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49 #include "gmx_fatal.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 */
240 /* Strange macro: first one fills the err_buf, and then one can check
241 * the condition, which will print the message and increase the error
244 #define CHECK(b) _low_check(b, err_buf, wi)
245 char err_buf[256], warn_buf[STRLEN];
251 t_lambda *fep = ir->fepvals;
252 t_expanded *expand = ir->expandedvals;
254 set_warning_line(wi, mdparin, -1);
256 /* BASIC CUT-OFF STUFF */
257 if (ir->rcoulomb < 0)
259 warning_error(wi, "rcoulomb should be >= 0");
263 warning_error(wi, "rvdw should be >= 0");
266 !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
268 warning_error(wi, "rlist should be >= 0");
271 process_interaction_modifier(ir, &ir->coulomb_modifier);
272 process_interaction_modifier(ir, &ir->vdw_modifier);
274 if (ir->cutoff_scheme == ecutsGROUP)
277 "The group cutoff scheme is deprecated in Gromacs 5.0 and will be removed in a future "
278 "release when all interaction forms are supported for the verlet scheme. The verlet "
279 "scheme already scales better, and it is compatible with GPUs and other accelerators.");
281 /* BASIC CUT-OFF STUFF */
282 if (ir->rlist == 0 ||
283 !((ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > ir->rlist) ||
284 (ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > ir->rlist)))
286 /* No switched potential and/or no twin-range:
287 * we can set the long-range cut-off to the maximum of the other cut-offs.
289 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
291 else if (ir->rlistlong < 0)
293 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
294 sprintf(warn_buf, "rlistlong was not set, setting it to %g (no buffer)",
296 warning(wi, warn_buf);
298 if (ir->rlistlong == 0 && ir->ePBC != epbcNONE)
300 warning_error(wi, "Can not have an infinite cut-off with PBC");
302 if (ir->rlistlong > 0 && (ir->rlist == 0 || ir->rlistlong < ir->rlist))
304 warning_error(wi, "rlistlong can not be shorter than rlist");
306 if (IR_TWINRANGE(*ir) && ir->nstlist <= 0)
308 warning_error(wi, "Can not have nstlist<=0 with twin-range interactions");
312 if (ir->rlistlong == ir->rlist)
316 else if (ir->rlistlong > ir->rlist && ir->nstcalclr == 0)
318 warning_error(wi, "With different cutoffs for electrostatics and VdW, nstcalclr must be -1 or a positive number");
321 if (ir->cutoff_scheme == ecutsVERLET)
325 /* Normal Verlet type neighbor-list, currently only limited feature support */
326 if (inputrec2nboundeddim(ir) < 3)
328 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
330 if (ir->rcoulomb != ir->rvdw)
332 warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported");
334 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
336 if (ir->vdw_modifier == eintmodNONE ||
337 ir->vdw_modifier == eintmodPOTSHIFT)
339 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
341 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]);
342 warning_note(wi, warn_buf);
344 ir->vdwtype = evdwCUT;
348 sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
349 warning_error(wi, warn_buf);
353 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
355 warning_error(wi, "With Verlet lists only cut-off and PME LJ interactions are supported");
357 if (!(ir->coulombtype == eelCUT ||
358 (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC) ||
359 EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
361 warning_error(wi, "With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
363 if (!(ir->coulomb_modifier == eintmodNONE ||
364 ir->coulomb_modifier == eintmodPOTSHIFT))
366 sprintf(warn_buf, "coulomb_modifier=%s is not supported with the Verlet cut-off scheme", eintmod_names[ir->coulomb_modifier]);
367 warning_error(wi, warn_buf);
370 if (ir->nstlist <= 0)
372 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
375 if (ir->nstlist < 10)
377 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.");
380 rc_max = max(ir->rvdw, ir->rcoulomb);
382 if (ir->verletbuf_tol <= 0)
384 if (ir->verletbuf_tol == 0)
386 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
389 if (ir->rlist < rc_max)
391 warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
394 if (ir->rlist == rc_max && ir->nstlist > 1)
396 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.");
401 if (ir->rlist > rc_max)
403 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.");
406 if (ir->nstlist == 1)
408 /* No buffer required */
413 if (EI_DYNAMICS(ir->eI))
415 if (inputrec2nboundeddim(ir) < 3)
417 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.");
419 /* Set rlist temporarily so we can continue processing */
424 /* Set the buffer to 5% of the cut-off */
425 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
430 /* No twin-range calculations with Verlet lists */
431 ir->rlistlong = ir->rlist;
434 if (ir->nstcalclr == -1)
436 /* if rlist=rlistlong, this will later be changed to nstcalclr=0 */
437 ir->nstcalclr = ir->nstlist;
439 else if (ir->nstcalclr > 0)
441 if (ir->nstlist > 0 && (ir->nstlist % ir->nstcalclr != 0))
443 warning_error(wi, "nstlist must be evenly divisible by nstcalclr. Use nstcalclr = -1 to automatically follow nstlist");
446 else if (ir->nstcalclr < -1)
448 warning_error(wi, "nstcalclr must be a positive number (divisor of nstcalclr), or -1 to follow nstlist.");
451 if (EEL_PME(ir->coulombtype) && ir->rcoulomb > ir->rvdw && ir->nstcalclr > 1)
453 warning_error(wi, "When used with PME, the long-range component of twin-range interactions must be updated every step (nstcalclr)");
456 /* GENERAL INTEGRATOR STUFF */
457 if (!(ir->eI == eiMD || EI_VV(ir->eI)))
461 if (ir->eI == eiVVAK)
463 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]);
464 warning_note(wi, warn_buf);
466 if (!EI_DYNAMICS(ir->eI))
470 if (EI_DYNAMICS(ir->eI))
472 if (ir->nstcalcenergy < 0)
474 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
475 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
477 /* nstcalcenergy larger than nstener does not make sense.
478 * We ideally want nstcalcenergy=nstener.
482 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
486 ir->nstcalcenergy = ir->nstenergy;
490 else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
491 (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
492 (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
495 const char *nsten = "nstenergy";
496 const char *nstdh = "nstdhdl";
497 const char *min_name = nsten;
498 int min_nst = ir->nstenergy;
500 /* find the smallest of ( nstenergy, nstdhdl ) */
501 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
502 (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
504 min_nst = ir->fepvals->nstdhdl;
507 /* If the user sets nstenergy small, we should respect that */
509 "Setting nstcalcenergy (%d) equal to %s (%d)",
510 ir->nstcalcenergy, min_name, min_nst);
511 warning_note(wi, warn_buf);
512 ir->nstcalcenergy = min_nst;
515 if (ir->epc != epcNO)
517 if (ir->nstpcouple < 0)
519 ir->nstpcouple = ir_optimal_nstpcouple(ir);
522 if (IR_TWINRANGE(*ir))
524 check_nst("nstlist", ir->nstlist,
525 "nstcalcenergy", &ir->nstcalcenergy, wi);
526 if (ir->epc != epcNO)
528 check_nst("nstlist", ir->nstlist,
529 "nstpcouple", &ir->nstpcouple, wi);
533 if (ir->nstcalcenergy > 0)
535 if (ir->efep != efepNO)
537 /* nstdhdl should be a multiple of nstcalcenergy */
538 check_nst("nstcalcenergy", ir->nstcalcenergy,
539 "nstdhdl", &ir->fepvals->nstdhdl, wi);
540 /* nstexpanded should be a multiple of nstcalcenergy */
541 check_nst("nstcalcenergy", ir->nstcalcenergy,
542 "nstexpanded", &ir->expandedvals->nstexpanded, wi);
544 /* for storing exact averages nstenergy should be
545 * a multiple of nstcalcenergy
547 check_nst("nstcalcenergy", ir->nstcalcenergy,
548 "nstenergy", &ir->nstenergy, wi);
553 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
554 ir->bContinuation && ir->ld_seed != -1)
556 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)");
562 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
563 CHECK(ir->ePBC != epbcXYZ);
564 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
565 CHECK(ir->ns_type != ensGRID);
566 sprintf(err_buf, "with TPI nstlist should be larger than zero");
567 CHECK(ir->nstlist <= 0);
568 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
569 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
573 if ( (opts->nshake > 0) && (opts->bMorse) )
576 "Using morse bond-potentials while constraining bonds is useless");
577 warning(wi, warn_buf);
580 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
581 ir->bContinuation && ir->ld_seed != -1)
583 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)");
585 /* verify simulated tempering options */
589 gmx_bool bAllTempZero = TRUE;
590 for (i = 0; i < fep->n_lambda; i++)
592 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]);
593 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
594 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
596 bAllTempZero = FALSE;
599 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
600 CHECK(bAllTempZero == TRUE);
602 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
603 CHECK(ir->eI != eiVV);
605 /* check compatability of the temperature coupling with simulated tempering */
607 if (ir->etc == etcNOSEHOOVER)
609 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
610 warning_note(wi, warn_buf);
613 /* check that the temperatures make sense */
615 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);
616 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
618 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
619 CHECK(ir->simtempvals->simtemp_high <= 0);
621 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
622 CHECK(ir->simtempvals->simtemp_low <= 0);
625 /* verify free energy options */
627 if (ir->efep != efepNO)
630 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
632 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
634 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
635 (int)fep->sc_r_power);
636 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
638 sprintf(err_buf, "Can't use postive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
639 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
641 sprintf(err_buf, "Can't use postive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
642 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
644 sprintf(err_buf, "Can only use expanded ensemble with md-vv for now; should be supported for other integrators in 5.0");
645 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
647 sprintf(err_buf, "Free-energy not implemented for Ewald");
648 CHECK(ir->coulombtype == eelEWALD);
650 /* check validty of lambda inputs */
651 if (fep->n_lambda == 0)
653 /* Clear output in case of no states:*/
654 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
655 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
659 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
660 CHECK((fep->init_fep_state >= fep->n_lambda));
663 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
664 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
666 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",
667 fep->init_lambda, fep->init_fep_state);
668 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
672 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
676 for (i = 0; i < efptNR; i++)
678 if (fep->separate_dvdl[i])
683 if (n_lambda_terms > 1)
685 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.");
686 warning(wi, warn_buf);
689 if (n_lambda_terms < 2 && fep->n_lambda > 0)
692 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
696 for (j = 0; j < efptNR; j++)
698 for (i = 0; i < fep->n_lambda; i++)
700 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]);
701 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
705 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
707 for (i = 0; i < fep->n_lambda; i++)
709 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],
710 fep->all_lambda[efptCOUL][i]);
711 CHECK((fep->sc_alpha > 0) &&
712 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
713 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
714 ((fep->all_lambda[efptVDW][i] > 0.0) &&
715 (fep->all_lambda[efptVDW][i] < 1.0))));
719 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
721 real sigma, lambda, r_sc;
724 /* Maximum estimate for A and B charges equal with lambda power 1 */
726 r_sc = pow(lambda*fep->sc_alpha*pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
727 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.",
729 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
730 warning_note(wi, warn_buf);
733 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
734 be treated differently, but that's the next step */
736 for (i = 0; i < efptNR; i++)
738 for (j = 0; j < fep->n_lambda; j++)
740 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
741 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
746 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
749 expand = ir->expandedvals;
751 /* checking equilibration of weights inputs for validity */
753 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
754 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
755 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
757 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
758 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
759 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
761 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
762 expand->equil_steps, elmceq_names[elmceqSTEPS]);
763 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
765 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
766 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
767 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
769 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
770 expand->equil_ratio, elmceq_names[elmceqRATIO]);
771 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
773 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
774 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
775 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
777 sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
778 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
779 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
781 sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
782 expand->equil_steps, elmceq_names[elmceqSTEPS]);
783 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
785 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
786 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
787 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
789 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
790 expand->equil_ratio, elmceq_names[elmceqRATIO]);
791 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
793 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
794 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
795 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
797 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
798 CHECK((expand->lmc_repeats <= 0));
799 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
800 CHECK((expand->minvarmin <= 0));
801 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
802 CHECK((expand->c_range < 0));
803 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
804 fep->init_fep_state, expand->lmc_forced_nstart);
805 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
806 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
807 CHECK((expand->lmc_forced_nstart < 0));
808 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
809 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
811 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
812 CHECK((expand->init_wl_delta < 0));
813 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
814 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
815 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
816 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
818 /* if there is no temperature control, we need to specify an MC temperature */
819 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
820 if (expand->nstTij > 0)
822 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
823 expand->nstTij, ir->nstlog);
824 CHECK((mod(expand->nstTij, ir->nstlog) != 0));
829 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
830 CHECK(ir->nwall && ir->ePBC != epbcXY);
833 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
835 if (ir->ePBC == epbcNONE)
837 if (ir->epc != epcNO)
839 warning(wi, "Turning off pressure coupling for vacuum system");
845 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
846 epbc_names[ir->ePBC]);
847 CHECK(ir->epc != epcNO);
849 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
850 CHECK(EEL_FULL(ir->coulombtype));
852 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
853 epbc_names[ir->ePBC]);
854 CHECK(ir->eDispCorr != edispcNO);
857 if (ir->rlist == 0.0)
859 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
860 "with coulombtype = %s or coulombtype = %s\n"
861 "without periodic boundary conditions (pbc = %s) and\n"
862 "rcoulomb and rvdw set to zero",
863 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
864 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
865 (ir->ePBC != epbcNONE) ||
866 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
870 warning_error(wi, "Can not have heuristic neighborlist updates without cut-off");
874 warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
879 if (ir->nstcomm == 0)
881 ir->comm_mode = ecmNO;
883 if (ir->comm_mode != ecmNO)
887 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");
888 ir->nstcomm = abs(ir->nstcomm);
891 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
893 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
894 ir->nstcomm = ir->nstcalcenergy;
897 if (ir->comm_mode == ecmANGULAR)
899 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
900 CHECK(ir->bPeriodicMols);
901 if (ir->ePBC != epbcNONE)
903 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).");
908 if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
910 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.");
913 sprintf(err_buf, "Twin-range neighbour searching (NS) with simple NS"
914 " algorithm not implemented");
915 CHECK(((ir->rcoulomb > ir->rlist) || (ir->rvdw > ir->rlist))
916 && (ir->ns_type == ensSIMPLE));
918 /* TEMPERATURE COUPLING */
919 if (ir->etc == etcYES)
921 ir->etc = etcBERENDSEN;
922 warning_note(wi, "Old option for temperature coupling given: "
923 "changing \"yes\" to \"Berendsen\"\n");
926 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
928 if (ir->opts.nhchainlength < 1)
930 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
931 ir->opts.nhchainlength = 1;
932 warning(wi, warn_buf);
935 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
937 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
938 ir->opts.nhchainlength = 1;
943 ir->opts.nhchainlength = 0;
946 if (ir->eI == eiVVAK)
948 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
950 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
953 if (ETC_ANDERSEN(ir->etc))
955 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
956 CHECK(!(EI_VV(ir->eI)));
958 for (i = 0; i < ir->opts.ngtc; i++)
960 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
961 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
962 sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
963 i, ir->opts.tau_t[i]);
964 CHECK(ir->opts.tau_t[i] < 0);
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));
975 for (i = 0; i < ir->opts.ngtc; i++)
977 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
978 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);
979 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
982 if (ir->etc == etcBERENDSEN)
984 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
985 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
986 warning_note(wi, warn_buf);
989 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
990 && ir->epc == epcBERENDSEN)
992 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
993 "true ensemble for the thermostat");
994 warning(wi, warn_buf);
997 /* PRESSURE COUPLING */
998 if (ir->epc == epcISOTROPIC)
1000 ir->epc = epcBERENDSEN;
1001 warning_note(wi, "Old option for pressure coupling given: "
1002 "changing \"Isotropic\" to \"Berendsen\"\n");
1005 if (ir->epc != epcNO)
1007 dt_pcoupl = ir->nstpcouple*ir->delta_t;
1009 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1010 CHECK(ir->tau_p <= 0);
1012 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc))
1014 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
1015 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1016 warning(wi, warn_buf);
1019 sprintf(err_buf, "compressibility must be > 0 when using pressure"
1020 " coupling %s\n", EPCOUPLTYPE(ir->epc));
1021 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
1022 ir->compress[ZZ][ZZ] < 0 ||
1023 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
1024 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
1026 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1029 "You are generating velocities so I am assuming you "
1030 "are equilibrating a system. You are using "
1031 "%s pressure coupling, but this can be "
1032 "unstable for equilibration. If your system crashes, try "
1033 "equilibrating first with Berendsen pressure coupling. If "
1034 "you are not equilibrating the system, you can probably "
1035 "ignore this warning.",
1036 epcoupl_names[ir->epc]);
1037 warning(wi, warn_buf);
1043 if (ir->epc > epcNO)
1045 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1047 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.");
1053 if (ir->epc == epcMTTK)
1055 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1059 /* ELECTROSTATICS */
1060 /* More checks are in triple check (grompp.c) */
1062 if (ir->coulombtype == eelSWITCH)
1064 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1065 "artifacts, advice: use coulombtype = %s",
1066 eel_names[ir->coulombtype],
1067 eel_names[eelRF_ZERO]);
1068 warning(wi, warn_buf);
1071 if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
1073 sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
1074 warning_note(wi, warn_buf);
1077 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1079 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);
1080 warning(wi, warn_buf);
1081 ir->epsilon_rf = ir->epsilon_r;
1082 ir->epsilon_r = 1.0;
1085 if (getenv("GALACTIC_DYNAMICS") == NULL)
1087 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1088 CHECK(ir->epsilon_r < 0);
1091 if (EEL_RF(ir->coulombtype))
1093 /* reaction field (at the cut-off) */
1095 if (ir->coulombtype == eelRF_ZERO)
1097 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1098 eel_names[ir->coulombtype]);
1099 CHECK(ir->epsilon_rf != 0);
1100 ir->epsilon_rf = 0.0;
1103 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1104 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1105 (ir->epsilon_r == 0));
1106 if (ir->epsilon_rf == ir->epsilon_r)
1108 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1109 eel_names[ir->coulombtype]);
1110 warning(wi, warn_buf);
1113 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1114 * means the interaction is zero outside rcoulomb, but it helps to
1115 * provide accurate energy conservation.
1117 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1119 if (ir_coulomb_switched(ir))
1122 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1123 eel_names[ir->coulombtype]);
1124 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1127 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1129 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1131 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1132 eel_names[ir->coulombtype]);
1133 CHECK(ir->rlist > ir->rcoulomb);
1137 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1138 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1141 "The switch/shift interaction settings are just for compatibility; you will get better "
1142 "performance from applying potential modifiers to your interactions!\n");
1143 warning_note(wi, warn_buf);
1146 if (ir->coulombtype == eelPMESWITCH)
1148 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1150 sprintf(warn_buf, "The switching range for %s should be 5%% or less, energy conservation will be good anyhow, since ewald_rtol = %g",
1151 eel_names[ir->coulombtype],
1153 warning(wi, warn_buf);
1157 if (EEL_FULL(ir->coulombtype))
1159 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1160 ir->coulombtype == eelPMEUSERSWITCH)
1162 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1163 eel_names[ir->coulombtype]);
1164 CHECK(ir->rcoulomb > ir->rlist);
1166 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1168 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1171 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
1172 "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
1173 "a potential modifier.", eel_names[ir->coulombtype]);
1174 if (ir->nstcalclr == 1)
1176 CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
1180 CHECK(ir->rcoulomb != ir->rlist);
1186 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1188 if (ir->pme_order < 3)
1190 warning_error(wi, "pme-order can not be smaller than 3");
1194 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1196 if (ir->ewald_geometry == eewg3D)
1198 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1199 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1200 warning(wi, warn_buf);
1202 /* This check avoids extra pbc coding for exclusion corrections */
1203 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1204 CHECK(ir->wall_ewald_zfac < 2);
1207 if (ir_vdw_switched(ir))
1209 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1210 CHECK(ir->rvdw_switch >= ir->rvdw);
1212 if (ir->rvdw_switch < 0.5*ir->rvdw)
1214 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.",
1215 ir->rvdw_switch, ir->rvdw);
1216 warning_note(wi, warn_buf);
1219 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1221 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1223 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1224 CHECK(ir->rlist > ir->rvdw);
1228 if (ir->cutoff_scheme == ecutsGROUP)
1230 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1231 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)) &&
1234 warning_note(wi, "With exact cut-offs, rlist should be "
1235 "larger than rcoulomb and rvdw, so that there "
1236 "is a buffer region for particle motion "
1237 "between neighborsearch steps");
1240 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlistlong <= ir->rcoulomb)
1242 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
1243 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1244 warning_note(wi, warn_buf);
1246 if (ir_vdw_switched(ir) && (ir->rlistlong <= ir->rvdw))
1248 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
1249 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1250 warning_note(wi, warn_buf);
1254 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1256 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.");
1259 if (ir->nstlist == -1)
1261 sprintf(err_buf, "With nstlist=-1 rvdw and rcoulomb should be smaller than rlist to account for diffusion and possibly charge-group radii");
1262 CHECK(ir->rvdw >= ir->rlist || ir->rcoulomb >= ir->rlist);
1264 sprintf(err_buf, "nstlist can not be smaller than -1");
1265 CHECK(ir->nstlist < -1);
1267 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1270 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1273 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1275 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1278 /* ENERGY CONSERVATION */
1279 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1281 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1283 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1284 evdw_names[evdwSHIFT]);
1285 warning_note(wi, warn_buf);
1287 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1289 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1290 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1291 warning_note(wi, warn_buf);
1295 /* IMPLICIT SOLVENT */
1296 if (ir->coulombtype == eelGB_NOTUSED)
1298 ir->coulombtype = eelCUT;
1299 ir->implicit_solvent = eisGBSA;
1300 fprintf(stderr, "Note: Old option for generalized born electrostatics given:\n"
1301 "Changing coulombtype from \"generalized-born\" to \"cut-off\" and instead\n"
1302 "setting implicit-solvent value to \"GBSA\" in input section.\n");
1305 if (ir->sa_algorithm == esaSTILL)
1307 sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
1308 CHECK(ir->sa_algorithm == esaSTILL);
1311 if (ir->implicit_solvent == eisGBSA)
1313 sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
1314 CHECK(ir->rgbradii != ir->rlist);
1316 if (ir->coulombtype != eelCUT)
1318 sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
1319 CHECK(ir->coulombtype != eelCUT);
1321 if (ir->vdwtype != evdwCUT)
1323 sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
1324 CHECK(ir->vdwtype != evdwCUT);
1326 if (ir->nstgbradii < 1)
1328 sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
1329 warning_note(wi, warn_buf);
1332 if (ir->sa_algorithm == esaNO)
1334 sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
1335 warning_note(wi, warn_buf);
1337 if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
1339 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");
1340 warning_note(wi, warn_buf);
1342 if (ir->gb_algorithm == egbSTILL)
1344 ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
1348 ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
1351 if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
1353 sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
1354 CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
1361 if (ir->cutoff_scheme != ecutsGROUP)
1363 warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
1367 warning_error(wi, "AdresS simulation supports only stochastic dynamics");
1369 if (ir->epc != epcNO)
1371 warning_error(wi, "AdresS simulation does not support pressure coupling");
1373 if (EEL_FULL(ir->coulombtype))
1375 warning_error(wi, "AdresS simulation does not support long-range electrostatics");
1380 /* count the number of text elemets separated by whitespace in a string.
1381 str = the input string
1382 maxptr = the maximum number of allowed elements
1383 ptr = the output array of pointers to the first character of each element
1384 returns: the number of elements. */
1385 int str_nelem(const char *str, int maxptr, char *ptr[])
1390 copy0 = strdup(str);
1393 while (*copy != '\0')
1397 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1405 while ((*copy != '\0') && !isspace(*copy))
1424 /* interpret a number of doubles from a string and put them in an array,
1425 after allocating space for them.
1426 str = the input string
1427 n = the (pre-allocated) number of doubles read
1428 r = the output array of doubles. */
1429 static void parse_n_real(char *str, int *n, real **r)
1434 *n = str_nelem(str, MAXPTR, ptr);
1437 for (i = 0; i < *n; i++)
1439 (*r)[i] = strtod(ptr[i], NULL);
1443 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
1446 int i, j, max_n_lambda, nweights, nfep[efptNR];
1447 t_lambda *fep = ir->fepvals;
1448 t_expanded *expand = ir->expandedvals;
1449 real **count_fep_lambdas;
1450 gmx_bool bOneLambda = TRUE;
1452 snew(count_fep_lambdas, efptNR);
1454 /* FEP input processing */
1455 /* first, identify the number of lambda values for each type.
1456 All that are nonzero must have the same number */
1458 for (i = 0; i < efptNR; i++)
1460 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
1463 /* now, determine the number of components. All must be either zero, or equal. */
1466 for (i = 0; i < efptNR; i++)
1468 if (nfep[i] > max_n_lambda)
1470 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1471 must have the same number if its not zero.*/
1476 for (i = 0; i < efptNR; i++)
1480 ir->fepvals->separate_dvdl[i] = FALSE;
1482 else if (nfep[i] == max_n_lambda)
1484 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1485 respect to the temperature currently */
1487 ir->fepvals->separate_dvdl[i] = TRUE;
1492 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1493 nfep[i], efpt_names[i], max_n_lambda);
1496 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1497 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1499 /* the number of lambdas is the number we've read in, which is either zero
1500 or the same for all */
1501 fep->n_lambda = max_n_lambda;
1503 /* allocate space for the array of lambda values */
1504 snew(fep->all_lambda, efptNR);
1505 /* if init_lambda is defined, we need to set lambda */
1506 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1508 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1510 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1511 for (i = 0; i < efptNR; i++)
1513 snew(fep->all_lambda[i], fep->n_lambda);
1514 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1517 for (j = 0; j < fep->n_lambda; j++)
1519 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1521 sfree(count_fep_lambdas[i]);
1524 sfree(count_fep_lambdas);
1526 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1527 bookkeeping -- for now, init_lambda */
1529 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1531 for (i = 0; i < fep->n_lambda; i++)
1533 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1537 /* check to see if only a single component lambda is defined, and soft core is defined.
1538 In this case, turn on coulomb soft core */
1540 if (max_n_lambda == 0)
1546 for (i = 0; i < efptNR; i++)
1548 if ((nfep[i] != 0) && (i != efptFEP))
1554 if ((bOneLambda) && (fep->sc_alpha > 0))
1556 fep->bScCoul = TRUE;
1559 /* Fill in the others with the efptFEP if they are not explicitly
1560 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1561 they are all zero. */
1563 for (i = 0; i < efptNR; i++)
1565 if ((nfep[i] == 0) && (i != efptFEP))
1567 for (j = 0; j < fep->n_lambda; j++)
1569 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1575 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1576 if (fep->sc_r_power == 48)
1578 if (fep->sc_alpha > 0.1)
1580 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1584 expand = ir->expandedvals;
1585 /* now read in the weights */
1586 parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
1589 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1591 else if (nweights != fep->n_lambda)
1593 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1594 nweights, fep->n_lambda);
1596 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1598 expand->nstexpanded = fep->nstdhdl;
1599 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1601 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1603 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1604 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1605 2*tau_t just to be careful so it's not to frequent */
1610 static void do_simtemp_params(t_inputrec *ir)
1613 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1614 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1619 static void do_wall_params(t_inputrec *ir,
1620 char *wall_atomtype, char *wall_density,
1624 char *names[MAXPTR];
1627 opts->wall_atomtype[0] = NULL;
1628 opts->wall_atomtype[1] = NULL;
1630 ir->wall_atomtype[0] = -1;
1631 ir->wall_atomtype[1] = -1;
1632 ir->wall_density[0] = 0;
1633 ir->wall_density[1] = 0;
1637 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1638 if (nstr != ir->nwall)
1640 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1643 for (i = 0; i < ir->nwall; i++)
1645 opts->wall_atomtype[i] = strdup(names[i]);
1648 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1650 nstr = str_nelem(wall_density, MAXPTR, names);
1651 if (nstr != ir->nwall)
1653 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1655 for (i = 0; i < ir->nwall; i++)
1657 sscanf(names[i], "%lf", &dbl);
1660 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1662 ir->wall_density[i] = dbl;
1668 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1676 srenew(groups->grpname, groups->ngrpname+nwall);
1677 grps = &(groups->grps[egcENER]);
1678 srenew(grps->nm_ind, grps->nr+nwall);
1679 for (i = 0; i < nwall; i++)
1681 sprintf(str, "wall%d", i);
1682 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1683 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1688 void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1689 t_expanded *expand, warninp_t wi)
1691 int ninp, nerror = 0;
1697 /* read expanded ensemble parameters */
1698 CCTYPE ("expanded ensemble variables");
1699 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1700 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1701 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1702 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1703 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1704 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1705 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1706 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1707 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1708 CCTYPE("Seed for Monte Carlo in lambda space");
1709 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1710 RTYPE ("mc-temperature", expand->mc_temp, -1);
1711 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1712 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1713 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1714 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1715 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1716 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1717 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1718 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1719 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1720 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1721 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
1729 void get_ir(const char *mdparin, const char *mdparout,
1730 t_inputrec *ir, t_gromppopts *opts,
1734 double dumdub[2][6];
1738 char warn_buf[STRLEN];
1739 t_lambda *fep = ir->fepvals;
1740 t_expanded *expand = ir->expandedvals;
1742 init_inputrec_strings();
1743 inp = read_inpfile(mdparin, &ninp, wi);
1745 snew(dumstr[0], STRLEN);
1746 snew(dumstr[1], STRLEN);
1748 if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
1751 "%s did not specify a value for the .mdp option "
1752 "\"cutoff-scheme\". Probably it was first intended for use "
1753 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1754 "introduced, but the group scheme was still the default. "
1755 "The default is now the Verlet scheme, so you will observe "
1756 "different behaviour.", mdparin);
1757 warning_note(wi, warn_buf);
1760 /* remove the following deprecated commands */
1763 REM_TYPE("domain-decomposition");
1764 REM_TYPE("andersen-seed");
1766 REM_TYPE("dihre-fc");
1767 REM_TYPE("dihre-tau");
1768 REM_TYPE("nstdihreout");
1769 REM_TYPE("nstcheckpoint");
1771 /* replace the following commands with the clearer new versions*/
1772 REPL_TYPE("unconstrained-start", "continuation");
1773 REPL_TYPE("foreign-lambda", "fep-lambdas");
1774 REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
1775 REPL_TYPE("nstxtcout", "nstxout-compressed");
1776 REPL_TYPE("xtc-grps", "compressed-x-grps");
1777 REPL_TYPE("xtc-precision", "compressed-x-precision");
1779 CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
1780 CTYPE ("Preprocessor information: use cpp syntax.");
1781 CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
1782 STYPE ("include", opts->include, NULL);
1783 CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1784 STYPE ("define", opts->define, NULL);
1786 CCTYPE ("RUN CONTROL PARAMETERS");
1787 EETYPE("integrator", ir->eI, ei_names);
1788 CTYPE ("Start time and timestep in ps");
1789 RTYPE ("tinit", ir->init_t, 0.0);
1790 RTYPE ("dt", ir->delta_t, 0.001);
1791 STEPTYPE ("nsteps", ir->nsteps, 0);
1792 CTYPE ("For exact run continuation or redoing part of a run");
1793 STEPTYPE ("init-step", ir->init_step, 0);
1794 CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
1795 ITYPE ("simulation-part", ir->simulation_part, 1);
1796 CTYPE ("mode for center of mass motion removal");
1797 EETYPE("comm-mode", ir->comm_mode, ecm_names);
1798 CTYPE ("number of steps for center of mass motion removal");
1799 ITYPE ("nstcomm", ir->nstcomm, 100);
1800 CTYPE ("group(s) for center of mass motion removal");
1801 STYPE ("comm-grps", is->vcm, NULL);
1803 CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
1804 CTYPE ("Friction coefficient (amu/ps) and random seed");
1805 RTYPE ("bd-fric", ir->bd_fric, 0.0);
1806 STEPTYPE ("ld-seed", ir->ld_seed, -1);
1809 CCTYPE ("ENERGY MINIMIZATION OPTIONS");
1810 CTYPE ("Force tolerance and initial step-size");
1811 RTYPE ("emtol", ir->em_tol, 10.0);
1812 RTYPE ("emstep", ir->em_stepsize, 0.01);
1813 CTYPE ("Max number of iterations in relax-shells");
1814 ITYPE ("niter", ir->niter, 20);
1815 CTYPE ("Step size (ps^2) for minimization of flexible constraints");
1816 RTYPE ("fcstep", ir->fc_stepsize, 0);
1817 CTYPE ("Frequency of steepest descents steps when doing CG");
1818 ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
1819 ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
1821 CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
1822 RTYPE ("rtpi", ir->rtpi, 0.05);
1824 /* Output options */
1825 CCTYPE ("OUTPUT CONTROL OPTIONS");
1826 CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
1827 ITYPE ("nstxout", ir->nstxout, 0);
1828 ITYPE ("nstvout", ir->nstvout, 0);
1829 ITYPE ("nstfout", ir->nstfout, 0);
1830 ir->nstcheckpoint = 1000;
1831 CTYPE ("Output frequency for energies to log file and energy file");
1832 ITYPE ("nstlog", ir->nstlog, 1000);
1833 ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
1834 ITYPE ("nstenergy", ir->nstenergy, 1000);
1835 CTYPE ("Output frequency and precision for .xtc file");
1836 ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
1837 RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
1838 CTYPE ("This selects the subset of atoms for the compressed");
1839 CTYPE ("trajectory file. You can select multiple groups. By");
1840 CTYPE ("default, all atoms will be written.");
1841 STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
1842 CTYPE ("Selection of energy groups");
1843 STYPE ("energygrps", is->energy, NULL);
1845 /* Neighbor searching */
1846 CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
1847 CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1848 EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
1849 CTYPE ("nblist update frequency");
1850 ITYPE ("nstlist", ir->nstlist, 10);
1851 CTYPE ("ns algorithm (simple or grid)");
1852 EETYPE("ns-type", ir->ns_type, ens_names);
1853 /* set ndelta to the optimal value of 2 */
1855 CTYPE ("Periodic boundary conditions: xyz, no, xy");
1856 EETYPE("pbc", ir->ePBC, epbc_names);
1857 EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
1858 CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1859 CTYPE ("a value of -1 means: use rlist");
1860 RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
1861 CTYPE ("nblist cut-off");
1862 RTYPE ("rlist", ir->rlist, 1.0);
1863 CTYPE ("long-range cut-off for switched potentials");
1864 RTYPE ("rlistlong", ir->rlistlong, -1);
1865 ITYPE ("nstcalclr", ir->nstcalclr, -1);
1867 /* Electrostatics */
1868 CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
1869 CTYPE ("Method for doing electrostatics");
1870 EETYPE("coulombtype", ir->coulombtype, eel_names);
1871 EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
1872 CTYPE ("cut-off lengths");
1873 RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
1874 RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
1875 CTYPE ("Relative dielectric constant for the medium and the reaction field");
1876 RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
1877 RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
1878 CTYPE ("Method for doing Van der Waals");
1879 EETYPE("vdw-type", ir->vdwtype, evdw_names);
1880 EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
1881 CTYPE ("cut-off lengths");
1882 RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
1883 RTYPE ("rvdw", ir->rvdw, 1.0);
1884 CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
1885 EETYPE("DispCorr", ir->eDispCorr, edispc_names);
1886 CTYPE ("Extension of the potential lookup tables beyond the cut-off");
1887 RTYPE ("table-extension", ir->tabext, 1.0);
1888 CTYPE ("Separate tables between energy group pairs");
1889 STYPE ("energygrp-table", is->egptable, NULL);
1890 CTYPE ("Spacing for the PME/PPPM FFT grid");
1891 RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
1892 CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
1893 ITYPE ("fourier-nx", ir->nkx, 0);
1894 ITYPE ("fourier-ny", ir->nky, 0);
1895 ITYPE ("fourier-nz", ir->nkz, 0);
1896 CTYPE ("EWALD/PME/PPPM parameters");
1897 ITYPE ("pme-order", ir->pme_order, 4);
1898 RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
1899 RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
1900 EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
1901 EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
1902 RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
1903 EETYPE("optimize-fft", ir->bOptFFT, yesno_names);
1905 CCTYPE("IMPLICIT SOLVENT ALGORITHM");
1906 EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
1908 CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
1909 CTYPE ("Algorithm for calculating Born radii");
1910 EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
1911 CTYPE ("Frequency of calculating the Born radii inside rlist");
1912 ITYPE ("nstgbradii", ir->nstgbradii, 1);
1913 CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
1914 CTYPE ("between rlist and rgbradii is updated every nstlist steps");
1915 RTYPE ("rgbradii", ir->rgbradii, 1.0);
1916 CTYPE ("Dielectric coefficient of the implicit solvent");
1917 RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
1918 CTYPE ("Salt concentration in M for Generalized Born models");
1919 RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
1920 CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
1921 RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
1922 RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
1923 RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
1924 RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
1925 EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
1926 CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
1927 CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
1928 RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
1930 /* Coupling stuff */
1931 CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
1932 CTYPE ("Temperature coupling");
1933 EETYPE("tcoupl", ir->etc, etcoupl_names);
1934 ITYPE ("nsttcouple", ir->nsttcouple, -1);
1935 ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
1936 EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
1937 CTYPE ("Groups to couple separately");
1938 STYPE ("tc-grps", is->tcgrps, NULL);
1939 CTYPE ("Time constant (ps) and reference temperature (K)");
1940 STYPE ("tau-t", is->tau_t, NULL);
1941 STYPE ("ref-t", is->ref_t, NULL);
1942 CTYPE ("pressure coupling");
1943 EETYPE("pcoupl", ir->epc, epcoupl_names);
1944 EETYPE("pcoupltype", ir->epct, epcoupltype_names);
1945 ITYPE ("nstpcouple", ir->nstpcouple, -1);
1946 CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
1947 RTYPE ("tau-p", ir->tau_p, 1.0);
1948 STYPE ("compressibility", dumstr[0], NULL);
1949 STYPE ("ref-p", dumstr[1], NULL);
1950 CTYPE ("Scaling of reference coordinates, No, All or COM");
1951 EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
1954 CCTYPE ("OPTIONS FOR QMMM calculations");
1955 EETYPE("QMMM", ir->bQMMM, yesno_names);
1956 CTYPE ("Groups treated Quantum Mechanically");
1957 STYPE ("QMMM-grps", is->QMMM, NULL);
1958 CTYPE ("QM method");
1959 STYPE("QMmethod", is->QMmethod, NULL);
1960 CTYPE ("QMMM scheme");
1961 EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
1962 CTYPE ("QM basisset");
1963 STYPE("QMbasis", is->QMbasis, NULL);
1964 CTYPE ("QM charge");
1965 STYPE ("QMcharge", is->QMcharge, NULL);
1966 CTYPE ("QM multiplicity");
1967 STYPE ("QMmult", is->QMmult, NULL);
1968 CTYPE ("Surface Hopping");
1969 STYPE ("SH", is->bSH, NULL);
1970 CTYPE ("CAS space options");
1971 STYPE ("CASorbitals", is->CASorbitals, NULL);
1972 STYPE ("CASelectrons", is->CASelectrons, NULL);
1973 STYPE ("SAon", is->SAon, NULL);
1974 STYPE ("SAoff", is->SAoff, NULL);
1975 STYPE ("SAsteps", is->SAsteps, NULL);
1976 CTYPE ("Scale factor for MM charges");
1977 RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
1978 CTYPE ("Optimization of QM subsystem");
1979 STYPE ("bOPT", is->bOPT, NULL);
1980 STYPE ("bTS", is->bTS, NULL);
1982 /* Simulated annealing */
1983 CCTYPE("SIMULATED ANNEALING");
1984 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
1985 STYPE ("annealing", is->anneal, NULL);
1986 CTYPE ("Number of time points to use for specifying annealing in each group");
1987 STYPE ("annealing-npoints", is->anneal_npoints, NULL);
1988 CTYPE ("List of times at the annealing points for each group");
1989 STYPE ("annealing-time", is->anneal_time, NULL);
1990 CTYPE ("Temp. at each annealing point, for each group.");
1991 STYPE ("annealing-temp", is->anneal_temp, NULL);
1994 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
1995 EETYPE("gen-vel", opts->bGenVel, yesno_names);
1996 RTYPE ("gen-temp", opts->tempi, 300.0);
1997 ITYPE ("gen-seed", opts->seed, -1);
2000 CCTYPE ("OPTIONS FOR BONDS");
2001 EETYPE("constraints", opts->nshake, constraints);
2002 CTYPE ("Type of constraint algorithm");
2003 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
2004 CTYPE ("Do not constrain the start configuration");
2005 EETYPE("continuation", ir->bContinuation, yesno_names);
2006 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
2007 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
2008 CTYPE ("Relative tolerance of shake");
2009 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
2010 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
2011 ITYPE ("lincs-order", ir->nProjOrder, 4);
2012 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
2013 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
2014 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
2015 ITYPE ("lincs-iter", ir->nLincsIter, 1);
2016 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
2017 CTYPE ("rotates over more degrees than");
2018 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
2019 CTYPE ("Convert harmonic bonds to morse potentials");
2020 EETYPE("morse", opts->bMorse, yesno_names);
2022 /* Energy group exclusions */
2023 CCTYPE ("ENERGY GROUP EXCLUSIONS");
2024 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
2025 STYPE ("energygrp-excl", is->egpexcl, NULL);
2029 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2030 ITYPE ("nwall", ir->nwall, 0);
2031 EETYPE("wall-type", ir->wall_type, ewt_names);
2032 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
2033 STYPE ("wall-atomtype", is->wall_atomtype, NULL);
2034 STYPE ("wall-density", is->wall_density, NULL);
2035 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
2038 CCTYPE("COM PULLING");
2039 CTYPE("Pull type: no, umbrella, constraint or constant-force");
2040 EETYPE("pull", ir->ePull, epull_names);
2041 if (ir->ePull != epullNO)
2044 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
2047 /* Enforced rotation */
2048 CCTYPE("ENFORCED ROTATION");
2049 CTYPE("Enforced rotation: No or Yes");
2050 EETYPE("rotation", ir->bRot, yesno_names);
2054 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2057 /* Interactive MD */
2059 CCTYPE("Group to display and/or manipulate in interactive MD session");
2060 STYPE ("IMD-group", is->imd_grp, NULL);
2061 if (is->imd_grp[0] != '\0')
2068 CCTYPE("NMR refinement stuff");
2069 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2070 EETYPE("disre", ir->eDisre, edisre_names);
2071 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2072 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2073 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2074 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2075 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2076 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2077 CTYPE ("Output frequency for pair distances to energy file");
2078 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2079 CTYPE ("Orientation restraints: No or Yes");
2080 EETYPE("orire", opts->bOrire, yesno_names);
2081 CTYPE ("Orientation restraints force constant and tau for time averaging");
2082 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2083 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2084 STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
2085 CTYPE ("Output frequency for trace(SD) and S to energy file");
2086 ITYPE ("nstorireout", ir->nstorireout, 100);
2088 /* free energy variables */
2089 CCTYPE ("Free energy variables");
2090 EETYPE("free-energy", ir->efep, efep_names);
2091 STYPE ("couple-moltype", is->couple_moltype, NULL);
2092 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2093 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2094 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2096 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2098 it was not entered */
2099 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2100 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2101 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2102 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
2103 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
2104 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
2105 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
2106 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
2107 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
2108 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
2109 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2110 STYPE ("init-lambda-weights", is->lambda_weights, NULL);
2111 EETYPE("dhdl-print-energy", fep->bPrintEnergy, yesno_names);
2112 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2113 ITYPE ("sc-power", fep->sc_power, 1);
2114 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2115 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2116 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2117 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2118 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2119 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2120 separate_dhdl_file_names);
2121 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2122 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2123 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2125 /* Non-equilibrium MD stuff */
2126 CCTYPE("Non-equilibrium MD stuff");
2127 STYPE ("acc-grps", is->accgrps, NULL);
2128 STYPE ("accelerate", is->acc, NULL);
2129 STYPE ("freezegrps", is->freeze, NULL);
2130 STYPE ("freezedim", is->frdim, NULL);
2131 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2132 STYPE ("deform", is->deform, NULL);
2134 /* simulated tempering variables */
2135 CCTYPE("simulated tempering variables");
2136 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2137 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2138 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2139 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2141 /* expanded ensemble variables */
2142 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2144 read_expandedparams(&ninp, &inp, expand, wi);
2147 /* Electric fields */
2148 CCTYPE("Electric fields");
2149 CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
2150 CTYPE ("and a phase angle (real)");
2151 STYPE ("E-x", is->efield_x, NULL);
2152 STYPE ("E-xt", is->efield_xt, NULL);
2153 STYPE ("E-y", is->efield_y, NULL);
2154 STYPE ("E-yt", is->efield_yt, NULL);
2155 STYPE ("E-z", is->efield_z, NULL);
2156 STYPE ("E-zt", is->efield_zt, NULL);
2158 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2159 CTYPE("Swap positions along direction: no, X, Y, Z");
2160 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2161 if (ir->eSwapCoords != eswapNO)
2164 CTYPE("Swap attempt frequency");
2165 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2166 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2167 STYPE("split-group0", splitgrp0, NULL);
2168 STYPE("split-group1", splitgrp1, NULL);
2169 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2170 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2171 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2173 CTYPE("Group name of ions that can be exchanged with solvent molecules");
2174 STYPE("swap-group", swapgrp, NULL);
2175 CTYPE("Group name of solvent molecules");
2176 STYPE("solvent-group", solgrp, NULL);
2178 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2179 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2180 CTYPE("however, if correctly defined, the ion permeation events are counted per channel");
2181 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2182 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2183 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2184 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2185 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2186 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2188 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2189 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2190 CTYPE("Requested number of anions and cations for each of the two compartments");
2191 CTYPE("-1 means fix the numbers as found in time step 0");
2192 ITYPE("anionsA", ir->swap->nanions[0], -1);
2193 ITYPE("cationsA", ir->swap->ncations[0], -1);
2194 ITYPE("anionsB", ir->swap->nanions[1], -1);
2195 ITYPE("cationsB", ir->swap->ncations[1], -1);
2196 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2197 RTYPE("threshold", ir->swap->threshold, 1.0);
2200 /* AdResS defined thingies */
2201 CCTYPE ("AdResS parameters");
2202 EETYPE("adress", ir->bAdress, yesno_names);
2205 snew(ir->adress, 1);
2206 read_adressparams(&ninp, &inp, ir->adress, wi);
2209 /* User defined thingies */
2210 CCTYPE ("User defined thingies");
2211 STYPE ("user1-grps", is->user1, NULL);
2212 STYPE ("user2-grps", is->user2, NULL);
2213 ITYPE ("userint1", ir->userint1, 0);
2214 ITYPE ("userint2", ir->userint2, 0);
2215 ITYPE ("userint3", ir->userint3, 0);
2216 ITYPE ("userint4", ir->userint4, 0);
2217 RTYPE ("userreal1", ir->userreal1, 0);
2218 RTYPE ("userreal2", ir->userreal2, 0);
2219 RTYPE ("userreal3", ir->userreal3, 0);
2220 RTYPE ("userreal4", ir->userreal4, 0);
2223 write_inpfile(mdparout, ninp, inp, FALSE, wi);
2224 for (i = 0; (i < ninp); i++)
2227 sfree(inp[i].value);
2231 /* Process options if necessary */
2232 for (m = 0; m < 2; m++)
2234 for (i = 0; i < 2*DIM; i++)
2243 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2245 warning_error(wi, "Pressure coupling not enough values (I need 1)");
2247 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2249 case epctSEMIISOTROPIC:
2250 case epctSURFACETENSION:
2251 if (sscanf(dumstr[m], "%lf%lf",
2252 &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2254 warning_error(wi, "Pressure coupling not enough values (I need 2)");
2256 dumdub[m][YY] = dumdub[m][XX];
2258 case epctANISOTROPIC:
2259 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2260 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2261 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2263 warning_error(wi, "Pressure coupling not enough values (I need 6)");
2267 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2268 epcoupltype_names[ir->epct]);
2272 clear_mat(ir->ref_p);
2273 clear_mat(ir->compress);
2274 for (i = 0; i < DIM; i++)
2276 ir->ref_p[i][i] = dumdub[1][i];
2277 ir->compress[i][i] = dumdub[0][i];
2279 if (ir->epct == epctANISOTROPIC)
2281 ir->ref_p[XX][YY] = dumdub[1][3];
2282 ir->ref_p[XX][ZZ] = dumdub[1][4];
2283 ir->ref_p[YY][ZZ] = dumdub[1][5];
2284 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2286 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2288 ir->compress[XX][YY] = dumdub[0][3];
2289 ir->compress[XX][ZZ] = dumdub[0][4];
2290 ir->compress[YY][ZZ] = dumdub[0][5];
2291 for (i = 0; i < DIM; i++)
2293 for (m = 0; m < i; m++)
2295 ir->ref_p[i][m] = ir->ref_p[m][i];
2296 ir->compress[i][m] = ir->compress[m][i];
2301 if (ir->comm_mode == ecmNO)
2306 opts->couple_moltype = NULL;
2307 if (strlen(is->couple_moltype) > 0)
2309 if (ir->efep != efepNO)
2311 opts->couple_moltype = strdup(is->couple_moltype);
2312 if (opts->couple_lam0 == opts->couple_lam1)
2314 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2316 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2317 opts->couple_lam1 == ecouplamNONE))
2319 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2324 warning(wi, "Can not couple a molecule with free_energy = no");
2327 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2328 if (ir->efep != efepNO)
2330 if (fep->delta_lambda > 0)
2332 ir->efep = efepSLOWGROWTH;
2338 fep->bPrintEnergy = TRUE;
2339 /* always print out the energy to dhdl if we are doing expanded ensemble, since we need the total energy
2340 if the temperature is changing. */
2343 if ((ir->efep != efepNO) || ir->bSimTemp)
2345 ir->bExpanded = FALSE;
2346 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2348 ir->bExpanded = TRUE;
2350 do_fep_params(ir, is->fep_lambda, is->lambda_weights);
2351 if (ir->bSimTemp) /* done after fep params */
2353 do_simtemp_params(ir);
2358 ir->fepvals->n_lambda = 0;
2361 /* WALL PARAMETERS */
2363 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2365 /* ORIENTATION RESTRAINT PARAMETERS */
2367 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
2369 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2372 /* DEFORMATION PARAMETERS */
2374 clear_mat(ir->deform);
2375 for (i = 0; i < 6; i++)
2379 m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
2380 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2381 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2382 for (i = 0; i < 3; i++)
2384 ir->deform[i][i] = dumdub[0][i];
2386 ir->deform[YY][XX] = dumdub[0][3];
2387 ir->deform[ZZ][XX] = dumdub[0][4];
2388 ir->deform[ZZ][YY] = dumdub[0][5];
2389 if (ir->epc != epcNO)
2391 for (i = 0; i < 3; i++)
2393 for (j = 0; j <= i; j++)
2395 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2397 warning_error(wi, "A box element has deform set and compressibility > 0");
2401 for (i = 0; i < 3; i++)
2403 for (j = 0; j < i; j++)
2405 if (ir->deform[i][j] != 0)
2407 for (m = j; m < DIM; m++)
2409 if (ir->compress[m][j] != 0)
2411 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.");
2412 warning(wi, warn_buf);
2420 /* Ion/water position swapping checks */
2421 if (ir->eSwapCoords != eswapNO)
2423 if (ir->swap->nstswap < 1)
2425 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2427 if (ir->swap->nAverage < 1)
2429 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2431 if (ir->swap->threshold < 1.0)
2433 warning_error(wi, "Ion count threshold must be at least 1.\n");
2441 static int search_QMstring(const char *s, int ng, const char *gn[])
2443 /* same as normal search_string, but this one searches QM strings */
2446 for (i = 0; (i < ng); i++)
2448 if (gmx_strcasecmp(s, gn[i]) == 0)
2454 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2458 } /* search_QMstring */
2460 /* We would like gn to be const as well, but C doesn't allow this */
2461 int search_string(const char *s, int ng, char *gn[])
2465 for (i = 0; (i < ng); i++)
2467 if (gmx_strcasecmp(s, gn[i]) == 0)
2474 "Group %s referenced in the .mdp file was not found in the index file.\n"
2475 "Group names must match either [moleculetype] names or custom index group\n"
2476 "names, in which case you must supply an index file to the '-n' option\n"
2483 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2484 t_blocka *block, char *gnames[],
2485 int gtype, int restnm,
2486 int grptp, gmx_bool bVerbose,
2489 unsigned short *cbuf;
2490 t_grps *grps = &(groups->grps[gtype]);
2491 int i, j, gid, aj, ognr, ntot = 0;
2494 char warn_buf[STRLEN];
2498 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2501 title = gtypes[gtype];
2504 /* Mark all id's as not set */
2505 for (i = 0; (i < natoms); i++)
2510 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2511 for (i = 0; (i < ng); i++)
2513 /* Lookup the group name in the block structure */
2514 gid = search_string(ptrs[i], block->nr, gnames);
2515 if ((grptp != egrptpONE) || (i == 0))
2517 grps->nm_ind[grps->nr++] = gid;
2521 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2524 /* Now go over the atoms in the group */
2525 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2530 /* Range checking */
2531 if ((aj < 0) || (aj >= natoms))
2533 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2535 /* Lookup up the old group number */
2539 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2540 aj+1, title, ognr+1, i+1);
2544 /* Store the group number in buffer */
2545 if (grptp == egrptpONE)
2558 /* Now check whether we have done all atoms */
2562 if (grptp == egrptpALL)
2564 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2565 natoms-ntot, title);
2567 else if (grptp == egrptpPART)
2569 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2570 natoms-ntot, title);
2571 warning_note(wi, warn_buf);
2573 /* Assign all atoms currently unassigned to a rest group */
2574 for (j = 0; (j < natoms); j++)
2576 if (cbuf[j] == NOGID)
2582 if (grptp != egrptpPART)
2587 "Making dummy/rest group for %s containing %d elements\n",
2588 title, natoms-ntot);
2590 /* Add group name "rest" */
2591 grps->nm_ind[grps->nr] = restnm;
2593 /* Assign the rest name to all atoms not currently assigned to a group */
2594 for (j = 0; (j < natoms); j++)
2596 if (cbuf[j] == NOGID)
2605 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2607 /* All atoms are part of one (or no) group, no index required */
2608 groups->ngrpnr[gtype] = 0;
2609 groups->grpnr[gtype] = NULL;
2613 groups->ngrpnr[gtype] = natoms;
2614 snew(groups->grpnr[gtype], natoms);
2615 for (j = 0; (j < natoms); j++)
2617 groups->grpnr[gtype][j] = cbuf[j];
2623 return (bRest && grptp == egrptpPART);
2626 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2629 gmx_groups_t *groups;
2631 int natoms, ai, aj, i, j, d, g, imin, jmin;
2633 int *nrdf2, *na_vcm, na_tot;
2634 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2635 gmx_mtop_atomloop_all_t aloop;
2637 int mb, mol, ftype, as;
2638 gmx_molblock_t *molb;
2639 gmx_moltype_t *molt;
2642 * First calc 3xnr-atoms for each group
2643 * then subtract half a degree of freedom for each constraint
2645 * Only atoms and nuclei contribute to the degrees of freedom...
2650 groups = &mtop->groups;
2651 natoms = mtop->natoms;
2653 /* Allocate one more for a possible rest group */
2654 /* We need to sum degrees of freedom into doubles,
2655 * since floats give too low nrdf's above 3 million atoms.
2657 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2658 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2659 snew(na_vcm, groups->grps[egcVCM].nr+1);
2661 for (i = 0; i < groups->grps[egcTC].nr; i++)
2665 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2670 snew(nrdf2, natoms);
2671 aloop = gmx_mtop_atomloop_all_init(mtop);
2672 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2675 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2677 g = ggrpnr(groups, egcFREEZE, i);
2678 /* Double count nrdf for particle i */
2679 for (d = 0; d < DIM; d++)
2681 if (opts->nFreeze[g][d] == 0)
2686 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2687 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2692 for (mb = 0; mb < mtop->nmolblock; mb++)
2694 molb = &mtop->molblock[mb];
2695 molt = &mtop->moltype[molb->type];
2696 atom = molt->atoms.atom;
2697 for (mol = 0; mol < molb->nmol; mol++)
2699 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2701 ia = molt->ilist[ftype].iatoms;
2702 for (i = 0; i < molt->ilist[ftype].nr; )
2704 /* Subtract degrees of freedom for the constraints,
2705 * if the particles still have degrees of freedom left.
2706 * If one of the particles is a vsite or a shell, then all
2707 * constraint motion will go there, but since they do not
2708 * contribute to the constraints the degrees of freedom do not
2713 if (((atom[ia[1]].ptype == eptNucleus) ||
2714 (atom[ia[1]].ptype == eptAtom)) &&
2715 ((atom[ia[2]].ptype == eptNucleus) ||
2716 (atom[ia[2]].ptype == eptAtom)))
2734 imin = min(imin, nrdf2[ai]);
2735 jmin = min(jmin, nrdf2[aj]);
2738 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2739 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2740 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2741 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2743 ia += interaction_function[ftype].nratoms+1;
2744 i += interaction_function[ftype].nratoms+1;
2747 ia = molt->ilist[F_SETTLE].iatoms;
2748 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2750 /* Subtract 1 dof from every atom in the SETTLE */
2751 for (j = 0; j < 3; j++)
2754 imin = min(2, nrdf2[ai]);
2756 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2757 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2762 as += molt->atoms.nr;
2766 if (ir->ePull == epullCONSTRAINT)
2768 /* Correct nrdf for the COM constraints.
2769 * We correct using the TC and VCM group of the first atom
2770 * in the reference and pull group. If atoms in one pull group
2771 * belong to different TC or VCM groups it is anyhow difficult
2772 * to determine the optimal nrdf assignment.
2776 for (i = 0; i < pull->ncoord; i++)
2780 for (j = 0; j < 2; j++)
2782 const t_pull_group *pgrp;
2784 pgrp = &pull->group[pull->coord[i].group[j]];
2788 /* Subtract 1/2 dof from each group */
2790 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2791 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2792 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2794 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)]]);
2799 /* We need to subtract the whole DOF from group j=1 */
2806 if (ir->nstcomm != 0)
2808 /* Subtract 3 from the number of degrees of freedom in each vcm group
2809 * when com translation is removed and 6 when rotation is removed
2812 switch (ir->comm_mode)
2815 n_sub = ndof_com(ir);
2822 gmx_incons("Checking comm_mode");
2825 for (i = 0; i < groups->grps[egcTC].nr; i++)
2827 /* Count the number of atoms of TC group i for every VCM group */
2828 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2833 for (ai = 0; ai < natoms; ai++)
2835 if (ggrpnr(groups, egcTC, ai) == i)
2837 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2841 /* Correct for VCM removal according to the fraction of each VCM
2842 * group present in this TC group.
2844 nrdf_uc = nrdf_tc[i];
2847 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2851 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2853 if (nrdf_vcm[j] > n_sub)
2855 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2856 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2860 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2861 j, nrdf_vcm[j], nrdf_tc[i]);
2866 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2868 opts->nrdf[i] = nrdf_tc[i];
2869 if (opts->nrdf[i] < 0)
2874 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2875 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
2884 static void decode_cos(char *s, t_cosines *cosine)
2887 char format[STRLEN], f1[STRLEN];
2899 sscanf(t, "%d", &(cosine->n));
2906 snew(cosine->a, cosine->n);
2907 snew(cosine->phi, cosine->n);
2909 sprintf(format, "%%*d");
2910 for (i = 0; (i < cosine->n); i++)
2913 strcat(f1, "%lf%lf");
2914 if (sscanf(t, f1, &a, &phi) < 2)
2916 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
2919 cosine->phi[i] = phi;
2920 strcat(format, "%*lf%*lf");
2927 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
2928 const char *option, const char *val, int flag)
2930 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
2931 * But since this is much larger than STRLEN, such a line can not be parsed.
2932 * The real maximum is the number of names that fit in a string: STRLEN/2.
2934 #define EGP_MAX (STRLEN/2)
2935 int nelem, i, j, k, nr;
2936 char *names[EGP_MAX];
2940 gnames = groups->grpname;
2942 nelem = str_nelem(val, EGP_MAX, names);
2945 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
2947 nr = groups->grps[egcENER].nr;
2949 for (i = 0; i < nelem/2; i++)
2953 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
2959 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
2960 names[2*i], option);
2964 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
2970 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
2971 names[2*i+1], option);
2973 if ((j < nr) && (k < nr))
2975 ir->opts.egp_flags[nr*j+k] |= flag;
2976 ir->opts.egp_flags[nr*k+j] |= flag;
2985 static void make_swap_groups(
2994 int ig = -1, i = 0, j;
2998 /* Just a quick check here, more thorough checks are in mdrun */
2999 if (strcmp(splitg0name, splitg1name) == 0)
3001 gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
3004 /* First get the swap group index atoms */
3005 ig = search_string(swapgname, grps->nr, gnames);
3006 swap->nat = grps->index[ig+1] - grps->index[ig];
3009 fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
3010 snew(swap->ind, swap->nat);
3011 for (i = 0; i < swap->nat; i++)
3013 swap->ind[i] = grps->a[grps->index[ig]+i];
3018 gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
3021 /* Now do so for the split groups */
3022 for (j = 0; j < 2; j++)
3026 splitg = splitg0name;
3030 splitg = splitg1name;
3033 ig = search_string(splitg, grps->nr, gnames);
3034 swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
3035 if (swap->nat_split[j] > 0)
3037 fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
3038 j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
3039 snew(swap->ind_split[j], swap->nat_split[j]);
3040 for (i = 0; i < swap->nat_split[j]; i++)
3042 swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
3047 gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
3051 /* Now get the solvent group index atoms */
3052 ig = search_string(solgname, grps->nr, gnames);
3053 swap->nat_sol = grps->index[ig+1] - grps->index[ig];
3054 if (swap->nat_sol > 0)
3056 fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
3057 snew(swap->ind_sol, swap->nat_sol);
3058 for (i = 0; i < swap->nat_sol; i++)
3060 swap->ind_sol[i] = grps->a[grps->index[ig]+i];
3065 gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
3070 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3075 ig = search_string(IMDgname, grps->nr, gnames);
3076 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3078 if (IMDgroup->nat > 0)
3080 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3081 IMDgname, IMDgroup->nat);
3082 snew(IMDgroup->ind, IMDgroup->nat);
3083 for (i = 0; i < IMDgroup->nat; i++)
3085 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3091 void do_index(const char* mdparin, const char *ndx,
3094 t_inputrec *ir, rvec *v,
3098 gmx_groups_t *groups;
3102 char warnbuf[STRLEN], **gnames;
3103 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3106 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3107 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3108 int i, j, k, restnm;
3110 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3111 int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
3112 nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
3113 char warn_buf[STRLEN];
3117 fprintf(stderr, "processing index file...\n");
3123 snew(grps->index, 1);
3125 atoms_all = gmx_mtop_global_atoms(mtop);
3126 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3127 free_t_atoms(&atoms_all, FALSE);
3131 grps = init_index(ndx, &gnames);
3134 groups = &mtop->groups;
3135 natoms = mtop->natoms;
3136 symtab = &mtop->symtab;
3138 snew(groups->grpname, grps->nr+1);
3140 for (i = 0; (i < grps->nr); i++)
3142 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3144 groups->grpname[i] = put_symtab(symtab, "rest");
3146 srenew(gnames, grps->nr+1);
3147 gnames[restnm] = *(groups->grpname[i]);
3148 groups->ngrpname = grps->nr+1;
3150 set_warning_line(wi, mdparin, -1);
3152 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3153 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3154 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3155 if ((ntau_t != ntcg) || (nref_t != ntcg))
3157 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3158 "%d tau-t values", ntcg, nref_t, ntau_t);
3161 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3162 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3163 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3164 nr = groups->grps[egcTC].nr;
3166 snew(ir->opts.nrdf, nr);
3167 snew(ir->opts.tau_t, nr);
3168 snew(ir->opts.ref_t, nr);
3169 if (ir->eI == eiBD && ir->bd_fric == 0)
3171 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3178 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3182 for (i = 0; (i < nr); i++)
3184 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
3185 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
3187 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3188 warning_error(wi, warn_buf);
3191 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3193 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.");
3196 if (ir->opts.tau_t[i] >= 0)
3198 tau_min = min(tau_min, ir->opts.tau_t[i]);
3201 if (ir->etc != etcNO && ir->nsttcouple == -1)
3203 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3208 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3210 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");
3212 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
3214 if (ir->nstpcouple != ir->nsttcouple)
3216 int mincouple = min(ir->nstpcouple, ir->nsttcouple);
3217 ir->nstpcouple = ir->nsttcouple = mincouple;
3218 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);
3219 warning_note(wi, warn_buf);
3223 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3224 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3226 if (ETC_ANDERSEN(ir->etc))
3228 if (ir->nsttcouple != 1)
3231 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");
3232 warning_note(wi, warn_buf);
3235 nstcmin = tcouple_min_integration_steps(ir->etc);
3238 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
3240 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3241 ETCOUPLTYPE(ir->etc),
3243 ir->nsttcouple*ir->delta_t);
3244 warning(wi, warn_buf);
3247 for (i = 0; (i < nr); i++)
3249 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
3250 if (ir->opts.ref_t[i] < 0)
3252 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3255 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3256 if we are in this conditional) if mc_temp is negative */
3257 if (ir->expandedvals->mc_temp < 0)
3259 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3263 /* Simulated annealing for each group. There are nr groups */
3264 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3265 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3269 if (nSA > 0 && nSA != nr)
3271 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3275 snew(ir->opts.annealing, nr);
3276 snew(ir->opts.anneal_npoints, nr);
3277 snew(ir->opts.anneal_time, nr);
3278 snew(ir->opts.anneal_temp, nr);
3279 for (i = 0; i < nr; i++)
3281 ir->opts.annealing[i] = eannNO;
3282 ir->opts.anneal_npoints[i] = 0;
3283 ir->opts.anneal_time[i] = NULL;
3284 ir->opts.anneal_temp[i] = NULL;
3289 for (i = 0; i < nr; i++)
3291 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3293 ir->opts.annealing[i] = eannNO;
3295 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3297 ir->opts.annealing[i] = eannSINGLE;
3300 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3302 ir->opts.annealing[i] = eannPERIODIC;
3308 /* Read the other fields too */
3309 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3310 if (nSA_points != nSA)
3312 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3314 for (k = 0, i = 0; i < nr; i++)
3316 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3317 if (ir->opts.anneal_npoints[i] == 1)
3319 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3321 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3322 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3323 k += ir->opts.anneal_npoints[i];
3326 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3329 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3331 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3334 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3337 for (i = 0, k = 0; i < nr; i++)
3340 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3342 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3343 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3346 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3348 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3354 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3356 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3357 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3360 if (ir->opts.anneal_temp[i][j] < 0)
3362 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3367 /* Print out some summary information, to make sure we got it right */
3368 for (i = 0, k = 0; i < nr; i++)
3370 if (ir->opts.annealing[i] != eannNO)
3372 j = groups->grps[egcTC].nm_ind[i];
3373 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3374 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3375 ir->opts.anneal_npoints[i]);
3376 fprintf(stderr, "Time (ps) Temperature (K)\n");
3377 /* All terms except the last one */
3378 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3380 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3383 /* Finally the last one */
3384 j = ir->opts.anneal_npoints[i]-1;
3385 if (ir->opts.annealing[i] == eannSINGLE)
3387 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3391 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3392 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3394 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3403 if (ir->ePull != epullNO)
3405 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3407 make_pull_coords(ir->pull);
3412 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3415 if (ir->eSwapCoords != eswapNO)
3417 make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
3420 /* Make indices for IMD session */
3423 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3426 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3427 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3428 if (nacg*DIM != nacc)
3430 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3433 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3434 restnm, egrptpALL_GENREST, bVerbose, wi);
3435 nr = groups->grps[egcACC].nr;
3436 snew(ir->opts.acc, nr);
3437 ir->opts.ngacc = nr;
3439 for (i = k = 0; (i < nacg); i++)
3441 for (j = 0; (j < DIM); j++, k++)
3443 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3446 for (; (i < nr); i++)
3448 for (j = 0; (j < DIM); j++)
3450 ir->opts.acc[i][j] = 0;
3454 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3455 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3456 if (nfrdim != DIM*nfreeze)
3458 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3461 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3462 restnm, egrptpALL_GENREST, bVerbose, wi);
3463 nr = groups->grps[egcFREEZE].nr;
3464 ir->opts.ngfrz = nr;
3465 snew(ir->opts.nFreeze, nr);
3466 for (i = k = 0; (i < nfreeze); i++)
3468 for (j = 0; (j < DIM); j++, k++)
3470 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3471 if (!ir->opts.nFreeze[i][j])
3473 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3475 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3476 "(not %s)", ptr1[k]);
3477 warning(wi, warn_buf);
3482 for (; (i < nr); i++)
3484 for (j = 0; (j < DIM); j++)
3486 ir->opts.nFreeze[i][j] = 0;
3490 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3491 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3492 restnm, egrptpALL_GENREST, bVerbose, wi);
3493 add_wall_energrps(groups, ir->nwall, symtab);
3494 ir->opts.ngener = groups->grps[egcENER].nr;
3495 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3497 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3498 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3501 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3502 "This may lead to artifacts.\n"
3503 "In most cases one should use one group for the whole system.");
3506 /* Now we have filled the freeze struct, so we can calculate NRDF */
3507 calc_nrdf(mtop, ir, gnames);
3513 /* Must check per group! */
3514 for (i = 0; (i < ir->opts.ngtc); i++)
3516 ntot += ir->opts.nrdf[i];
3518 if (ntot != (DIM*natoms))
3520 fac = sqrt(ntot/(DIM*natoms));
3523 fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
3524 "and removal of center of mass motion\n", fac);
3526 for (i = 0; (i < natoms); i++)
3528 svmul(fac, v[i], v[i]);
3533 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3534 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3535 restnm, egrptpALL_GENREST, bVerbose, wi);
3536 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3537 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3538 restnm, egrptpALL_GENREST, bVerbose, wi);
3539 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3540 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3541 restnm, egrptpONE, bVerbose, wi);
3542 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3543 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3544 restnm, egrptpALL_GENREST, bVerbose, wi);
3546 /* QMMM input processing */
3547 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3548 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3549 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3550 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3552 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3553 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3555 /* group rest, if any, is always MM! */
3556 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3557 restnm, egrptpALL_GENREST, bVerbose, wi);
3558 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3559 ir->opts.ngQM = nQMg;
3560 snew(ir->opts.QMmethod, nr);
3561 snew(ir->opts.QMbasis, nr);
3562 for (i = 0; i < nr; i++)
3564 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3565 * converted to the corresponding enum in names.c
3567 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3569 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3573 nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
3574 nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
3575 nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
3576 snew(ir->opts.QMmult, nr);
3577 snew(ir->opts.QMcharge, nr);
3578 snew(ir->opts.bSH, nr);
3580 for (i = 0; i < nr; i++)
3582 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3583 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3584 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3587 nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
3588 nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
3589 snew(ir->opts.CASelectrons, nr);
3590 snew(ir->opts.CASorbitals, nr);
3591 for (i = 0; i < nr; i++)
3593 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3594 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3596 /* special optimization options */
3598 nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
3599 nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
3600 snew(ir->opts.bOPT, nr);
3601 snew(ir->opts.bTS, nr);
3602 for (i = 0; i < nr; i++)
3604 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3605 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3607 nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
3608 nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
3609 nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
3610 snew(ir->opts.SAon, nr);
3611 snew(ir->opts.SAoff, nr);
3612 snew(ir->opts.SAsteps, nr);
3614 for (i = 0; i < nr; i++)
3616 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3617 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3618 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3620 /* end of QMMM input */
3624 for (i = 0; (i < egcNR); i++)
3626 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3627 for (j = 0; (j < groups->grps[i].nr); j++)
3629 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3631 fprintf(stderr, "\n");
3635 nr = groups->grps[egcENER].nr;
3636 snew(ir->opts.egp_flags, nr*nr);
3638 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3639 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3641 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3643 if (bExcl && EEL_FULL(ir->coulombtype))
3645 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3648 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3649 if (bTable && !(ir->vdwtype == evdwUSER) &&
3650 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3651 !(ir->coulombtype == eelPMEUSERSWITCH))
3653 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3656 decode_cos(is->efield_x, &(ir->ex[XX]));
3657 decode_cos(is->efield_xt, &(ir->et[XX]));
3658 decode_cos(is->efield_y, &(ir->ex[YY]));
3659 decode_cos(is->efield_yt, &(ir->et[YY]));
3660 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3661 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3665 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3668 for (i = 0; (i < grps->nr); i++)
3680 static void check_disre(gmx_mtop_t *mtop)
3682 gmx_ffparams_t *ffparams;
3683 t_functype *functype;
3685 int i, ndouble, ftype;
3686 int label, old_label;
3688 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3690 ffparams = &mtop->ffparams;
3691 functype = ffparams->functype;
3692 ip = ffparams->iparams;
3695 for (i = 0; i < ffparams->ntypes; i++)
3697 ftype = functype[i];
3698 if (ftype == F_DISRES)
3700 label = ip[i].disres.label;
3701 if (label == old_label)
3703 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3711 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3712 "probably the parameters for multiple pairs in one restraint "
3713 "are not identical\n", ndouble);
3718 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3719 gmx_bool posres_only,
3723 gmx_mtop_ilistloop_t iloop;
3733 for (d = 0; d < DIM; d++)
3735 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3737 /* Check for freeze groups */
3738 for (g = 0; g < ir->opts.ngfrz; g++)
3740 for (d = 0; d < DIM; d++)
3742 if (ir->opts.nFreeze[g][d] != 0)
3750 /* Check for position restraints */
3751 iloop = gmx_mtop_ilistloop_init(sys);
3752 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3755 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3757 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3759 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3760 for (d = 0; d < DIM; d++)
3762 if (pr->posres.fcA[d] != 0)
3768 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3770 /* Check for flat-bottom posres */
3771 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3772 if (pr->fbposres.k != 0)
3774 switch (pr->fbposres.geom)
3776 case efbposresSPHERE:
3777 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3779 case efbposresCYLINDER:
3780 AbsRef[XX] = AbsRef[YY] = 1;
3782 case efbposresX: /* d=XX */
3783 case efbposresY: /* d=YY */
3784 case efbposresZ: /* d=ZZ */
3785 d = pr->fbposres.geom - efbposresX;
3789 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3790 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3798 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3802 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3803 gmx_bool *bC6ParametersWorkWithGeometricRules,
3804 gmx_bool *bC6ParametersWorkWithLBRules,
3805 gmx_bool *bLBRulesPossible)
3807 int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
3810 double geometricdiff, LBdiff;
3811 double c6i, c6j, c12i, c12j;
3812 double c6, c6_geometric, c6_LB;
3813 double sigmai, sigmaj, epsi, epsj;
3814 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3817 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3818 * force-field floating point parameters.
3821 ptr = getenv("GMX_LJCOMB_TOL");
3826 sscanf(ptr, "%lf", &dbl);
3830 *bC6ParametersWorkWithLBRules = TRUE;
3831 *bC6ParametersWorkWithGeometricRules = TRUE;
3832 bCanDoLBRules = TRUE;
3833 bCanDoGeometricRules = TRUE;
3834 ntypes = mtop->ffparams.atnr;
3835 snew(typecount, ntypes);
3836 gmx_mtop_count_atomtypes(mtop, state, typecount);
3837 geometricdiff = LBdiff = 0.0;
3838 *bLBRulesPossible = TRUE;
3839 for (tpi = 0; tpi < ntypes; ++tpi)
3841 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3842 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3843 for (tpj = tpi; tpj < ntypes; ++tpj)
3845 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3846 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3847 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3848 c6_geometric = sqrt(c6i * c6j);
3849 if (!gmx_numzero(c6_geometric))
3851 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3853 sigmai = pow(c12i / c6i, 1.0/6.0);
3854 sigmaj = pow(c12j / c6j, 1.0/6.0);
3855 epsi = c6i * c6i /(4.0 * c12i);
3856 epsj = c6j * c6j /(4.0 * c12j);
3857 c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
3861 *bLBRulesPossible = FALSE;
3862 c6_LB = c6_geometric;
3864 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3867 if (FALSE == bCanDoLBRules)
3869 *bC6ParametersWorkWithLBRules = FALSE;
3872 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3874 if (FALSE == bCanDoGeometricRules)
3876 *bC6ParametersWorkWithGeometricRules = FALSE;
3884 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3888 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3890 check_combination_rule_differences(mtop, 0,
3891 &bC6ParametersWorkWithGeometricRules,
3892 &bC6ParametersWorkWithLBRules,
3894 if (ir->ljpme_combination_rule == eljpmeLB)
3896 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
3898 warning(wi, "You are using arithmetic-geometric combination rules "
3899 "in LJ-PME, but your non-bonded C6 parameters do not "
3900 "follow these rules.");
3905 if (FALSE == bC6ParametersWorkWithGeometricRules)
3907 if (ir->eDispCorr != edispcNO)
3909 warning_note(wi, "You are using geometric combination rules in "
3910 "LJ-PME, but your non-bonded C6 parameters do "
3911 "not follow these rules. "
3912 "This will introduce very small errors in the forces and energies in "
3913 "your simulations. Dispersion correction will correct total energy "
3914 "and/or pressure for isotropic systems, but not forces or surface tensions.");
3918 warning_note(wi, "You are using geometric combination rules in "
3919 "LJ-PME, but your non-bonded C6 parameters do "
3920 "not follow these rules. "
3921 "This will introduce very small errors in the forces and energies in "
3922 "your simulations. If your system is homogeneous, consider using dispersion correction "
3923 "for the total energy and pressure.");
3929 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
3933 int i, m, c, nmol, npct;
3934 gmx_bool bCharge, bAcc;
3935 real gdt_max, *mgrp, mt;
3937 gmx_mtop_atomloop_block_t aloopb;
3938 gmx_mtop_atomloop_all_t aloop;
3941 char warn_buf[STRLEN];
3943 set_warning_line(wi, mdparin, -1);
3945 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
3946 ir->comm_mode == ecmNO &&
3947 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
3948 !ETC_ANDERSEN(ir->etc))
3950 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");
3953 /* Check for pressure coupling with absolute position restraints */
3954 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
3956 absolute_reference(ir, sys, TRUE, AbsRef);
3958 for (m = 0; m < DIM; m++)
3960 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
3962 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
3970 aloopb = gmx_mtop_atomloop_block_init(sys);
3971 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
3973 if (atom->q != 0 || atom->qB != 0)
3981 if (EEL_FULL(ir->coulombtype))
3984 "You are using full electrostatics treatment %s for a system without charges.\n"
3985 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
3986 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
3987 warning(wi, err_buf);
3992 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
3995 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
3996 "You might want to consider using %s electrostatics.\n",
3998 warning_note(wi, err_buf);
4002 /* Check if combination rules used in LJ-PME are the same as in the force field */
4003 if (EVDW_PME(ir->vdwtype))
4005 check_combination_rules(ir, sys, wi);
4008 /* Generalized reaction field */
4009 if (ir->opts.ngtc == 0)
4011 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4013 CHECK(ir->coulombtype == eelGRF);
4017 sprintf(err_buf, "When using coulombtype = %s"
4018 " ref-t for temperature coupling should be > 0",
4020 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4023 if (ir->eI == eiSD1 &&
4024 (gmx_mtop_ftype_count(sys, F_CONSTR) > 0 ||
4025 gmx_mtop_ftype_count(sys, F_SETTLE) > 0))
4027 sprintf(warn_buf, "With constraints integrator %s is less accurate, consider using %s instead", ei_names[ir->eI], ei_names[eiSD2]);
4028 warning_note(wi, warn_buf);
4032 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4034 for (m = 0; (m < DIM); m++)
4036 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4045 snew(mgrp, sys->groups.grps[egcACC].nr);
4046 aloop = gmx_mtop_atomloop_all_init(sys);
4047 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4049 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4052 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4054 for (m = 0; (m < DIM); m++)
4056 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4060 for (m = 0; (m < DIM); m++)
4062 if (fabs(acc[m]) > 1e-6)
4064 const char *dim[DIM] = { "X", "Y", "Z" };
4066 "Net Acceleration in %s direction, will %s be corrected\n",
4067 dim[m], ir->nstcomm != 0 ? "" : "not");
4068 if (ir->nstcomm != 0 && m < ndof_com(ir))
4071 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4073 ir->opts.acc[i][m] -= acc[m];
4081 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4082 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4084 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4087 if (ir->ePull != epullNO)
4089 gmx_bool bPullAbsoluteRef;
4091 bPullAbsoluteRef = FALSE;
4092 for (i = 0; i < ir->pull->ncoord; i++)
4094 bPullAbsoluteRef = bPullAbsoluteRef ||
4095 ir->pull->coord[i].group[0] == 0 ||
4096 ir->pull->coord[i].group[1] == 0;
4098 if (bPullAbsoluteRef)
4100 absolute_reference(ir, sys, FALSE, AbsRef);
4101 for (m = 0; m < DIM; m++)
4103 if (ir->pull->dim[m] && !AbsRef[m])
4105 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.");
4111 if (ir->pull->eGeom == epullgDIRPBC)
4113 for (i = 0; i < 3; i++)
4115 for (m = 0; m <= i; m++)
4117 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4118 ir->deform[i][m] != 0)
4120 for (c = 0; c < ir->pull->ncoord; c++)
4122 if (ir->pull->coord[c].vec[m] != 0)
4124 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->eGeom), 'x'+m);
4136 void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr, warninp_t wi)
4140 char warn_buf[STRLEN];
4143 ptr = check_box(ir->ePBC, box);
4146 warning_error(wi, ptr);
4149 if (bConstr && ir->eConstrAlg == econtSHAKE)
4151 if (ir->shake_tol <= 0.0)
4153 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4155 warning_error(wi, warn_buf);
4158 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
4160 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
4161 if (ir->epc == epcNO)
4163 warning(wi, warn_buf);
4167 warning_error(wi, warn_buf);
4172 if ( (ir->eConstrAlg == econtLINCS) && bConstr)
4174 /* If we have Lincs constraints: */
4175 if (ir->eI == eiMD && ir->etc == etcNO &&
4176 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4178 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4179 warning_note(wi, warn_buf);
4182 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4184 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4185 warning_note(wi, warn_buf);
4187 if (ir->epc == epcMTTK)
4189 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4193 if (bConstr && ir->epc == epcMTTK)
4195 warning_note(wi, "MTTK with constraints is deprecated, and will be removed in GROMACS 5.1");
4198 if (ir->LincsWarnAngle > 90.0)
4200 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4201 warning(wi, warn_buf);
4202 ir->LincsWarnAngle = 90.0;
4205 if (ir->ePBC != epbcNONE)
4207 if (ir->nstlist == 0)
4209 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4211 bTWIN = (ir->rlistlong > ir->rlist);
4212 if (ir->ns_type == ensGRID)
4214 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
4216 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",
4217 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
4218 warning_error(wi, warn_buf);
4223 min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
4224 if (2*ir->rlistlong >= min_size)
4226 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4227 warning_error(wi, warn_buf);
4230 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4237 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4241 real rvdw1, rvdw2, rcoul1, rcoul2;
4242 char warn_buf[STRLEN];
4244 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4248 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4253 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4259 if (rvdw1 + rvdw2 > ir->rlist ||
4260 rcoul1 + rcoul2 > ir->rlist)
4263 "The sum of the two largest charge group radii (%f) "
4264 "is larger than rlist (%f)\n",
4265 max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4266 warning(wi, warn_buf);
4270 /* Here we do not use the zero at cut-off macro,
4271 * since user defined interactions might purposely
4272 * not be zero at the cut-off.
4274 if (ir_vdw_is_zero_at_cutoff(ir) &&
4275 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
4277 sprintf(warn_buf, "The sum of the two largest charge group "
4278 "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
4279 "With exact cut-offs, better performance can be "
4280 "obtained with cutoff-scheme = %s, because it "
4281 "does not use charge groups at all.",
4283 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4284 ir->rlistlong, ir->rvdw,
4285 ecutscheme_names[ecutsVERLET]);
4288 warning(wi, warn_buf);
4292 warning_note(wi, warn_buf);
4295 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4296 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
4298 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
4299 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4301 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4302 ir->rlistlong, ir->rcoulomb,
4303 ecutscheme_names[ecutsVERLET]);
4306 warning(wi, warn_buf);
4310 warning_note(wi, warn_buf);