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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->edHdLPrintEnergy, edHdLPrintEnergy_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;
2367 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2369 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2370 warning_note(wi, "Old option for dhdl-print-energy given: "
2371 "changing \"yes\" to \"total\"\n");
2374 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2376 /* always print out the energy to dhdl if we are doing
2377 expanded ensemble, since we need the total energy for
2378 analysis if the temperature is changing. In some
2379 conditions one may only want the potential energy, so
2380 we will allow that if the appropriate mdp setting has
2381 been enabled. Otherwise, total it is:
2383 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2386 if ((ir->efep != efepNO) || ir->bSimTemp)
2388 ir->bExpanded = FALSE;
2389 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2391 ir->bExpanded = TRUE;
2393 do_fep_params(ir, is->fep_lambda, is->lambda_weights);
2394 if (ir->bSimTemp) /* done after fep params */
2396 do_simtemp_params(ir);
2401 ir->fepvals->n_lambda = 0;
2404 /* WALL PARAMETERS */
2406 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2408 /* ORIENTATION RESTRAINT PARAMETERS */
2410 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
2412 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2415 /* DEFORMATION PARAMETERS */
2417 clear_mat(ir->deform);
2418 for (i = 0; i < 6; i++)
2422 m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
2423 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2424 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2425 for (i = 0; i < 3; i++)
2427 ir->deform[i][i] = dumdub[0][i];
2429 ir->deform[YY][XX] = dumdub[0][3];
2430 ir->deform[ZZ][XX] = dumdub[0][4];
2431 ir->deform[ZZ][YY] = dumdub[0][5];
2432 if (ir->epc != epcNO)
2434 for (i = 0; i < 3; i++)
2436 for (j = 0; j <= i; j++)
2438 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2440 warning_error(wi, "A box element has deform set and compressibility > 0");
2444 for (i = 0; i < 3; i++)
2446 for (j = 0; j < i; j++)
2448 if (ir->deform[i][j] != 0)
2450 for (m = j; m < DIM; m++)
2452 if (ir->compress[m][j] != 0)
2454 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.");
2455 warning(wi, warn_buf);
2463 /* Ion/water position swapping checks */
2464 if (ir->eSwapCoords != eswapNO)
2466 if (ir->swap->nstswap < 1)
2468 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2470 if (ir->swap->nAverage < 1)
2472 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2474 if (ir->swap->threshold < 1.0)
2476 warning_error(wi, "Ion count threshold must be at least 1.\n");
2484 static int search_QMstring(const char *s, int ng, const char *gn[])
2486 /* same as normal search_string, but this one searches QM strings */
2489 for (i = 0; (i < ng); i++)
2491 if (gmx_strcasecmp(s, gn[i]) == 0)
2497 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2501 } /* search_QMstring */
2503 /* We would like gn to be const as well, but C doesn't allow this */
2504 int search_string(const char *s, int ng, char *gn[])
2508 for (i = 0; (i < ng); i++)
2510 if (gmx_strcasecmp(s, gn[i]) == 0)
2517 "Group %s referenced in the .mdp file was not found in the index file.\n"
2518 "Group names must match either [moleculetype] names or custom index group\n"
2519 "names, in which case you must supply an index file to the '-n' option\n"
2526 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2527 t_blocka *block, char *gnames[],
2528 int gtype, int restnm,
2529 int grptp, gmx_bool bVerbose,
2532 unsigned short *cbuf;
2533 t_grps *grps = &(groups->grps[gtype]);
2534 int i, j, gid, aj, ognr, ntot = 0;
2537 char warn_buf[STRLEN];
2541 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2544 title = gtypes[gtype];
2547 /* Mark all id's as not set */
2548 for (i = 0; (i < natoms); i++)
2553 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2554 for (i = 0; (i < ng); i++)
2556 /* Lookup the group name in the block structure */
2557 gid = search_string(ptrs[i], block->nr, gnames);
2558 if ((grptp != egrptpONE) || (i == 0))
2560 grps->nm_ind[grps->nr++] = gid;
2564 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2567 /* Now go over the atoms in the group */
2568 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2573 /* Range checking */
2574 if ((aj < 0) || (aj >= natoms))
2576 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2578 /* Lookup up the old group number */
2582 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2583 aj+1, title, ognr+1, i+1);
2587 /* Store the group number in buffer */
2588 if (grptp == egrptpONE)
2601 /* Now check whether we have done all atoms */
2605 if (grptp == egrptpALL)
2607 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2608 natoms-ntot, title);
2610 else if (grptp == egrptpPART)
2612 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2613 natoms-ntot, title);
2614 warning_note(wi, warn_buf);
2616 /* Assign all atoms currently unassigned to a rest group */
2617 for (j = 0; (j < natoms); j++)
2619 if (cbuf[j] == NOGID)
2625 if (grptp != egrptpPART)
2630 "Making dummy/rest group for %s containing %d elements\n",
2631 title, natoms-ntot);
2633 /* Add group name "rest" */
2634 grps->nm_ind[grps->nr] = restnm;
2636 /* Assign the rest name to all atoms not currently assigned to a group */
2637 for (j = 0; (j < natoms); j++)
2639 if (cbuf[j] == NOGID)
2648 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2650 /* All atoms are part of one (or no) group, no index required */
2651 groups->ngrpnr[gtype] = 0;
2652 groups->grpnr[gtype] = NULL;
2656 groups->ngrpnr[gtype] = natoms;
2657 snew(groups->grpnr[gtype], natoms);
2658 for (j = 0; (j < natoms); j++)
2660 groups->grpnr[gtype][j] = cbuf[j];
2666 return (bRest && grptp == egrptpPART);
2669 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2672 gmx_groups_t *groups;
2674 int natoms, ai, aj, i, j, d, g, imin, jmin;
2676 int *nrdf2, *na_vcm, na_tot;
2677 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2678 gmx_mtop_atomloop_all_t aloop;
2680 int mb, mol, ftype, as;
2681 gmx_molblock_t *molb;
2682 gmx_moltype_t *molt;
2685 * First calc 3xnr-atoms for each group
2686 * then subtract half a degree of freedom for each constraint
2688 * Only atoms and nuclei contribute to the degrees of freedom...
2693 groups = &mtop->groups;
2694 natoms = mtop->natoms;
2696 /* Allocate one more for a possible rest group */
2697 /* We need to sum degrees of freedom into doubles,
2698 * since floats give too low nrdf's above 3 million atoms.
2700 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2701 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2702 snew(na_vcm, groups->grps[egcVCM].nr+1);
2704 for (i = 0; i < groups->grps[egcTC].nr; i++)
2708 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2713 snew(nrdf2, natoms);
2714 aloop = gmx_mtop_atomloop_all_init(mtop);
2715 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2718 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2720 g = ggrpnr(groups, egcFREEZE, i);
2721 /* Double count nrdf for particle i */
2722 for (d = 0; d < DIM; d++)
2724 if (opts->nFreeze[g][d] == 0)
2729 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2730 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2735 for (mb = 0; mb < mtop->nmolblock; mb++)
2737 molb = &mtop->molblock[mb];
2738 molt = &mtop->moltype[molb->type];
2739 atom = molt->atoms.atom;
2740 for (mol = 0; mol < molb->nmol; mol++)
2742 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2744 ia = molt->ilist[ftype].iatoms;
2745 for (i = 0; i < molt->ilist[ftype].nr; )
2747 /* Subtract degrees of freedom for the constraints,
2748 * if the particles still have degrees of freedom left.
2749 * If one of the particles is a vsite or a shell, then all
2750 * constraint motion will go there, but since they do not
2751 * contribute to the constraints the degrees of freedom do not
2756 if (((atom[ia[1]].ptype == eptNucleus) ||
2757 (atom[ia[1]].ptype == eptAtom)) &&
2758 ((atom[ia[2]].ptype == eptNucleus) ||
2759 (atom[ia[2]].ptype == eptAtom)))
2777 imin = min(imin, nrdf2[ai]);
2778 jmin = min(jmin, nrdf2[aj]);
2781 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2782 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2783 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2784 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2786 ia += interaction_function[ftype].nratoms+1;
2787 i += interaction_function[ftype].nratoms+1;
2790 ia = molt->ilist[F_SETTLE].iatoms;
2791 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2793 /* Subtract 1 dof from every atom in the SETTLE */
2794 for (j = 0; j < 3; j++)
2797 imin = min(2, nrdf2[ai]);
2799 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2800 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2805 as += molt->atoms.nr;
2809 if (ir->ePull == epullCONSTRAINT)
2811 /* Correct nrdf for the COM constraints.
2812 * We correct using the TC and VCM group of the first atom
2813 * in the reference and pull group. If atoms in one pull group
2814 * belong to different TC or VCM groups it is anyhow difficult
2815 * to determine the optimal nrdf assignment.
2819 for (i = 0; i < pull->ncoord; i++)
2823 for (j = 0; j < 2; j++)
2825 const t_pull_group *pgrp;
2827 pgrp = &pull->group[pull->coord[i].group[j]];
2831 /* Subtract 1/2 dof from each group */
2833 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2834 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2835 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2837 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)]]);
2842 /* We need to subtract the whole DOF from group j=1 */
2849 if (ir->nstcomm != 0)
2851 /* Subtract 3 from the number of degrees of freedom in each vcm group
2852 * when com translation is removed and 6 when rotation is removed
2855 switch (ir->comm_mode)
2858 n_sub = ndof_com(ir);
2865 gmx_incons("Checking comm_mode");
2868 for (i = 0; i < groups->grps[egcTC].nr; i++)
2870 /* Count the number of atoms of TC group i for every VCM group */
2871 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2876 for (ai = 0; ai < natoms; ai++)
2878 if (ggrpnr(groups, egcTC, ai) == i)
2880 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2884 /* Correct for VCM removal according to the fraction of each VCM
2885 * group present in this TC group.
2887 nrdf_uc = nrdf_tc[i];
2890 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2894 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2896 if (nrdf_vcm[j] > n_sub)
2898 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2899 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2903 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2904 j, nrdf_vcm[j], nrdf_tc[i]);
2909 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2911 opts->nrdf[i] = nrdf_tc[i];
2912 if (opts->nrdf[i] < 0)
2917 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2918 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
2927 static void decode_cos(char *s, t_cosines *cosine)
2930 char format[STRLEN], f1[STRLEN];
2942 sscanf(t, "%d", &(cosine->n));
2949 snew(cosine->a, cosine->n);
2950 snew(cosine->phi, cosine->n);
2952 sprintf(format, "%%*d");
2953 for (i = 0; (i < cosine->n); i++)
2956 strcat(f1, "%lf%lf");
2957 if (sscanf(t, f1, &a, &phi) < 2)
2959 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
2962 cosine->phi[i] = phi;
2963 strcat(format, "%*lf%*lf");
2970 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
2971 const char *option, const char *val, int flag)
2973 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
2974 * But since this is much larger than STRLEN, such a line can not be parsed.
2975 * The real maximum is the number of names that fit in a string: STRLEN/2.
2977 #define EGP_MAX (STRLEN/2)
2978 int nelem, i, j, k, nr;
2979 char *names[EGP_MAX];
2983 gnames = groups->grpname;
2985 nelem = str_nelem(val, EGP_MAX, names);
2988 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
2990 nr = groups->grps[egcENER].nr;
2992 for (i = 0; i < nelem/2; i++)
2996 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
3002 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3003 names[2*i], option);
3007 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
3013 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3014 names[2*i+1], option);
3016 if ((j < nr) && (k < nr))
3018 ir->opts.egp_flags[nr*j+k] |= flag;
3019 ir->opts.egp_flags[nr*k+j] |= flag;
3028 static void make_swap_groups(
3037 int ig = -1, i = 0, j;
3041 /* Just a quick check here, more thorough checks are in mdrun */
3042 if (strcmp(splitg0name, splitg1name) == 0)
3044 gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
3047 /* First get the swap group index atoms */
3048 ig = search_string(swapgname, grps->nr, gnames);
3049 swap->nat = grps->index[ig+1] - grps->index[ig];
3052 fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
3053 snew(swap->ind, swap->nat);
3054 for (i = 0; i < swap->nat; i++)
3056 swap->ind[i] = grps->a[grps->index[ig]+i];
3061 gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
3064 /* Now do so for the split groups */
3065 for (j = 0; j < 2; j++)
3069 splitg = splitg0name;
3073 splitg = splitg1name;
3076 ig = search_string(splitg, grps->nr, gnames);
3077 swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
3078 if (swap->nat_split[j] > 0)
3080 fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
3081 j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
3082 snew(swap->ind_split[j], swap->nat_split[j]);
3083 for (i = 0; i < swap->nat_split[j]; i++)
3085 swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
3090 gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
3094 /* Now get the solvent group index atoms */
3095 ig = search_string(solgname, grps->nr, gnames);
3096 swap->nat_sol = grps->index[ig+1] - grps->index[ig];
3097 if (swap->nat_sol > 0)
3099 fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
3100 snew(swap->ind_sol, swap->nat_sol);
3101 for (i = 0; i < swap->nat_sol; i++)
3103 swap->ind_sol[i] = grps->a[grps->index[ig]+i];
3108 gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
3113 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3118 ig = search_string(IMDgname, grps->nr, gnames);
3119 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3121 if (IMDgroup->nat > 0)
3123 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3124 IMDgname, IMDgroup->nat);
3125 snew(IMDgroup->ind, IMDgroup->nat);
3126 for (i = 0; i < IMDgroup->nat; i++)
3128 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3134 void do_index(const char* mdparin, const char *ndx,
3137 t_inputrec *ir, rvec *v,
3141 gmx_groups_t *groups;
3145 char warnbuf[STRLEN], **gnames;
3146 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3149 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3150 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3151 int i, j, k, restnm;
3153 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3154 int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
3155 nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
3156 char warn_buf[STRLEN];
3160 fprintf(stderr, "processing index file...\n");
3166 snew(grps->index, 1);
3168 atoms_all = gmx_mtop_global_atoms(mtop);
3169 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3170 free_t_atoms(&atoms_all, FALSE);
3174 grps = init_index(ndx, &gnames);
3177 groups = &mtop->groups;
3178 natoms = mtop->natoms;
3179 symtab = &mtop->symtab;
3181 snew(groups->grpname, grps->nr+1);
3183 for (i = 0; (i < grps->nr); i++)
3185 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3187 groups->grpname[i] = put_symtab(symtab, "rest");
3189 srenew(gnames, grps->nr+1);
3190 gnames[restnm] = *(groups->grpname[i]);
3191 groups->ngrpname = grps->nr+1;
3193 set_warning_line(wi, mdparin, -1);
3195 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3196 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3197 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3198 if ((ntau_t != ntcg) || (nref_t != ntcg))
3200 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3201 "%d tau-t values", ntcg, nref_t, ntau_t);
3204 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3205 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3206 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3207 nr = groups->grps[egcTC].nr;
3209 snew(ir->opts.nrdf, nr);
3210 snew(ir->opts.tau_t, nr);
3211 snew(ir->opts.ref_t, nr);
3212 if (ir->eI == eiBD && ir->bd_fric == 0)
3214 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3221 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3225 for (i = 0; (i < nr); i++)
3227 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
3228 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
3230 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3231 warning_error(wi, warn_buf);
3234 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3236 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.");
3239 if (ir->opts.tau_t[i] >= 0)
3241 tau_min = min(tau_min, ir->opts.tau_t[i]);
3244 if (ir->etc != etcNO && ir->nsttcouple == -1)
3246 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3251 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3253 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");
3255 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
3257 if (ir->nstpcouple != ir->nsttcouple)
3259 int mincouple = min(ir->nstpcouple, ir->nsttcouple);
3260 ir->nstpcouple = ir->nsttcouple = mincouple;
3261 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);
3262 warning_note(wi, warn_buf);
3266 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3267 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3269 if (ETC_ANDERSEN(ir->etc))
3271 if (ir->nsttcouple != 1)
3274 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");
3275 warning_note(wi, warn_buf);
3278 nstcmin = tcouple_min_integration_steps(ir->etc);
3281 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
3283 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3284 ETCOUPLTYPE(ir->etc),
3286 ir->nsttcouple*ir->delta_t);
3287 warning(wi, warn_buf);
3290 for (i = 0; (i < nr); i++)
3292 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
3293 if (ir->opts.ref_t[i] < 0)
3295 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3298 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3299 if we are in this conditional) if mc_temp is negative */
3300 if (ir->expandedvals->mc_temp < 0)
3302 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3306 /* Simulated annealing for each group. There are nr groups */
3307 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3308 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3312 if (nSA > 0 && nSA != nr)
3314 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3318 snew(ir->opts.annealing, nr);
3319 snew(ir->opts.anneal_npoints, nr);
3320 snew(ir->opts.anneal_time, nr);
3321 snew(ir->opts.anneal_temp, nr);
3322 for (i = 0; i < nr; i++)
3324 ir->opts.annealing[i] = eannNO;
3325 ir->opts.anneal_npoints[i] = 0;
3326 ir->opts.anneal_time[i] = NULL;
3327 ir->opts.anneal_temp[i] = NULL;
3332 for (i = 0; i < nr; i++)
3334 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3336 ir->opts.annealing[i] = eannNO;
3338 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3340 ir->opts.annealing[i] = eannSINGLE;
3343 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3345 ir->opts.annealing[i] = eannPERIODIC;
3351 /* Read the other fields too */
3352 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3353 if (nSA_points != nSA)
3355 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3357 for (k = 0, i = 0; i < nr; i++)
3359 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3360 if (ir->opts.anneal_npoints[i] == 1)
3362 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3364 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3365 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3366 k += ir->opts.anneal_npoints[i];
3369 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3372 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3374 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3377 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3380 for (i = 0, k = 0; i < nr; i++)
3383 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3385 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3386 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3389 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3391 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3397 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3399 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3400 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3403 if (ir->opts.anneal_temp[i][j] < 0)
3405 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3410 /* Print out some summary information, to make sure we got it right */
3411 for (i = 0, k = 0; i < nr; i++)
3413 if (ir->opts.annealing[i] != eannNO)
3415 j = groups->grps[egcTC].nm_ind[i];
3416 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3417 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3418 ir->opts.anneal_npoints[i]);
3419 fprintf(stderr, "Time (ps) Temperature (K)\n");
3420 /* All terms except the last one */
3421 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3423 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3426 /* Finally the last one */
3427 j = ir->opts.anneal_npoints[i]-1;
3428 if (ir->opts.annealing[i] == eannSINGLE)
3430 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3434 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3435 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3437 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3446 if (ir->ePull != epullNO)
3448 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3450 make_pull_coords(ir->pull);
3455 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3458 if (ir->eSwapCoords != eswapNO)
3460 make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
3463 /* Make indices for IMD session */
3466 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3469 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3470 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3471 if (nacg*DIM != nacc)
3473 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3476 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3477 restnm, egrptpALL_GENREST, bVerbose, wi);
3478 nr = groups->grps[egcACC].nr;
3479 snew(ir->opts.acc, nr);
3480 ir->opts.ngacc = nr;
3482 for (i = k = 0; (i < nacg); i++)
3484 for (j = 0; (j < DIM); j++, k++)
3486 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3489 for (; (i < nr); i++)
3491 for (j = 0; (j < DIM); j++)
3493 ir->opts.acc[i][j] = 0;
3497 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3498 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3499 if (nfrdim != DIM*nfreeze)
3501 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3504 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3505 restnm, egrptpALL_GENREST, bVerbose, wi);
3506 nr = groups->grps[egcFREEZE].nr;
3507 ir->opts.ngfrz = nr;
3508 snew(ir->opts.nFreeze, nr);
3509 for (i = k = 0; (i < nfreeze); i++)
3511 for (j = 0; (j < DIM); j++, k++)
3513 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3514 if (!ir->opts.nFreeze[i][j])
3516 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3518 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3519 "(not %s)", ptr1[k]);
3520 warning(wi, warn_buf);
3525 for (; (i < nr); i++)
3527 for (j = 0; (j < DIM); j++)
3529 ir->opts.nFreeze[i][j] = 0;
3533 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3534 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3535 restnm, egrptpALL_GENREST, bVerbose, wi);
3536 add_wall_energrps(groups, ir->nwall, symtab);
3537 ir->opts.ngener = groups->grps[egcENER].nr;
3538 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3540 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3541 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3544 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3545 "This may lead to artifacts.\n"
3546 "In most cases one should use one group for the whole system.");
3549 /* Now we have filled the freeze struct, so we can calculate NRDF */
3550 calc_nrdf(mtop, ir, gnames);
3556 /* Must check per group! */
3557 for (i = 0; (i < ir->opts.ngtc); i++)
3559 ntot += ir->opts.nrdf[i];
3561 if (ntot != (DIM*natoms))
3563 fac = sqrt(ntot/(DIM*natoms));
3566 fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
3567 "and removal of center of mass motion\n", fac);
3569 for (i = 0; (i < natoms); i++)
3571 svmul(fac, v[i], v[i]);
3576 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3577 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3578 restnm, egrptpALL_GENREST, bVerbose, wi);
3579 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3580 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3581 restnm, egrptpALL_GENREST, bVerbose, wi);
3582 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3583 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3584 restnm, egrptpONE, bVerbose, wi);
3585 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3586 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3587 restnm, egrptpALL_GENREST, bVerbose, wi);
3589 /* QMMM input processing */
3590 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3591 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3592 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3593 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3595 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3596 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3598 /* group rest, if any, is always MM! */
3599 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3600 restnm, egrptpALL_GENREST, bVerbose, wi);
3601 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3602 ir->opts.ngQM = nQMg;
3603 snew(ir->opts.QMmethod, nr);
3604 snew(ir->opts.QMbasis, nr);
3605 for (i = 0; i < nr; i++)
3607 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3608 * converted to the corresponding enum in names.c
3610 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3612 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3616 nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
3617 nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
3618 nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
3619 snew(ir->opts.QMmult, nr);
3620 snew(ir->opts.QMcharge, nr);
3621 snew(ir->opts.bSH, nr);
3623 for (i = 0; i < nr; i++)
3625 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3626 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3627 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3630 nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
3631 nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
3632 snew(ir->opts.CASelectrons, nr);
3633 snew(ir->opts.CASorbitals, nr);
3634 for (i = 0; i < nr; i++)
3636 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3637 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3639 /* special optimization options */
3641 nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
3642 nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
3643 snew(ir->opts.bOPT, nr);
3644 snew(ir->opts.bTS, nr);
3645 for (i = 0; i < nr; i++)
3647 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3648 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3650 nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
3651 nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
3652 nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
3653 snew(ir->opts.SAon, nr);
3654 snew(ir->opts.SAoff, nr);
3655 snew(ir->opts.SAsteps, nr);
3657 for (i = 0; i < nr; i++)
3659 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3660 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3661 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3663 /* end of QMMM input */
3667 for (i = 0; (i < egcNR); i++)
3669 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3670 for (j = 0; (j < groups->grps[i].nr); j++)
3672 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3674 fprintf(stderr, "\n");
3678 nr = groups->grps[egcENER].nr;
3679 snew(ir->opts.egp_flags, nr*nr);
3681 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3682 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3684 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3686 if (bExcl && EEL_FULL(ir->coulombtype))
3688 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3691 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3692 if (bTable && !(ir->vdwtype == evdwUSER) &&
3693 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3694 !(ir->coulombtype == eelPMEUSERSWITCH))
3696 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3699 decode_cos(is->efield_x, &(ir->ex[XX]));
3700 decode_cos(is->efield_xt, &(ir->et[XX]));
3701 decode_cos(is->efield_y, &(ir->ex[YY]));
3702 decode_cos(is->efield_yt, &(ir->et[YY]));
3703 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3704 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3708 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3711 for (i = 0; (i < grps->nr); i++)
3723 static void check_disre(gmx_mtop_t *mtop)
3725 gmx_ffparams_t *ffparams;
3726 t_functype *functype;
3728 int i, ndouble, ftype;
3729 int label, old_label;
3731 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3733 ffparams = &mtop->ffparams;
3734 functype = ffparams->functype;
3735 ip = ffparams->iparams;
3738 for (i = 0; i < ffparams->ntypes; i++)
3740 ftype = functype[i];
3741 if (ftype == F_DISRES)
3743 label = ip[i].disres.label;
3744 if (label == old_label)
3746 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3754 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3755 "probably the parameters for multiple pairs in one restraint "
3756 "are not identical\n", ndouble);
3761 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3762 gmx_bool posres_only,
3766 gmx_mtop_ilistloop_t iloop;
3776 for (d = 0; d < DIM; d++)
3778 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3780 /* Check for freeze groups */
3781 for (g = 0; g < ir->opts.ngfrz; g++)
3783 for (d = 0; d < DIM; d++)
3785 if (ir->opts.nFreeze[g][d] != 0)
3793 /* Check for position restraints */
3794 iloop = gmx_mtop_ilistloop_init(sys);
3795 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3798 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3800 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3802 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3803 for (d = 0; d < DIM; d++)
3805 if (pr->posres.fcA[d] != 0)
3811 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3813 /* Check for flat-bottom posres */
3814 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3815 if (pr->fbposres.k != 0)
3817 switch (pr->fbposres.geom)
3819 case efbposresSPHERE:
3820 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3822 case efbposresCYLINDER:
3823 AbsRef[XX] = AbsRef[YY] = 1;
3825 case efbposresX: /* d=XX */
3826 case efbposresY: /* d=YY */
3827 case efbposresZ: /* d=ZZ */
3828 d = pr->fbposres.geom - efbposresX;
3832 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3833 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3841 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3845 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3846 gmx_bool *bC6ParametersWorkWithGeometricRules,
3847 gmx_bool *bC6ParametersWorkWithLBRules,
3848 gmx_bool *bLBRulesPossible)
3850 int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
3853 double geometricdiff, LBdiff;
3854 double c6i, c6j, c12i, c12j;
3855 double c6, c6_geometric, c6_LB;
3856 double sigmai, sigmaj, epsi, epsj;
3857 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3860 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3861 * force-field floating point parameters.
3864 ptr = getenv("GMX_LJCOMB_TOL");
3869 sscanf(ptr, "%lf", &dbl);
3873 *bC6ParametersWorkWithLBRules = TRUE;
3874 *bC6ParametersWorkWithGeometricRules = TRUE;
3875 bCanDoLBRules = TRUE;
3876 bCanDoGeometricRules = TRUE;
3877 ntypes = mtop->ffparams.atnr;
3878 snew(typecount, ntypes);
3879 gmx_mtop_count_atomtypes(mtop, state, typecount);
3880 geometricdiff = LBdiff = 0.0;
3881 *bLBRulesPossible = TRUE;
3882 for (tpi = 0; tpi < ntypes; ++tpi)
3884 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3885 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3886 for (tpj = tpi; tpj < ntypes; ++tpj)
3888 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3889 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3890 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3891 c6_geometric = sqrt(c6i * c6j);
3892 if (!gmx_numzero(c6_geometric))
3894 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3896 sigmai = pow(c12i / c6i, 1.0/6.0);
3897 sigmaj = pow(c12j / c6j, 1.0/6.0);
3898 epsi = c6i * c6i /(4.0 * c12i);
3899 epsj = c6j * c6j /(4.0 * c12j);
3900 c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
3904 *bLBRulesPossible = FALSE;
3905 c6_LB = c6_geometric;
3907 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3910 if (FALSE == bCanDoLBRules)
3912 *bC6ParametersWorkWithLBRules = FALSE;
3915 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3917 if (FALSE == bCanDoGeometricRules)
3919 *bC6ParametersWorkWithGeometricRules = FALSE;
3927 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3931 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3933 check_combination_rule_differences(mtop, 0,
3934 &bC6ParametersWorkWithGeometricRules,
3935 &bC6ParametersWorkWithLBRules,
3937 if (ir->ljpme_combination_rule == eljpmeLB)
3939 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
3941 warning(wi, "You are using arithmetic-geometric combination rules "
3942 "in LJ-PME, but your non-bonded C6 parameters do not "
3943 "follow these rules.");
3948 if (FALSE == bC6ParametersWorkWithGeometricRules)
3950 if (ir->eDispCorr != edispcNO)
3952 warning_note(wi, "You are using geometric combination rules in "
3953 "LJ-PME, but your non-bonded C6 parameters do "
3954 "not follow these rules. "
3955 "This will introduce very small errors in the forces and energies in "
3956 "your simulations. Dispersion correction will correct total energy "
3957 "and/or pressure for isotropic systems, but not forces or surface tensions.");
3961 warning_note(wi, "You are using geometric combination rules in "
3962 "LJ-PME, but your non-bonded C6 parameters do "
3963 "not follow these rules. "
3964 "This will introduce very small errors in the forces and energies in "
3965 "your simulations. If your system is homogeneous, consider using dispersion correction "
3966 "for the total energy and pressure.");
3972 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
3975 char err_buf[STRLEN];
3976 int i, m, c, nmol, npct;
3977 gmx_bool bCharge, bAcc;
3978 real gdt_max, *mgrp, mt;
3980 gmx_mtop_atomloop_block_t aloopb;
3981 gmx_mtop_atomloop_all_t aloop;
3984 char warn_buf[STRLEN];
3986 set_warning_line(wi, mdparin, -1);
3988 if (ir->cutoff_scheme == ecutsVERLET &&
3989 ir->verletbuf_tol > 0 &&
3991 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
3992 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
3994 /* Check if a too small Verlet buffer might potentially
3995 * cause more drift than the thermostat can couple off.
3997 /* Temperature error fraction for warning and suggestion */
3998 const real T_error_warn = 0.002;
3999 const real T_error_suggest = 0.001;
4000 /* For safety: 2 DOF per atom (typical with constraints) */
4001 const real nrdf_at = 2;
4002 real T, tau, max_T_error;
4007 for (i = 0; i < ir->opts.ngtc; i++)
4009 T = max(T, ir->opts.ref_t[i]);
4010 tau = max(tau, ir->opts.tau_t[i]);
4014 /* This is a worst case estimate of the temperature error,
4015 * assuming perfect buffer estimation and no cancelation
4016 * of errors. The factor 0.5 is because energy distributes
4017 * equally over Ekin and Epot.
4019 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4020 if (max_T_error > T_error_warn)
4022 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.",
4023 ir->verletbuf_tol, T, tau,
4025 100*T_error_suggest,
4026 ir->verletbuf_tol*T_error_suggest/max_T_error);
4027 warning(wi, warn_buf);
4032 if (ETC_ANDERSEN(ir->etc))
4036 for (i = 0; i < ir->opts.ngtc; i++)
4038 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4039 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4040 sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
4041 i, ir->opts.tau_t[i]);
4042 CHECK(ir->opts.tau_t[i] < 0);
4045 for (i = 0; i < ir->opts.ngtc; i++)
4047 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
4048 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);
4049 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
4053 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4054 ir->comm_mode == ecmNO &&
4055 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4056 !ETC_ANDERSEN(ir->etc))
4058 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");
4061 /* Check for pressure coupling with absolute position restraints */
4062 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4064 absolute_reference(ir, sys, TRUE, AbsRef);
4066 for (m = 0; m < DIM; m++)
4068 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4070 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4078 aloopb = gmx_mtop_atomloop_block_init(sys);
4079 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4081 if (atom->q != 0 || atom->qB != 0)
4089 if (EEL_FULL(ir->coulombtype))
4092 "You are using full electrostatics treatment %s for a system without charges.\n"
4093 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4094 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4095 warning(wi, err_buf);
4100 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4103 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4104 "You might want to consider using %s electrostatics.\n",
4106 warning_note(wi, err_buf);
4110 /* Check if combination rules used in LJ-PME are the same as in the force field */
4111 if (EVDW_PME(ir->vdwtype))
4113 check_combination_rules(ir, sys, wi);
4116 /* Generalized reaction field */
4117 if (ir->opts.ngtc == 0)
4119 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4121 CHECK(ir->coulombtype == eelGRF);
4125 sprintf(err_buf, "When using coulombtype = %s"
4126 " ref-t for temperature coupling should be > 0",
4128 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4131 if (ir->eI == eiSD2)
4133 sprintf(warn_buf, "The stochastic dynamics integrator %s is deprecated, since\n"
4134 "it is slower than integrator %s and is slightly less accurate\n"
4135 "with constraints. Use the %s integrator.",
4136 ei_names[ir->eI], ei_names[eiSD1], ei_names[eiSD1]);
4137 warning_note(wi, warn_buf);
4141 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4143 for (m = 0; (m < DIM); m++)
4145 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4154 snew(mgrp, sys->groups.grps[egcACC].nr);
4155 aloop = gmx_mtop_atomloop_all_init(sys);
4156 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4158 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4161 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4163 for (m = 0; (m < DIM); m++)
4165 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4169 for (m = 0; (m < DIM); m++)
4171 if (fabs(acc[m]) > 1e-6)
4173 const char *dim[DIM] = { "X", "Y", "Z" };
4175 "Net Acceleration in %s direction, will %s be corrected\n",
4176 dim[m], ir->nstcomm != 0 ? "" : "not");
4177 if (ir->nstcomm != 0 && m < ndof_com(ir))
4180 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4182 ir->opts.acc[i][m] -= acc[m];
4190 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4191 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4193 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4196 if (ir->ePull != epullNO)
4198 gmx_bool bPullAbsoluteRef;
4200 bPullAbsoluteRef = FALSE;
4201 for (i = 0; i < ir->pull->ncoord; i++)
4203 bPullAbsoluteRef = bPullAbsoluteRef ||
4204 ir->pull->coord[i].group[0] == 0 ||
4205 ir->pull->coord[i].group[1] == 0;
4207 if (bPullAbsoluteRef)
4209 absolute_reference(ir, sys, FALSE, AbsRef);
4210 for (m = 0; m < DIM; m++)
4212 if (ir->pull->dim[m] && !AbsRef[m])
4214 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.");
4220 if (ir->pull->eGeom == epullgDIRPBC)
4222 for (i = 0; i < 3; i++)
4224 for (m = 0; m <= i; m++)
4226 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4227 ir->deform[i][m] != 0)
4229 for (c = 0; c < ir->pull->ncoord; c++)
4231 if (ir->pull->coord[c].vec[m] != 0)
4233 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->eGeom), 'x'+m);
4245 void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr, warninp_t wi)
4249 char warn_buf[STRLEN];
4252 ptr = check_box(ir->ePBC, box);
4255 warning_error(wi, ptr);
4258 if (bConstr && ir->eConstrAlg == econtSHAKE)
4260 if (ir->shake_tol <= 0.0)
4262 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4264 warning_error(wi, warn_buf);
4267 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
4269 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
4270 if (ir->epc == epcNO)
4272 warning(wi, warn_buf);
4276 warning_error(wi, warn_buf);
4281 if ( (ir->eConstrAlg == econtLINCS) && bConstr)
4283 /* If we have Lincs constraints: */
4284 if (ir->eI == eiMD && ir->etc == etcNO &&
4285 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4287 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4288 warning_note(wi, warn_buf);
4291 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4293 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4294 warning_note(wi, warn_buf);
4296 if (ir->epc == epcMTTK)
4298 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4302 if (bConstr && ir->epc == epcMTTK)
4304 warning_note(wi, "MTTK with constraints is deprecated, and will be removed in GROMACS 5.1");
4307 if (ir->LincsWarnAngle > 90.0)
4309 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4310 warning(wi, warn_buf);
4311 ir->LincsWarnAngle = 90.0;
4314 if (ir->ePBC != epbcNONE)
4316 if (ir->nstlist == 0)
4318 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4320 bTWIN = (ir->rlistlong > ir->rlist);
4321 if (ir->ns_type == ensGRID)
4323 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
4325 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",
4326 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
4327 warning_error(wi, warn_buf);
4332 min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
4333 if (2*ir->rlistlong >= min_size)
4335 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4336 warning_error(wi, warn_buf);
4339 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4346 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4350 real rvdw1, rvdw2, rcoul1, rcoul2;
4351 char warn_buf[STRLEN];
4353 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4357 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4362 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4368 if (rvdw1 + rvdw2 > ir->rlist ||
4369 rcoul1 + rcoul2 > ir->rlist)
4372 "The sum of the two largest charge group radii (%f) "
4373 "is larger than rlist (%f)\n",
4374 max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4375 warning(wi, warn_buf);
4379 /* Here we do not use the zero at cut-off macro,
4380 * since user defined interactions might purposely
4381 * not be zero at the cut-off.
4383 if (ir_vdw_is_zero_at_cutoff(ir) &&
4384 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
4386 sprintf(warn_buf, "The sum of the two largest charge group "
4387 "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
4388 "With exact cut-offs, better performance can be "
4389 "obtained with cutoff-scheme = %s, because it "
4390 "does not use charge groups at all.",
4392 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4393 ir->rlistlong, ir->rvdw,
4394 ecutscheme_names[ecutsVERLET]);
4397 warning(wi, warn_buf);
4401 warning_note(wi, warn_buf);
4404 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4405 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
4407 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
4408 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4410 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4411 ir->rlistlong, ir->rcoulomb,
4412 ecutscheme_names[ecutsVERLET]);
4415 warning(wi, warn_buf);
4419 warning_note(wi, warn_buf);