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49 #include "gmx_fatal.h"
62 #include "mtop_util.h"
63 #include "chargegroup.h"
65 #include "calc_verletbuf.h"
70 /* Resource parameters
71 * Do not change any of these until you read the instruction
72 * in readinp.h. Some cpp's do not take spaces after the backslash
73 * (like the c-shell), which will give you a very weird compiler
77 typedef struct t_inputrec_strings
79 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN],
80 acc[STRLEN], accgrps[STRLEN], freeze[STRLEN], frdim[STRLEN],
81 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
82 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
83 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN];
84 char fep_lambda[efptNR][STRLEN];
85 char lambda_weights[STRLEN];
88 char anneal[STRLEN], anneal_npoints[STRLEN],
89 anneal_time[STRLEN], anneal_temp[STRLEN];
90 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
91 bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
92 SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
93 char efield_x[STRLEN], efield_xt[STRLEN], efield_y[STRLEN],
94 efield_yt[STRLEN], efield_z[STRLEN], efield_zt[STRLEN];
96 } gmx_inputrec_strings;
98 static gmx_inputrec_strings *is = NULL;
100 void init_inputrec_strings()
104 gmx_incons("Attempted to call init_inputrec_strings before calling done_inputrec_strings. Only one inputrec (i.e. .mdp file) can be parsed at a time.");
109 void done_inputrec_strings()
115 static char swapgrp[STRLEN], splitgrp0[STRLEN], splitgrp1[STRLEN], solgrp[STRLEN];
118 egrptpALL, /* All particles have to be a member of a group. */
119 egrptpALL_GENREST, /* A rest group with name is generated for particles *
120 * that are not part of any group. */
121 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
122 * for the rest group. */
123 egrptpONE /* Merge all selected groups into one group, *
124 * make a rest group for the remaining particles. */
127 static const char *constraints[eshNR+1] = {
128 "none", "h-bonds", "all-bonds", "h-angles", "all-angles", NULL
131 static const char *couple_lam[ecouplamNR+1] = {
132 "vdw-q", "vdw", "q", "none", NULL
135 void init_ir(t_inputrec *ir, t_gromppopts *opts)
137 snew(opts->include, STRLEN);
138 snew(opts->define, STRLEN);
139 snew(ir->fepvals, 1);
140 snew(ir->expandedvals, 1);
141 snew(ir->simtempvals, 1);
144 static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
149 for (i = 0; i < ntemps; i++)
151 /* simple linear scaling -- allows more control */
152 if (simtemp->eSimTempScale == esimtempLINEAR)
154 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*temperature_lambdas[i];
156 else if (simtemp->eSimTempScale == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
158 simtemp->temperatures[i] = simtemp->simtemp_low * pow(simtemp->simtemp_high/simtemp->simtemp_low, (1.0*i)/(ntemps-1));
160 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
162 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*((exp(temperature_lambdas[i])-1)/(exp(1.0)-1));
167 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
168 gmx_fatal(FARGS, errorstr);
175 static void _low_check(gmx_bool b, char *s, warninp_t wi)
179 warning_error(wi, s);
183 static void check_nst(const char *desc_nst, int nst,
184 const char *desc_p, int *p,
189 if (*p > 0 && *p % nst != 0)
191 /* Round up to the next multiple of nst */
192 *p = ((*p)/nst + 1)*nst;
193 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n",
194 desc_p, desc_nst, desc_p, *p);
199 static gmx_bool ir_NVE(const t_inputrec *ir)
201 return ((ir->eI == eiMD || EI_VV(ir->eI)) && ir->etc == etcNO);
204 static int lcd(int n1, int n2)
209 for (i = 2; (i <= n1 && i <= n2); i++)
211 if (n1 % i == 0 && n2 % i == 0)
220 static void process_interaction_modifier(const t_inputrec *ir, int *eintmod)
222 if (*eintmod == eintmodPOTSHIFT_VERLET)
224 if (ir->cutoff_scheme == ecutsVERLET)
226 *eintmod = eintmodPOTSHIFT;
230 *eintmod = eintmodNONE;
235 void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
237 /* Check internal consistency */
239 /* Strange macro: first one fills the err_buf, and then one can check
240 * the condition, which will print the message and increase the error
243 #define CHECK(b) _low_check(b, err_buf, wi)
244 char err_buf[256], warn_buf[STRLEN];
250 t_lambda *fep = ir->fepvals;
251 t_expanded *expand = ir->expandedvals;
253 set_warning_line(wi, mdparin, -1);
255 /* BASIC CUT-OFF STUFF */
256 if (ir->rcoulomb < 0)
258 warning_error(wi, "rcoulomb should be >= 0");
262 warning_error(wi, "rvdw should be >= 0");
265 !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
267 warning_error(wi, "rlist should be >= 0");
270 process_interaction_modifier(ir, &ir->coulomb_modifier);
271 process_interaction_modifier(ir, &ir->vdw_modifier);
273 if (ir->cutoff_scheme == ecutsGROUP)
275 /* BASIC CUT-OFF STUFF */
276 if (ir->rlist == 0 ||
277 !((EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > ir->rlist) ||
278 (EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && ir->rvdw > ir->rlist)))
280 /* No switched potential and/or no twin-range:
281 * we can set the long-range cut-off to the maximum of the other cut-offs.
283 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
285 else if (ir->rlistlong < 0)
287 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
288 sprintf(warn_buf, "rlistlong was not set, setting it to %g (no buffer)",
290 warning(wi, warn_buf);
292 if (ir->rlistlong == 0 && ir->ePBC != epbcNONE)
294 warning_error(wi, "Can not have an infinite cut-off with PBC");
296 if (ir->rlistlong > 0 && (ir->rlist == 0 || ir->rlistlong < ir->rlist))
298 warning_error(wi, "rlistlong can not be shorter than rlist");
300 if (IR_TWINRANGE(*ir) && ir->nstlist <= 0)
302 warning_error(wi, "Can not have nstlist<=0 with twin-range interactions");
306 if (ir->rlistlong == ir->rlist)
310 else if (ir->rlistlong > ir->rlist && ir->nstcalclr == 0)
312 warning_error(wi, "With different cutoffs for electrostatics and VdW, nstcalclr must be -1 or a positive number");
315 if (ir->cutoff_scheme == ecutsVERLET)
319 /* Normal Verlet type neighbor-list, currently only limited feature support */
320 if (inputrec2nboundeddim(ir) < 3)
322 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
324 if (ir->rcoulomb != ir->rvdw)
326 warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported");
328 if (ir->vdwtype != evdwCUT)
330 warning_error(wi, "With Verlet lists only cut-off LJ interactions are supported");
332 if (!(ir->coulombtype == eelCUT ||
333 (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC) ||
334 EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
336 warning_error(wi, "With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
339 if (ir->nstlist <= 0)
341 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
344 if (ir->nstlist < 10)
346 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.");
349 rc_max = max(ir->rvdw, ir->rcoulomb);
351 if (ir->verletbuf_tol <= 0)
353 if (ir->verletbuf_tol == 0)
355 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
358 if (ir->rlist < rc_max)
360 warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
363 if (ir->rlist == rc_max && ir->nstlist > 1)
365 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.");
370 if (ir->rlist > rc_max)
372 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.");
375 if (ir->nstlist == 1)
377 /* No buffer required */
382 if (EI_DYNAMICS(ir->eI))
384 if (inputrec2nboundeddim(ir) < 3)
386 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.");
388 /* Set rlist temporarily so we can continue processing */
393 /* Set the buffer to 5% of the cut-off */
394 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
399 /* No twin-range calculations with Verlet lists */
400 ir->rlistlong = ir->rlist;
403 if (ir->nstcalclr == -1)
405 /* if rlist=rlistlong, this will later be changed to nstcalclr=0 */
406 ir->nstcalclr = ir->nstlist;
408 else if (ir->nstcalclr > 0)
410 if (ir->nstlist > 0 && (ir->nstlist % ir->nstcalclr != 0))
412 warning_error(wi, "nstlist must be evenly divisible by nstcalclr. Use nstcalclr = -1 to automatically follow nstlist");
415 else if (ir->nstcalclr < -1)
417 warning_error(wi, "nstcalclr must be a positive number (divisor of nstcalclr), or -1 to follow nstlist.");
420 if (EEL_PME(ir->coulombtype) && ir->rcoulomb > ir->rvdw && ir->nstcalclr > 1)
422 warning_error(wi, "When used with PME, the long-range component of twin-range interactions must be updated every step (nstcalclr)");
425 /* GENERAL INTEGRATOR STUFF */
426 if (!(ir->eI == eiMD || EI_VV(ir->eI)))
430 if (ir->eI == eiVVAK)
432 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]);
433 warning_note(wi, warn_buf);
435 if (!EI_DYNAMICS(ir->eI))
439 if (EI_DYNAMICS(ir->eI))
441 if (ir->nstcalcenergy < 0)
443 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
444 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
446 /* nstcalcenergy larger than nstener does not make sense.
447 * We ideally want nstcalcenergy=nstener.
451 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
455 ir->nstcalcenergy = ir->nstenergy;
459 else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
460 (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
461 (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
464 const char *nsten = "nstenergy";
465 const char *nstdh = "nstdhdl";
466 const char *min_name = nsten;
467 int min_nst = ir->nstenergy;
469 /* find the smallest of ( nstenergy, nstdhdl ) */
470 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
471 (ir->fepvals->nstdhdl < ir->nstenergy) )
473 min_nst = ir->fepvals->nstdhdl;
476 /* If the user sets nstenergy small, we should respect that */
478 "Setting nstcalcenergy (%d) equal to %s (%d)",
479 ir->nstcalcenergy, min_name, min_nst);
480 warning_note(wi, warn_buf);
481 ir->nstcalcenergy = min_nst;
484 if (ir->epc != epcNO)
486 if (ir->nstpcouple < 0)
488 ir->nstpcouple = ir_optimal_nstpcouple(ir);
491 if (IR_TWINRANGE(*ir))
493 check_nst("nstlist", ir->nstlist,
494 "nstcalcenergy", &ir->nstcalcenergy, wi);
495 if (ir->epc != epcNO)
497 check_nst("nstlist", ir->nstlist,
498 "nstpcouple", &ir->nstpcouple, wi);
502 if (ir->nstcalcenergy > 0)
504 if (ir->efep != efepNO)
506 /* nstdhdl should be a multiple of nstcalcenergy */
507 check_nst("nstcalcenergy", ir->nstcalcenergy,
508 "nstdhdl", &ir->fepvals->nstdhdl, wi);
509 /* nstexpanded should be a multiple of nstcalcenergy */
510 check_nst("nstcalcenergy", ir->nstcalcenergy,
511 "nstexpanded", &ir->expandedvals->nstexpanded, wi);
513 /* for storing exact averages nstenergy should be
514 * a multiple of nstcalcenergy
516 check_nst("nstcalcenergy", ir->nstcalcenergy,
517 "nstenergy", &ir->nstenergy, wi);
522 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
523 ir->bContinuation && ir->ld_seed != -1)
525 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)");
531 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
532 CHECK(ir->ePBC != epbcXYZ);
533 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
534 CHECK(ir->ns_type != ensGRID);
535 sprintf(err_buf, "with TPI nstlist should be larger than zero");
536 CHECK(ir->nstlist <= 0);
537 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
538 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
542 if ( (opts->nshake > 0) && (opts->bMorse) )
545 "Using morse bond-potentials while constraining bonds is useless");
546 warning(wi, warn_buf);
549 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
550 ir->bContinuation && ir->ld_seed != -1)
552 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)");
554 /* verify simulated tempering options */
558 gmx_bool bAllTempZero = TRUE;
559 for (i = 0; i < fep->n_lambda; i++)
561 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]);
562 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
563 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
565 bAllTempZero = FALSE;
568 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
569 CHECK(bAllTempZero == TRUE);
571 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
572 CHECK(ir->eI != eiVV);
574 /* check compatability of the temperature coupling with simulated tempering */
576 if (ir->etc == etcNOSEHOOVER)
578 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
579 warning_note(wi, warn_buf);
582 /* check that the temperatures make sense */
584 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);
585 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
587 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
588 CHECK(ir->simtempvals->simtemp_high <= 0);
590 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
591 CHECK(ir->simtempvals->simtemp_low <= 0);
594 /* verify free energy options */
596 if (ir->efep != efepNO)
599 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
601 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
603 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
604 (int)fep->sc_r_power);
605 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
607 sprintf(err_buf, "Can't use postive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
608 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
610 sprintf(err_buf, "Can't use postive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
611 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
613 sprintf(err_buf, "Can only use expanded ensemble with md-vv for now; should be supported for other integrators in 5.0");
614 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
616 sprintf(err_buf, "Free-energy not implemented for Ewald");
617 CHECK(ir->coulombtype == eelEWALD);
619 /* check validty of lambda inputs */
620 if (fep->n_lambda == 0)
622 /* Clear output in case of no states:*/
623 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
624 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
628 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
629 CHECK((fep->init_fep_state >= fep->n_lambda));
632 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
633 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
635 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",
636 fep->init_lambda, fep->init_fep_state);
637 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
641 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
645 for (i = 0; i < efptNR; i++)
647 if (fep->separate_dvdl[i])
652 if (n_lambda_terms > 1)
654 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.");
655 warning(wi, warn_buf);
658 if (n_lambda_terms < 2 && fep->n_lambda > 0)
661 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
665 for (j = 0; j < efptNR; j++)
667 for (i = 0; i < fep->n_lambda; i++)
669 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]);
670 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
674 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
676 for (i = 0; i < fep->n_lambda; i++)
678 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],
679 fep->all_lambda[efptCOUL][i]);
680 CHECK((fep->sc_alpha > 0) &&
681 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
682 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
683 ((fep->all_lambda[efptVDW][i] > 0.0) &&
684 (fep->all_lambda[efptVDW][i] < 1.0))));
688 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
690 real sigma, lambda, r_sc;
693 /* Maximum estimate for A and B charges equal with lambda power 1 */
695 r_sc = pow(lambda*fep->sc_alpha*pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
696 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.",
698 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
699 warning_note(wi, warn_buf);
702 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
703 be treated differently, but that's the next step */
705 for (i = 0; i < efptNR; i++)
707 for (j = 0; j < fep->n_lambda; j++)
709 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
710 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
715 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
718 expand = ir->expandedvals;
720 /* checking equilibration of weights inputs for validity */
722 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
723 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
724 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
726 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
727 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
728 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
730 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
731 expand->equil_steps, elmceq_names[elmceqSTEPS]);
732 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
734 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
735 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
736 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
738 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
739 expand->equil_ratio, elmceq_names[elmceqRATIO]);
740 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
742 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
743 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
744 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
746 sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
747 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
748 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
750 sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
751 expand->equil_steps, elmceq_names[elmceqSTEPS]);
752 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
754 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
755 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
756 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
758 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
759 expand->equil_ratio, elmceq_names[elmceqRATIO]);
760 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
762 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
763 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
764 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
766 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
767 CHECK((expand->lmc_repeats <= 0));
768 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
769 CHECK((expand->minvarmin <= 0));
770 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
771 CHECK((expand->c_range < 0));
772 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
773 fep->init_fep_state, expand->lmc_forced_nstart);
774 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
775 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
776 CHECK((expand->lmc_forced_nstart < 0));
777 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
778 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
780 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
781 CHECK((expand->init_wl_delta < 0));
782 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
783 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
784 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
785 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
787 /* if there is no temperature control, we need to specify an MC temperature */
788 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
789 if (expand->nstTij > 0)
791 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
792 expand->nstTij, ir->nstlog);
793 CHECK((mod(expand->nstTij, ir->nstlog) != 0));
798 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
799 CHECK(ir->nwall && ir->ePBC != epbcXY);
802 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
804 if (ir->ePBC == epbcNONE)
806 if (ir->epc != epcNO)
808 warning(wi, "Turning off pressure coupling for vacuum system");
814 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
815 epbc_names[ir->ePBC]);
816 CHECK(ir->epc != epcNO);
818 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
819 CHECK(EEL_FULL(ir->coulombtype));
821 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
822 epbc_names[ir->ePBC]);
823 CHECK(ir->eDispCorr != edispcNO);
826 if (ir->rlist == 0.0)
828 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
829 "with coulombtype = %s or coulombtype = %s\n"
830 "without periodic boundary conditions (pbc = %s) and\n"
831 "rcoulomb and rvdw set to zero",
832 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
833 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
834 (ir->ePBC != epbcNONE) ||
835 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
839 warning_error(wi, "Can not have heuristic neighborlist updates without cut-off");
843 warning_note(wi, "Simulating without cut-offs is usually (slightly) faster with nstlist=0, nstype=simple and particle decomposition");
848 if (ir->nstcomm == 0)
850 ir->comm_mode = ecmNO;
852 if (ir->comm_mode != ecmNO)
856 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");
857 ir->nstcomm = abs(ir->nstcomm);
860 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
862 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
863 ir->nstcomm = ir->nstcalcenergy;
866 if (ir->comm_mode == ecmANGULAR)
868 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
869 CHECK(ir->bPeriodicMols);
870 if (ir->ePBC != epbcNONE)
872 warning(wi, "Removing the rotation around the center of mass in a periodic system (this is not a problem when you have only one molecule).");
877 if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
879 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.");
882 sprintf(err_buf, "Twin-range neighbour searching (NS) with simple NS"
883 " algorithm not implemented");
884 CHECK(((ir->rcoulomb > ir->rlist) || (ir->rvdw > ir->rlist))
885 && (ir->ns_type == ensSIMPLE));
887 /* TEMPERATURE COUPLING */
888 if (ir->etc == etcYES)
890 ir->etc = etcBERENDSEN;
891 warning_note(wi, "Old option for temperature coupling given: "
892 "changing \"yes\" to \"Berendsen\"\n");
895 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
897 if (ir->opts.nhchainlength < 1)
899 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
900 ir->opts.nhchainlength = 1;
901 warning(wi, warn_buf);
904 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
906 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
907 ir->opts.nhchainlength = 1;
912 ir->opts.nhchainlength = 0;
915 if (ir->eI == eiVVAK)
917 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
919 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
922 if (ETC_ANDERSEN(ir->etc))
924 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
925 CHECK(!(EI_VV(ir->eI)));
927 for (i = 0; i < ir->opts.ngtc; i++)
929 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
930 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
931 sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
932 i, ir->opts.tau_t[i]);
933 CHECK(ir->opts.tau_t[i] < 0);
935 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
937 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]);
938 warning_note(wi, warn_buf);
941 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]);
942 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
944 for (i = 0; i < ir->opts.ngtc; i++)
946 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
947 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);
948 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
951 if (ir->etc == etcBERENDSEN)
953 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
954 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
955 warning_note(wi, warn_buf);
958 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
959 && ir->epc == epcBERENDSEN)
961 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
962 "true ensemble for the thermostat");
963 warning(wi, warn_buf);
966 /* PRESSURE COUPLING */
967 if (ir->epc == epcISOTROPIC)
969 ir->epc = epcBERENDSEN;
970 warning_note(wi, "Old option for pressure coupling given: "
971 "changing \"Isotropic\" to \"Berendsen\"\n");
974 if (ir->epc != epcNO)
976 dt_pcoupl = ir->nstpcouple*ir->delta_t;
978 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
979 CHECK(ir->tau_p <= 0);
981 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc))
983 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
984 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
985 warning(wi, warn_buf);
988 sprintf(err_buf, "compressibility must be > 0 when using pressure"
989 " coupling %s\n", EPCOUPLTYPE(ir->epc));
990 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
991 ir->compress[ZZ][ZZ] < 0 ||
992 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
993 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
995 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
998 "You are generating velocities so I am assuming you "
999 "are equilibrating a system. You are using "
1000 "%s pressure coupling, but this can be "
1001 "unstable for equilibration. If your system crashes, try "
1002 "equilibrating first with Berendsen pressure coupling. If "
1003 "you are not equilibrating the system, you can probably "
1004 "ignore this warning.",
1005 epcoupl_names[ir->epc]);
1006 warning(wi, warn_buf);
1012 if (ir->epc > epcNO)
1014 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1016 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.");
1021 /* ELECTROSTATICS */
1022 /* More checks are in triple check (grompp.c) */
1024 if (ir->coulombtype == eelSWITCH)
1026 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1027 "artifacts, advice: use coulombtype = %s",
1028 eel_names[ir->coulombtype],
1029 eel_names[eelRF_ZERO]);
1030 warning(wi, warn_buf);
1033 if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
1035 sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
1036 warning_note(wi, warn_buf);
1039 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1041 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);
1042 warning(wi, warn_buf);
1043 ir->epsilon_rf = ir->epsilon_r;
1044 ir->epsilon_r = 1.0;
1047 if (getenv("GALACTIC_DYNAMICS") == NULL)
1049 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1050 CHECK(ir->epsilon_r < 0);
1053 if (EEL_RF(ir->coulombtype))
1055 /* reaction field (at the cut-off) */
1057 if (ir->coulombtype == eelRF_ZERO)
1059 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1060 eel_names[ir->coulombtype]);
1061 CHECK(ir->epsilon_rf != 0);
1062 ir->epsilon_rf = 0.0;
1065 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1066 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1067 (ir->epsilon_r == 0));
1068 if (ir->epsilon_rf == ir->epsilon_r)
1070 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1071 eel_names[ir->coulombtype]);
1072 warning(wi, warn_buf);
1075 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1076 * means the interaction is zero outside rcoulomb, but it helps to
1077 * provide accurate energy conservation.
1079 if (EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype))
1081 if (EEL_SWITCHED(ir->coulombtype))
1084 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1085 eel_names[ir->coulombtype]);
1086 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1089 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1091 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1093 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1094 eel_names[ir->coulombtype]);
1095 CHECK(ir->rlist > ir->rcoulomb);
1099 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1100 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1103 "The switch/shift interaction settings are just for compatibility; you will get better "
1104 "performance from applying potential modifiers to your interactions!\n");
1105 warning_note(wi, warn_buf);
1108 if (ir->coulombtype == eelPMESWITCH)
1110 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1112 sprintf(warn_buf, "The switching range for %s should be 5%% or less, energy conservation will be good anyhow, since ewald_rtol = %g",
1113 eel_names[ir->coulombtype],
1115 warning(wi, warn_buf);
1119 if (EEL_FULL(ir->coulombtype))
1121 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1122 ir->coulombtype == eelPMEUSERSWITCH)
1124 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1125 eel_names[ir->coulombtype]);
1126 CHECK(ir->rcoulomb > ir->rlist);
1128 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1130 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1133 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
1134 "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
1135 "a potential modifier.", eel_names[ir->coulombtype]);
1136 if (ir->nstcalclr == 1)
1138 CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
1142 CHECK(ir->rcoulomb != ir->rlist);
1148 if (EVDW_PME(ir->vdwtype))
1150 if (EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype))
1152 sprintf(err_buf, "With vdwtype = %s, rvdw must be <= rlist",
1153 evdw_names[ir->vdwtype]);
1154 CHECK(ir->rvdw > ir->rlist);
1159 "With vdwtype = %s, rvdw must be equal to rlist\n",
1160 evdw_names[ir->vdwtype]);
1161 CHECK(ir->rvdw != ir->rlist);
1165 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1167 if (ir->pme_order < 3)
1169 warning_error(wi, "pme-order can not be smaller than 3");
1173 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1175 if (ir->ewald_geometry == eewg3D)
1177 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1178 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1179 warning(wi, warn_buf);
1181 /* This check avoids extra pbc coding for exclusion corrections */
1182 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1183 CHECK(ir->wall_ewald_zfac < 2);
1186 if (EVDW_SWITCHED(ir->vdwtype))
1188 sprintf(err_buf, "With vdwtype = %s rvdw-switch must be < rvdw. Or, better - use a potential modifier.",
1189 evdw_names[ir->vdwtype]);
1190 CHECK(ir->rvdw_switch >= ir->rvdw);
1192 else if (ir->vdwtype == evdwCUT)
1194 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1196 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1197 CHECK(ir->rlist > ir->rvdw);
1200 if (ir->cutoff_scheme == ecutsGROUP)
1202 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1203 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)) &&
1206 warning_note(wi, "With exact cut-offs, rlist should be "
1207 "larger than rcoulomb and rvdw, so that there "
1208 "is a buffer region for particle motion "
1209 "between neighborsearch steps");
1212 if (EEL_IS_ZERO_AT_CUTOFF(ir->coulombtype)
1213 && (ir->rlistlong <= ir->rcoulomb))
1215 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
1216 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1217 warning_note(wi, warn_buf);
1219 if (EVDW_SWITCHED(ir->vdwtype) && (ir->rlistlong <= ir->rvdw))
1221 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
1222 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1223 warning_note(wi, warn_buf);
1227 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1229 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.");
1232 if (ir->nstlist == -1)
1234 sprintf(err_buf, "With nstlist=-1 rvdw and rcoulomb should be smaller than rlist to account for diffusion and possibly charge-group radii");
1235 CHECK(ir->rvdw >= ir->rlist || ir->rcoulomb >= ir->rlist);
1237 sprintf(err_buf, "nstlist can not be smaller than -1");
1238 CHECK(ir->nstlist < -1);
1240 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1243 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1246 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1248 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1251 /* ENERGY CONSERVATION */
1252 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1254 if (!EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1256 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1257 evdw_names[evdwSHIFT]);
1258 warning_note(wi, warn_buf);
1260 if (!EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > 0 && ir->coulomb_modifier == eintmodNONE)
1262 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1263 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1264 warning_note(wi, warn_buf);
1268 /* IMPLICIT SOLVENT */
1269 if (ir->coulombtype == eelGB_NOTUSED)
1271 ir->coulombtype = eelCUT;
1272 ir->implicit_solvent = eisGBSA;
1273 fprintf(stderr, "Note: Old option for generalized born electrostatics given:\n"
1274 "Changing coulombtype from \"generalized-born\" to \"cut-off\" and instead\n"
1275 "setting implicit-solvent value to \"GBSA\" in input section.\n");
1278 if (ir->sa_algorithm == esaSTILL)
1280 sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
1281 CHECK(ir->sa_algorithm == esaSTILL);
1284 if (ir->implicit_solvent == eisGBSA)
1286 sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
1287 CHECK(ir->rgbradii != ir->rlist);
1289 if (ir->coulombtype != eelCUT)
1291 sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
1292 CHECK(ir->coulombtype != eelCUT);
1294 if (ir->vdwtype != evdwCUT)
1296 sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
1297 CHECK(ir->vdwtype != evdwCUT);
1299 if (ir->nstgbradii < 1)
1301 sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
1302 warning_note(wi, warn_buf);
1305 if (ir->sa_algorithm == esaNO)
1307 sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
1308 warning_note(wi, warn_buf);
1310 if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
1312 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");
1313 warning_note(wi, warn_buf);
1315 if (ir->gb_algorithm == egbSTILL)
1317 ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
1321 ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
1324 if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
1326 sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
1327 CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
1334 if (ir->cutoff_scheme != ecutsGROUP)
1336 warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
1340 warning_error(wi, "AdresS simulation supports only stochastic dynamics");
1342 if (ir->epc != epcNO)
1344 warning_error(wi, "AdresS simulation does not support pressure coupling");
1346 if (EEL_FULL(ir->coulombtype))
1348 warning_error(wi, "AdresS simulation does not support long-range electrostatics");
1353 /* count the number of text elemets separated by whitespace in a string.
1354 str = the input string
1355 maxptr = the maximum number of allowed elements
1356 ptr = the output array of pointers to the first character of each element
1357 returns: the number of elements. */
1358 int str_nelem(const char *str, int maxptr, char *ptr[])
1363 copy0 = strdup(str);
1366 while (*copy != '\0')
1370 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1378 while ((*copy != '\0') && !isspace(*copy))
1397 /* interpret a number of doubles from a string and put them in an array,
1398 after allocating space for them.
1399 str = the input string
1400 n = the (pre-allocated) number of doubles read
1401 r = the output array of doubles. */
1402 static void parse_n_real(char *str, int *n, real **r)
1407 *n = str_nelem(str, MAXPTR, ptr);
1410 for (i = 0; i < *n; i++)
1412 (*r)[i] = strtod(ptr[i], NULL);
1416 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
1419 int i, j, max_n_lambda, nweights, nfep[efptNR];
1420 t_lambda *fep = ir->fepvals;
1421 t_expanded *expand = ir->expandedvals;
1422 real **count_fep_lambdas;
1423 gmx_bool bOneLambda = TRUE;
1425 snew(count_fep_lambdas, efptNR);
1427 /* FEP input processing */
1428 /* first, identify the number of lambda values for each type.
1429 All that are nonzero must have the same number */
1431 for (i = 0; i < efptNR; i++)
1433 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
1436 /* now, determine the number of components. All must be either zero, or equal. */
1439 for (i = 0; i < efptNR; i++)
1441 if (nfep[i] > max_n_lambda)
1443 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1444 must have the same number if its not zero.*/
1449 for (i = 0; i < efptNR; i++)
1453 ir->fepvals->separate_dvdl[i] = FALSE;
1455 else if (nfep[i] == max_n_lambda)
1457 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1458 respect to the temperature currently */
1460 ir->fepvals->separate_dvdl[i] = TRUE;
1465 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1466 nfep[i], efpt_names[i], max_n_lambda);
1469 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1470 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1472 /* the number of lambdas is the number we've read in, which is either zero
1473 or the same for all */
1474 fep->n_lambda = max_n_lambda;
1476 /* allocate space for the array of lambda values */
1477 snew(fep->all_lambda, efptNR);
1478 /* if init_lambda is defined, we need to set lambda */
1479 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1481 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1483 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1484 for (i = 0; i < efptNR; i++)
1486 snew(fep->all_lambda[i], fep->n_lambda);
1487 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1490 for (j = 0; j < fep->n_lambda; j++)
1492 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1494 sfree(count_fep_lambdas[i]);
1497 sfree(count_fep_lambdas);
1499 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1500 bookkeeping -- for now, init_lambda */
1502 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1504 for (i = 0; i < fep->n_lambda; i++)
1506 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1510 /* check to see if only a single component lambda is defined, and soft core is defined.
1511 In this case, turn on coulomb soft core */
1513 if (max_n_lambda == 0)
1519 for (i = 0; i < efptNR; i++)
1521 if ((nfep[i] != 0) && (i != efptFEP))
1527 if ((bOneLambda) && (fep->sc_alpha > 0))
1529 fep->bScCoul = TRUE;
1532 /* Fill in the others with the efptFEP if they are not explicitly
1533 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1534 they are all zero. */
1536 for (i = 0; i < efptNR; i++)
1538 if ((nfep[i] == 0) && (i != efptFEP))
1540 for (j = 0; j < fep->n_lambda; j++)
1542 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1548 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1549 if (fep->sc_r_power == 48)
1551 if (fep->sc_alpha > 0.1)
1553 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1557 expand = ir->expandedvals;
1558 /* now read in the weights */
1559 parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
1562 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1564 else if (nweights != fep->n_lambda)
1566 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1567 nweights, fep->n_lambda);
1569 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1571 expand->nstexpanded = fep->nstdhdl;
1572 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1574 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1576 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1577 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1578 2*tau_t just to be careful so it's not to frequent */
1583 static void do_simtemp_params(t_inputrec *ir)
1586 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1587 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1592 static void do_wall_params(t_inputrec *ir,
1593 char *wall_atomtype, char *wall_density,
1597 char *names[MAXPTR];
1600 opts->wall_atomtype[0] = NULL;
1601 opts->wall_atomtype[1] = NULL;
1603 ir->wall_atomtype[0] = -1;
1604 ir->wall_atomtype[1] = -1;
1605 ir->wall_density[0] = 0;
1606 ir->wall_density[1] = 0;
1610 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1611 if (nstr != ir->nwall)
1613 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1616 for (i = 0; i < ir->nwall; i++)
1618 opts->wall_atomtype[i] = strdup(names[i]);
1621 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1623 nstr = str_nelem(wall_density, MAXPTR, names);
1624 if (nstr != ir->nwall)
1626 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1628 for (i = 0; i < ir->nwall; i++)
1630 sscanf(names[i], "%lf", &dbl);
1633 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1635 ir->wall_density[i] = dbl;
1641 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1649 srenew(groups->grpname, groups->ngrpname+nwall);
1650 grps = &(groups->grps[egcENER]);
1651 srenew(grps->nm_ind, grps->nr+nwall);
1652 for (i = 0; i < nwall; i++)
1654 sprintf(str, "wall%d", i);
1655 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1656 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1661 void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1662 t_expanded *expand, warninp_t wi)
1664 int ninp, nerror = 0;
1670 /* read expanded ensemble parameters */
1671 CCTYPE ("expanded ensemble variables");
1672 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1673 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1674 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1675 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1676 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1677 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1678 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1679 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1680 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1681 CCTYPE("Seed for Monte Carlo in lambda space");
1682 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1683 RTYPE ("mc-temperature", expand->mc_temp, -1);
1684 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1685 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1686 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1687 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1688 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1689 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1690 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1691 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1692 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1693 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1694 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
1702 void get_ir(const char *mdparin, const char *mdparout,
1703 t_inputrec *ir, t_gromppopts *opts,
1707 double dumdub[2][6];
1711 char warn_buf[STRLEN];
1712 t_lambda *fep = ir->fepvals;
1713 t_expanded *expand = ir->expandedvals;
1715 init_inputrec_strings();
1716 inp = read_inpfile(mdparin, &ninp, wi);
1718 snew(dumstr[0], STRLEN);
1719 snew(dumstr[1], STRLEN);
1721 if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
1724 "%s did not specify a value for the .mdp option "
1725 "\"cutoff-scheme\". Probably it was first intended for use "
1726 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1727 "introduced, but the group scheme was still the default. "
1728 "The default is now the Verlet scheme, so you will observe "
1729 "different behaviour.", mdparin);
1730 warning_note(wi, warn_buf);
1733 /* remove the following deprecated commands */
1736 REM_TYPE("domain-decomposition");
1737 REM_TYPE("andersen-seed");
1739 REM_TYPE("dihre-fc");
1740 REM_TYPE("dihre-tau");
1741 REM_TYPE("nstdihreout");
1742 REM_TYPE("nstcheckpoint");
1744 /* replace the following commands with the clearer new versions*/
1745 REPL_TYPE("unconstrained-start", "continuation");
1746 REPL_TYPE("foreign-lambda", "fep-lambdas");
1747 REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
1748 REPL_TYPE("nstxtcout", "nstxout-compressed");
1749 REPL_TYPE("xtc-grps", "compressed-x-grps");
1750 REPL_TYPE("xtc-precision", "compressed-x-precision");
1752 CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
1753 CTYPE ("Preprocessor information: use cpp syntax.");
1754 CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
1755 STYPE ("include", opts->include, NULL);
1756 CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1757 STYPE ("define", opts->define, NULL);
1759 CCTYPE ("RUN CONTROL PARAMETERS");
1760 EETYPE("integrator", ir->eI, ei_names);
1761 CTYPE ("Start time and timestep in ps");
1762 RTYPE ("tinit", ir->init_t, 0.0);
1763 RTYPE ("dt", ir->delta_t, 0.001);
1764 STEPTYPE ("nsteps", ir->nsteps, 0);
1765 CTYPE ("For exact run continuation or redoing part of a run");
1766 STEPTYPE ("init-step", ir->init_step, 0);
1767 CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
1768 ITYPE ("simulation-part", ir->simulation_part, 1);
1769 CTYPE ("mode for center of mass motion removal");
1770 EETYPE("comm-mode", ir->comm_mode, ecm_names);
1771 CTYPE ("number of steps for center of mass motion removal");
1772 ITYPE ("nstcomm", ir->nstcomm, 100);
1773 CTYPE ("group(s) for center of mass motion removal");
1774 STYPE ("comm-grps", is->vcm, NULL);
1776 CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
1777 CTYPE ("Friction coefficient (amu/ps) and random seed");
1778 RTYPE ("bd-fric", ir->bd_fric, 0.0);
1779 ITYPE ("ld-seed", ir->ld_seed, 1993);
1782 CCTYPE ("ENERGY MINIMIZATION OPTIONS");
1783 CTYPE ("Force tolerance and initial step-size");
1784 RTYPE ("emtol", ir->em_tol, 10.0);
1785 RTYPE ("emstep", ir->em_stepsize, 0.01);
1786 CTYPE ("Max number of iterations in relax-shells");
1787 ITYPE ("niter", ir->niter, 20);
1788 CTYPE ("Step size (ps^2) for minimization of flexible constraints");
1789 RTYPE ("fcstep", ir->fc_stepsize, 0);
1790 CTYPE ("Frequency of steepest descents steps when doing CG");
1791 ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
1792 ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
1794 CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
1795 RTYPE ("rtpi", ir->rtpi, 0.05);
1797 /* Output options */
1798 CCTYPE ("OUTPUT CONTROL OPTIONS");
1799 CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
1800 ITYPE ("nstxout", ir->nstxout, 0);
1801 ITYPE ("nstvout", ir->nstvout, 0);
1802 ITYPE ("nstfout", ir->nstfout, 0);
1803 ir->nstcheckpoint = 1000;
1804 CTYPE ("Output frequency for energies to log file and energy file");
1805 ITYPE ("nstlog", ir->nstlog, 1000);
1806 ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
1807 ITYPE ("nstenergy", ir->nstenergy, 1000);
1808 CTYPE ("Output frequency and precision for .xtc file");
1809 ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
1810 RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
1811 CTYPE ("This selects the subset of atoms for the compressed");
1812 CTYPE ("trajectory file. You can select multiple groups. By");
1813 CTYPE ("default, all atoms will be written.");
1814 STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
1815 CTYPE ("Selection of energy groups");
1816 STYPE ("energygrps", is->energy, NULL);
1818 /* Neighbor searching */
1819 CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
1820 CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1821 EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
1822 CTYPE ("nblist update frequency");
1823 ITYPE ("nstlist", ir->nstlist, 10);
1824 CTYPE ("ns algorithm (simple or grid)");
1825 EETYPE("ns-type", ir->ns_type, ens_names);
1826 /* set ndelta to the optimal value of 2 */
1828 CTYPE ("Periodic boundary conditions: xyz, no, xy");
1829 EETYPE("pbc", ir->ePBC, epbc_names);
1830 EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
1831 CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1832 CTYPE ("a value of -1 means: use rlist");
1833 RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
1834 CTYPE ("nblist cut-off");
1835 RTYPE ("rlist", ir->rlist, 1.0);
1836 CTYPE ("long-range cut-off for switched potentials");
1837 RTYPE ("rlistlong", ir->rlistlong, -1);
1838 ITYPE ("nstcalclr", ir->nstcalclr, -1);
1840 /* Electrostatics */
1841 CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
1842 CTYPE ("Method for doing electrostatics");
1843 EETYPE("coulombtype", ir->coulombtype, eel_names);
1844 EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
1845 CTYPE ("cut-off lengths");
1846 RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
1847 RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
1848 CTYPE ("Relative dielectric constant for the medium and the reaction field");
1849 RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
1850 RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
1851 CTYPE ("Method for doing Van der Waals");
1852 EETYPE("vdw-type", ir->vdwtype, evdw_names);
1853 EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
1854 CTYPE ("cut-off lengths");
1855 RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
1856 RTYPE ("rvdw", ir->rvdw, 1.0);
1857 CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
1858 EETYPE("DispCorr", ir->eDispCorr, edispc_names);
1859 CTYPE ("Extension of the potential lookup tables beyond the cut-off");
1860 RTYPE ("table-extension", ir->tabext, 1.0);
1861 CTYPE ("Separate tables between energy group pairs");
1862 STYPE ("energygrp-table", is->egptable, NULL);
1863 CTYPE ("Spacing for the PME/PPPM FFT grid");
1864 RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
1865 CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
1866 ITYPE ("fourier-nx", ir->nkx, 0);
1867 ITYPE ("fourier-ny", ir->nky, 0);
1868 ITYPE ("fourier-nz", ir->nkz, 0);
1869 CTYPE ("EWALD/PME/PPPM parameters");
1870 ITYPE ("pme-order", ir->pme_order, 4);
1871 RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
1872 RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
1873 EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
1874 EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
1875 RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
1876 EETYPE("optimize-fft", ir->bOptFFT, yesno_names);
1878 CCTYPE("IMPLICIT SOLVENT ALGORITHM");
1879 EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
1881 CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
1882 CTYPE ("Algorithm for calculating Born radii");
1883 EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
1884 CTYPE ("Frequency of calculating the Born radii inside rlist");
1885 ITYPE ("nstgbradii", ir->nstgbradii, 1);
1886 CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
1887 CTYPE ("between rlist and rgbradii is updated every nstlist steps");
1888 RTYPE ("rgbradii", ir->rgbradii, 1.0);
1889 CTYPE ("Dielectric coefficient of the implicit solvent");
1890 RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
1891 CTYPE ("Salt concentration in M for Generalized Born models");
1892 RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
1893 CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
1894 RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
1895 RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
1896 RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
1897 RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
1898 EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
1899 CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
1900 CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
1901 RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
1903 /* Coupling stuff */
1904 CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
1905 CTYPE ("Temperature coupling");
1906 EETYPE("tcoupl", ir->etc, etcoupl_names);
1907 ITYPE ("nsttcouple", ir->nsttcouple, -1);
1908 ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
1909 EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
1910 CTYPE ("Groups to couple separately");
1911 STYPE ("tc-grps", is->tcgrps, NULL);
1912 CTYPE ("Time constant (ps) and reference temperature (K)");
1913 STYPE ("tau-t", is->tau_t, NULL);
1914 STYPE ("ref-t", is->ref_t, NULL);
1915 CTYPE ("pressure coupling");
1916 EETYPE("pcoupl", ir->epc, epcoupl_names);
1917 EETYPE("pcoupltype", ir->epct, epcoupltype_names);
1918 ITYPE ("nstpcouple", ir->nstpcouple, -1);
1919 CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
1920 RTYPE ("tau-p", ir->tau_p, 1.0);
1921 STYPE ("compressibility", dumstr[0], NULL);
1922 STYPE ("ref-p", dumstr[1], NULL);
1923 CTYPE ("Scaling of reference coordinates, No, All or COM");
1924 EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
1927 CCTYPE ("OPTIONS FOR QMMM calculations");
1928 EETYPE("QMMM", ir->bQMMM, yesno_names);
1929 CTYPE ("Groups treated Quantum Mechanically");
1930 STYPE ("QMMM-grps", is->QMMM, NULL);
1931 CTYPE ("QM method");
1932 STYPE("QMmethod", is->QMmethod, NULL);
1933 CTYPE ("QMMM scheme");
1934 EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
1935 CTYPE ("QM basisset");
1936 STYPE("QMbasis", is->QMbasis, NULL);
1937 CTYPE ("QM charge");
1938 STYPE ("QMcharge", is->QMcharge, NULL);
1939 CTYPE ("QM multiplicity");
1940 STYPE ("QMmult", is->QMmult, NULL);
1941 CTYPE ("Surface Hopping");
1942 STYPE ("SH", is->bSH, NULL);
1943 CTYPE ("CAS space options");
1944 STYPE ("CASorbitals", is->CASorbitals, NULL);
1945 STYPE ("CASelectrons", is->CASelectrons, NULL);
1946 STYPE ("SAon", is->SAon, NULL);
1947 STYPE ("SAoff", is->SAoff, NULL);
1948 STYPE ("SAsteps", is->SAsteps, NULL);
1949 CTYPE ("Scale factor for MM charges");
1950 RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
1951 CTYPE ("Optimization of QM subsystem");
1952 STYPE ("bOPT", is->bOPT, NULL);
1953 STYPE ("bTS", is->bTS, NULL);
1955 /* Simulated annealing */
1956 CCTYPE("SIMULATED ANNEALING");
1957 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
1958 STYPE ("annealing", is->anneal, NULL);
1959 CTYPE ("Number of time points to use for specifying annealing in each group");
1960 STYPE ("annealing-npoints", is->anneal_npoints, NULL);
1961 CTYPE ("List of times at the annealing points for each group");
1962 STYPE ("annealing-time", is->anneal_time, NULL);
1963 CTYPE ("Temp. at each annealing point, for each group.");
1964 STYPE ("annealing-temp", is->anneal_temp, NULL);
1967 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
1968 EETYPE("gen-vel", opts->bGenVel, yesno_names);
1969 RTYPE ("gen-temp", opts->tempi, 300.0);
1970 ITYPE ("gen-seed", opts->seed, 173529);
1973 CCTYPE ("OPTIONS FOR BONDS");
1974 EETYPE("constraints", opts->nshake, constraints);
1975 CTYPE ("Type of constraint algorithm");
1976 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
1977 CTYPE ("Do not constrain the start configuration");
1978 EETYPE("continuation", ir->bContinuation, yesno_names);
1979 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
1980 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
1981 CTYPE ("Relative tolerance of shake");
1982 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
1983 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
1984 ITYPE ("lincs-order", ir->nProjOrder, 4);
1985 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
1986 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
1987 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
1988 ITYPE ("lincs-iter", ir->nLincsIter, 1);
1989 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
1990 CTYPE ("rotates over more degrees than");
1991 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
1992 CTYPE ("Convert harmonic bonds to morse potentials");
1993 EETYPE("morse", opts->bMorse, yesno_names);
1995 /* Energy group exclusions */
1996 CCTYPE ("ENERGY GROUP EXCLUSIONS");
1997 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
1998 STYPE ("energygrp-excl", is->egpexcl, NULL);
2002 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2003 ITYPE ("nwall", ir->nwall, 0);
2004 EETYPE("wall-type", ir->wall_type, ewt_names);
2005 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
2006 STYPE ("wall-atomtype", is->wall_atomtype, NULL);
2007 STYPE ("wall-density", is->wall_density, NULL);
2008 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
2011 CCTYPE("COM PULLING");
2012 CTYPE("Pull type: no, umbrella, constraint or constant-force");
2013 EETYPE("pull", ir->ePull, epull_names);
2014 if (ir->ePull != epullNO)
2017 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
2020 /* Enforced rotation */
2021 CCTYPE("ENFORCED ROTATION");
2022 CTYPE("Enforced rotation: No or Yes");
2023 EETYPE("rotation", ir->bRot, yesno_names);
2027 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2031 CCTYPE("NMR refinement stuff");
2032 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2033 EETYPE("disre", ir->eDisre, edisre_names);
2034 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2035 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2036 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2037 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2038 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2039 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2040 CTYPE ("Output frequency for pair distances to energy file");
2041 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2042 CTYPE ("Orientation restraints: No or Yes");
2043 EETYPE("orire", opts->bOrire, yesno_names);
2044 CTYPE ("Orientation restraints force constant and tau for time averaging");
2045 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2046 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2047 STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
2048 CTYPE ("Output frequency for trace(SD) and S to energy file");
2049 ITYPE ("nstorireout", ir->nstorireout, 100);
2051 /* free energy variables */
2052 CCTYPE ("Free energy variables");
2053 EETYPE("free-energy", ir->efep, efep_names);
2054 STYPE ("couple-moltype", is->couple_moltype, NULL);
2055 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2056 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2057 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2059 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2061 it was not entered */
2062 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2063 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2064 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2065 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
2066 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
2067 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
2068 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
2069 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
2070 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
2071 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
2072 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2073 STYPE ("init-lambda-weights", is->lambda_weights, NULL);
2074 EETYPE("dhdl-print-energy", fep->bPrintEnergy, yesno_names);
2075 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2076 ITYPE ("sc-power", fep->sc_power, 1);
2077 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2078 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2079 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2080 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2081 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2082 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2083 separate_dhdl_file_names);
2084 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2085 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2086 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2088 /* Non-equilibrium MD stuff */
2089 CCTYPE("Non-equilibrium MD stuff");
2090 STYPE ("acc-grps", is->accgrps, NULL);
2091 STYPE ("accelerate", is->acc, NULL);
2092 STYPE ("freezegrps", is->freeze, NULL);
2093 STYPE ("freezedim", is->frdim, NULL);
2094 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2095 STYPE ("deform", is->deform, NULL);
2097 /* simulated tempering variables */
2098 CCTYPE("simulated tempering variables");
2099 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2100 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2101 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2102 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2104 /* expanded ensemble variables */
2105 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2107 read_expandedparams(&ninp, &inp, expand, wi);
2110 /* Electric fields */
2111 CCTYPE("Electric fields");
2112 CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
2113 CTYPE ("and a phase angle (real)");
2114 STYPE ("E-x", is->efield_x, NULL);
2115 STYPE ("E-xt", is->efield_xt, NULL);
2116 STYPE ("E-y", is->efield_y, NULL);
2117 STYPE ("E-yt", is->efield_yt, NULL);
2118 STYPE ("E-z", is->efield_z, NULL);
2119 STYPE ("E-zt", is->efield_zt, NULL);
2121 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2122 CTYPE("Swap positions along direction: no, X, Y, Z");
2123 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2124 if (ir->eSwapCoords != eswapNO)
2127 CTYPE("Swap attempt frequency");
2128 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2129 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2130 STYPE("split-group0", splitgrp0, NULL);
2131 STYPE("split-group1", splitgrp1, NULL);
2132 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2133 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2134 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2136 CTYPE("Group name of ions that can be exchanged with solvent molecules");
2137 STYPE("swap-group", swapgrp, NULL);
2138 CTYPE("Group name of solvent molecules");
2139 STYPE("solvent-group", solgrp, NULL);
2141 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2142 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2143 CTYPE("however, if correctly defined, the ion permeation events are counted per channel");
2144 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2145 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2146 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2147 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2148 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2149 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2151 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2152 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2153 CTYPE("Requested number of anions and cations for each of the two compartments");
2154 CTYPE("-1 means fix the numbers as found in time step 0");
2155 ITYPE("anionsA", ir->swap->nanions[0], -1);
2156 ITYPE("cationsA", ir->swap->ncations[0], -1);
2157 ITYPE("anionsB", ir->swap->nanions[1], -1);
2158 ITYPE("cationsB", ir->swap->ncations[1], -1);
2159 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2160 RTYPE("threshold", ir->swap->threshold, 1.0);
2163 /* AdResS defined thingies */
2164 CCTYPE ("AdResS parameters");
2165 EETYPE("adress", ir->bAdress, yesno_names);
2168 snew(ir->adress, 1);
2169 read_adressparams(&ninp, &inp, ir->adress, wi);
2172 /* User defined thingies */
2173 CCTYPE ("User defined thingies");
2174 STYPE ("user1-grps", is->user1, NULL);
2175 STYPE ("user2-grps", is->user2, NULL);
2176 ITYPE ("userint1", ir->userint1, 0);
2177 ITYPE ("userint2", ir->userint2, 0);
2178 ITYPE ("userint3", ir->userint3, 0);
2179 ITYPE ("userint4", ir->userint4, 0);
2180 RTYPE ("userreal1", ir->userreal1, 0);
2181 RTYPE ("userreal2", ir->userreal2, 0);
2182 RTYPE ("userreal3", ir->userreal3, 0);
2183 RTYPE ("userreal4", ir->userreal4, 0);
2186 write_inpfile(mdparout, ninp, inp, FALSE, wi);
2187 for (i = 0; (i < ninp); i++)
2190 sfree(inp[i].value);
2194 /* Process options if necessary */
2195 for (m = 0; m < 2; m++)
2197 for (i = 0; i < 2*DIM; i++)
2206 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2208 warning_error(wi, "Pressure coupling not enough values (I need 1)");
2210 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2212 case epctSEMIISOTROPIC:
2213 case epctSURFACETENSION:
2214 if (sscanf(dumstr[m], "%lf%lf",
2215 &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2217 warning_error(wi, "Pressure coupling not enough values (I need 2)");
2219 dumdub[m][YY] = dumdub[m][XX];
2221 case epctANISOTROPIC:
2222 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2223 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2224 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2226 warning_error(wi, "Pressure coupling not enough values (I need 6)");
2230 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2231 epcoupltype_names[ir->epct]);
2235 clear_mat(ir->ref_p);
2236 clear_mat(ir->compress);
2237 for (i = 0; i < DIM; i++)
2239 ir->ref_p[i][i] = dumdub[1][i];
2240 ir->compress[i][i] = dumdub[0][i];
2242 if (ir->epct == epctANISOTROPIC)
2244 ir->ref_p[XX][YY] = dumdub[1][3];
2245 ir->ref_p[XX][ZZ] = dumdub[1][4];
2246 ir->ref_p[YY][ZZ] = dumdub[1][5];
2247 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2249 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2251 ir->compress[XX][YY] = dumdub[0][3];
2252 ir->compress[XX][ZZ] = dumdub[0][4];
2253 ir->compress[YY][ZZ] = dumdub[0][5];
2254 for (i = 0; i < DIM; i++)
2256 for (m = 0; m < i; m++)
2258 ir->ref_p[i][m] = ir->ref_p[m][i];
2259 ir->compress[i][m] = ir->compress[m][i];
2264 if (ir->comm_mode == ecmNO)
2269 opts->couple_moltype = NULL;
2270 if (strlen(is->couple_moltype) > 0)
2272 if (ir->efep != efepNO)
2274 opts->couple_moltype = strdup(is->couple_moltype);
2275 if (opts->couple_lam0 == opts->couple_lam1)
2277 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2279 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2280 opts->couple_lam1 == ecouplamNONE))
2282 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2287 warning(wi, "Can not couple a molecule with free_energy = no");
2290 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2291 if (ir->efep != efepNO)
2293 if (fep->delta_lambda > 0)
2295 ir->efep = efepSLOWGROWTH;
2301 fep->bPrintEnergy = TRUE;
2302 /* always print out the energy to dhdl if we are doing expanded ensemble, since we need the total energy
2303 if the temperature is changing. */
2306 if ((ir->efep != efepNO) || ir->bSimTemp)
2308 ir->bExpanded = FALSE;
2309 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2311 ir->bExpanded = TRUE;
2313 do_fep_params(ir, is->fep_lambda, is->lambda_weights);
2314 if (ir->bSimTemp) /* done after fep params */
2316 do_simtemp_params(ir);
2321 ir->fepvals->n_lambda = 0;
2324 /* WALL PARAMETERS */
2326 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2328 /* ORIENTATION RESTRAINT PARAMETERS */
2330 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
2332 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2335 /* DEFORMATION PARAMETERS */
2337 clear_mat(ir->deform);
2338 for (i = 0; i < 6; i++)
2342 m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
2343 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2344 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2345 for (i = 0; i < 3; i++)
2347 ir->deform[i][i] = dumdub[0][i];
2349 ir->deform[YY][XX] = dumdub[0][3];
2350 ir->deform[ZZ][XX] = dumdub[0][4];
2351 ir->deform[ZZ][YY] = dumdub[0][5];
2352 if (ir->epc != epcNO)
2354 for (i = 0; i < 3; i++)
2356 for (j = 0; j <= i; j++)
2358 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2360 warning_error(wi, "A box element has deform set and compressibility > 0");
2364 for (i = 0; i < 3; i++)
2366 for (j = 0; j < i; j++)
2368 if (ir->deform[i][j] != 0)
2370 for (m = j; m < DIM; m++)
2372 if (ir->compress[m][j] != 0)
2374 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.");
2375 warning(wi, warn_buf);
2383 /* Ion/water position swapping checks */
2384 if (ir->eSwapCoords != eswapNO)
2386 if (ir->swap->nstswap < 1)
2388 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2390 if (ir->swap->nAverage < 1)
2392 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2394 if (ir->swap->threshold < 1.0)
2396 warning_error(wi, "Ion count threshold must be at least 1.\n");
2404 static int search_QMstring(const char *s, int ng, const char *gn[])
2406 /* same as normal search_string, but this one searches QM strings */
2409 for (i = 0; (i < ng); i++)
2411 if (gmx_strcasecmp(s, gn[i]) == 0)
2417 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2421 } /* search_QMstring */
2423 /* We would like gn to be const as well, but C doesn't allow this */
2424 int search_string(const char *s, int ng, char *gn[])
2428 for (i = 0; (i < ng); i++)
2430 if (gmx_strcasecmp(s, gn[i]) == 0)
2437 "Group %s referenced in the .mdp file was not found in the index file.\n"
2438 "Group names must match either [moleculetype] names or custom index group\n"
2439 "names, in which case you must supply an index file to the '-n' option\n"
2446 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2447 t_blocka *block, char *gnames[],
2448 int gtype, int restnm,
2449 int grptp, gmx_bool bVerbose,
2452 unsigned short *cbuf;
2453 t_grps *grps = &(groups->grps[gtype]);
2454 int i, j, gid, aj, ognr, ntot = 0;
2457 char warn_buf[STRLEN];
2461 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2464 title = gtypes[gtype];
2467 /* Mark all id's as not set */
2468 for (i = 0; (i < natoms); i++)
2473 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2474 for (i = 0; (i < ng); i++)
2476 /* Lookup the group name in the block structure */
2477 gid = search_string(ptrs[i], block->nr, gnames);
2478 if ((grptp != egrptpONE) || (i == 0))
2480 grps->nm_ind[grps->nr++] = gid;
2484 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2487 /* Now go over the atoms in the group */
2488 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2493 /* Range checking */
2494 if ((aj < 0) || (aj >= natoms))
2496 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2498 /* Lookup up the old group number */
2502 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2503 aj+1, title, ognr+1, i+1);
2507 /* Store the group number in buffer */
2508 if (grptp == egrptpONE)
2521 /* Now check whether we have done all atoms */
2525 if (grptp == egrptpALL)
2527 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2528 natoms-ntot, title);
2530 else if (grptp == egrptpPART)
2532 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2533 natoms-ntot, title);
2534 warning_note(wi, warn_buf);
2536 /* Assign all atoms currently unassigned to a rest group */
2537 for (j = 0; (j < natoms); j++)
2539 if (cbuf[j] == NOGID)
2545 if (grptp != egrptpPART)
2550 "Making dummy/rest group for %s containing %d elements\n",
2551 title, natoms-ntot);
2553 /* Add group name "rest" */
2554 grps->nm_ind[grps->nr] = restnm;
2556 /* Assign the rest name to all atoms not currently assigned to a group */
2557 for (j = 0; (j < natoms); j++)
2559 if (cbuf[j] == NOGID)
2568 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2570 /* All atoms are part of one (or no) group, no index required */
2571 groups->ngrpnr[gtype] = 0;
2572 groups->grpnr[gtype] = NULL;
2576 groups->ngrpnr[gtype] = natoms;
2577 snew(groups->grpnr[gtype], natoms);
2578 for (j = 0; (j < natoms); j++)
2580 groups->grpnr[gtype][j] = cbuf[j];
2586 return (bRest && grptp == egrptpPART);
2589 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2592 gmx_groups_t *groups;
2594 int natoms, ai, aj, i, j, d, g, imin, jmin;
2596 int *nrdf2, *na_vcm, na_tot;
2597 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2598 gmx_mtop_atomloop_all_t aloop;
2600 int mb, mol, ftype, as;
2601 gmx_molblock_t *molb;
2602 gmx_moltype_t *molt;
2605 * First calc 3xnr-atoms for each group
2606 * then subtract half a degree of freedom for each constraint
2608 * Only atoms and nuclei contribute to the degrees of freedom...
2613 groups = &mtop->groups;
2614 natoms = mtop->natoms;
2616 /* Allocate one more for a possible rest group */
2617 /* We need to sum degrees of freedom into doubles,
2618 * since floats give too low nrdf's above 3 million atoms.
2620 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2621 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2622 snew(na_vcm, groups->grps[egcVCM].nr+1);
2624 for (i = 0; i < groups->grps[egcTC].nr; i++)
2628 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2633 snew(nrdf2, natoms);
2634 aloop = gmx_mtop_atomloop_all_init(mtop);
2635 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2638 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2640 g = ggrpnr(groups, egcFREEZE, i);
2641 /* Double count nrdf for particle i */
2642 for (d = 0; d < DIM; d++)
2644 if (opts->nFreeze[g][d] == 0)
2649 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2650 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2655 for (mb = 0; mb < mtop->nmolblock; mb++)
2657 molb = &mtop->molblock[mb];
2658 molt = &mtop->moltype[molb->type];
2659 atom = molt->atoms.atom;
2660 for (mol = 0; mol < molb->nmol; mol++)
2662 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2664 ia = molt->ilist[ftype].iatoms;
2665 for (i = 0; i < molt->ilist[ftype].nr; )
2667 /* Subtract degrees of freedom for the constraints,
2668 * if the particles still have degrees of freedom left.
2669 * If one of the particles is a vsite or a shell, then all
2670 * constraint motion will go there, but since they do not
2671 * contribute to the constraints the degrees of freedom do not
2676 if (((atom[ia[1]].ptype == eptNucleus) ||
2677 (atom[ia[1]].ptype == eptAtom)) &&
2678 ((atom[ia[2]].ptype == eptNucleus) ||
2679 (atom[ia[2]].ptype == eptAtom)))
2697 imin = min(imin, nrdf2[ai]);
2698 jmin = min(jmin, nrdf2[aj]);
2701 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2702 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2703 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2704 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2706 ia += interaction_function[ftype].nratoms+1;
2707 i += interaction_function[ftype].nratoms+1;
2710 ia = molt->ilist[F_SETTLE].iatoms;
2711 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2713 /* Subtract 1 dof from every atom in the SETTLE */
2714 for (j = 0; j < 3; j++)
2717 imin = min(2, nrdf2[ai]);
2719 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2720 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2725 as += molt->atoms.nr;
2729 if (ir->ePull == epullCONSTRAINT)
2731 /* Correct nrdf for the COM constraints.
2732 * We correct using the TC and VCM group of the first atom
2733 * in the reference and pull group. If atoms in one pull group
2734 * belong to different TC or VCM groups it is anyhow difficult
2735 * to determine the optimal nrdf assignment.
2739 for (i = 0; i < pull->ncoord; i++)
2743 for (j = 0; j < 2; j++)
2745 const t_pull_group *pgrp;
2747 pgrp = &pull->group[pull->coord[i].group[j]];
2751 /* Subtract 1/2 dof from each group */
2753 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2754 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2755 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2757 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)]]);
2762 /* We need to subtract the whole DOF from group j=1 */
2769 if (ir->nstcomm != 0)
2771 /* Subtract 3 from the number of degrees of freedom in each vcm group
2772 * when com translation is removed and 6 when rotation is removed
2775 switch (ir->comm_mode)
2778 n_sub = ndof_com(ir);
2785 gmx_incons("Checking comm_mode");
2788 for (i = 0; i < groups->grps[egcTC].nr; i++)
2790 /* Count the number of atoms of TC group i for every VCM group */
2791 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2796 for (ai = 0; ai < natoms; ai++)
2798 if (ggrpnr(groups, egcTC, ai) == i)
2800 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2804 /* Correct for VCM removal according to the fraction of each VCM
2805 * group present in this TC group.
2807 nrdf_uc = nrdf_tc[i];
2810 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2814 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2816 if (nrdf_vcm[j] > n_sub)
2818 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2819 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2823 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2824 j, nrdf_vcm[j], nrdf_tc[i]);
2829 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2831 opts->nrdf[i] = nrdf_tc[i];
2832 if (opts->nrdf[i] < 0)
2837 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2838 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
2847 static void decode_cos(char *s, t_cosines *cosine)
2850 char format[STRLEN], f1[STRLEN];
2862 sscanf(t, "%d", &(cosine->n));
2869 snew(cosine->a, cosine->n);
2870 snew(cosine->phi, cosine->n);
2872 sprintf(format, "%%*d");
2873 for (i = 0; (i < cosine->n); i++)
2876 strcat(f1, "%lf%lf");
2877 if (sscanf(t, f1, &a, &phi) < 2)
2879 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
2882 cosine->phi[i] = phi;
2883 strcat(format, "%*lf%*lf");
2890 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
2891 const char *option, const char *val, int flag)
2893 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
2894 * But since this is much larger than STRLEN, such a line can not be parsed.
2895 * The real maximum is the number of names that fit in a string: STRLEN/2.
2897 #define EGP_MAX (STRLEN/2)
2898 int nelem, i, j, k, nr;
2899 char *names[EGP_MAX];
2903 gnames = groups->grpname;
2905 nelem = str_nelem(val, EGP_MAX, names);
2908 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
2910 nr = groups->grps[egcENER].nr;
2912 for (i = 0; i < nelem/2; i++)
2916 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
2922 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
2923 names[2*i], option);
2927 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
2933 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
2934 names[2*i+1], option);
2936 if ((j < nr) && (k < nr))
2938 ir->opts.egp_flags[nr*j+k] |= flag;
2939 ir->opts.egp_flags[nr*k+j] |= flag;
2948 static void make_swap_groups(
2957 int ig = -1, i = 0, j;
2961 /* Just a quick check here, more thorough checks are in mdrun */
2962 if (strcmp(splitg0name, splitg1name) == 0)
2964 gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
2967 /* First get the swap group index atoms */
2968 ig = search_string(swapgname, grps->nr, gnames);
2969 swap->nat = grps->index[ig+1] - grps->index[ig];
2972 fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
2973 snew(swap->ind, swap->nat);
2974 for (i = 0; i < swap->nat; i++)
2976 swap->ind[i] = grps->a[grps->index[ig]+i];
2981 gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
2984 /* Now do so for the split groups */
2985 for (j = 0; j < 2; j++)
2989 splitg = splitg0name;
2993 splitg = splitg1name;
2996 ig = search_string(splitg, grps->nr, gnames);
2997 swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
2998 if (swap->nat_split[j] > 0)
3000 fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
3001 j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
3002 snew(swap->ind_split[j], swap->nat_split[j]);
3003 for (i = 0; i < swap->nat_split[j]; i++)
3005 swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
3010 gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
3014 /* Now get the solvent group index atoms */
3015 ig = search_string(solgname, grps->nr, gnames);
3016 swap->nat_sol = grps->index[ig+1] - grps->index[ig];
3017 if (swap->nat_sol > 0)
3019 fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
3020 snew(swap->ind_sol, swap->nat_sol);
3021 for (i = 0; i < swap->nat_sol; i++)
3023 swap->ind_sol[i] = grps->a[grps->index[ig]+i];
3028 gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
3033 void do_index(const char* mdparin, const char *ndx,
3036 t_inputrec *ir, rvec *v,
3040 gmx_groups_t *groups;
3044 char warnbuf[STRLEN], **gnames;
3045 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3048 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3049 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3050 int i, j, k, restnm;
3052 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3053 int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
3054 nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
3055 char warn_buf[STRLEN];
3059 fprintf(stderr, "processing index file...\n");
3065 snew(grps->index, 1);
3067 atoms_all = gmx_mtop_global_atoms(mtop);
3068 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3069 free_t_atoms(&atoms_all, FALSE);
3073 grps = init_index(ndx, &gnames);
3076 groups = &mtop->groups;
3077 natoms = mtop->natoms;
3078 symtab = &mtop->symtab;
3080 snew(groups->grpname, grps->nr+1);
3082 for (i = 0; (i < grps->nr); i++)
3084 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3086 groups->grpname[i] = put_symtab(symtab, "rest");
3088 srenew(gnames, grps->nr+1);
3089 gnames[restnm] = *(groups->grpname[i]);
3090 groups->ngrpname = grps->nr+1;
3092 set_warning_line(wi, mdparin, -1);
3094 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3095 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3096 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3097 if ((ntau_t != ntcg) || (nref_t != ntcg))
3099 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3100 "%d tau-t values", ntcg, nref_t, ntau_t);
3103 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3104 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3105 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3106 nr = groups->grps[egcTC].nr;
3108 snew(ir->opts.nrdf, nr);
3109 snew(ir->opts.tau_t, nr);
3110 snew(ir->opts.ref_t, nr);
3111 if (ir->eI == eiBD && ir->bd_fric == 0)
3113 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3120 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3124 for (i = 0; (i < nr); i++)
3126 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
3127 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
3129 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3130 warning_error(wi, warn_buf);
3133 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3135 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.");
3138 if (ir->opts.tau_t[i] >= 0)
3140 tau_min = min(tau_min, ir->opts.tau_t[i]);
3143 if (ir->etc != etcNO && ir->nsttcouple == -1)
3145 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3150 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3152 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");
3154 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
3156 if (ir->nstpcouple != ir->nsttcouple)
3158 int mincouple = min(ir->nstpcouple, ir->nsttcouple);
3159 ir->nstpcouple = ir->nsttcouple = mincouple;
3160 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);
3161 warning_note(wi, warn_buf);
3165 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3166 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3168 if (ETC_ANDERSEN(ir->etc))
3170 if (ir->nsttcouple != 1)
3173 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");
3174 warning_note(wi, warn_buf);
3177 nstcmin = tcouple_min_integration_steps(ir->etc);
3180 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
3182 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3183 ETCOUPLTYPE(ir->etc),
3185 ir->nsttcouple*ir->delta_t);
3186 warning(wi, warn_buf);
3189 for (i = 0; (i < nr); i++)
3191 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
3192 if (ir->opts.ref_t[i] < 0)
3194 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3197 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3198 if we are in this conditional) if mc_temp is negative */
3199 if (ir->expandedvals->mc_temp < 0)
3201 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3205 /* Simulated annealing for each group. There are nr groups */
3206 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3207 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3211 if (nSA > 0 && nSA != nr)
3213 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3217 snew(ir->opts.annealing, nr);
3218 snew(ir->opts.anneal_npoints, nr);
3219 snew(ir->opts.anneal_time, nr);
3220 snew(ir->opts.anneal_temp, nr);
3221 for (i = 0; i < nr; i++)
3223 ir->opts.annealing[i] = eannNO;
3224 ir->opts.anneal_npoints[i] = 0;
3225 ir->opts.anneal_time[i] = NULL;
3226 ir->opts.anneal_temp[i] = NULL;
3231 for (i = 0; i < nr; i++)
3233 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3235 ir->opts.annealing[i] = eannNO;
3237 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3239 ir->opts.annealing[i] = eannSINGLE;
3242 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3244 ir->opts.annealing[i] = eannPERIODIC;
3250 /* Read the other fields too */
3251 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3252 if (nSA_points != nSA)
3254 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3256 for (k = 0, i = 0; i < nr; i++)
3258 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3259 if (ir->opts.anneal_npoints[i] == 1)
3261 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3263 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3264 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3265 k += ir->opts.anneal_npoints[i];
3268 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3271 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3273 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3276 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3279 for (i = 0, k = 0; i < nr; i++)
3282 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3284 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3285 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3288 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3290 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3296 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3298 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3299 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3302 if (ir->opts.anneal_temp[i][j] < 0)
3304 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3309 /* Print out some summary information, to make sure we got it right */
3310 for (i = 0, k = 0; i < nr; i++)
3312 if (ir->opts.annealing[i] != eannNO)
3314 j = groups->grps[egcTC].nm_ind[i];
3315 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3316 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3317 ir->opts.anneal_npoints[i]);
3318 fprintf(stderr, "Time (ps) Temperature (K)\n");
3319 /* All terms except the last one */
3320 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3322 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3325 /* Finally the last one */
3326 j = ir->opts.anneal_npoints[i]-1;
3327 if (ir->opts.annealing[i] == eannSINGLE)
3329 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3333 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3334 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3336 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3345 if (ir->ePull != epullNO)
3347 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3349 make_pull_coords(ir->pull);
3354 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3357 if (ir->eSwapCoords != eswapNO)
3359 make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
3362 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3363 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3364 if (nacg*DIM != nacc)
3366 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3369 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3370 restnm, egrptpALL_GENREST, bVerbose, wi);
3371 nr = groups->grps[egcACC].nr;
3372 snew(ir->opts.acc, nr);
3373 ir->opts.ngacc = nr;
3375 for (i = k = 0; (i < nacg); i++)
3377 for (j = 0; (j < DIM); j++, k++)
3379 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3382 for (; (i < nr); i++)
3384 for (j = 0; (j < DIM); j++)
3386 ir->opts.acc[i][j] = 0;
3390 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3391 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3392 if (nfrdim != DIM*nfreeze)
3394 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3397 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3398 restnm, egrptpALL_GENREST, bVerbose, wi);
3399 nr = groups->grps[egcFREEZE].nr;
3400 ir->opts.ngfrz = nr;
3401 snew(ir->opts.nFreeze, nr);
3402 for (i = k = 0; (i < nfreeze); i++)
3404 for (j = 0; (j < DIM); j++, k++)
3406 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3407 if (!ir->opts.nFreeze[i][j])
3409 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3411 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3412 "(not %s)", ptr1[k]);
3413 warning(wi, warn_buf);
3418 for (; (i < nr); i++)
3420 for (j = 0; (j < DIM); j++)
3422 ir->opts.nFreeze[i][j] = 0;
3426 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3427 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3428 restnm, egrptpALL_GENREST, bVerbose, wi);
3429 add_wall_energrps(groups, ir->nwall, symtab);
3430 ir->opts.ngener = groups->grps[egcENER].nr;
3431 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3433 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3434 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3437 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3438 "This may lead to artifacts.\n"
3439 "In most cases one should use one group for the whole system.");
3442 /* Now we have filled the freeze struct, so we can calculate NRDF */
3443 calc_nrdf(mtop, ir, gnames);
3449 /* Must check per group! */
3450 for (i = 0; (i < ir->opts.ngtc); i++)
3452 ntot += ir->opts.nrdf[i];
3454 if (ntot != (DIM*natoms))
3456 fac = sqrt(ntot/(DIM*natoms));
3459 fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
3460 "and removal of center of mass motion\n", fac);
3462 for (i = 0; (i < natoms); i++)
3464 svmul(fac, v[i], v[i]);
3469 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3470 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3471 restnm, egrptpALL_GENREST, bVerbose, wi);
3472 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3473 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3474 restnm, egrptpALL_GENREST, bVerbose, wi);
3475 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3476 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3477 restnm, egrptpONE, bVerbose, wi);
3478 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3479 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3480 restnm, egrptpALL_GENREST, bVerbose, wi);
3482 /* QMMM input processing */
3483 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3484 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3485 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3486 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3488 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3489 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3491 /* group rest, if any, is always MM! */
3492 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3493 restnm, egrptpALL_GENREST, bVerbose, wi);
3494 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3495 ir->opts.ngQM = nQMg;
3496 snew(ir->opts.QMmethod, nr);
3497 snew(ir->opts.QMbasis, nr);
3498 for (i = 0; i < nr; i++)
3500 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3501 * converted to the corresponding enum in names.c
3503 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3505 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3509 nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
3510 nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
3511 nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
3512 snew(ir->opts.QMmult, nr);
3513 snew(ir->opts.QMcharge, nr);
3514 snew(ir->opts.bSH, nr);
3516 for (i = 0; i < nr; i++)
3518 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3519 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3520 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3523 nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
3524 nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
3525 snew(ir->opts.CASelectrons, nr);
3526 snew(ir->opts.CASorbitals, nr);
3527 for (i = 0; i < nr; i++)
3529 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3530 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3532 /* special optimization options */
3534 nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
3535 nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
3536 snew(ir->opts.bOPT, nr);
3537 snew(ir->opts.bTS, nr);
3538 for (i = 0; i < nr; i++)
3540 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3541 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3543 nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
3544 nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
3545 nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
3546 snew(ir->opts.SAon, nr);
3547 snew(ir->opts.SAoff, nr);
3548 snew(ir->opts.SAsteps, nr);
3550 for (i = 0; i < nr; i++)
3552 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3553 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3554 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3556 /* end of QMMM input */
3560 for (i = 0; (i < egcNR); i++)
3562 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3563 for (j = 0; (j < groups->grps[i].nr); j++)
3565 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3567 fprintf(stderr, "\n");
3571 nr = groups->grps[egcENER].nr;
3572 snew(ir->opts.egp_flags, nr*nr);
3574 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3575 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3577 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3579 if (bExcl && EEL_FULL(ir->coulombtype))
3581 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3584 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3585 if (bTable && !(ir->vdwtype == evdwUSER) &&
3586 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3587 !(ir->coulombtype == eelPMEUSERSWITCH))
3589 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3592 decode_cos(is->efield_x, &(ir->ex[XX]));
3593 decode_cos(is->efield_xt, &(ir->et[XX]));
3594 decode_cos(is->efield_y, &(ir->ex[YY]));
3595 decode_cos(is->efield_yt, &(ir->et[YY]));
3596 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3597 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3601 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3604 for (i = 0; (i < grps->nr); i++)
3616 static void check_disre(gmx_mtop_t *mtop)
3618 gmx_ffparams_t *ffparams;
3619 t_functype *functype;
3621 int i, ndouble, ftype;
3622 int label, old_label;
3624 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3626 ffparams = &mtop->ffparams;
3627 functype = ffparams->functype;
3628 ip = ffparams->iparams;
3631 for (i = 0; i < ffparams->ntypes; i++)
3633 ftype = functype[i];
3634 if (ftype == F_DISRES)
3636 label = ip[i].disres.label;
3637 if (label == old_label)
3639 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3647 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3648 "probably the parameters for multiple pairs in one restraint "
3649 "are not identical\n", ndouble);
3654 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3655 gmx_bool posres_only,
3659 gmx_mtop_ilistloop_t iloop;
3669 for (d = 0; d < DIM; d++)
3671 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3673 /* Check for freeze groups */
3674 for (g = 0; g < ir->opts.ngfrz; g++)
3676 for (d = 0; d < DIM; d++)
3678 if (ir->opts.nFreeze[g][d] != 0)
3686 /* Check for position restraints */
3687 iloop = gmx_mtop_ilistloop_init(sys);
3688 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3691 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3693 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3695 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3696 for (d = 0; d < DIM; d++)
3698 if (pr->posres.fcA[d] != 0)
3704 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3706 /* Check for flat-bottom posres */
3707 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3708 if (pr->fbposres.k != 0)
3710 switch (pr->fbposres.geom)
3712 case efbposresSPHERE:
3713 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3715 case efbposresCYLINDER:
3716 AbsRef[XX] = AbsRef[YY] = 1;
3718 case efbposresX: /* d=XX */
3719 case efbposresY: /* d=YY */
3720 case efbposresZ: /* d=ZZ */
3721 d = pr->fbposres.geom - efbposresX;
3725 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3726 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3734 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3738 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3739 gmx_bool *bC6ParametersWorkWithGeometricRules,
3740 gmx_bool *bC6ParametersWorkWithLBRules,
3741 gmx_bool *bLBRulesPossible)
3743 int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
3746 double geometricdiff, LBdiff;
3747 double c6i, c6j, c12i, c12j;
3748 double c6, c6_geometric, c6_LB;
3749 double sigmai, sigmaj, epsi, epsj;
3750 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3753 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3754 * force-field floating point parameters.
3757 ptr = getenv("GMX_LJCOMB_TOL");
3762 sscanf(ptr, "%lf", &dbl);
3766 *bC6ParametersWorkWithLBRules = TRUE;
3767 *bC6ParametersWorkWithGeometricRules = TRUE;
3768 bCanDoLBRules = TRUE;
3769 bCanDoGeometricRules = TRUE;
3770 ntypes = mtop->ffparams.atnr;
3771 snew(typecount, ntypes);
3772 gmx_mtop_count_atomtypes(mtop, state, typecount);
3773 geometricdiff = LBdiff = 0.0;
3774 *bLBRulesPossible = TRUE;
3775 for (tpi = 0; tpi < ntypes; ++tpi)
3777 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3778 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3779 for (tpj = tpi; tpj < ntypes; ++tpj)
3781 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3782 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3783 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3784 c6_geometric = sqrt(c6i * c6j);
3785 if (!gmx_numzero(c6_geometric))
3787 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3789 sigmai = pow(c12i / c6i, 1.0/6.0);
3790 sigmaj = pow(c12j / c6j, 1.0/6.0);
3791 epsi = c6i * c6i /(4.0 * c12i);
3792 epsj = c6j * c6j /(4.0 * c12j);
3793 c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
3797 *bLBRulesPossible = FALSE;
3798 c6_LB = c6_geometric;
3800 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3803 if (FALSE == bCanDoLBRules)
3805 *bC6ParametersWorkWithLBRules = FALSE;
3808 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3810 if (FALSE == bCanDoGeometricRules)
3812 *bC6ParametersWorkWithGeometricRules = FALSE;
3820 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3824 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3826 check_combination_rule_differences(mtop, 0,
3827 &bC6ParametersWorkWithGeometricRules,
3828 &bC6ParametersWorkWithLBRules,
3830 if (ir->ljpme_combination_rule == eljpmeLB)
3832 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
3834 warning(wi, "You are using arithmetic-geometric combination rules "
3835 "in LJ-PME, but your non-bonded C6 parameters do not "
3836 "follow these rules.");
3841 if (FALSE == bC6ParametersWorkWithGeometricRules)
3843 if (ir->eDispCorr != edispcNO)
3845 warning_note(wi, "You are using geometric combination rules in "
3846 "LJ-PME, but your non-bonded C6 parameters do "
3847 "not follow these rules. "
3848 "If your force field uses Lorentz-Berthelot combination rules this "
3849 "will introduce small errors in the forces and energies in "
3850 "your simulations. Dispersion correction will correct total "
3851 "energy and/or pressure, but not forces or surface tensions. "
3852 "Please check the LJ-PME section in the manual "
3853 "before proceeding further.");
3857 warning_note(wi, "You are using geometric combination rules in "
3858 "LJ-PME, but your non-bonded C6 parameters do "
3859 "not follow these rules. "
3860 "If your force field uses Lorentz-Berthelot combination rules this "
3861 "will introduce small errors in the forces and energies in "
3862 "your simulations. Consider using dispersion correction "
3863 "for the total energy and pressure. "
3864 "Please check the LJ-PME section in the manual "
3865 "before proceeding further.");
3871 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
3875 int i, m, c, nmol, npct;
3876 gmx_bool bCharge, bAcc;
3877 real gdt_max, *mgrp, mt;
3879 gmx_mtop_atomloop_block_t aloopb;
3880 gmx_mtop_atomloop_all_t aloop;
3883 char warn_buf[STRLEN];
3885 set_warning_line(wi, mdparin, -1);
3887 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
3888 ir->comm_mode == ecmNO &&
3889 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10))
3891 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");
3894 /* Check for pressure coupling with absolute position restraints */
3895 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
3897 absolute_reference(ir, sys, TRUE, AbsRef);
3899 for (m = 0; m < DIM; m++)
3901 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
3903 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
3911 aloopb = gmx_mtop_atomloop_block_init(sys);
3912 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
3914 if (atom->q != 0 || atom->qB != 0)
3922 if (EEL_FULL(ir->coulombtype))
3925 "You are using full electrostatics treatment %s for a system without charges.\n"
3926 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
3927 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
3928 warning(wi, err_buf);
3933 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
3936 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
3937 "You might want to consider using %s electrostatics.\n",
3939 warning_note(wi, err_buf);
3943 /* Check if combination rules used in LJ-PME are the same as in the force field */
3944 if (EVDW_PME(ir->vdwtype))
3946 check_combination_rules(ir, sys, wi);
3949 /* Generalized reaction field */
3950 if (ir->opts.ngtc == 0)
3952 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
3954 CHECK(ir->coulombtype == eelGRF);
3958 sprintf(err_buf, "When using coulombtype = %s"
3959 " ref-t for temperature coupling should be > 0",
3961 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
3964 if (ir->eI == eiSD1 &&
3965 (gmx_mtop_ftype_count(sys, F_CONSTR) > 0 ||
3966 gmx_mtop_ftype_count(sys, F_SETTLE) > 0))
3968 sprintf(warn_buf, "With constraints integrator %s is less accurate, consider using %s instead", ei_names[ir->eI], ei_names[eiSD2]);
3969 warning_note(wi, warn_buf);
3973 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
3975 for (m = 0; (m < DIM); m++)
3977 if (fabs(ir->opts.acc[i][m]) > 1e-6)
3986 snew(mgrp, sys->groups.grps[egcACC].nr);
3987 aloop = gmx_mtop_atomloop_all_init(sys);
3988 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
3990 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
3993 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
3995 for (m = 0; (m < DIM); m++)
3997 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4001 for (m = 0; (m < DIM); m++)
4003 if (fabs(acc[m]) > 1e-6)
4005 const char *dim[DIM] = { "X", "Y", "Z" };
4007 "Net Acceleration in %s direction, will %s be corrected\n",
4008 dim[m], ir->nstcomm != 0 ? "" : "not");
4009 if (ir->nstcomm != 0 && m < ndof_com(ir))
4012 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4014 ir->opts.acc[i][m] -= acc[m];
4022 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4023 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4025 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4028 if (ir->ePull != epullNO)
4030 gmx_bool bPullAbsoluteRef;
4032 bPullAbsoluteRef = FALSE;
4033 for (i = 0; i < ir->pull->ncoord; i++)
4035 bPullAbsoluteRef = bPullAbsoluteRef ||
4036 ir->pull->coord[i].group[0] == 0 ||
4037 ir->pull->coord[i].group[1] == 0;
4039 if (bPullAbsoluteRef)
4041 absolute_reference(ir, sys, FALSE, AbsRef);
4042 for (m = 0; m < DIM; m++)
4044 if (ir->pull->dim[m] && !AbsRef[m])
4046 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.");
4052 if (ir->pull->eGeom == epullgDIRPBC)
4054 for (i = 0; i < 3; i++)
4056 for (m = 0; m <= i; m++)
4058 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4059 ir->deform[i][m] != 0)
4061 for (c = 0; c < ir->pull->ncoord; c++)
4063 if (ir->pull->coord[c].vec[m] != 0)
4065 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->eGeom), 'x'+m);
4077 void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr, warninp_t wi)
4081 char warn_buf[STRLEN];
4084 ptr = check_box(ir->ePBC, box);
4087 warning_error(wi, ptr);
4090 if (bConstr && ir->eConstrAlg == econtSHAKE)
4092 if (ir->shake_tol <= 0.0)
4094 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4096 warning_error(wi, warn_buf);
4099 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
4101 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
4102 if (ir->epc == epcNO)
4104 warning(wi, warn_buf);
4108 warning_error(wi, warn_buf);
4113 if ( (ir->eConstrAlg == econtLINCS) && bConstr)
4115 /* If we have Lincs constraints: */
4116 if (ir->eI == eiMD && ir->etc == etcNO &&
4117 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4119 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4120 warning_note(wi, warn_buf);
4123 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4125 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4126 warning_note(wi, warn_buf);
4128 if (ir->epc == epcMTTK)
4130 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4134 if (ir->LincsWarnAngle > 90.0)
4136 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4137 warning(wi, warn_buf);
4138 ir->LincsWarnAngle = 90.0;
4141 if (ir->ePBC != epbcNONE)
4143 if (ir->nstlist == 0)
4145 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4147 bTWIN = (ir->rlistlong > ir->rlist);
4148 if (ir->ns_type == ensGRID)
4150 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
4152 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",
4153 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
4154 warning_error(wi, warn_buf);
4159 min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
4160 if (2*ir->rlistlong >= min_size)
4162 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4163 warning_error(wi, warn_buf);
4166 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4173 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4177 real rvdw1, rvdw2, rcoul1, rcoul2;
4178 char warn_buf[STRLEN];
4180 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4184 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4189 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4195 if (rvdw1 + rvdw2 > ir->rlist ||
4196 rcoul1 + rcoul2 > ir->rlist)
4199 "The sum of the two largest charge group radii (%f) "
4200 "is larger than rlist (%f)\n",
4201 max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4202 warning(wi, warn_buf);
4206 /* Here we do not use the zero at cut-off macro,
4207 * since user defined interactions might purposely
4208 * not be zero at the cut-off.
4210 if ((EVDW_IS_ZERO_AT_CUTOFF(ir->vdwtype) ||
4211 ir->vdw_modifier != eintmodNONE) &&
4212 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
4214 sprintf(warn_buf, "The sum of the two largest charge group "
4215 "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
4216 "With exact cut-offs, better performance can be "
4217 "obtained with cutoff-scheme = %s, because it "
4218 "does not use charge groups at all.",
4220 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4221 ir->rlistlong, ir->rvdw,
4222 ecutscheme_names[ecutsVERLET]);
4225 warning(wi, warn_buf);
4229 warning_note(wi, warn_buf);
4232 if ((EEL_IS_ZERO_AT_CUTOFF(ir->coulombtype) ||
4233 ir->coulomb_modifier != eintmodNONE) &&
4234 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
4236 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
4237 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4239 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4240 ir->rlistlong, ir->rcoulomb,
4241 ecutscheme_names[ecutsVERLET]);
4244 warning(wi, warn_buf);
4248 warning_note(wi, warn_buf);