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45 #include "gromacs/gmxpreprocess/toputil.h"
46 #include "gromacs/legacyheaders/chargegroup.h"
47 #include "gromacs/legacyheaders/inputrec.h"
48 #include "gromacs/legacyheaders/macros.h"
49 #include "gromacs/legacyheaders/names.h"
50 #include "gromacs/legacyheaders/network.h"
51 #include "gromacs/legacyheaders/readinp.h"
52 #include "gromacs/legacyheaders/typedefs.h"
53 #include "gromacs/legacyheaders/warninp.h"
54 #include "gromacs/math/units.h"
55 #include "gromacs/math/vec.h"
56 #include "gromacs/mdlib/calc_verletbuf.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)*(gmx_expm1(temperature_lambdas[i])/gmx_expm1(1.0));
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 /* TODO this is utility functionality (search for the index of a
2536 string in a collection), so should be refactored and located more
2538 int search_string(const char *s, int ng, char *gn[])
2542 for (i = 0; (i < ng); i++)
2544 if (gmx_strcasecmp(s, gn[i]) == 0)
2551 "Group %s referenced in the .mdp file was not found in the index file.\n"
2552 "Group names must match either [moleculetype] names or custom index group\n"
2553 "names, in which case you must supply an index file to the '-n' option\n"
2560 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2561 t_blocka *block, char *gnames[],
2562 int gtype, int restnm,
2563 int grptp, gmx_bool bVerbose,
2566 unsigned short *cbuf;
2567 t_grps *grps = &(groups->grps[gtype]);
2568 int i, j, gid, aj, ognr, ntot = 0;
2571 char warn_buf[STRLEN];
2575 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2578 title = gtypes[gtype];
2581 /* Mark all id's as not set */
2582 for (i = 0; (i < natoms); i++)
2587 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2588 for (i = 0; (i < ng); i++)
2590 /* Lookup the group name in the block structure */
2591 gid = search_string(ptrs[i], block->nr, gnames);
2592 if ((grptp != egrptpONE) || (i == 0))
2594 grps->nm_ind[grps->nr++] = gid;
2598 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2601 /* Now go over the atoms in the group */
2602 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2607 /* Range checking */
2608 if ((aj < 0) || (aj >= natoms))
2610 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2612 /* Lookup up the old group number */
2616 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2617 aj+1, title, ognr+1, i+1);
2621 /* Store the group number in buffer */
2622 if (grptp == egrptpONE)
2635 /* Now check whether we have done all atoms */
2639 if (grptp == egrptpALL)
2641 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2642 natoms-ntot, title);
2644 else if (grptp == egrptpPART)
2646 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2647 natoms-ntot, title);
2648 warning_note(wi, warn_buf);
2650 /* Assign all atoms currently unassigned to a rest group */
2651 for (j = 0; (j < natoms); j++)
2653 if (cbuf[j] == NOGID)
2659 if (grptp != egrptpPART)
2664 "Making dummy/rest group for %s containing %d elements\n",
2665 title, natoms-ntot);
2667 /* Add group name "rest" */
2668 grps->nm_ind[grps->nr] = restnm;
2670 /* Assign the rest name to all atoms not currently assigned to a group */
2671 for (j = 0; (j < natoms); j++)
2673 if (cbuf[j] == NOGID)
2682 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2684 /* All atoms are part of one (or no) group, no index required */
2685 groups->ngrpnr[gtype] = 0;
2686 groups->grpnr[gtype] = NULL;
2690 groups->ngrpnr[gtype] = natoms;
2691 snew(groups->grpnr[gtype], natoms);
2692 for (j = 0; (j < natoms); j++)
2694 groups->grpnr[gtype][j] = cbuf[j];
2700 return (bRest && grptp == egrptpPART);
2703 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2706 gmx_groups_t *groups;
2708 int natoms, ai, aj, i, j, d, g, imin, jmin;
2710 int *nrdf2, *na_vcm, na_tot;
2711 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2712 gmx_mtop_atomloop_all_t aloop;
2714 int mb, mol, ftype, as;
2715 gmx_molblock_t *molb;
2716 gmx_moltype_t *molt;
2719 * First calc 3xnr-atoms for each group
2720 * then subtract half a degree of freedom for each constraint
2722 * Only atoms and nuclei contribute to the degrees of freedom...
2727 groups = &mtop->groups;
2728 natoms = mtop->natoms;
2730 /* Allocate one more for a possible rest group */
2731 /* We need to sum degrees of freedom into doubles,
2732 * since floats give too low nrdf's above 3 million atoms.
2734 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2735 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2736 snew(na_vcm, groups->grps[egcVCM].nr+1);
2738 for (i = 0; i < groups->grps[egcTC].nr; i++)
2742 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2747 snew(nrdf2, natoms);
2748 aloop = gmx_mtop_atomloop_all_init(mtop);
2749 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2752 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2754 g = ggrpnr(groups, egcFREEZE, i);
2755 /* Double count nrdf for particle i */
2756 for (d = 0; d < DIM; d++)
2758 if (opts->nFreeze[g][d] == 0)
2763 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2764 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2769 for (mb = 0; mb < mtop->nmolblock; mb++)
2771 molb = &mtop->molblock[mb];
2772 molt = &mtop->moltype[molb->type];
2773 atom = molt->atoms.atom;
2774 for (mol = 0; mol < molb->nmol; mol++)
2776 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2778 ia = molt->ilist[ftype].iatoms;
2779 for (i = 0; i < molt->ilist[ftype].nr; )
2781 /* Subtract degrees of freedom for the constraints,
2782 * if the particles still have degrees of freedom left.
2783 * If one of the particles is a vsite or a shell, then all
2784 * constraint motion will go there, but since they do not
2785 * contribute to the constraints the degrees of freedom do not
2790 if (((atom[ia[1]].ptype == eptNucleus) ||
2791 (atom[ia[1]].ptype == eptAtom)) &&
2792 ((atom[ia[2]].ptype == eptNucleus) ||
2793 (atom[ia[2]].ptype == eptAtom)))
2811 imin = min(imin, nrdf2[ai]);
2812 jmin = min(jmin, nrdf2[aj]);
2815 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2816 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2817 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2818 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2820 ia += interaction_function[ftype].nratoms+1;
2821 i += interaction_function[ftype].nratoms+1;
2824 ia = molt->ilist[F_SETTLE].iatoms;
2825 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2827 /* Subtract 1 dof from every atom in the SETTLE */
2828 for (j = 0; j < 3; j++)
2831 imin = min(2, nrdf2[ai]);
2833 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2834 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2839 as += molt->atoms.nr;
2843 if (ir->ePull == epullCONSTRAINT)
2845 /* Correct nrdf for the COM constraints.
2846 * We correct using the TC and VCM group of the first atom
2847 * in the reference and pull group. If atoms in one pull group
2848 * belong to different TC or VCM groups it is anyhow difficult
2849 * to determine the optimal nrdf assignment.
2853 for (i = 0; i < pull->ncoord; i++)
2857 for (j = 0; j < 2; j++)
2859 const t_pull_group *pgrp;
2861 pgrp = &pull->group[pull->coord[i].group[j]];
2865 /* Subtract 1/2 dof from each group */
2867 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2868 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2869 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2871 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)]]);
2876 /* We need to subtract the whole DOF from group j=1 */
2883 if (ir->nstcomm != 0)
2885 /* Subtract 3 from the number of degrees of freedom in each vcm group
2886 * when com translation is removed and 6 when rotation is removed
2889 switch (ir->comm_mode)
2892 n_sub = ndof_com(ir);
2899 gmx_incons("Checking comm_mode");
2902 for (i = 0; i < groups->grps[egcTC].nr; i++)
2904 /* Count the number of atoms of TC group i for every VCM group */
2905 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2910 for (ai = 0; ai < natoms; ai++)
2912 if (ggrpnr(groups, egcTC, ai) == i)
2914 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2918 /* Correct for VCM removal according to the fraction of each VCM
2919 * group present in this TC group.
2921 nrdf_uc = nrdf_tc[i];
2924 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2928 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2930 if (nrdf_vcm[j] > n_sub)
2932 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2933 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2937 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2938 j, nrdf_vcm[j], nrdf_tc[i]);
2943 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2945 opts->nrdf[i] = nrdf_tc[i];
2946 if (opts->nrdf[i] < 0)
2951 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2952 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
2961 static void decode_cos(char *s, t_cosines *cosine)
2964 char format[STRLEN], f1[STRLEN];
2976 sscanf(t, "%d", &(cosine->n));
2983 snew(cosine->a, cosine->n);
2984 snew(cosine->phi, cosine->n);
2986 sprintf(format, "%%*d");
2987 for (i = 0; (i < cosine->n); i++)
2990 strcat(f1, "%lf%lf");
2991 if (sscanf(t, f1, &a, &phi) < 2)
2993 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
2996 cosine->phi[i] = phi;
2997 strcat(format, "%*lf%*lf");
3004 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
3005 const char *option, const char *val, int flag)
3007 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3008 * But since this is much larger than STRLEN, such a line can not be parsed.
3009 * The real maximum is the number of names that fit in a string: STRLEN/2.
3011 #define EGP_MAX (STRLEN/2)
3012 int nelem, i, j, k, nr;
3013 char *names[EGP_MAX];
3017 gnames = groups->grpname;
3019 nelem = str_nelem(val, EGP_MAX, names);
3022 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3024 nr = groups->grps[egcENER].nr;
3026 for (i = 0; i < nelem/2; i++)
3030 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
3036 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3037 names[2*i], option);
3041 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
3047 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3048 names[2*i+1], option);
3050 if ((j < nr) && (k < nr))
3052 ir->opts.egp_flags[nr*j+k] |= flag;
3053 ir->opts.egp_flags[nr*k+j] |= flag;
3062 static void make_swap_groups(
3071 int ig = -1, i = 0, j;
3075 /* Just a quick check here, more thorough checks are in mdrun */
3076 if (strcmp(splitg0name, splitg1name) == 0)
3078 gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
3081 /* First get the swap group index atoms */
3082 ig = search_string(swapgname, grps->nr, gnames);
3083 swap->nat = grps->index[ig+1] - grps->index[ig];
3086 fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
3087 snew(swap->ind, swap->nat);
3088 for (i = 0; i < swap->nat; i++)
3090 swap->ind[i] = grps->a[grps->index[ig]+i];
3095 gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
3098 /* Now do so for the split groups */
3099 for (j = 0; j < 2; j++)
3103 splitg = splitg0name;
3107 splitg = splitg1name;
3110 ig = search_string(splitg, grps->nr, gnames);
3111 swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
3112 if (swap->nat_split[j] > 0)
3114 fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
3115 j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
3116 snew(swap->ind_split[j], swap->nat_split[j]);
3117 for (i = 0; i < swap->nat_split[j]; i++)
3119 swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
3124 gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
3128 /* Now get the solvent group index atoms */
3129 ig = search_string(solgname, grps->nr, gnames);
3130 swap->nat_sol = grps->index[ig+1] - grps->index[ig];
3131 if (swap->nat_sol > 0)
3133 fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
3134 snew(swap->ind_sol, swap->nat_sol);
3135 for (i = 0; i < swap->nat_sol; i++)
3137 swap->ind_sol[i] = grps->a[grps->index[ig]+i];
3142 gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
3147 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3152 ig = search_string(IMDgname, grps->nr, gnames);
3153 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3155 if (IMDgroup->nat > 0)
3157 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3158 IMDgname, IMDgroup->nat);
3159 snew(IMDgroup->ind, IMDgroup->nat);
3160 for (i = 0; i < IMDgroup->nat; i++)
3162 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3168 void do_index(const char* mdparin, const char *ndx,
3171 t_inputrec *ir, rvec *v,
3175 gmx_groups_t *groups;
3179 char warnbuf[STRLEN], **gnames;
3180 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3183 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3184 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3185 int i, j, k, restnm;
3187 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3188 int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
3189 nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
3190 char warn_buf[STRLEN];
3194 fprintf(stderr, "processing index file...\n");
3200 snew(grps->index, 1);
3202 atoms_all = gmx_mtop_global_atoms(mtop);
3203 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3204 free_t_atoms(&atoms_all, FALSE);
3208 grps = init_index(ndx, &gnames);
3211 groups = &mtop->groups;
3212 natoms = mtop->natoms;
3213 symtab = &mtop->symtab;
3215 snew(groups->grpname, grps->nr+1);
3217 for (i = 0; (i < grps->nr); i++)
3219 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3221 groups->grpname[i] = put_symtab(symtab, "rest");
3223 srenew(gnames, grps->nr+1);
3224 gnames[restnm] = *(groups->grpname[i]);
3225 groups->ngrpname = grps->nr+1;
3227 set_warning_line(wi, mdparin, -1);
3229 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3230 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3231 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3232 if ((ntau_t != ntcg) || (nref_t != ntcg))
3234 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3235 "%d tau-t values", ntcg, nref_t, ntau_t);
3238 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3239 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3240 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3241 nr = groups->grps[egcTC].nr;
3243 snew(ir->opts.nrdf, nr);
3244 snew(ir->opts.tau_t, nr);
3245 snew(ir->opts.ref_t, nr);
3246 if (ir->eI == eiBD && ir->bd_fric == 0)
3248 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3255 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3259 for (i = 0; (i < nr); i++)
3261 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
3262 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
3264 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3265 warning_error(wi, warn_buf);
3268 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3270 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.");
3273 if (ir->opts.tau_t[i] >= 0)
3275 tau_min = min(tau_min, ir->opts.tau_t[i]);
3278 if (ir->etc != etcNO && ir->nsttcouple == -1)
3280 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3285 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3287 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");
3289 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
3291 if (ir->nstpcouple != ir->nsttcouple)
3293 int mincouple = min(ir->nstpcouple, ir->nsttcouple);
3294 ir->nstpcouple = ir->nsttcouple = mincouple;
3295 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);
3296 warning_note(wi, warn_buf);
3300 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3301 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3303 if (ETC_ANDERSEN(ir->etc))
3305 if (ir->nsttcouple != 1)
3308 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");
3309 warning_note(wi, warn_buf);
3312 nstcmin = tcouple_min_integration_steps(ir->etc);
3315 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin - 10*GMX_REAL_EPS)
3317 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3318 ETCOUPLTYPE(ir->etc),
3320 ir->nsttcouple*ir->delta_t);
3321 warning(wi, warn_buf);
3324 for (i = 0; (i < nr); i++)
3326 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
3327 if (ir->opts.ref_t[i] < 0)
3329 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3332 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3333 if we are in this conditional) if mc_temp is negative */
3334 if (ir->expandedvals->mc_temp < 0)
3336 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3340 /* Simulated annealing for each group. There are nr groups */
3341 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3342 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3346 if (nSA > 0 && nSA != nr)
3348 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3352 snew(ir->opts.annealing, nr);
3353 snew(ir->opts.anneal_npoints, nr);
3354 snew(ir->opts.anneal_time, nr);
3355 snew(ir->opts.anneal_temp, nr);
3356 for (i = 0; i < nr; i++)
3358 ir->opts.annealing[i] = eannNO;
3359 ir->opts.anneal_npoints[i] = 0;
3360 ir->opts.anneal_time[i] = NULL;
3361 ir->opts.anneal_temp[i] = NULL;
3366 for (i = 0; i < nr; i++)
3368 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3370 ir->opts.annealing[i] = eannNO;
3372 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3374 ir->opts.annealing[i] = eannSINGLE;
3377 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3379 ir->opts.annealing[i] = eannPERIODIC;
3385 /* Read the other fields too */
3386 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3387 if (nSA_points != nSA)
3389 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3391 for (k = 0, i = 0; i < nr; i++)
3393 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3394 if (ir->opts.anneal_npoints[i] == 1)
3396 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3398 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3399 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3400 k += ir->opts.anneal_npoints[i];
3403 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3406 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3408 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3411 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3414 for (i = 0, k = 0; i < nr; i++)
3417 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3419 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3420 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3423 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3425 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3431 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3433 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3434 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3437 if (ir->opts.anneal_temp[i][j] < 0)
3439 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3444 /* Print out some summary information, to make sure we got it right */
3445 for (i = 0, k = 0; i < nr; i++)
3447 if (ir->opts.annealing[i] != eannNO)
3449 j = groups->grps[egcTC].nm_ind[i];
3450 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3451 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3452 ir->opts.anneal_npoints[i]);
3453 fprintf(stderr, "Time (ps) Temperature (K)\n");
3454 /* All terms except the last one */
3455 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3457 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3460 /* Finally the last one */
3461 j = ir->opts.anneal_npoints[i]-1;
3462 if (ir->opts.annealing[i] == eannSINGLE)
3464 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3468 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3469 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3471 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3480 if (ir->ePull != epullNO)
3482 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3484 make_pull_coords(ir->pull);
3489 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3492 if (ir->eSwapCoords != eswapNO)
3494 make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
3497 /* Make indices for IMD session */
3500 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3503 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3504 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3505 if (nacg*DIM != nacc)
3507 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3510 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3511 restnm, egrptpALL_GENREST, bVerbose, wi);
3512 nr = groups->grps[egcACC].nr;
3513 snew(ir->opts.acc, nr);
3514 ir->opts.ngacc = nr;
3516 for (i = k = 0; (i < nacg); i++)
3518 for (j = 0; (j < DIM); j++, k++)
3520 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3523 for (; (i < nr); i++)
3525 for (j = 0; (j < DIM); j++)
3527 ir->opts.acc[i][j] = 0;
3531 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3532 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3533 if (nfrdim != DIM*nfreeze)
3535 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3538 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3539 restnm, egrptpALL_GENREST, bVerbose, wi);
3540 nr = groups->grps[egcFREEZE].nr;
3541 ir->opts.ngfrz = nr;
3542 snew(ir->opts.nFreeze, nr);
3543 for (i = k = 0; (i < nfreeze); i++)
3545 for (j = 0; (j < DIM); j++, k++)
3547 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3548 if (!ir->opts.nFreeze[i][j])
3550 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3552 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3553 "(not %s)", ptr1[k]);
3554 warning(wi, warn_buf);
3559 for (; (i < nr); i++)
3561 for (j = 0; (j < DIM); j++)
3563 ir->opts.nFreeze[i][j] = 0;
3567 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3568 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3569 restnm, egrptpALL_GENREST, bVerbose, wi);
3570 add_wall_energrps(groups, ir->nwall, symtab);
3571 ir->opts.ngener = groups->grps[egcENER].nr;
3572 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3574 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3575 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3578 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3579 "This may lead to artifacts.\n"
3580 "In most cases one should use one group for the whole system.");
3583 /* Now we have filled the freeze struct, so we can calculate NRDF */
3584 calc_nrdf(mtop, ir, gnames);
3590 /* Must check per group! */
3591 for (i = 0; (i < ir->opts.ngtc); i++)
3593 ntot += ir->opts.nrdf[i];
3595 if (ntot != (DIM*natoms))
3597 fac = sqrt(ntot/(DIM*natoms));
3600 fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
3601 "and removal of center of mass motion\n", fac);
3603 for (i = 0; (i < natoms); i++)
3605 svmul(fac, v[i], v[i]);
3610 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3611 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3612 restnm, egrptpALL_GENREST, bVerbose, wi);
3613 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3614 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3615 restnm, egrptpALL_GENREST, bVerbose, wi);
3616 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3617 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3618 restnm, egrptpONE, bVerbose, wi);
3619 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3620 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3621 restnm, egrptpALL_GENREST, bVerbose, wi);
3623 /* QMMM input processing */
3624 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3625 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3626 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3627 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3629 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3630 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3632 /* group rest, if any, is always MM! */
3633 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3634 restnm, egrptpALL_GENREST, bVerbose, wi);
3635 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3636 ir->opts.ngQM = nQMg;
3637 snew(ir->opts.QMmethod, nr);
3638 snew(ir->opts.QMbasis, nr);
3639 for (i = 0; i < nr; i++)
3641 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3642 * converted to the corresponding enum in names.c
3644 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3646 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3650 nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
3651 nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
3652 nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
3653 snew(ir->opts.QMmult, nr);
3654 snew(ir->opts.QMcharge, nr);
3655 snew(ir->opts.bSH, nr);
3657 for (i = 0; i < nr; i++)
3659 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3660 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3661 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3664 nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
3665 nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
3666 snew(ir->opts.CASelectrons, nr);
3667 snew(ir->opts.CASorbitals, nr);
3668 for (i = 0; i < nr; i++)
3670 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3671 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3673 /* special optimization options */
3675 nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
3676 nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
3677 snew(ir->opts.bOPT, nr);
3678 snew(ir->opts.bTS, nr);
3679 for (i = 0; i < nr; i++)
3681 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3682 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3684 nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
3685 nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
3686 nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
3687 snew(ir->opts.SAon, nr);
3688 snew(ir->opts.SAoff, nr);
3689 snew(ir->opts.SAsteps, nr);
3691 for (i = 0; i < nr; i++)
3693 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3694 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3695 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3697 /* end of QMMM input */
3701 for (i = 0; (i < egcNR); i++)
3703 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3704 for (j = 0; (j < groups->grps[i].nr); j++)
3706 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3708 fprintf(stderr, "\n");
3712 nr = groups->grps[egcENER].nr;
3713 snew(ir->opts.egp_flags, nr*nr);
3715 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3716 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3718 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3720 if (bExcl && EEL_FULL(ir->coulombtype))
3722 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3725 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3726 if (bTable && !(ir->vdwtype == evdwUSER) &&
3727 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3728 !(ir->coulombtype == eelPMEUSERSWITCH))
3730 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3733 decode_cos(is->efield_x, &(ir->ex[XX]));
3734 decode_cos(is->efield_xt, &(ir->et[XX]));
3735 decode_cos(is->efield_y, &(ir->ex[YY]));
3736 decode_cos(is->efield_yt, &(ir->et[YY]));
3737 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3738 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3742 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3745 for (i = 0; (i < grps->nr); i++)
3757 static void check_disre(gmx_mtop_t *mtop)
3759 gmx_ffparams_t *ffparams;
3760 t_functype *functype;
3762 int i, ndouble, ftype;
3763 int label, old_label;
3765 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3767 ffparams = &mtop->ffparams;
3768 functype = ffparams->functype;
3769 ip = ffparams->iparams;
3772 for (i = 0; i < ffparams->ntypes; i++)
3774 ftype = functype[i];
3775 if (ftype == F_DISRES)
3777 label = ip[i].disres.label;
3778 if (label == old_label)
3780 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3788 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3789 "probably the parameters for multiple pairs in one restraint "
3790 "are not identical\n", ndouble);
3795 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3796 gmx_bool posres_only,
3800 gmx_mtop_ilistloop_t iloop;
3810 for (d = 0; d < DIM; d++)
3812 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3814 /* Check for freeze groups */
3815 for (g = 0; g < ir->opts.ngfrz; g++)
3817 for (d = 0; d < DIM; d++)
3819 if (ir->opts.nFreeze[g][d] != 0)
3827 /* Check for position restraints */
3828 iloop = gmx_mtop_ilistloop_init(sys);
3829 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3832 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3834 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3836 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3837 for (d = 0; d < DIM; d++)
3839 if (pr->posres.fcA[d] != 0)
3845 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3847 /* Check for flat-bottom posres */
3848 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3849 if (pr->fbposres.k != 0)
3851 switch (pr->fbposres.geom)
3853 case efbposresSPHERE:
3854 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3856 case efbposresCYLINDERX:
3857 AbsRef[YY] = AbsRef[ZZ] = 1;
3859 case efbposresCYLINDERY:
3860 AbsRef[XX] = AbsRef[ZZ] = 1;
3862 case efbposresCYLINDER:
3863 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3864 case efbposresCYLINDERZ:
3865 AbsRef[XX] = AbsRef[YY] = 1;
3867 case efbposresX: /* d=XX */
3868 case efbposresY: /* d=YY */
3869 case efbposresZ: /* d=ZZ */
3870 d = pr->fbposres.geom - efbposresX;
3874 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3875 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3883 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3887 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3888 gmx_bool *bC6ParametersWorkWithGeometricRules,
3889 gmx_bool *bC6ParametersWorkWithLBRules,
3890 gmx_bool *bLBRulesPossible)
3892 int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
3895 double geometricdiff, LBdiff;
3896 double c6i, c6j, c12i, c12j;
3897 double c6, c6_geometric, c6_LB;
3898 double sigmai, sigmaj, epsi, epsj;
3899 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3902 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3903 * force-field floating point parameters.
3906 ptr = getenv("GMX_LJCOMB_TOL");
3911 sscanf(ptr, "%lf", &dbl);
3915 *bC6ParametersWorkWithLBRules = TRUE;
3916 *bC6ParametersWorkWithGeometricRules = TRUE;
3917 bCanDoLBRules = TRUE;
3918 bCanDoGeometricRules = TRUE;
3919 ntypes = mtop->ffparams.atnr;
3920 snew(typecount, ntypes);
3921 gmx_mtop_count_atomtypes(mtop, state, typecount);
3922 geometricdiff = LBdiff = 0.0;
3923 *bLBRulesPossible = TRUE;
3924 for (tpi = 0; tpi < ntypes; ++tpi)
3926 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3927 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3928 for (tpj = tpi; tpj < ntypes; ++tpj)
3930 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3931 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3932 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3933 c6_geometric = sqrt(c6i * c6j);
3934 if (!gmx_numzero(c6_geometric))
3936 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3938 sigmai = pow(c12i / c6i, 1.0/6.0);
3939 sigmaj = pow(c12j / c6j, 1.0/6.0);
3940 epsi = c6i * c6i /(4.0 * c12i);
3941 epsj = c6j * c6j /(4.0 * c12j);
3942 c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
3946 *bLBRulesPossible = FALSE;
3947 c6_LB = c6_geometric;
3949 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3952 if (FALSE == bCanDoLBRules)
3954 *bC6ParametersWorkWithLBRules = FALSE;
3957 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3959 if (FALSE == bCanDoGeometricRules)
3961 *bC6ParametersWorkWithGeometricRules = FALSE;
3969 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3973 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3975 check_combination_rule_differences(mtop, 0,
3976 &bC6ParametersWorkWithGeometricRules,
3977 &bC6ParametersWorkWithLBRules,
3979 if (ir->ljpme_combination_rule == eljpmeLB)
3981 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
3983 warning(wi, "You are using arithmetic-geometric combination rules "
3984 "in LJ-PME, but your non-bonded C6 parameters do not "
3985 "follow these rules.");
3990 if (FALSE == bC6ParametersWorkWithGeometricRules)
3992 if (ir->eDispCorr != edispcNO)
3994 warning_note(wi, "You are using geometric combination rules in "
3995 "LJ-PME, but your non-bonded C6 parameters do "
3996 "not follow these rules. "
3997 "This will introduce very small errors in the forces and energies in "
3998 "your simulations. Dispersion correction will correct total energy "
3999 "and/or pressure for isotropic systems, but not forces or surface tensions.");
4003 warning_note(wi, "You are using geometric combination rules in "
4004 "LJ-PME, but your non-bonded C6 parameters do "
4005 "not follow these rules. "
4006 "This will introduce very small errors in the forces and energies in "
4007 "your simulations. If your system is homogeneous, consider using dispersion correction "
4008 "for the total energy and pressure.");
4014 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
4017 char err_buf[STRLEN];
4018 int i, m, c, nmol, npct;
4019 gmx_bool bCharge, bAcc;
4020 real gdt_max, *mgrp, mt;
4022 gmx_mtop_atomloop_block_t aloopb;
4023 gmx_mtop_atomloop_all_t aloop;
4026 char warn_buf[STRLEN];
4028 set_warning_line(wi, mdparin, -1);
4030 if (ir->cutoff_scheme == ecutsVERLET &&
4031 ir->verletbuf_tol > 0 &&
4033 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
4034 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4036 /* Check if a too small Verlet buffer might potentially
4037 * cause more drift than the thermostat can couple off.
4039 /* Temperature error fraction for warning and suggestion */
4040 const real T_error_warn = 0.002;
4041 const real T_error_suggest = 0.001;
4042 /* For safety: 2 DOF per atom (typical with constraints) */
4043 const real nrdf_at = 2;
4044 real T, tau, max_T_error;
4049 for (i = 0; i < ir->opts.ngtc; i++)
4051 T = max(T, ir->opts.ref_t[i]);
4052 tau = max(tau, ir->opts.tau_t[i]);
4056 /* This is a worst case estimate of the temperature error,
4057 * assuming perfect buffer estimation and no cancelation
4058 * of errors. The factor 0.5 is because energy distributes
4059 * equally over Ekin and Epot.
4061 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4062 if (max_T_error > T_error_warn)
4064 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.",
4065 ir->verletbuf_tol, T, tau,
4067 100*T_error_suggest,
4068 ir->verletbuf_tol*T_error_suggest/max_T_error);
4069 warning(wi, warn_buf);
4074 if (ETC_ANDERSEN(ir->etc))
4078 for (i = 0; i < ir->opts.ngtc; i++)
4080 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4081 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4082 sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
4083 i, ir->opts.tau_t[i]);
4084 CHECK(ir->opts.tau_t[i] < 0);
4087 for (i = 0; i < ir->opts.ngtc; i++)
4089 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
4090 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);
4091 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
4095 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4096 ir->comm_mode == ecmNO &&
4097 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4098 !ETC_ANDERSEN(ir->etc))
4100 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");
4103 /* Check for pressure coupling with absolute position restraints */
4104 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4106 absolute_reference(ir, sys, TRUE, AbsRef);
4108 for (m = 0; m < DIM; m++)
4110 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4112 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4120 aloopb = gmx_mtop_atomloop_block_init(sys);
4121 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4123 if (atom->q != 0 || atom->qB != 0)
4131 if (EEL_FULL(ir->coulombtype))
4134 "You are using full electrostatics treatment %s for a system without charges.\n"
4135 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4136 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4137 warning(wi, err_buf);
4142 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4145 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4146 "You might want to consider using %s electrostatics.\n",
4148 warning_note(wi, err_buf);
4152 /* Check if combination rules used in LJ-PME are the same as in the force field */
4153 if (EVDW_PME(ir->vdwtype))
4155 check_combination_rules(ir, sys, wi);
4158 /* Generalized reaction field */
4159 if (ir->opts.ngtc == 0)
4161 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4163 CHECK(ir->coulombtype == eelGRF);
4167 sprintf(err_buf, "When using coulombtype = %s"
4168 " ref-t for temperature coupling should be > 0",
4170 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4173 if (ir->eI == eiSD2)
4175 sprintf(warn_buf, "The stochastic dynamics integrator %s is deprecated, since\n"
4176 "it is slower than integrator %s and is slightly less accurate\n"
4177 "with constraints. Use the %s integrator.",
4178 ei_names[ir->eI], ei_names[eiSD1], ei_names[eiSD1]);
4179 warning_note(wi, warn_buf);
4183 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4185 for (m = 0; (m < DIM); m++)
4187 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4196 snew(mgrp, sys->groups.grps[egcACC].nr);
4197 aloop = gmx_mtop_atomloop_all_init(sys);
4198 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4200 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4203 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4205 for (m = 0; (m < DIM); m++)
4207 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4211 for (m = 0; (m < DIM); m++)
4213 if (fabs(acc[m]) > 1e-6)
4215 const char *dim[DIM] = { "X", "Y", "Z" };
4217 "Net Acceleration in %s direction, will %s be corrected\n",
4218 dim[m], ir->nstcomm != 0 ? "" : "not");
4219 if (ir->nstcomm != 0 && m < ndof_com(ir))
4222 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4224 ir->opts.acc[i][m] -= acc[m];
4232 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4233 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4235 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4238 if (ir->ePull != epullNO)
4240 gmx_bool bPullAbsoluteRef;
4242 bPullAbsoluteRef = FALSE;
4243 for (i = 0; i < ir->pull->ncoord; i++)
4245 bPullAbsoluteRef = bPullAbsoluteRef ||
4246 ir->pull->coord[i].group[0] == 0 ||
4247 ir->pull->coord[i].group[1] == 0;
4249 if (bPullAbsoluteRef)
4251 absolute_reference(ir, sys, FALSE, AbsRef);
4252 for (m = 0; m < DIM; m++)
4254 if (ir->pull->dim[m] && !AbsRef[m])
4256 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.");
4262 if (ir->pull->eGeom == epullgDIRPBC)
4264 for (i = 0; i < 3; i++)
4266 for (m = 0; m <= i; m++)
4268 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4269 ir->deform[i][m] != 0)
4271 for (c = 0; c < ir->pull->ncoord; c++)
4273 if (ir->pull->coord[c].vec[m] != 0)
4275 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->eGeom), 'x'+m);
4287 void double_check(t_inputrec *ir, matrix box,
4288 gmx_bool bHasNormalConstraints,
4289 gmx_bool bHasAnyConstraints,
4294 char warn_buf[STRLEN];
4297 ptr = check_box(ir->ePBC, box);
4300 warning_error(wi, ptr);
4303 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4305 if (ir->shake_tol <= 0.0)
4307 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4309 warning_error(wi, warn_buf);
4312 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
4314 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
4315 if (ir->epc == epcNO)
4317 warning(wi, warn_buf);
4321 warning_error(wi, warn_buf);
4326 if ( (ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4328 /* If we have Lincs constraints: */
4329 if (ir->eI == eiMD && ir->etc == etcNO &&
4330 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4332 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4333 warning_note(wi, warn_buf);
4336 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4338 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4339 warning_note(wi, warn_buf);
4341 if (ir->epc == epcMTTK)
4343 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4347 if (bHasAnyConstraints && ir->epc == epcMTTK)
4349 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4352 if (ir->LincsWarnAngle > 90.0)
4354 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4355 warning(wi, warn_buf);
4356 ir->LincsWarnAngle = 90.0;
4359 if (ir->ePBC != epbcNONE)
4361 if (ir->nstlist == 0)
4363 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4365 bTWIN = (ir->rlistlong > ir->rlist);
4366 if (ir->ns_type == ensGRID)
4368 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
4370 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",
4371 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
4372 warning_error(wi, warn_buf);
4377 min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
4378 if (2*ir->rlistlong >= min_size)
4380 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4381 warning_error(wi, warn_buf);
4384 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4391 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4395 real rvdw1, rvdw2, rcoul1, rcoul2;
4396 char warn_buf[STRLEN];
4398 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4402 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4407 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4413 if (rvdw1 + rvdw2 > ir->rlist ||
4414 rcoul1 + rcoul2 > ir->rlist)
4417 "The sum of the two largest charge group radii (%f) "
4418 "is larger than rlist (%f)\n",
4419 max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4420 warning(wi, warn_buf);
4424 /* Here we do not use the zero at cut-off macro,
4425 * since user defined interactions might purposely
4426 * not be zero at the cut-off.
4428 if (ir_vdw_is_zero_at_cutoff(ir) &&
4429 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
4431 sprintf(warn_buf, "The sum of the two largest charge group "
4432 "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
4433 "With exact cut-offs, better performance can be "
4434 "obtained with cutoff-scheme = %s, because it "
4435 "does not use charge groups at all.",
4437 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4438 ir->rlistlong, ir->rvdw,
4439 ecutscheme_names[ecutsVERLET]);
4442 warning(wi, warn_buf);
4446 warning_note(wi, warn_buf);
4449 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4450 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
4452 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
4453 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4455 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4456 ir->rlistlong, ir->rcoulomb,
4457 ecutscheme_names[ecutsVERLET]);
4460 warning(wi, warn_buf);
4464 warning_note(wi, warn_buf);