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45 #include "gromacs/utility/smalloc.h"
49 #include "gromacs/utility/fatalerror.h"
53 #include "gromacs/utility/cstringutil.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],
85 char fep_lambda[efptNR][STRLEN];
86 char lambda_weights[STRLEN];
89 char anneal[STRLEN], anneal_npoints[STRLEN],
90 anneal_time[STRLEN], anneal_temp[STRLEN];
91 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
92 bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
93 SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
94 char efield_x[STRLEN], efield_xt[STRLEN], efield_y[STRLEN],
95 efield_yt[STRLEN], efield_z[STRLEN], efield_zt[STRLEN];
97 } gmx_inputrec_strings;
99 static gmx_inputrec_strings *is = NULL;
101 void init_inputrec_strings()
105 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.");
110 void done_inputrec_strings()
116 static char swapgrp[STRLEN], splitgrp0[STRLEN], splitgrp1[STRLEN], solgrp[STRLEN];
119 egrptpALL, /* All particles have to be a member of a group. */
120 egrptpALL_GENREST, /* A rest group with name is generated for particles *
121 * that are not part of any group. */
122 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
123 * for the rest group. */
124 egrptpONE /* Merge all selected groups into one group, *
125 * make a rest group for the remaining particles. */
128 static const char *constraints[eshNR+1] = {
129 "none", "h-bonds", "all-bonds", "h-angles", "all-angles", NULL
132 static const char *couple_lam[ecouplamNR+1] = {
133 "vdw-q", "vdw", "q", "none", NULL
136 void init_ir(t_inputrec *ir, t_gromppopts *opts)
138 snew(opts->include, STRLEN);
139 snew(opts->define, STRLEN);
140 snew(ir->fepvals, 1);
141 snew(ir->expandedvals, 1);
142 snew(ir->simtempvals, 1);
145 static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
150 for (i = 0; i < ntemps; i++)
152 /* simple linear scaling -- allows more control */
153 if (simtemp->eSimTempScale == esimtempLINEAR)
155 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*temperature_lambdas[i];
157 else if (simtemp->eSimTempScale == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
159 simtemp->temperatures[i] = simtemp->simtemp_low * pow(simtemp->simtemp_high/simtemp->simtemp_low, (1.0*i)/(ntemps-1));
161 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
163 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*((exp(temperature_lambdas[i])-1)/(exp(1.0)-1));
168 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
169 gmx_fatal(FARGS, errorstr);
176 static void _low_check(gmx_bool b, char *s, warninp_t wi)
180 warning_error(wi, s);
184 static void check_nst(const char *desc_nst, int nst,
185 const char *desc_p, int *p,
190 if (*p > 0 && *p % nst != 0)
192 /* Round up to the next multiple of nst */
193 *p = ((*p)/nst + 1)*nst;
194 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n",
195 desc_p, desc_nst, desc_p, *p);
200 static gmx_bool ir_NVE(const t_inputrec *ir)
202 return ((ir->eI == eiMD || EI_VV(ir->eI)) && ir->etc == etcNO);
205 static int lcd(int n1, int n2)
210 for (i = 2; (i <= n1 && i <= n2); i++)
212 if (n1 % i == 0 && n2 % i == 0)
221 static void process_interaction_modifier(const t_inputrec *ir, int *eintmod)
223 if (*eintmod == eintmodPOTSHIFT_VERLET)
225 if (ir->cutoff_scheme == ecutsVERLET)
227 *eintmod = eintmodPOTSHIFT;
231 *eintmod = eintmodNONE;
236 void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
238 /* Check internal consistency */
240 /* Strange macro: first one fills the err_buf, and then one can check
241 * the condition, which will print the message and increase the error
244 #define CHECK(b) _low_check(b, err_buf, wi)
245 char err_buf[256], warn_buf[STRLEN];
251 t_lambda *fep = ir->fepvals;
252 t_expanded *expand = ir->expandedvals;
254 set_warning_line(wi, mdparin, -1);
256 /* BASIC CUT-OFF STUFF */
257 if (ir->rcoulomb < 0)
259 warning_error(wi, "rcoulomb should be >= 0");
263 warning_error(wi, "rvdw should be >= 0");
266 !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
268 warning_error(wi, "rlist should be >= 0");
271 process_interaction_modifier(ir, &ir->coulomb_modifier);
272 process_interaction_modifier(ir, &ir->vdw_modifier);
274 if (ir->cutoff_scheme == ecutsGROUP)
277 "The group cutoff scheme is deprecated in Gromacs 5.0 and will be removed in a future "
278 "release when all interaction forms are supported for the verlet scheme. The verlet "
279 "scheme already scales better, and it is compatible with GPUs and other accelerators.");
281 /* BASIC CUT-OFF STUFF */
282 if (ir->rlist == 0 ||
283 !((ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > ir->rlist) ||
284 (ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > ir->rlist)))
286 /* No switched potential and/or no twin-range:
287 * we can set the long-range cut-off to the maximum of the other cut-offs.
289 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
291 else if (ir->rlistlong < 0)
293 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
294 sprintf(warn_buf, "rlistlong was not set, setting it to %g (no buffer)",
296 warning(wi, warn_buf);
298 if (ir->rlistlong == 0 && ir->ePBC != epbcNONE)
300 warning_error(wi, "Can not have an infinite cut-off with PBC");
302 if (ir->rlistlong > 0 && (ir->rlist == 0 || ir->rlistlong < ir->rlist))
304 warning_error(wi, "rlistlong can not be shorter than rlist");
306 if (IR_TWINRANGE(*ir) && ir->nstlist <= 0)
308 warning_error(wi, "Can not have nstlist<=0 with twin-range interactions");
312 if (ir->rlistlong == ir->rlist)
316 else if (ir->rlistlong > ir->rlist && ir->nstcalclr == 0)
318 warning_error(wi, "With different cutoffs for electrostatics and VdW, nstcalclr must be -1 or a positive number");
321 if (ir->cutoff_scheme == ecutsVERLET)
325 /* Normal Verlet type neighbor-list, currently only limited feature support */
326 if (inputrec2nboundeddim(ir) < 3)
328 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
330 if (ir->rcoulomb != ir->rvdw)
332 warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported");
334 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
336 if (ir->vdw_modifier == eintmodNONE ||
337 ir->vdw_modifier == eintmodPOTSHIFT)
339 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
341 sprintf(warn_buf, "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], evdw_names[evdwCUT], eintmod_names[ir->vdw_modifier]);
342 warning_note(wi, warn_buf);
344 ir->vdwtype = evdwCUT;
348 sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
349 warning_error(wi, warn_buf);
353 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
355 warning_error(wi, "With Verlet lists only cut-off and PME LJ interactions are supported");
357 if (!(ir->coulombtype == eelCUT ||
358 (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC) ||
359 EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
361 warning_error(wi, "With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
363 if (!(ir->coulomb_modifier == eintmodNONE ||
364 ir->coulomb_modifier == eintmodPOTSHIFT))
366 sprintf(warn_buf, "coulomb_modifier=%s is not supported with the Verlet cut-off scheme", eintmod_names[ir->coulomb_modifier]);
367 warning_error(wi, warn_buf);
370 if (ir->nstlist <= 0)
372 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
375 if (ir->nstlist < 10)
377 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.");
380 rc_max = max(ir->rvdw, ir->rcoulomb);
382 if (ir->verletbuf_tol <= 0)
384 if (ir->verletbuf_tol == 0)
386 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
389 if (ir->rlist < rc_max)
391 warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
394 if (ir->rlist == rc_max && ir->nstlist > 1)
396 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.");
401 if (ir->rlist > rc_max)
403 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.");
406 if (ir->nstlist == 1)
408 /* No buffer required */
413 if (EI_DYNAMICS(ir->eI))
415 if (inputrec2nboundeddim(ir) < 3)
417 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.");
419 /* Set rlist temporarily so we can continue processing */
424 /* Set the buffer to 5% of the cut-off */
425 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
430 /* No twin-range calculations with Verlet lists */
431 ir->rlistlong = ir->rlist;
434 if (ir->nstcalclr == -1)
436 /* if rlist=rlistlong, this will later be changed to nstcalclr=0 */
437 ir->nstcalclr = ir->nstlist;
439 else if (ir->nstcalclr > 0)
441 if (ir->nstlist > 0 && (ir->nstlist % ir->nstcalclr != 0))
443 warning_error(wi, "nstlist must be evenly divisible by nstcalclr. Use nstcalclr = -1 to automatically follow nstlist");
446 else if (ir->nstcalclr < -1)
448 warning_error(wi, "nstcalclr must be a positive number (divisor of nstcalclr), or -1 to follow nstlist.");
451 if (EEL_PME(ir->coulombtype) && ir->rcoulomb > ir->rvdw && ir->nstcalclr > 1)
453 warning_error(wi, "When used with PME, the long-range component of twin-range interactions must be updated every step (nstcalclr)");
456 /* GENERAL INTEGRATOR STUFF */
457 if (!(ir->eI == eiMD || EI_VV(ir->eI)))
461 if (ir->eI == eiVVAK)
463 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]);
464 warning_note(wi, warn_buf);
466 if (!EI_DYNAMICS(ir->eI))
470 if (EI_DYNAMICS(ir->eI))
472 if (ir->nstcalcenergy < 0)
474 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
475 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
477 /* nstcalcenergy larger than nstener does not make sense.
478 * We ideally want nstcalcenergy=nstener.
482 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
486 ir->nstcalcenergy = ir->nstenergy;
490 else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
491 (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
492 (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
495 const char *nsten = "nstenergy";
496 const char *nstdh = "nstdhdl";
497 const char *min_name = nsten;
498 int min_nst = ir->nstenergy;
500 /* find the smallest of ( nstenergy, nstdhdl ) */
501 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
502 (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
504 min_nst = ir->fepvals->nstdhdl;
507 /* If the user sets nstenergy small, we should respect that */
509 "Setting nstcalcenergy (%d) equal to %s (%d)",
510 ir->nstcalcenergy, min_name, min_nst);
511 warning_note(wi, warn_buf);
512 ir->nstcalcenergy = min_nst;
515 if (ir->epc != epcNO)
517 if (ir->nstpcouple < 0)
519 ir->nstpcouple = ir_optimal_nstpcouple(ir);
522 if (IR_TWINRANGE(*ir))
524 check_nst("nstlist", ir->nstlist,
525 "nstcalcenergy", &ir->nstcalcenergy, wi);
526 if (ir->epc != epcNO)
528 check_nst("nstlist", ir->nstlist,
529 "nstpcouple", &ir->nstpcouple, wi);
533 if (ir->nstcalcenergy > 0)
535 if (ir->efep != efepNO)
537 /* nstdhdl should be a multiple of nstcalcenergy */
538 check_nst("nstcalcenergy", ir->nstcalcenergy,
539 "nstdhdl", &ir->fepvals->nstdhdl, wi);
540 /* nstexpanded should be a multiple of nstcalcenergy */
541 check_nst("nstcalcenergy", ir->nstcalcenergy,
542 "nstexpanded", &ir->expandedvals->nstexpanded, wi);
544 /* for storing exact averages nstenergy should be
545 * a multiple of nstcalcenergy
547 check_nst("nstcalcenergy", ir->nstcalcenergy,
548 "nstenergy", &ir->nstenergy, wi);
553 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
554 ir->bContinuation && ir->ld_seed != -1)
556 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)");
562 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
563 CHECK(ir->ePBC != epbcXYZ);
564 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
565 CHECK(ir->ns_type != ensGRID);
566 sprintf(err_buf, "with TPI nstlist should be larger than zero");
567 CHECK(ir->nstlist <= 0);
568 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
569 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
573 if ( (opts->nshake > 0) && (opts->bMorse) )
576 "Using morse bond-potentials while constraining bonds is useless");
577 warning(wi, warn_buf);
580 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
581 ir->bContinuation && ir->ld_seed != -1)
583 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)");
585 /* verify simulated tempering options */
589 gmx_bool bAllTempZero = TRUE;
590 for (i = 0; i < fep->n_lambda; i++)
592 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]);
593 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
594 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
596 bAllTempZero = FALSE;
599 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
600 CHECK(bAllTempZero == TRUE);
602 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
603 CHECK(ir->eI != eiVV);
605 /* check compatability of the temperature coupling with simulated tempering */
607 if (ir->etc == etcNOSEHOOVER)
609 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
610 warning_note(wi, warn_buf);
613 /* check that the temperatures make sense */
615 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);
616 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
618 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
619 CHECK(ir->simtempvals->simtemp_high <= 0);
621 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
622 CHECK(ir->simtempvals->simtemp_low <= 0);
625 /* verify free energy options */
627 if (ir->efep != efepNO)
630 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
632 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
634 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
635 (int)fep->sc_r_power);
636 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
638 sprintf(err_buf, "Can't use postive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
639 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
641 sprintf(err_buf, "Can't use postive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
642 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
644 sprintf(err_buf, "Can only use expanded ensemble with md-vv for now; should be supported for other integrators in 5.0");
645 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
647 sprintf(err_buf, "Free-energy not implemented for Ewald");
648 CHECK(ir->coulombtype == eelEWALD);
650 /* check validty of lambda inputs */
651 if (fep->n_lambda == 0)
653 /* Clear output in case of no states:*/
654 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
655 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
659 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
660 CHECK((fep->init_fep_state >= fep->n_lambda));
663 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
664 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
666 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",
667 fep->init_lambda, fep->init_fep_state);
668 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
672 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
676 for (i = 0; i < efptNR; i++)
678 if (fep->separate_dvdl[i])
683 if (n_lambda_terms > 1)
685 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.");
686 warning(wi, warn_buf);
689 if (n_lambda_terms < 2 && fep->n_lambda > 0)
692 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
696 for (j = 0; j < efptNR; j++)
698 for (i = 0; i < fep->n_lambda; i++)
700 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]);
701 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
705 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
707 for (i = 0; i < fep->n_lambda; i++)
709 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],
710 fep->all_lambda[efptCOUL][i]);
711 CHECK((fep->sc_alpha > 0) &&
712 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
713 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
714 ((fep->all_lambda[efptVDW][i] > 0.0) &&
715 (fep->all_lambda[efptVDW][i] < 1.0))));
719 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
721 real sigma, lambda, r_sc;
724 /* Maximum estimate for A and B charges equal with lambda power 1 */
726 r_sc = pow(lambda*fep->sc_alpha*pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
727 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.",
729 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
730 warning_note(wi, warn_buf);
733 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
734 be treated differently, but that's the next step */
736 for (i = 0; i < efptNR; i++)
738 for (j = 0; j < fep->n_lambda; j++)
740 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
741 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
746 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
749 expand = ir->expandedvals;
751 /* checking equilibration of weights inputs for validity */
753 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
754 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
755 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
757 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
758 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
759 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
761 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
762 expand->equil_steps, elmceq_names[elmceqSTEPS]);
763 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
765 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
766 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
767 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
769 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
770 expand->equil_ratio, elmceq_names[elmceqRATIO]);
771 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
773 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
774 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
775 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
777 sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
778 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
779 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
781 sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
782 expand->equil_steps, elmceq_names[elmceqSTEPS]);
783 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
785 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
786 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
787 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
789 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
790 expand->equil_ratio, elmceq_names[elmceqRATIO]);
791 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
793 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
794 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
795 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
797 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
798 CHECK((expand->lmc_repeats <= 0));
799 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
800 CHECK((expand->minvarmin <= 0));
801 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
802 CHECK((expand->c_range < 0));
803 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
804 fep->init_fep_state, expand->lmc_forced_nstart);
805 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
806 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
807 CHECK((expand->lmc_forced_nstart < 0));
808 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
809 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
811 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
812 CHECK((expand->init_wl_delta < 0));
813 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
814 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
815 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
816 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
818 /* if there is no temperature control, we need to specify an MC temperature */
819 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
820 if (expand->nstTij > 0)
822 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
823 expand->nstTij, ir->nstlog);
824 CHECK((mod(expand->nstTij, ir->nstlog) != 0));
829 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
830 CHECK(ir->nwall && ir->ePBC != epbcXY);
833 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
835 if (ir->ePBC == epbcNONE)
837 if (ir->epc != epcNO)
839 warning(wi, "Turning off pressure coupling for vacuum system");
845 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
846 epbc_names[ir->ePBC]);
847 CHECK(ir->epc != epcNO);
849 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
850 CHECK(EEL_FULL(ir->coulombtype));
852 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
853 epbc_names[ir->ePBC]);
854 CHECK(ir->eDispCorr != edispcNO);
857 if (ir->rlist == 0.0)
859 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
860 "with coulombtype = %s or coulombtype = %s\n"
861 "without periodic boundary conditions (pbc = %s) and\n"
862 "rcoulomb and rvdw set to zero",
863 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
864 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
865 (ir->ePBC != epbcNONE) ||
866 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
870 warning_error(wi, "Can not have heuristic neighborlist updates without cut-off");
874 warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
879 if (ir->nstcomm == 0)
881 ir->comm_mode = ecmNO;
883 if (ir->comm_mode != ecmNO)
887 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");
888 ir->nstcomm = abs(ir->nstcomm);
891 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
893 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
894 ir->nstcomm = ir->nstcalcenergy;
897 if (ir->comm_mode == ecmANGULAR)
899 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
900 CHECK(ir->bPeriodicMols);
901 if (ir->ePBC != epbcNONE)
903 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).");
908 if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
910 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.");
913 sprintf(err_buf, "Twin-range neighbour searching (NS) with simple NS"
914 " algorithm not implemented");
915 CHECK(((ir->rcoulomb > ir->rlist) || (ir->rvdw > ir->rlist))
916 && (ir->ns_type == ensSIMPLE));
918 /* TEMPERATURE COUPLING */
919 if (ir->etc == etcYES)
921 ir->etc = etcBERENDSEN;
922 warning_note(wi, "Old option for temperature coupling given: "
923 "changing \"yes\" to \"Berendsen\"\n");
926 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
928 if (ir->opts.nhchainlength < 1)
930 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
931 ir->opts.nhchainlength = 1;
932 warning(wi, warn_buf);
935 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
937 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
938 ir->opts.nhchainlength = 1;
943 ir->opts.nhchainlength = 0;
946 if (ir->eI == eiVVAK)
948 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
950 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
953 if (ETC_ANDERSEN(ir->etc))
955 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
956 CHECK(!(EI_VV(ir->eI)));
958 for (i = 0; i < ir->opts.ngtc; i++)
960 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
961 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
962 sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
963 i, ir->opts.tau_t[i]);
964 CHECK(ir->opts.tau_t[i] < 0);
966 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
968 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]);
969 warning_note(wi, warn_buf);
972 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]);
973 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
975 for (i = 0; i < ir->opts.ngtc; i++)
977 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
978 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);
979 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
982 if (ir->etc == etcBERENDSEN)
984 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
985 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
986 warning_note(wi, warn_buf);
989 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
990 && ir->epc == epcBERENDSEN)
992 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
993 "true ensemble for the thermostat");
994 warning(wi, warn_buf);
997 /* PRESSURE COUPLING */
998 if (ir->epc == epcISOTROPIC)
1000 ir->epc = epcBERENDSEN;
1001 warning_note(wi, "Old option for pressure coupling given: "
1002 "changing \"Isotropic\" to \"Berendsen\"\n");
1005 if (ir->epc != epcNO)
1007 dt_pcoupl = ir->nstpcouple*ir->delta_t;
1009 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1010 CHECK(ir->tau_p <= 0);
1012 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc))
1014 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
1015 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1016 warning(wi, warn_buf);
1019 sprintf(err_buf, "compressibility must be > 0 when using pressure"
1020 " coupling %s\n", EPCOUPLTYPE(ir->epc));
1021 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
1022 ir->compress[ZZ][ZZ] < 0 ||
1023 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
1024 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
1026 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1029 "You are generating velocities so I am assuming you "
1030 "are equilibrating a system. You are using "
1031 "%s pressure coupling, but this can be "
1032 "unstable for equilibration. If your system crashes, try "
1033 "equilibrating first with Berendsen pressure coupling. If "
1034 "you are not equilibrating the system, you can probably "
1035 "ignore this warning.",
1036 epcoupl_names[ir->epc]);
1037 warning(wi, warn_buf);
1043 if (ir->epc > epcNO)
1045 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1047 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.");
1053 if (ir->epc == epcMTTK)
1055 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1059 /* ELECTROSTATICS */
1060 /* More checks are in triple check (grompp.c) */
1062 if (ir->coulombtype == eelSWITCH)
1064 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1065 "artifacts, advice: use coulombtype = %s",
1066 eel_names[ir->coulombtype],
1067 eel_names[eelRF_ZERO]);
1068 warning(wi, warn_buf);
1071 if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
1073 sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
1074 warning_note(wi, warn_buf);
1077 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1079 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);
1080 warning(wi, warn_buf);
1081 ir->epsilon_rf = ir->epsilon_r;
1082 ir->epsilon_r = 1.0;
1085 if (getenv("GALACTIC_DYNAMICS") == NULL)
1087 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1088 CHECK(ir->epsilon_r < 0);
1091 if (EEL_RF(ir->coulombtype))
1093 /* reaction field (at the cut-off) */
1095 if (ir->coulombtype == eelRF_ZERO)
1097 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1098 eel_names[ir->coulombtype]);
1099 CHECK(ir->epsilon_rf != 0);
1100 ir->epsilon_rf = 0.0;
1103 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1104 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1105 (ir->epsilon_r == 0));
1106 if (ir->epsilon_rf == ir->epsilon_r)
1108 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1109 eel_names[ir->coulombtype]);
1110 warning(wi, warn_buf);
1113 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1114 * means the interaction is zero outside rcoulomb, but it helps to
1115 * provide accurate energy conservation.
1117 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1119 if (ir_coulomb_switched(ir))
1122 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1123 eel_names[ir->coulombtype]);
1124 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1127 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1129 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1131 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1132 eel_names[ir->coulombtype]);
1133 CHECK(ir->rlist > ir->rcoulomb);
1137 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1138 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1141 "The switch/shift interaction settings are just for compatibility; you will get better "
1142 "performance from applying potential modifiers to your interactions!\n");
1143 warning_note(wi, warn_buf);
1146 if (ir->coulombtype == eelPMESWITCH)
1148 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1150 sprintf(warn_buf, "The switching range for %s should be 5%% or less, energy conservation will be good anyhow, since ewald_rtol = %g",
1151 eel_names[ir->coulombtype],
1153 warning(wi, warn_buf);
1157 if (EEL_FULL(ir->coulombtype))
1159 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1160 ir->coulombtype == eelPMEUSERSWITCH)
1162 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1163 eel_names[ir->coulombtype]);
1164 CHECK(ir->rcoulomb > ir->rlist);
1166 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1168 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1171 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
1172 "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
1173 "a potential modifier.", eel_names[ir->coulombtype]);
1174 if (ir->nstcalclr == 1)
1176 CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
1180 CHECK(ir->rcoulomb != ir->rlist);
1186 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1188 if (ir->pme_order < 3)
1190 warning_error(wi, "pme-order can not be smaller than 3");
1194 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1196 if (ir->ewald_geometry == eewg3D)
1198 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1199 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1200 warning(wi, warn_buf);
1202 /* This check avoids extra pbc coding for exclusion corrections */
1203 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1204 CHECK(ir->wall_ewald_zfac < 2);
1207 if (ir_vdw_switched(ir))
1209 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1210 CHECK(ir->rvdw_switch >= ir->rvdw);
1212 if (ir->rvdw_switch < 0.5*ir->rvdw)
1214 sprintf(warn_buf, "You are applying a switch function to vdw forces or potentials from %g to %g nm, which is more than half the interaction range, whereas switch functions are intended to act only close to the cut-off.",
1215 ir->rvdw_switch, ir->rvdw);
1216 warning_note(wi, warn_buf);
1219 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1221 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1223 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1224 CHECK(ir->rlist > ir->rvdw);
1228 if (ir->vdwtype == evdwPME)
1230 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1232 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s a\
1234 evdw_names[ir->vdwtype],
1235 eintmod_names[eintmodPOTSHIFT],
1236 eintmod_names[eintmodNONE]);
1240 if (ir->cutoff_scheme == ecutsGROUP)
1242 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1243 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)) &&
1246 warning_note(wi, "With exact cut-offs, rlist should be "
1247 "larger than rcoulomb and rvdw, so that there "
1248 "is a buffer region for particle motion "
1249 "between neighborsearch steps");
1252 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlistlong <= ir->rcoulomb)
1254 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
1255 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1256 warning_note(wi, warn_buf);
1258 if (ir_vdw_switched(ir) && (ir->rlistlong <= ir->rvdw))
1260 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
1261 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1262 warning_note(wi, warn_buf);
1266 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1268 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.");
1271 if (ir->nstlist == -1)
1273 sprintf(err_buf, "With nstlist=-1 rvdw and rcoulomb should be smaller than rlist to account for diffusion and possibly charge-group radii");
1274 CHECK(ir->rvdw >= ir->rlist || ir->rcoulomb >= ir->rlist);
1276 sprintf(err_buf, "nstlist can not be smaller than -1");
1277 CHECK(ir->nstlist < -1);
1279 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1282 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1285 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1287 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1290 /* ENERGY CONSERVATION */
1291 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1293 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1295 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1296 evdw_names[evdwSHIFT]);
1297 warning_note(wi, warn_buf);
1299 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1301 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1302 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1303 warning_note(wi, warn_buf);
1307 /* IMPLICIT SOLVENT */
1308 if (ir->coulombtype == eelGB_NOTUSED)
1310 ir->coulombtype = eelCUT;
1311 ir->implicit_solvent = eisGBSA;
1312 fprintf(stderr, "Note: Old option for generalized born electrostatics given:\n"
1313 "Changing coulombtype from \"generalized-born\" to \"cut-off\" and instead\n"
1314 "setting implicit-solvent value to \"GBSA\" in input section.\n");
1317 if (ir->sa_algorithm == esaSTILL)
1319 sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
1320 CHECK(ir->sa_algorithm == esaSTILL);
1323 if (ir->implicit_solvent == eisGBSA)
1325 sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
1326 CHECK(ir->rgbradii != ir->rlist);
1328 if (ir->coulombtype != eelCUT)
1330 sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
1331 CHECK(ir->coulombtype != eelCUT);
1333 if (ir->vdwtype != evdwCUT)
1335 sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
1336 CHECK(ir->vdwtype != evdwCUT);
1338 if (ir->nstgbradii < 1)
1340 sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
1341 warning_note(wi, warn_buf);
1344 if (ir->sa_algorithm == esaNO)
1346 sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
1347 warning_note(wi, warn_buf);
1349 if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
1351 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");
1352 warning_note(wi, warn_buf);
1354 if (ir->gb_algorithm == egbSTILL)
1356 ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
1360 ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
1363 if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
1365 sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
1366 CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
1373 if (ir->cutoff_scheme != ecutsGROUP)
1375 warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
1379 warning_error(wi, "AdresS simulation supports only stochastic dynamics");
1381 if (ir->epc != epcNO)
1383 warning_error(wi, "AdresS simulation does not support pressure coupling");
1385 if (EEL_FULL(ir->coulombtype))
1387 warning_error(wi, "AdresS simulation does not support long-range electrostatics");
1392 /* count the number of text elemets separated by whitespace in a string.
1393 str = the input string
1394 maxptr = the maximum number of allowed elements
1395 ptr = the output array of pointers to the first character of each element
1396 returns: the number of elements. */
1397 int str_nelem(const char *str, int maxptr, char *ptr[])
1402 copy0 = strdup(str);
1405 while (*copy != '\0')
1409 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1417 while ((*copy != '\0') && !isspace(*copy))
1436 /* interpret a number of doubles from a string and put them in an array,
1437 after allocating space for them.
1438 str = the input string
1439 n = the (pre-allocated) number of doubles read
1440 r = the output array of doubles. */
1441 static void parse_n_real(char *str, int *n, real **r)
1446 *n = str_nelem(str, MAXPTR, ptr);
1449 for (i = 0; i < *n; i++)
1451 (*r)[i] = strtod(ptr[i], NULL);
1455 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
1458 int i, j, max_n_lambda, nweights, nfep[efptNR];
1459 t_lambda *fep = ir->fepvals;
1460 t_expanded *expand = ir->expandedvals;
1461 real **count_fep_lambdas;
1462 gmx_bool bOneLambda = TRUE;
1464 snew(count_fep_lambdas, efptNR);
1466 /* FEP input processing */
1467 /* first, identify the number of lambda values for each type.
1468 All that are nonzero must have the same number */
1470 for (i = 0; i < efptNR; i++)
1472 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
1475 /* now, determine the number of components. All must be either zero, or equal. */
1478 for (i = 0; i < efptNR; i++)
1480 if (nfep[i] > max_n_lambda)
1482 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1483 must have the same number if its not zero.*/
1488 for (i = 0; i < efptNR; i++)
1492 ir->fepvals->separate_dvdl[i] = FALSE;
1494 else if (nfep[i] == max_n_lambda)
1496 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1497 respect to the temperature currently */
1499 ir->fepvals->separate_dvdl[i] = TRUE;
1504 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1505 nfep[i], efpt_names[i], max_n_lambda);
1508 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1509 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1511 /* the number of lambdas is the number we've read in, which is either zero
1512 or the same for all */
1513 fep->n_lambda = max_n_lambda;
1515 /* allocate space for the array of lambda values */
1516 snew(fep->all_lambda, efptNR);
1517 /* if init_lambda is defined, we need to set lambda */
1518 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1520 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1522 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1523 for (i = 0; i < efptNR; i++)
1525 snew(fep->all_lambda[i], fep->n_lambda);
1526 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1529 for (j = 0; j < fep->n_lambda; j++)
1531 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1533 sfree(count_fep_lambdas[i]);
1536 sfree(count_fep_lambdas);
1538 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1539 bookkeeping -- for now, init_lambda */
1541 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1543 for (i = 0; i < fep->n_lambda; i++)
1545 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1549 /* check to see if only a single component lambda is defined, and soft core is defined.
1550 In this case, turn on coulomb soft core */
1552 if (max_n_lambda == 0)
1558 for (i = 0; i < efptNR; i++)
1560 if ((nfep[i] != 0) && (i != efptFEP))
1566 if ((bOneLambda) && (fep->sc_alpha > 0))
1568 fep->bScCoul = TRUE;
1571 /* Fill in the others with the efptFEP if they are not explicitly
1572 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1573 they are all zero. */
1575 for (i = 0; i < efptNR; i++)
1577 if ((nfep[i] == 0) && (i != efptFEP))
1579 for (j = 0; j < fep->n_lambda; j++)
1581 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1587 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1588 if (fep->sc_r_power == 48)
1590 if (fep->sc_alpha > 0.1)
1592 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1596 expand = ir->expandedvals;
1597 /* now read in the weights */
1598 parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
1601 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1603 else if (nweights != fep->n_lambda)
1605 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1606 nweights, fep->n_lambda);
1608 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1610 expand->nstexpanded = fep->nstdhdl;
1611 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1613 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1615 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1616 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1617 2*tau_t just to be careful so it's not to frequent */
1622 static void do_simtemp_params(t_inputrec *ir)
1625 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1626 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1631 static void do_wall_params(t_inputrec *ir,
1632 char *wall_atomtype, char *wall_density,
1636 char *names[MAXPTR];
1639 opts->wall_atomtype[0] = NULL;
1640 opts->wall_atomtype[1] = NULL;
1642 ir->wall_atomtype[0] = -1;
1643 ir->wall_atomtype[1] = -1;
1644 ir->wall_density[0] = 0;
1645 ir->wall_density[1] = 0;
1649 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1650 if (nstr != ir->nwall)
1652 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1655 for (i = 0; i < ir->nwall; i++)
1657 opts->wall_atomtype[i] = strdup(names[i]);
1660 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1662 nstr = str_nelem(wall_density, MAXPTR, names);
1663 if (nstr != ir->nwall)
1665 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1667 for (i = 0; i < ir->nwall; i++)
1669 sscanf(names[i], "%lf", &dbl);
1672 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1674 ir->wall_density[i] = dbl;
1680 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1688 srenew(groups->grpname, groups->ngrpname+nwall);
1689 grps = &(groups->grps[egcENER]);
1690 srenew(grps->nm_ind, grps->nr+nwall);
1691 for (i = 0; i < nwall; i++)
1693 sprintf(str, "wall%d", i);
1694 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1695 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1700 void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1701 t_expanded *expand, warninp_t wi)
1703 int ninp, nerror = 0;
1709 /* read expanded ensemble parameters */
1710 CCTYPE ("expanded ensemble variables");
1711 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1712 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1713 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1714 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1715 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1716 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1717 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1718 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1719 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1720 CCTYPE("Seed for Monte Carlo in lambda space");
1721 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1722 RTYPE ("mc-temperature", expand->mc_temp, -1);
1723 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1724 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1725 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1726 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1727 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1728 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1729 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1730 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1731 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1732 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1733 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
1741 void get_ir(const char *mdparin, const char *mdparout,
1742 t_inputrec *ir, t_gromppopts *opts,
1746 double dumdub[2][6];
1750 char warn_buf[STRLEN];
1751 t_lambda *fep = ir->fepvals;
1752 t_expanded *expand = ir->expandedvals;
1754 init_inputrec_strings();
1755 inp = read_inpfile(mdparin, &ninp, wi);
1757 snew(dumstr[0], STRLEN);
1758 snew(dumstr[1], STRLEN);
1760 if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
1763 "%s did not specify a value for the .mdp option "
1764 "\"cutoff-scheme\". Probably it was first intended for use "
1765 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1766 "introduced, but the group scheme was still the default. "
1767 "The default is now the Verlet scheme, so you will observe "
1768 "different behaviour.", mdparin);
1769 warning_note(wi, warn_buf);
1772 /* remove the following deprecated commands */
1775 REM_TYPE("domain-decomposition");
1776 REM_TYPE("andersen-seed");
1778 REM_TYPE("dihre-fc");
1779 REM_TYPE("dihre-tau");
1780 REM_TYPE("nstdihreout");
1781 REM_TYPE("nstcheckpoint");
1783 /* replace the following commands with the clearer new versions*/
1784 REPL_TYPE("unconstrained-start", "continuation");
1785 REPL_TYPE("foreign-lambda", "fep-lambdas");
1786 REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
1787 REPL_TYPE("nstxtcout", "nstxout-compressed");
1788 REPL_TYPE("xtc-grps", "compressed-x-grps");
1789 REPL_TYPE("xtc-precision", "compressed-x-precision");
1791 CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
1792 CTYPE ("Preprocessor information: use cpp syntax.");
1793 CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
1794 STYPE ("include", opts->include, NULL);
1795 CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1796 STYPE ("define", opts->define, NULL);
1798 CCTYPE ("RUN CONTROL PARAMETERS");
1799 EETYPE("integrator", ir->eI, ei_names);
1800 CTYPE ("Start time and timestep in ps");
1801 RTYPE ("tinit", ir->init_t, 0.0);
1802 RTYPE ("dt", ir->delta_t, 0.001);
1803 STEPTYPE ("nsteps", ir->nsteps, 0);
1804 CTYPE ("For exact run continuation or redoing part of a run");
1805 STEPTYPE ("init-step", ir->init_step, 0);
1806 CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
1807 ITYPE ("simulation-part", ir->simulation_part, 1);
1808 CTYPE ("mode for center of mass motion removal");
1809 EETYPE("comm-mode", ir->comm_mode, ecm_names);
1810 CTYPE ("number of steps for center of mass motion removal");
1811 ITYPE ("nstcomm", ir->nstcomm, 100);
1812 CTYPE ("group(s) for center of mass motion removal");
1813 STYPE ("comm-grps", is->vcm, NULL);
1815 CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
1816 CTYPE ("Friction coefficient (amu/ps) and random seed");
1817 RTYPE ("bd-fric", ir->bd_fric, 0.0);
1818 STEPTYPE ("ld-seed", ir->ld_seed, -1);
1821 CCTYPE ("ENERGY MINIMIZATION OPTIONS");
1822 CTYPE ("Force tolerance and initial step-size");
1823 RTYPE ("emtol", ir->em_tol, 10.0);
1824 RTYPE ("emstep", ir->em_stepsize, 0.01);
1825 CTYPE ("Max number of iterations in relax-shells");
1826 ITYPE ("niter", ir->niter, 20);
1827 CTYPE ("Step size (ps^2) for minimization of flexible constraints");
1828 RTYPE ("fcstep", ir->fc_stepsize, 0);
1829 CTYPE ("Frequency of steepest descents steps when doing CG");
1830 ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
1831 ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
1833 CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
1834 RTYPE ("rtpi", ir->rtpi, 0.05);
1836 /* Output options */
1837 CCTYPE ("OUTPUT CONTROL OPTIONS");
1838 CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
1839 ITYPE ("nstxout", ir->nstxout, 0);
1840 ITYPE ("nstvout", ir->nstvout, 0);
1841 ITYPE ("nstfout", ir->nstfout, 0);
1842 ir->nstcheckpoint = 1000;
1843 CTYPE ("Output frequency for energies to log file and energy file");
1844 ITYPE ("nstlog", ir->nstlog, 1000);
1845 ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
1846 ITYPE ("nstenergy", ir->nstenergy, 1000);
1847 CTYPE ("Output frequency and precision for .xtc file");
1848 ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
1849 RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
1850 CTYPE ("This selects the subset of atoms for the compressed");
1851 CTYPE ("trajectory file. You can select multiple groups. By");
1852 CTYPE ("default, all atoms will be written.");
1853 STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
1854 CTYPE ("Selection of energy groups");
1855 STYPE ("energygrps", is->energy, NULL);
1857 /* Neighbor searching */
1858 CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
1859 CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1860 EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
1861 CTYPE ("nblist update frequency");
1862 ITYPE ("nstlist", ir->nstlist, 10);
1863 CTYPE ("ns algorithm (simple or grid)");
1864 EETYPE("ns-type", ir->ns_type, ens_names);
1865 /* set ndelta to the optimal value of 2 */
1867 CTYPE ("Periodic boundary conditions: xyz, no, xy");
1868 EETYPE("pbc", ir->ePBC, epbc_names);
1869 EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
1870 CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1871 CTYPE ("a value of -1 means: use rlist");
1872 RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
1873 CTYPE ("nblist cut-off");
1874 RTYPE ("rlist", ir->rlist, 1.0);
1875 CTYPE ("long-range cut-off for switched potentials");
1876 RTYPE ("rlistlong", ir->rlistlong, -1);
1877 ITYPE ("nstcalclr", ir->nstcalclr, -1);
1879 /* Electrostatics */
1880 CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
1881 CTYPE ("Method for doing electrostatics");
1882 EETYPE("coulombtype", ir->coulombtype, eel_names);
1883 EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
1884 CTYPE ("cut-off lengths");
1885 RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
1886 RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
1887 CTYPE ("Relative dielectric constant for the medium and the reaction field");
1888 RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
1889 RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
1890 CTYPE ("Method for doing Van der Waals");
1891 EETYPE("vdw-type", ir->vdwtype, evdw_names);
1892 EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
1893 CTYPE ("cut-off lengths");
1894 RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
1895 RTYPE ("rvdw", ir->rvdw, 1.0);
1896 CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
1897 EETYPE("DispCorr", ir->eDispCorr, edispc_names);
1898 CTYPE ("Extension of the potential lookup tables beyond the cut-off");
1899 RTYPE ("table-extension", ir->tabext, 1.0);
1900 CTYPE ("Separate tables between energy group pairs");
1901 STYPE ("energygrp-table", is->egptable, NULL);
1902 CTYPE ("Spacing for the PME/PPPM FFT grid");
1903 RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
1904 CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
1905 ITYPE ("fourier-nx", ir->nkx, 0);
1906 ITYPE ("fourier-ny", ir->nky, 0);
1907 ITYPE ("fourier-nz", ir->nkz, 0);
1908 CTYPE ("EWALD/PME/PPPM parameters");
1909 ITYPE ("pme-order", ir->pme_order, 4);
1910 RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
1911 RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
1912 EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
1913 EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
1914 RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
1915 EETYPE("optimize-fft", ir->bOptFFT, yesno_names);
1917 CCTYPE("IMPLICIT SOLVENT ALGORITHM");
1918 EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
1920 CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
1921 CTYPE ("Algorithm for calculating Born radii");
1922 EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
1923 CTYPE ("Frequency of calculating the Born radii inside rlist");
1924 ITYPE ("nstgbradii", ir->nstgbradii, 1);
1925 CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
1926 CTYPE ("between rlist and rgbradii is updated every nstlist steps");
1927 RTYPE ("rgbradii", ir->rgbradii, 1.0);
1928 CTYPE ("Dielectric coefficient of the implicit solvent");
1929 RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
1930 CTYPE ("Salt concentration in M for Generalized Born models");
1931 RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
1932 CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
1933 RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
1934 RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
1935 RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
1936 RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
1937 EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
1938 CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
1939 CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
1940 RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
1942 /* Coupling stuff */
1943 CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
1944 CTYPE ("Temperature coupling");
1945 EETYPE("tcoupl", ir->etc, etcoupl_names);
1946 ITYPE ("nsttcouple", ir->nsttcouple, -1);
1947 ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
1948 EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
1949 CTYPE ("Groups to couple separately");
1950 STYPE ("tc-grps", is->tcgrps, NULL);
1951 CTYPE ("Time constant (ps) and reference temperature (K)");
1952 STYPE ("tau-t", is->tau_t, NULL);
1953 STYPE ("ref-t", is->ref_t, NULL);
1954 CTYPE ("pressure coupling");
1955 EETYPE("pcoupl", ir->epc, epcoupl_names);
1956 EETYPE("pcoupltype", ir->epct, epcoupltype_names);
1957 ITYPE ("nstpcouple", ir->nstpcouple, -1);
1958 CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
1959 RTYPE ("tau-p", ir->tau_p, 1.0);
1960 STYPE ("compressibility", dumstr[0], NULL);
1961 STYPE ("ref-p", dumstr[1], NULL);
1962 CTYPE ("Scaling of reference coordinates, No, All or COM");
1963 EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
1966 CCTYPE ("OPTIONS FOR QMMM calculations");
1967 EETYPE("QMMM", ir->bQMMM, yesno_names);
1968 CTYPE ("Groups treated Quantum Mechanically");
1969 STYPE ("QMMM-grps", is->QMMM, NULL);
1970 CTYPE ("QM method");
1971 STYPE("QMmethod", is->QMmethod, NULL);
1972 CTYPE ("QMMM scheme");
1973 EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
1974 CTYPE ("QM basisset");
1975 STYPE("QMbasis", is->QMbasis, NULL);
1976 CTYPE ("QM charge");
1977 STYPE ("QMcharge", is->QMcharge, NULL);
1978 CTYPE ("QM multiplicity");
1979 STYPE ("QMmult", is->QMmult, NULL);
1980 CTYPE ("Surface Hopping");
1981 STYPE ("SH", is->bSH, NULL);
1982 CTYPE ("CAS space options");
1983 STYPE ("CASorbitals", is->CASorbitals, NULL);
1984 STYPE ("CASelectrons", is->CASelectrons, NULL);
1985 STYPE ("SAon", is->SAon, NULL);
1986 STYPE ("SAoff", is->SAoff, NULL);
1987 STYPE ("SAsteps", is->SAsteps, NULL);
1988 CTYPE ("Scale factor for MM charges");
1989 RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
1990 CTYPE ("Optimization of QM subsystem");
1991 STYPE ("bOPT", is->bOPT, NULL);
1992 STYPE ("bTS", is->bTS, NULL);
1994 /* Simulated annealing */
1995 CCTYPE("SIMULATED ANNEALING");
1996 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
1997 STYPE ("annealing", is->anneal, NULL);
1998 CTYPE ("Number of time points to use for specifying annealing in each group");
1999 STYPE ("annealing-npoints", is->anneal_npoints, NULL);
2000 CTYPE ("List of times at the annealing points for each group");
2001 STYPE ("annealing-time", is->anneal_time, NULL);
2002 CTYPE ("Temp. at each annealing point, for each group.");
2003 STYPE ("annealing-temp", is->anneal_temp, NULL);
2006 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
2007 EETYPE("gen-vel", opts->bGenVel, yesno_names);
2008 RTYPE ("gen-temp", opts->tempi, 300.0);
2009 ITYPE ("gen-seed", opts->seed, -1);
2012 CCTYPE ("OPTIONS FOR BONDS");
2013 EETYPE("constraints", opts->nshake, constraints);
2014 CTYPE ("Type of constraint algorithm");
2015 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
2016 CTYPE ("Do not constrain the start configuration");
2017 EETYPE("continuation", ir->bContinuation, yesno_names);
2018 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
2019 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
2020 CTYPE ("Relative tolerance of shake");
2021 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
2022 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
2023 ITYPE ("lincs-order", ir->nProjOrder, 4);
2024 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
2025 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
2026 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
2027 ITYPE ("lincs-iter", ir->nLincsIter, 1);
2028 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
2029 CTYPE ("rotates over more degrees than");
2030 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
2031 CTYPE ("Convert harmonic bonds to morse potentials");
2032 EETYPE("morse", opts->bMorse, yesno_names);
2034 /* Energy group exclusions */
2035 CCTYPE ("ENERGY GROUP EXCLUSIONS");
2036 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
2037 STYPE ("energygrp-excl", is->egpexcl, NULL);
2041 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2042 ITYPE ("nwall", ir->nwall, 0);
2043 EETYPE("wall-type", ir->wall_type, ewt_names);
2044 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
2045 STYPE ("wall-atomtype", is->wall_atomtype, NULL);
2046 STYPE ("wall-density", is->wall_density, NULL);
2047 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
2050 CCTYPE("COM PULLING");
2051 CTYPE("Pull type: no, umbrella, constraint or constant-force");
2052 EETYPE("pull", ir->ePull, epull_names);
2053 if (ir->ePull != epullNO)
2056 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
2059 /* Enforced rotation */
2060 CCTYPE("ENFORCED ROTATION");
2061 CTYPE("Enforced rotation: No or Yes");
2062 EETYPE("rotation", ir->bRot, yesno_names);
2066 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2069 /* Interactive MD */
2071 CCTYPE("Group to display and/or manipulate in interactive MD session");
2072 STYPE ("IMD-group", is->imd_grp, NULL);
2073 if (is->imd_grp[0] != '\0')
2080 CCTYPE("NMR refinement stuff");
2081 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2082 EETYPE("disre", ir->eDisre, edisre_names);
2083 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2084 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2085 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2086 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2087 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2088 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2089 CTYPE ("Output frequency for pair distances to energy file");
2090 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2091 CTYPE ("Orientation restraints: No or Yes");
2092 EETYPE("orire", opts->bOrire, yesno_names);
2093 CTYPE ("Orientation restraints force constant and tau for time averaging");
2094 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2095 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2096 STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
2097 CTYPE ("Output frequency for trace(SD) and S to energy file");
2098 ITYPE ("nstorireout", ir->nstorireout, 100);
2100 /* free energy variables */
2101 CCTYPE ("Free energy variables");
2102 EETYPE("free-energy", ir->efep, efep_names);
2103 STYPE ("couple-moltype", is->couple_moltype, NULL);
2104 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2105 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2106 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2108 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2110 it was not entered */
2111 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2112 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2113 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2114 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
2115 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
2116 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
2117 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
2118 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
2119 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
2120 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
2121 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2122 STYPE ("init-lambda-weights", is->lambda_weights, NULL);
2123 EETYPE("dhdl-print-energy", fep->bPrintEnergy, yesno_names);
2124 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2125 ITYPE ("sc-power", fep->sc_power, 1);
2126 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2127 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2128 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2129 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2130 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2131 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2132 separate_dhdl_file_names);
2133 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2134 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2135 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2137 /* Non-equilibrium MD stuff */
2138 CCTYPE("Non-equilibrium MD stuff");
2139 STYPE ("acc-grps", is->accgrps, NULL);
2140 STYPE ("accelerate", is->acc, NULL);
2141 STYPE ("freezegrps", is->freeze, NULL);
2142 STYPE ("freezedim", is->frdim, NULL);
2143 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2144 STYPE ("deform", is->deform, NULL);
2146 /* simulated tempering variables */
2147 CCTYPE("simulated tempering variables");
2148 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2149 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2150 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2151 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2153 /* expanded ensemble variables */
2154 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2156 read_expandedparams(&ninp, &inp, expand, wi);
2159 /* Electric fields */
2160 CCTYPE("Electric fields");
2161 CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
2162 CTYPE ("and a phase angle (real)");
2163 STYPE ("E-x", is->efield_x, NULL);
2164 STYPE ("E-xt", is->efield_xt, NULL);
2165 STYPE ("E-y", is->efield_y, NULL);
2166 STYPE ("E-yt", is->efield_yt, NULL);
2167 STYPE ("E-z", is->efield_z, NULL);
2168 STYPE ("E-zt", is->efield_zt, NULL);
2170 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2171 CTYPE("Swap positions along direction: no, X, Y, Z");
2172 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2173 if (ir->eSwapCoords != eswapNO)
2176 CTYPE("Swap attempt frequency");
2177 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2178 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2179 STYPE("split-group0", splitgrp0, NULL);
2180 STYPE("split-group1", splitgrp1, NULL);
2181 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2182 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2183 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2185 CTYPE("Group name of ions that can be exchanged with solvent molecules");
2186 STYPE("swap-group", swapgrp, NULL);
2187 CTYPE("Group name of solvent molecules");
2188 STYPE("solvent-group", solgrp, NULL);
2190 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2191 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2192 CTYPE("however, if correctly defined, the ion permeation events are counted per channel");
2193 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2194 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2195 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2196 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2197 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2198 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2200 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2201 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2202 CTYPE("Requested number of anions and cations for each of the two compartments");
2203 CTYPE("-1 means fix the numbers as found in time step 0");
2204 ITYPE("anionsA", ir->swap->nanions[0], -1);
2205 ITYPE("cationsA", ir->swap->ncations[0], -1);
2206 ITYPE("anionsB", ir->swap->nanions[1], -1);
2207 ITYPE("cationsB", ir->swap->ncations[1], -1);
2208 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2209 RTYPE("threshold", ir->swap->threshold, 1.0);
2212 /* AdResS defined thingies */
2213 CCTYPE ("AdResS parameters");
2214 EETYPE("adress", ir->bAdress, yesno_names);
2217 snew(ir->adress, 1);
2218 read_adressparams(&ninp, &inp, ir->adress, wi);
2221 /* User defined thingies */
2222 CCTYPE ("User defined thingies");
2223 STYPE ("user1-grps", is->user1, NULL);
2224 STYPE ("user2-grps", is->user2, NULL);
2225 ITYPE ("userint1", ir->userint1, 0);
2226 ITYPE ("userint2", ir->userint2, 0);
2227 ITYPE ("userint3", ir->userint3, 0);
2228 ITYPE ("userint4", ir->userint4, 0);
2229 RTYPE ("userreal1", ir->userreal1, 0);
2230 RTYPE ("userreal2", ir->userreal2, 0);
2231 RTYPE ("userreal3", ir->userreal3, 0);
2232 RTYPE ("userreal4", ir->userreal4, 0);
2235 write_inpfile(mdparout, ninp, inp, FALSE, wi);
2236 for (i = 0; (i < ninp); i++)
2239 sfree(inp[i].value);
2243 /* Process options if necessary */
2244 for (m = 0; m < 2; m++)
2246 for (i = 0; i < 2*DIM; i++)
2255 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2257 warning_error(wi, "Pressure coupling not enough values (I need 1)");
2259 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2261 case epctSEMIISOTROPIC:
2262 case epctSURFACETENSION:
2263 if (sscanf(dumstr[m], "%lf%lf",
2264 &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2266 warning_error(wi, "Pressure coupling not enough values (I need 2)");
2268 dumdub[m][YY] = dumdub[m][XX];
2270 case epctANISOTROPIC:
2271 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2272 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2273 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2275 warning_error(wi, "Pressure coupling not enough values (I need 6)");
2279 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2280 epcoupltype_names[ir->epct]);
2284 clear_mat(ir->ref_p);
2285 clear_mat(ir->compress);
2286 for (i = 0; i < DIM; i++)
2288 ir->ref_p[i][i] = dumdub[1][i];
2289 ir->compress[i][i] = dumdub[0][i];
2291 if (ir->epct == epctANISOTROPIC)
2293 ir->ref_p[XX][YY] = dumdub[1][3];
2294 ir->ref_p[XX][ZZ] = dumdub[1][4];
2295 ir->ref_p[YY][ZZ] = dumdub[1][5];
2296 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2298 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2300 ir->compress[XX][YY] = dumdub[0][3];
2301 ir->compress[XX][ZZ] = dumdub[0][4];
2302 ir->compress[YY][ZZ] = dumdub[0][5];
2303 for (i = 0; i < DIM; i++)
2305 for (m = 0; m < i; m++)
2307 ir->ref_p[i][m] = ir->ref_p[m][i];
2308 ir->compress[i][m] = ir->compress[m][i];
2313 if (ir->comm_mode == ecmNO)
2318 opts->couple_moltype = NULL;
2319 if (strlen(is->couple_moltype) > 0)
2321 if (ir->efep != efepNO)
2323 opts->couple_moltype = strdup(is->couple_moltype);
2324 if (opts->couple_lam0 == opts->couple_lam1)
2326 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2328 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2329 opts->couple_lam1 == ecouplamNONE))
2331 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2336 warning(wi, "Can not couple a molecule with free_energy = no");
2339 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2340 if (ir->efep != efepNO)
2342 if (fep->delta_lambda > 0)
2344 ir->efep = efepSLOWGROWTH;
2350 fep->bPrintEnergy = TRUE;
2351 /* always print out the energy to dhdl if we are doing expanded ensemble, since we need the total energy
2352 if the temperature is changing. */
2355 if ((ir->efep != efepNO) || ir->bSimTemp)
2357 ir->bExpanded = FALSE;
2358 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2360 ir->bExpanded = TRUE;
2362 do_fep_params(ir, is->fep_lambda, is->lambda_weights);
2363 if (ir->bSimTemp) /* done after fep params */
2365 do_simtemp_params(ir);
2370 ir->fepvals->n_lambda = 0;
2373 /* WALL PARAMETERS */
2375 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2377 /* ORIENTATION RESTRAINT PARAMETERS */
2379 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
2381 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2384 /* DEFORMATION PARAMETERS */
2386 clear_mat(ir->deform);
2387 for (i = 0; i < 6; i++)
2391 m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
2392 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2393 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2394 for (i = 0; i < 3; i++)
2396 ir->deform[i][i] = dumdub[0][i];
2398 ir->deform[YY][XX] = dumdub[0][3];
2399 ir->deform[ZZ][XX] = dumdub[0][4];
2400 ir->deform[ZZ][YY] = dumdub[0][5];
2401 if (ir->epc != epcNO)
2403 for (i = 0; i < 3; i++)
2405 for (j = 0; j <= i; j++)
2407 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2409 warning_error(wi, "A box element has deform set and compressibility > 0");
2413 for (i = 0; i < 3; i++)
2415 for (j = 0; j < i; j++)
2417 if (ir->deform[i][j] != 0)
2419 for (m = j; m < DIM; m++)
2421 if (ir->compress[m][j] != 0)
2423 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.");
2424 warning(wi, warn_buf);
2432 /* Ion/water position swapping checks */
2433 if (ir->eSwapCoords != eswapNO)
2435 if (ir->swap->nstswap < 1)
2437 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2439 if (ir->swap->nAverage < 1)
2441 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2443 if (ir->swap->threshold < 1.0)
2445 warning_error(wi, "Ion count threshold must be at least 1.\n");
2453 static int search_QMstring(const char *s, int ng, const char *gn[])
2455 /* same as normal search_string, but this one searches QM strings */
2458 for (i = 0; (i < ng); i++)
2460 if (gmx_strcasecmp(s, gn[i]) == 0)
2466 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2470 } /* search_QMstring */
2472 /* We would like gn to be const as well, but C doesn't allow this */
2473 int search_string(const char *s, int ng, char *gn[])
2477 for (i = 0; (i < ng); i++)
2479 if (gmx_strcasecmp(s, gn[i]) == 0)
2486 "Group %s referenced in the .mdp file was not found in the index file.\n"
2487 "Group names must match either [moleculetype] names or custom index group\n"
2488 "names, in which case you must supply an index file to the '-n' option\n"
2495 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2496 t_blocka *block, char *gnames[],
2497 int gtype, int restnm,
2498 int grptp, gmx_bool bVerbose,
2501 unsigned short *cbuf;
2502 t_grps *grps = &(groups->grps[gtype]);
2503 int i, j, gid, aj, ognr, ntot = 0;
2506 char warn_buf[STRLEN];
2510 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2513 title = gtypes[gtype];
2516 /* Mark all id's as not set */
2517 for (i = 0; (i < natoms); i++)
2522 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2523 for (i = 0; (i < ng); i++)
2525 /* Lookup the group name in the block structure */
2526 gid = search_string(ptrs[i], block->nr, gnames);
2527 if ((grptp != egrptpONE) || (i == 0))
2529 grps->nm_ind[grps->nr++] = gid;
2533 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2536 /* Now go over the atoms in the group */
2537 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2542 /* Range checking */
2543 if ((aj < 0) || (aj >= natoms))
2545 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2547 /* Lookup up the old group number */
2551 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2552 aj+1, title, ognr+1, i+1);
2556 /* Store the group number in buffer */
2557 if (grptp == egrptpONE)
2570 /* Now check whether we have done all atoms */
2574 if (grptp == egrptpALL)
2576 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2577 natoms-ntot, title);
2579 else if (grptp == egrptpPART)
2581 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2582 natoms-ntot, title);
2583 warning_note(wi, warn_buf);
2585 /* Assign all atoms currently unassigned to a rest group */
2586 for (j = 0; (j < natoms); j++)
2588 if (cbuf[j] == NOGID)
2594 if (grptp != egrptpPART)
2599 "Making dummy/rest group for %s containing %d elements\n",
2600 title, natoms-ntot);
2602 /* Add group name "rest" */
2603 grps->nm_ind[grps->nr] = restnm;
2605 /* Assign the rest name to all atoms not currently assigned to a group */
2606 for (j = 0; (j < natoms); j++)
2608 if (cbuf[j] == NOGID)
2617 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2619 /* All atoms are part of one (or no) group, no index required */
2620 groups->ngrpnr[gtype] = 0;
2621 groups->grpnr[gtype] = NULL;
2625 groups->ngrpnr[gtype] = natoms;
2626 snew(groups->grpnr[gtype], natoms);
2627 for (j = 0; (j < natoms); j++)
2629 groups->grpnr[gtype][j] = cbuf[j];
2635 return (bRest && grptp == egrptpPART);
2638 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2641 gmx_groups_t *groups;
2643 int natoms, ai, aj, i, j, d, g, imin, jmin;
2645 int *nrdf2, *na_vcm, na_tot;
2646 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2647 gmx_mtop_atomloop_all_t aloop;
2649 int mb, mol, ftype, as;
2650 gmx_molblock_t *molb;
2651 gmx_moltype_t *molt;
2654 * First calc 3xnr-atoms for each group
2655 * then subtract half a degree of freedom for each constraint
2657 * Only atoms and nuclei contribute to the degrees of freedom...
2662 groups = &mtop->groups;
2663 natoms = mtop->natoms;
2665 /* Allocate one more for a possible rest group */
2666 /* We need to sum degrees of freedom into doubles,
2667 * since floats give too low nrdf's above 3 million atoms.
2669 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2670 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2671 snew(na_vcm, groups->grps[egcVCM].nr+1);
2673 for (i = 0; i < groups->grps[egcTC].nr; i++)
2677 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2682 snew(nrdf2, natoms);
2683 aloop = gmx_mtop_atomloop_all_init(mtop);
2684 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2687 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2689 g = ggrpnr(groups, egcFREEZE, i);
2690 /* Double count nrdf for particle i */
2691 for (d = 0; d < DIM; d++)
2693 if (opts->nFreeze[g][d] == 0)
2698 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2699 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2704 for (mb = 0; mb < mtop->nmolblock; mb++)
2706 molb = &mtop->molblock[mb];
2707 molt = &mtop->moltype[molb->type];
2708 atom = molt->atoms.atom;
2709 for (mol = 0; mol < molb->nmol; mol++)
2711 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2713 ia = molt->ilist[ftype].iatoms;
2714 for (i = 0; i < molt->ilist[ftype].nr; )
2716 /* Subtract degrees of freedom for the constraints,
2717 * if the particles still have degrees of freedom left.
2718 * If one of the particles is a vsite or a shell, then all
2719 * constraint motion will go there, but since they do not
2720 * contribute to the constraints the degrees of freedom do not
2725 if (((atom[ia[1]].ptype == eptNucleus) ||
2726 (atom[ia[1]].ptype == eptAtom)) &&
2727 ((atom[ia[2]].ptype == eptNucleus) ||
2728 (atom[ia[2]].ptype == eptAtom)))
2746 imin = min(imin, nrdf2[ai]);
2747 jmin = min(jmin, nrdf2[aj]);
2750 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2751 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2752 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2753 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2755 ia += interaction_function[ftype].nratoms+1;
2756 i += interaction_function[ftype].nratoms+1;
2759 ia = molt->ilist[F_SETTLE].iatoms;
2760 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2762 /* Subtract 1 dof from every atom in the SETTLE */
2763 for (j = 0; j < 3; j++)
2766 imin = min(2, nrdf2[ai]);
2768 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2769 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2774 as += molt->atoms.nr;
2778 if (ir->ePull == epullCONSTRAINT)
2780 /* Correct nrdf for the COM constraints.
2781 * We correct using the TC and VCM group of the first atom
2782 * in the reference and pull group. If atoms in one pull group
2783 * belong to different TC or VCM groups it is anyhow difficult
2784 * to determine the optimal nrdf assignment.
2788 for (i = 0; i < pull->ncoord; i++)
2792 for (j = 0; j < 2; j++)
2794 const t_pull_group *pgrp;
2796 pgrp = &pull->group[pull->coord[i].group[j]];
2800 /* Subtract 1/2 dof from each group */
2802 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2803 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2804 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2806 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)]]);
2811 /* We need to subtract the whole DOF from group j=1 */
2818 if (ir->nstcomm != 0)
2820 /* Subtract 3 from the number of degrees of freedom in each vcm group
2821 * when com translation is removed and 6 when rotation is removed
2824 switch (ir->comm_mode)
2827 n_sub = ndof_com(ir);
2834 gmx_incons("Checking comm_mode");
2837 for (i = 0; i < groups->grps[egcTC].nr; i++)
2839 /* Count the number of atoms of TC group i for every VCM group */
2840 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2845 for (ai = 0; ai < natoms; ai++)
2847 if (ggrpnr(groups, egcTC, ai) == i)
2849 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2853 /* Correct for VCM removal according to the fraction of each VCM
2854 * group present in this TC group.
2856 nrdf_uc = nrdf_tc[i];
2859 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2863 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2865 if (nrdf_vcm[j] > n_sub)
2867 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2868 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2872 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2873 j, nrdf_vcm[j], nrdf_tc[i]);
2878 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2880 opts->nrdf[i] = nrdf_tc[i];
2881 if (opts->nrdf[i] < 0)
2886 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2887 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
2896 static void decode_cos(char *s, t_cosines *cosine)
2899 char format[STRLEN], f1[STRLEN];
2911 sscanf(t, "%d", &(cosine->n));
2918 snew(cosine->a, cosine->n);
2919 snew(cosine->phi, cosine->n);
2921 sprintf(format, "%%*d");
2922 for (i = 0; (i < cosine->n); i++)
2925 strcat(f1, "%lf%lf");
2926 if (sscanf(t, f1, &a, &phi) < 2)
2928 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
2931 cosine->phi[i] = phi;
2932 strcat(format, "%*lf%*lf");
2939 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
2940 const char *option, const char *val, int flag)
2942 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
2943 * But since this is much larger than STRLEN, such a line can not be parsed.
2944 * The real maximum is the number of names that fit in a string: STRLEN/2.
2946 #define EGP_MAX (STRLEN/2)
2947 int nelem, i, j, k, nr;
2948 char *names[EGP_MAX];
2952 gnames = groups->grpname;
2954 nelem = str_nelem(val, EGP_MAX, names);
2957 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
2959 nr = groups->grps[egcENER].nr;
2961 for (i = 0; i < nelem/2; i++)
2965 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
2971 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
2972 names[2*i], option);
2976 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
2982 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
2983 names[2*i+1], option);
2985 if ((j < nr) && (k < nr))
2987 ir->opts.egp_flags[nr*j+k] |= flag;
2988 ir->opts.egp_flags[nr*k+j] |= flag;
2997 static void make_swap_groups(
3006 int ig = -1, i = 0, j;
3010 /* Just a quick check here, more thorough checks are in mdrun */
3011 if (strcmp(splitg0name, splitg1name) == 0)
3013 gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
3016 /* First get the swap group index atoms */
3017 ig = search_string(swapgname, grps->nr, gnames);
3018 swap->nat = grps->index[ig+1] - grps->index[ig];
3021 fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
3022 snew(swap->ind, swap->nat);
3023 for (i = 0; i < swap->nat; i++)
3025 swap->ind[i] = grps->a[grps->index[ig]+i];
3030 gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
3033 /* Now do so for the split groups */
3034 for (j = 0; j < 2; j++)
3038 splitg = splitg0name;
3042 splitg = splitg1name;
3045 ig = search_string(splitg, grps->nr, gnames);
3046 swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
3047 if (swap->nat_split[j] > 0)
3049 fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
3050 j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
3051 snew(swap->ind_split[j], swap->nat_split[j]);
3052 for (i = 0; i < swap->nat_split[j]; i++)
3054 swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
3059 gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
3063 /* Now get the solvent group index atoms */
3064 ig = search_string(solgname, grps->nr, gnames);
3065 swap->nat_sol = grps->index[ig+1] - grps->index[ig];
3066 if (swap->nat_sol > 0)
3068 fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
3069 snew(swap->ind_sol, swap->nat_sol);
3070 for (i = 0; i < swap->nat_sol; i++)
3072 swap->ind_sol[i] = grps->a[grps->index[ig]+i];
3077 gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
3082 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3087 ig = search_string(IMDgname, grps->nr, gnames);
3088 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3090 if (IMDgroup->nat > 0)
3092 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3093 IMDgname, IMDgroup->nat);
3094 snew(IMDgroup->ind, IMDgroup->nat);
3095 for (i = 0; i < IMDgroup->nat; i++)
3097 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3103 void do_index(const char* mdparin, const char *ndx,
3106 t_inputrec *ir, rvec *v,
3110 gmx_groups_t *groups;
3114 char warnbuf[STRLEN], **gnames;
3115 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3118 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3119 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3120 int i, j, k, restnm;
3122 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3123 int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
3124 nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
3125 char warn_buf[STRLEN];
3129 fprintf(stderr, "processing index file...\n");
3135 snew(grps->index, 1);
3137 atoms_all = gmx_mtop_global_atoms(mtop);
3138 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3139 free_t_atoms(&atoms_all, FALSE);
3143 grps = init_index(ndx, &gnames);
3146 groups = &mtop->groups;
3147 natoms = mtop->natoms;
3148 symtab = &mtop->symtab;
3150 snew(groups->grpname, grps->nr+1);
3152 for (i = 0; (i < grps->nr); i++)
3154 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3156 groups->grpname[i] = put_symtab(symtab, "rest");
3158 srenew(gnames, grps->nr+1);
3159 gnames[restnm] = *(groups->grpname[i]);
3160 groups->ngrpname = grps->nr+1;
3162 set_warning_line(wi, mdparin, -1);
3164 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3165 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3166 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3167 if ((ntau_t != ntcg) || (nref_t != ntcg))
3169 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3170 "%d tau-t values", ntcg, nref_t, ntau_t);
3173 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3174 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3175 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3176 nr = groups->grps[egcTC].nr;
3178 snew(ir->opts.nrdf, nr);
3179 snew(ir->opts.tau_t, nr);
3180 snew(ir->opts.ref_t, nr);
3181 if (ir->eI == eiBD && ir->bd_fric == 0)
3183 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3190 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3194 for (i = 0; (i < nr); i++)
3196 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
3197 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
3199 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3200 warning_error(wi, warn_buf);
3203 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3205 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.");
3208 if (ir->opts.tau_t[i] >= 0)
3210 tau_min = min(tau_min, ir->opts.tau_t[i]);
3213 if (ir->etc != etcNO && ir->nsttcouple == -1)
3215 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3220 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3222 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");
3224 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
3226 if (ir->nstpcouple != ir->nsttcouple)
3228 int mincouple = min(ir->nstpcouple, ir->nsttcouple);
3229 ir->nstpcouple = ir->nsttcouple = mincouple;
3230 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);
3231 warning_note(wi, warn_buf);
3235 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3236 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3238 if (ETC_ANDERSEN(ir->etc))
3240 if (ir->nsttcouple != 1)
3243 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");
3244 warning_note(wi, warn_buf);
3247 nstcmin = tcouple_min_integration_steps(ir->etc);
3250 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
3252 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3253 ETCOUPLTYPE(ir->etc),
3255 ir->nsttcouple*ir->delta_t);
3256 warning(wi, warn_buf);
3259 for (i = 0; (i < nr); i++)
3261 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
3262 if (ir->opts.ref_t[i] < 0)
3264 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3267 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3268 if we are in this conditional) if mc_temp is negative */
3269 if (ir->expandedvals->mc_temp < 0)
3271 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3275 /* Simulated annealing for each group. There are nr groups */
3276 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3277 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3281 if (nSA > 0 && nSA != nr)
3283 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3287 snew(ir->opts.annealing, nr);
3288 snew(ir->opts.anneal_npoints, nr);
3289 snew(ir->opts.anneal_time, nr);
3290 snew(ir->opts.anneal_temp, nr);
3291 for (i = 0; i < nr; i++)
3293 ir->opts.annealing[i] = eannNO;
3294 ir->opts.anneal_npoints[i] = 0;
3295 ir->opts.anneal_time[i] = NULL;
3296 ir->opts.anneal_temp[i] = NULL;
3301 for (i = 0; i < nr; i++)
3303 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3305 ir->opts.annealing[i] = eannNO;
3307 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3309 ir->opts.annealing[i] = eannSINGLE;
3312 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3314 ir->opts.annealing[i] = eannPERIODIC;
3320 /* Read the other fields too */
3321 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3322 if (nSA_points != nSA)
3324 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3326 for (k = 0, i = 0; i < nr; i++)
3328 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3329 if (ir->opts.anneal_npoints[i] == 1)
3331 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3333 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3334 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3335 k += ir->opts.anneal_npoints[i];
3338 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3341 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3343 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3346 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3349 for (i = 0, k = 0; i < nr; i++)
3352 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3354 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3355 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3358 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3360 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3366 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3368 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3369 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3372 if (ir->opts.anneal_temp[i][j] < 0)
3374 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3379 /* Print out some summary information, to make sure we got it right */
3380 for (i = 0, k = 0; i < nr; i++)
3382 if (ir->opts.annealing[i] != eannNO)
3384 j = groups->grps[egcTC].nm_ind[i];
3385 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3386 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3387 ir->opts.anneal_npoints[i]);
3388 fprintf(stderr, "Time (ps) Temperature (K)\n");
3389 /* All terms except the last one */
3390 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3392 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3395 /* Finally the last one */
3396 j = ir->opts.anneal_npoints[i]-1;
3397 if (ir->opts.annealing[i] == eannSINGLE)
3399 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3403 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3404 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3406 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3415 if (ir->ePull != epullNO)
3417 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3419 make_pull_coords(ir->pull);
3424 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3427 if (ir->eSwapCoords != eswapNO)
3429 make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
3432 /* Make indices for IMD session */
3435 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3438 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3439 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3440 if (nacg*DIM != nacc)
3442 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3445 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3446 restnm, egrptpALL_GENREST, bVerbose, wi);
3447 nr = groups->grps[egcACC].nr;
3448 snew(ir->opts.acc, nr);
3449 ir->opts.ngacc = nr;
3451 for (i = k = 0; (i < nacg); i++)
3453 for (j = 0; (j < DIM); j++, k++)
3455 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3458 for (; (i < nr); i++)
3460 for (j = 0; (j < DIM); j++)
3462 ir->opts.acc[i][j] = 0;
3466 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3467 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3468 if (nfrdim != DIM*nfreeze)
3470 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3473 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3474 restnm, egrptpALL_GENREST, bVerbose, wi);
3475 nr = groups->grps[egcFREEZE].nr;
3476 ir->opts.ngfrz = nr;
3477 snew(ir->opts.nFreeze, nr);
3478 for (i = k = 0; (i < nfreeze); i++)
3480 for (j = 0; (j < DIM); j++, k++)
3482 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3483 if (!ir->opts.nFreeze[i][j])
3485 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3487 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3488 "(not %s)", ptr1[k]);
3489 warning(wi, warn_buf);
3494 for (; (i < nr); i++)
3496 for (j = 0; (j < DIM); j++)
3498 ir->opts.nFreeze[i][j] = 0;
3502 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3503 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3504 restnm, egrptpALL_GENREST, bVerbose, wi);
3505 add_wall_energrps(groups, ir->nwall, symtab);
3506 ir->opts.ngener = groups->grps[egcENER].nr;
3507 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3509 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3510 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3513 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3514 "This may lead to artifacts.\n"
3515 "In most cases one should use one group for the whole system.");
3518 /* Now we have filled the freeze struct, so we can calculate NRDF */
3519 calc_nrdf(mtop, ir, gnames);
3525 /* Must check per group! */
3526 for (i = 0; (i < ir->opts.ngtc); i++)
3528 ntot += ir->opts.nrdf[i];
3530 if (ntot != (DIM*natoms))
3532 fac = sqrt(ntot/(DIM*natoms));
3535 fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
3536 "and removal of center of mass motion\n", fac);
3538 for (i = 0; (i < natoms); i++)
3540 svmul(fac, v[i], v[i]);
3545 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3546 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3547 restnm, egrptpALL_GENREST, bVerbose, wi);
3548 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3549 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3550 restnm, egrptpALL_GENREST, bVerbose, wi);
3551 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3552 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3553 restnm, egrptpONE, bVerbose, wi);
3554 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3555 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3556 restnm, egrptpALL_GENREST, bVerbose, wi);
3558 /* QMMM input processing */
3559 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3560 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3561 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3562 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3564 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3565 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3567 /* group rest, if any, is always MM! */
3568 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3569 restnm, egrptpALL_GENREST, bVerbose, wi);
3570 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3571 ir->opts.ngQM = nQMg;
3572 snew(ir->opts.QMmethod, nr);
3573 snew(ir->opts.QMbasis, nr);
3574 for (i = 0; i < nr; i++)
3576 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3577 * converted to the corresponding enum in names.c
3579 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3581 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3585 nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
3586 nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
3587 nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
3588 snew(ir->opts.QMmult, nr);
3589 snew(ir->opts.QMcharge, nr);
3590 snew(ir->opts.bSH, nr);
3592 for (i = 0; i < nr; i++)
3594 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3595 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3596 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3599 nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
3600 nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
3601 snew(ir->opts.CASelectrons, nr);
3602 snew(ir->opts.CASorbitals, nr);
3603 for (i = 0; i < nr; i++)
3605 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3606 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3608 /* special optimization options */
3610 nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
3611 nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
3612 snew(ir->opts.bOPT, nr);
3613 snew(ir->opts.bTS, nr);
3614 for (i = 0; i < nr; i++)
3616 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3617 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3619 nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
3620 nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
3621 nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
3622 snew(ir->opts.SAon, nr);
3623 snew(ir->opts.SAoff, nr);
3624 snew(ir->opts.SAsteps, nr);
3626 for (i = 0; i < nr; i++)
3628 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3629 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3630 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3632 /* end of QMMM input */
3636 for (i = 0; (i < egcNR); i++)
3638 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3639 for (j = 0; (j < groups->grps[i].nr); j++)
3641 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3643 fprintf(stderr, "\n");
3647 nr = groups->grps[egcENER].nr;
3648 snew(ir->opts.egp_flags, nr*nr);
3650 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3651 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3653 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3655 if (bExcl && EEL_FULL(ir->coulombtype))
3657 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3660 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3661 if (bTable && !(ir->vdwtype == evdwUSER) &&
3662 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3663 !(ir->coulombtype == eelPMEUSERSWITCH))
3665 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3668 decode_cos(is->efield_x, &(ir->ex[XX]));
3669 decode_cos(is->efield_xt, &(ir->et[XX]));
3670 decode_cos(is->efield_y, &(ir->ex[YY]));
3671 decode_cos(is->efield_yt, &(ir->et[YY]));
3672 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3673 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3677 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3680 for (i = 0; (i < grps->nr); i++)
3692 static void check_disre(gmx_mtop_t *mtop)
3694 gmx_ffparams_t *ffparams;
3695 t_functype *functype;
3697 int i, ndouble, ftype;
3698 int label, old_label;
3700 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3702 ffparams = &mtop->ffparams;
3703 functype = ffparams->functype;
3704 ip = ffparams->iparams;
3707 for (i = 0; i < ffparams->ntypes; i++)
3709 ftype = functype[i];
3710 if (ftype == F_DISRES)
3712 label = ip[i].disres.label;
3713 if (label == old_label)
3715 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3723 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3724 "probably the parameters for multiple pairs in one restraint "
3725 "are not identical\n", ndouble);
3730 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3731 gmx_bool posres_only,
3735 gmx_mtop_ilistloop_t iloop;
3745 for (d = 0; d < DIM; d++)
3747 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3749 /* Check for freeze groups */
3750 for (g = 0; g < ir->opts.ngfrz; g++)
3752 for (d = 0; d < DIM; d++)
3754 if (ir->opts.nFreeze[g][d] != 0)
3762 /* Check for position restraints */
3763 iloop = gmx_mtop_ilistloop_init(sys);
3764 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3767 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3769 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3771 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3772 for (d = 0; d < DIM; d++)
3774 if (pr->posres.fcA[d] != 0)
3780 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3782 /* Check for flat-bottom posres */
3783 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3784 if (pr->fbposres.k != 0)
3786 switch (pr->fbposres.geom)
3788 case efbposresSPHERE:
3789 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3791 case efbposresCYLINDER:
3792 AbsRef[XX] = AbsRef[YY] = 1;
3794 case efbposresX: /* d=XX */
3795 case efbposresY: /* d=YY */
3796 case efbposresZ: /* d=ZZ */
3797 d = pr->fbposres.geom - efbposresX;
3801 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3802 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3810 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3814 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3815 gmx_bool *bC6ParametersWorkWithGeometricRules,
3816 gmx_bool *bC6ParametersWorkWithLBRules,
3817 gmx_bool *bLBRulesPossible)
3819 int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
3822 double geometricdiff, LBdiff;
3823 double c6i, c6j, c12i, c12j;
3824 double c6, c6_geometric, c6_LB;
3825 double sigmai, sigmaj, epsi, epsj;
3826 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3829 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3830 * force-field floating point parameters.
3833 ptr = getenv("GMX_LJCOMB_TOL");
3838 sscanf(ptr, "%lf", &dbl);
3842 *bC6ParametersWorkWithLBRules = TRUE;
3843 *bC6ParametersWorkWithGeometricRules = TRUE;
3844 bCanDoLBRules = TRUE;
3845 bCanDoGeometricRules = TRUE;
3846 ntypes = mtop->ffparams.atnr;
3847 snew(typecount, ntypes);
3848 gmx_mtop_count_atomtypes(mtop, state, typecount);
3849 geometricdiff = LBdiff = 0.0;
3850 *bLBRulesPossible = TRUE;
3851 for (tpi = 0; tpi < ntypes; ++tpi)
3853 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3854 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3855 for (tpj = tpi; tpj < ntypes; ++tpj)
3857 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3858 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3859 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3860 c6_geometric = sqrt(c6i * c6j);
3861 if (!gmx_numzero(c6_geometric))
3863 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3865 sigmai = pow(c12i / c6i, 1.0/6.0);
3866 sigmaj = pow(c12j / c6j, 1.0/6.0);
3867 epsi = c6i * c6i /(4.0 * c12i);
3868 epsj = c6j * c6j /(4.0 * c12j);
3869 c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
3873 *bLBRulesPossible = FALSE;
3874 c6_LB = c6_geometric;
3876 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3879 if (FALSE == bCanDoLBRules)
3881 *bC6ParametersWorkWithLBRules = FALSE;
3884 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3886 if (FALSE == bCanDoGeometricRules)
3888 *bC6ParametersWorkWithGeometricRules = FALSE;
3896 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3900 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3902 check_combination_rule_differences(mtop, 0,
3903 &bC6ParametersWorkWithGeometricRules,
3904 &bC6ParametersWorkWithLBRules,
3906 if (ir->ljpme_combination_rule == eljpmeLB)
3908 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
3910 warning(wi, "You are using arithmetic-geometric combination rules "
3911 "in LJ-PME, but your non-bonded C6 parameters do not "
3912 "follow these rules.");
3917 if (FALSE == bC6ParametersWorkWithGeometricRules)
3919 if (ir->eDispCorr != edispcNO)
3921 warning_note(wi, "You are using geometric combination rules in "
3922 "LJ-PME, but your non-bonded C6 parameters do "
3923 "not follow these rules. "
3924 "This will introduce very small errors in the forces and energies in "
3925 "your simulations. Dispersion correction will correct total energy "
3926 "and/or pressure for isotropic systems, but not forces or surface tensions.");
3930 warning_note(wi, "You are using geometric combination rules in "
3931 "LJ-PME, but your non-bonded C6 parameters do "
3932 "not follow these rules. "
3933 "This will introduce very small errors in the forces and energies in "
3934 "your simulations. If your system is homogeneous, consider using dispersion correction "
3935 "for the total energy and pressure.");
3941 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
3945 int i, m, c, nmol, npct;
3946 gmx_bool bCharge, bAcc;
3947 real gdt_max, *mgrp, mt;
3949 gmx_mtop_atomloop_block_t aloopb;
3950 gmx_mtop_atomloop_all_t aloop;
3953 char warn_buf[STRLEN];
3955 set_warning_line(wi, mdparin, -1);
3957 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
3958 ir->comm_mode == ecmNO &&
3959 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
3960 !ETC_ANDERSEN(ir->etc))
3962 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");
3965 /* Check for pressure coupling with absolute position restraints */
3966 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
3968 absolute_reference(ir, sys, TRUE, AbsRef);
3970 for (m = 0; m < DIM; m++)
3972 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
3974 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
3982 aloopb = gmx_mtop_atomloop_block_init(sys);
3983 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
3985 if (atom->q != 0 || atom->qB != 0)
3993 if (EEL_FULL(ir->coulombtype))
3996 "You are using full electrostatics treatment %s for a system without charges.\n"
3997 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
3998 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
3999 warning(wi, err_buf);
4004 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4007 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4008 "You might want to consider using %s electrostatics.\n",
4010 warning_note(wi, err_buf);
4014 /* Check if combination rules used in LJ-PME are the same as in the force field */
4015 if (EVDW_PME(ir->vdwtype))
4017 check_combination_rules(ir, sys, wi);
4020 /* Generalized reaction field */
4021 if (ir->opts.ngtc == 0)
4023 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4025 CHECK(ir->coulombtype == eelGRF);
4029 sprintf(err_buf, "When using coulombtype = %s"
4030 " ref-t for temperature coupling should be > 0",
4032 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4035 if (ir->eI == eiSD1 &&
4036 (gmx_mtop_ftype_count(sys, F_CONSTR) > 0 ||
4037 gmx_mtop_ftype_count(sys, F_SETTLE) > 0))
4039 sprintf(warn_buf, "With constraints integrator %s is less accurate, consider using %s instead", ei_names[ir->eI], ei_names[eiSD2]);
4040 warning_note(wi, warn_buf);
4044 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4046 for (m = 0; (m < DIM); m++)
4048 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4057 snew(mgrp, sys->groups.grps[egcACC].nr);
4058 aloop = gmx_mtop_atomloop_all_init(sys);
4059 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4061 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4064 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4066 for (m = 0; (m < DIM); m++)
4068 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4072 for (m = 0; (m < DIM); m++)
4074 if (fabs(acc[m]) > 1e-6)
4076 const char *dim[DIM] = { "X", "Y", "Z" };
4078 "Net Acceleration in %s direction, will %s be corrected\n",
4079 dim[m], ir->nstcomm != 0 ? "" : "not");
4080 if (ir->nstcomm != 0 && m < ndof_com(ir))
4083 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4085 ir->opts.acc[i][m] -= acc[m];
4093 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4094 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4096 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4099 if (ir->ePull != epullNO)
4101 gmx_bool bPullAbsoluteRef;
4103 bPullAbsoluteRef = FALSE;
4104 for (i = 0; i < ir->pull->ncoord; i++)
4106 bPullAbsoluteRef = bPullAbsoluteRef ||
4107 ir->pull->coord[i].group[0] == 0 ||
4108 ir->pull->coord[i].group[1] == 0;
4110 if (bPullAbsoluteRef)
4112 absolute_reference(ir, sys, FALSE, AbsRef);
4113 for (m = 0; m < DIM; m++)
4115 if (ir->pull->dim[m] && !AbsRef[m])
4117 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.");
4123 if (ir->pull->eGeom == epullgDIRPBC)
4125 for (i = 0; i < 3; i++)
4127 for (m = 0; m <= i; m++)
4129 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4130 ir->deform[i][m] != 0)
4132 for (c = 0; c < ir->pull->ncoord; c++)
4134 if (ir->pull->coord[c].vec[m] != 0)
4136 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->eGeom), 'x'+m);
4148 void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr, warninp_t wi)
4152 char warn_buf[STRLEN];
4155 ptr = check_box(ir->ePBC, box);
4158 warning_error(wi, ptr);
4161 if (bConstr && ir->eConstrAlg == econtSHAKE)
4163 if (ir->shake_tol <= 0.0)
4165 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4167 warning_error(wi, warn_buf);
4170 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
4172 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
4173 if (ir->epc == epcNO)
4175 warning(wi, warn_buf);
4179 warning_error(wi, warn_buf);
4184 if ( (ir->eConstrAlg == econtLINCS) && bConstr)
4186 /* If we have Lincs constraints: */
4187 if (ir->eI == eiMD && ir->etc == etcNO &&
4188 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4190 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4191 warning_note(wi, warn_buf);
4194 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4196 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4197 warning_note(wi, warn_buf);
4199 if (ir->epc == epcMTTK)
4201 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4205 if (bConstr && ir->epc == epcMTTK)
4207 warning_note(wi, "MTTK with constraints is deprecated, and will be removed in GROMACS 5.1");
4210 if (ir->LincsWarnAngle > 90.0)
4212 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4213 warning(wi, warn_buf);
4214 ir->LincsWarnAngle = 90.0;
4217 if (ir->ePBC != epbcNONE)
4219 if (ir->nstlist == 0)
4221 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4223 bTWIN = (ir->rlistlong > ir->rlist);
4224 if (ir->ns_type == ensGRID)
4226 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
4228 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",
4229 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
4230 warning_error(wi, warn_buf);
4235 min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
4236 if (2*ir->rlistlong >= min_size)
4238 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4239 warning_error(wi, warn_buf);
4242 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4249 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4253 real rvdw1, rvdw2, rcoul1, rcoul2;
4254 char warn_buf[STRLEN];
4256 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4260 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4265 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4271 if (rvdw1 + rvdw2 > ir->rlist ||
4272 rcoul1 + rcoul2 > ir->rlist)
4275 "The sum of the two largest charge group radii (%f) "
4276 "is larger than rlist (%f)\n",
4277 max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4278 warning(wi, warn_buf);
4282 /* Here we do not use the zero at cut-off macro,
4283 * since user defined interactions might purposely
4284 * not be zero at the cut-off.
4286 if (ir_vdw_is_zero_at_cutoff(ir) &&
4287 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
4289 sprintf(warn_buf, "The sum of the two largest charge group "
4290 "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
4291 "With exact cut-offs, better performance can be "
4292 "obtained with cutoff-scheme = %s, because it "
4293 "does not use charge groups at all.",
4295 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4296 ir->rlistlong, ir->rvdw,
4297 ecutscheme_names[ecutsVERLET]);
4300 warning(wi, warn_buf);
4304 warning_note(wi, warn_buf);
4307 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4308 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
4310 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
4311 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4313 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4314 ir->rlistlong, ir->rcoulomb,
4315 ecutscheme_names[ecutsVERLET]);
4318 warning(wi, warn_buf);
4322 warning_note(wi, warn_buf);