-range multiple time stepping does not work with integrator %s.", ei_names[ir->eI]);
1326 warning_error(wi, warn_buf);
1329 /* IMPLICIT SOLVENT */
1330 if (ir->coulombtype == eelGB_NOTUSED)
1332 ir->coulombtype = eelCUT;
1333 ir->implicit_solvent = eisGBSA;
1334 fprintf(stderr, "Note: Old option for generalized born electrostatics given:\n"
1335 "Changing coulombtype from \"generalized-born\" to \"cut-off\" and instead\n"
1336 "setting implicit-solvent value to \"GBSA\" in input section.\n");
1339 if (ir->sa_algorithm == esaSTILL)
1341 sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
1342 CHECK(ir->sa_algorithm == esaSTILL);
1345 if (ir->implicit_solvent == eisGBSA)
1347 sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
1348 CHECK(ir->rgbradii != ir->rlist);
1350 if (ir->coulombtype != eelCUT)
1352 sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
1353 CHECK(ir->coulombtype != eelCUT);
1355 if (ir->vdwtype != evdwCUT)
1357 sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
1358 CHECK(ir->vdwtype != evdwCUT);
1360 if (ir->nstgbradii < 1)
1362 sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
1363 warning_note(wi, warn_buf);
1366 if (ir->sa_algorithm == esaNO)
1368 sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
1369 warning_note(wi, warn_buf);
1371 if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
1373 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");
1374 warning_note(wi, warn_buf);
1376 if (ir->gb_algorithm == egbSTILL)
1378 ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
1382 ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
1385 if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
1387 sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
1388 CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
1395 if (ir->cutoff_scheme != ecutsGROUP)
1397 warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
1401 warning_error(wi, "AdresS simulation supports only stochastic dynamics");
1403 if (ir->epc != epcNO)
1405 warning_error(wi, "AdresS simulation does not support pressure coupling");
1407 if (EEL_FULL(ir->coulombtype))
1409 warning_error(wi, "AdresS simulation does not support long-range electrostatics");
1414 /* count the number of text elemets separated by whitespace in a string.
1415 str = the input string
1416 maxptr = the maximum number of allowed elements
1417 ptr = the output array of pointers to the first character of each element
1418 returns: the number of elements. */
1419 int str_nelem(const char *str, int maxptr, char *ptr[])
1424 copy0 = strdup(str);
1427 while (*copy != '\0')
1431 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1439 while ((*copy != '\0') && !isspace(*copy))
1458 /* interpret a number of doubles from a string and put them in an array,
1459 after allocating space for them.
1460 str = the input string
1461 n = the (pre-allocated) number of doubles read
1462 r = the output array of doubles. */
1463 static void parse_n_real(char *str, int *n, real **r)
1468 *n = str_nelem(str, MAXPTR, ptr);
1471 for (i = 0; i < *n; i++)
1473 (*r)[i] = strtod(ptr[i], NULL);
1477 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
1480 int i, j, max_n_lambda, nweights, nfep[efptNR];
1481 t_lambda *fep = ir->fepvals;
1482 t_expanded *expand = ir->expandedvals;
1483 real **count_fep_lambdas;
1484 gmx_bool bOneLambda = TRUE;
1486 snew(count_fep_lambdas, efptNR);
1488 /* FEP input processing */
1489 /* first, identify the number of lambda values for each type.
1490 All that are nonzero must have the same number */
1492 for (i = 0; i < efptNR; i++)
1494 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
1497 /* now, determine the number of components. All must be either zero, or equal. */
1500 for (i = 0; i < efptNR; i++)
1502 if (nfep[i] > max_n_lambda)
1504 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1505 must have the same number if its not zero.*/
1510 for (i = 0; i < efptNR; i++)
1514 ir->fepvals->separate_dvdl[i] = FALSE;
1516 else if (nfep[i] == max_n_lambda)
1518 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1519 respect to the temperature currently */
1521 ir->fepvals->separate_dvdl[i] = TRUE;
1526 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1527 nfep[i], efpt_names[i], max_n_lambda);
1530 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1531 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1533 /* the number of lambdas is the number we've read in, which is either zero
1534 or the same for all */
1535 fep->n_lambda = max_n_lambda;
1537 /* allocate space for the array of lambda values */
1538 snew(fep->all_lambda, efptNR);
1539 /* if init_lambda is defined, we need to set lambda */
1540 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1542 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1544 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1545 for (i = 0; i < efptNR; i++)
1547 snew(fep->all_lambda[i], fep->n_lambda);
1548 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1551 for (j = 0; j < fep->n_lambda; j++)
1553 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1555 sfree(count_fep_lambdas[i]);
1558 sfree(count_fep_lambdas);
1560 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1561 bookkeeping -- for now, init_lambda */
1563 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1565 for (i = 0; i < fep->n_lambda; i++)
1567 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1571 /* check to see if only a single component lambda is defined, and soft core is defined.
1572 In this case, turn on coulomb soft core */
1574 if (max_n_lambda == 0)
1580 for (i = 0; i < efptNR; i++)
1582 if ((nfep[i] != 0) && (i != efptFEP))
1588 if ((bOneLambda) && (fep->sc_alpha > 0))
1590 fep->bScCoul = TRUE;
1593 /* Fill in the others with the efptFEP if they are not explicitly
1594 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1595 they are all zero. */
1597 for (i = 0; i < efptNR; i++)
1599 if ((nfep[i] == 0) && (i != efptFEP))
1601 for (j = 0; j < fep->n_lambda; j++)
1603 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1609 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1610 if (fep->sc_r_power == 48)
1612 if (fep->sc_alpha > 0.1)
1614 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1618 expand = ir->expandedvals;
1619 /* now read in the weights */
1620 parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
1623 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1625 else if (nweights != fep->n_lambda)
1627 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1628 nweights, fep->n_lambda);
1630 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1632 expand->nstexpanded = fep->nstdhdl;
1633 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1635 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1637 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1638 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1639 2*tau_t just to be careful so it's not to frequent */
1644 static void do_simtemp_params(t_inputrec *ir)
1647 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1648 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1653 static void do_wall_params(t_inputrec *ir,
1654 char *wall_atomtype, char *wall_density,
1658 char *names[MAXPTR];
1661 opts->wall_atomtype[0] = NULL;
1662 opts->wall_atomtype[1] = NULL;
1664 ir->wall_atomtype[0] = -1;
1665 ir->wall_atomtype[1] = -1;
1666 ir->wall_density[0] = 0;
1667 ir->wall_density[1] = 0;
1671 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1672 if (nstr != ir->nwall)
1674 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1677 for (i = 0; i < ir->nwall; i++)
1679 opts->wall_atomtype[i] = strdup(names[i]);
1682 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1684 nstr = str_nelem(wall_density, MAXPTR, names);
1685 if (nstr != ir->nwall)
1687 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1689 for (i = 0; i < ir->nwall; i++)
1691 sscanf(names[i], "%lf", &dbl);
1694 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1696 ir->wall_density[i] = dbl;
1702 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1710 srenew(groups->grpname, groups->ngrpname+nwall);
1711 grps = &(groups->grps[egcENER]);
1712 srenew(grps->nm_ind, grps->nr+nwall);
1713 for (i = 0; i < nwall; i++)
1715 sprintf(str, "wall%d", i);
1716 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1717 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1722 void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1723 t_expanded *expand, warninp_t wi)
1725 int ninp, nerror = 0;
1731 /* read expanded ensemble parameters */
1732 CCTYPE ("expanded ensemble variables");
1733 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1734 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1735 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1736 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1737 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1738 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1739 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1740 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1741 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1742 CCTYPE("Seed for Monte Carlo in lambda space");
1743 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1744 RTYPE ("mc-temperature", expand->mc_temp, -1);
1745 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1746 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1747 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1748 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1749 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1750 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1751 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1752 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1753 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1754 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1755 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
1763 void get_ir(const char *mdparin, const char *mdparout,
1764 t_inputrec *ir, t_gromppopts *opts,
1768 double dumdub[2][6];
1772 char warn_buf[STRLEN];
1773 t_lambda *fep = ir->fepvals;
1774 t_expanded *expand = ir->expandedvals;
1776 init_inputrec_strings();
1777 inp = read_inpfile(mdparin, &ninp, wi);
1779 snew(dumstr[0], STRLEN);
1780 snew(dumstr[1], STRLEN);
1782 if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
1785 "%s did not specify a value for the .mdp option "
1786 "\"cutoff-scheme\". Probably it was first intended for use "
1787 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1788 "introduced, but the group scheme was still the default. "
1789 "The default is now the Verlet scheme, so you will observe "
1790 "different behaviour.", mdparin);
1791 warning_note(wi, warn_buf);
1794 /* ignore the following deprecated commands */
1797 REM_TYPE("domain-decomposition");
1798 REM_TYPE("andersen-seed");
1800 REM_TYPE("dihre-fc");
1801 REM_TYPE("dihre-tau");
1802 REM_TYPE("nstdihreout");
1803 REM_TYPE("nstcheckpoint");
1804 REM_TYPE("optimize-fft");
1806 /* replace the following commands with the clearer new versions*/
1807 REPL_TYPE("unconstrained-start", "continuation");
1808 REPL_TYPE("foreign-lambda", "fep-lambdas");
1809 REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
1810 REPL_TYPE("nstxtcout", "nstxout-compressed");
1811 REPL_TYPE("xtc-grps", "compressed-x-grps");
1812 REPL_TYPE("xtc-precision", "compressed-x-precision");
1814 CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
1815 CTYPE ("Preprocessor information: use cpp syntax.");
1816 CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
1817 STYPE ("include", opts->include, NULL);
1818 CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1819 STYPE ("define", opts->define, NULL);
1821 CCTYPE ("RUN CONTROL PARAMETERS");
1822 EETYPE("integrator", ir->eI, ei_names);
1823 CTYPE ("Start time and timestep in ps");
1824 RTYPE ("tinit", ir->init_t, 0.0);
1825 RTYPE ("dt", ir->delta_t, 0.001);
1826 STEPTYPE ("nsteps", ir->nsteps, 0);
1827 CTYPE ("For exact run continuation or redoing part of a run");
1828 STEPTYPE ("init-step", ir->init_step, 0);
1829 CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
1830 ITYPE ("simulation-part", ir->simulation_part, 1);
1831 CTYPE ("mode for center of mass motion removal");
1832 EETYPE("comm-mode", ir->comm_mode, ecm_names);
1833 CTYPE ("number of steps for center of mass motion removal");
1834 ITYPE ("nstcomm", ir->nstcomm, 100);
1835 CTYPE ("group(s) for center of mass motion removal");
1836 STYPE ("comm-grps", is->vcm, NULL);
1838 CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
1839 CTYPE ("Friction coefficient (amu/ps) and random seed");
1840 RTYPE ("bd-fric", ir->bd_fric, 0.0);
1841 STEPTYPE ("ld-seed", ir->ld_seed, -1);
1844 CCTYPE ("ENERGY MINIMIZATION OPTIONS");
1845 CTYPE ("Force tolerance and initial step-size");
1846 RTYPE ("emtol", ir->em_tol, 10.0);
1847 RTYPE ("emstep", ir->em_stepsize, 0.01);
1848 CTYPE ("Max number of iterations in relax-shells");
1849 ITYPE ("niter", ir->niter, 20);
1850 CTYPE ("Step size (ps^2) for minimization of flexible constraints");
1851 RTYPE ("fcstep", ir->fc_stepsize, 0);
1852 CTYPE ("Frequency of steepest descents steps when doing CG");
1853 ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
1854 ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
1856 CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
1857 RTYPE ("rtpi", ir->rtpi, 0.05);
1859 /* Output options */
1860 CCTYPE ("OUTPUT CONTROL OPTIONS");
1861 CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
1862 ITYPE ("nstxout", ir->nstxout, 0);
1863 ITYPE ("nstvout", ir->nstvout, 0);
1864 ITYPE ("nstfout", ir->nstfout, 0);
1865 CTYPE ("Output frequency for energies to log file and energy file");
1866 ITYPE ("nstlog", ir->nstlog, 1000);
1867 ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
1868 ITYPE ("nstenergy", ir->nstenergy, 1000);
1869 CTYPE ("Output frequency and precision for .xtc file");
1870 ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
1871 RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
1872 CTYPE ("This selects the subset of atoms for the compressed");
1873 CTYPE ("trajectory file. You can select multiple groups. By");
1874 CTYPE ("default, all atoms will be written.");
1875 STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
1876 CTYPE ("Selection of energy groups");
1877 STYPE ("energygrps", is->energy, NULL);
1879 /* Neighbor searching */
1880 CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
1881 CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1882 EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
1883 CTYPE ("nblist update frequency");
1884 ITYPE ("nstlist", ir->nstlist, 10);
1885 CTYPE ("ns algorithm (simple or grid)");
1886 EETYPE("ns-type", ir->ns_type, ens_names);
1887 CTYPE ("Periodic boundary conditions: xyz, no, xy");
1888 EETYPE("pbc", ir->ePBC, epbc_names);
1889 EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
1890 CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1891 CTYPE ("a value of -1 means: use rlist");
1892 RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
1893 CTYPE ("nblist cut-off");
1894 RTYPE ("rlist", ir->rlist, 1.0);
1895 CTYPE ("long-range cut-off for switched potentials");
1896 RTYPE ("rlistlong", ir->rlistlong, -1);
1897 ITYPE ("nstcalclr", ir->nstcalclr, -1);
1899 /* Electrostatics */
1900 CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
1901 CTYPE ("Method for doing electrostatics");
1902 EETYPE("coulombtype", ir->coulombtype, eel_names);
1903 EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
1904 CTYPE ("cut-off lengths");
1905 RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
1906 RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
1907 CTYPE ("Relative dielectric constant for the medium and the reaction field");
1908 RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
1909 RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
1910 CTYPE ("Method for doing Van der Waals");
1911 EETYPE("vdw-type", ir->vdwtype, evdw_names);
1912 EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
1913 CTYPE ("cut-off lengths");
1914 RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
1915 RTYPE ("rvdw", ir->rvdw, 1.0);
1916 CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
1917 EETYPE("DispCorr", ir->eDispCorr, edispc_names);
1918 CTYPE ("Extension of the potential lookup tables beyond the cut-off");
1919 RTYPE ("table-extension", ir->tabext, 1.0);
1920 CTYPE ("Separate tables between energy group pairs");
1921 STYPE ("energygrp-table", is->egptable, NULL);
1922 CTYPE ("Spacing for the PME/PPPM FFT grid");
1923 RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
1924 CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
1925 ITYPE ("fourier-nx", ir->nkx, 0);
1926 ITYPE ("fourier-ny", ir->nky, 0);
1927 ITYPE ("fourier-nz", ir->nkz, 0);
1928 CTYPE ("EWALD/PME/PPPM parameters");
1929 ITYPE ("pme-order", ir->pme_order, 4);
1930 RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
1931 RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
1932 EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
1933 EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
1934 RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
1936 CCTYPE("IMPLICIT SOLVENT ALGORITHM");
1937 EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
1939 CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
1940 CTYPE ("Algorithm for calculating Born radii");
1941 EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
1942 CTYPE ("Frequency of calculating the Born radii inside rlist");
1943 ITYPE ("nstgbradii", ir->nstgbradii, 1);
1944 CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
1945 CTYPE ("between rlist and rgbradii is updated every nstlist steps");
1946 RTYPE ("rgbradii", ir->rgbradii, 1.0);
1947 CTYPE ("Dielectric coefficient of the implicit solvent");
1948 RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
1949 CTYPE ("Salt concentration in M for Generalized Born models");
1950 RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
1951 CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
1952 RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
1953 RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
1954 RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
1955 RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
1956 EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
1957 CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
1958 CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
1959 RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
1961 /* Coupling stuff */
1962 CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
1963 CTYPE ("Temperature coupling");
1964 EETYPE("tcoupl", ir->etc, etcoupl_names);
1965 ITYPE ("nsttcouple", ir->nsttcouple, -1);
1966 ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
1967 EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
1968 CTYPE ("Groups to couple separately");
1969 STYPE ("tc-grps", is->tcgrps, NULL);
1970 CTYPE ("Time constant (ps) and reference temperature (K)");
1971 STYPE ("tau-t", is->tau_t, NULL);
1972 STYPE ("ref-t", is->ref_t, NULL);
1973 CTYPE ("pressure coupling");
1974 EETYPE("pcoupl", ir->epc, epcoupl_names);
1975 EETYPE("pcoupltype", ir->epct, epcoupltype_names);
1976 ITYPE ("nstpcouple", ir->nstpcouple, -1);
1977 CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
1978 RTYPE ("tau-p", ir->tau_p, 1.0);
1979 STYPE ("compressibility", dumstr[0], NULL);
1980 STYPE ("ref-p", dumstr[1], NULL);
1981 CTYPE ("Scaling of reference coordinates, No, All or COM");
1982 EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
1985 CCTYPE ("OPTIONS FOR QMMM calculations");
1986 EETYPE("QMMM", ir->bQMMM, yesno_names);
1987 CTYPE ("Groups treated Quantum Mechanically");
1988 STYPE ("QMMM-grps", is->QMMM, NULL);
1989 CTYPE ("QM method");
1990 STYPE("QMmethod", is->QMmethod, NULL);
1991 CTYPE ("QMMM scheme");
1992 EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
1993 CTYPE ("QM basisset");
1994 STYPE("QMbasis", is->QMbasis, NULL);
1995 CTYPE ("QM charge");
1996 STYPE ("QMcharge", is->QMcharge, NULL);
1997 CTYPE ("QM multiplicity");
1998 STYPE ("QMmult", is->QMmult, NULL);
1999 CTYPE ("Surface Hopping");
2000 STYPE ("SH", is->bSH, NULL);
2001 CTYPE ("CAS space options");
2002 STYPE ("CASorbitals", is->CASorbitals, NULL);
2003 STYPE ("CASelectrons", is->CASelectrons, NULL);
2004 STYPE ("SAon", is->SAon, NULL);
2005 STYPE ("SAoff", is->SAoff, NULL);
2006 STYPE ("SAsteps", is->SAsteps, NULL);
2007 CTYPE ("Scale factor for MM charges");
2008 RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
2009 CTYPE ("Optimization of QM subsystem");
2010 STYPE ("bOPT", is->bOPT, NULL);
2011 STYPE ("bTS", is->bTS, NULL);
2013 /* Simulated annealing */
2014 CCTYPE("SIMULATED ANNEALING");
2015 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
2016 STYPE ("annealing", is->anneal, NULL);
2017 CTYPE ("Number of time points to use for specifying annealing in each group");
2018 STYPE ("annealing-npoints", is->anneal_npoints, NULL);
2019 CTYPE ("List of times at the annealing points for each group");
2020 STYPE ("annealing-time", is->anneal_time, NULL);
2021 CTYPE ("Temp. at each annealing point, for each group.");
2022 STYPE ("annealing-temp", is->anneal_temp, NULL);
2025 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
2026 EETYPE("gen-vel", opts->bGenVel, yesno_names);
2027 RTYPE ("gen-temp", opts->tempi, 300.0);
2028 ITYPE ("gen-seed", opts->seed, -1);
2031 CCTYPE ("OPTIONS FOR BONDS");
2032 EETYPE("constraints", opts->nshake, constraints);
2033 CTYPE ("Type of constraint algorithm");
2034 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
2035 CTYPE ("Do not constrain the start configuration");
2036 EETYPE("continuation", ir->bContinuation, yesno_names);
2037 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
2038 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
2039 CTYPE ("Relative tolerance of shake");
2040 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
2041 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
2042 ITYPE ("lincs-order", ir->nProjOrder, 4);
2043 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
2044 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
2045 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
2046 ITYPE ("lincs-iter", ir->nLincsIter, 1);
2047 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
2048 CTYPE ("rotates over more degrees than");
2049 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
2050 CTYPE ("Convert harmonic bonds to morse potentials");
2051 EETYPE("morse", opts->bMorse, yesno_names);
2053 /* Energy group exclusions */
2054 CCTYPE ("ENERGY GROUP EXCLUSIONS");
2055 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
2056 STYPE ("energygrp-excl", is->egpexcl, NULL);
2060 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2061 ITYPE ("nwall", ir->nwall, 0);
2062 EETYPE("wall-type", ir->wall_type, ewt_names);
2063 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
2064 STYPE ("wall-atomtype", is->wall_atomtype, NULL);
2065 STYPE ("wall-density", is->wall_density, NULL);
2066 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
2069 CCTYPE("COM PULLING");
2070 CTYPE("Pull type: no, umbrella, constraint or constant-force");
2071 EETYPE("pull", ir->ePull, epull_names);
2072 if (ir->ePull != epullNO)
2075 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
2078 /* Enforced rotation */
2079 CCTYPE("ENFORCED ROTATION");
2080 CTYPE("Enforced rotation: No or Yes");
2081 EETYPE("rotation", ir->bRot, yesno_names);
2085 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2088 /* Interactive MD */
2090 CCTYPE("Group to display and/or manipulate in interactive MD session");
2091 STYPE ("IMD-group", is->imd_grp, NULL);
2092 if (is->imd_grp[0] != '\0')
2099 CCTYPE("NMR refinement stuff");
2100 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2101 EETYPE("disre", ir->eDisre, edisre_names);
2102 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2103 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2104 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2105 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2106 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2107 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2108 CTYPE ("Output frequency for pair distances to energy file");
2109 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2110 CTYPE ("Orientation restraints: No or Yes");
2111 EETYPE("orire", opts->bOrire, yesno_names);
2112 CTYPE ("Orientation restraints force constant and tau for time averaging");
2113 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2114 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2115 STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
2116 CTYPE ("Output frequency for trace(SD) and S to energy file");
2117 ITYPE ("nstorireout", ir->nstorireout, 100);
2119 /* free energy variables */
2120 CCTYPE ("Free energy variables");
2121 EETYPE("free-energy", ir->efep, efep_names);
2122 STYPE ("couple-moltype", is->couple_moltype, NULL);
2123 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2124 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2125 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2127 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2129 it was not entered */
2130 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2131 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2132 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2133 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
2134 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
2135 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
2136 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
2137 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
2138 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
2139 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
2140 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2141 STYPE ("init-lambda-weights", is->lambda_weights, NULL);
2142 EETYPE("dhdl-print-energy", fep->bPrintEnergy, yesno_names);
2143 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2144 ITYPE ("sc-power", fep->sc_power, 1);
2145 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2146 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2147 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2148 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2149 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2150 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2151 separate_dhdl_file_names);
2152 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2153 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2154 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2156 /* Non-equilibrium MD stuff */
2157 CCTYPE("Non-equilibrium MD stuff");
2158 STYPE ("acc-grps", is->accgrps, NULL);
2159 STYPE ("accelerate", is->acc, NULL);
2160 STYPE ("freezegrps", is->freeze, NULL);
2161 STYPE ("freezedim", is->frdim, NULL);
2162 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2163 STYPE ("deform", is->deform, NULL);
2165 /* simulated tempering variables */
2166 CCTYPE("simulated tempering variables");
2167 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2168 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2169 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2170 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2172 /* expanded ensemble variables */
2173 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2175 read_expandedparams(&ninp, &inp, expand, wi);
2178 /* Electric fields */
2179 CCTYPE("Electric fields");
2180 CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
2181 CTYPE ("and a phase angle (real)");
2182 STYPE ("E-x", is->efield_x, NULL);
2183 STYPE ("E-xt", is->efield_xt, NULL);
2184 STYPE ("E-y", is->efield_y, NULL);
2185 STYPE ("E-yt", is->efield_yt, NULL);
2186 STYPE ("E-z", is->efield_z, NULL);
2187 STYPE ("E-zt", is->efield_zt, NULL);
2189 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2190 CTYPE("Swap positions along direction: no, X, Y, Z");
2191 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2192 if (ir->eSwapCoords != eswapNO)
2195 CTYPE("Swap attempt frequency");
2196 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2197 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2198 STYPE("split-group0", splitgrp0, NULL);
2199 STYPE("split-group1", splitgrp1, NULL);
2200 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2201 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2202 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2204 CTYPE("Group name of ions that can be exchanged with solvent molecules");
2205 STYPE("swap-group", swapgrp, NULL);
2206 CTYPE("Group name of solvent molecules");
2207 STYPE("solvent-group", solgrp, NULL);
2209 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2210 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2211 CTYPE("however, if correctly defined, the ion permeation events are counted per channel");
2212 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2213 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2214 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2215 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2216 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2217 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2219 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2220 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2221 CTYPE("Requested number of anions and cations for each of the two compartments");
2222 CTYPE("-1 means fix the numbers as found in time step 0");
2223 ITYPE("anionsA", ir->swap->nanions[0], -1);
2224 ITYPE("cationsA", ir->swap->ncations[0], -1);
2225 ITYPE("anionsB", ir->swap->nanions[1], -1);
2226 ITYPE("cationsB", ir->swap->ncations[1], -1);
2227 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2228 RTYPE("threshold", ir->swap->threshold, 1.0);
2231 /* AdResS defined thingies */
2232 CCTYPE ("AdResS parameters");
2233 EETYPE("adress", ir->bAdress, yesno_names);
2236 snew(ir->adress, 1);
2237 read_adressparams(&ninp, &inp, ir->adress, wi);
2240 /* User defined thingies */
2241 CCTYPE ("User defined thingies");
2242 STYPE ("user1-grps", is->user1, NULL);
2243 STYPE ("user2-grps", is->user2, NULL);
2244 ITYPE ("userint1", ir->userint1, 0);
2245 ITYPE ("userint2", ir->userint2, 0);
2246 ITYPE ("userint3", ir->userint3, 0);
2247 ITYPE ("userint4", ir->userint4, 0);
2248 RTYPE ("userreal1", ir->userreal1, 0);
2249 RTYPE ("userreal2", ir->userreal2, 0);
2250 RTYPE ("userreal3", ir->userreal3, 0);
2251 RTYPE ("userreal4", ir->userreal4, 0);
2254 write_inpfile(mdparout, ninp, inp, FALSE, wi);
2255 for (i = 0; (i < ninp); i++)
2258 sfree(inp[i].value);
2262 /* Process options if necessary */
2263 for (m = 0; m < 2; m++)
2265 for (i = 0; i < 2*DIM; i++)
2274 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2276 warning_error(wi, "Pressure coupling not enough values (I need 1)");
2278 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2280 case epctSEMIISOTROPIC:
2281 case epctSURFACETENSION:
2282 if (sscanf(dumstr[m], "%lf%lf",
2283 &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2285 warning_error(wi, "Pressure coupling not enough values (I need 2)");
2287 dumdub[m][YY] = dumdub[m][XX];
2289 case epctANISOTROPIC:
2290 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2291 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2292 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2294 warning_error(wi, "Pressure coupling not enough values (I need 6)");
2298 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2299 epcoupltype_names[ir->epct]);
2303 clear_mat(ir->ref_p);
2304 clear_mat(ir->compress);
2305 for (i = 0; i < DIM; i++)
2307 ir->ref_p[i][i] = dumdub[1][i];
2308 ir->compress[i][i] = dumdub[0][i];
2310 if (ir->epct == epctANISOTROPIC)
2312 ir->ref_p[XX][YY] = dumdub[1][3];
2313 ir->ref_p[XX][ZZ] = dumdub[1][4];
2314 ir->ref_p[YY][ZZ] = dumdub[1][5];
2315 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2317 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2319 ir->compress[XX][YY] = dumdub[0][3];
2320 ir->compress[XX][ZZ] = dumdub[0][4];
2321 ir->compress[YY][ZZ] = dumdub[0][5];
2322 for (i = 0; i < DIM; i++)
2324 for (m = 0; m < i; m++)
2326 ir->ref_p[i][m] = ir->ref_p[m][i];
2327 ir->compress[i][m] = ir->compress[m][i];
2332 if (ir->comm_mode == ecmNO)
2337 opts->couple_moltype = NULL;
2338 if (strlen(is->couple_moltype) > 0)
2340 if (ir->efep != efepNO)
2342 opts->couple_moltype = strdup(is->couple_moltype);
2343 if (opts->couple_lam0 == opts->couple_lam1)
2345 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2347 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2348 opts->couple_lam1 == ecouplamNONE))
2350 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2355 warning_note(wi, "Free energy is turned off, so we will not decouple the molecule listed in your input.");
2358 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2359 if (ir->efep != efepNO)
2361 if (fep->delta_lambda > 0)
2363 ir->efep = efepSLOWGROWTH;
2369 fep->bPrintEnergy = TRUE;
2370 /* always print out the energy to dhdl if we are doing expanded ensemble, since we need the total energy
2371 if the temperature is changing. */
2374 if ((ir->efep != efepNO) || ir->bSimTemp)
2376 ir->bExpanded = FALSE;
2377 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2379 ir->bExpanded = TRUE;
2381 do_fep_params(ir, is->fep_lambda, is->lambda_weights);
2382 if (ir->bSimTemp) /* done after fep params */
2384 do_simtemp_params(ir);
2389 ir->fepvals->n_lambda = 0;
2392 /* WALL PARAMETERS */
2394 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2396 /* ORIENTATION RESTRAINT PARAMETERS */
2398 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
2400 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2403 /* DEFORMATION PARAMETERS */
2405 clear_mat(ir->deform);
2406 for (i = 0; i < 6; i++)
2410 m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
2411 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2412 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2413 for (i = 0; i < 3; i++)
2415 ir->deform[i][i] = dumdub[0][i];
2417 ir->deform[YY][XX] = dumdub[0][3];
2418 ir->deform[ZZ][XX] = dumdub[0][4];
2419 ir->deform[ZZ][YY] = dumdub[0][5];
2420 if (ir->epc != epcNO)
2422 for (i = 0; i < 3; i++)
2424 for (j = 0; j <= i; j++)
2426 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2428 warning_error(wi, "A box element has deform set and compressibility > 0");
2432 for (i = 0; i < 3; i++)
2434 for (j = 0; j < i; j++)
2436 if (ir->deform[i][j] != 0)
2438 for (m = j; m < DIM; m++)
2440 if (ir->compress[m][j] != 0)
2442 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.");
2443 warning(wi, warn_buf);
2451 /* Ion/water position swapping checks */
2452 if (ir->eSwapCoords != eswapNO)
2454 if (ir->swap->nstswap < 1)
2456 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2458 if (ir->swap->nAverage < 1)
2460 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2462 if (ir->swap->threshold < 1.0)
2464 warning_error(wi, "Ion count threshold must be at least 1.\n");
2472 static int search_QMstring(const char *s, int ng, const char *gn[])
2474 /* same as normal search_string, but this one searches QM strings */
2477 for (i = 0; (i < ng); i++)
2479 if (gmx_strcasecmp(s, gn[i]) == 0)
2485 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2489 } /* search_QMstring */
2491 /* We would like gn to be const as well, but C doesn't allow this */
2492 int search_string(const char *s, int ng, char *gn[])
2496 for (i = 0; (i < ng); i++)
2498 if (gmx_strcasecmp(s, gn[i]) == 0)
2505 "Group %s referenced in the .mdp file was not found in the index file.\n"
2506 "Group names must match either [moleculetype] names or custom index group\n"
2507 "names, in which case you must supply an index file to the '-n' option\n"
2514 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2515 t_blocka *block, char *gnames[],
2516 int gtype, int restnm,
2517 int grptp, gmx_bool bVerbose,
2520 unsigned short *cbuf;
2521 t_grps *grps = &(groups->grps[gtype]);
2522 int i, j, gid, aj, ognr, ntot = 0;
2525 char warn_buf[STRLEN];
2529 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2532 title = gtypes[gtype];
2535 /* Mark all id's as not set */
2536 for (i = 0; (i < natoms); i++)
2541 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2542 for (i = 0; (i < ng); i++)
2544 /* Lookup the group name in the block structure */
2545 gid = search_string(ptrs[i], block->nr, gnames);
2546 if ((grptp != egrptpONE) || (i == 0))
2548 grps->nm_ind[grps->nr++] = gid;
2552 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2555 /* Now go over the atoms in the group */
2556 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2561 /* Range checking */
2562 if ((aj < 0) || (aj >= natoms))
2564 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2566 /* Lookup up the old group number */
2570 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2571 aj+1, title, ognr+1, i+1);
2575 /* Store the group number in buffer */
2576 if (grptp == egrptpONE)
2589 /* Now check whether we have done all atoms */
2593 if (grptp == egrptpALL)
2595 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2596 natoms-ntot, title);
2598 else if (grptp == egrptpPART)
2600 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2601 natoms-ntot, title);
2602 warning_note(wi, warn_buf);
2604 /* Assign all atoms currently unassigned to a rest group */
2605 for (j = 0; (j < natoms); j++)
2607 if (cbuf[j] == NOGID)
2613 if (grptp != egrptpPART)
2618 "Making dummy/rest group for %s containing %d elements\n",
2619 title, natoms-ntot);
2621 /* Add group name "rest" */
2622 grps->nm_ind[grps->nr] = restnm;
2624 /* Assign the rest name to all atoms not currently assigned to a group */
2625 for (j = 0; (j < natoms); j++)
2627 if (cbuf[j] == NOGID)
2636 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2638 /* All atoms are part of one (or no) group, no index required */
2639 groups->ngrpnr[gtype] = 0;
2640 groups->grpnr[gtype] = NULL;
2644 groups->ngrpnr[gtype] = natoms;
2645 snew(groups->grpnr[gtype], natoms);
2646 for (j = 0; (j < natoms); j++)
2648 groups->grpnr[gtype][j] = cbuf[j];
2654 return (bRest && grptp == egrptpPART);
2657 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2660 gmx_groups_t *groups;
2662 int natoms, ai, aj, i, j, d, g, imin, jmin;
2664 int *nrdf2, *na_vcm, na_tot;
2665 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2666 gmx_mtop_atomloop_all_t aloop;
2668 int mb, mol, ftype, as;
2669 gmx_molblock_t *molb;
2670 gmx_moltype_t *molt;
2673 * First calc 3xnr-atoms for each group
2674 * then subtract half a degree of freedom for each constraint
2676 * Only atoms and nuclei contribute to the degrees of freedom...
2681 groups = &mtop->groups;
2682 natoms = mtop->natoms;
2684 /* Allocate one more for a possible rest group */
2685 /* We need to sum degrees of freedom into doubles,
2686 * since floats give too low nrdf's above 3 million atoms.
2688 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2689 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2690 snew(na_vcm, groups->grps[egcVCM].nr+1);
2692 for (i = 0; i < groups->grps[egcTC].nr; i++)
2696 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2701 snew(nrdf2, natoms);
2702 aloop = gmx_mtop_atomloop_all_init(mtop);
2703 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2706 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2708 g = ggrpnr(groups, egcFREEZE, i);
2709 /* Double count nrdf for particle i */
2710 for (d = 0; d < DIM; d++)
2712 if (opts->nFreeze[g][d] == 0)
2717 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2718 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2723 for (mb = 0; mb < mtop->nmolblock; mb++)
2725 molb = &mtop->molblock[mb];
2726 molt = &mtop->moltype[molb->type];
2727 atom = molt->atoms.atom;
2728 for (mol = 0; mol < molb->nmol; mol++)
2730 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2732 ia = molt->ilist[ftype].iatoms;
2733 for (i = 0; i < molt->ilist[ftype].nr; )
2735 /* Subtract degrees of freedom for the constraints,
2736 * if the particles still have degrees of freedom left.
2737 * If one of the particles is a vsite or a shell, then all
2738 * constraint motion will go there, but since they do not
2739 * contribute to the constraints the degrees of freedom do not
2744 if (((atom[ia[1]].ptype == eptNucleus) ||
2745 (atom[ia[1]].ptype == eptAtom)) &&
2746 ((atom[ia[2]].ptype == eptNucleus) ||
2747 (atom[ia[2]].ptype == eptAtom)))
2765 imin = min(imin, nrdf2[ai]);
2766 jmin = min(jmin, nrdf2[aj]);
2769 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2770 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2771 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2772 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2774 ia += interaction_function[ftype].nratoms+1;
2775 i += interaction_function[ftype].nratoms+1;
2778 ia = molt->ilist[F_SETTLE].iatoms;
2779 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2781 /* Subtract 1 dof from every atom in the SETTLE */
2782 for (j = 0; j < 3; j++)
2785 imin = min(2, nrdf2[ai]);
2787 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2788 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2793 as += molt->atoms.nr;
2797 if (ir->ePull == epullCONSTRAINT)
2799 /* Correct nrdf for the COM constraints.
2800 * We correct using the TC and VCM group of the first atom
2801 * in the reference and pull group. If atoms in one pull group
2802 * belong to different TC or VCM groups it is anyhow difficult
2803 * to determine the optimal nrdf assignment.
2807 for (i = 0; i < pull->ncoord; i++)
2811 for (j = 0; j < 2; j++)
2813 const t_pull_group *pgrp;
2815 pgrp = &pull->group[pull->coord[i].group[j]];
2819 /* Subtract 1/2 dof from each group */
2821 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2822 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2823 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2825 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)]]);
2830 /* We need to subtract the whole DOF from group j=1 */
2837 if (ir->nstcomm != 0)
2839 /* Subtract 3 from the number of degrees of freedom in each vcm group
2840 * when com translation is removed and 6 when rotation is removed
2843 switch (ir->comm_mode)
2846 n_sub = ndof_com(ir);
2853 gmx_incons("Checking comm_mode");
2856 for (i = 0; i < groups->grps[egcTC].nr; i++)
2858 /* Count the number of atoms of TC group i for every VCM group */
2859 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2864 for (ai = 0; ai < natoms; ai++)
2866 if (ggrpnr(groups, egcTC, ai) == i)
2868 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2872 /* Correct for VCM removal according to the fraction of each VCM
2873 * group present in this TC group.
2875 nrdf_uc = nrdf_tc[i];
2878 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2882 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2884 if (nrdf_vcm[j] > n_sub)
2886 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2887 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2891 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2892 j, nrdf_vcm[j], nrdf_tc[i]);
2897 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2899 opts->nrdf[i] = nrdf_tc[i];
2900 if (opts->nrdf[i] < 0)
2905 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2906 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
2915 static void decode_cos(char *s, t_cosines *cosine)
2918 char format[STRLEN], f1[STRLEN];
2930 sscanf(t, "%d", &(cosine->n));
2937 snew(cosine->a, cosine->n);
2938 snew(cosine->phi, cosine->n);
2940 sprintf(format, "%%*d");
2941 for (i = 0; (i < cosine->n); i++)
2944 strcat(f1, "%lf%lf");
2945 if (sscanf(t, f1, &a, &phi) < 2)
2947 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
2950 cosine->phi[i] = phi;
2951 strcat(format, "%*lf%*lf");
2958 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
2959 const char *option, const char *val, int flag)
2961 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
2962 * But since this is much larger than STRLEN, such a line can not be parsed.
2963 * The real maximum is the number of names that fit in a string: STRLEN/2.
2965 #define EGP_MAX (STRLEN/2)
2966 int nelem, i, j, k, nr;
2967 char *names[EGP_MAX];
2971 gnames = groups->grpname;
2973 nelem = str_nelem(val, EGP_MAX, names);
2976 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
2978 nr = groups->grps[egcENER].nr;
2980 for (i = 0; i < nelem/2; i++)
2984 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
2990 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
2991 names[2*i], option);
2995 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
3001 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3002 names[2*i+1], option);
3004 if ((j < nr) && (k < nr))
3006 ir->opts.egp_flags[nr*j+k] |= flag;
3007 ir->opts.egp_flags[nr*k+j] |= flag;
3016 static void make_swap_groups(
3025 int ig = -1, i = 0, j;
3029 /* Just a quick check here, more thorough checks are in mdrun */
3030 if (strcmp(splitg0name, splitg1name) == 0)
3032 gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
3035 /* First get the swap group index atoms */
3036 ig = search_string(swapgname, grps->nr, gnames);
3037 swap->nat = grps->index[ig+1] - grps->index[ig];
3040 fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
3041 snew(swap->ind, swap->nat);
3042 for (i = 0; i < swap->nat; i++)
3044 swap->ind[i] = grps->a[grps->index[ig]+i];
3049 gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
3052 /* Now do so for the split groups */
3053 for (j = 0; j < 2; j++)
3057 splitg = splitg0name;
3061 splitg = splitg1name;
3064 ig = search_string(splitg, grps->nr, gnames);
3065 swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
3066 if (swap->nat_split[j] > 0)
3068 fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
3069 j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
3070 snew(swap->ind_split[j], swap->nat_split[j]);
3071 for (i = 0; i < swap->nat_split[j]; i++)
3073 swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
3078 gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
3082 /* Now get the solvent group index atoms */
3083 ig = search_string(solgname, grps->nr, gnames);
3084 swap->nat_sol = grps->index[ig+1] - grps->index[ig];
3085 if (swap->nat_sol > 0)
3087 fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
3088 snew(swap->ind_sol, swap->nat_sol);
3089 for (i = 0; i < swap->nat_sol; i++)
3091 swap->ind_sol[i] = grps->a[grps->index[ig]+i];
3096 gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
3101 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3106 ig = search_string(IMDgname, grps->nr, gnames);
3107 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3109 if (IMDgroup->nat > 0)
3111 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3112 IMDgname, IMDgroup->nat);
3113 snew(IMDgroup->ind, IMDgroup->nat);
3114 for (i = 0; i < IMDgroup->nat; i++)
3116 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3122 void do_index(const char* mdparin, const char *ndx,
3125 t_inputrec *ir, rvec *v,
3129 gmx_groups_t *groups;
3133 char warnbuf[STRLEN], **gnames;
3134 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3137 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3138 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3139 int i, j, k, restnm;
3141 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3142 int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
3143 nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
3144 char warn_buf[STRLEN];
3148 fprintf(stderr, "processing index file...\n");
3154 snew(grps->index, 1);
3156 atoms_all = gmx_mtop_global_atoms(mtop);
3157 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3158 free_t_atoms(&atoms_all, FALSE);
3162 grps = init_index(ndx, &gnames);
3165 groups = &mtop->groups;
3166 natoms = mtop->natoms;
3167 symtab = &mtop->symtab;
3169 snew(groups->grpname, grps->nr+1);
3171 for (i = 0; (i < grps->nr); i++)
3173 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3175 groups->grpname[i] = put_symtab(symtab, "rest");
3177 srenew(gnames, grps->nr+1);
3178 gnames[restnm] = *(groups->grpname[i]);
3179 groups->ngrpname = grps->nr+1;
3181 set_warning_line(wi, mdparin, -1);
3183 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3184 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3185 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3186 if ((ntau_t != ntcg) || (nref_t != ntcg))
3188 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3189 "%d tau-t values", ntcg, nref_t, ntau_t);
3192 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3193 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3194 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3195 nr = groups->grps[egcTC].nr;
3197 snew(ir->opts.nrdf, nr);
3198 snew(ir->opts.tau_t, nr);
3199 snew(ir->opts.ref_t, nr);
3200 if (ir->eI == eiBD && ir->bd_fric == 0)
3202 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3209 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3213 for (i = 0; (i < nr); i++)
3215 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
3216 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
3218 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3219 warning_error(wi, warn_buf);
3222 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3224 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.");
3227 if (ir->opts.tau_t[i] >= 0)
3229 tau_min = min(tau_min, ir->opts.tau_t[i]);
3232 if (ir->etc != etcNO && ir->nsttcouple == -1)
3234 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3239 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3241 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");
3243 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
3245 if (ir->nstpcouple != ir->nsttcouple)
3247 int mincouple = min(ir->nstpcouple, ir->nsttcouple);
3248 ir->nstpcouple = ir->nsttcouple = mincouple;
3249 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);
3250 warning_note(wi, warn_buf);
3254 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3255 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3257 if (ETC_ANDERSEN(ir->etc))
3259 if (ir->nsttcouple != 1)
3262 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");
3263 warning_note(wi, warn_buf);
3266 nstcmin = tcouple_min_integration_steps(ir->etc);
3269 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
3271 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3272 ETCOUPLTYPE(ir->etc),
3274 ir->nsttcouple*ir->delta_t);
3275 warning(wi, warn_buf);
3278 for (i = 0; (i < nr); i++)
3280 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
3281 if (ir->opts.ref_t[i] < 0)
3283 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3286 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3287 if we are in this conditional) if mc_temp is negative */
3288 if (ir->expandedvals->mc_temp < 0)
3290 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3294 /* Simulated annealing for each group. There are nr groups */
3295 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3296 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3300 if (nSA > 0 && nSA != nr)
3302 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3306 snew(ir->opts.annealing, nr);
3307 snew(ir->opts.anneal_npoints, nr);
3308 snew(ir->opts.anneal_time, nr);
3309 snew(ir->opts.anneal_temp, nr);
3310 for (i = 0; i < nr; i++)
3312 ir->opts.annealing[i] = eannNO;
3313 ir->opts.anneal_npoints[i] = 0;
3314 ir->opts.anneal_time[i] = NULL;
3315 ir->opts.anneal_temp[i] = NULL;
3320 for (i = 0; i < nr; i++)
3322 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3324 ir->opts.annealing[i] = eannNO;
3326 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3328 ir->opts.annealing[i] = eannSINGLE;
3331 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3333 ir->opts.annealing[i] = eannPERIODIC;
3339 /* Read the other fields too */
3340 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3341 if (nSA_points != nSA)
3343 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3345 for (k = 0, i = 0; i < nr; i++)
3347 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3348 if (ir->opts.anneal_npoints[i] == 1)
3350 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3352 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3353 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3354 k += ir->opts.anneal_npoints[i];
3357 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3360 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3362 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3365 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3368 for (i = 0, k = 0; i < nr; i++)
3371 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3373 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3374 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3377 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3379 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3385 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3387 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3388 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3391 if (ir->opts.anneal_temp[i][j] < 0)
3393 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3398 /* Print out some summary information, to make sure we got it right */
3399 for (i = 0, k = 0; i < nr; i++)
3401 if (ir->opts.annealing[i] != eannNO)
3403 j = groups->grps[egcTC].nm_ind[i];
3404 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3405 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3406 ir->opts.anneal_npoints[i]);
3407 fprintf(stderr, "Time (ps) Temperature (K)\n");
3408 /* All terms except the last one */
3409 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3411 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3414 /* Finally the last one */
3415 j = ir->opts.anneal_npoints[i]-1;
3416 if (ir->opts.annealing[i] == eannSINGLE)
3418 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3422 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3423 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3425 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3434 if (ir->ePull != epullNO)
3436 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3438 make_pull_coords(ir->pull);
3443 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3446 if (ir->eSwapCoords != eswapNO)
3448 make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
3451 /* Make indices for IMD session */
3454 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3457 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3458 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3459 if (nacg*DIM != nacc)
3461 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3464 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3465 restnm, egrptpALL_GENREST, bVerbose, wi);
3466 nr = groups->grps[egcACC].nr;
3467 snew(ir->opts.acc, nr);
3468 ir->opts.ngacc = nr;
3470 for (i = k = 0; (i < nacg); i++)
3472 for (j = 0; (j < DIM); j++, k++)
3474 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3477 for (; (i < nr); i++)
3479 for (j = 0; (j < DIM); j++)
3481 ir->opts.acc[i][j] = 0;
3485 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3486 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3487 if (nfrdim != DIM*nfreeze)
3489 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3492 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3493 restnm, egrptpALL_GENREST, bVerbose, wi);
3494 nr = groups->grps[egcFREEZE].nr;
3495 ir->opts.ngfrz = nr;
3496 snew(ir->opts.nFreeze, nr);
3497 for (i = k = 0; (i < nfreeze); i++)
3499 for (j = 0; (j < DIM); j++, k++)
3501 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3502 if (!ir->opts.nFreeze[i][j])
3504 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3506 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3507 "(not %s)", ptr1[k]);
3508 warning(wi, warn_buf);
3513 for (; (i < nr); i++)
3515 for (j = 0; (j < DIM); j++)
3517 ir->opts.nFreeze[i][j] = 0;
3521 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3522 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3523 restnm, egrptpALL_GENREST, bVerbose, wi);
3524 add_wall_energrps(groups, ir->nwall, symtab);
3525 ir->opts.ngener = groups->grps[egcENER].nr;
3526 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3528 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3529 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3532 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3533 "This may lead to artifacts.\n"
3534 "In most cases one should use one group for the whole system.");
3537 /* Now we have filled the freeze struct, so we can calculate NRDF */
3538 calc_nrdf(mtop, ir, gnames);
3544 /* Must check per group! */
3545 for (i = 0; (i < ir->opts.ngtc); i++)
3547 ntot += ir->opts.nrdf[i];
3549 if (ntot != (DIM*natoms))
3551 fac = sqrt(ntot/(DIM*natoms));
3554 fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
3555 "and removal of center of mass motion\n", fac);
3557 for (i = 0; (i < natoms); i++)
3559 svmul(fac, v[i], v[i]);
3564 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3565 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3566 restnm, egrptpALL_GENREST, bVerbose, wi);
3567 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3568 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3569 restnm, egrptpALL_GENREST, bVerbose, wi);
3570 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3571 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3572 restnm, egrptpONE, bVerbose, wi);
3573 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3574 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3575 restnm, egrptpALL_GENREST, bVerbose, wi);
3577 /* QMMM input processing */
3578 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3579 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3580 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3581 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3583 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3584 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3586 /* group rest, if any, is always MM! */
3587 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3588 restnm, egrptpALL_GENREST, bVerbose, wi);
3589 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3590 ir->opts.ngQM = nQMg;
3591 snew(ir->opts.QMmethod, nr);
3592 snew(ir->opts.QMbasis, nr);
3593 for (i = 0; i < nr; i++)
3595 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3596 * converted to the corresponding enum in names.c
3598 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3600 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3604 nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
3605 nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
3606 nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
3607 snew(ir->opts.QMmult, nr);
3608 snew(ir->opts.QMcharge, nr);
3609 snew(ir->opts.bSH, nr);
3611 for (i = 0; i < nr; i++)
3613 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3614 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3615 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3618 nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
3619 nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
3620 snew(ir->opts.CASelectrons, nr);
3621 snew(ir->opts.CASorbitals, nr);
3622 for (i = 0; i < nr; i++)
3624 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3625 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3627 /* special optimization options */
3629 nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
3630 nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
3631 snew(ir->opts.bOPT, nr);
3632 snew(ir->opts.bTS, nr);
3633 for (i = 0; i < nr; i++)
3635 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3636 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3638 nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
3639 nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
3640 nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
3641 snew(ir->opts.SAon, nr);
3642 snew(ir->opts.SAoff, nr);
3643 snew(ir->opts.SAsteps, nr);
3645 for (i = 0; i < nr; i++)
3647 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3648 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3649 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3651 /* end of QMMM input */
3655 for (i = 0; (i < egcNR); i++)
3657 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3658 for (j = 0; (j < groups->grps[i].nr); j++)
3660 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3662 fprintf(stderr, "\n");
3666 nr = groups->grps[egcENER].nr;
3667 snew(ir->opts.egp_flags, nr*nr);
3669 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3670 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3672 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3674 if (bExcl && EEL_FULL(ir->coulombtype))
3676 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3679 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3680 if (bTable && !(ir->vdwtype == evdwUSER) &&
3681 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3682 !(ir->coulombtype == eelPMEUSERSWITCH))
3684 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3687 decode_cos(is->efield_x, &(ir->ex[XX]));
3688 decode_cos(is->efield_xt, &(ir->et[XX]));
3689 decode_cos(is->efield_y, &(ir->ex[YY]));
3690 decode_cos(is->efield_yt, &(ir->et[YY]));
3691 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3692 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3696 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3699 for (i = 0; (i < grps->nr); i++)
3711 static void check_disre(gmx_mtop_t *mtop)
3713 gmx_ffparams_t *ffparams;
3714 t_functype *functype;
3716 int i, ndouble, ftype;
3717 int label, old_label;
3719 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3721 ffparams = &mtop->ffparams;
3722 functype = ffparams->functype;
3723 ip = ffparams->iparams;
3726 for (i = 0; i < ffparams->ntypes; i++)
3728 ftype = functype[i];
3729 if (ftype == F_DISRES)
3731 label = ip[i].disres.label;
3732 if (label == old_label)
3734 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3742 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3743 "probably the parameters for multiple pairs in one restraint "
3744 "are not identical\n", ndouble);
3749 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3750 gmx_bool posres_only,
3754 gmx_mtop_ilistloop_t iloop;
3764 for (d = 0; d < DIM; d++)
3766 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3768 /* Check for freeze groups */
3769 for (g = 0; g < ir->opts.ngfrz; g++)
3771 for (d = 0; d < DIM; d++)
3773 if (ir->opts.nFreeze[g][d] != 0)
3781 /* Check for position restraints */
3782 iloop = gmx_mtop_ilistloop_init(sys);
3783 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3786 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3788 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3790 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3791 for (d = 0; d < DIM; d++)
3793 if (pr->posres.fcA[d] != 0)
3799 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3801 /* Check for flat-bottom posres */
3802 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3803 if (pr->fbposres.k != 0)
3805 switch (pr->fbposres.geom)
3807 case efbposresSPHERE:
3808 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3810 case efbposresCYLINDER:
3811 AbsRef[XX] = AbsRef[YY] = 1;
3813 case efbposresX: /* d=XX */
3814 case efbposresY: /* d=YY */
3815 case efbposresZ: /* d=ZZ */
3816 d = pr->fbposres.geom - efbposresX;
3820 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3821 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3829 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3833 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3834 gmx_bool *bC6ParametersWorkWithGeometricRules,
3835 gmx_bool *bC6ParametersWorkWithLBRules,
3836 gmx_bool *bLBRulesPossible)
3838 int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
3841 double geometricdiff, LBdiff;
3842 double c6i, c6j, c12i, c12j;
3843 double c6, c6_geometric, c6_LB;
3844 double sigmai, sigmaj, epsi, epsj;
3845 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3848 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3849 * force-field floating point parameters.
3852 ptr = getenv("GMX_LJCOMB_TOL");
3857 sscanf(ptr, "%lf", &dbl);
3861 *bC6ParametersWorkWithLBRules = TRUE;
3862 *bC6ParametersWorkWithGeometricRules = TRUE;
3863 bCanDoLBRules = TRUE;
3864 bCanDoGeometricRules = TRUE;
3865 ntypes = mtop->ffparams.atnr;
3866 snew(typecount, ntypes);
3867 gmx_mtop_count_atomtypes(mtop, state, typecount);
3868 geometricdiff = LBdiff = 0.0;
3869 *bLBRulesPossible = TRUE;
3870 for (tpi = 0; tpi < ntypes; ++tpi)
3872 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3873 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3874 for (tpj = tpi; tpj < ntypes; ++tpj)
3876 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3877 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3878 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3879 c6_geometric = sqrt(c6i * c6j);
3880 if (!gmx_numzero(c6_geometric))
3882 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3884 sigmai = pow(c12i / c6i, 1.0/6.0);
3885 sigmaj = pow(c12j / c6j, 1.0/6.0);
3886 epsi = c6i * c6i /(4.0 * c12i);
3887 epsj = c6j * c6j /(4.0 * c12j);
3888 c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
3892 *bLBRulesPossible = FALSE;
3893 c6_LB = c6_geometric;
3895 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3898 if (FALSE == bCanDoLBRules)
3900 *bC6ParametersWorkWithLBRules = FALSE;
3903 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3905 if (FALSE == bCanDoGeometricRules)
3907 *bC6ParametersWorkWithGeometricRules = FALSE;
3915 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3919 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3921 check_combination_rule_differences(mtop, 0,
3922 &bC6ParametersWorkWithGeometricRules,
3923 &bC6ParametersWorkWithLBRules,
3925 if (ir->ljpme_combination_rule == eljpmeLB)
3927 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
3929 warning(wi, "You are using arithmetic-geometric combination rules "
3930 "in LJ-PME, but your non-bonded C6 parameters do not "
3931 "follow these rules.");
3936 if (FALSE == bC6ParametersWorkWithGeometricRules)
3938 if (ir->eDispCorr != edispcNO)
3940 warning_note(wi, "You are using geometric combination rules in "
3941 "LJ-PME, but your non-bonded C6 parameters do "
3942 "not follow these rules. "
3943 "This will introduce very small errors in the forces and energies in "
3944 "your simulations. Dispersion correction will correct total energy "
3945 "and/or pressure for isotropic systems, but not forces or surface tensions.");
3949 warning_note(wi, "You are using geometric combination rules in "
3950 "LJ-PME, but your non-bonded C6 parameters do "
3951 "not follow these rules. "
3952 "This will introduce very small errors in the forces and energies in "
3953 "your simulations. If your system is homogeneous, consider using dispersion correction "
3954 "for the total energy and pressure.");
3960 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
3963 char err_buf[STRLEN];
3964 int i, m, c, nmol, npct;
3965 gmx_bool bCharge, bAcc;
3966 real gdt_max, *mgrp, mt;
3968 gmx_mtop_atomloop_block_t aloopb;
3969 gmx_mtop_atomloop_all_t aloop;
3972 char warn_buf[STRLEN];
3974 set_warning_line(wi, mdparin, -1);
3976 if (ir->cutoff_scheme == ecutsVERLET &&
3977 ir->verletbuf_tol > 0 &&
3979 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
3980 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
3982 /* Check if a too small Verlet buffer might potentially
3983 * cause more drift than the thermostat can couple off.
3985 /* Temperature error fraction for warning and suggestion */
3986 const real T_error_warn = 0.002;
3987 const real T_error_suggest = 0.001;
3988 /* For safety: 2 DOF per atom (typical with constraints) */
3989 const real nrdf_at = 2;
3990 real T, tau, max_T_error;
3995 for (i = 0; i < ir->opts.ngtc; i++)
3997 T = max(T, ir->opts.ref_t[i]);
3998 tau = max(tau, ir->opts.tau_t[i]);
4002 /* This is a worst case estimate of the temperature error,
4003 * assuming perfect buffer estimation and no cancelation
4004 * of errors. The factor 0.5 is because energy distributes
4005 * equally over Ekin and Epot.
4007 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4008 if (max_T_error > T_error_warn)
4010 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.",
4011 ir->verletbuf_tol, T, tau,
4013 100*T_error_suggest,
4014 ir->verletbuf_tol*T_error_suggest/max_T_error);
4015 warning(wi, warn_buf);
4020 if (ETC_ANDERSEN(ir->etc))
4024 for (i = 0; i < ir->opts.ngtc; i++)
4026 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4027 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4028 sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
4029 i, ir->opts.tau_t[i]);
4030 CHECK(ir->opts.tau_t[i] < 0);
4033 for (i = 0; i < ir->opts.ngtc; i++)
4035 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
4036 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);
4037 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
4041 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4042 ir->comm_mode == ecmNO &&
4043 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4044 !ETC_ANDERSEN(ir->etc))
4046 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");
4049 /* Check for pressure coupling with absolute position restraints */
4050 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4052 absolute_reference(ir, sys, TRUE, AbsRef);
4054 for (m = 0; m < DIM; m++)
4056 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4058 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4066 aloopb = gmx_mtop_atomloop_block_init(sys);
4067 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4069 if (atom->q != 0 || atom->qB != 0)
4077 if (EEL_FULL(ir->coulombtype))
4080 "You are using full electrostatics treatment %s for a system without charges.\n"
4081 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4082 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4083 warning(wi, err_buf);
4088 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4091 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4092 "You might want to consider using %s electrostatics.\n",
4094 warning_note(wi, err_buf);
4098 /* Check if combination rules used in LJ-PME are the same as in the force field */
4099 if (EVDW_PME(ir->vdwtype))
4101 check_combination_rules(ir, sys, wi);
4104 /* Generalized reaction field */
4105 if (ir->opts.ngtc == 0)
4107 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4109 CHECK(ir->coulombtype == eelGRF);
4113 sprintf(err_buf, "When using coulombtype = %s"
4114 " ref-t for temperature coupling should be > 0",
4116 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4119 if (ir->eI == eiSD1 &&
4120 (gmx_mtop_ftype_count(sys, F_CONSTR) > 0 ||
4121 gmx_mtop_ftype_count(sys, F_SETTLE) > 0))
4123 sprintf(warn_buf, "With constraints integrator %s is less accurate, consider using %s instead", ei_names[ir->eI], ei_names[eiSD2]);
4124 warning_note(wi, warn_buf);
4128 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4130 for (m = 0; (m < DIM); m++)
4132 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4141 snew(mgrp, sys->groups.grps[egcACC].nr);
4142 aloop = gmx_mtop_atomloop_all_init(sys);
4143 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4145 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4148 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4150 for (m = 0; (m < DIM); m++)
4152 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4156 for (m = 0; (m < DIM); m++)
4158 if (fabs(acc[m]) > 1e-6)
4160 const char *dim[DIM] = { "X", "Y", "Z" };
4162 "Net Acceleration in %s direction, will %s be corrected\n",
4163 dim[m], ir->nstcomm != 0 ? "" : "not");
4164 if (ir->nstcomm != 0 && m < ndof_com(ir))
4167 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4169 ir->opts.acc[i][m] -= acc[m];
4177 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4178 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4180 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4183 if (ir->ePull != epullNO)
4185 gmx_bool bPullAbsoluteRef;
4187 bPullAbsoluteRef = FALSE;
4188 for (i = 0; i < ir->pull->ncoord; i++)
4190 bPullAbsoluteRef = bPullAbsoluteRef ||
4191 ir->pull->coord[i].group[0] == 0 ||
4192 ir->pull->coord[i].group[1] == 0;
4194 if (bPullAbsoluteRef)
4196 absolute_reference(ir, sys, FALSE, AbsRef);
4197 for (m = 0; m < DIM; m++)
4199 if (ir->pull->dim[m] && !AbsRef[m])
4201 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.");
4207 if (ir->pull->eGeom == epullgDIRPBC)
4209 for (i = 0; i < 3; i++)
4211 for (m = 0; m <= i; m++)
4213 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4214 ir->deform[i][m] != 0)
4216 for (c = 0; c < ir->pull->ncoord; c++)
4218 if (ir->pull->coord[c].vec[m] != 0)
4220 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->eGeom), 'x'+m);
4232 void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr, warninp_t wi)
4236 char warn_buf[STRLEN];
4239 ptr = check_box(ir->ePBC, box);
4242 warning_error(wi, ptr);
4245 if (bConstr && ir->eConstrAlg == econtSHAKE)
4247 if (ir->shake_tol <= 0.0)
4249 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4251 warning_error(wi, warn_buf);
4254 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
4256 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
4257 if (ir->epc == epcNO)
4259 warning(wi, warn_buf);
4263 warning_error(wi, warn_buf);
4268 if ( (ir->eConstrAlg == econtLINCS) && bConstr)
4270 /* If we have Lincs constraints: */
4271 if (ir->eI == eiMD && ir->etc == etcNO &&
4272 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4274 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4275 warning_note(wi, warn_buf);
4278 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4280 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4281 warning_note(wi, warn_buf);
4283 if (ir->epc == epcMTTK)
4285 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4289 if (bConstr && ir->epc == epcMTTK)
4291 warning_note(wi, "MTTK with constraints is deprecated, and will be removed in GROMACS 5.1");
4294 if (ir->LincsWarnAngle > 90.0)
4296 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4297 warning(wi, warn_buf);
4298 ir->LincsWarnAngle = 90.0;
4301 if (ir->ePBC != epbcNONE)
4303 if (ir->nstlist == 0)
4305 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4307 bTWIN = (ir->rlistlong > ir->rlist);
4308 if (ir->ns_type == ensGRID)
4310 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
4312 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",
4313 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
4314 warning_error(wi, warn_buf);
4319 min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
4320 if (2*ir->rlistlong >= min_size)
4322 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4323 warning_error(wi, warn_buf);
4326 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4333 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4337 real rvdw1, rvdw2, rcoul1, rcoul2;
4338 char warn_buf[STRLEN];
4340 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4344 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4349 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4355 if (rvdw1 + rvdw2 > ir->rlist ||
4356 rcoul1 + rcoul2 > ir->rlist)
4359 "The sum of the two largest charge group radii (%f) "
4360 "is larger than rlist (%f)\n",
4361 max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4362 warning(wi, warn_buf);
4366 /* Here we do not use the zero at cut-off macro,
4367 * since user defined interactions might purposely
4368 * not be zero at the cut-off.
4370 if (ir_vdw_is_zero_at_cutoff(ir) &&
4371 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
4373 sprintf(warn_buf, "The sum of the two largest charge group "
4374 "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
4375 "With exact cut-offs, better performance can be "
4376 "obtained with cutoff-scheme = %s, because it "
4377 "does not use charge groups at all.",
4379 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4380 ir->rlistlong, ir->rvdw,
4381 ecutscheme_names[ecutsVERLET]);
4384 warning(wi, warn_buf);
4388 warning_note(wi, warn_buf);
4391 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4392 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
4394 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
4395 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4397 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4398 ir->rlistlong, ir->rcoulomb,
4399 ecutscheme_names[ecutsVERLET]);
4402 warning(wi, warn_buf);
4406 warning_note(wi, warn_buf);