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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->edHdLPrintEnergy, edHdLPrintEnergy_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;
2368 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2370 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2371 warning_note(wi, "Old option for dhdl-print-energy given: "
2372 "changing \"yes\" to \"total\"\n");
2375 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2377 /* always print out the energy to dhdl if we are doing
2378 expanded ensemble, since we need the total energy for
2379 analysis if the temperature is changing. In some
2380 conditions one may only want the potential energy, so
2381 we will allow that if the appropriate mdp setting has
2382 been enabled. Otherwise, total it is:
2384 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2387 if ((ir->efep != efepNO) || ir->bSimTemp)
2389 ir->bExpanded = FALSE;
2390 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2392 ir->bExpanded = TRUE;
2394 do_fep_params(ir, is->fep_lambda, is->lambda_weights);
2395 if (ir->bSimTemp) /* done after fep params */
2397 do_simtemp_params(ir);
2402 ir->fepvals->n_lambda = 0;
2405 /* WALL PARAMETERS */
2407 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2409 /* ORIENTATION RESTRAINT PARAMETERS */
2411 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
2413 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2416 /* DEFORMATION PARAMETERS */
2418 clear_mat(ir->deform);
2419 for (i = 0; i < 6; i++)
2423 m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
2424 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2425 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2426 for (i = 0; i < 3; i++)
2428 ir->deform[i][i] = dumdub[0][i];
2430 ir->deform[YY][XX] = dumdub[0][3];
2431 ir->deform[ZZ][XX] = dumdub[0][4];
2432 ir->deform[ZZ][YY] = dumdub[0][5];
2433 if (ir->epc != epcNO)
2435 for (i = 0; i < 3; i++)
2437 for (j = 0; j <= i; j++)
2439 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2441 warning_error(wi, "A box element has deform set and compressibility > 0");
2445 for (i = 0; i < 3; i++)
2447 for (j = 0; j < i; j++)
2449 if (ir->deform[i][j] != 0)
2451 for (m = j; m < DIM; m++)
2453 if (ir->compress[m][j] != 0)
2455 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.");
2456 warning(wi, warn_buf);
2464 /* Ion/water position swapping checks */
2465 if (ir->eSwapCoords != eswapNO)
2467 if (ir->swap->nstswap < 1)
2469 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2471 if (ir->swap->nAverage < 1)
2473 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2475 if (ir->swap->threshold < 1.0)
2477 warning_error(wi, "Ion count threshold must be at least 1.\n");
2485 static int search_QMstring(const char *s, int ng, const char *gn[])
2487 /* same as normal search_string, but this one searches QM strings */
2490 for (i = 0; (i < ng); i++)
2492 if (gmx_strcasecmp(s, gn[i]) == 0)
2498 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2502 } /* search_QMstring */
2504 /* We would like gn to be const as well, but C doesn't allow this */
2505 int search_string(const char *s, int ng, char *gn[])
2509 for (i = 0; (i < ng); i++)
2511 if (gmx_strcasecmp(s, gn[i]) == 0)
2518 "Group %s referenced in the .mdp file was not found in the index file.\n"
2519 "Group names must match either [moleculetype] names or custom index group\n"
2520 "names, in which case you must supply an index file to the '-n' option\n"
2527 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2528 t_blocka *block, char *gnames[],
2529 int gtype, int restnm,
2530 int grptp, gmx_bool bVerbose,
2533 unsigned short *cbuf;
2534 t_grps *grps = &(groups->grps[gtype]);
2535 int i, j, gid, aj, ognr, ntot = 0;
2538 char warn_buf[STRLEN];
2542 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2545 title = gtypes[gtype];
2548 /* Mark all id's as not set */
2549 for (i = 0; (i < natoms); i++)
2554 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2555 for (i = 0; (i < ng); i++)
2557 /* Lookup the group name in the block structure */
2558 gid = search_string(ptrs[i], block->nr, gnames);
2559 if ((grptp != egrptpONE) || (i == 0))
2561 grps->nm_ind[grps->nr++] = gid;
2565 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2568 /* Now go over the atoms in the group */
2569 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2574 /* Range checking */
2575 if ((aj < 0) || (aj >= natoms))
2577 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2579 /* Lookup up the old group number */
2583 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2584 aj+1, title, ognr+1, i+1);
2588 /* Store the group number in buffer */
2589 if (grptp == egrptpONE)
2602 /* Now check whether we have done all atoms */
2606 if (grptp == egrptpALL)
2608 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2609 natoms-ntot, title);
2611 else if (grptp == egrptpPART)
2613 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2614 natoms-ntot, title);
2615 warning_note(wi, warn_buf);
2617 /* Assign all atoms currently unassigned to a rest group */
2618 for (j = 0; (j < natoms); j++)
2620 if (cbuf[j] == NOGID)
2626 if (grptp != egrptpPART)
2631 "Making dummy/rest group for %s containing %d elements\n",
2632 title, natoms-ntot);
2634 /* Add group name "rest" */
2635 grps->nm_ind[grps->nr] = restnm;
2637 /* Assign the rest name to all atoms not currently assigned to a group */
2638 for (j = 0; (j < natoms); j++)
2640 if (cbuf[j] == NOGID)
2649 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2651 /* All atoms are part of one (or no) group, no index required */
2652 groups->ngrpnr[gtype] = 0;
2653 groups->grpnr[gtype] = NULL;
2657 groups->ngrpnr[gtype] = natoms;
2658 snew(groups->grpnr[gtype], natoms);
2659 for (j = 0; (j < natoms); j++)
2661 groups->grpnr[gtype][j] = cbuf[j];
2667 return (bRest && grptp == egrptpPART);
2670 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2673 gmx_groups_t *groups;
2675 int natoms, ai, aj, i, j, d, g, imin, jmin;
2677 int *nrdf2, *na_vcm, na_tot;
2678 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2679 gmx_mtop_atomloop_all_t aloop;
2681 int mb, mol, ftype, as;
2682 gmx_molblock_t *molb;
2683 gmx_moltype_t *molt;
2686 * First calc 3xnr-atoms for each group
2687 * then subtract half a degree of freedom for each constraint
2689 * Only atoms and nuclei contribute to the degrees of freedom...
2694 groups = &mtop->groups;
2695 natoms = mtop->natoms;
2697 /* Allocate one more for a possible rest group */
2698 /* We need to sum degrees of freedom into doubles,
2699 * since floats give too low nrdf's above 3 million atoms.
2701 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2702 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2703 snew(na_vcm, groups->grps[egcVCM].nr+1);
2705 for (i = 0; i < groups->grps[egcTC].nr; i++)
2709 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2714 snew(nrdf2, natoms);
2715 aloop = gmx_mtop_atomloop_all_init(mtop);
2716 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2719 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2721 g = ggrpnr(groups, egcFREEZE, i);
2722 /* Double count nrdf for particle i */
2723 for (d = 0; d < DIM; d++)
2725 if (opts->nFreeze[g][d] == 0)
2730 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2731 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2736 for (mb = 0; mb < mtop->nmolblock; mb++)
2738 molb = &mtop->molblock[mb];
2739 molt = &mtop->moltype[molb->type];
2740 atom = molt->atoms.atom;
2741 for (mol = 0; mol < molb->nmol; mol++)
2743 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2745 ia = molt->ilist[ftype].iatoms;
2746 for (i = 0; i < molt->ilist[ftype].nr; )
2748 /* Subtract degrees of freedom for the constraints,
2749 * if the particles still have degrees of freedom left.
2750 * If one of the particles is a vsite or a shell, then all
2751 * constraint motion will go there, but since they do not
2752 * contribute to the constraints the degrees of freedom do not
2757 if (((atom[ia[1]].ptype == eptNucleus) ||
2758 (atom[ia[1]].ptype == eptAtom)) &&
2759 ((atom[ia[2]].ptype == eptNucleus) ||
2760 (atom[ia[2]].ptype == eptAtom)))
2778 imin = min(imin, nrdf2[ai]);
2779 jmin = min(jmin, nrdf2[aj]);
2782 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2783 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2784 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2785 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2787 ia += interaction_function[ftype].nratoms+1;
2788 i += interaction_function[ftype].nratoms+1;
2791 ia = molt->ilist[F_SETTLE].iatoms;
2792 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2794 /* Subtract 1 dof from every atom in the SETTLE */
2795 for (j = 0; j < 3; j++)
2798 imin = min(2, nrdf2[ai]);
2800 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2801 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2806 as += molt->atoms.nr;
2810 if (ir->ePull == epullCONSTRAINT)
2812 /* Correct nrdf for the COM constraints.
2813 * We correct using the TC and VCM group of the first atom
2814 * in the reference and pull group. If atoms in one pull group
2815 * belong to different TC or VCM groups it is anyhow difficult
2816 * to determine the optimal nrdf assignment.
2820 for (i = 0; i < pull->ncoord; i++)
2824 for (j = 0; j < 2; j++)
2826 const t_pull_group *pgrp;
2828 pgrp = &pull->group[pull->coord[i].group[j]];
2832 /* Subtract 1/2 dof from each group */
2834 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2835 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2836 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2838 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)]]);
2843 /* We need to subtract the whole DOF from group j=1 */
2850 if (ir->nstcomm != 0)
2852 /* Subtract 3 from the number of degrees of freedom in each vcm group
2853 * when com translation is removed and 6 when rotation is removed
2856 switch (ir->comm_mode)
2859 n_sub = ndof_com(ir);
2866 gmx_incons("Checking comm_mode");
2869 for (i = 0; i < groups->grps[egcTC].nr; i++)
2871 /* Count the number of atoms of TC group i for every VCM group */
2872 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2877 for (ai = 0; ai < natoms; ai++)
2879 if (ggrpnr(groups, egcTC, ai) == i)
2881 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2885 /* Correct for VCM removal according to the fraction of each VCM
2886 * group present in this TC group.
2888 nrdf_uc = nrdf_tc[i];
2891 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2895 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2897 if (nrdf_vcm[j] > n_sub)
2899 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2900 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2904 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2905 j, nrdf_vcm[j], nrdf_tc[i]);
2910 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2912 opts->nrdf[i] = nrdf_tc[i];
2913 if (opts->nrdf[i] < 0)
2918 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2919 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
2928 static void decode_cos(char *s, t_cosines *cosine)
2931 char format[STRLEN], f1[STRLEN];
2943 sscanf(t, "%d", &(cosine->n));
2950 snew(cosine->a, cosine->n);
2951 snew(cosine->phi, cosine->n);
2953 sprintf(format, "%%*d");
2954 for (i = 0; (i < cosine->n); i++)
2957 strcat(f1, "%lf%lf");
2958 if (sscanf(t, f1, &a, &phi) < 2)
2960 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
2963 cosine->phi[i] = phi;
2964 strcat(format, "%*lf%*lf");
2971 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
2972 const char *option, const char *val, int flag)
2974 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
2975 * But since this is much larger than STRLEN, such a line can not be parsed.
2976 * The real maximum is the number of names that fit in a string: STRLEN/2.
2978 #define EGP_MAX (STRLEN/2)
2979 int nelem, i, j, k, nr;
2980 char *names[EGP_MAX];
2984 gnames = groups->grpname;
2986 nelem = str_nelem(val, EGP_MAX, names);
2989 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
2991 nr = groups->grps[egcENER].nr;
2993 for (i = 0; i < nelem/2; i++)
2997 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
3003 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3004 names[2*i], option);
3008 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
3014 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3015 names[2*i+1], option);
3017 if ((j < nr) && (k < nr))
3019 ir->opts.egp_flags[nr*j+k] |= flag;
3020 ir->opts.egp_flags[nr*k+j] |= flag;
3029 static void make_swap_groups(
3038 int ig = -1, i = 0, j;
3042 /* Just a quick check here, more thorough checks are in mdrun */
3043 if (strcmp(splitg0name, splitg1name) == 0)
3045 gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
3048 /* First get the swap group index atoms */
3049 ig = search_string(swapgname, grps->nr, gnames);
3050 swap->nat = grps->index[ig+1] - grps->index[ig];
3053 fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
3054 snew(swap->ind, swap->nat);
3055 for (i = 0; i < swap->nat; i++)
3057 swap->ind[i] = grps->a[grps->index[ig]+i];
3062 gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
3065 /* Now do so for the split groups */
3066 for (j = 0; j < 2; j++)
3070 splitg = splitg0name;
3074 splitg = splitg1name;
3077 ig = search_string(splitg, grps->nr, gnames);
3078 swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
3079 if (swap->nat_split[j] > 0)
3081 fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
3082 j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
3083 snew(swap->ind_split[j], swap->nat_split[j]);
3084 for (i = 0; i < swap->nat_split[j]; i++)
3086 swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
3091 gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
3095 /* Now get the solvent group index atoms */
3096 ig = search_string(solgname, grps->nr, gnames);
3097 swap->nat_sol = grps->index[ig+1] - grps->index[ig];
3098 if (swap->nat_sol > 0)
3100 fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
3101 snew(swap->ind_sol, swap->nat_sol);
3102 for (i = 0; i < swap->nat_sol; i++)
3104 swap->ind_sol[i] = grps->a[grps->index[ig]+i];
3109 gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
3114 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3119 ig = search_string(IMDgname, grps->nr, gnames);
3120 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3122 if (IMDgroup->nat > 0)
3124 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3125 IMDgname, IMDgroup->nat);
3126 snew(IMDgroup->ind, IMDgroup->nat);
3127 for (i = 0; i < IMDgroup->nat; i++)
3129 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3135 void do_index(const char* mdparin, const char *ndx,
3138 t_inputrec *ir, rvec *v,
3142 gmx_groups_t *groups;
3146 char warnbuf[STRLEN], **gnames;
3147 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3150 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3151 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3152 int i, j, k, restnm;
3154 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3155 int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
3156 nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
3157 char warn_buf[STRLEN];
3161 fprintf(stderr, "processing index file...\n");
3167 snew(grps->index, 1);
3169 atoms_all = gmx_mtop_global_atoms(mtop);
3170 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3171 free_t_atoms(&atoms_all, FALSE);
3175 grps = init_index(ndx, &gnames);
3178 groups = &mtop->groups;
3179 natoms = mtop->natoms;
3180 symtab = &mtop->symtab;
3182 snew(groups->grpname, grps->nr+1);
3184 for (i = 0; (i < grps->nr); i++)
3186 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3188 groups->grpname[i] = put_symtab(symtab, "rest");
3190 srenew(gnames, grps->nr+1);
3191 gnames[restnm] = *(groups->grpname[i]);
3192 groups->ngrpname = grps->nr+1;
3194 set_warning_line(wi, mdparin, -1);
3196 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3197 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3198 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3199 if ((ntau_t != ntcg) || (nref_t != ntcg))
3201 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3202 "%d tau-t values", ntcg, nref_t, ntau_t);
3205 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3206 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3207 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3208 nr = groups->grps[egcTC].nr;
3210 snew(ir->opts.nrdf, nr);
3211 snew(ir->opts.tau_t, nr);
3212 snew(ir->opts.ref_t, nr);
3213 if (ir->eI == eiBD && ir->bd_fric == 0)
3215 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3222 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3226 for (i = 0; (i < nr); i++)
3228 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
3229 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
3231 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3232 warning_error(wi, warn_buf);
3235 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3237 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.");
3240 if (ir->opts.tau_t[i] >= 0)
3242 tau_min = min(tau_min, ir->opts.tau_t[i]);
3245 if (ir->etc != etcNO && ir->nsttcouple == -1)
3247 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3252 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3254 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");
3256 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
3258 if (ir->nstpcouple != ir->nsttcouple)
3260 int mincouple = min(ir->nstpcouple, ir->nsttcouple);
3261 ir->nstpcouple = ir->nsttcouple = mincouple;
3262 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);
3263 warning_note(wi, warn_buf);
3267 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3268 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3270 if (ETC_ANDERSEN(ir->etc))
3272 if (ir->nsttcouple != 1)
3275 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");
3276 warning_note(wi, warn_buf);
3279 nstcmin = tcouple_min_integration_steps(ir->etc);
3282 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
3284 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3285 ETCOUPLTYPE(ir->etc),
3287 ir->nsttcouple*ir->delta_t);
3288 warning(wi, warn_buf);
3291 for (i = 0; (i < nr); i++)
3293 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
3294 if (ir->opts.ref_t[i] < 0)
3296 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3299 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3300 if we are in this conditional) if mc_temp is negative */
3301 if (ir->expandedvals->mc_temp < 0)
3303 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3307 /* Simulated annealing for each group. There are nr groups */
3308 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3309 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3313 if (nSA > 0 && nSA != nr)
3315 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3319 snew(ir->opts.annealing, nr);
3320 snew(ir->opts.anneal_npoints, nr);
3321 snew(ir->opts.anneal_time, nr);
3322 snew(ir->opts.anneal_temp, nr);
3323 for (i = 0; i < nr; i++)
3325 ir->opts.annealing[i] = eannNO;
3326 ir->opts.anneal_npoints[i] = 0;
3327 ir->opts.anneal_time[i] = NULL;
3328 ir->opts.anneal_temp[i] = NULL;
3333 for (i = 0; i < nr; i++)
3335 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3337 ir->opts.annealing[i] = eannNO;
3339 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3341 ir->opts.annealing[i] = eannSINGLE;
3344 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3346 ir->opts.annealing[i] = eannPERIODIC;
3352 /* Read the other fields too */
3353 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3354 if (nSA_points != nSA)
3356 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3358 for (k = 0, i = 0; i < nr; i++)
3360 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3361 if (ir->opts.anneal_npoints[i] == 1)
3363 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3365 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3366 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3367 k += ir->opts.anneal_npoints[i];
3370 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3373 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3375 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3378 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3381 for (i = 0, k = 0; i < nr; i++)
3384 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3386 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3387 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3390 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3392 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3398 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3400 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3401 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3404 if (ir->opts.anneal_temp[i][j] < 0)
3406 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3411 /* Print out some summary information, to make sure we got it right */
3412 for (i = 0, k = 0; i < nr; i++)
3414 if (ir->opts.annealing[i] != eannNO)
3416 j = groups->grps[egcTC].nm_ind[i];
3417 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3418 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3419 ir->opts.anneal_npoints[i]);
3420 fprintf(stderr, "Time (ps) Temperature (K)\n");
3421 /* All terms except the last one */
3422 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3424 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3427 /* Finally the last one */
3428 j = ir->opts.anneal_npoints[i]-1;
3429 if (ir->opts.annealing[i] == eannSINGLE)
3431 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3435 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3436 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3438 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3447 if (ir->ePull != epullNO)
3449 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3451 make_pull_coords(ir->pull);
3456 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3459 if (ir->eSwapCoords != eswapNO)
3461 make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
3464 /* Make indices for IMD session */
3467 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3470 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3471 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3472 if (nacg*DIM != nacc)
3474 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3477 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3478 restnm, egrptpALL_GENREST, bVerbose, wi);
3479 nr = groups->grps[egcACC].nr;
3480 snew(ir->opts.acc, nr);
3481 ir->opts.ngacc = nr;
3483 for (i = k = 0; (i < nacg); i++)
3485 for (j = 0; (j < DIM); j++, k++)
3487 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3490 for (; (i < nr); i++)
3492 for (j = 0; (j < DIM); j++)
3494 ir->opts.acc[i][j] = 0;
3498 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3499 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3500 if (nfrdim != DIM*nfreeze)
3502 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3505 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3506 restnm, egrptpALL_GENREST, bVerbose, wi);
3507 nr = groups->grps[egcFREEZE].nr;
3508 ir->opts.ngfrz = nr;
3509 snew(ir->opts.nFreeze, nr);
3510 for (i = k = 0; (i < nfreeze); i++)
3512 for (j = 0; (j < DIM); j++, k++)
3514 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3515 if (!ir->opts.nFreeze[i][j])
3517 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3519 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3520 "(not %s)", ptr1[k]);
3521 warning(wi, warn_buf);
3526 for (; (i < nr); i++)
3528 for (j = 0; (j < DIM); j++)
3530 ir->opts.nFreeze[i][j] = 0;
3534 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3535 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3536 restnm, egrptpALL_GENREST, bVerbose, wi);
3537 add_wall_energrps(groups, ir->nwall, symtab);
3538 ir->opts.ngener = groups->grps[egcENER].nr;
3539 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3541 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3542 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3545 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3546 "This may lead to artifacts.\n"
3547 "In most cases one should use one group for the whole system.");
3550 /* Now we have filled the freeze struct, so we can calculate NRDF */
3551 calc_nrdf(mtop, ir, gnames);
3557 /* Must check per group! */
3558 for (i = 0; (i < ir->opts.ngtc); i++)
3560 ntot += ir->opts.nrdf[i];
3562 if (ntot != (DIM*natoms))
3564 fac = sqrt(ntot/(DIM*natoms));
3567 fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
3568 "and removal of center of mass motion\n", fac);
3570 for (i = 0; (i < natoms); i++)
3572 svmul(fac, v[i], v[i]);
3577 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3578 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3579 restnm, egrptpALL_GENREST, bVerbose, wi);
3580 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3581 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3582 restnm, egrptpALL_GENREST, bVerbose, wi);
3583 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3584 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3585 restnm, egrptpONE, bVerbose, wi);
3586 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3587 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3588 restnm, egrptpALL_GENREST, bVerbose, wi);
3590 /* QMMM input processing */
3591 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3592 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3593 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3594 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3596 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3597 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3599 /* group rest, if any, is always MM! */
3600 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3601 restnm, egrptpALL_GENREST, bVerbose, wi);
3602 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3603 ir->opts.ngQM = nQMg;
3604 snew(ir->opts.QMmethod, nr);
3605 snew(ir->opts.QMbasis, nr);
3606 for (i = 0; i < nr; i++)
3608 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3609 * converted to the corresponding enum in names.c
3611 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3613 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3617 nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
3618 nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
3619 nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
3620 snew(ir->opts.QMmult, nr);
3621 snew(ir->opts.QMcharge, nr);
3622 snew(ir->opts.bSH, nr);
3624 for (i = 0; i < nr; i++)
3626 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3627 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3628 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3631 nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
3632 nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
3633 snew(ir->opts.CASelectrons, nr);
3634 snew(ir->opts.CASorbitals, nr);
3635 for (i = 0; i < nr; i++)
3637 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3638 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3640 /* special optimization options */
3642 nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
3643 nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
3644 snew(ir->opts.bOPT, nr);
3645 snew(ir->opts.bTS, nr);
3646 for (i = 0; i < nr; i++)
3648 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3649 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3651 nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
3652 nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
3653 nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
3654 snew(ir->opts.SAon, nr);
3655 snew(ir->opts.SAoff, nr);
3656 snew(ir->opts.SAsteps, nr);
3658 for (i = 0; i < nr; i++)
3660 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3661 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3662 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3664 /* end of QMMM input */
3668 for (i = 0; (i < egcNR); i++)
3670 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3671 for (j = 0; (j < groups->grps[i].nr); j++)
3673 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3675 fprintf(stderr, "\n");
3679 nr = groups->grps[egcENER].nr;
3680 snew(ir->opts.egp_flags, nr*nr);
3682 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3683 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3685 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3687 if (bExcl && EEL_FULL(ir->coulombtype))
3689 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3692 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3693 if (bTable && !(ir->vdwtype == evdwUSER) &&
3694 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3695 !(ir->coulombtype == eelPMEUSERSWITCH))
3697 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3700 decode_cos(is->efield_x, &(ir->ex[XX]));
3701 decode_cos(is->efield_xt, &(ir->et[XX]));
3702 decode_cos(is->efield_y, &(ir->ex[YY]));
3703 decode_cos(is->efield_yt, &(ir->et[YY]));
3704 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3705 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3709 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3712 for (i = 0; (i < grps->nr); i++)
3724 static void check_disre(gmx_mtop_t *mtop)
3726 gmx_ffparams_t *ffparams;
3727 t_functype *functype;
3729 int i, ndouble, ftype;
3730 int label, old_label;
3732 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3734 ffparams = &mtop->ffparams;
3735 functype = ffparams->functype;
3736 ip = ffparams->iparams;
3739 for (i = 0; i < ffparams->ntypes; i++)
3741 ftype = functype[i];
3742 if (ftype == F_DISRES)
3744 label = ip[i].disres.label;
3745 if (label == old_label)
3747 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3755 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3756 "probably the parameters for multiple pairs in one restraint "
3757 "are not identical\n", ndouble);
3762 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3763 gmx_bool posres_only,
3767 gmx_mtop_ilistloop_t iloop;
3777 for (d = 0; d < DIM; d++)
3779 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3781 /* Check for freeze groups */
3782 for (g = 0; g < ir->opts.ngfrz; g++)
3784 for (d = 0; d < DIM; d++)
3786 if (ir->opts.nFreeze[g][d] != 0)
3794 /* Check for position restraints */
3795 iloop = gmx_mtop_ilistloop_init(sys);
3796 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3799 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3801 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3803 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3804 for (d = 0; d < DIM; d++)
3806 if (pr->posres.fcA[d] != 0)
3812 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3814 /* Check for flat-bottom posres */
3815 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3816 if (pr->fbposres.k != 0)
3818 switch (pr->fbposres.geom)
3820 case efbposresSPHERE:
3821 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3823 case efbposresCYLINDER:
3824 AbsRef[XX] = AbsRef[YY] = 1;
3826 case efbposresX: /* d=XX */
3827 case efbposresY: /* d=YY */
3828 case efbposresZ: /* d=ZZ */
3829 d = pr->fbposres.geom - efbposresX;
3833 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3834 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3842 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3846 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3847 gmx_bool *bC6ParametersWorkWithGeometricRules,
3848 gmx_bool *bC6ParametersWorkWithLBRules,
3849 gmx_bool *bLBRulesPossible)
3851 int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
3854 double geometricdiff, LBdiff;
3855 double c6i, c6j, c12i, c12j;
3856 double c6, c6_geometric, c6_LB;
3857 double sigmai, sigmaj, epsi, epsj;
3858 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3861 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3862 * force-field floating point parameters.
3865 ptr = getenv("GMX_LJCOMB_TOL");
3870 sscanf(ptr, "%lf", &dbl);
3874 *bC6ParametersWorkWithLBRules = TRUE;
3875 *bC6ParametersWorkWithGeometricRules = TRUE;
3876 bCanDoLBRules = TRUE;
3877 bCanDoGeometricRules = TRUE;
3878 ntypes = mtop->ffparams.atnr;
3879 snew(typecount, ntypes);
3880 gmx_mtop_count_atomtypes(mtop, state, typecount);
3881 geometricdiff = LBdiff = 0.0;
3882 *bLBRulesPossible = TRUE;
3883 for (tpi = 0; tpi < ntypes; ++tpi)
3885 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3886 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3887 for (tpj = tpi; tpj < ntypes; ++tpj)
3889 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3890 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3891 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3892 c6_geometric = sqrt(c6i * c6j);
3893 if (!gmx_numzero(c6_geometric))
3895 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3897 sigmai = pow(c12i / c6i, 1.0/6.0);
3898 sigmaj = pow(c12j / c6j, 1.0/6.0);
3899 epsi = c6i * c6i /(4.0 * c12i);
3900 epsj = c6j * c6j /(4.0 * c12j);
3901 c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
3905 *bLBRulesPossible = FALSE;
3906 c6_LB = c6_geometric;
3908 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3911 if (FALSE == bCanDoLBRules)
3913 *bC6ParametersWorkWithLBRules = FALSE;
3916 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3918 if (FALSE == bCanDoGeometricRules)
3920 *bC6ParametersWorkWithGeometricRules = FALSE;
3928 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3932 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3934 check_combination_rule_differences(mtop, 0,
3935 &bC6ParametersWorkWithGeometricRules,
3936 &bC6ParametersWorkWithLBRules,
3938 if (ir->ljpme_combination_rule == eljpmeLB)
3940 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
3942 warning(wi, "You are using arithmetic-geometric combination rules "
3943 "in LJ-PME, but your non-bonded C6 parameters do not "
3944 "follow these rules.");
3949 if (FALSE == bC6ParametersWorkWithGeometricRules)
3951 if (ir->eDispCorr != edispcNO)
3953 warning_note(wi, "You are using geometric combination rules in "
3954 "LJ-PME, but your non-bonded C6 parameters do "
3955 "not follow these rules. "
3956 "This will introduce very small errors in the forces and energies in "
3957 "your simulations. Dispersion correction will correct total energy "
3958 "and/or pressure for isotropic systems, but not forces or surface tensions.");
3962 warning_note(wi, "You are using geometric combination rules in "
3963 "LJ-PME, but your non-bonded C6 parameters do "
3964 "not follow these rules. "
3965 "This will introduce very small errors in the forces and energies in "
3966 "your simulations. If your system is homogeneous, consider using dispersion correction "
3967 "for the total energy and pressure.");
3973 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
3976 char err_buf[STRLEN];
3977 int i, m, c, nmol, npct;
3978 gmx_bool bCharge, bAcc;
3979 real gdt_max, *mgrp, mt;
3981 gmx_mtop_atomloop_block_t aloopb;
3982 gmx_mtop_atomloop_all_t aloop;
3985 char warn_buf[STRLEN];
3987 set_warning_line(wi, mdparin, -1);
3989 if (ir->cutoff_scheme == ecutsVERLET &&
3990 ir->verletbuf_tol > 0 &&
3992 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
3993 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
3995 /* Check if a too small Verlet buffer might potentially
3996 * cause more drift than the thermostat can couple off.
3998 /* Temperature error fraction for warning and suggestion */
3999 const real T_error_warn = 0.002;
4000 const real T_error_suggest = 0.001;
4001 /* For safety: 2 DOF per atom (typical with constraints) */
4002 const real nrdf_at = 2;
4003 real T, tau, max_T_error;
4008 for (i = 0; i < ir->opts.ngtc; i++)
4010 T = max(T, ir->opts.ref_t[i]);
4011 tau = max(tau, ir->opts.tau_t[i]);
4015 /* This is a worst case estimate of the temperature error,
4016 * assuming perfect buffer estimation and no cancelation
4017 * of errors. The factor 0.5 is because energy distributes
4018 * equally over Ekin and Epot.
4020 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4021 if (max_T_error > T_error_warn)
4023 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.",
4024 ir->verletbuf_tol, T, tau,
4026 100*T_error_suggest,
4027 ir->verletbuf_tol*T_error_suggest/max_T_error);
4028 warning(wi, warn_buf);
4033 if (ETC_ANDERSEN(ir->etc))
4037 for (i = 0; i < ir->opts.ngtc; i++)
4039 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4040 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4041 sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
4042 i, ir->opts.tau_t[i]);
4043 CHECK(ir->opts.tau_t[i] < 0);
4046 for (i = 0; i < ir->opts.ngtc; i++)
4048 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
4049 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);
4050 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
4054 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4055 ir->comm_mode == ecmNO &&
4056 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4057 !ETC_ANDERSEN(ir->etc))
4059 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");
4062 /* Check for pressure coupling with absolute position restraints */
4063 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4065 absolute_reference(ir, sys, TRUE, AbsRef);
4067 for (m = 0; m < DIM; m++)
4069 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4071 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4079 aloopb = gmx_mtop_atomloop_block_init(sys);
4080 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4082 if (atom->q != 0 || atom->qB != 0)
4090 if (EEL_FULL(ir->coulombtype))
4093 "You are using full electrostatics treatment %s for a system without charges.\n"
4094 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4095 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4096 warning(wi, err_buf);
4101 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4104 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4105 "You might want to consider using %s electrostatics.\n",
4107 warning_note(wi, err_buf);
4111 /* Check if combination rules used in LJ-PME are the same as in the force field */
4112 if (EVDW_PME(ir->vdwtype))
4114 check_combination_rules(ir, sys, wi);
4117 /* Generalized reaction field */
4118 if (ir->opts.ngtc == 0)
4120 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4122 CHECK(ir->coulombtype == eelGRF);
4126 sprintf(err_buf, "When using coulombtype = %s"
4127 " ref-t for temperature coupling should be > 0",
4129 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4132 if (ir->eI == eiSD2)
4134 sprintf(warn_buf, "The stochastic dynamics integrator %s is deprecated, since\n"
4135 "it is slower than integrator %s and is slightly less accurate\n"
4136 "with constraints. Use the %s integrator.",
4137 ei_names[ir->eI], ei_names[eiSD1], ei_names[eiSD1]);
4138 warning_note(wi, warn_buf);
4142 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4144 for (m = 0; (m < DIM); m++)
4146 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4155 snew(mgrp, sys->groups.grps[egcACC].nr);
4156 aloop = gmx_mtop_atomloop_all_init(sys);
4157 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4159 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4162 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4164 for (m = 0; (m < DIM); m++)
4166 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4170 for (m = 0; (m < DIM); m++)
4172 if (fabs(acc[m]) > 1e-6)
4174 const char *dim[DIM] = { "X", "Y", "Z" };
4176 "Net Acceleration in %s direction, will %s be corrected\n",
4177 dim[m], ir->nstcomm != 0 ? "" : "not");
4178 if (ir->nstcomm != 0 && m < ndof_com(ir))
4181 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4183 ir->opts.acc[i][m] -= acc[m];
4191 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4192 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4194 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4197 if (ir->ePull != epullNO)
4199 gmx_bool bPullAbsoluteRef;
4201 bPullAbsoluteRef = FALSE;
4202 for (i = 0; i < ir->pull->ncoord; i++)
4204 bPullAbsoluteRef = bPullAbsoluteRef ||
4205 ir->pull->coord[i].group[0] == 0 ||
4206 ir->pull->coord[i].group[1] == 0;
4208 if (bPullAbsoluteRef)
4210 absolute_reference(ir, sys, FALSE, AbsRef);
4211 for (m = 0; m < DIM; m++)
4213 if (ir->pull->dim[m] && !AbsRef[m])
4215 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.");
4221 if (ir->pull->eGeom == epullgDIRPBC)
4223 for (i = 0; i < 3; i++)
4225 for (m = 0; m <= i; m++)
4227 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4228 ir->deform[i][m] != 0)
4230 for (c = 0; c < ir->pull->ncoord; c++)
4232 if (ir->pull->coord[c].vec[m] != 0)
4234 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->eGeom), 'x'+m);
4246 void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr, warninp_t wi)
4250 char warn_buf[STRLEN];
4253 ptr = check_box(ir->ePBC, box);
4256 warning_error(wi, ptr);
4259 if (bConstr && ir->eConstrAlg == econtSHAKE)
4261 if (ir->shake_tol <= 0.0)
4263 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4265 warning_error(wi, warn_buf);
4268 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
4270 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
4271 if (ir->epc == epcNO)
4273 warning(wi, warn_buf);
4277 warning_error(wi, warn_buf);
4282 if ( (ir->eConstrAlg == econtLINCS) && bConstr)
4284 /* If we have Lincs constraints: */
4285 if (ir->eI == eiMD && ir->etc == etcNO &&
4286 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4288 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4289 warning_note(wi, warn_buf);
4292 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4294 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4295 warning_note(wi, warn_buf);
4297 if (ir->epc == epcMTTK)
4299 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4303 if (bConstr && ir->epc == epcMTTK)
4305 warning_note(wi, "MTTK with constraints is deprecated, and will be removed in GROMACS 5.1");
4308 if (ir->LincsWarnAngle > 90.0)
4310 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4311 warning(wi, warn_buf);
4312 ir->LincsWarnAngle = 90.0;
4315 if (ir->ePBC != epbcNONE)
4317 if (ir->nstlist == 0)
4319 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4321 bTWIN = (ir->rlistlong > ir->rlist);
4322 if (ir->ns_type == ensGRID)
4324 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
4326 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",
4327 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
4328 warning_error(wi, warn_buf);
4333 min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
4334 if (2*ir->rlistlong >= min_size)
4336 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4337 warning_error(wi, warn_buf);
4340 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4347 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4351 real rvdw1, rvdw2, rcoul1, rcoul2;
4352 char warn_buf[STRLEN];
4354 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4358 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4363 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4369 if (rvdw1 + rvdw2 > ir->rlist ||
4370 rcoul1 + rcoul2 > ir->rlist)
4373 "The sum of the two largest charge group radii (%f) "
4374 "is larger than rlist (%f)\n",
4375 max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4376 warning(wi, warn_buf);
4380 /* Here we do not use the zero at cut-off macro,
4381 * since user defined interactions might purposely
4382 * not be zero at the cut-off.
4384 if (ir_vdw_is_zero_at_cutoff(ir) &&
4385 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
4387 sprintf(warn_buf, "The sum of the two largest charge group "
4388 "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
4389 "With exact cut-offs, better performance can be "
4390 "obtained with cutoff-scheme = %s, because it "
4391 "does not use charge groups at all.",
4393 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4394 ir->rlistlong, ir->rvdw,
4395 ecutscheme_names[ecutsVERLET]);
4398 warning(wi, warn_buf);
4402 warning_note(wi, warn_buf);
4405 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4406 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
4408 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
4409 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4411 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4412 ir->rlistlong, ir->rcoulomb,
4413 ecutscheme_names[ecutsVERLET]);
4416 warning(wi, warn_buf);
4420 warning_note(wi, warn_buf);