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45 #include "gromacs/gmxpreprocess/calc_verletbuf.h"
46 #include "gromacs/gmxpreprocess/toputil.h"
47 #include "gromacs/legacyheaders/chargegroup.h"
48 #include "gromacs/legacyheaders/inputrec.h"
49 #include "gromacs/legacyheaders/macros.h"
50 #include "gromacs/legacyheaders/names.h"
51 #include "gromacs/legacyheaders/network.h"
52 #include "gromacs/legacyheaders/readinp.h"
53 #include "gromacs/legacyheaders/typedefs.h"
54 #include "gromacs/legacyheaders/warninp.h"
55 #include "gromacs/math/units.h"
56 #include "gromacs/math/vec.h"
57 #include "gromacs/pbcutil/pbc.h"
58 #include "gromacs/topology/block.h"
59 #include "gromacs/topology/index.h"
60 #include "gromacs/topology/mtop_util.h"
61 #include "gromacs/topology/symtab.h"
62 #include "gromacs/utility/cstringutil.h"
63 #include "gromacs/utility/fatalerror.h"
64 #include "gromacs/utility/smalloc.h"
69 /* Resource parameters
70 * Do not change any of these until you read the instruction
71 * in readinp.h. Some cpp's do not take spaces after the backslash
72 * (like the c-shell), which will give you a very weird compiler
76 typedef struct t_inputrec_strings
78 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN],
79 acc[STRLEN], accgrps[STRLEN], freeze[STRLEN], frdim[STRLEN],
80 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
81 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
82 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN],
84 char fep_lambda[efptNR][STRLEN];
85 char lambda_weights[STRLEN];
88 char anneal[STRLEN], anneal_npoints[STRLEN],
89 anneal_time[STRLEN], anneal_temp[STRLEN];
90 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
91 bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
92 SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
93 char efield_x[STRLEN], efield_xt[STRLEN], efield_y[STRLEN],
94 efield_yt[STRLEN], efield_z[STRLEN], efield_zt[STRLEN];
96 } gmx_inputrec_strings;
98 static gmx_inputrec_strings *is = NULL;
100 void init_inputrec_strings()
104 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.");
109 void done_inputrec_strings()
115 static char swapgrp[STRLEN], splitgrp0[STRLEN], splitgrp1[STRLEN], solgrp[STRLEN];
118 egrptpALL, /* All particles have to be a member of a group. */
119 egrptpALL_GENREST, /* A rest group with name is generated for particles *
120 * that are not part of any group. */
121 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
122 * for the rest group. */
123 egrptpONE /* Merge all selected groups into one group, *
124 * make a rest group for the remaining particles. */
127 static const char *constraints[eshNR+1] = {
128 "none", "h-bonds", "all-bonds", "h-angles", "all-angles", NULL
131 static const char *couple_lam[ecouplamNR+1] = {
132 "vdw-q", "vdw", "q", "none", NULL
135 void init_ir(t_inputrec *ir, t_gromppopts *opts)
137 snew(opts->include, STRLEN);
138 snew(opts->define, STRLEN);
139 snew(ir->fepvals, 1);
140 snew(ir->expandedvals, 1);
141 snew(ir->simtempvals, 1);
144 static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
149 for (i = 0; i < ntemps; i++)
151 /* simple linear scaling -- allows more control */
152 if (simtemp->eSimTempScale == esimtempLINEAR)
154 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*temperature_lambdas[i];
156 else if (simtemp->eSimTempScale == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
158 simtemp->temperatures[i] = simtemp->simtemp_low * pow(simtemp->simtemp_high/simtemp->simtemp_low, (1.0*i)/(ntemps-1));
160 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
162 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*((exp(temperature_lambdas[i])-1)/(exp(1.0)-1));
167 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
168 gmx_fatal(FARGS, errorstr);
175 static void _low_check(gmx_bool b, char *s, warninp_t wi)
179 warning_error(wi, s);
183 static void check_nst(const char *desc_nst, int nst,
184 const char *desc_p, int *p,
189 if (*p > 0 && *p % nst != 0)
191 /* Round up to the next multiple of nst */
192 *p = ((*p)/nst + 1)*nst;
193 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n",
194 desc_p, desc_nst, desc_p, *p);
199 static gmx_bool ir_NVE(const t_inputrec *ir)
201 return ((ir->eI == eiMD || EI_VV(ir->eI)) && ir->etc == etcNO);
204 static int lcd(int n1, int n2)
209 for (i = 2; (i <= n1 && i <= n2); i++)
211 if (n1 % i == 0 && n2 % i == 0)
220 static void process_interaction_modifier(const t_inputrec *ir, int *eintmod)
222 if (*eintmod == eintmodPOTSHIFT_VERLET)
224 if (ir->cutoff_scheme == ecutsVERLET)
226 *eintmod = eintmodPOTSHIFT;
230 *eintmod = eintmodNONE;
235 void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
237 /* Check internal consistency.
238 * NOTE: index groups are not set here yet, don't check things
239 * like temperature coupling group options here, but in triple_check
242 /* Strange macro: first one fills the err_buf, and then one can check
243 * the condition, which will print the message and increase the error
246 #define CHECK(b) _low_check(b, err_buf, wi)
247 char err_buf[256], warn_buf[STRLEN];
253 t_lambda *fep = ir->fepvals;
254 t_expanded *expand = ir->expandedvals;
256 set_warning_line(wi, mdparin, -1);
258 /* BASIC CUT-OFF STUFF */
259 if (ir->rcoulomb < 0)
261 warning_error(wi, "rcoulomb should be >= 0");
265 warning_error(wi, "rvdw should be >= 0");
268 !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
270 warning_error(wi, "rlist should be >= 0");
272 sprintf(err_buf, "nstlist can not be smaller than 0. (If you were trying to use the heuristic neighbour-list update scheme for efficient buffering for improved energy conservation, please use the Verlet cut-off scheme instead.)");
273 CHECK(ir->nstlist < 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->implicit_solvent != eisNO)
376 warning_error(wi, "Implicit solvent is not (yet) supported with the with Verlet lists.");
379 if (ir->nstlist <= 0)
381 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
384 if (ir->nstlist < 10)
386 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.");
389 rc_max = max(ir->rvdw, ir->rcoulomb);
391 if (ir->verletbuf_tol <= 0)
393 if (ir->verletbuf_tol == 0)
395 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
398 if (ir->rlist < rc_max)
400 warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
403 if (ir->rlist == rc_max && ir->nstlist > 1)
405 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.");
410 if (ir->rlist > rc_max)
412 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.");
415 if (ir->nstlist == 1)
417 /* No buffer required */
422 if (EI_DYNAMICS(ir->eI))
424 if (inputrec2nboundeddim(ir) < 3)
426 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.");
428 /* Set rlist temporarily so we can continue processing */
433 /* Set the buffer to 5% of the cut-off */
434 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
439 /* No twin-range calculations with Verlet lists */
440 ir->rlistlong = ir->rlist;
443 if (ir->nstcalclr == -1)
445 /* if rlist=rlistlong, this will later be changed to nstcalclr=0 */
446 ir->nstcalclr = ir->nstlist;
448 else if (ir->nstcalclr > 0)
450 if (ir->nstlist > 0 && (ir->nstlist % ir->nstcalclr != 0))
452 warning_error(wi, "nstlist must be evenly divisible by nstcalclr. Use nstcalclr = -1 to automatically follow nstlist");
455 else if (ir->nstcalclr < -1)
457 warning_error(wi, "nstcalclr must be a positive number (divisor of nstcalclr), or -1 to follow nstlist.");
460 if (EEL_PME(ir->coulombtype) && ir->rcoulomb > ir->rlist && ir->nstcalclr > 1)
462 warning_error(wi, "When used with PME, the long-range component of twin-range interactions must be updated every step (nstcalclr)");
465 /* GENERAL INTEGRATOR STUFF */
466 if (!(ir->eI == eiMD || EI_VV(ir->eI)))
470 if (ir->eI == eiVVAK)
472 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]);
473 warning_note(wi, warn_buf);
475 if (!EI_DYNAMICS(ir->eI))
479 if (EI_DYNAMICS(ir->eI))
481 if (ir->nstcalcenergy < 0)
483 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
484 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
486 /* nstcalcenergy larger than nstener does not make sense.
487 * We ideally want nstcalcenergy=nstener.
491 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
495 ir->nstcalcenergy = ir->nstenergy;
499 else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
500 (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
501 (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
504 const char *nsten = "nstenergy";
505 const char *nstdh = "nstdhdl";
506 const char *min_name = nsten;
507 int min_nst = ir->nstenergy;
509 /* find the smallest of ( nstenergy, nstdhdl ) */
510 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
511 (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
513 min_nst = ir->fepvals->nstdhdl;
516 /* If the user sets nstenergy small, we should respect that */
518 "Setting nstcalcenergy (%d) equal to %s (%d)",
519 ir->nstcalcenergy, min_name, min_nst);
520 warning_note(wi, warn_buf);
521 ir->nstcalcenergy = min_nst;
524 if (ir->epc != epcNO)
526 if (ir->nstpcouple < 0)
528 ir->nstpcouple = ir_optimal_nstpcouple(ir);
531 if (IR_TWINRANGE(*ir))
533 check_nst("nstlist", ir->nstlist,
534 "nstcalcenergy", &ir->nstcalcenergy, wi);
535 if (ir->epc != epcNO)
537 check_nst("nstlist", ir->nstlist,
538 "nstpcouple", &ir->nstpcouple, wi);
542 if (ir->nstcalcenergy > 0)
544 if (ir->efep != efepNO)
546 /* nstdhdl should be a multiple of nstcalcenergy */
547 check_nst("nstcalcenergy", ir->nstcalcenergy,
548 "nstdhdl", &ir->fepvals->nstdhdl, wi);
549 /* nstexpanded should be a multiple of nstcalcenergy */
550 check_nst("nstcalcenergy", ir->nstcalcenergy,
551 "nstexpanded", &ir->expandedvals->nstexpanded, wi);
553 /* for storing exact averages nstenergy should be
554 * a multiple of nstcalcenergy
556 check_nst("nstcalcenergy", ir->nstcalcenergy,
557 "nstenergy", &ir->nstenergy, wi);
561 if (ir->nsteps == 0 && !ir->bContinuation)
563 warning_note(wi, "For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates.");
567 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
568 ir->bContinuation && ir->ld_seed != -1)
570 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)");
576 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
577 CHECK(ir->ePBC != epbcXYZ);
578 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
579 CHECK(ir->ns_type != ensGRID);
580 sprintf(err_buf, "with TPI nstlist should be larger than zero");
581 CHECK(ir->nstlist <= 0);
582 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
583 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
584 sprintf(err_buf, "TPI does not work (yet) with the Verlet cut-off scheme");
585 CHECK(ir->cutoff_scheme == ecutsVERLET);
589 if ( (opts->nshake > 0) && (opts->bMorse) )
592 "Using morse bond-potentials while constraining bonds is useless");
593 warning(wi, warn_buf);
596 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
597 ir->bContinuation && ir->ld_seed != -1)
599 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)");
601 /* verify simulated tempering options */
605 gmx_bool bAllTempZero = TRUE;
606 for (i = 0; i < fep->n_lambda; i++)
608 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]);
609 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
610 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
612 bAllTempZero = FALSE;
615 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
616 CHECK(bAllTempZero == TRUE);
618 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
619 CHECK(ir->eI != eiVV);
621 /* check compatability of the temperature coupling with simulated tempering */
623 if (ir->etc == etcNOSEHOOVER)
625 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
626 warning_note(wi, warn_buf);
629 /* check that the temperatures make sense */
631 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);
632 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
634 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
635 CHECK(ir->simtempvals->simtemp_high <= 0);
637 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
638 CHECK(ir->simtempvals->simtemp_low <= 0);
641 /* verify free energy options */
643 if (ir->efep != efepNO)
646 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
648 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
650 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
651 (int)fep->sc_r_power);
652 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
654 sprintf(err_buf, "Can't use postive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
655 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
657 sprintf(err_buf, "Can't use postive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
658 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
660 sprintf(err_buf, "Can only use expanded ensemble with md-vv for now; should be supported for other integrators in 5.0");
661 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
663 sprintf(err_buf, "Free-energy not implemented for Ewald");
664 CHECK(ir->coulombtype == eelEWALD);
666 /* check validty of lambda inputs */
667 if (fep->n_lambda == 0)
669 /* Clear output in case of no states:*/
670 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
671 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
675 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
676 CHECK((fep->init_fep_state >= fep->n_lambda));
679 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
680 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
682 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",
683 fep->init_lambda, fep->init_fep_state);
684 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
688 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
692 for (i = 0; i < efptNR; i++)
694 if (fep->separate_dvdl[i])
699 if (n_lambda_terms > 1)
701 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.");
702 warning(wi, warn_buf);
705 if (n_lambda_terms < 2 && fep->n_lambda > 0)
708 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
712 for (j = 0; j < efptNR; j++)
714 for (i = 0; i < fep->n_lambda; i++)
716 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]);
717 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
721 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
723 for (i = 0; i < fep->n_lambda; i++)
725 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],
726 fep->all_lambda[efptCOUL][i]);
727 CHECK((fep->sc_alpha > 0) &&
728 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
729 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
730 ((fep->all_lambda[efptVDW][i] > 0.0) &&
731 (fep->all_lambda[efptVDW][i] < 1.0))));
735 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
737 real sigma, lambda, r_sc;
740 /* Maximum estimate for A and B charges equal with lambda power 1 */
742 r_sc = pow(lambda*fep->sc_alpha*pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
743 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.",
745 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
746 warning_note(wi, warn_buf);
749 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
750 be treated differently, but that's the next step */
752 for (i = 0; i < efptNR; i++)
754 for (j = 0; j < fep->n_lambda; j++)
756 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
757 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
762 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
765 expand = ir->expandedvals;
767 /* checking equilibration of weights inputs for validity */
769 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
770 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
771 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
773 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
774 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
775 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
777 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
778 expand->equil_steps, elmceq_names[elmceqSTEPS]);
779 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
781 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
782 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
783 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
785 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
786 expand->equil_ratio, elmceq_names[elmceqRATIO]);
787 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
789 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
790 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
791 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
793 sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
794 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
795 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
797 sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
798 expand->equil_steps, elmceq_names[elmceqSTEPS]);
799 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
801 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
802 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
803 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
805 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
806 expand->equil_ratio, elmceq_names[elmceqRATIO]);
807 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
809 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
810 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
811 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
813 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
814 CHECK((expand->lmc_repeats <= 0));
815 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
816 CHECK((expand->minvarmin <= 0));
817 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
818 CHECK((expand->c_range < 0));
819 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
820 fep->init_fep_state, expand->lmc_forced_nstart);
821 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
822 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
823 CHECK((expand->lmc_forced_nstart < 0));
824 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
825 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
827 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
828 CHECK((expand->init_wl_delta < 0));
829 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
830 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
831 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
832 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
834 /* if there is no temperature control, we need to specify an MC temperature */
835 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
836 if (expand->nstTij > 0)
838 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
839 expand->nstTij, ir->nstlog);
840 CHECK((mod(expand->nstTij, ir->nstlog) != 0));
845 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
846 CHECK(ir->nwall && ir->ePBC != epbcXY);
849 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
851 if (ir->ePBC == epbcNONE)
853 if (ir->epc != epcNO)
855 warning(wi, "Turning off pressure coupling for vacuum system");
861 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
862 epbc_names[ir->ePBC]);
863 CHECK(ir->epc != epcNO);
865 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
866 CHECK(EEL_FULL(ir->coulombtype));
868 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
869 epbc_names[ir->ePBC]);
870 CHECK(ir->eDispCorr != edispcNO);
873 if (ir->rlist == 0.0)
875 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
876 "with coulombtype = %s or coulombtype = %s\n"
877 "without periodic boundary conditions (pbc = %s) and\n"
878 "rcoulomb and rvdw set to zero",
879 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
880 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
881 (ir->ePBC != epbcNONE) ||
882 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
886 warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
891 if (ir->nstcomm == 0)
893 ir->comm_mode = ecmNO;
895 if (ir->comm_mode != ecmNO)
899 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");
900 ir->nstcomm = abs(ir->nstcomm);
903 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
905 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
906 ir->nstcomm = ir->nstcalcenergy;
909 if (ir->comm_mode == ecmANGULAR)
911 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
912 CHECK(ir->bPeriodicMols);
913 if (ir->ePBC != epbcNONE)
915 warning(wi, "Removing the rotation around the center of mass in a periodic system, this can lead to artifacts. Only use this on a single (cluster of) molecules. This cluster should not cross periodic boundaries.");
920 if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
922 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.");
925 sprintf(err_buf, "Twin-range neighbour searching (NS) with simple NS"
926 " algorithm not implemented");
927 CHECK(((ir->rcoulomb > ir->rlist) || (ir->rvdw > ir->rlist))
928 && (ir->ns_type == ensSIMPLE));
930 /* TEMPERATURE COUPLING */
931 if (ir->etc == etcYES)
933 ir->etc = etcBERENDSEN;
934 warning_note(wi, "Old option for temperature coupling given: "
935 "changing \"yes\" to \"Berendsen\"\n");
938 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
940 if (ir->opts.nhchainlength < 1)
942 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
943 ir->opts.nhchainlength = 1;
944 warning(wi, warn_buf);
947 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
949 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
950 ir->opts.nhchainlength = 1;
955 ir->opts.nhchainlength = 0;
958 if (ir->eI == eiVVAK)
960 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
962 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
965 if (ETC_ANDERSEN(ir->etc))
967 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
968 CHECK(!(EI_VV(ir->eI)));
970 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
972 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]);
973 warning_note(wi, warn_buf);
976 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]);
977 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
980 if (ir->etc == etcBERENDSEN)
982 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
983 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
984 warning_note(wi, warn_buf);
987 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
988 && ir->epc == epcBERENDSEN)
990 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
991 "true ensemble for the thermostat");
992 warning(wi, warn_buf);
995 /* PRESSURE COUPLING */
996 if (ir->epc == epcISOTROPIC)
998 ir->epc = epcBERENDSEN;
999 warning_note(wi, "Old option for pressure coupling given: "
1000 "changing \"Isotropic\" to \"Berendsen\"\n");
1003 if (ir->epc != epcNO)
1005 dt_pcoupl = ir->nstpcouple*ir->delta_t;
1007 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1008 CHECK(ir->tau_p <= 0);
1010 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10*GMX_REAL_EPS)
1012 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
1013 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1014 warning(wi, warn_buf);
1017 sprintf(err_buf, "compressibility must be > 0 when using pressure"
1018 " coupling %s\n", EPCOUPLTYPE(ir->epc));
1019 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
1020 ir->compress[ZZ][ZZ] < 0 ||
1021 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
1022 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
1024 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1027 "You are generating velocities so I am assuming you "
1028 "are equilibrating a system. You are using "
1029 "%s pressure coupling, but this can be "
1030 "unstable for equilibration. If your system crashes, try "
1031 "equilibrating first with Berendsen pressure coupling. If "
1032 "you are not equilibrating the system, you can probably "
1033 "ignore this warning.",
1034 epcoupl_names[ir->epc]);
1035 warning(wi, warn_buf);
1041 if (ir->epc > epcNO)
1043 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1045 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.");
1051 if (ir->epc == epcMTTK)
1053 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1057 /* ELECTROSTATICS */
1058 /* More checks are in triple check (grompp.c) */
1060 if (ir->coulombtype == eelSWITCH)
1062 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1063 "artifacts, advice: use coulombtype = %s",
1064 eel_names[ir->coulombtype],
1065 eel_names[eelRF_ZERO]);
1066 warning(wi, warn_buf);
1069 if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
1071 sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
1072 warning_note(wi, warn_buf);
1075 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1077 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);
1078 warning(wi, warn_buf);
1079 ir->epsilon_rf = ir->epsilon_r;
1080 ir->epsilon_r = 1.0;
1083 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == NULL)
1085 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1086 CHECK(ir->epsilon_r < 0);
1089 if (EEL_RF(ir->coulombtype))
1091 /* reaction field (at the cut-off) */
1093 if (ir->coulombtype == eelRF_ZERO)
1095 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1096 eel_names[ir->coulombtype]);
1097 CHECK(ir->epsilon_rf != 0);
1098 ir->epsilon_rf = 0.0;
1101 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1102 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1103 (ir->epsilon_r == 0));
1104 if (ir->epsilon_rf == ir->epsilon_r)
1106 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1107 eel_names[ir->coulombtype]);
1108 warning(wi, warn_buf);
1111 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1112 * means the interaction is zero outside rcoulomb, but it helps to
1113 * provide accurate energy conservation.
1115 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1117 if (ir_coulomb_switched(ir))
1120 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1121 eel_names[ir->coulombtype]);
1122 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1125 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1127 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1129 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1130 eel_names[ir->coulombtype]);
1131 CHECK(ir->rlist > ir->rcoulomb);
1135 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1138 "Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier.");
1139 CHECK( ir->coulomb_modifier != eintmodNONE);
1141 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1144 "Explicit switch/shift vdw interactions cannot be used in combination with a secondary vdw-modifier.");
1145 CHECK( ir->vdw_modifier != eintmodNONE);
1148 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1149 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1152 "The switch/shift interaction settings are just for compatibility; you will get better "
1153 "performance from applying potential modifiers to your interactions!\n");
1154 warning_note(wi, warn_buf);
1157 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1159 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1161 real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
1162 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.",
1163 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1164 warning(wi, warn_buf);
1168 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1170 if (ir->rvdw_switch == 0)
1172 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.");
1173 warning(wi, warn_buf);
1177 if (EEL_FULL(ir->coulombtype))
1179 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1180 ir->coulombtype == eelPMEUSERSWITCH)
1182 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1183 eel_names[ir->coulombtype]);
1184 CHECK(ir->rcoulomb > ir->rlist);
1186 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1188 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1191 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
1192 "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
1193 "a potential modifier.", eel_names[ir->coulombtype]);
1194 if (ir->nstcalclr == 1)
1196 CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
1200 CHECK(ir->rcoulomb != ir->rlist);
1206 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1208 if (ir->pme_order < 3)
1210 warning_error(wi, "pme-order can not be smaller than 3");
1214 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1216 if (ir->ewald_geometry == eewg3D)
1218 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1219 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1220 warning(wi, warn_buf);
1222 /* This check avoids extra pbc coding for exclusion corrections */
1223 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1224 CHECK(ir->wall_ewald_zfac < 2);
1226 if ((ir->ewald_geometry == eewg3DC) && (ir->ePBC != epbcXY) &&
1227 EEL_FULL(ir->coulombtype))
1229 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1230 eel_names[ir->coulombtype], eewg_names[eewg3DC], epbc_names[epbcXY]);
1231 warning(wi, warn_buf);
1233 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1235 if (ir->cutoff_scheme == ecutsVERLET)
1237 sprintf(warn_buf, "Since molecules/charge groups are broken using the Verlet scheme, you can not use a dipole correction to the %s electrostatics.",
1238 eel_names[ir->coulombtype]);
1239 warning(wi, warn_buf);
1243 sprintf(warn_buf, "Dipole corrections to %s electrostatics only work if all charge groups that can cross PBC boundaries are dipoles. If this is not the case set epsilon_surface to 0",
1244 eel_names[ir->coulombtype]);
1245 warning_note(wi, warn_buf);
1249 if (ir_vdw_switched(ir))
1251 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1252 CHECK(ir->rvdw_switch >= ir->rvdw);
1254 if (ir->rvdw_switch < 0.5*ir->rvdw)
1256 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.",
1257 ir->rvdw_switch, ir->rvdw);
1258 warning_note(wi, warn_buf);
1261 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1263 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1265 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1266 CHECK(ir->rlist > ir->rvdw);
1270 if (ir->vdwtype == evdwPME)
1272 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1274 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s a\
1276 evdw_names[ir->vdwtype],
1277 eintmod_names[eintmodPOTSHIFT],
1278 eintmod_names[eintmodNONE]);
1282 if (ir->cutoff_scheme == ecutsGROUP)
1284 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1285 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)))
1287 warning_note(wi, "With exact cut-offs, rlist should be "
1288 "larger than rcoulomb and rvdw, so that there "
1289 "is a buffer region for particle motion "
1290 "between neighborsearch steps");
1293 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlistlong <= ir->rcoulomb)
1295 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
1296 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1297 warning_note(wi, warn_buf);
1299 if (ir_vdw_switched(ir) && (ir->rlistlong <= ir->rvdw))
1301 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
1302 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1303 warning_note(wi, warn_buf);
1307 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1309 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.");
1312 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1315 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1318 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1320 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1323 /* ENERGY CONSERVATION */
1324 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1326 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1328 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1329 evdw_names[evdwSHIFT]);
1330 warning_note(wi, warn_buf);
1332 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1334 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1335 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1336 warning_note(wi, warn_buf);
1340 if (EI_VV(ir->eI) && IR_TWINRANGE(*ir) && ir->nstlist > 1)
1342 sprintf(warn_buf, "Twin-range multiple time stepping does not work with integrator %s.", ei_names[ir->eI]);
1343 warning_error(wi, warn_buf);
1346 /* IMPLICIT SOLVENT */
1347 if (ir->coulombtype == eelGB_NOTUSED)
1349 sprintf(warn_buf, "Invalid option %s for coulombtype",
1350 eel_names[ir->coulombtype]);
1351 warning_error(wi, warn_buf);
1354 if (ir->sa_algorithm == esaSTILL)
1356 sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
1357 CHECK(ir->sa_algorithm == esaSTILL);
1360 if (ir->implicit_solvent == eisGBSA)
1362 sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
1363 CHECK(ir->rgbradii != ir->rlist);
1365 if (ir->coulombtype != eelCUT)
1367 sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
1368 CHECK(ir->coulombtype != eelCUT);
1370 if (ir->vdwtype != evdwCUT)
1372 sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
1373 CHECK(ir->vdwtype != evdwCUT);
1375 if (ir->nstgbradii < 1)
1377 sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
1378 warning_note(wi, warn_buf);
1381 if (ir->sa_algorithm == esaNO)
1383 sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
1384 warning_note(wi, warn_buf);
1386 if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
1388 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");
1389 warning_note(wi, warn_buf);
1391 if (ir->gb_algorithm == egbSTILL)
1393 ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
1397 ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
1400 if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
1402 sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
1403 CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
1410 if (ir->cutoff_scheme != ecutsGROUP)
1412 warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
1416 warning_error(wi, "AdresS simulation supports only stochastic dynamics");
1418 if (ir->epc != epcNO)
1420 warning_error(wi, "AdresS simulation does not support pressure coupling");
1422 if (EEL_FULL(ir->coulombtype))
1424 warning_error(wi, "AdresS simulation does not support long-range electrostatics");
1429 /* count the number of text elemets separated by whitespace in a string.
1430 str = the input string
1431 maxptr = the maximum number of allowed elements
1432 ptr = the output array of pointers to the first character of each element
1433 returns: the number of elements. */
1434 int str_nelem(const char *str, int maxptr, char *ptr[])
1439 copy0 = gmx_strdup(str);
1442 while (*copy != '\0')
1446 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1454 while ((*copy != '\0') && !isspace(*copy))
1473 /* interpret a number of doubles from a string and put them in an array,
1474 after allocating space for them.
1475 str = the input string
1476 n = the (pre-allocated) number of doubles read
1477 r = the output array of doubles. */
1478 static void parse_n_real(char *str, int *n, real **r)
1483 *n = str_nelem(str, MAXPTR, ptr);
1486 for (i = 0; i < *n; i++)
1488 (*r)[i] = strtod(ptr[i], NULL);
1492 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
1495 int i, j, max_n_lambda, nweights, nfep[efptNR];
1496 t_lambda *fep = ir->fepvals;
1497 t_expanded *expand = ir->expandedvals;
1498 real **count_fep_lambdas;
1499 gmx_bool bOneLambda = TRUE;
1501 snew(count_fep_lambdas, efptNR);
1503 /* FEP input processing */
1504 /* first, identify the number of lambda values for each type.
1505 All that are nonzero must have the same number */
1507 for (i = 0; i < efptNR; i++)
1509 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
1512 /* now, determine the number of components. All must be either zero, or equal. */
1515 for (i = 0; i < efptNR; i++)
1517 if (nfep[i] > max_n_lambda)
1519 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1520 must have the same number if its not zero.*/
1525 for (i = 0; i < efptNR; i++)
1529 ir->fepvals->separate_dvdl[i] = FALSE;
1531 else if (nfep[i] == max_n_lambda)
1533 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1534 respect to the temperature currently */
1536 ir->fepvals->separate_dvdl[i] = TRUE;
1541 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1542 nfep[i], efpt_names[i], max_n_lambda);
1545 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1546 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1548 /* the number of lambdas is the number we've read in, which is either zero
1549 or the same for all */
1550 fep->n_lambda = max_n_lambda;
1552 /* allocate space for the array of lambda values */
1553 snew(fep->all_lambda, efptNR);
1554 /* if init_lambda is defined, we need to set lambda */
1555 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1557 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1559 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1560 for (i = 0; i < efptNR; i++)
1562 snew(fep->all_lambda[i], fep->n_lambda);
1563 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1566 for (j = 0; j < fep->n_lambda; j++)
1568 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1570 sfree(count_fep_lambdas[i]);
1573 sfree(count_fep_lambdas);
1575 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1576 bookkeeping -- for now, init_lambda */
1578 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1580 for (i = 0; i < fep->n_lambda; i++)
1582 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1586 /* check to see if only a single component lambda is defined, and soft core is defined.
1587 In this case, turn on coulomb soft core */
1589 if (max_n_lambda == 0)
1595 for (i = 0; i < efptNR; i++)
1597 if ((nfep[i] != 0) && (i != efptFEP))
1603 if ((bOneLambda) && (fep->sc_alpha > 0))
1605 fep->bScCoul = TRUE;
1608 /* Fill in the others with the efptFEP if they are not explicitly
1609 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1610 they are all zero. */
1612 for (i = 0; i < efptNR; i++)
1614 if ((nfep[i] == 0) && (i != efptFEP))
1616 for (j = 0; j < fep->n_lambda; j++)
1618 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1624 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1625 if (fep->sc_r_power == 48)
1627 if (fep->sc_alpha > 0.1)
1629 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1633 expand = ir->expandedvals;
1634 /* now read in the weights */
1635 parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
1638 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1640 else if (nweights != fep->n_lambda)
1642 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1643 nweights, fep->n_lambda);
1645 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1647 expand->nstexpanded = fep->nstdhdl;
1648 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1650 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1652 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1653 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1654 2*tau_t just to be careful so it's not to frequent */
1659 static void do_simtemp_params(t_inputrec *ir)
1662 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1663 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1668 static void do_wall_params(t_inputrec *ir,
1669 char *wall_atomtype, char *wall_density,
1673 char *names[MAXPTR];
1676 opts->wall_atomtype[0] = NULL;
1677 opts->wall_atomtype[1] = NULL;
1679 ir->wall_atomtype[0] = -1;
1680 ir->wall_atomtype[1] = -1;
1681 ir->wall_density[0] = 0;
1682 ir->wall_density[1] = 0;
1686 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1687 if (nstr != ir->nwall)
1689 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1692 for (i = 0; i < ir->nwall; i++)
1694 opts->wall_atomtype[i] = gmx_strdup(names[i]);
1697 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1699 nstr = str_nelem(wall_density, MAXPTR, names);
1700 if (nstr != ir->nwall)
1702 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1704 for (i = 0; i < ir->nwall; i++)
1706 sscanf(names[i], "%lf", &dbl);
1709 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1711 ir->wall_density[i] = dbl;
1717 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1725 srenew(groups->grpname, groups->ngrpname+nwall);
1726 grps = &(groups->grps[egcENER]);
1727 srenew(grps->nm_ind, grps->nr+nwall);
1728 for (i = 0; i < nwall; i++)
1730 sprintf(str, "wall%d", i);
1731 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1732 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1737 void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1738 t_expanded *expand, warninp_t wi)
1740 int ninp, nerror = 0;
1746 /* read expanded ensemble parameters */
1747 CCTYPE ("expanded ensemble variables");
1748 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1749 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1750 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1751 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1752 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1753 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1754 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1755 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1756 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1757 CCTYPE("Seed for Monte Carlo in lambda space");
1758 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1759 RTYPE ("mc-temperature", expand->mc_temp, -1);
1760 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1761 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1762 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1763 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1764 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1765 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1766 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1767 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1768 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1769 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1770 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
1778 void get_ir(const char *mdparin, const char *mdparout,
1779 t_inputrec *ir, t_gromppopts *opts,
1783 double dumdub[2][6];
1787 char warn_buf[STRLEN];
1788 t_lambda *fep = ir->fepvals;
1789 t_expanded *expand = ir->expandedvals;
1791 init_inputrec_strings();
1792 inp = read_inpfile(mdparin, &ninp, wi);
1794 snew(dumstr[0], STRLEN);
1795 snew(dumstr[1], STRLEN);
1797 if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
1800 "%s did not specify a value for the .mdp option "
1801 "\"cutoff-scheme\". Probably it was first intended for use "
1802 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1803 "introduced, but the group scheme was still the default. "
1804 "The default is now the Verlet scheme, so you will observe "
1805 "different behaviour.", mdparin);
1806 warning_note(wi, warn_buf);
1809 /* ignore the following deprecated commands */
1812 REM_TYPE("domain-decomposition");
1813 REM_TYPE("andersen-seed");
1815 REM_TYPE("dihre-fc");
1816 REM_TYPE("dihre-tau");
1817 REM_TYPE("nstdihreout");
1818 REM_TYPE("nstcheckpoint");
1819 REM_TYPE("optimize-fft");
1821 /* replace the following commands with the clearer new versions*/
1822 REPL_TYPE("unconstrained-start", "continuation");
1823 REPL_TYPE("foreign-lambda", "fep-lambdas");
1824 REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
1825 REPL_TYPE("nstxtcout", "nstxout-compressed");
1826 REPL_TYPE("xtc-grps", "compressed-x-grps");
1827 REPL_TYPE("xtc-precision", "compressed-x-precision");
1829 CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
1830 CTYPE ("Preprocessor information: use cpp syntax.");
1831 CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
1832 STYPE ("include", opts->include, NULL);
1833 CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1834 STYPE ("define", opts->define, NULL);
1836 CCTYPE ("RUN CONTROL PARAMETERS");
1837 EETYPE("integrator", ir->eI, ei_names);
1838 CTYPE ("Start time and timestep in ps");
1839 RTYPE ("tinit", ir->init_t, 0.0);
1840 RTYPE ("dt", ir->delta_t, 0.001);
1841 STEPTYPE ("nsteps", ir->nsteps, 0);
1842 CTYPE ("For exact run continuation or redoing part of a run");
1843 STEPTYPE ("init-step", ir->init_step, 0);
1844 CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
1845 ITYPE ("simulation-part", ir->simulation_part, 1);
1846 CTYPE ("mode for center of mass motion removal");
1847 EETYPE("comm-mode", ir->comm_mode, ecm_names);
1848 CTYPE ("number of steps for center of mass motion removal");
1849 ITYPE ("nstcomm", ir->nstcomm, 100);
1850 CTYPE ("group(s) for center of mass motion removal");
1851 STYPE ("comm-grps", is->vcm, NULL);
1853 CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
1854 CTYPE ("Friction coefficient (amu/ps) and random seed");
1855 RTYPE ("bd-fric", ir->bd_fric, 0.0);
1856 STEPTYPE ("ld-seed", ir->ld_seed, -1);
1859 CCTYPE ("ENERGY MINIMIZATION OPTIONS");
1860 CTYPE ("Force tolerance and initial step-size");
1861 RTYPE ("emtol", ir->em_tol, 10.0);
1862 RTYPE ("emstep", ir->em_stepsize, 0.01);
1863 CTYPE ("Max number of iterations in relax-shells");
1864 ITYPE ("niter", ir->niter, 20);
1865 CTYPE ("Step size (ps^2) for minimization of flexible constraints");
1866 RTYPE ("fcstep", ir->fc_stepsize, 0);
1867 CTYPE ("Frequency of steepest descents steps when doing CG");
1868 ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
1869 ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
1871 CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
1872 RTYPE ("rtpi", ir->rtpi, 0.05);
1874 /* Output options */
1875 CCTYPE ("OUTPUT CONTROL OPTIONS");
1876 CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
1877 ITYPE ("nstxout", ir->nstxout, 0);
1878 ITYPE ("nstvout", ir->nstvout, 0);
1879 ITYPE ("nstfout", ir->nstfout, 0);
1880 CTYPE ("Output frequency for energies to log file and energy file");
1881 ITYPE ("nstlog", ir->nstlog, 1000);
1882 ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
1883 ITYPE ("nstenergy", ir->nstenergy, 1000);
1884 CTYPE ("Output frequency and precision for .xtc file");
1885 ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
1886 RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
1887 CTYPE ("This selects the subset of atoms for the compressed");
1888 CTYPE ("trajectory file. You can select multiple groups. By");
1889 CTYPE ("default, all atoms will be written.");
1890 STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
1891 CTYPE ("Selection of energy groups");
1892 STYPE ("energygrps", is->energy, NULL);
1894 /* Neighbor searching */
1895 CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
1896 CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1897 EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
1898 CTYPE ("nblist update frequency");
1899 ITYPE ("nstlist", ir->nstlist, 10);
1900 CTYPE ("ns algorithm (simple or grid)");
1901 EETYPE("ns-type", ir->ns_type, ens_names);
1902 CTYPE ("Periodic boundary conditions: xyz, no, xy");
1903 EETYPE("pbc", ir->ePBC, epbc_names);
1904 EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
1905 CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1906 CTYPE ("a value of -1 means: use rlist");
1907 RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
1908 CTYPE ("nblist cut-off");
1909 RTYPE ("rlist", ir->rlist, 1.0);
1910 CTYPE ("long-range cut-off for switched potentials");
1911 RTYPE ("rlistlong", ir->rlistlong, -1);
1912 ITYPE ("nstcalclr", ir->nstcalclr, -1);
1914 /* Electrostatics */
1915 CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
1916 CTYPE ("Method for doing electrostatics");
1917 EETYPE("coulombtype", ir->coulombtype, eel_names);
1918 EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
1919 CTYPE ("cut-off lengths");
1920 RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
1921 RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
1922 CTYPE ("Relative dielectric constant for the medium and the reaction field");
1923 RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
1924 RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
1925 CTYPE ("Method for doing Van der Waals");
1926 EETYPE("vdw-type", ir->vdwtype, evdw_names);
1927 EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
1928 CTYPE ("cut-off lengths");
1929 RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
1930 RTYPE ("rvdw", ir->rvdw, 1.0);
1931 CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
1932 EETYPE("DispCorr", ir->eDispCorr, edispc_names);
1933 CTYPE ("Extension of the potential lookup tables beyond the cut-off");
1934 RTYPE ("table-extension", ir->tabext, 1.0);
1935 CTYPE ("Separate tables between energy group pairs");
1936 STYPE ("energygrp-table", is->egptable, NULL);
1937 CTYPE ("Spacing for the PME/PPPM FFT grid");
1938 RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
1939 CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
1940 ITYPE ("fourier-nx", ir->nkx, 0);
1941 ITYPE ("fourier-ny", ir->nky, 0);
1942 ITYPE ("fourier-nz", ir->nkz, 0);
1943 CTYPE ("EWALD/PME/PPPM parameters");
1944 ITYPE ("pme-order", ir->pme_order, 4);
1945 RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
1946 RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
1947 EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
1948 EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
1949 RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
1951 CCTYPE("IMPLICIT SOLVENT ALGORITHM");
1952 EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
1954 CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
1955 CTYPE ("Algorithm for calculating Born radii");
1956 EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
1957 CTYPE ("Frequency of calculating the Born radii inside rlist");
1958 ITYPE ("nstgbradii", ir->nstgbradii, 1);
1959 CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
1960 CTYPE ("between rlist and rgbradii is updated every nstlist steps");
1961 RTYPE ("rgbradii", ir->rgbradii, 1.0);
1962 CTYPE ("Dielectric coefficient of the implicit solvent");
1963 RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
1964 CTYPE ("Salt concentration in M for Generalized Born models");
1965 RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
1966 CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
1967 RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
1968 RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
1969 RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
1970 RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
1971 EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
1972 CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
1973 CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
1974 RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
1976 /* Coupling stuff */
1977 CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
1978 CTYPE ("Temperature coupling");
1979 EETYPE("tcoupl", ir->etc, etcoupl_names);
1980 ITYPE ("nsttcouple", ir->nsttcouple, -1);
1981 ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
1982 EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
1983 CTYPE ("Groups to couple separately");
1984 STYPE ("tc-grps", is->tcgrps, NULL);
1985 CTYPE ("Time constant (ps) and reference temperature (K)");
1986 STYPE ("tau-t", is->tau_t, NULL);
1987 STYPE ("ref-t", is->ref_t, NULL);
1988 CTYPE ("pressure coupling");
1989 EETYPE("pcoupl", ir->epc, epcoupl_names);
1990 EETYPE("pcoupltype", ir->epct, epcoupltype_names);
1991 ITYPE ("nstpcouple", ir->nstpcouple, -1);
1992 CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
1993 RTYPE ("tau-p", ir->tau_p, 1.0);
1994 STYPE ("compressibility", dumstr[0], NULL);
1995 STYPE ("ref-p", dumstr[1], NULL);
1996 CTYPE ("Scaling of reference coordinates, No, All or COM");
1997 EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
2000 CCTYPE ("OPTIONS FOR QMMM calculations");
2001 EETYPE("QMMM", ir->bQMMM, yesno_names);
2002 CTYPE ("Groups treated Quantum Mechanically");
2003 STYPE ("QMMM-grps", is->QMMM, NULL);
2004 CTYPE ("QM method");
2005 STYPE("QMmethod", is->QMmethod, NULL);
2006 CTYPE ("QMMM scheme");
2007 EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
2008 CTYPE ("QM basisset");
2009 STYPE("QMbasis", is->QMbasis, NULL);
2010 CTYPE ("QM charge");
2011 STYPE ("QMcharge", is->QMcharge, NULL);
2012 CTYPE ("QM multiplicity");
2013 STYPE ("QMmult", is->QMmult, NULL);
2014 CTYPE ("Surface Hopping");
2015 STYPE ("SH", is->bSH, NULL);
2016 CTYPE ("CAS space options");
2017 STYPE ("CASorbitals", is->CASorbitals, NULL);
2018 STYPE ("CASelectrons", is->CASelectrons, NULL);
2019 STYPE ("SAon", is->SAon, NULL);
2020 STYPE ("SAoff", is->SAoff, NULL);
2021 STYPE ("SAsteps", is->SAsteps, NULL);
2022 CTYPE ("Scale factor for MM charges");
2023 RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
2024 CTYPE ("Optimization of QM subsystem");
2025 STYPE ("bOPT", is->bOPT, NULL);
2026 STYPE ("bTS", is->bTS, NULL);
2028 /* Simulated annealing */
2029 CCTYPE("SIMULATED ANNEALING");
2030 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
2031 STYPE ("annealing", is->anneal, NULL);
2032 CTYPE ("Number of time points to use for specifying annealing in each group");
2033 STYPE ("annealing-npoints", is->anneal_npoints, NULL);
2034 CTYPE ("List of times at the annealing points for each group");
2035 STYPE ("annealing-time", is->anneal_time, NULL);
2036 CTYPE ("Temp. at each annealing point, for each group.");
2037 STYPE ("annealing-temp", is->anneal_temp, NULL);
2040 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
2041 EETYPE("gen-vel", opts->bGenVel, yesno_names);
2042 RTYPE ("gen-temp", opts->tempi, 300.0);
2043 ITYPE ("gen-seed", opts->seed, -1);
2046 CCTYPE ("OPTIONS FOR BONDS");
2047 EETYPE("constraints", opts->nshake, constraints);
2048 CTYPE ("Type of constraint algorithm");
2049 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
2050 CTYPE ("Do not constrain the start configuration");
2051 EETYPE("continuation", ir->bContinuation, yesno_names);
2052 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
2053 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
2054 CTYPE ("Relative tolerance of shake");
2055 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
2056 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
2057 ITYPE ("lincs-order", ir->nProjOrder, 4);
2058 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
2059 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
2060 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
2061 ITYPE ("lincs-iter", ir->nLincsIter, 1);
2062 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
2063 CTYPE ("rotates over more degrees than");
2064 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
2065 CTYPE ("Convert harmonic bonds to morse potentials");
2066 EETYPE("morse", opts->bMorse, yesno_names);
2068 /* Energy group exclusions */
2069 CCTYPE ("ENERGY GROUP EXCLUSIONS");
2070 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
2071 STYPE ("energygrp-excl", is->egpexcl, NULL);
2075 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2076 ITYPE ("nwall", ir->nwall, 0);
2077 EETYPE("wall-type", ir->wall_type, ewt_names);
2078 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
2079 STYPE ("wall-atomtype", is->wall_atomtype, NULL);
2080 STYPE ("wall-density", is->wall_density, NULL);
2081 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
2084 CCTYPE("COM PULLING");
2085 CTYPE("Pull type: no, umbrella, constraint or constant-force");
2086 EETYPE("pull", ir->ePull, epull_names);
2087 if (ir->ePull != epullNO)
2090 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
2093 /* Enforced rotation */
2094 CCTYPE("ENFORCED ROTATION");
2095 CTYPE("Enforced rotation: No or Yes");
2096 EETYPE("rotation", ir->bRot, yesno_names);
2100 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2103 /* Interactive MD */
2105 CCTYPE("Group to display and/or manipulate in interactive MD session");
2106 STYPE ("IMD-group", is->imd_grp, NULL);
2107 if (is->imd_grp[0] != '\0')
2114 CCTYPE("NMR refinement stuff");
2115 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2116 EETYPE("disre", ir->eDisre, edisre_names);
2117 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2118 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2119 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2120 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2121 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2122 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2123 CTYPE ("Output frequency for pair distances to energy file");
2124 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2125 CTYPE ("Orientation restraints: No or Yes");
2126 EETYPE("orire", opts->bOrire, yesno_names);
2127 CTYPE ("Orientation restraints force constant and tau for time averaging");
2128 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2129 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2130 STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
2131 CTYPE ("Output frequency for trace(SD) and S to energy file");
2132 ITYPE ("nstorireout", ir->nstorireout, 100);
2134 /* free energy variables */
2135 CCTYPE ("Free energy variables");
2136 EETYPE("free-energy", ir->efep, efep_names);
2137 STYPE ("couple-moltype", is->couple_moltype, NULL);
2138 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2139 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2140 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2142 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2144 it was not entered */
2145 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2146 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2147 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2148 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
2149 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
2150 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
2151 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
2152 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
2153 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
2154 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
2155 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2156 STYPE ("init-lambda-weights", is->lambda_weights, NULL);
2157 EETYPE("dhdl-print-energy", fep->edHdLPrintEnergy, edHdLPrintEnergy_names);
2158 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2159 ITYPE ("sc-power", fep->sc_power, 1);
2160 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2161 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2162 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2163 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2164 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2165 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2166 separate_dhdl_file_names);
2167 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2168 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2169 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2171 /* Non-equilibrium MD stuff */
2172 CCTYPE("Non-equilibrium MD stuff");
2173 STYPE ("acc-grps", is->accgrps, NULL);
2174 STYPE ("accelerate", is->acc, NULL);
2175 STYPE ("freezegrps", is->freeze, NULL);
2176 STYPE ("freezedim", is->frdim, NULL);
2177 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2178 STYPE ("deform", is->deform, NULL);
2180 /* simulated tempering variables */
2181 CCTYPE("simulated tempering variables");
2182 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2183 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2184 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2185 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2187 /* expanded ensemble variables */
2188 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2190 read_expandedparams(&ninp, &inp, expand, wi);
2193 /* Electric fields */
2194 CCTYPE("Electric fields");
2195 CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
2196 CTYPE ("and a phase angle (real)");
2197 STYPE ("E-x", is->efield_x, NULL);
2198 STYPE ("E-xt", is->efield_xt, NULL);
2199 STYPE ("E-y", is->efield_y, NULL);
2200 STYPE ("E-yt", is->efield_yt, NULL);
2201 STYPE ("E-z", is->efield_z, NULL);
2202 STYPE ("E-zt", is->efield_zt, NULL);
2204 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2205 CTYPE("Swap positions along direction: no, X, Y, Z");
2206 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2207 if (ir->eSwapCoords != eswapNO)
2210 CTYPE("Swap attempt frequency");
2211 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2212 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2213 STYPE("split-group0", splitgrp0, NULL);
2214 STYPE("split-group1", splitgrp1, NULL);
2215 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2216 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2217 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2219 CTYPE("Group name of ions that can be exchanged with solvent molecules");
2220 STYPE("swap-group", swapgrp, NULL);
2221 CTYPE("Group name of solvent molecules");
2222 STYPE("solvent-group", solgrp, NULL);
2224 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2225 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2226 CTYPE("however, if correctly defined, the ion permeation events are counted per channel");
2227 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2228 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2229 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2230 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2231 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2232 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2234 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2235 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2236 CTYPE("Requested number of anions and cations for each of the two compartments");
2237 CTYPE("-1 means fix the numbers as found in time step 0");
2238 ITYPE("anionsA", ir->swap->nanions[0], -1);
2239 ITYPE("cationsA", ir->swap->ncations[0], -1);
2240 ITYPE("anionsB", ir->swap->nanions[1], -1);
2241 ITYPE("cationsB", ir->swap->ncations[1], -1);
2242 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2243 RTYPE("threshold", ir->swap->threshold, 1.0);
2246 /* AdResS defined thingies */
2247 CCTYPE ("AdResS parameters");
2248 EETYPE("adress", ir->bAdress, yesno_names);
2251 snew(ir->adress, 1);
2252 read_adressparams(&ninp, &inp, ir->adress, wi);
2255 /* User defined thingies */
2256 CCTYPE ("User defined thingies");
2257 STYPE ("user1-grps", is->user1, NULL);
2258 STYPE ("user2-grps", is->user2, NULL);
2259 ITYPE ("userint1", ir->userint1, 0);
2260 ITYPE ("userint2", ir->userint2, 0);
2261 ITYPE ("userint3", ir->userint3, 0);
2262 ITYPE ("userint4", ir->userint4, 0);
2263 RTYPE ("userreal1", ir->userreal1, 0);
2264 RTYPE ("userreal2", ir->userreal2, 0);
2265 RTYPE ("userreal3", ir->userreal3, 0);
2266 RTYPE ("userreal4", ir->userreal4, 0);
2269 write_inpfile(mdparout, ninp, inp, FALSE, wi);
2270 for (i = 0; (i < ninp); i++)
2273 sfree(inp[i].value);
2277 /* Process options if necessary */
2278 for (m = 0; m < 2; m++)
2280 for (i = 0; i < 2*DIM; i++)
2289 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2291 warning_error(wi, "Pressure coupling not enough values (I need 1)");
2293 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2295 case epctSEMIISOTROPIC:
2296 case epctSURFACETENSION:
2297 if (sscanf(dumstr[m], "%lf%lf",
2298 &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2300 warning_error(wi, "Pressure coupling not enough values (I need 2)");
2302 dumdub[m][YY] = dumdub[m][XX];
2304 case epctANISOTROPIC:
2305 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2306 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2307 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2309 warning_error(wi, "Pressure coupling not enough values (I need 6)");
2313 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2314 epcoupltype_names[ir->epct]);
2318 clear_mat(ir->ref_p);
2319 clear_mat(ir->compress);
2320 for (i = 0; i < DIM; i++)
2322 ir->ref_p[i][i] = dumdub[1][i];
2323 ir->compress[i][i] = dumdub[0][i];
2325 if (ir->epct == epctANISOTROPIC)
2327 ir->ref_p[XX][YY] = dumdub[1][3];
2328 ir->ref_p[XX][ZZ] = dumdub[1][4];
2329 ir->ref_p[YY][ZZ] = dumdub[1][5];
2330 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2332 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2334 ir->compress[XX][YY] = dumdub[0][3];
2335 ir->compress[XX][ZZ] = dumdub[0][4];
2336 ir->compress[YY][ZZ] = dumdub[0][5];
2337 for (i = 0; i < DIM; i++)
2339 for (m = 0; m < i; m++)
2341 ir->ref_p[i][m] = ir->ref_p[m][i];
2342 ir->compress[i][m] = ir->compress[m][i];
2347 if (ir->comm_mode == ecmNO)
2352 opts->couple_moltype = NULL;
2353 if (strlen(is->couple_moltype) > 0)
2355 if (ir->efep != efepNO)
2357 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2358 if (opts->couple_lam0 == opts->couple_lam1)
2360 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2362 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2363 opts->couple_lam1 == ecouplamNONE))
2365 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2370 warning_note(wi, "Free energy is turned off, so we will not decouple the molecule listed in your input.");
2373 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2374 if (ir->efep != efepNO)
2376 if (fep->delta_lambda > 0)
2378 ir->efep = efepSLOWGROWTH;
2382 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2384 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2385 warning_note(wi, "Old option for dhdl-print-energy given: "
2386 "changing \"yes\" to \"total\"\n");
2389 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2391 /* always print out the energy to dhdl if we are doing
2392 expanded ensemble, since we need the total energy for
2393 analysis if the temperature is changing. In some
2394 conditions one may only want the potential energy, so
2395 we will allow that if the appropriate mdp setting has
2396 been enabled. Otherwise, total it is:
2398 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2401 if ((ir->efep != efepNO) || ir->bSimTemp)
2403 ir->bExpanded = FALSE;
2404 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2406 ir->bExpanded = TRUE;
2408 do_fep_params(ir, is->fep_lambda, is->lambda_weights);
2409 if (ir->bSimTemp) /* done after fep params */
2411 do_simtemp_params(ir);
2414 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2415 * setup and not on the old way of specifying the free-energy setup,
2416 * we should check for using soft-core when not needed, since that
2417 * can complicate the sampling significantly.
2418 * Note that we only check for the automated coupling setup.
2419 * If the (advanced) user does FEP through manual topology changes,
2420 * this check will not be triggered.
2422 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 &&
2423 ir->fepvals->sc_alpha != 0 &&
2424 ((opts->couple_lam0 == ecouplamVDW && opts->couple_lam0 == ecouplamVDWQ) ||
2425 (opts->couple_lam1 == ecouplamVDWQ && opts->couple_lam1 == ecouplamVDW)))
2427 warning(wi, "You are using soft-core interactions while the Van der Waals interactions are not decoupled (note that the sc-coul option is only active when using lambda states). Although this will not lead to errors, you will need much more sampling than without soft-core interactions. Consider using sc-alpha=0.");
2432 ir->fepvals->n_lambda = 0;
2435 /* WALL PARAMETERS */
2437 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2439 /* ORIENTATION RESTRAINT PARAMETERS */
2441 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
2443 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2446 /* DEFORMATION PARAMETERS */
2448 clear_mat(ir->deform);
2449 for (i = 0; i < 6; i++)
2453 m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
2454 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2455 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2456 for (i = 0; i < 3; i++)
2458 ir->deform[i][i] = dumdub[0][i];
2460 ir->deform[YY][XX] = dumdub[0][3];
2461 ir->deform[ZZ][XX] = dumdub[0][4];
2462 ir->deform[ZZ][YY] = dumdub[0][5];
2463 if (ir->epc != epcNO)
2465 for (i = 0; i < 3; i++)
2467 for (j = 0; j <= i; j++)
2469 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2471 warning_error(wi, "A box element has deform set and compressibility > 0");
2475 for (i = 0; i < 3; i++)
2477 for (j = 0; j < i; j++)
2479 if (ir->deform[i][j] != 0)
2481 for (m = j; m < DIM; m++)
2483 if (ir->compress[m][j] != 0)
2485 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.");
2486 warning(wi, warn_buf);
2494 /* Ion/water position swapping checks */
2495 if (ir->eSwapCoords != eswapNO)
2497 if (ir->swap->nstswap < 1)
2499 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2501 if (ir->swap->nAverage < 1)
2503 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2505 if (ir->swap->threshold < 1.0)
2507 warning_error(wi, "Ion count threshold must be at least 1.\n");
2515 static int search_QMstring(const char *s, int ng, const char *gn[])
2517 /* same as normal search_string, but this one searches QM strings */
2520 for (i = 0; (i < ng); i++)
2522 if (gmx_strcasecmp(s, gn[i]) == 0)
2528 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2532 } /* search_QMstring */
2534 /* We would like gn to be const as well, but C doesn't allow this */
2535 int search_string(const char *s, int ng, char *gn[])
2539 for (i = 0; (i < ng); i++)
2541 if (gmx_strcasecmp(s, gn[i]) == 0)
2548 "Group %s referenced in the .mdp file was not found in the index file.\n"
2549 "Group names must match either [moleculetype] names or custom index group\n"
2550 "names, in which case you must supply an index file to the '-n' option\n"
2557 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2558 t_blocka *block, char *gnames[],
2559 int gtype, int restnm,
2560 int grptp, gmx_bool bVerbose,
2563 unsigned short *cbuf;
2564 t_grps *grps = &(groups->grps[gtype]);
2565 int i, j, gid, aj, ognr, ntot = 0;
2568 char warn_buf[STRLEN];
2572 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2575 title = gtypes[gtype];
2578 /* Mark all id's as not set */
2579 for (i = 0; (i < natoms); i++)
2584 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2585 for (i = 0; (i < ng); i++)
2587 /* Lookup the group name in the block structure */
2588 gid = search_string(ptrs[i], block->nr, gnames);
2589 if ((grptp != egrptpONE) || (i == 0))
2591 grps->nm_ind[grps->nr++] = gid;
2595 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2598 /* Now go over the atoms in the group */
2599 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2604 /* Range checking */
2605 if ((aj < 0) || (aj >= natoms))
2607 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2609 /* Lookup up the old group number */
2613 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2614 aj+1, title, ognr+1, i+1);
2618 /* Store the group number in buffer */
2619 if (grptp == egrptpONE)
2632 /* Now check whether we have done all atoms */
2636 if (grptp == egrptpALL)
2638 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2639 natoms-ntot, title);
2641 else if (grptp == egrptpPART)
2643 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2644 natoms-ntot, title);
2645 warning_note(wi, warn_buf);
2647 /* Assign all atoms currently unassigned to a rest group */
2648 for (j = 0; (j < natoms); j++)
2650 if (cbuf[j] == NOGID)
2656 if (grptp != egrptpPART)
2661 "Making dummy/rest group for %s containing %d elements\n",
2662 title, natoms-ntot);
2664 /* Add group name "rest" */
2665 grps->nm_ind[grps->nr] = restnm;
2667 /* Assign the rest name to all atoms not currently assigned to a group */
2668 for (j = 0; (j < natoms); j++)
2670 if (cbuf[j] == NOGID)
2679 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2681 /* All atoms are part of one (or no) group, no index required */
2682 groups->ngrpnr[gtype] = 0;
2683 groups->grpnr[gtype] = NULL;
2687 groups->ngrpnr[gtype] = natoms;
2688 snew(groups->grpnr[gtype], natoms);
2689 for (j = 0; (j < natoms); j++)
2691 groups->grpnr[gtype][j] = cbuf[j];
2697 return (bRest && grptp == egrptpPART);
2700 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2703 gmx_groups_t *groups;
2705 int natoms, ai, aj, i, j, d, g, imin, jmin;
2707 int *nrdf2, *na_vcm, na_tot;
2708 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2709 gmx_mtop_atomloop_all_t aloop;
2711 int mb, mol, ftype, as;
2712 gmx_molblock_t *molb;
2713 gmx_moltype_t *molt;
2716 * First calc 3xnr-atoms for each group
2717 * then subtract half a degree of freedom for each constraint
2719 * Only atoms and nuclei contribute to the degrees of freedom...
2724 groups = &mtop->groups;
2725 natoms = mtop->natoms;
2727 /* Allocate one more for a possible rest group */
2728 /* We need to sum degrees of freedom into doubles,
2729 * since floats give too low nrdf's above 3 million atoms.
2731 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2732 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2733 snew(na_vcm, groups->grps[egcVCM].nr+1);
2735 for (i = 0; i < groups->grps[egcTC].nr; i++)
2739 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2744 snew(nrdf2, natoms);
2745 aloop = gmx_mtop_atomloop_all_init(mtop);
2746 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2749 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2751 g = ggrpnr(groups, egcFREEZE, i);
2752 /* Double count nrdf for particle i */
2753 for (d = 0; d < DIM; d++)
2755 if (opts->nFreeze[g][d] == 0)
2760 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2761 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2766 for (mb = 0; mb < mtop->nmolblock; mb++)
2768 molb = &mtop->molblock[mb];
2769 molt = &mtop->moltype[molb->type];
2770 atom = molt->atoms.atom;
2771 for (mol = 0; mol < molb->nmol; mol++)
2773 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2775 ia = molt->ilist[ftype].iatoms;
2776 for (i = 0; i < molt->ilist[ftype].nr; )
2778 /* Subtract degrees of freedom for the constraints,
2779 * if the particles still have degrees of freedom left.
2780 * If one of the particles is a vsite or a shell, then all
2781 * constraint motion will go there, but since they do not
2782 * contribute to the constraints the degrees of freedom do not
2787 if (((atom[ia[1]].ptype == eptNucleus) ||
2788 (atom[ia[1]].ptype == eptAtom)) &&
2789 ((atom[ia[2]].ptype == eptNucleus) ||
2790 (atom[ia[2]].ptype == eptAtom)))
2808 imin = min(imin, nrdf2[ai]);
2809 jmin = min(jmin, nrdf2[aj]);
2812 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2813 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2814 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2815 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2817 ia += interaction_function[ftype].nratoms+1;
2818 i += interaction_function[ftype].nratoms+1;
2821 ia = molt->ilist[F_SETTLE].iatoms;
2822 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2824 /* Subtract 1 dof from every atom in the SETTLE */
2825 for (j = 0; j < 3; j++)
2828 imin = min(2, nrdf2[ai]);
2830 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2831 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2836 as += molt->atoms.nr;
2840 if (ir->ePull == epullCONSTRAINT)
2842 /* Correct nrdf for the COM constraints.
2843 * We correct using the TC and VCM group of the first atom
2844 * in the reference and pull group. If atoms in one pull group
2845 * belong to different TC or VCM groups it is anyhow difficult
2846 * to determine the optimal nrdf assignment.
2850 for (i = 0; i < pull->ncoord; i++)
2854 for (j = 0; j < 2; j++)
2856 const t_pull_group *pgrp;
2858 pgrp = &pull->group[pull->coord[i].group[j]];
2862 /* Subtract 1/2 dof from each group */
2864 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2865 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2866 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2868 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)]]);
2873 /* We need to subtract the whole DOF from group j=1 */
2880 if (ir->nstcomm != 0)
2882 /* Subtract 3 from the number of degrees of freedom in each vcm group
2883 * when com translation is removed and 6 when rotation is removed
2886 switch (ir->comm_mode)
2889 n_sub = ndof_com(ir);
2896 gmx_incons("Checking comm_mode");
2899 for (i = 0; i < groups->grps[egcTC].nr; i++)
2901 /* Count the number of atoms of TC group i for every VCM group */
2902 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2907 for (ai = 0; ai < natoms; ai++)
2909 if (ggrpnr(groups, egcTC, ai) == i)
2911 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2915 /* Correct for VCM removal according to the fraction of each VCM
2916 * group present in this TC group.
2918 nrdf_uc = nrdf_tc[i];
2921 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2925 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2927 if (nrdf_vcm[j] > n_sub)
2929 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2930 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2934 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2935 j, nrdf_vcm[j], nrdf_tc[i]);
2940 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2942 opts->nrdf[i] = nrdf_tc[i];
2943 if (opts->nrdf[i] < 0)
2948 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2949 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
2958 static void decode_cos(char *s, t_cosines *cosine)
2961 char format[STRLEN], f1[STRLEN];
2973 sscanf(t, "%d", &(cosine->n));
2980 snew(cosine->a, cosine->n);
2981 snew(cosine->phi, cosine->n);
2983 sprintf(format, "%%*d");
2984 for (i = 0; (i < cosine->n); i++)
2987 strcat(f1, "%lf%lf");
2988 if (sscanf(t, f1, &a, &phi) < 2)
2990 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
2993 cosine->phi[i] = phi;
2994 strcat(format, "%*lf%*lf");
3001 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
3002 const char *option, const char *val, int flag)
3004 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3005 * But since this is much larger than STRLEN, such a line can not be parsed.
3006 * The real maximum is the number of names that fit in a string: STRLEN/2.
3008 #define EGP_MAX (STRLEN/2)
3009 int nelem, i, j, k, nr;
3010 char *names[EGP_MAX];
3014 gnames = groups->grpname;
3016 nelem = str_nelem(val, EGP_MAX, names);
3019 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3021 nr = groups->grps[egcENER].nr;
3023 for (i = 0; i < nelem/2; i++)
3027 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
3033 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3034 names[2*i], option);
3038 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
3044 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3045 names[2*i+1], option);
3047 if ((j < nr) && (k < nr))
3049 ir->opts.egp_flags[nr*j+k] |= flag;
3050 ir->opts.egp_flags[nr*k+j] |= flag;
3059 static void make_swap_groups(
3068 int ig = -1, i = 0, j;
3072 /* Just a quick check here, more thorough checks are in mdrun */
3073 if (strcmp(splitg0name, splitg1name) == 0)
3075 gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
3078 /* First get the swap group index atoms */
3079 ig = search_string(swapgname, grps->nr, gnames);
3080 swap->nat = grps->index[ig+1] - grps->index[ig];
3083 fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
3084 snew(swap->ind, swap->nat);
3085 for (i = 0; i < swap->nat; i++)
3087 swap->ind[i] = grps->a[grps->index[ig]+i];
3092 gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
3095 /* Now do so for the split groups */
3096 for (j = 0; j < 2; j++)
3100 splitg = splitg0name;
3104 splitg = splitg1name;
3107 ig = search_string(splitg, grps->nr, gnames);
3108 swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
3109 if (swap->nat_split[j] > 0)
3111 fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
3112 j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
3113 snew(swap->ind_split[j], swap->nat_split[j]);
3114 for (i = 0; i < swap->nat_split[j]; i++)
3116 swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
3121 gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
3125 /* Now get the solvent group index atoms */
3126 ig = search_string(solgname, grps->nr, gnames);
3127 swap->nat_sol = grps->index[ig+1] - grps->index[ig];
3128 if (swap->nat_sol > 0)
3130 fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
3131 snew(swap->ind_sol, swap->nat_sol);
3132 for (i = 0; i < swap->nat_sol; i++)
3134 swap->ind_sol[i] = grps->a[grps->index[ig]+i];
3139 gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
3144 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3149 ig = search_string(IMDgname, grps->nr, gnames);
3150 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3152 if (IMDgroup->nat > 0)
3154 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3155 IMDgname, IMDgroup->nat);
3156 snew(IMDgroup->ind, IMDgroup->nat);
3157 for (i = 0; i < IMDgroup->nat; i++)
3159 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3165 void do_index(const char* mdparin, const char *ndx,
3168 t_inputrec *ir, rvec *v,
3172 gmx_groups_t *groups;
3176 char warnbuf[STRLEN], **gnames;
3177 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3180 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3181 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3182 int i, j, k, restnm;
3184 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3185 int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
3186 nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
3187 char warn_buf[STRLEN];
3191 fprintf(stderr, "processing index file...\n");
3197 snew(grps->index, 1);
3199 atoms_all = gmx_mtop_global_atoms(mtop);
3200 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3201 free_t_atoms(&atoms_all, FALSE);
3205 grps = init_index(ndx, &gnames);
3208 groups = &mtop->groups;
3209 natoms = mtop->natoms;
3210 symtab = &mtop->symtab;
3212 snew(groups->grpname, grps->nr+1);
3214 for (i = 0; (i < grps->nr); i++)
3216 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3218 groups->grpname[i] = put_symtab(symtab, "rest");
3220 srenew(gnames, grps->nr+1);
3221 gnames[restnm] = *(groups->grpname[i]);
3222 groups->ngrpname = grps->nr+1;
3224 set_warning_line(wi, mdparin, -1);
3226 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3227 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3228 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3229 if ((ntau_t != ntcg) || (nref_t != ntcg))
3231 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3232 "%d tau-t values", ntcg, nref_t, ntau_t);
3235 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3236 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3237 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3238 nr = groups->grps[egcTC].nr;
3240 snew(ir->opts.nrdf, nr);
3241 snew(ir->opts.tau_t, nr);
3242 snew(ir->opts.ref_t, nr);
3243 if (ir->eI == eiBD && ir->bd_fric == 0)
3245 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3252 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3256 for (i = 0; (i < nr); i++)
3258 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
3259 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
3261 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3262 warning_error(wi, warn_buf);
3265 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3267 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.");
3270 if (ir->opts.tau_t[i] >= 0)
3272 tau_min = min(tau_min, ir->opts.tau_t[i]);
3275 if (ir->etc != etcNO && ir->nsttcouple == -1)
3277 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3282 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3284 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");
3286 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
3288 if (ir->nstpcouple != ir->nsttcouple)
3290 int mincouple = min(ir->nstpcouple, ir->nsttcouple);
3291 ir->nstpcouple = ir->nsttcouple = mincouple;
3292 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);
3293 warning_note(wi, warn_buf);
3297 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3298 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3300 if (ETC_ANDERSEN(ir->etc))
3302 if (ir->nsttcouple != 1)
3305 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");
3306 warning_note(wi, warn_buf);
3309 nstcmin = tcouple_min_integration_steps(ir->etc);
3312 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin - 10*GMX_REAL_EPS)
3314 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3315 ETCOUPLTYPE(ir->etc),
3317 ir->nsttcouple*ir->delta_t);
3318 warning(wi, warn_buf);
3321 for (i = 0; (i < nr); i++)
3323 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
3324 if (ir->opts.ref_t[i] < 0)
3326 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3329 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3330 if we are in this conditional) if mc_temp is negative */
3331 if (ir->expandedvals->mc_temp < 0)
3333 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3337 /* Simulated annealing for each group. There are nr groups */
3338 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3339 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3343 if (nSA > 0 && nSA != nr)
3345 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3349 snew(ir->opts.annealing, nr);
3350 snew(ir->opts.anneal_npoints, nr);
3351 snew(ir->opts.anneal_time, nr);
3352 snew(ir->opts.anneal_temp, nr);
3353 for (i = 0; i < nr; i++)
3355 ir->opts.annealing[i] = eannNO;
3356 ir->opts.anneal_npoints[i] = 0;
3357 ir->opts.anneal_time[i] = NULL;
3358 ir->opts.anneal_temp[i] = NULL;
3363 for (i = 0; i < nr; i++)
3365 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3367 ir->opts.annealing[i] = eannNO;
3369 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3371 ir->opts.annealing[i] = eannSINGLE;
3374 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3376 ir->opts.annealing[i] = eannPERIODIC;
3382 /* Read the other fields too */
3383 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3384 if (nSA_points != nSA)
3386 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3388 for (k = 0, i = 0; i < nr; i++)
3390 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3391 if (ir->opts.anneal_npoints[i] == 1)
3393 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3395 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3396 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3397 k += ir->opts.anneal_npoints[i];
3400 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3403 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3405 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3408 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3411 for (i = 0, k = 0; i < nr; i++)
3414 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3416 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3417 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3420 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3422 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3428 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3430 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3431 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3434 if (ir->opts.anneal_temp[i][j] < 0)
3436 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3441 /* Print out some summary information, to make sure we got it right */
3442 for (i = 0, k = 0; i < nr; i++)
3444 if (ir->opts.annealing[i] != eannNO)
3446 j = groups->grps[egcTC].nm_ind[i];
3447 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3448 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3449 ir->opts.anneal_npoints[i]);
3450 fprintf(stderr, "Time (ps) Temperature (K)\n");
3451 /* All terms except the last one */
3452 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3454 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3457 /* Finally the last one */
3458 j = ir->opts.anneal_npoints[i]-1;
3459 if (ir->opts.annealing[i] == eannSINGLE)
3461 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3465 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3466 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3468 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3477 if (ir->ePull != epullNO)
3479 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3481 make_pull_coords(ir->pull);
3486 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3489 if (ir->eSwapCoords != eswapNO)
3491 make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
3494 /* Make indices for IMD session */
3497 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3500 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3501 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3502 if (nacg*DIM != nacc)
3504 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3507 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3508 restnm, egrptpALL_GENREST, bVerbose, wi);
3509 nr = groups->grps[egcACC].nr;
3510 snew(ir->opts.acc, nr);
3511 ir->opts.ngacc = nr;
3513 for (i = k = 0; (i < nacg); i++)
3515 for (j = 0; (j < DIM); j++, k++)
3517 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3520 for (; (i < nr); i++)
3522 for (j = 0; (j < DIM); j++)
3524 ir->opts.acc[i][j] = 0;
3528 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3529 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3530 if (nfrdim != DIM*nfreeze)
3532 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3535 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3536 restnm, egrptpALL_GENREST, bVerbose, wi);
3537 nr = groups->grps[egcFREEZE].nr;
3538 ir->opts.ngfrz = nr;
3539 snew(ir->opts.nFreeze, nr);
3540 for (i = k = 0; (i < nfreeze); i++)
3542 for (j = 0; (j < DIM); j++, k++)
3544 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3545 if (!ir->opts.nFreeze[i][j])
3547 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3549 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3550 "(not %s)", ptr1[k]);
3551 warning(wi, warn_buf);
3556 for (; (i < nr); i++)
3558 for (j = 0; (j < DIM); j++)
3560 ir->opts.nFreeze[i][j] = 0;
3564 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3565 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3566 restnm, egrptpALL_GENREST, bVerbose, wi);
3567 add_wall_energrps(groups, ir->nwall, symtab);
3568 ir->opts.ngener = groups->grps[egcENER].nr;
3569 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3571 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3572 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3575 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3576 "This may lead to artifacts.\n"
3577 "In most cases one should use one group for the whole system.");
3580 /* Now we have filled the freeze struct, so we can calculate NRDF */
3581 calc_nrdf(mtop, ir, gnames);
3587 /* Must check per group! */
3588 for (i = 0; (i < ir->opts.ngtc); i++)
3590 ntot += ir->opts.nrdf[i];
3592 if (ntot != (DIM*natoms))
3594 fac = sqrt(ntot/(DIM*natoms));
3597 fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
3598 "and removal of center of mass motion\n", fac);
3600 for (i = 0; (i < natoms); i++)
3602 svmul(fac, v[i], v[i]);
3607 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3608 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3609 restnm, egrptpALL_GENREST, bVerbose, wi);
3610 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3611 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3612 restnm, egrptpALL_GENREST, bVerbose, wi);
3613 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3614 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3615 restnm, egrptpONE, bVerbose, wi);
3616 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3617 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3618 restnm, egrptpALL_GENREST, bVerbose, wi);
3620 /* QMMM input processing */
3621 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3622 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3623 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3624 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3626 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3627 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3629 /* group rest, if any, is always MM! */
3630 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3631 restnm, egrptpALL_GENREST, bVerbose, wi);
3632 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3633 ir->opts.ngQM = nQMg;
3634 snew(ir->opts.QMmethod, nr);
3635 snew(ir->opts.QMbasis, nr);
3636 for (i = 0; i < nr; i++)
3638 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3639 * converted to the corresponding enum in names.c
3641 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3643 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3647 nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
3648 nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
3649 nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
3650 snew(ir->opts.QMmult, nr);
3651 snew(ir->opts.QMcharge, nr);
3652 snew(ir->opts.bSH, nr);
3654 for (i = 0; i < nr; i++)
3656 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3657 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3658 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3661 nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
3662 nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
3663 snew(ir->opts.CASelectrons, nr);
3664 snew(ir->opts.CASorbitals, nr);
3665 for (i = 0; i < nr; i++)
3667 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3668 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3670 /* special optimization options */
3672 nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
3673 nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
3674 snew(ir->opts.bOPT, nr);
3675 snew(ir->opts.bTS, nr);
3676 for (i = 0; i < nr; i++)
3678 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3679 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3681 nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
3682 nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
3683 nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
3684 snew(ir->opts.SAon, nr);
3685 snew(ir->opts.SAoff, nr);
3686 snew(ir->opts.SAsteps, nr);
3688 for (i = 0; i < nr; i++)
3690 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3691 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3692 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3694 /* end of QMMM input */
3698 for (i = 0; (i < egcNR); i++)
3700 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3701 for (j = 0; (j < groups->grps[i].nr); j++)
3703 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3705 fprintf(stderr, "\n");
3709 nr = groups->grps[egcENER].nr;
3710 snew(ir->opts.egp_flags, nr*nr);
3712 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3713 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3715 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3717 if (bExcl && EEL_FULL(ir->coulombtype))
3719 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3722 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3723 if (bTable && !(ir->vdwtype == evdwUSER) &&
3724 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3725 !(ir->coulombtype == eelPMEUSERSWITCH))
3727 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3730 decode_cos(is->efield_x, &(ir->ex[XX]));
3731 decode_cos(is->efield_xt, &(ir->et[XX]));
3732 decode_cos(is->efield_y, &(ir->ex[YY]));
3733 decode_cos(is->efield_yt, &(ir->et[YY]));
3734 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3735 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3739 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3742 for (i = 0; (i < grps->nr); i++)
3754 static void check_disre(gmx_mtop_t *mtop)
3756 gmx_ffparams_t *ffparams;
3757 t_functype *functype;
3759 int i, ndouble, ftype;
3760 int label, old_label;
3762 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3764 ffparams = &mtop->ffparams;
3765 functype = ffparams->functype;
3766 ip = ffparams->iparams;
3769 for (i = 0; i < ffparams->ntypes; i++)
3771 ftype = functype[i];
3772 if (ftype == F_DISRES)
3774 label = ip[i].disres.label;
3775 if (label == old_label)
3777 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3785 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3786 "probably the parameters for multiple pairs in one restraint "
3787 "are not identical\n", ndouble);
3792 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3793 gmx_bool posres_only,
3797 gmx_mtop_ilistloop_t iloop;
3807 for (d = 0; d < DIM; d++)
3809 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3811 /* Check for freeze groups */
3812 for (g = 0; g < ir->opts.ngfrz; g++)
3814 for (d = 0; d < DIM; d++)
3816 if (ir->opts.nFreeze[g][d] != 0)
3824 /* Check for position restraints */
3825 iloop = gmx_mtop_ilistloop_init(sys);
3826 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3829 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3831 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3833 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3834 for (d = 0; d < DIM; d++)
3836 if (pr->posres.fcA[d] != 0)
3842 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3844 /* Check for flat-bottom posres */
3845 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3846 if (pr->fbposres.k != 0)
3848 switch (pr->fbposres.geom)
3850 case efbposresSPHERE:
3851 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3853 case efbposresCYLINDERX:
3854 AbsRef[YY] = AbsRef[ZZ] = 1;
3856 case efbposresCYLINDERY:
3857 AbsRef[XX] = AbsRef[ZZ] = 1;
3859 case efbposresCYLINDER:
3860 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3861 case efbposresCYLINDERZ:
3862 AbsRef[XX] = AbsRef[YY] = 1;
3864 case efbposresX: /* d=XX */
3865 case efbposresY: /* d=YY */
3866 case efbposresZ: /* d=ZZ */
3867 d = pr->fbposres.geom - efbposresX;
3871 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3872 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3880 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3884 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3885 gmx_bool *bC6ParametersWorkWithGeometricRules,
3886 gmx_bool *bC6ParametersWorkWithLBRules,
3887 gmx_bool *bLBRulesPossible)
3889 int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
3892 double geometricdiff, LBdiff;
3893 double c6i, c6j, c12i, c12j;
3894 double c6, c6_geometric, c6_LB;
3895 double sigmai, sigmaj, epsi, epsj;
3896 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3899 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3900 * force-field floating point parameters.
3903 ptr = getenv("GMX_LJCOMB_TOL");
3908 sscanf(ptr, "%lf", &dbl);
3912 *bC6ParametersWorkWithLBRules = TRUE;
3913 *bC6ParametersWorkWithGeometricRules = TRUE;
3914 bCanDoLBRules = TRUE;
3915 bCanDoGeometricRules = TRUE;
3916 ntypes = mtop->ffparams.atnr;
3917 snew(typecount, ntypes);
3918 gmx_mtop_count_atomtypes(mtop, state, typecount);
3919 geometricdiff = LBdiff = 0.0;
3920 *bLBRulesPossible = TRUE;
3921 for (tpi = 0; tpi < ntypes; ++tpi)
3923 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3924 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3925 for (tpj = tpi; tpj < ntypes; ++tpj)
3927 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3928 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3929 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3930 c6_geometric = sqrt(c6i * c6j);
3931 if (!gmx_numzero(c6_geometric))
3933 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3935 sigmai = pow(c12i / c6i, 1.0/6.0);
3936 sigmaj = pow(c12j / c6j, 1.0/6.0);
3937 epsi = c6i * c6i /(4.0 * c12i);
3938 epsj = c6j * c6j /(4.0 * c12j);
3939 c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
3943 *bLBRulesPossible = FALSE;
3944 c6_LB = c6_geometric;
3946 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3949 if (FALSE == bCanDoLBRules)
3951 *bC6ParametersWorkWithLBRules = FALSE;
3954 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3956 if (FALSE == bCanDoGeometricRules)
3958 *bC6ParametersWorkWithGeometricRules = FALSE;
3966 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3970 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3972 check_combination_rule_differences(mtop, 0,
3973 &bC6ParametersWorkWithGeometricRules,
3974 &bC6ParametersWorkWithLBRules,
3976 if (ir->ljpme_combination_rule == eljpmeLB)
3978 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
3980 warning(wi, "You are using arithmetic-geometric combination rules "
3981 "in LJ-PME, but your non-bonded C6 parameters do not "
3982 "follow these rules.");
3987 if (FALSE == bC6ParametersWorkWithGeometricRules)
3989 if (ir->eDispCorr != edispcNO)
3991 warning_note(wi, "You are using geometric combination rules in "
3992 "LJ-PME, but your non-bonded C6 parameters do "
3993 "not follow these rules. "
3994 "This will introduce very small errors in the forces and energies in "
3995 "your simulations. Dispersion correction will correct total energy "
3996 "and/or pressure for isotropic systems, but not forces or surface tensions.");
4000 warning_note(wi, "You are using geometric combination rules in "
4001 "LJ-PME, but your non-bonded C6 parameters do "
4002 "not follow these rules. "
4003 "This will introduce very small errors in the forces and energies in "
4004 "your simulations. If your system is homogeneous, consider using dispersion correction "
4005 "for the total energy and pressure.");
4011 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
4014 char err_buf[STRLEN];
4015 int i, m, c, nmol, npct;
4016 gmx_bool bCharge, bAcc;
4017 real gdt_max, *mgrp, mt;
4019 gmx_mtop_atomloop_block_t aloopb;
4020 gmx_mtop_atomloop_all_t aloop;
4023 char warn_buf[STRLEN];
4025 set_warning_line(wi, mdparin, -1);
4027 if (ir->cutoff_scheme == ecutsVERLET &&
4028 ir->verletbuf_tol > 0 &&
4030 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
4031 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4033 /* Check if a too small Verlet buffer might potentially
4034 * cause more drift than the thermostat can couple off.
4036 /* Temperature error fraction for warning and suggestion */
4037 const real T_error_warn = 0.002;
4038 const real T_error_suggest = 0.001;
4039 /* For safety: 2 DOF per atom (typical with constraints) */
4040 const real nrdf_at = 2;
4041 real T, tau, max_T_error;
4046 for (i = 0; i < ir->opts.ngtc; i++)
4048 T = max(T, ir->opts.ref_t[i]);
4049 tau = max(tau, ir->opts.tau_t[i]);
4053 /* This is a worst case estimate of the temperature error,
4054 * assuming perfect buffer estimation and no cancelation
4055 * of errors. The factor 0.5 is because energy distributes
4056 * equally over Ekin and Epot.
4058 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4059 if (max_T_error > T_error_warn)
4061 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.",
4062 ir->verletbuf_tol, T, tau,
4064 100*T_error_suggest,
4065 ir->verletbuf_tol*T_error_suggest/max_T_error);
4066 warning(wi, warn_buf);
4071 if (ETC_ANDERSEN(ir->etc))
4075 for (i = 0; i < ir->opts.ngtc; i++)
4077 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4078 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4079 sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
4080 i, ir->opts.tau_t[i]);
4081 CHECK(ir->opts.tau_t[i] < 0);
4084 for (i = 0; i < ir->opts.ngtc; i++)
4086 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
4087 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);
4088 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
4092 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4093 ir->comm_mode == ecmNO &&
4094 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4095 !ETC_ANDERSEN(ir->etc))
4097 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");
4100 /* Check for pressure coupling with absolute position restraints */
4101 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4103 absolute_reference(ir, sys, TRUE, AbsRef);
4105 for (m = 0; m < DIM; m++)
4107 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4109 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4117 aloopb = gmx_mtop_atomloop_block_init(sys);
4118 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4120 if (atom->q != 0 || atom->qB != 0)
4128 if (EEL_FULL(ir->coulombtype))
4131 "You are using full electrostatics treatment %s for a system without charges.\n"
4132 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4133 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4134 warning(wi, err_buf);
4139 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4142 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4143 "You might want to consider using %s electrostatics.\n",
4145 warning_note(wi, err_buf);
4149 /* Check if combination rules used in LJ-PME are the same as in the force field */
4150 if (EVDW_PME(ir->vdwtype))
4152 check_combination_rules(ir, sys, wi);
4155 /* Generalized reaction field */
4156 if (ir->opts.ngtc == 0)
4158 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4160 CHECK(ir->coulombtype == eelGRF);
4164 sprintf(err_buf, "When using coulombtype = %s"
4165 " ref-t for temperature coupling should be > 0",
4167 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4170 if (ir->eI == eiSD2)
4172 sprintf(warn_buf, "The stochastic dynamics integrator %s is deprecated, since\n"
4173 "it is slower than integrator %s and is slightly less accurate\n"
4174 "with constraints. Use the %s integrator.",
4175 ei_names[ir->eI], ei_names[eiSD1], ei_names[eiSD1]);
4176 warning_note(wi, warn_buf);
4180 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4182 for (m = 0; (m < DIM); m++)
4184 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4193 snew(mgrp, sys->groups.grps[egcACC].nr);
4194 aloop = gmx_mtop_atomloop_all_init(sys);
4195 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4197 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4200 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4202 for (m = 0; (m < DIM); m++)
4204 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4208 for (m = 0; (m < DIM); m++)
4210 if (fabs(acc[m]) > 1e-6)
4212 const char *dim[DIM] = { "X", "Y", "Z" };
4214 "Net Acceleration in %s direction, will %s be corrected\n",
4215 dim[m], ir->nstcomm != 0 ? "" : "not");
4216 if (ir->nstcomm != 0 && m < ndof_com(ir))
4219 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4221 ir->opts.acc[i][m] -= acc[m];
4229 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4230 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4232 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4235 if (ir->ePull != epullNO)
4237 gmx_bool bPullAbsoluteRef;
4239 bPullAbsoluteRef = FALSE;
4240 for (i = 0; i < ir->pull->ncoord; i++)
4242 bPullAbsoluteRef = bPullAbsoluteRef ||
4243 ir->pull->coord[i].group[0] == 0 ||
4244 ir->pull->coord[i].group[1] == 0;
4246 if (bPullAbsoluteRef)
4248 absolute_reference(ir, sys, FALSE, AbsRef);
4249 for (m = 0; m < DIM; m++)
4251 if (ir->pull->dim[m] && !AbsRef[m])
4253 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.");
4259 if (ir->pull->eGeom == epullgDIRPBC)
4261 for (i = 0; i < 3; i++)
4263 for (m = 0; m <= i; m++)
4265 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4266 ir->deform[i][m] != 0)
4268 for (c = 0; c < ir->pull->ncoord; c++)
4270 if (ir->pull->coord[c].vec[m] != 0)
4272 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->eGeom), 'x'+m);
4284 void double_check(t_inputrec *ir, matrix box,
4285 gmx_bool bHasNormalConstraints,
4286 gmx_bool bHasAnyConstraints,
4291 char warn_buf[STRLEN];
4294 ptr = check_box(ir->ePBC, box);
4297 warning_error(wi, ptr);
4300 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4302 if (ir->shake_tol <= 0.0)
4304 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4306 warning_error(wi, warn_buf);
4309 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
4311 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
4312 if (ir->epc == epcNO)
4314 warning(wi, warn_buf);
4318 warning_error(wi, warn_buf);
4323 if ( (ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4325 /* If we have Lincs constraints: */
4326 if (ir->eI == eiMD && ir->etc == etcNO &&
4327 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4329 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4330 warning_note(wi, warn_buf);
4333 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4335 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4336 warning_note(wi, warn_buf);
4338 if (ir->epc == epcMTTK)
4340 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4344 if (bHasAnyConstraints && ir->epc == epcMTTK)
4346 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4349 if (ir->LincsWarnAngle > 90.0)
4351 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4352 warning(wi, warn_buf);
4353 ir->LincsWarnAngle = 90.0;
4356 if (ir->ePBC != epbcNONE)
4358 if (ir->nstlist == 0)
4360 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4362 bTWIN = (ir->rlistlong > ir->rlist);
4363 if (ir->ns_type == ensGRID)
4365 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
4367 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",
4368 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
4369 warning_error(wi, warn_buf);
4374 min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
4375 if (2*ir->rlistlong >= min_size)
4377 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4378 warning_error(wi, warn_buf);
4381 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4388 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4392 real rvdw1, rvdw2, rcoul1, rcoul2;
4393 char warn_buf[STRLEN];
4395 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4399 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4404 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4410 if (rvdw1 + rvdw2 > ir->rlist ||
4411 rcoul1 + rcoul2 > ir->rlist)
4414 "The sum of the two largest charge group radii (%f) "
4415 "is larger than rlist (%f)\n",
4416 max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4417 warning(wi, warn_buf);
4421 /* Here we do not use the zero at cut-off macro,
4422 * since user defined interactions might purposely
4423 * not be zero at the cut-off.
4425 if (ir_vdw_is_zero_at_cutoff(ir) &&
4426 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
4428 sprintf(warn_buf, "The sum of the two largest charge group "
4429 "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
4430 "With exact cut-offs, better performance can be "
4431 "obtained with cutoff-scheme = %s, because it "
4432 "does not use charge groups at all.",
4434 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4435 ir->rlistlong, ir->rvdw,
4436 ecutscheme_names[ecutsVERLET]);
4439 warning(wi, warn_buf);
4443 warning_note(wi, warn_buf);
4446 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4447 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
4449 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
4450 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4452 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4453 ir->rlistlong, ir->rcoulomb,
4454 ecutscheme_names[ecutsVERLET]);
4457 warning(wi, warn_buf);
4461 warning_note(wi, warn_buf);