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46 #include "gromacs/math/units.h"
49 #include "gromacs/topology/index.h"
50 #include "gromacs/utility/cstringutil.h"
56 #include "gromacs/math/vec.h"
57 #include "gromacs/pbcutil/pbc.h"
58 #include "gromacs/topology/mtop_util.h"
59 #include "chargegroup.h"
61 #include "calc_verletbuf.h"
63 #include "gromacs/topology/block.h"
64 #include "gromacs/topology/symtab.h"
65 #include "gromacs/utility/fatalerror.h"
66 #include "gromacs/utility/smalloc.h"
71 /* Resource parameters
72 * Do not change any of these until you read the instruction
73 * in readinp.h. Some cpp's do not take spaces after the backslash
74 * (like the c-shell), which will give you a very weird compiler
78 typedef struct t_inputrec_strings
80 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN],
81 acc[STRLEN], accgrps[STRLEN], freeze[STRLEN], frdim[STRLEN],
82 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
83 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
84 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN],
86 char fep_lambda[efptNR][STRLEN];
87 char lambda_weights[STRLEN];
90 char anneal[STRLEN], anneal_npoints[STRLEN],
91 anneal_time[STRLEN], anneal_temp[STRLEN];
92 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
93 bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
94 SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
95 char efield_x[STRLEN], efield_xt[STRLEN], efield_y[STRLEN],
96 efield_yt[STRLEN], efield_z[STRLEN], efield_zt[STRLEN];
98 } gmx_inputrec_strings;
100 static gmx_inputrec_strings *is = NULL;
102 void init_inputrec_strings()
106 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.");
111 void done_inputrec_strings()
117 static char swapgrp[STRLEN], splitgrp0[STRLEN], splitgrp1[STRLEN], solgrp[STRLEN];
120 egrptpALL, /* All particles have to be a member of a group. */
121 egrptpALL_GENREST, /* A rest group with name is generated for particles *
122 * that are not part of any group. */
123 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
124 * for the rest group. */
125 egrptpONE /* Merge all selected groups into one group, *
126 * make a rest group for the remaining particles. */
129 static const char *constraints[eshNR+1] = {
130 "none", "h-bonds", "all-bonds", "h-angles", "all-angles", NULL
133 static const char *couple_lam[ecouplamNR+1] = {
134 "vdw-q", "vdw", "q", "none", NULL
137 void init_ir(t_inputrec *ir, t_gromppopts *opts)
139 snew(opts->include, STRLEN);
140 snew(opts->define, STRLEN);
141 snew(ir->fepvals, 1);
142 snew(ir->expandedvals, 1);
143 snew(ir->simtempvals, 1);
146 static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
151 for (i = 0; i < ntemps; i++)
153 /* simple linear scaling -- allows more control */
154 if (simtemp->eSimTempScale == esimtempLINEAR)
156 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*temperature_lambdas[i];
158 else if (simtemp->eSimTempScale == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
160 simtemp->temperatures[i] = simtemp->simtemp_low * pow(simtemp->simtemp_high/simtemp->simtemp_low, (1.0*i)/(ntemps-1));
162 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
164 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*((exp(temperature_lambdas[i])-1)/(exp(1.0)-1));
169 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
170 gmx_fatal(FARGS, errorstr);
177 static void _low_check(gmx_bool b, char *s, warninp_t wi)
181 warning_error(wi, s);
185 static void check_nst(const char *desc_nst, int nst,
186 const char *desc_p, int *p,
191 if (*p > 0 && *p % nst != 0)
193 /* Round up to the next multiple of nst */
194 *p = ((*p)/nst + 1)*nst;
195 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n",
196 desc_p, desc_nst, desc_p, *p);
201 static gmx_bool ir_NVE(const t_inputrec *ir)
203 return ((ir->eI == eiMD || EI_VV(ir->eI)) && ir->etc == etcNO);
206 static int lcd(int n1, int n2)
211 for (i = 2; (i <= n1 && i <= n2); i++)
213 if (n1 % i == 0 && n2 % i == 0)
222 static void process_interaction_modifier(const t_inputrec *ir, int *eintmod)
224 if (*eintmod == eintmodPOTSHIFT_VERLET)
226 if (ir->cutoff_scheme == ecutsVERLET)
228 *eintmod = eintmodPOTSHIFT;
232 *eintmod = eintmodNONE;
237 void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
239 /* Check internal consistency.
240 * NOTE: index groups are not set here yet, don't check things
241 * like temperature coupling group options here, but in triple_check
244 /* Strange macro: first one fills the err_buf, and then one can check
245 * the condition, which will print the message and increase the error
248 #define CHECK(b) _low_check(b, err_buf, wi)
249 char err_buf[256], warn_buf[STRLEN];
255 t_lambda *fep = ir->fepvals;
256 t_expanded *expand = ir->expandedvals;
258 set_warning_line(wi, mdparin, -1);
260 /* BASIC CUT-OFF STUFF */
261 if (ir->rcoulomb < 0)
263 warning_error(wi, "rcoulomb should be >= 0");
267 warning_error(wi, "rvdw should be >= 0");
270 !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
272 warning_error(wi, "rlist should be >= 0");
275 process_interaction_modifier(ir, &ir->coulomb_modifier);
276 process_interaction_modifier(ir, &ir->vdw_modifier);
278 if (ir->cutoff_scheme == ecutsGROUP)
281 "The group cutoff scheme is deprecated in Gromacs 5.0 and will be removed in a future "
282 "release when all interaction forms are supported for the verlet scheme. The verlet "
283 "scheme already scales better, and it is compatible with GPUs and other accelerators.");
285 /* BASIC CUT-OFF STUFF */
286 if (ir->rlist == 0 ||
287 !((ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > ir->rlist) ||
288 (ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > ir->rlist)))
290 /* No switched potential and/or no twin-range:
291 * we can set the long-range cut-off to the maximum of the other cut-offs.
293 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
295 else if (ir->rlistlong < 0)
297 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
298 sprintf(warn_buf, "rlistlong was not set, setting it to %g (no buffer)",
300 warning(wi, warn_buf);
302 if (ir->rlistlong == 0 && ir->ePBC != epbcNONE)
304 warning_error(wi, "Can not have an infinite cut-off with PBC");
306 if (ir->rlistlong > 0 && (ir->rlist == 0 || ir->rlistlong < ir->rlist))
308 warning_error(wi, "rlistlong can not be shorter than rlist");
310 if (IR_TWINRANGE(*ir) && ir->nstlist <= 0)
312 warning_error(wi, "Can not have nstlist<=0 with twin-range interactions");
316 if (ir->rlistlong == ir->rlist)
320 else if (ir->rlistlong > ir->rlist && ir->nstcalclr == 0)
322 warning_error(wi, "With different cutoffs for electrostatics and VdW, nstcalclr must be -1 or a positive number");
325 if (ir->cutoff_scheme == ecutsVERLET)
329 /* Normal Verlet type neighbor-list, currently only limited feature support */
330 if (inputrec2nboundeddim(ir) < 3)
332 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
334 if (ir->rcoulomb != ir->rvdw)
336 warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported");
338 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
340 if (ir->vdw_modifier == eintmodNONE ||
341 ir->vdw_modifier == eintmodPOTSHIFT)
343 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
345 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]);
346 warning_note(wi, warn_buf);
348 ir->vdwtype = evdwCUT;
352 sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
353 warning_error(wi, warn_buf);
357 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
359 warning_error(wi, "With Verlet lists only cut-off and PME LJ interactions are supported");
361 if (!(ir->coulombtype == eelCUT ||
362 (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC) ||
363 EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
365 warning_error(wi, "With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
367 if (!(ir->coulomb_modifier == eintmodNONE ||
368 ir->coulomb_modifier == eintmodPOTSHIFT))
370 sprintf(warn_buf, "coulomb_modifier=%s is not supported with the Verlet cut-off scheme", eintmod_names[ir->coulomb_modifier]);
371 warning_error(wi, warn_buf);
374 if (ir->nstlist <= 0)
376 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
379 if (ir->nstlist < 10)
381 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.");
384 rc_max = max(ir->rvdw, ir->rcoulomb);
386 if (ir->verletbuf_tol <= 0)
388 if (ir->verletbuf_tol == 0)
390 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
393 if (ir->rlist < rc_max)
395 warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
398 if (ir->rlist == rc_max && ir->nstlist > 1)
400 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.");
405 if (ir->rlist > rc_max)
407 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.");
410 if (ir->nstlist == 1)
412 /* No buffer required */
417 if (EI_DYNAMICS(ir->eI))
419 if (inputrec2nboundeddim(ir) < 3)
421 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.");
423 /* Set rlist temporarily so we can continue processing */
428 /* Set the buffer to 5% of the cut-off */
429 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
434 /* No twin-range calculations with Verlet lists */
435 ir->rlistlong = ir->rlist;
438 if (ir->nstcalclr == -1)
440 /* if rlist=rlistlong, this will later be changed to nstcalclr=0 */
441 ir->nstcalclr = ir->nstlist;
443 else if (ir->nstcalclr > 0)
445 if (ir->nstlist > 0 && (ir->nstlist % ir->nstcalclr != 0))
447 warning_error(wi, "nstlist must be evenly divisible by nstcalclr. Use nstcalclr = -1 to automatically follow nstlist");
450 else if (ir->nstcalclr < -1)
452 warning_error(wi, "nstcalclr must be a positive number (divisor of nstcalclr), or -1 to follow nstlist.");
455 if (EEL_PME(ir->coulombtype) && ir->rcoulomb > ir->rvdw && ir->nstcalclr > 1)
457 warning_error(wi, "When used with PME, the long-range component of twin-range interactions must be updated every step (nstcalclr)");
460 /* GENERAL INTEGRATOR STUFF */
461 if (!(ir->eI == eiMD || EI_VV(ir->eI)))
465 if (ir->eI == eiVVAK)
467 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]);
468 warning_note(wi, warn_buf);
470 if (!EI_DYNAMICS(ir->eI))
474 if (EI_DYNAMICS(ir->eI))
476 if (ir->nstcalcenergy < 0)
478 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
479 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
481 /* nstcalcenergy larger than nstener does not make sense.
482 * We ideally want nstcalcenergy=nstener.
486 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
490 ir->nstcalcenergy = ir->nstenergy;
494 else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
495 (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
496 (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
499 const char *nsten = "nstenergy";
500 const char *nstdh = "nstdhdl";
501 const char *min_name = nsten;
502 int min_nst = ir->nstenergy;
504 /* find the smallest of ( nstenergy, nstdhdl ) */
505 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
506 (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
508 min_nst = ir->fepvals->nstdhdl;
511 /* If the user sets nstenergy small, we should respect that */
513 "Setting nstcalcenergy (%d) equal to %s (%d)",
514 ir->nstcalcenergy, min_name, min_nst);
515 warning_note(wi, warn_buf);
516 ir->nstcalcenergy = min_nst;
519 if (ir->epc != epcNO)
521 if (ir->nstpcouple < 0)
523 ir->nstpcouple = ir_optimal_nstpcouple(ir);
526 if (IR_TWINRANGE(*ir))
528 check_nst("nstlist", ir->nstlist,
529 "nstcalcenergy", &ir->nstcalcenergy, wi);
530 if (ir->epc != epcNO)
532 check_nst("nstlist", ir->nstlist,
533 "nstpcouple", &ir->nstpcouple, wi);
537 if (ir->nstcalcenergy > 0)
539 if (ir->efep != efepNO)
541 /* nstdhdl should be a multiple of nstcalcenergy */
542 check_nst("nstcalcenergy", ir->nstcalcenergy,
543 "nstdhdl", &ir->fepvals->nstdhdl, wi);
544 /* nstexpanded should be a multiple of nstcalcenergy */
545 check_nst("nstcalcenergy", ir->nstcalcenergy,
546 "nstexpanded", &ir->expandedvals->nstexpanded, wi);
548 /* for storing exact averages nstenergy should be
549 * a multiple of nstcalcenergy
551 check_nst("nstcalcenergy", ir->nstcalcenergy,
552 "nstenergy", &ir->nstenergy, wi);
556 if (ir->nsteps == 0 && !ir->bContinuation)
558 warning_note(wi, "For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates.");
562 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
563 ir->bContinuation && ir->ld_seed != -1)
565 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)");
571 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
572 CHECK(ir->ePBC != epbcXYZ);
573 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
574 CHECK(ir->ns_type != ensGRID);
575 sprintf(err_buf, "with TPI nstlist should be larger than zero");
576 CHECK(ir->nstlist <= 0);
577 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
578 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
582 if ( (opts->nshake > 0) && (opts->bMorse) )
585 "Using morse bond-potentials while constraining bonds is useless");
586 warning(wi, warn_buf);
589 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
590 ir->bContinuation && ir->ld_seed != -1)
592 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)");
594 /* verify simulated tempering options */
598 gmx_bool bAllTempZero = TRUE;
599 for (i = 0; i < fep->n_lambda; i++)
601 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]);
602 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
603 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
605 bAllTempZero = FALSE;
608 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
609 CHECK(bAllTempZero == TRUE);
611 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
612 CHECK(ir->eI != eiVV);
614 /* check compatability of the temperature coupling with simulated tempering */
616 if (ir->etc == etcNOSEHOOVER)
618 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
619 warning_note(wi, warn_buf);
622 /* check that the temperatures make sense */
624 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);
625 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
627 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
628 CHECK(ir->simtempvals->simtemp_high <= 0);
630 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
631 CHECK(ir->simtempvals->simtemp_low <= 0);
634 /* verify free energy options */
636 if (ir->efep != efepNO)
639 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
641 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
643 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
644 (int)fep->sc_r_power);
645 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
647 sprintf(err_buf, "Can't use postive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
648 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
650 sprintf(err_buf, "Can't use postive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
651 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
653 sprintf(err_buf, "Can only use expanded ensemble with md-vv for now; should be supported for other integrators in 5.0");
654 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
656 sprintf(err_buf, "Free-energy not implemented for Ewald");
657 CHECK(ir->coulombtype == eelEWALD);
659 /* check validty of lambda inputs */
660 if (fep->n_lambda == 0)
662 /* Clear output in case of no states:*/
663 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
664 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
668 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
669 CHECK((fep->init_fep_state >= fep->n_lambda));
672 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
673 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
675 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",
676 fep->init_lambda, fep->init_fep_state);
677 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
681 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
685 for (i = 0; i < efptNR; i++)
687 if (fep->separate_dvdl[i])
692 if (n_lambda_terms > 1)
694 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.");
695 warning(wi, warn_buf);
698 if (n_lambda_terms < 2 && fep->n_lambda > 0)
701 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
705 for (j = 0; j < efptNR; j++)
707 for (i = 0; i < fep->n_lambda; i++)
709 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]);
710 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
714 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
716 for (i = 0; i < fep->n_lambda; i++)
718 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],
719 fep->all_lambda[efptCOUL][i]);
720 CHECK((fep->sc_alpha > 0) &&
721 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
722 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
723 ((fep->all_lambda[efptVDW][i] > 0.0) &&
724 (fep->all_lambda[efptVDW][i] < 1.0))));
728 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
730 real sigma, lambda, r_sc;
733 /* Maximum estimate for A and B charges equal with lambda power 1 */
735 r_sc = pow(lambda*fep->sc_alpha*pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
736 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.",
738 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
739 warning_note(wi, warn_buf);
742 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
743 be treated differently, but that's the next step */
745 for (i = 0; i < efptNR; i++)
747 for (j = 0; j < fep->n_lambda; j++)
749 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
750 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
755 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
758 expand = ir->expandedvals;
760 /* checking equilibration of weights inputs for validity */
762 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
763 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
764 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
766 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
767 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
768 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
770 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
771 expand->equil_steps, elmceq_names[elmceqSTEPS]);
772 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
774 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
775 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
776 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
778 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
779 expand->equil_ratio, elmceq_names[elmceqRATIO]);
780 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
782 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
783 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
784 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
786 sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
787 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
788 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
790 sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
791 expand->equil_steps, elmceq_names[elmceqSTEPS]);
792 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
794 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
795 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
796 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
798 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
799 expand->equil_ratio, elmceq_names[elmceqRATIO]);
800 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
802 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
803 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
804 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
806 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
807 CHECK((expand->lmc_repeats <= 0));
808 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
809 CHECK((expand->minvarmin <= 0));
810 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
811 CHECK((expand->c_range < 0));
812 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
813 fep->init_fep_state, expand->lmc_forced_nstart);
814 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
815 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
816 CHECK((expand->lmc_forced_nstart < 0));
817 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
818 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
820 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
821 CHECK((expand->init_wl_delta < 0));
822 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
823 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
824 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
825 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
827 /* if there is no temperature control, we need to specify an MC temperature */
828 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
829 if (expand->nstTij > 0)
831 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
832 expand->nstTij, ir->nstlog);
833 CHECK((mod(expand->nstTij, ir->nstlog) != 0));
838 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
839 CHECK(ir->nwall && ir->ePBC != epbcXY);
842 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
844 if (ir->ePBC == epbcNONE)
846 if (ir->epc != epcNO)
848 warning(wi, "Turning off pressure coupling for vacuum system");
854 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
855 epbc_names[ir->ePBC]);
856 CHECK(ir->epc != epcNO);
858 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
859 CHECK(EEL_FULL(ir->coulombtype));
861 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
862 epbc_names[ir->ePBC]);
863 CHECK(ir->eDispCorr != edispcNO);
866 if (ir->rlist == 0.0)
868 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
869 "with coulombtype = %s or coulombtype = %s\n"
870 "without periodic boundary conditions (pbc = %s) and\n"
871 "rcoulomb and rvdw set to zero",
872 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
873 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
874 (ir->ePBC != epbcNONE) ||
875 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
879 warning_error(wi, "Can not have heuristic neighborlist updates without cut-off");
883 warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
888 if (ir->nstcomm == 0)
890 ir->comm_mode = ecmNO;
892 if (ir->comm_mode != ecmNO)
896 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");
897 ir->nstcomm = abs(ir->nstcomm);
900 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
902 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
903 ir->nstcomm = ir->nstcalcenergy;
906 if (ir->comm_mode == ecmANGULAR)
908 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
909 CHECK(ir->bPeriodicMols);
910 if (ir->ePBC != epbcNONE)
912 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).");
917 if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
919 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.");
922 sprintf(err_buf, "Twin-range neighbour searching (NS) with simple NS"
923 " algorithm not implemented");
924 CHECK(((ir->rcoulomb > ir->rlist) || (ir->rvdw > ir->rlist))
925 && (ir->ns_type == ensSIMPLE));
927 /* TEMPERATURE COUPLING */
928 if (ir->etc == etcYES)
930 ir->etc = etcBERENDSEN;
931 warning_note(wi, "Old option for temperature coupling given: "
932 "changing \"yes\" to \"Berendsen\"\n");
935 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
937 if (ir->opts.nhchainlength < 1)
939 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
940 ir->opts.nhchainlength = 1;
941 warning(wi, warn_buf);
944 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
946 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
947 ir->opts.nhchainlength = 1;
952 ir->opts.nhchainlength = 0;
955 if (ir->eI == eiVVAK)
957 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
959 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
962 if (ETC_ANDERSEN(ir->etc))
964 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
965 CHECK(!(EI_VV(ir->eI)));
967 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
969 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]);
970 warning_note(wi, warn_buf);
973 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]);
974 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
977 if (ir->etc == etcBERENDSEN)
979 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
980 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
981 warning_note(wi, warn_buf);
984 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
985 && ir->epc == epcBERENDSEN)
987 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
988 "true ensemble for the thermostat");
989 warning(wi, warn_buf);
992 /* PRESSURE COUPLING */
993 if (ir->epc == epcISOTROPIC)
995 ir->epc = epcBERENDSEN;
996 warning_note(wi, "Old option for pressure coupling given: "
997 "changing \"Isotropic\" to \"Berendsen\"\n");
1000 if (ir->epc != epcNO)
1002 dt_pcoupl = ir->nstpcouple*ir->delta_t;
1004 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1005 CHECK(ir->tau_p <= 0);
1007 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc))
1009 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
1010 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1011 warning(wi, warn_buf);
1014 sprintf(err_buf, "compressibility must be > 0 when using pressure"
1015 " coupling %s\n", EPCOUPLTYPE(ir->epc));
1016 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
1017 ir->compress[ZZ][ZZ] < 0 ||
1018 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
1019 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
1021 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1024 "You are generating velocities so I am assuming you "
1025 "are equilibrating a system. You are using "
1026 "%s pressure coupling, but this can be "
1027 "unstable for equilibration. If your system crashes, try "
1028 "equilibrating first with Berendsen pressure coupling. If "
1029 "you are not equilibrating the system, you can probably "
1030 "ignore this warning.",
1031 epcoupl_names[ir->epc]);
1032 warning(wi, warn_buf);
1038 if (ir->epc > epcNO)
1040 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1042 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.");
1048 if (ir->epc == epcMTTK)
1050 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1054 /* ELECTROSTATICS */
1055 /* More checks are in triple check (grompp.c) */
1057 if (ir->coulombtype == eelSWITCH)
1059 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1060 "artifacts, advice: use coulombtype = %s",
1061 eel_names[ir->coulombtype],
1062 eel_names[eelRF_ZERO]);
1063 warning(wi, warn_buf);
1066 if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
1068 sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
1069 warning_note(wi, warn_buf);
1072 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1074 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);
1075 warning(wi, warn_buf);
1076 ir->epsilon_rf = ir->epsilon_r;
1077 ir->epsilon_r = 1.0;
1080 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == NULL)
1082 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1083 CHECK(ir->epsilon_r < 0);
1086 if (EEL_RF(ir->coulombtype))
1088 /* reaction field (at the cut-off) */
1090 if (ir->coulombtype == eelRF_ZERO)
1092 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1093 eel_names[ir->coulombtype]);
1094 CHECK(ir->epsilon_rf != 0);
1095 ir->epsilon_rf = 0.0;
1098 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1099 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1100 (ir->epsilon_r == 0));
1101 if (ir->epsilon_rf == ir->epsilon_r)
1103 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1104 eel_names[ir->coulombtype]);
1105 warning(wi, warn_buf);
1108 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1109 * means the interaction is zero outside rcoulomb, but it helps to
1110 * provide accurate energy conservation.
1112 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1114 if (ir_coulomb_switched(ir))
1117 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1118 eel_names[ir->coulombtype]);
1119 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1122 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1124 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1126 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1127 eel_names[ir->coulombtype]);
1128 CHECK(ir->rlist > ir->rcoulomb);
1132 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1135 "Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier.");
1136 CHECK( ir->coulomb_modifier != eintmodNONE);
1138 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1141 "Explicit switch/shift vdw interactions cannot be used in combination with a secondary vdw-modifier.");
1142 CHECK( ir->vdw_modifier != eintmodNONE);
1145 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1146 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1149 "The switch/shift interaction settings are just for compatibility; you will get better "
1150 "performance from applying potential modifiers to your interactions!\n");
1151 warning_note(wi, warn_buf);
1154 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1156 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1158 real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
1159 sprintf(warn_buf, "The switching range should be 5%% or less (currently %.2f%% using a switching range of %4f-%4f) for accurate electrostatic energies, energy conservation will be good regardless, since ewald_rtol = %g.",
1160 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1161 warning(wi, warn_buf);
1165 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1167 if (ir->rvdw_switch == 0)
1169 sprintf(warn_buf, "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones potential. This suggests it was not set in the mdp, which can lead to large energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw switching range.");
1170 warning(wi, warn_buf);
1174 if (EEL_FULL(ir->coulombtype))
1176 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1177 ir->coulombtype == eelPMEUSERSWITCH)
1179 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1180 eel_names[ir->coulombtype]);
1181 CHECK(ir->rcoulomb > ir->rlist);
1183 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1185 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1188 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
1189 "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
1190 "a potential modifier.", eel_names[ir->coulombtype]);
1191 if (ir->nstcalclr == 1)
1193 CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
1197 CHECK(ir->rcoulomb != ir->rlist);
1203 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1205 if (ir->pme_order < 3)
1207 warning_error(wi, "pme-order can not be smaller than 3");
1211 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1213 if (ir->ewald_geometry == eewg3D)
1215 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1216 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1217 warning(wi, warn_buf);
1219 /* This check avoids extra pbc coding for exclusion corrections */
1220 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1221 CHECK(ir->wall_ewald_zfac < 2);
1224 if (ir_vdw_switched(ir))
1226 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1227 CHECK(ir->rvdw_switch >= ir->rvdw);
1229 if (ir->rvdw_switch < 0.5*ir->rvdw)
1231 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.",
1232 ir->rvdw_switch, ir->rvdw);
1233 warning_note(wi, warn_buf);
1236 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1238 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1240 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1241 CHECK(ir->rlist > ir->rvdw);
1245 if (ir->vdwtype == evdwPME)
1247 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1249 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s a\
1251 evdw_names[ir->vdwtype],
1252 eintmod_names[eintmodPOTSHIFT],
1253 eintmod_names[eintmodNONE]);
1257 if (ir->cutoff_scheme == ecutsGROUP)
1259 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1260 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)) &&
1263 warning_note(wi, "With exact cut-offs, rlist should be "
1264 "larger than rcoulomb and rvdw, so that there "
1265 "is a buffer region for particle motion "
1266 "between neighborsearch steps");
1269 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlistlong <= ir->rcoulomb)
1271 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
1272 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1273 warning_note(wi, warn_buf);
1275 if (ir_vdw_switched(ir) && (ir->rlistlong <= ir->rvdw))
1277 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
1278 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1279 warning_note(wi, warn_buf);
1283 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1285 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.");
1288 if (ir->nstlist == -1)
1290 sprintf(err_buf, "With nstlist=-1 rvdw and rcoulomb should be smaller than rlist to account for diffusion and possibly charge-group radii");
1291 CHECK(ir->rvdw >= ir->rlist || ir->rcoulomb >= ir->rlist);
1293 sprintf(err_buf, "nstlist can not be smaller than -1");
1294 CHECK(ir->nstlist < -1);
1296 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1299 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1302 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1304 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1307 /* ENERGY CONSERVATION */
1308 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1310 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1312 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1313 evdw_names[evdwSHIFT]);
1314 warning_note(wi, warn_buf);
1316 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1318 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1319 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1320 warning_note(wi, warn_buf);
1324 if (EI_VV(ir->eI) && IR_TWINRANGE(*ir) && ir->nstlist > 1)
1326 sprintf(warn_buf, "Twin-range multiple time stepping does not work with integrator %s.", ei_names[ir->eI]);
1327 warning_error(wi, warn_buf);
1330 /* IMPLICIT SOLVENT */
1331 if (ir->coulombtype == eelGB_NOTUSED)
1333 ir->coulombtype = eelCUT;
1334 ir->implicit_solvent = eisGBSA;
1335 fprintf(stderr, "Note: Old option for generalized born electrostatics given:\n"
1336 "Changing coulombtype from \"generalized-born\" to \"cut-off\" and instead\n"
1337 "setting implicit-solvent value to \"GBSA\" in input section.\n");
1340 if (ir->sa_algorithm == esaSTILL)
1342 sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
1343 CHECK(ir->sa_algorithm == esaSTILL);
1346 if (ir->implicit_solvent == eisGBSA)
1348 sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
1349 CHECK(ir->rgbradii != ir->rlist);
1351 if (ir->coulombtype != eelCUT)
1353 sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
1354 CHECK(ir->coulombtype != eelCUT);
1356 if (ir->vdwtype != evdwCUT)
1358 sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
1359 CHECK(ir->vdwtype != evdwCUT);
1361 if (ir->nstgbradii < 1)
1363 sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
1364 warning_note(wi, warn_buf);
1367 if (ir->sa_algorithm == esaNO)
1369 sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
1370 warning_note(wi, warn_buf);
1372 if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
1374 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");
1375 warning_note(wi, warn_buf);
1377 if (ir->gb_algorithm == egbSTILL)
1379 ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
1383 ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
1386 if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
1388 sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
1389 CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
1396 if (ir->cutoff_scheme != ecutsGROUP)
1398 warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
1402 warning_error(wi, "AdresS simulation supports only stochastic dynamics");
1404 if (ir->epc != epcNO)
1406 warning_error(wi, "AdresS simulation does not support pressure coupling");
1408 if (EEL_FULL(ir->coulombtype))
1410 warning_error(wi, "AdresS simulation does not support long-range electrostatics");
1415 /* count the number of text elemets separated by whitespace in a string.
1416 str = the input string
1417 maxptr = the maximum number of allowed elements
1418 ptr = the output array of pointers to the first character of each element
1419 returns: the number of elements. */
1420 int str_nelem(const char *str, int maxptr, char *ptr[])
1425 copy0 = strdup(str);
1428 while (*copy != '\0')
1432 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1440 while ((*copy != '\0') && !isspace(*copy))
1459 /* interpret a number of doubles from a string and put them in an array,
1460 after allocating space for them.
1461 str = the input string
1462 n = the (pre-allocated) number of doubles read
1463 r = the output array of doubles. */
1464 static void parse_n_real(char *str, int *n, real **r)
1469 *n = str_nelem(str, MAXPTR, ptr);
1472 for (i = 0; i < *n; i++)
1474 (*r)[i] = strtod(ptr[i], NULL);
1478 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
1481 int i, j, max_n_lambda, nweights, nfep[efptNR];
1482 t_lambda *fep = ir->fepvals;
1483 t_expanded *expand = ir->expandedvals;
1484 real **count_fep_lambdas;
1485 gmx_bool bOneLambda = TRUE;
1487 snew(count_fep_lambdas, efptNR);
1489 /* FEP input processing */
1490 /* first, identify the number of lambda values for each type.
1491 All that are nonzero must have the same number */
1493 for (i = 0; i < efptNR; i++)
1495 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
1498 /* now, determine the number of components. All must be either zero, or equal. */
1501 for (i = 0; i < efptNR; i++)
1503 if (nfep[i] > max_n_lambda)
1505 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1506 must have the same number if its not zero.*/
1511 for (i = 0; i < efptNR; i++)
1515 ir->fepvals->separate_dvdl[i] = FALSE;
1517 else if (nfep[i] == max_n_lambda)
1519 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1520 respect to the temperature currently */
1522 ir->fepvals->separate_dvdl[i] = TRUE;
1527 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1528 nfep[i], efpt_names[i], max_n_lambda);
1531 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1532 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1534 /* the number of lambdas is the number we've read in, which is either zero
1535 or the same for all */
1536 fep->n_lambda = max_n_lambda;
1538 /* allocate space for the array of lambda values */
1539 snew(fep->all_lambda, efptNR);
1540 /* if init_lambda is defined, we need to set lambda */
1541 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1543 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1545 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1546 for (i = 0; i < efptNR; i++)
1548 snew(fep->all_lambda[i], fep->n_lambda);
1549 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1552 for (j = 0; j < fep->n_lambda; j++)
1554 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1556 sfree(count_fep_lambdas[i]);
1559 sfree(count_fep_lambdas);
1561 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1562 bookkeeping -- for now, init_lambda */
1564 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1566 for (i = 0; i < fep->n_lambda; i++)
1568 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1572 /* check to see if only a single component lambda is defined, and soft core is defined.
1573 In this case, turn on coulomb soft core */
1575 if (max_n_lambda == 0)
1581 for (i = 0; i < efptNR; i++)
1583 if ((nfep[i] != 0) && (i != efptFEP))
1589 if ((bOneLambda) && (fep->sc_alpha > 0))
1591 fep->bScCoul = TRUE;
1594 /* Fill in the others with the efptFEP if they are not explicitly
1595 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1596 they are all zero. */
1598 for (i = 0; i < efptNR; i++)
1600 if ((nfep[i] == 0) && (i != efptFEP))
1602 for (j = 0; j < fep->n_lambda; j++)
1604 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1610 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1611 if (fep->sc_r_power == 48)
1613 if (fep->sc_alpha > 0.1)
1615 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1619 expand = ir->expandedvals;
1620 /* now read in the weights */
1621 parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
1624 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1626 else if (nweights != fep->n_lambda)
1628 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1629 nweights, fep->n_lambda);
1631 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1633 expand->nstexpanded = fep->nstdhdl;
1634 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1636 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1638 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1639 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1640 2*tau_t just to be careful so it's not to frequent */
1645 static void do_simtemp_params(t_inputrec *ir)
1648 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1649 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1654 static void do_wall_params(t_inputrec *ir,
1655 char *wall_atomtype, char *wall_density,
1659 char *names[MAXPTR];
1662 opts->wall_atomtype[0] = NULL;
1663 opts->wall_atomtype[1] = NULL;
1665 ir->wall_atomtype[0] = -1;
1666 ir->wall_atomtype[1] = -1;
1667 ir->wall_density[0] = 0;
1668 ir->wall_density[1] = 0;
1672 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1673 if (nstr != ir->nwall)
1675 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1678 for (i = 0; i < ir->nwall; i++)
1680 opts->wall_atomtype[i] = strdup(names[i]);
1683 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1685 nstr = str_nelem(wall_density, MAXPTR, names);
1686 if (nstr != ir->nwall)
1688 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1690 for (i = 0; i < ir->nwall; i++)
1692 sscanf(names[i], "%lf", &dbl);
1695 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1697 ir->wall_density[i] = dbl;
1703 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1711 srenew(groups->grpname, groups->ngrpname+nwall);
1712 grps = &(groups->grps[egcENER]);
1713 srenew(grps->nm_ind, grps->nr+nwall);
1714 for (i = 0; i < nwall; i++)
1716 sprintf(str, "wall%d", i);
1717 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1718 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1723 void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1724 t_expanded *expand, warninp_t wi)
1726 int ninp, nerror = 0;
1732 /* read expanded ensemble parameters */
1733 CCTYPE ("expanded ensemble variables");
1734 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1735 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1736 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1737 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1738 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1739 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1740 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1741 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1742 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1743 CCTYPE("Seed for Monte Carlo in lambda space");
1744 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1745 RTYPE ("mc-temperature", expand->mc_temp, -1);
1746 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1747 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1748 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1749 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1750 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1751 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1752 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1753 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1754 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1755 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1756 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
1764 void get_ir(const char *mdparin, const char *mdparout,
1765 t_inputrec *ir, t_gromppopts *opts,
1769 double dumdub[2][6];
1773 char warn_buf[STRLEN];
1774 t_lambda *fep = ir->fepvals;
1775 t_expanded *expand = ir->expandedvals;
1777 init_inputrec_strings();
1778 inp = read_inpfile(mdparin, &ninp, wi);
1780 snew(dumstr[0], STRLEN);
1781 snew(dumstr[1], STRLEN);
1783 if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
1786 "%s did not specify a value for the .mdp option "
1787 "\"cutoff-scheme\". Probably it was first intended for use "
1788 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1789 "introduced, but the group scheme was still the default. "
1790 "The default is now the Verlet scheme, so you will observe "
1791 "different behaviour.", mdparin);
1792 warning_note(wi, warn_buf);
1795 /* ignore the following deprecated commands */
1798 REM_TYPE("domain-decomposition");
1799 REM_TYPE("andersen-seed");
1801 REM_TYPE("dihre-fc");
1802 REM_TYPE("dihre-tau");
1803 REM_TYPE("nstdihreout");
1804 REM_TYPE("nstcheckpoint");
1805 REM_TYPE("optimize-fft");
1807 /* replace the following commands with the clearer new versions*/
1808 REPL_TYPE("unconstrained-start", "continuation");
1809 REPL_TYPE("foreign-lambda", "fep-lambdas");
1810 REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
1811 REPL_TYPE("nstxtcout", "nstxout-compressed");
1812 REPL_TYPE("xtc-grps", "compressed-x-grps");
1813 REPL_TYPE("xtc-precision", "compressed-x-precision");
1815 CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
1816 CTYPE ("Preprocessor information: use cpp syntax.");
1817 CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
1818 STYPE ("include", opts->include, NULL);
1819 CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1820 STYPE ("define", opts->define, NULL);
1822 CCTYPE ("RUN CONTROL PARAMETERS");
1823 EETYPE("integrator", ir->eI, ei_names);
1824 CTYPE ("Start time and timestep in ps");
1825 RTYPE ("tinit", ir->init_t, 0.0);
1826 RTYPE ("dt", ir->delta_t, 0.001);
1827 STEPTYPE ("nsteps", ir->nsteps, 0);
1828 CTYPE ("For exact run continuation or redoing part of a run");
1829 STEPTYPE ("init-step", ir->init_step, 0);
1830 CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
1831 ITYPE ("simulation-part", ir->simulation_part, 1);
1832 CTYPE ("mode for center of mass motion removal");
1833 EETYPE("comm-mode", ir->comm_mode, ecm_names);
1834 CTYPE ("number of steps for center of mass motion removal");
1835 ITYPE ("nstcomm", ir->nstcomm, 100);
1836 CTYPE ("group(s) for center of mass motion removal");
1837 STYPE ("comm-grps", is->vcm, NULL);
1839 CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
1840 CTYPE ("Friction coefficient (amu/ps) and random seed");
1841 RTYPE ("bd-fric", ir->bd_fric, 0.0);
1842 STEPTYPE ("ld-seed", ir->ld_seed, -1);
1845 CCTYPE ("ENERGY MINIMIZATION OPTIONS");
1846 CTYPE ("Force tolerance and initial step-size");
1847 RTYPE ("emtol", ir->em_tol, 10.0);
1848 RTYPE ("emstep", ir->em_stepsize, 0.01);
1849 CTYPE ("Max number of iterations in relax-shells");
1850 ITYPE ("niter", ir->niter, 20);
1851 CTYPE ("Step size (ps^2) for minimization of flexible constraints");
1852 RTYPE ("fcstep", ir->fc_stepsize, 0);
1853 CTYPE ("Frequency of steepest descents steps when doing CG");
1854 ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
1855 ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
1857 CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
1858 RTYPE ("rtpi", ir->rtpi, 0.05);
1860 /* Output options */
1861 CCTYPE ("OUTPUT CONTROL OPTIONS");
1862 CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
1863 ITYPE ("nstxout", ir->nstxout, 0);
1864 ITYPE ("nstvout", ir->nstvout, 0);
1865 ITYPE ("nstfout", ir->nstfout, 0);
1866 CTYPE ("Output frequency for energies to log file and energy file");
1867 ITYPE ("nstlog", ir->nstlog, 1000);
1868 ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
1869 ITYPE ("nstenergy", ir->nstenergy, 1000);
1870 CTYPE ("Output frequency and precision for .xtc file");
1871 ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
1872 RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
1873 CTYPE ("This selects the subset of atoms for the compressed");
1874 CTYPE ("trajectory file. You can select multiple groups. By");
1875 CTYPE ("default, all atoms will be written.");
1876 STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
1877 CTYPE ("Selection of energy groups");
1878 STYPE ("energygrps", is->energy, NULL);
1880 /* Neighbor searching */
1881 CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
1882 CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1883 EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
1884 CTYPE ("nblist update frequency");
1885 ITYPE ("nstlist", ir->nstlist, 10);
1886 CTYPE ("ns algorithm (simple or grid)");
1887 EETYPE("ns-type", ir->ns_type, ens_names);
1888 CTYPE ("Periodic boundary conditions: xyz, no, xy");
1889 EETYPE("pbc", ir->ePBC, epbc_names);
1890 EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
1891 CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1892 CTYPE ("a value of -1 means: use rlist");
1893 RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
1894 CTYPE ("nblist cut-off");
1895 RTYPE ("rlist", ir->rlist, 1.0);
1896 CTYPE ("long-range cut-off for switched potentials");
1897 RTYPE ("rlistlong", ir->rlistlong, -1);
1898 ITYPE ("nstcalclr", ir->nstcalclr, -1);
1900 /* Electrostatics */
1901 CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
1902 CTYPE ("Method for doing electrostatics");
1903 EETYPE("coulombtype", ir->coulombtype, eel_names);
1904 EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
1905 CTYPE ("cut-off lengths");
1906 RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
1907 RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
1908 CTYPE ("Relative dielectric constant for the medium and the reaction field");
1909 RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
1910 RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
1911 CTYPE ("Method for doing Van der Waals");
1912 EETYPE("vdw-type", ir->vdwtype, evdw_names);
1913 EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
1914 CTYPE ("cut-off lengths");
1915 RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
1916 RTYPE ("rvdw", ir->rvdw, 1.0);
1917 CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
1918 EETYPE("DispCorr", ir->eDispCorr, edispc_names);
1919 CTYPE ("Extension of the potential lookup tables beyond the cut-off");
1920 RTYPE ("table-extension", ir->tabext, 1.0);
1921 CTYPE ("Separate tables between energy group pairs");
1922 STYPE ("energygrp-table", is->egptable, NULL);
1923 CTYPE ("Spacing for the PME/PPPM FFT grid");
1924 RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
1925 CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
1926 ITYPE ("fourier-nx", ir->nkx, 0);
1927 ITYPE ("fourier-ny", ir->nky, 0);
1928 ITYPE ("fourier-nz", ir->nkz, 0);
1929 CTYPE ("EWALD/PME/PPPM parameters");
1930 ITYPE ("pme-order", ir->pme_order, 4);
1931 RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
1932 RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
1933 EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
1934 EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
1935 RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
1937 CCTYPE("IMPLICIT SOLVENT ALGORITHM");
1938 EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
1940 CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
1941 CTYPE ("Algorithm for calculating Born radii");
1942 EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
1943 CTYPE ("Frequency of calculating the Born radii inside rlist");
1944 ITYPE ("nstgbradii", ir->nstgbradii, 1);
1945 CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
1946 CTYPE ("between rlist and rgbradii is updated every nstlist steps");
1947 RTYPE ("rgbradii", ir->rgbradii, 1.0);
1948 CTYPE ("Dielectric coefficient of the implicit solvent");
1949 RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
1950 CTYPE ("Salt concentration in M for Generalized Born models");
1951 RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
1952 CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
1953 RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
1954 RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
1955 RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
1956 RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
1957 EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
1958 CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
1959 CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
1960 RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
1962 /* Coupling stuff */
1963 CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
1964 CTYPE ("Temperature coupling");
1965 EETYPE("tcoupl", ir->etc, etcoupl_names);
1966 ITYPE ("nsttcouple", ir->nsttcouple, -1);
1967 ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
1968 EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
1969 CTYPE ("Groups to couple separately");
1970 STYPE ("tc-grps", is->tcgrps, NULL);
1971 CTYPE ("Time constant (ps) and reference temperature (K)");
1972 STYPE ("tau-t", is->tau_t, NULL);
1973 STYPE ("ref-t", is->ref_t, NULL);
1974 CTYPE ("pressure coupling");
1975 EETYPE("pcoupl", ir->epc, epcoupl_names);
1976 EETYPE("pcoupltype", ir->epct, epcoupltype_names);
1977 ITYPE ("nstpcouple", ir->nstpcouple, -1);
1978 CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
1979 RTYPE ("tau-p", ir->tau_p, 1.0);
1980 STYPE ("compressibility", dumstr[0], NULL);
1981 STYPE ("ref-p", dumstr[1], NULL);
1982 CTYPE ("Scaling of reference coordinates, No, All or COM");
1983 EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
1986 CCTYPE ("OPTIONS FOR QMMM calculations");
1987 EETYPE("QMMM", ir->bQMMM, yesno_names);
1988 CTYPE ("Groups treated Quantum Mechanically");
1989 STYPE ("QMMM-grps", is->QMMM, NULL);
1990 CTYPE ("QM method");
1991 STYPE("QMmethod", is->QMmethod, NULL);
1992 CTYPE ("QMMM scheme");
1993 EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
1994 CTYPE ("QM basisset");
1995 STYPE("QMbasis", is->QMbasis, NULL);
1996 CTYPE ("QM charge");
1997 STYPE ("QMcharge", is->QMcharge, NULL);
1998 CTYPE ("QM multiplicity");
1999 STYPE ("QMmult", is->QMmult, NULL);
2000 CTYPE ("Surface Hopping");
2001 STYPE ("SH", is->bSH, NULL);
2002 CTYPE ("CAS space options");
2003 STYPE ("CASorbitals", is->CASorbitals, NULL);
2004 STYPE ("CASelectrons", is->CASelectrons, NULL);
2005 STYPE ("SAon", is->SAon, NULL);
2006 STYPE ("SAoff", is->SAoff, NULL);
2007 STYPE ("SAsteps", is->SAsteps, NULL);
2008 CTYPE ("Scale factor for MM charges");
2009 RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
2010 CTYPE ("Optimization of QM subsystem");
2011 STYPE ("bOPT", is->bOPT, NULL);
2012 STYPE ("bTS", is->bTS, NULL);
2014 /* Simulated annealing */
2015 CCTYPE("SIMULATED ANNEALING");
2016 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
2017 STYPE ("annealing", is->anneal, NULL);
2018 CTYPE ("Number of time points to use for specifying annealing in each group");
2019 STYPE ("annealing-npoints", is->anneal_npoints, NULL);
2020 CTYPE ("List of times at the annealing points for each group");
2021 STYPE ("annealing-time", is->anneal_time, NULL);
2022 CTYPE ("Temp. at each annealing point, for each group.");
2023 STYPE ("annealing-temp", is->anneal_temp, NULL);
2026 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
2027 EETYPE("gen-vel", opts->bGenVel, yesno_names);
2028 RTYPE ("gen-temp", opts->tempi, 300.0);
2029 ITYPE ("gen-seed", opts->seed, -1);
2032 CCTYPE ("OPTIONS FOR BONDS");
2033 EETYPE("constraints", opts->nshake, constraints);
2034 CTYPE ("Type of constraint algorithm");
2035 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
2036 CTYPE ("Do not constrain the start configuration");
2037 EETYPE("continuation", ir->bContinuation, yesno_names);
2038 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
2039 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
2040 CTYPE ("Relative tolerance of shake");
2041 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
2042 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
2043 ITYPE ("lincs-order", ir->nProjOrder, 4);
2044 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
2045 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
2046 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
2047 ITYPE ("lincs-iter", ir->nLincsIter, 1);
2048 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
2049 CTYPE ("rotates over more degrees than");
2050 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
2051 CTYPE ("Convert harmonic bonds to morse potentials");
2052 EETYPE("morse", opts->bMorse, yesno_names);
2054 /* Energy group exclusions */
2055 CCTYPE ("ENERGY GROUP EXCLUSIONS");
2056 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
2057 STYPE ("energygrp-excl", is->egpexcl, NULL);
2061 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2062 ITYPE ("nwall", ir->nwall, 0);
2063 EETYPE("wall-type", ir->wall_type, ewt_names);
2064 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
2065 STYPE ("wall-atomtype", is->wall_atomtype, NULL);
2066 STYPE ("wall-density", is->wall_density, NULL);
2067 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
2070 CCTYPE("COM PULLING");
2071 CTYPE("Pull type: no, umbrella, constraint or constant-force");
2072 EETYPE("pull", ir->ePull, epull_names);
2073 if (ir->ePull != epullNO)
2076 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
2079 /* Enforced rotation */
2080 CCTYPE("ENFORCED ROTATION");
2081 CTYPE("Enforced rotation: No or Yes");
2082 EETYPE("rotation", ir->bRot, yesno_names);
2086 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2089 /* Interactive MD */
2091 CCTYPE("Group to display and/or manipulate in interactive MD session");
2092 STYPE ("IMD-group", is->imd_grp, NULL);
2093 if (is->imd_grp[0] != '\0')
2100 CCTYPE("NMR refinement stuff");
2101 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2102 EETYPE("disre", ir->eDisre, edisre_names);
2103 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2104 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2105 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2106 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2107 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2108 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2109 CTYPE ("Output frequency for pair distances to energy file");
2110 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2111 CTYPE ("Orientation restraints: No or Yes");
2112 EETYPE("orire", opts->bOrire, yesno_names);
2113 CTYPE ("Orientation restraints force constant and tau for time averaging");
2114 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2115 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2116 STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
2117 CTYPE ("Output frequency for trace(SD) and S to energy file");
2118 ITYPE ("nstorireout", ir->nstorireout, 100);
2120 /* free energy variables */
2121 CCTYPE ("Free energy variables");
2122 EETYPE("free-energy", ir->efep, efep_names);
2123 STYPE ("couple-moltype", is->couple_moltype, NULL);
2124 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2125 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2126 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2128 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2130 it was not entered */
2131 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2132 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2133 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2134 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
2135 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
2136 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
2137 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
2138 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
2139 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
2140 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
2141 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2142 STYPE ("init-lambda-weights", is->lambda_weights, NULL);
2143 EETYPE("dhdl-print-energy", fep->bPrintEnergy, yesno_names);
2144 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2145 ITYPE ("sc-power", fep->sc_power, 1);
2146 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2147 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2148 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2149 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2150 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2151 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2152 separate_dhdl_file_names);
2153 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2154 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2155 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2157 /* Non-equilibrium MD stuff */
2158 CCTYPE("Non-equilibrium MD stuff");
2159 STYPE ("acc-grps", is->accgrps, NULL);
2160 STYPE ("accelerate", is->acc, NULL);
2161 STYPE ("freezegrps", is->freeze, NULL);
2162 STYPE ("freezedim", is->frdim, NULL);
2163 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2164 STYPE ("deform", is->deform, NULL);
2166 /* simulated tempering variables */
2167 CCTYPE("simulated tempering variables");
2168 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2169 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2170 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2171 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2173 /* expanded ensemble variables */
2174 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2176 read_expandedparams(&ninp, &inp, expand, wi);
2179 /* Electric fields */
2180 CCTYPE("Electric fields");
2181 CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
2182 CTYPE ("and a phase angle (real)");
2183 STYPE ("E-x", is->efield_x, NULL);
2184 STYPE ("E-xt", is->efield_xt, NULL);
2185 STYPE ("E-y", is->efield_y, NULL);
2186 STYPE ("E-yt", is->efield_yt, NULL);
2187 STYPE ("E-z", is->efield_z, NULL);
2188 STYPE ("E-zt", is->efield_zt, NULL);
2190 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2191 CTYPE("Swap positions along direction: no, X, Y, Z");
2192 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2193 if (ir->eSwapCoords != eswapNO)
2196 CTYPE("Swap attempt frequency");
2197 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2198 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2199 STYPE("split-group0", splitgrp0, NULL);
2200 STYPE("split-group1", splitgrp1, NULL);
2201 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2202 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2203 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2205 CTYPE("Group name of ions that can be exchanged with solvent molecules");
2206 STYPE("swap-group", swapgrp, NULL);
2207 CTYPE("Group name of solvent molecules");
2208 STYPE("solvent-group", solgrp, NULL);
2210 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2211 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2212 CTYPE("however, if correctly defined, the ion permeation events are counted per channel");
2213 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2214 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2215 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2216 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2217 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2218 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2220 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2221 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2222 CTYPE("Requested number of anions and cations for each of the two compartments");
2223 CTYPE("-1 means fix the numbers as found in time step 0");
2224 ITYPE("anionsA", ir->swap->nanions[0], -1);
2225 ITYPE("cationsA", ir->swap->ncations[0], -1);
2226 ITYPE("anionsB", ir->swap->nanions[1], -1);
2227 ITYPE("cationsB", ir->swap->ncations[1], -1);
2228 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2229 RTYPE("threshold", ir->swap->threshold, 1.0);
2232 /* AdResS defined thingies */
2233 CCTYPE ("AdResS parameters");
2234 EETYPE("adress", ir->bAdress, yesno_names);
2237 snew(ir->adress, 1);
2238 read_adressparams(&ninp, &inp, ir->adress, wi);
2241 /* User defined thingies */
2242 CCTYPE ("User defined thingies");
2243 STYPE ("user1-grps", is->user1, NULL);
2244 STYPE ("user2-grps", is->user2, NULL);
2245 ITYPE ("userint1", ir->userint1, 0);
2246 ITYPE ("userint2", ir->userint2, 0);
2247 ITYPE ("userint3", ir->userint3, 0);
2248 ITYPE ("userint4", ir->userint4, 0);
2249 RTYPE ("userreal1", ir->userreal1, 0);
2250 RTYPE ("userreal2", ir->userreal2, 0);
2251 RTYPE ("userreal3", ir->userreal3, 0);
2252 RTYPE ("userreal4", ir->userreal4, 0);
2255 write_inpfile(mdparout, ninp, inp, FALSE, wi);
2256 for (i = 0; (i < ninp); i++)
2259 sfree(inp[i].value);
2263 /* Process options if necessary */
2264 for (m = 0; m < 2; m++)
2266 for (i = 0; i < 2*DIM; i++)
2275 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2277 warning_error(wi, "Pressure coupling not enough values (I need 1)");
2279 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2281 case epctSEMIISOTROPIC:
2282 case epctSURFACETENSION:
2283 if (sscanf(dumstr[m], "%lf%lf",
2284 &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2286 warning_error(wi, "Pressure coupling not enough values (I need 2)");
2288 dumdub[m][YY] = dumdub[m][XX];
2290 case epctANISOTROPIC:
2291 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2292 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2293 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2295 warning_error(wi, "Pressure coupling not enough values (I need 6)");
2299 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2300 epcoupltype_names[ir->epct]);
2304 clear_mat(ir->ref_p);
2305 clear_mat(ir->compress);
2306 for (i = 0; i < DIM; i++)
2308 ir->ref_p[i][i] = dumdub[1][i];
2309 ir->compress[i][i] = dumdub[0][i];
2311 if (ir->epct == epctANISOTROPIC)
2313 ir->ref_p[XX][YY] = dumdub[1][3];
2314 ir->ref_p[XX][ZZ] = dumdub[1][4];
2315 ir->ref_p[YY][ZZ] = dumdub[1][5];
2316 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2318 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2320 ir->compress[XX][YY] = dumdub[0][3];
2321 ir->compress[XX][ZZ] = dumdub[0][4];
2322 ir->compress[YY][ZZ] = dumdub[0][5];
2323 for (i = 0; i < DIM; i++)
2325 for (m = 0; m < i; m++)
2327 ir->ref_p[i][m] = ir->ref_p[m][i];
2328 ir->compress[i][m] = ir->compress[m][i];
2333 if (ir->comm_mode == ecmNO)
2338 opts->couple_moltype = NULL;
2339 if (strlen(is->couple_moltype) > 0)
2341 if (ir->efep != efepNO)
2343 opts->couple_moltype = strdup(is->couple_moltype);
2344 if (opts->couple_lam0 == opts->couple_lam1)
2346 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2348 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2349 opts->couple_lam1 == ecouplamNONE))
2351 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2356 warning_note(wi, "Free energy is turned off, so we will not decouple the molecule listed in your input.");
2359 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2360 if (ir->efep != efepNO)
2362 if (fep->delta_lambda > 0)
2364 ir->efep = efepSLOWGROWTH;
2370 fep->bPrintEnergy = TRUE;
2371 /* always print out the energy to dhdl if we are doing expanded ensemble, since we need the total energy
2372 if the temperature is changing. */
2375 if ((ir->efep != efepNO) || ir->bSimTemp)
2377 ir->bExpanded = FALSE;
2378 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2380 ir->bExpanded = TRUE;
2382 do_fep_params(ir, is->fep_lambda, is->lambda_weights);
2383 if (ir->bSimTemp) /* done after fep params */
2385 do_simtemp_params(ir);
2390 ir->fepvals->n_lambda = 0;
2393 /* WALL PARAMETERS */
2395 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2397 /* ORIENTATION RESTRAINT PARAMETERS */
2399 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
2401 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2404 /* DEFORMATION PARAMETERS */
2406 clear_mat(ir->deform);
2407 for (i = 0; i < 6; i++)
2411 m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
2412 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2413 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2414 for (i = 0; i < 3; i++)
2416 ir->deform[i][i] = dumdub[0][i];
2418 ir->deform[YY][XX] = dumdub[0][3];
2419 ir->deform[ZZ][XX] = dumdub[0][4];
2420 ir->deform[ZZ][YY] = dumdub[0][5];
2421 if (ir->epc != epcNO)
2423 for (i = 0; i < 3; i++)
2425 for (j = 0; j <= i; j++)
2427 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2429 warning_error(wi, "A box element has deform set and compressibility > 0");
2433 for (i = 0; i < 3; i++)
2435 for (j = 0; j < i; j++)
2437 if (ir->deform[i][j] != 0)
2439 for (m = j; m < DIM; m++)
2441 if (ir->compress[m][j] != 0)
2443 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.");
2444 warning(wi, warn_buf);
2452 /* Ion/water position swapping checks */
2453 if (ir->eSwapCoords != eswapNO)
2455 if (ir->swap->nstswap < 1)
2457 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2459 if (ir->swap->nAverage < 1)
2461 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2463 if (ir->swap->threshold < 1.0)
2465 warning_error(wi, "Ion count threshold must be at least 1.\n");
2473 static int search_QMstring(const char *s, int ng, const char *gn[])
2475 /* same as normal search_string, but this one searches QM strings */
2478 for (i = 0; (i < ng); i++)
2480 if (gmx_strcasecmp(s, gn[i]) == 0)
2486 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2490 } /* search_QMstring */
2492 /* We would like gn to be const as well, but C doesn't allow this */
2493 int search_string(const char *s, int ng, char *gn[])
2497 for (i = 0; (i < ng); i++)
2499 if (gmx_strcasecmp(s, gn[i]) == 0)
2506 "Group %s referenced in the .mdp file was not found in the index file.\n"
2507 "Group names must match either [moleculetype] names or custom index group\n"
2508 "names, in which case you must supply an index file to the '-n' option\n"
2515 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2516 t_blocka *block, char *gnames[],
2517 int gtype, int restnm,
2518 int grptp, gmx_bool bVerbose,
2521 unsigned short *cbuf;
2522 t_grps *grps = &(groups->grps[gtype]);
2523 int i, j, gid, aj, ognr, ntot = 0;
2526 char warn_buf[STRLEN];
2530 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2533 title = gtypes[gtype];
2536 /* Mark all id's as not set */
2537 for (i = 0; (i < natoms); i++)
2542 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2543 for (i = 0; (i < ng); i++)
2545 /* Lookup the group name in the block structure */
2546 gid = search_string(ptrs[i], block->nr, gnames);
2547 if ((grptp != egrptpONE) || (i == 0))
2549 grps->nm_ind[grps->nr++] = gid;
2553 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2556 /* Now go over the atoms in the group */
2557 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2562 /* Range checking */
2563 if ((aj < 0) || (aj >= natoms))
2565 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2567 /* Lookup up the old group number */
2571 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2572 aj+1, title, ognr+1, i+1);
2576 /* Store the group number in buffer */
2577 if (grptp == egrptpONE)
2590 /* Now check whether we have done all atoms */
2594 if (grptp == egrptpALL)
2596 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2597 natoms-ntot, title);
2599 else if (grptp == egrptpPART)
2601 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2602 natoms-ntot, title);
2603 warning_note(wi, warn_buf);
2605 /* Assign all atoms currently unassigned to a rest group */
2606 for (j = 0; (j < natoms); j++)
2608 if (cbuf[j] == NOGID)
2614 if (grptp != egrptpPART)
2619 "Making dummy/rest group for %s containing %d elements\n",
2620 title, natoms-ntot);
2622 /* Add group name "rest" */
2623 grps->nm_ind[grps->nr] = restnm;
2625 /* Assign the rest name to all atoms not currently assigned to a group */
2626 for (j = 0; (j < natoms); j++)
2628 if (cbuf[j] == NOGID)
2637 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2639 /* All atoms are part of one (or no) group, no index required */
2640 groups->ngrpnr[gtype] = 0;
2641 groups->grpnr[gtype] = NULL;
2645 groups->ngrpnr[gtype] = natoms;
2646 snew(groups->grpnr[gtype], natoms);
2647 for (j = 0; (j < natoms); j++)
2649 groups->grpnr[gtype][j] = cbuf[j];
2655 return (bRest && grptp == egrptpPART);
2658 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2661 gmx_groups_t *groups;
2663 int natoms, ai, aj, i, j, d, g, imin, jmin;
2665 int *nrdf2, *na_vcm, na_tot;
2666 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2667 gmx_mtop_atomloop_all_t aloop;
2669 int mb, mol, ftype, as;
2670 gmx_molblock_t *molb;
2671 gmx_moltype_t *molt;
2674 * First calc 3xnr-atoms for each group
2675 * then subtract half a degree of freedom for each constraint
2677 * Only atoms and nuclei contribute to the degrees of freedom...
2682 groups = &mtop->groups;
2683 natoms = mtop->natoms;
2685 /* Allocate one more for a possible rest group */
2686 /* We need to sum degrees of freedom into doubles,
2687 * since floats give too low nrdf's above 3 million atoms.
2689 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2690 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2691 snew(na_vcm, groups->grps[egcVCM].nr+1);
2693 for (i = 0; i < groups->grps[egcTC].nr; i++)
2697 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2702 snew(nrdf2, natoms);
2703 aloop = gmx_mtop_atomloop_all_init(mtop);
2704 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2707 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2709 g = ggrpnr(groups, egcFREEZE, i);
2710 /* Double count nrdf for particle i */
2711 for (d = 0; d < DIM; d++)
2713 if (opts->nFreeze[g][d] == 0)
2718 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2719 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2724 for (mb = 0; mb < mtop->nmolblock; mb++)
2726 molb = &mtop->molblock[mb];
2727 molt = &mtop->moltype[molb->type];
2728 atom = molt->atoms.atom;
2729 for (mol = 0; mol < molb->nmol; mol++)
2731 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2733 ia = molt->ilist[ftype].iatoms;
2734 for (i = 0; i < molt->ilist[ftype].nr; )
2736 /* Subtract degrees of freedom for the constraints,
2737 * if the particles still have degrees of freedom left.
2738 * If one of the particles is a vsite or a shell, then all
2739 * constraint motion will go there, but since they do not
2740 * contribute to the constraints the degrees of freedom do not
2745 if (((atom[ia[1]].ptype == eptNucleus) ||
2746 (atom[ia[1]].ptype == eptAtom)) &&
2747 ((atom[ia[2]].ptype == eptNucleus) ||
2748 (atom[ia[2]].ptype == eptAtom)))
2766 imin = min(imin, nrdf2[ai]);
2767 jmin = min(jmin, nrdf2[aj]);
2770 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2771 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2772 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2773 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2775 ia += interaction_function[ftype].nratoms+1;
2776 i += interaction_function[ftype].nratoms+1;
2779 ia = molt->ilist[F_SETTLE].iatoms;
2780 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2782 /* Subtract 1 dof from every atom in the SETTLE */
2783 for (j = 0; j < 3; j++)
2786 imin = min(2, nrdf2[ai]);
2788 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2789 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2794 as += molt->atoms.nr;
2798 if (ir->ePull == epullCONSTRAINT)
2800 /* Correct nrdf for the COM constraints.
2801 * We correct using the TC and VCM group of the first atom
2802 * in the reference and pull group. If atoms in one pull group
2803 * belong to different TC or VCM groups it is anyhow difficult
2804 * to determine the optimal nrdf assignment.
2808 for (i = 0; i < pull->ncoord; i++)
2812 for (j = 0; j < 2; j++)
2814 const t_pull_group *pgrp;
2816 pgrp = &pull->group[pull->coord[i].group[j]];
2820 /* Subtract 1/2 dof from each group */
2822 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2823 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2824 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2826 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)]]);
2831 /* We need to subtract the whole DOF from group j=1 */
2838 if (ir->nstcomm != 0)
2840 /* Subtract 3 from the number of degrees of freedom in each vcm group
2841 * when com translation is removed and 6 when rotation is removed
2844 switch (ir->comm_mode)
2847 n_sub = ndof_com(ir);
2854 gmx_incons("Checking comm_mode");
2857 for (i = 0; i < groups->grps[egcTC].nr; i++)
2859 /* Count the number of atoms of TC group i for every VCM group */
2860 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2865 for (ai = 0; ai < natoms; ai++)
2867 if (ggrpnr(groups, egcTC, ai) == i)
2869 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2873 /* Correct for VCM removal according to the fraction of each VCM
2874 * group present in this TC group.
2876 nrdf_uc = nrdf_tc[i];
2879 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2883 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2885 if (nrdf_vcm[j] > n_sub)
2887 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2888 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2892 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2893 j, nrdf_vcm[j], nrdf_tc[i]);
2898 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2900 opts->nrdf[i] = nrdf_tc[i];
2901 if (opts->nrdf[i] < 0)
2906 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2907 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
2916 static void decode_cos(char *s, t_cosines *cosine)
2919 char format[STRLEN], f1[STRLEN];
2931 sscanf(t, "%d", &(cosine->n));
2938 snew(cosine->a, cosine->n);
2939 snew(cosine->phi, cosine->n);
2941 sprintf(format, "%%*d");
2942 for (i = 0; (i < cosine->n); i++)
2945 strcat(f1, "%lf%lf");
2946 if (sscanf(t, f1, &a, &phi) < 2)
2948 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
2951 cosine->phi[i] = phi;
2952 strcat(format, "%*lf%*lf");
2959 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
2960 const char *option, const char *val, int flag)
2962 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
2963 * But since this is much larger than STRLEN, such a line can not be parsed.
2964 * The real maximum is the number of names that fit in a string: STRLEN/2.
2966 #define EGP_MAX (STRLEN/2)
2967 int nelem, i, j, k, nr;
2968 char *names[EGP_MAX];
2972 gnames = groups->grpname;
2974 nelem = str_nelem(val, EGP_MAX, names);
2977 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
2979 nr = groups->grps[egcENER].nr;
2981 for (i = 0; i < nelem/2; i++)
2985 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
2991 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
2992 names[2*i], option);
2996 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
3002 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3003 names[2*i+1], option);
3005 if ((j < nr) && (k < nr))
3007 ir->opts.egp_flags[nr*j+k] |= flag;
3008 ir->opts.egp_flags[nr*k+j] |= flag;
3017 static void make_swap_groups(
3026 int ig = -1, i = 0, j;
3030 /* Just a quick check here, more thorough checks are in mdrun */
3031 if (strcmp(splitg0name, splitg1name) == 0)
3033 gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
3036 /* First get the swap group index atoms */
3037 ig = search_string(swapgname, grps->nr, gnames);
3038 swap->nat = grps->index[ig+1] - grps->index[ig];
3041 fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
3042 snew(swap->ind, swap->nat);
3043 for (i = 0; i < swap->nat; i++)
3045 swap->ind[i] = grps->a[grps->index[ig]+i];
3050 gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
3053 /* Now do so for the split groups */
3054 for (j = 0; j < 2; j++)
3058 splitg = splitg0name;
3062 splitg = splitg1name;
3065 ig = search_string(splitg, grps->nr, gnames);
3066 swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
3067 if (swap->nat_split[j] > 0)
3069 fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
3070 j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
3071 snew(swap->ind_split[j], swap->nat_split[j]);
3072 for (i = 0; i < swap->nat_split[j]; i++)
3074 swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
3079 gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
3083 /* Now get the solvent group index atoms */
3084 ig = search_string(solgname, grps->nr, gnames);
3085 swap->nat_sol = grps->index[ig+1] - grps->index[ig];
3086 if (swap->nat_sol > 0)
3088 fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
3089 snew(swap->ind_sol, swap->nat_sol);
3090 for (i = 0; i < swap->nat_sol; i++)
3092 swap->ind_sol[i] = grps->a[grps->index[ig]+i];
3097 gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
3102 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3107 ig = search_string(IMDgname, grps->nr, gnames);
3108 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3110 if (IMDgroup->nat > 0)
3112 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3113 IMDgname, IMDgroup->nat);
3114 snew(IMDgroup->ind, IMDgroup->nat);
3115 for (i = 0; i < IMDgroup->nat; i++)
3117 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3123 void do_index(const char* mdparin, const char *ndx,
3126 t_inputrec *ir, rvec *v,
3130 gmx_groups_t *groups;
3134 char warnbuf[STRLEN], **gnames;
3135 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3138 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3139 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3140 int i, j, k, restnm;
3142 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3143 int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
3144 nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
3145 char warn_buf[STRLEN];
3149 fprintf(stderr, "processing index file...\n");
3155 snew(grps->index, 1);
3157 atoms_all = gmx_mtop_global_atoms(mtop);
3158 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3159 free_t_atoms(&atoms_all, FALSE);
3163 grps = init_index(ndx, &gnames);
3166 groups = &mtop->groups;
3167 natoms = mtop->natoms;
3168 symtab = &mtop->symtab;
3170 snew(groups->grpname, grps->nr+1);
3172 for (i = 0; (i < grps->nr); i++)
3174 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3176 groups->grpname[i] = put_symtab(symtab, "rest");
3178 srenew(gnames, grps->nr+1);
3179 gnames[restnm] = *(groups->grpname[i]);
3180 groups->ngrpname = grps->nr+1;
3182 set_warning_line(wi, mdparin, -1);
3184 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3185 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3186 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3187 if ((ntau_t != ntcg) || (nref_t != ntcg))
3189 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3190 "%d tau-t values", ntcg, nref_t, ntau_t);
3193 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3194 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3195 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3196 nr = groups->grps[egcTC].nr;
3198 snew(ir->opts.nrdf, nr);
3199 snew(ir->opts.tau_t, nr);
3200 snew(ir->opts.ref_t, nr);
3201 if (ir->eI == eiBD && ir->bd_fric == 0)
3203 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3210 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3214 for (i = 0; (i < nr); i++)
3216 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
3217 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
3219 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3220 warning_error(wi, warn_buf);
3223 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3225 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.");
3228 if (ir->opts.tau_t[i] >= 0)
3230 tau_min = min(tau_min, ir->opts.tau_t[i]);
3233 if (ir->etc != etcNO && ir->nsttcouple == -1)
3235 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3240 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3242 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");
3244 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
3246 if (ir->nstpcouple != ir->nsttcouple)
3248 int mincouple = min(ir->nstpcouple, ir->nsttcouple);
3249 ir->nstpcouple = ir->nsttcouple = mincouple;
3250 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);
3251 warning_note(wi, warn_buf);
3255 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3256 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3258 if (ETC_ANDERSEN(ir->etc))
3260 if (ir->nsttcouple != 1)
3263 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");
3264 warning_note(wi, warn_buf);
3267 nstcmin = tcouple_min_integration_steps(ir->etc);
3270 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
3272 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3273 ETCOUPLTYPE(ir->etc),
3275 ir->nsttcouple*ir->delta_t);
3276 warning(wi, warn_buf);
3279 for (i = 0; (i < nr); i++)
3281 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
3282 if (ir->opts.ref_t[i] < 0)
3284 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3287 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3288 if we are in this conditional) if mc_temp is negative */
3289 if (ir->expandedvals->mc_temp < 0)
3291 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3295 /* Simulated annealing for each group. There are nr groups */
3296 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3297 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3301 if (nSA > 0 && nSA != nr)
3303 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3307 snew(ir->opts.annealing, nr);
3308 snew(ir->opts.anneal_npoints, nr);
3309 snew(ir->opts.anneal_time, nr);
3310 snew(ir->opts.anneal_temp, nr);
3311 for (i = 0; i < nr; i++)
3313 ir->opts.annealing[i] = eannNO;
3314 ir->opts.anneal_npoints[i] = 0;
3315 ir->opts.anneal_time[i] = NULL;
3316 ir->opts.anneal_temp[i] = NULL;
3321 for (i = 0; i < nr; i++)
3323 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3325 ir->opts.annealing[i] = eannNO;
3327 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3329 ir->opts.annealing[i] = eannSINGLE;
3332 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3334 ir->opts.annealing[i] = eannPERIODIC;
3340 /* Read the other fields too */
3341 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3342 if (nSA_points != nSA)
3344 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3346 for (k = 0, i = 0; i < nr; i++)
3348 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3349 if (ir->opts.anneal_npoints[i] == 1)
3351 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3353 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3354 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3355 k += ir->opts.anneal_npoints[i];
3358 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3361 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3363 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3366 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3369 for (i = 0, k = 0; i < nr; i++)
3372 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3374 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3375 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3378 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3380 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3386 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3388 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3389 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3392 if (ir->opts.anneal_temp[i][j] < 0)
3394 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3399 /* Print out some summary information, to make sure we got it right */
3400 for (i = 0, k = 0; i < nr; i++)
3402 if (ir->opts.annealing[i] != eannNO)
3404 j = groups->grps[egcTC].nm_ind[i];
3405 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3406 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3407 ir->opts.anneal_npoints[i]);
3408 fprintf(stderr, "Time (ps) Temperature (K)\n");
3409 /* All terms except the last one */
3410 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3412 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3415 /* Finally the last one */
3416 j = ir->opts.anneal_npoints[i]-1;
3417 if (ir->opts.annealing[i] == eannSINGLE)
3419 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3423 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3424 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3426 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3435 if (ir->ePull != epullNO)
3437 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3439 make_pull_coords(ir->pull);
3444 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3447 if (ir->eSwapCoords != eswapNO)
3449 make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
3452 /* Make indices for IMD session */
3455 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3458 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3459 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3460 if (nacg*DIM != nacc)
3462 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3465 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3466 restnm, egrptpALL_GENREST, bVerbose, wi);
3467 nr = groups->grps[egcACC].nr;
3468 snew(ir->opts.acc, nr);
3469 ir->opts.ngacc = nr;
3471 for (i = k = 0; (i < nacg); i++)
3473 for (j = 0; (j < DIM); j++, k++)
3475 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3478 for (; (i < nr); i++)
3480 for (j = 0; (j < DIM); j++)
3482 ir->opts.acc[i][j] = 0;
3486 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3487 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3488 if (nfrdim != DIM*nfreeze)
3490 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3493 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3494 restnm, egrptpALL_GENREST, bVerbose, wi);
3495 nr = groups->grps[egcFREEZE].nr;
3496 ir->opts.ngfrz = nr;
3497 snew(ir->opts.nFreeze, nr);
3498 for (i = k = 0; (i < nfreeze); i++)
3500 for (j = 0; (j < DIM); j++, k++)
3502 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3503 if (!ir->opts.nFreeze[i][j])
3505 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3507 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3508 "(not %s)", ptr1[k]);
3509 warning(wi, warn_buf);
3514 for (; (i < nr); i++)
3516 for (j = 0; (j < DIM); j++)
3518 ir->opts.nFreeze[i][j] = 0;
3522 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3523 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3524 restnm, egrptpALL_GENREST, bVerbose, wi);
3525 add_wall_energrps(groups, ir->nwall, symtab);
3526 ir->opts.ngener = groups->grps[egcENER].nr;
3527 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3529 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3530 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3533 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3534 "This may lead to artifacts.\n"
3535 "In most cases one should use one group for the whole system.");
3538 /* Now we have filled the freeze struct, so we can calculate NRDF */
3539 calc_nrdf(mtop, ir, gnames);
3545 /* Must check per group! */
3546 for (i = 0; (i < ir->opts.ngtc); i++)
3548 ntot += ir->opts.nrdf[i];
3550 if (ntot != (DIM*natoms))
3552 fac = sqrt(ntot/(DIM*natoms));
3555 fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
3556 "and removal of center of mass motion\n", fac);
3558 for (i = 0; (i < natoms); i++)
3560 svmul(fac, v[i], v[i]);
3565 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3566 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3567 restnm, egrptpALL_GENREST, bVerbose, wi);
3568 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3569 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3570 restnm, egrptpALL_GENREST, bVerbose, wi);
3571 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3572 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3573 restnm, egrptpONE, bVerbose, wi);
3574 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3575 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3576 restnm, egrptpALL_GENREST, bVerbose, wi);
3578 /* QMMM input processing */
3579 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3580 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3581 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3582 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3584 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3585 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3587 /* group rest, if any, is always MM! */
3588 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3589 restnm, egrptpALL_GENREST, bVerbose, wi);
3590 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3591 ir->opts.ngQM = nQMg;
3592 snew(ir->opts.QMmethod, nr);
3593 snew(ir->opts.QMbasis, nr);
3594 for (i = 0; i < nr; i++)
3596 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3597 * converted to the corresponding enum in names.c
3599 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3601 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3605 nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
3606 nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
3607 nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
3608 snew(ir->opts.QMmult, nr);
3609 snew(ir->opts.QMcharge, nr);
3610 snew(ir->opts.bSH, nr);
3612 for (i = 0; i < nr; i++)
3614 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3615 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3616 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3619 nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
3620 nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
3621 snew(ir->opts.CASelectrons, nr);
3622 snew(ir->opts.CASorbitals, nr);
3623 for (i = 0; i < nr; i++)
3625 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3626 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3628 /* special optimization options */
3630 nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
3631 nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
3632 snew(ir->opts.bOPT, nr);
3633 snew(ir->opts.bTS, nr);
3634 for (i = 0; i < nr; i++)
3636 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3637 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3639 nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
3640 nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
3641 nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
3642 snew(ir->opts.SAon, nr);
3643 snew(ir->opts.SAoff, nr);
3644 snew(ir->opts.SAsteps, nr);
3646 for (i = 0; i < nr; i++)
3648 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3649 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3650 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3652 /* end of QMMM input */
3656 for (i = 0; (i < egcNR); i++)
3658 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3659 for (j = 0; (j < groups->grps[i].nr); j++)
3661 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3663 fprintf(stderr, "\n");
3667 nr = groups->grps[egcENER].nr;
3668 snew(ir->opts.egp_flags, nr*nr);
3670 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3671 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3673 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3675 if (bExcl && EEL_FULL(ir->coulombtype))
3677 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3680 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3681 if (bTable && !(ir->vdwtype == evdwUSER) &&
3682 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3683 !(ir->coulombtype == eelPMEUSERSWITCH))
3685 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3688 decode_cos(is->efield_x, &(ir->ex[XX]));
3689 decode_cos(is->efield_xt, &(ir->et[XX]));
3690 decode_cos(is->efield_y, &(ir->ex[YY]));
3691 decode_cos(is->efield_yt, &(ir->et[YY]));
3692 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3693 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3697 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3700 for (i = 0; (i < grps->nr); i++)
3712 static void check_disre(gmx_mtop_t *mtop)
3714 gmx_ffparams_t *ffparams;
3715 t_functype *functype;
3717 int i, ndouble, ftype;
3718 int label, old_label;
3720 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3722 ffparams = &mtop->ffparams;
3723 functype = ffparams->functype;
3724 ip = ffparams->iparams;
3727 for (i = 0; i < ffparams->ntypes; i++)
3729 ftype = functype[i];
3730 if (ftype == F_DISRES)
3732 label = ip[i].disres.label;
3733 if (label == old_label)
3735 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3743 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3744 "probably the parameters for multiple pairs in one restraint "
3745 "are not identical\n", ndouble);
3750 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3751 gmx_bool posres_only,
3755 gmx_mtop_ilistloop_t iloop;
3765 for (d = 0; d < DIM; d++)
3767 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3769 /* Check for freeze groups */
3770 for (g = 0; g < ir->opts.ngfrz; g++)
3772 for (d = 0; d < DIM; d++)
3774 if (ir->opts.nFreeze[g][d] != 0)
3782 /* Check for position restraints */
3783 iloop = gmx_mtop_ilistloop_init(sys);
3784 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3787 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3789 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3791 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3792 for (d = 0; d < DIM; d++)
3794 if (pr->posres.fcA[d] != 0)
3800 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3802 /* Check for flat-bottom posres */
3803 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3804 if (pr->fbposres.k != 0)
3806 switch (pr->fbposres.geom)
3808 case efbposresSPHERE:
3809 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3811 case efbposresCYLINDER:
3812 AbsRef[XX] = AbsRef[YY] = 1;
3814 case efbposresX: /* d=XX */
3815 case efbposresY: /* d=YY */
3816 case efbposresZ: /* d=ZZ */
3817 d = pr->fbposres.geom - efbposresX;
3821 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3822 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3830 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3834 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3835 gmx_bool *bC6ParametersWorkWithGeometricRules,
3836 gmx_bool *bC6ParametersWorkWithLBRules,
3837 gmx_bool *bLBRulesPossible)
3839 int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
3842 double geometricdiff, LBdiff;
3843 double c6i, c6j, c12i, c12j;
3844 double c6, c6_geometric, c6_LB;
3845 double sigmai, sigmaj, epsi, epsj;
3846 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3849 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3850 * force-field floating point parameters.
3853 ptr = getenv("GMX_LJCOMB_TOL");
3858 sscanf(ptr, "%lf", &dbl);
3862 *bC6ParametersWorkWithLBRules = TRUE;
3863 *bC6ParametersWorkWithGeometricRules = TRUE;
3864 bCanDoLBRules = TRUE;
3865 bCanDoGeometricRules = TRUE;
3866 ntypes = mtop->ffparams.atnr;
3867 snew(typecount, ntypes);
3868 gmx_mtop_count_atomtypes(mtop, state, typecount);
3869 geometricdiff = LBdiff = 0.0;
3870 *bLBRulesPossible = TRUE;
3871 for (tpi = 0; tpi < ntypes; ++tpi)
3873 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3874 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3875 for (tpj = tpi; tpj < ntypes; ++tpj)
3877 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3878 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3879 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3880 c6_geometric = sqrt(c6i * c6j);
3881 if (!gmx_numzero(c6_geometric))
3883 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3885 sigmai = pow(c12i / c6i, 1.0/6.0);
3886 sigmaj = pow(c12j / c6j, 1.0/6.0);
3887 epsi = c6i * c6i /(4.0 * c12i);
3888 epsj = c6j * c6j /(4.0 * c12j);
3889 c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
3893 *bLBRulesPossible = FALSE;
3894 c6_LB = c6_geometric;
3896 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3899 if (FALSE == bCanDoLBRules)
3901 *bC6ParametersWorkWithLBRules = FALSE;
3904 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3906 if (FALSE == bCanDoGeometricRules)
3908 *bC6ParametersWorkWithGeometricRules = FALSE;
3916 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3920 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3922 check_combination_rule_differences(mtop, 0,
3923 &bC6ParametersWorkWithGeometricRules,
3924 &bC6ParametersWorkWithLBRules,
3926 if (ir->ljpme_combination_rule == eljpmeLB)
3928 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
3930 warning(wi, "You are using arithmetic-geometric combination rules "
3931 "in LJ-PME, but your non-bonded C6 parameters do not "
3932 "follow these rules.");
3937 if (FALSE == bC6ParametersWorkWithGeometricRules)
3939 if (ir->eDispCorr != edispcNO)
3941 warning_note(wi, "You are using geometric combination rules in "
3942 "LJ-PME, but your non-bonded C6 parameters do "
3943 "not follow these rules. "
3944 "This will introduce very small errors in the forces and energies in "
3945 "your simulations. Dispersion correction will correct total energy "
3946 "and/or pressure for isotropic systems, but not forces or surface tensions.");
3950 warning_note(wi, "You are using geometric combination rules in "
3951 "LJ-PME, but your non-bonded C6 parameters do "
3952 "not follow these rules. "
3953 "This will introduce very small errors in the forces and energies in "
3954 "your simulations. If your system is homogeneous, consider using dispersion correction "
3955 "for the total energy and pressure.");
3961 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
3964 char err_buf[STRLEN];
3965 int i, m, c, nmol, npct;
3966 gmx_bool bCharge, bAcc;
3967 real gdt_max, *mgrp, mt;
3969 gmx_mtop_atomloop_block_t aloopb;
3970 gmx_mtop_atomloop_all_t aloop;
3973 char warn_buf[STRLEN];
3975 set_warning_line(wi, mdparin, -1);
3977 if (ir->cutoff_scheme == ecutsVERLET &&
3978 ir->verletbuf_tol > 0 &&
3980 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
3981 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
3983 /* Check if a too small Verlet buffer might potentially
3984 * cause more drift than the thermostat can couple off.
3986 /* Temperature error fraction for warning and suggestion */
3987 const real T_error_warn = 0.002;
3988 const real T_error_suggest = 0.001;
3989 /* For safety: 2 DOF per atom (typical with constraints) */
3990 const real nrdf_at = 2;
3991 real T, tau, max_T_error;
3996 for (i = 0; i < ir->opts.ngtc; i++)
3998 T = max(T, ir->opts.ref_t[i]);
3999 tau = max(tau, ir->opts.tau_t[i]);
4003 /* This is a worst case estimate of the temperature error,
4004 * assuming perfect buffer estimation and no cancelation
4005 * of errors. The factor 0.5 is because energy distributes
4006 * equally over Ekin and Epot.
4008 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4009 if (max_T_error > T_error_warn)
4011 sprintf(warn_buf, "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to %.0e or decrease tau_t.",
4012 ir->verletbuf_tol, T, tau,
4014 100*T_error_suggest,
4015 ir->verletbuf_tol*T_error_suggest/max_T_error);
4016 warning(wi, warn_buf);
4021 if (ETC_ANDERSEN(ir->etc))
4025 for (i = 0; i < ir->opts.ngtc; i++)
4027 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4028 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4029 sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
4030 i, ir->opts.tau_t[i]);
4031 CHECK(ir->opts.tau_t[i] < 0);
4034 for (i = 0; i < ir->opts.ngtc; i++)
4036 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
4037 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);
4038 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
4042 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4043 ir->comm_mode == ecmNO &&
4044 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4045 !ETC_ANDERSEN(ir->etc))
4047 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");
4050 /* Check for pressure coupling with absolute position restraints */
4051 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4053 absolute_reference(ir, sys, TRUE, AbsRef);
4055 for (m = 0; m < DIM; m++)
4057 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4059 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4067 aloopb = gmx_mtop_atomloop_block_init(sys);
4068 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4070 if (atom->q != 0 || atom->qB != 0)
4078 if (EEL_FULL(ir->coulombtype))
4081 "You are using full electrostatics treatment %s for a system without charges.\n"
4082 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4083 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4084 warning(wi, err_buf);
4089 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4092 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4093 "You might want to consider using %s electrostatics.\n",
4095 warning_note(wi, err_buf);
4099 /* Check if combination rules used in LJ-PME are the same as in the force field */
4100 if (EVDW_PME(ir->vdwtype))
4102 check_combination_rules(ir, sys, wi);
4105 /* Generalized reaction field */
4106 if (ir->opts.ngtc == 0)
4108 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4110 CHECK(ir->coulombtype == eelGRF);
4114 sprintf(err_buf, "When using coulombtype = %s"
4115 " ref-t for temperature coupling should be > 0",
4117 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4120 if (ir->eI == eiSD1 &&
4121 (gmx_mtop_ftype_count(sys, F_CONSTR) > 0 ||
4122 gmx_mtop_ftype_count(sys, F_SETTLE) > 0))
4124 sprintf(warn_buf, "With constraints integrator %s is less accurate, consider using %s instead", ei_names[ir->eI], ei_names[eiSD2]);
4125 warning_note(wi, warn_buf);
4129 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4131 for (m = 0; (m < DIM); m++)
4133 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4142 snew(mgrp, sys->groups.grps[egcACC].nr);
4143 aloop = gmx_mtop_atomloop_all_init(sys);
4144 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4146 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4149 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4151 for (m = 0; (m < DIM); m++)
4153 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4157 for (m = 0; (m < DIM); m++)
4159 if (fabs(acc[m]) > 1e-6)
4161 const char *dim[DIM] = { "X", "Y", "Z" };
4163 "Net Acceleration in %s direction, will %s be corrected\n",
4164 dim[m], ir->nstcomm != 0 ? "" : "not");
4165 if (ir->nstcomm != 0 && m < ndof_com(ir))
4168 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4170 ir->opts.acc[i][m] -= acc[m];
4178 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4179 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4181 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4184 if (ir->ePull != epullNO)
4186 gmx_bool bPullAbsoluteRef;
4188 bPullAbsoluteRef = FALSE;
4189 for (i = 0; i < ir->pull->ncoord; i++)
4191 bPullAbsoluteRef = bPullAbsoluteRef ||
4192 ir->pull->coord[i].group[0] == 0 ||
4193 ir->pull->coord[i].group[1] == 0;
4195 if (bPullAbsoluteRef)
4197 absolute_reference(ir, sys, FALSE, AbsRef);
4198 for (m = 0; m < DIM; m++)
4200 if (ir->pull->dim[m] && !AbsRef[m])
4202 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.");
4208 if (ir->pull->eGeom == epullgDIRPBC)
4210 for (i = 0; i < 3; i++)
4212 for (m = 0; m <= i; m++)
4214 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4215 ir->deform[i][m] != 0)
4217 for (c = 0; c < ir->pull->ncoord; c++)
4219 if (ir->pull->coord[c].vec[m] != 0)
4221 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->eGeom), 'x'+m);
4233 void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr, warninp_t wi)
4237 char warn_buf[STRLEN];
4240 ptr = check_box(ir->ePBC, box);
4243 warning_error(wi, ptr);
4246 if (bConstr && ir->eConstrAlg == econtSHAKE)
4248 if (ir->shake_tol <= 0.0)
4250 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4252 warning_error(wi, warn_buf);
4255 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
4257 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
4258 if (ir->epc == epcNO)
4260 warning(wi, warn_buf);
4264 warning_error(wi, warn_buf);
4269 if ( (ir->eConstrAlg == econtLINCS) && bConstr)
4271 /* If we have Lincs constraints: */
4272 if (ir->eI == eiMD && ir->etc == etcNO &&
4273 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4275 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4276 warning_note(wi, warn_buf);
4279 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4281 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4282 warning_note(wi, warn_buf);
4284 if (ir->epc == epcMTTK)
4286 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4290 if (bConstr && ir->epc == epcMTTK)
4292 warning_note(wi, "MTTK with constraints is deprecated, and will be removed in GROMACS 5.1");
4295 if (ir->LincsWarnAngle > 90.0)
4297 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4298 warning(wi, warn_buf);
4299 ir->LincsWarnAngle = 90.0;
4302 if (ir->ePBC != epbcNONE)
4304 if (ir->nstlist == 0)
4306 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4308 bTWIN = (ir->rlistlong > ir->rlist);
4309 if (ir->ns_type == ensGRID)
4311 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
4313 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",
4314 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
4315 warning_error(wi, warn_buf);
4320 min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
4321 if (2*ir->rlistlong >= min_size)
4323 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4324 warning_error(wi, warn_buf);
4327 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4334 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4338 real rvdw1, rvdw2, rcoul1, rcoul2;
4339 char warn_buf[STRLEN];
4341 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4345 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4350 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4356 if (rvdw1 + rvdw2 > ir->rlist ||
4357 rcoul1 + rcoul2 > ir->rlist)
4360 "The sum of the two largest charge group radii (%f) "
4361 "is larger than rlist (%f)\n",
4362 max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4363 warning(wi, warn_buf);
4367 /* Here we do not use the zero at cut-off macro,
4368 * since user defined interactions might purposely
4369 * not be zero at the cut-off.
4371 if (ir_vdw_is_zero_at_cutoff(ir) &&
4372 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
4374 sprintf(warn_buf, "The sum of the two largest charge group "
4375 "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
4376 "With exact cut-offs, better performance can be "
4377 "obtained with cutoff-scheme = %s, because it "
4378 "does not use charge groups at all.",
4380 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4381 ir->rlistlong, ir->rvdw,
4382 ecutscheme_names[ecutsVERLET]);
4385 warning(wi, warn_buf);
4389 warning_note(wi, warn_buf);
4392 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4393 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
4395 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
4396 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4398 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4399 ir->rlistlong, ir->rcoulomb,
4400 ecutscheme_names[ecutsVERLET]);
4403 warning(wi, warn_buf);
4407 warning_note(wi, warn_buf);