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45 #include "gromacs/utility/smalloc.h"
49 #include "gmx_fatal.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 || ir->coulomb_modifier == eintmodPOTSWITCH)
1148 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1150 real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
1151 sprintf(warn_buf, "The switching range for should be 5%% or less (currently %.2f%% using a switching range of %4f-%4f) for accurate electrostatic energies, energy conservation will be good regardless, since ewald_rtol = %g.",
1152 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1153 warning(wi, warn_buf);
1157 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1159 if (ir->rvdw_switch == 0)
1161 sprintf(warn_buf, "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones potential. This suggests it was not set in the mdp, which can lead to large energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw switching range.");
1162 warning(wi, warn_buf);
1166 if (EEL_FULL(ir->coulombtype))
1168 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1169 ir->coulombtype == eelPMEUSERSWITCH)
1171 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1172 eel_names[ir->coulombtype]);
1173 CHECK(ir->rcoulomb > ir->rlist);
1175 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1177 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1180 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
1181 "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
1182 "a potential modifier.", eel_names[ir->coulombtype]);
1183 if (ir->nstcalclr == 1)
1185 CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
1189 CHECK(ir->rcoulomb != ir->rlist);
1195 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1197 if (ir->pme_order < 3)
1199 warning_error(wi, "pme-order can not be smaller than 3");
1203 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1205 if (ir->ewald_geometry == eewg3D)
1207 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1208 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1209 warning(wi, warn_buf);
1211 /* This check avoids extra pbc coding for exclusion corrections */
1212 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1213 CHECK(ir->wall_ewald_zfac < 2);
1216 if (ir_vdw_switched(ir))
1218 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1219 CHECK(ir->rvdw_switch >= ir->rvdw);
1221 if (ir->rvdw_switch < 0.5*ir->rvdw)
1223 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.",
1224 ir->rvdw_switch, ir->rvdw);
1225 warning_note(wi, warn_buf);
1228 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1230 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1232 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1233 CHECK(ir->rlist > ir->rvdw);
1237 if (ir->vdwtype == evdwPME)
1239 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1241 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s a\
1243 evdw_names[ir->vdwtype],
1244 eintmod_names[eintmodPOTSHIFT],
1245 eintmod_names[eintmodNONE]);
1249 if (ir->cutoff_scheme == ecutsGROUP)
1251 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1252 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)) &&
1255 warning_note(wi, "With exact cut-offs, rlist should be "
1256 "larger than rcoulomb and rvdw, so that there "
1257 "is a buffer region for particle motion "
1258 "between neighborsearch steps");
1261 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlistlong <= ir->rcoulomb)
1263 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
1264 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1265 warning_note(wi, warn_buf);
1267 if (ir_vdw_switched(ir) && (ir->rlistlong <= ir->rvdw))
1269 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
1270 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1271 warning_note(wi, warn_buf);
1275 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1277 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.");
1280 if (ir->nstlist == -1)
1282 sprintf(err_buf, "With nstlist=-1 rvdw and rcoulomb should be smaller than rlist to account for diffusion and possibly charge-group radii");
1283 CHECK(ir->rvdw >= ir->rlist || ir->rcoulomb >= ir->rlist);
1285 sprintf(err_buf, "nstlist can not be smaller than -1");
1286 CHECK(ir->nstlist < -1);
1288 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1291 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1294 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1296 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1299 /* ENERGY CONSERVATION */
1300 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1302 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1304 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1305 evdw_names[evdwSHIFT]);
1306 warning_note(wi, warn_buf);
1308 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1310 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1311 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1312 warning_note(wi, warn_buf);
1316 /* IMPLICIT SOLVENT */
1317 if (ir->coulombtype == eelGB_NOTUSED)
1319 ir->coulombtype = eelCUT;
1320 ir->implicit_solvent = eisGBSA;
1321 fprintf(stderr, "Note: Old option for generalized born electrostatics given:\n"
1322 "Changing coulombtype from \"generalized-born\" to \"cut-off\" and instead\n"
1323 "setting implicit-solvent value to \"GBSA\" in input section.\n");
1326 if (ir->sa_algorithm == esaSTILL)
1328 sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
1329 CHECK(ir->sa_algorithm == esaSTILL);
1332 if (ir->implicit_solvent == eisGBSA)
1334 sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
1335 CHECK(ir->rgbradii != ir->rlist);
1337 if (ir->coulombtype != eelCUT)
1339 sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
1340 CHECK(ir->coulombtype != eelCUT);
1342 if (ir->vdwtype != evdwCUT)
1344 sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
1345 CHECK(ir->vdwtype != evdwCUT);
1347 if (ir->nstgbradii < 1)
1349 sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
1350 warning_note(wi, warn_buf);
1353 if (ir->sa_algorithm == esaNO)
1355 sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
1356 warning_note(wi, warn_buf);
1358 if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
1360 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");
1361 warning_note(wi, warn_buf);
1363 if (ir->gb_algorithm == egbSTILL)
1365 ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
1369 ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
1372 if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
1374 sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
1375 CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
1382 if (ir->cutoff_scheme != ecutsGROUP)
1384 warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
1388 warning_error(wi, "AdresS simulation supports only stochastic dynamics");
1390 if (ir->epc != epcNO)
1392 warning_error(wi, "AdresS simulation does not support pressure coupling");
1394 if (EEL_FULL(ir->coulombtype))
1396 warning_error(wi, "AdresS simulation does not support long-range electrostatics");
1401 /* count the number of text elemets separated by whitespace in a string.
1402 str = the input string
1403 maxptr = the maximum number of allowed elements
1404 ptr = the output array of pointers to the first character of each element
1405 returns: the number of elements. */
1406 int str_nelem(const char *str, int maxptr, char *ptr[])
1411 copy0 = strdup(str);
1414 while (*copy != '\0')
1418 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1426 while ((*copy != '\0') && !isspace(*copy))
1445 /* interpret a number of doubles from a string and put them in an array,
1446 after allocating space for them.
1447 str = the input string
1448 n = the (pre-allocated) number of doubles read
1449 r = the output array of doubles. */
1450 static void parse_n_real(char *str, int *n, real **r)
1455 *n = str_nelem(str, MAXPTR, ptr);
1458 for (i = 0; i < *n; i++)
1460 (*r)[i] = strtod(ptr[i], NULL);
1464 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
1467 int i, j, max_n_lambda, nweights, nfep[efptNR];
1468 t_lambda *fep = ir->fepvals;
1469 t_expanded *expand = ir->expandedvals;
1470 real **count_fep_lambdas;
1471 gmx_bool bOneLambda = TRUE;
1473 snew(count_fep_lambdas, efptNR);
1475 /* FEP input processing */
1476 /* first, identify the number of lambda values for each type.
1477 All that are nonzero must have the same number */
1479 for (i = 0; i < efptNR; i++)
1481 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
1484 /* now, determine the number of components. All must be either zero, or equal. */
1487 for (i = 0; i < efptNR; i++)
1489 if (nfep[i] > max_n_lambda)
1491 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1492 must have the same number if its not zero.*/
1497 for (i = 0; i < efptNR; i++)
1501 ir->fepvals->separate_dvdl[i] = FALSE;
1503 else if (nfep[i] == max_n_lambda)
1505 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1506 respect to the temperature currently */
1508 ir->fepvals->separate_dvdl[i] = TRUE;
1513 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1514 nfep[i], efpt_names[i], max_n_lambda);
1517 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1518 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1520 /* the number of lambdas is the number we've read in, which is either zero
1521 or the same for all */
1522 fep->n_lambda = max_n_lambda;
1524 /* allocate space for the array of lambda values */
1525 snew(fep->all_lambda, efptNR);
1526 /* if init_lambda is defined, we need to set lambda */
1527 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1529 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1531 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1532 for (i = 0; i < efptNR; i++)
1534 snew(fep->all_lambda[i], fep->n_lambda);
1535 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1538 for (j = 0; j < fep->n_lambda; j++)
1540 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1542 sfree(count_fep_lambdas[i]);
1545 sfree(count_fep_lambdas);
1547 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1548 bookkeeping -- for now, init_lambda */
1550 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1552 for (i = 0; i < fep->n_lambda; i++)
1554 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1558 /* check to see if only a single component lambda is defined, and soft core is defined.
1559 In this case, turn on coulomb soft core */
1561 if (max_n_lambda == 0)
1567 for (i = 0; i < efptNR; i++)
1569 if ((nfep[i] != 0) && (i != efptFEP))
1575 if ((bOneLambda) && (fep->sc_alpha > 0))
1577 fep->bScCoul = TRUE;
1580 /* Fill in the others with the efptFEP if they are not explicitly
1581 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1582 they are all zero. */
1584 for (i = 0; i < efptNR; i++)
1586 if ((nfep[i] == 0) && (i != efptFEP))
1588 for (j = 0; j < fep->n_lambda; j++)
1590 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1596 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1597 if (fep->sc_r_power == 48)
1599 if (fep->sc_alpha > 0.1)
1601 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1605 expand = ir->expandedvals;
1606 /* now read in the weights */
1607 parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
1610 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1612 else if (nweights != fep->n_lambda)
1614 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1615 nweights, fep->n_lambda);
1617 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1619 expand->nstexpanded = fep->nstdhdl;
1620 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1622 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1624 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1625 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1626 2*tau_t just to be careful so it's not to frequent */
1631 static void do_simtemp_params(t_inputrec *ir)
1634 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1635 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1640 static void do_wall_params(t_inputrec *ir,
1641 char *wall_atomtype, char *wall_density,
1645 char *names[MAXPTR];
1648 opts->wall_atomtype[0] = NULL;
1649 opts->wall_atomtype[1] = NULL;
1651 ir->wall_atomtype[0] = -1;
1652 ir->wall_atomtype[1] = -1;
1653 ir->wall_density[0] = 0;
1654 ir->wall_density[1] = 0;
1658 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1659 if (nstr != ir->nwall)
1661 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1664 for (i = 0; i < ir->nwall; i++)
1666 opts->wall_atomtype[i] = strdup(names[i]);
1669 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1671 nstr = str_nelem(wall_density, MAXPTR, names);
1672 if (nstr != ir->nwall)
1674 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1676 for (i = 0; i < ir->nwall; i++)
1678 sscanf(names[i], "%lf", &dbl);
1681 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1683 ir->wall_density[i] = dbl;
1689 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1697 srenew(groups->grpname, groups->ngrpname+nwall);
1698 grps = &(groups->grps[egcENER]);
1699 srenew(grps->nm_ind, grps->nr+nwall);
1700 for (i = 0; i < nwall; i++)
1702 sprintf(str, "wall%d", i);
1703 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1704 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1709 void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1710 t_expanded *expand, warninp_t wi)
1712 int ninp, nerror = 0;
1718 /* read expanded ensemble parameters */
1719 CCTYPE ("expanded ensemble variables");
1720 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1721 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1722 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1723 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1724 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1725 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1726 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1727 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1728 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1729 CCTYPE("Seed for Monte Carlo in lambda space");
1730 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1731 RTYPE ("mc-temperature", expand->mc_temp, -1);
1732 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1733 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1734 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1735 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1736 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1737 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1738 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1739 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1740 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1741 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1742 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
1750 void get_ir(const char *mdparin, const char *mdparout,
1751 t_inputrec *ir, t_gromppopts *opts,
1755 double dumdub[2][6];
1759 char warn_buf[STRLEN];
1760 t_lambda *fep = ir->fepvals;
1761 t_expanded *expand = ir->expandedvals;
1763 init_inputrec_strings();
1764 inp = read_inpfile(mdparin, &ninp, wi);
1766 snew(dumstr[0], STRLEN);
1767 snew(dumstr[1], STRLEN);
1769 if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
1772 "%s did not specify a value for the .mdp option "
1773 "\"cutoff-scheme\". Probably it was first intended for use "
1774 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1775 "introduced, but the group scheme was still the default. "
1776 "The default is now the Verlet scheme, so you will observe "
1777 "different behaviour.", mdparin);
1778 warning_note(wi, warn_buf);
1781 /* remove the following deprecated commands */
1784 REM_TYPE("domain-decomposition");
1785 REM_TYPE("andersen-seed");
1787 REM_TYPE("dihre-fc");
1788 REM_TYPE("dihre-tau");
1789 REM_TYPE("nstdihreout");
1790 REM_TYPE("nstcheckpoint");
1792 /* replace the following commands with the clearer new versions*/
1793 REPL_TYPE("unconstrained-start", "continuation");
1794 REPL_TYPE("foreign-lambda", "fep-lambdas");
1795 REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
1796 REPL_TYPE("nstxtcout", "nstxout-compressed");
1797 REPL_TYPE("xtc-grps", "compressed-x-grps");
1798 REPL_TYPE("xtc-precision", "compressed-x-precision");
1800 CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
1801 CTYPE ("Preprocessor information: use cpp syntax.");
1802 CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
1803 STYPE ("include", opts->include, NULL);
1804 CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1805 STYPE ("define", opts->define, NULL);
1807 CCTYPE ("RUN CONTROL PARAMETERS");
1808 EETYPE("integrator", ir->eI, ei_names);
1809 CTYPE ("Start time and timestep in ps");
1810 RTYPE ("tinit", ir->init_t, 0.0);
1811 RTYPE ("dt", ir->delta_t, 0.001);
1812 STEPTYPE ("nsteps", ir->nsteps, 0);
1813 CTYPE ("For exact run continuation or redoing part of a run");
1814 STEPTYPE ("init-step", ir->init_step, 0);
1815 CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
1816 ITYPE ("simulation-part", ir->simulation_part, 1);
1817 CTYPE ("mode for center of mass motion removal");
1818 EETYPE("comm-mode", ir->comm_mode, ecm_names);
1819 CTYPE ("number of steps for center of mass motion removal");
1820 ITYPE ("nstcomm", ir->nstcomm, 100);
1821 CTYPE ("group(s) for center of mass motion removal");
1822 STYPE ("comm-grps", is->vcm, NULL);
1824 CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
1825 CTYPE ("Friction coefficient (amu/ps) and random seed");
1826 RTYPE ("bd-fric", ir->bd_fric, 0.0);
1827 STEPTYPE ("ld-seed", ir->ld_seed, -1);
1830 CCTYPE ("ENERGY MINIMIZATION OPTIONS");
1831 CTYPE ("Force tolerance and initial step-size");
1832 RTYPE ("emtol", ir->em_tol, 10.0);
1833 RTYPE ("emstep", ir->em_stepsize, 0.01);
1834 CTYPE ("Max number of iterations in relax-shells");
1835 ITYPE ("niter", ir->niter, 20);
1836 CTYPE ("Step size (ps^2) for minimization of flexible constraints");
1837 RTYPE ("fcstep", ir->fc_stepsize, 0);
1838 CTYPE ("Frequency of steepest descents steps when doing CG");
1839 ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
1840 ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
1842 CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
1843 RTYPE ("rtpi", ir->rtpi, 0.05);
1845 /* Output options */
1846 CCTYPE ("OUTPUT CONTROL OPTIONS");
1847 CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
1848 ITYPE ("nstxout", ir->nstxout, 0);
1849 ITYPE ("nstvout", ir->nstvout, 0);
1850 ITYPE ("nstfout", ir->nstfout, 0);
1851 ir->nstcheckpoint = 1000;
1852 CTYPE ("Output frequency for energies to log file and energy file");
1853 ITYPE ("nstlog", ir->nstlog, 1000);
1854 ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
1855 ITYPE ("nstenergy", ir->nstenergy, 1000);
1856 CTYPE ("Output frequency and precision for .xtc file");
1857 ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
1858 RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
1859 CTYPE ("This selects the subset of atoms for the compressed");
1860 CTYPE ("trajectory file. You can select multiple groups. By");
1861 CTYPE ("default, all atoms will be written.");
1862 STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
1863 CTYPE ("Selection of energy groups");
1864 STYPE ("energygrps", is->energy, NULL);
1866 /* Neighbor searching */
1867 CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
1868 CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1869 EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
1870 CTYPE ("nblist update frequency");
1871 ITYPE ("nstlist", ir->nstlist, 10);
1872 CTYPE ("ns algorithm (simple or grid)");
1873 EETYPE("ns-type", ir->ns_type, ens_names);
1874 /* set ndelta to the optimal value of 2 */
1876 CTYPE ("Periodic boundary conditions: xyz, no, xy");
1877 EETYPE("pbc", ir->ePBC, epbc_names);
1878 EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
1879 CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1880 CTYPE ("a value of -1 means: use rlist");
1881 RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
1882 CTYPE ("nblist cut-off");
1883 RTYPE ("rlist", ir->rlist, 1.0);
1884 CTYPE ("long-range cut-off for switched potentials");
1885 RTYPE ("rlistlong", ir->rlistlong, -1);
1886 ITYPE ("nstcalclr", ir->nstcalclr, -1);
1888 /* Electrostatics */
1889 CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
1890 CTYPE ("Method for doing electrostatics");
1891 EETYPE("coulombtype", ir->coulombtype, eel_names);
1892 EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
1893 CTYPE ("cut-off lengths");
1894 RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
1895 RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
1896 CTYPE ("Relative dielectric constant for the medium and the reaction field");
1897 RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
1898 RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
1899 CTYPE ("Method for doing Van der Waals");
1900 EETYPE("vdw-type", ir->vdwtype, evdw_names);
1901 EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
1902 CTYPE ("cut-off lengths");
1903 RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
1904 RTYPE ("rvdw", ir->rvdw, 1.0);
1905 CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
1906 EETYPE("DispCorr", ir->eDispCorr, edispc_names);
1907 CTYPE ("Extension of the potential lookup tables beyond the cut-off");
1908 RTYPE ("table-extension", ir->tabext, 1.0);
1909 CTYPE ("Separate tables between energy group pairs");
1910 STYPE ("energygrp-table", is->egptable, NULL);
1911 CTYPE ("Spacing for the PME/PPPM FFT grid");
1912 RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
1913 CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
1914 ITYPE ("fourier-nx", ir->nkx, 0);
1915 ITYPE ("fourier-ny", ir->nky, 0);
1916 ITYPE ("fourier-nz", ir->nkz, 0);
1917 CTYPE ("EWALD/PME/PPPM parameters");
1918 ITYPE ("pme-order", ir->pme_order, 4);
1919 RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
1920 RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
1921 EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
1922 EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
1923 RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
1924 EETYPE("optimize-fft", ir->bOptFFT, yesno_names);
1926 CCTYPE("IMPLICIT SOLVENT ALGORITHM");
1927 EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
1929 CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
1930 CTYPE ("Algorithm for calculating Born radii");
1931 EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
1932 CTYPE ("Frequency of calculating the Born radii inside rlist");
1933 ITYPE ("nstgbradii", ir->nstgbradii, 1);
1934 CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
1935 CTYPE ("between rlist and rgbradii is updated every nstlist steps");
1936 RTYPE ("rgbradii", ir->rgbradii, 1.0);
1937 CTYPE ("Dielectric coefficient of the implicit solvent");
1938 RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
1939 CTYPE ("Salt concentration in M for Generalized Born models");
1940 RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
1941 CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
1942 RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
1943 RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
1944 RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
1945 RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
1946 EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
1947 CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
1948 CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
1949 RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
1951 /* Coupling stuff */
1952 CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
1953 CTYPE ("Temperature coupling");
1954 EETYPE("tcoupl", ir->etc, etcoupl_names);
1955 ITYPE ("nsttcouple", ir->nsttcouple, -1);
1956 ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
1957 EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
1958 CTYPE ("Groups to couple separately");
1959 STYPE ("tc-grps", is->tcgrps, NULL);
1960 CTYPE ("Time constant (ps) and reference temperature (K)");
1961 STYPE ("tau-t", is->tau_t, NULL);
1962 STYPE ("ref-t", is->ref_t, NULL);
1963 CTYPE ("pressure coupling");
1964 EETYPE("pcoupl", ir->epc, epcoupl_names);
1965 EETYPE("pcoupltype", ir->epct, epcoupltype_names);
1966 ITYPE ("nstpcouple", ir->nstpcouple, -1);
1967 CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
1968 RTYPE ("tau-p", ir->tau_p, 1.0);
1969 STYPE ("compressibility", dumstr[0], NULL);
1970 STYPE ("ref-p", dumstr[1], NULL);
1971 CTYPE ("Scaling of reference coordinates, No, All or COM");
1972 EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
1975 CCTYPE ("OPTIONS FOR QMMM calculations");
1976 EETYPE("QMMM", ir->bQMMM, yesno_names);
1977 CTYPE ("Groups treated Quantum Mechanically");
1978 STYPE ("QMMM-grps", is->QMMM, NULL);
1979 CTYPE ("QM method");
1980 STYPE("QMmethod", is->QMmethod, NULL);
1981 CTYPE ("QMMM scheme");
1982 EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
1983 CTYPE ("QM basisset");
1984 STYPE("QMbasis", is->QMbasis, NULL);
1985 CTYPE ("QM charge");
1986 STYPE ("QMcharge", is->QMcharge, NULL);
1987 CTYPE ("QM multiplicity");
1988 STYPE ("QMmult", is->QMmult, NULL);
1989 CTYPE ("Surface Hopping");
1990 STYPE ("SH", is->bSH, NULL);
1991 CTYPE ("CAS space options");
1992 STYPE ("CASorbitals", is->CASorbitals, NULL);
1993 STYPE ("CASelectrons", is->CASelectrons, NULL);
1994 STYPE ("SAon", is->SAon, NULL);
1995 STYPE ("SAoff", is->SAoff, NULL);
1996 STYPE ("SAsteps", is->SAsteps, NULL);
1997 CTYPE ("Scale factor for MM charges");
1998 RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
1999 CTYPE ("Optimization of QM subsystem");
2000 STYPE ("bOPT", is->bOPT, NULL);
2001 STYPE ("bTS", is->bTS, NULL);
2003 /* Simulated annealing */
2004 CCTYPE("SIMULATED ANNEALING");
2005 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
2006 STYPE ("annealing", is->anneal, NULL);
2007 CTYPE ("Number of time points to use for specifying annealing in each group");
2008 STYPE ("annealing-npoints", is->anneal_npoints, NULL);
2009 CTYPE ("List of times at the annealing points for each group");
2010 STYPE ("annealing-time", is->anneal_time, NULL);
2011 CTYPE ("Temp. at each annealing point, for each group.");
2012 STYPE ("annealing-temp", is->anneal_temp, NULL);
2015 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
2016 EETYPE("gen-vel", opts->bGenVel, yesno_names);
2017 RTYPE ("gen-temp", opts->tempi, 300.0);
2018 ITYPE ("gen-seed", opts->seed, -1);
2021 CCTYPE ("OPTIONS FOR BONDS");
2022 EETYPE("constraints", opts->nshake, constraints);
2023 CTYPE ("Type of constraint algorithm");
2024 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
2025 CTYPE ("Do not constrain the start configuration");
2026 EETYPE("continuation", ir->bContinuation, yesno_names);
2027 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
2028 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
2029 CTYPE ("Relative tolerance of shake");
2030 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
2031 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
2032 ITYPE ("lincs-order", ir->nProjOrder, 4);
2033 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
2034 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
2035 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
2036 ITYPE ("lincs-iter", ir->nLincsIter, 1);
2037 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
2038 CTYPE ("rotates over more degrees than");
2039 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
2040 CTYPE ("Convert harmonic bonds to morse potentials");
2041 EETYPE("morse", opts->bMorse, yesno_names);
2043 /* Energy group exclusions */
2044 CCTYPE ("ENERGY GROUP EXCLUSIONS");
2045 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
2046 STYPE ("energygrp-excl", is->egpexcl, NULL);
2050 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2051 ITYPE ("nwall", ir->nwall, 0);
2052 EETYPE("wall-type", ir->wall_type, ewt_names);
2053 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
2054 STYPE ("wall-atomtype", is->wall_atomtype, NULL);
2055 STYPE ("wall-density", is->wall_density, NULL);
2056 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
2059 CCTYPE("COM PULLING");
2060 CTYPE("Pull type: no, umbrella, constraint or constant-force");
2061 EETYPE("pull", ir->ePull, epull_names);
2062 if (ir->ePull != epullNO)
2065 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
2068 /* Enforced rotation */
2069 CCTYPE("ENFORCED ROTATION");
2070 CTYPE("Enforced rotation: No or Yes");
2071 EETYPE("rotation", ir->bRot, yesno_names);
2075 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2078 /* Interactive MD */
2080 CCTYPE("Group to display and/or manipulate in interactive MD session");
2081 STYPE ("IMD-group", is->imd_grp, NULL);
2082 if (is->imd_grp[0] != '\0')
2089 CCTYPE("NMR refinement stuff");
2090 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2091 EETYPE("disre", ir->eDisre, edisre_names);
2092 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2093 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2094 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2095 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2096 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2097 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2098 CTYPE ("Output frequency for pair distances to energy file");
2099 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2100 CTYPE ("Orientation restraints: No or Yes");
2101 EETYPE("orire", opts->bOrire, yesno_names);
2102 CTYPE ("Orientation restraints force constant and tau for time averaging");
2103 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2104 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2105 STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
2106 CTYPE ("Output frequency for trace(SD) and S to energy file");
2107 ITYPE ("nstorireout", ir->nstorireout, 100);
2109 /* free energy variables */
2110 CCTYPE ("Free energy variables");
2111 EETYPE("free-energy", ir->efep, efep_names);
2112 STYPE ("couple-moltype", is->couple_moltype, NULL);
2113 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2114 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2115 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2117 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2119 it was not entered */
2120 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2121 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2122 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2123 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
2124 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
2125 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
2126 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
2127 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
2128 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
2129 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
2130 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2131 STYPE ("init-lambda-weights", is->lambda_weights, NULL);
2132 EETYPE("dhdl-print-energy", fep->bPrintEnergy, yesno_names);
2133 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2134 ITYPE ("sc-power", fep->sc_power, 1);
2135 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2136 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2137 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2138 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2139 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2140 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2141 separate_dhdl_file_names);
2142 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2143 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2144 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2146 /* Non-equilibrium MD stuff */
2147 CCTYPE("Non-equilibrium MD stuff");
2148 STYPE ("acc-grps", is->accgrps, NULL);
2149 STYPE ("accelerate", is->acc, NULL);
2150 STYPE ("freezegrps", is->freeze, NULL);
2151 STYPE ("freezedim", is->frdim, NULL);
2152 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2153 STYPE ("deform", is->deform, NULL);
2155 /* simulated tempering variables */
2156 CCTYPE("simulated tempering variables");
2157 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2158 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2159 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2160 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2162 /* expanded ensemble variables */
2163 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2165 read_expandedparams(&ninp, &inp, expand, wi);
2168 /* Electric fields */
2169 CCTYPE("Electric fields");
2170 CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
2171 CTYPE ("and a phase angle (real)");
2172 STYPE ("E-x", is->efield_x, NULL);
2173 STYPE ("E-xt", is->efield_xt, NULL);
2174 STYPE ("E-y", is->efield_y, NULL);
2175 STYPE ("E-yt", is->efield_yt, NULL);
2176 STYPE ("E-z", is->efield_z, NULL);
2177 STYPE ("E-zt", is->efield_zt, NULL);
2179 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2180 CTYPE("Swap positions along direction: no, X, Y, Z");
2181 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2182 if (ir->eSwapCoords != eswapNO)
2185 CTYPE("Swap attempt frequency");
2186 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2187 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2188 STYPE("split-group0", splitgrp0, NULL);
2189 STYPE("split-group1", splitgrp1, NULL);
2190 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2191 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2192 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2194 CTYPE("Group name of ions that can be exchanged with solvent molecules");
2195 STYPE("swap-group", swapgrp, NULL);
2196 CTYPE("Group name of solvent molecules");
2197 STYPE("solvent-group", solgrp, NULL);
2199 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2200 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2201 CTYPE("however, if correctly defined, the ion permeation events are counted per channel");
2202 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2203 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2204 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2205 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2206 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2207 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2209 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2210 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2211 CTYPE("Requested number of anions and cations for each of the two compartments");
2212 CTYPE("-1 means fix the numbers as found in time step 0");
2213 ITYPE("anionsA", ir->swap->nanions[0], -1);
2214 ITYPE("cationsA", ir->swap->ncations[0], -1);
2215 ITYPE("anionsB", ir->swap->nanions[1], -1);
2216 ITYPE("cationsB", ir->swap->ncations[1], -1);
2217 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2218 RTYPE("threshold", ir->swap->threshold, 1.0);
2221 /* AdResS defined thingies */
2222 CCTYPE ("AdResS parameters");
2223 EETYPE("adress", ir->bAdress, yesno_names);
2226 snew(ir->adress, 1);
2227 read_adressparams(&ninp, &inp, ir->adress, wi);
2230 /* User defined thingies */
2231 CCTYPE ("User defined thingies");
2232 STYPE ("user1-grps", is->user1, NULL);
2233 STYPE ("user2-grps", is->user2, NULL);
2234 ITYPE ("userint1", ir->userint1, 0);
2235 ITYPE ("userint2", ir->userint2, 0);
2236 ITYPE ("userint3", ir->userint3, 0);
2237 ITYPE ("userint4", ir->userint4, 0);
2238 RTYPE ("userreal1", ir->userreal1, 0);
2239 RTYPE ("userreal2", ir->userreal2, 0);
2240 RTYPE ("userreal3", ir->userreal3, 0);
2241 RTYPE ("userreal4", ir->userreal4, 0);
2244 write_inpfile(mdparout, ninp, inp, FALSE, wi);
2245 for (i = 0; (i < ninp); i++)
2248 sfree(inp[i].value);
2252 /* Process options if necessary */
2253 for (m = 0; m < 2; m++)
2255 for (i = 0; i < 2*DIM; i++)
2264 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2266 warning_error(wi, "Pressure coupling not enough values (I need 1)");
2268 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2270 case epctSEMIISOTROPIC:
2271 case epctSURFACETENSION:
2272 if (sscanf(dumstr[m], "%lf%lf",
2273 &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2275 warning_error(wi, "Pressure coupling not enough values (I need 2)");
2277 dumdub[m][YY] = dumdub[m][XX];
2279 case epctANISOTROPIC:
2280 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2281 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2282 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2284 warning_error(wi, "Pressure coupling not enough values (I need 6)");
2288 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2289 epcoupltype_names[ir->epct]);
2293 clear_mat(ir->ref_p);
2294 clear_mat(ir->compress);
2295 for (i = 0; i < DIM; i++)
2297 ir->ref_p[i][i] = dumdub[1][i];
2298 ir->compress[i][i] = dumdub[0][i];
2300 if (ir->epct == epctANISOTROPIC)
2302 ir->ref_p[XX][YY] = dumdub[1][3];
2303 ir->ref_p[XX][ZZ] = dumdub[1][4];
2304 ir->ref_p[YY][ZZ] = dumdub[1][5];
2305 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2307 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2309 ir->compress[XX][YY] = dumdub[0][3];
2310 ir->compress[XX][ZZ] = dumdub[0][4];
2311 ir->compress[YY][ZZ] = dumdub[0][5];
2312 for (i = 0; i < DIM; i++)
2314 for (m = 0; m < i; m++)
2316 ir->ref_p[i][m] = ir->ref_p[m][i];
2317 ir->compress[i][m] = ir->compress[m][i];
2322 if (ir->comm_mode == ecmNO)
2327 opts->couple_moltype = NULL;
2328 if (strlen(is->couple_moltype) > 0)
2330 if (ir->efep != efepNO)
2332 opts->couple_moltype = strdup(is->couple_moltype);
2333 if (opts->couple_lam0 == opts->couple_lam1)
2335 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2337 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2338 opts->couple_lam1 == ecouplamNONE))
2340 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2345 warning(wi, "Can not couple a molecule with free_energy = no");
2348 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2349 if (ir->efep != efepNO)
2351 if (fep->delta_lambda > 0)
2353 ir->efep = efepSLOWGROWTH;
2359 fep->bPrintEnergy = TRUE;
2360 /* always print out the energy to dhdl if we are doing expanded ensemble, since we need the total energy
2361 if the temperature is changing. */
2364 if ((ir->efep != efepNO) || ir->bSimTemp)
2366 ir->bExpanded = FALSE;
2367 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2369 ir->bExpanded = TRUE;
2371 do_fep_params(ir, is->fep_lambda, is->lambda_weights);
2372 if (ir->bSimTemp) /* done after fep params */
2374 do_simtemp_params(ir);
2379 ir->fepvals->n_lambda = 0;
2382 /* WALL PARAMETERS */
2384 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2386 /* ORIENTATION RESTRAINT PARAMETERS */
2388 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
2390 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2393 /* DEFORMATION PARAMETERS */
2395 clear_mat(ir->deform);
2396 for (i = 0; i < 6; i++)
2400 m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
2401 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2402 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2403 for (i = 0; i < 3; i++)
2405 ir->deform[i][i] = dumdub[0][i];
2407 ir->deform[YY][XX] = dumdub[0][3];
2408 ir->deform[ZZ][XX] = dumdub[0][4];
2409 ir->deform[ZZ][YY] = dumdub[0][5];
2410 if (ir->epc != epcNO)
2412 for (i = 0; i < 3; i++)
2414 for (j = 0; j <= i; j++)
2416 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2418 warning_error(wi, "A box element has deform set and compressibility > 0");
2422 for (i = 0; i < 3; i++)
2424 for (j = 0; j < i; j++)
2426 if (ir->deform[i][j] != 0)
2428 for (m = j; m < DIM; m++)
2430 if (ir->compress[m][j] != 0)
2432 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.");
2433 warning(wi, warn_buf);
2441 /* Ion/water position swapping checks */
2442 if (ir->eSwapCoords != eswapNO)
2444 if (ir->swap->nstswap < 1)
2446 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2448 if (ir->swap->nAverage < 1)
2450 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2452 if (ir->swap->threshold < 1.0)
2454 warning_error(wi, "Ion count threshold must be at least 1.\n");
2462 static int search_QMstring(const char *s, int ng, const char *gn[])
2464 /* same as normal search_string, but this one searches QM strings */
2467 for (i = 0; (i < ng); i++)
2469 if (gmx_strcasecmp(s, gn[i]) == 0)
2475 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2479 } /* search_QMstring */
2481 /* We would like gn to be const as well, but C doesn't allow this */
2482 int search_string(const char *s, int ng, char *gn[])
2486 for (i = 0; (i < ng); i++)
2488 if (gmx_strcasecmp(s, gn[i]) == 0)
2495 "Group %s referenced in the .mdp file was not found in the index file.\n"
2496 "Group names must match either [moleculetype] names or custom index group\n"
2497 "names, in which case you must supply an index file to the '-n' option\n"
2504 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2505 t_blocka *block, char *gnames[],
2506 int gtype, int restnm,
2507 int grptp, gmx_bool bVerbose,
2510 unsigned short *cbuf;
2511 t_grps *grps = &(groups->grps[gtype]);
2512 int i, j, gid, aj, ognr, ntot = 0;
2515 char warn_buf[STRLEN];
2519 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2522 title = gtypes[gtype];
2525 /* Mark all id's as not set */
2526 for (i = 0; (i < natoms); i++)
2531 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2532 for (i = 0; (i < ng); i++)
2534 /* Lookup the group name in the block structure */
2535 gid = search_string(ptrs[i], block->nr, gnames);
2536 if ((grptp != egrptpONE) || (i == 0))
2538 grps->nm_ind[grps->nr++] = gid;
2542 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2545 /* Now go over the atoms in the group */
2546 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2551 /* Range checking */
2552 if ((aj < 0) || (aj >= natoms))
2554 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2556 /* Lookup up the old group number */
2560 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2561 aj+1, title, ognr+1, i+1);
2565 /* Store the group number in buffer */
2566 if (grptp == egrptpONE)
2579 /* Now check whether we have done all atoms */
2583 if (grptp == egrptpALL)
2585 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2586 natoms-ntot, title);
2588 else if (grptp == egrptpPART)
2590 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2591 natoms-ntot, title);
2592 warning_note(wi, warn_buf);
2594 /* Assign all atoms currently unassigned to a rest group */
2595 for (j = 0; (j < natoms); j++)
2597 if (cbuf[j] == NOGID)
2603 if (grptp != egrptpPART)
2608 "Making dummy/rest group for %s containing %d elements\n",
2609 title, natoms-ntot);
2611 /* Add group name "rest" */
2612 grps->nm_ind[grps->nr] = restnm;
2614 /* Assign the rest name to all atoms not currently assigned to a group */
2615 for (j = 0; (j < natoms); j++)
2617 if (cbuf[j] == NOGID)
2626 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2628 /* All atoms are part of one (or no) group, no index required */
2629 groups->ngrpnr[gtype] = 0;
2630 groups->grpnr[gtype] = NULL;
2634 groups->ngrpnr[gtype] = natoms;
2635 snew(groups->grpnr[gtype], natoms);
2636 for (j = 0; (j < natoms); j++)
2638 groups->grpnr[gtype][j] = cbuf[j];
2644 return (bRest && grptp == egrptpPART);
2647 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2650 gmx_groups_t *groups;
2652 int natoms, ai, aj, i, j, d, g, imin, jmin;
2654 int *nrdf2, *na_vcm, na_tot;
2655 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2656 gmx_mtop_atomloop_all_t aloop;
2658 int mb, mol, ftype, as;
2659 gmx_molblock_t *molb;
2660 gmx_moltype_t *molt;
2663 * First calc 3xnr-atoms for each group
2664 * then subtract half a degree of freedom for each constraint
2666 * Only atoms and nuclei contribute to the degrees of freedom...
2671 groups = &mtop->groups;
2672 natoms = mtop->natoms;
2674 /* Allocate one more for a possible rest group */
2675 /* We need to sum degrees of freedom into doubles,
2676 * since floats give too low nrdf's above 3 million atoms.
2678 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2679 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2680 snew(na_vcm, groups->grps[egcVCM].nr+1);
2682 for (i = 0; i < groups->grps[egcTC].nr; i++)
2686 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2691 snew(nrdf2, natoms);
2692 aloop = gmx_mtop_atomloop_all_init(mtop);
2693 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2696 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2698 g = ggrpnr(groups, egcFREEZE, i);
2699 /* Double count nrdf for particle i */
2700 for (d = 0; d < DIM; d++)
2702 if (opts->nFreeze[g][d] == 0)
2707 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2708 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2713 for (mb = 0; mb < mtop->nmolblock; mb++)
2715 molb = &mtop->molblock[mb];
2716 molt = &mtop->moltype[molb->type];
2717 atom = molt->atoms.atom;
2718 for (mol = 0; mol < molb->nmol; mol++)
2720 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2722 ia = molt->ilist[ftype].iatoms;
2723 for (i = 0; i < molt->ilist[ftype].nr; )
2725 /* Subtract degrees of freedom for the constraints,
2726 * if the particles still have degrees of freedom left.
2727 * If one of the particles is a vsite or a shell, then all
2728 * constraint motion will go there, but since they do not
2729 * contribute to the constraints the degrees of freedom do not
2734 if (((atom[ia[1]].ptype == eptNucleus) ||
2735 (atom[ia[1]].ptype == eptAtom)) &&
2736 ((atom[ia[2]].ptype == eptNucleus) ||
2737 (atom[ia[2]].ptype == eptAtom)))
2755 imin = min(imin, nrdf2[ai]);
2756 jmin = min(jmin, nrdf2[aj]);
2759 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2760 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2761 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2762 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2764 ia += interaction_function[ftype].nratoms+1;
2765 i += interaction_function[ftype].nratoms+1;
2768 ia = molt->ilist[F_SETTLE].iatoms;
2769 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2771 /* Subtract 1 dof from every atom in the SETTLE */
2772 for (j = 0; j < 3; j++)
2775 imin = min(2, nrdf2[ai]);
2777 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2778 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2783 as += molt->atoms.nr;
2787 if (ir->ePull == epullCONSTRAINT)
2789 /* Correct nrdf for the COM constraints.
2790 * We correct using the TC and VCM group of the first atom
2791 * in the reference and pull group. If atoms in one pull group
2792 * belong to different TC or VCM groups it is anyhow difficult
2793 * to determine the optimal nrdf assignment.
2797 for (i = 0; i < pull->ncoord; i++)
2801 for (j = 0; j < 2; j++)
2803 const t_pull_group *pgrp;
2805 pgrp = &pull->group[pull->coord[i].group[j]];
2809 /* Subtract 1/2 dof from each group */
2811 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2812 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2813 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2815 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)]]);
2820 /* We need to subtract the whole DOF from group j=1 */
2827 if (ir->nstcomm != 0)
2829 /* Subtract 3 from the number of degrees of freedom in each vcm group
2830 * when com translation is removed and 6 when rotation is removed
2833 switch (ir->comm_mode)
2836 n_sub = ndof_com(ir);
2843 gmx_incons("Checking comm_mode");
2846 for (i = 0; i < groups->grps[egcTC].nr; i++)
2848 /* Count the number of atoms of TC group i for every VCM group */
2849 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2854 for (ai = 0; ai < natoms; ai++)
2856 if (ggrpnr(groups, egcTC, ai) == i)
2858 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2862 /* Correct for VCM removal according to the fraction of each VCM
2863 * group present in this TC group.
2865 nrdf_uc = nrdf_tc[i];
2868 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2872 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2874 if (nrdf_vcm[j] > n_sub)
2876 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2877 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2881 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2882 j, nrdf_vcm[j], nrdf_tc[i]);
2887 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2889 opts->nrdf[i] = nrdf_tc[i];
2890 if (opts->nrdf[i] < 0)
2895 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2896 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
2905 static void decode_cos(char *s, t_cosines *cosine)
2908 char format[STRLEN], f1[STRLEN];
2920 sscanf(t, "%d", &(cosine->n));
2927 snew(cosine->a, cosine->n);
2928 snew(cosine->phi, cosine->n);
2930 sprintf(format, "%%*d");
2931 for (i = 0; (i < cosine->n); i++)
2934 strcat(f1, "%lf%lf");
2935 if (sscanf(t, f1, &a, &phi) < 2)
2937 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
2940 cosine->phi[i] = phi;
2941 strcat(format, "%*lf%*lf");
2948 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
2949 const char *option, const char *val, int flag)
2951 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
2952 * But since this is much larger than STRLEN, such a line can not be parsed.
2953 * The real maximum is the number of names that fit in a string: STRLEN/2.
2955 #define EGP_MAX (STRLEN/2)
2956 int nelem, i, j, k, nr;
2957 char *names[EGP_MAX];
2961 gnames = groups->grpname;
2963 nelem = str_nelem(val, EGP_MAX, names);
2966 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
2968 nr = groups->grps[egcENER].nr;
2970 for (i = 0; i < nelem/2; i++)
2974 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
2980 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
2981 names[2*i], option);
2985 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
2991 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
2992 names[2*i+1], option);
2994 if ((j < nr) && (k < nr))
2996 ir->opts.egp_flags[nr*j+k] |= flag;
2997 ir->opts.egp_flags[nr*k+j] |= flag;
3006 static void make_swap_groups(
3015 int ig = -1, i = 0, j;
3019 /* Just a quick check here, more thorough checks are in mdrun */
3020 if (strcmp(splitg0name, splitg1name) == 0)
3022 gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
3025 /* First get the swap group index atoms */
3026 ig = search_string(swapgname, grps->nr, gnames);
3027 swap->nat = grps->index[ig+1] - grps->index[ig];
3030 fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
3031 snew(swap->ind, swap->nat);
3032 for (i = 0; i < swap->nat; i++)
3034 swap->ind[i] = grps->a[grps->index[ig]+i];
3039 gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
3042 /* Now do so for the split groups */
3043 for (j = 0; j < 2; j++)
3047 splitg = splitg0name;
3051 splitg = splitg1name;
3054 ig = search_string(splitg, grps->nr, gnames);
3055 swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
3056 if (swap->nat_split[j] > 0)
3058 fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
3059 j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
3060 snew(swap->ind_split[j], swap->nat_split[j]);
3061 for (i = 0; i < swap->nat_split[j]; i++)
3063 swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
3068 gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
3072 /* Now get the solvent group index atoms */
3073 ig = search_string(solgname, grps->nr, gnames);
3074 swap->nat_sol = grps->index[ig+1] - grps->index[ig];
3075 if (swap->nat_sol > 0)
3077 fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
3078 snew(swap->ind_sol, swap->nat_sol);
3079 for (i = 0; i < swap->nat_sol; i++)
3081 swap->ind_sol[i] = grps->a[grps->index[ig]+i];
3086 gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
3091 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3096 ig = search_string(IMDgname, grps->nr, gnames);
3097 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3099 if (IMDgroup->nat > 0)
3101 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3102 IMDgname, IMDgroup->nat);
3103 snew(IMDgroup->ind, IMDgroup->nat);
3104 for (i = 0; i < IMDgroup->nat; i++)
3106 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3112 void do_index(const char* mdparin, const char *ndx,
3115 t_inputrec *ir, rvec *v,
3119 gmx_groups_t *groups;
3123 char warnbuf[STRLEN], **gnames;
3124 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3127 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3128 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3129 int i, j, k, restnm;
3131 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3132 int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
3133 nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
3134 char warn_buf[STRLEN];
3138 fprintf(stderr, "processing index file...\n");
3144 snew(grps->index, 1);
3146 atoms_all = gmx_mtop_global_atoms(mtop);
3147 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3148 free_t_atoms(&atoms_all, FALSE);
3152 grps = init_index(ndx, &gnames);
3155 groups = &mtop->groups;
3156 natoms = mtop->natoms;
3157 symtab = &mtop->symtab;
3159 snew(groups->grpname, grps->nr+1);
3161 for (i = 0; (i < grps->nr); i++)
3163 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3165 groups->grpname[i] = put_symtab(symtab, "rest");
3167 srenew(gnames, grps->nr+1);
3168 gnames[restnm] = *(groups->grpname[i]);
3169 groups->ngrpname = grps->nr+1;
3171 set_warning_line(wi, mdparin, -1);
3173 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3174 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3175 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3176 if ((ntau_t != ntcg) || (nref_t != ntcg))
3178 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3179 "%d tau-t values", ntcg, nref_t, ntau_t);
3182 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3183 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3184 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3185 nr = groups->grps[egcTC].nr;
3187 snew(ir->opts.nrdf, nr);
3188 snew(ir->opts.tau_t, nr);
3189 snew(ir->opts.ref_t, nr);
3190 if (ir->eI == eiBD && ir->bd_fric == 0)
3192 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3199 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3203 for (i = 0; (i < nr); i++)
3205 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
3206 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
3208 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3209 warning_error(wi, warn_buf);
3212 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3214 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.");
3217 if (ir->opts.tau_t[i] >= 0)
3219 tau_min = min(tau_min, ir->opts.tau_t[i]);
3222 if (ir->etc != etcNO && ir->nsttcouple == -1)
3224 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3229 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3231 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");
3233 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
3235 if (ir->nstpcouple != ir->nsttcouple)
3237 int mincouple = min(ir->nstpcouple, ir->nsttcouple);
3238 ir->nstpcouple = ir->nsttcouple = mincouple;
3239 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);
3240 warning_note(wi, warn_buf);
3244 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3245 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3247 if (ETC_ANDERSEN(ir->etc))
3249 if (ir->nsttcouple != 1)
3252 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");
3253 warning_note(wi, warn_buf);
3256 nstcmin = tcouple_min_integration_steps(ir->etc);
3259 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
3261 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3262 ETCOUPLTYPE(ir->etc),
3264 ir->nsttcouple*ir->delta_t);
3265 warning(wi, warn_buf);
3268 for (i = 0; (i < nr); i++)
3270 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
3271 if (ir->opts.ref_t[i] < 0)
3273 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3276 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3277 if we are in this conditional) if mc_temp is negative */
3278 if (ir->expandedvals->mc_temp < 0)
3280 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3284 /* Simulated annealing for each group. There are nr groups */
3285 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3286 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3290 if (nSA > 0 && nSA != nr)
3292 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3296 snew(ir->opts.annealing, nr);
3297 snew(ir->opts.anneal_npoints, nr);
3298 snew(ir->opts.anneal_time, nr);
3299 snew(ir->opts.anneal_temp, nr);
3300 for (i = 0; i < nr; i++)
3302 ir->opts.annealing[i] = eannNO;
3303 ir->opts.anneal_npoints[i] = 0;
3304 ir->opts.anneal_time[i] = NULL;
3305 ir->opts.anneal_temp[i] = NULL;
3310 for (i = 0; i < nr; i++)
3312 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3314 ir->opts.annealing[i] = eannNO;
3316 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3318 ir->opts.annealing[i] = eannSINGLE;
3321 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3323 ir->opts.annealing[i] = eannPERIODIC;
3329 /* Read the other fields too */
3330 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3331 if (nSA_points != nSA)
3333 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3335 for (k = 0, i = 0; i < nr; i++)
3337 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3338 if (ir->opts.anneal_npoints[i] == 1)
3340 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3342 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3343 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3344 k += ir->opts.anneal_npoints[i];
3347 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3350 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3352 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3355 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3358 for (i = 0, k = 0; i < nr; i++)
3361 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3363 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3364 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3367 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3369 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3375 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3377 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3378 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3381 if (ir->opts.anneal_temp[i][j] < 0)
3383 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3388 /* Print out some summary information, to make sure we got it right */
3389 for (i = 0, k = 0; i < nr; i++)
3391 if (ir->opts.annealing[i] != eannNO)
3393 j = groups->grps[egcTC].nm_ind[i];
3394 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3395 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3396 ir->opts.anneal_npoints[i]);
3397 fprintf(stderr, "Time (ps) Temperature (K)\n");
3398 /* All terms except the last one */
3399 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3401 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3404 /* Finally the last one */
3405 j = ir->opts.anneal_npoints[i]-1;
3406 if (ir->opts.annealing[i] == eannSINGLE)
3408 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3412 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3413 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3415 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3424 if (ir->ePull != epullNO)
3426 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3428 make_pull_coords(ir->pull);
3433 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3436 if (ir->eSwapCoords != eswapNO)
3438 make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
3441 /* Make indices for IMD session */
3444 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3447 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3448 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3449 if (nacg*DIM != nacc)
3451 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3454 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3455 restnm, egrptpALL_GENREST, bVerbose, wi);
3456 nr = groups->grps[egcACC].nr;
3457 snew(ir->opts.acc, nr);
3458 ir->opts.ngacc = nr;
3460 for (i = k = 0; (i < nacg); i++)
3462 for (j = 0; (j < DIM); j++, k++)
3464 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3467 for (; (i < nr); i++)
3469 for (j = 0; (j < DIM); j++)
3471 ir->opts.acc[i][j] = 0;
3475 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3476 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3477 if (nfrdim != DIM*nfreeze)
3479 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3482 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3483 restnm, egrptpALL_GENREST, bVerbose, wi);
3484 nr = groups->grps[egcFREEZE].nr;
3485 ir->opts.ngfrz = nr;
3486 snew(ir->opts.nFreeze, nr);
3487 for (i = k = 0; (i < nfreeze); i++)
3489 for (j = 0; (j < DIM); j++, k++)
3491 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3492 if (!ir->opts.nFreeze[i][j])
3494 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3496 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3497 "(not %s)", ptr1[k]);
3498 warning(wi, warn_buf);
3503 for (; (i < nr); i++)
3505 for (j = 0; (j < DIM); j++)
3507 ir->opts.nFreeze[i][j] = 0;
3511 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3512 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3513 restnm, egrptpALL_GENREST, bVerbose, wi);
3514 add_wall_energrps(groups, ir->nwall, symtab);
3515 ir->opts.ngener = groups->grps[egcENER].nr;
3516 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3518 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3519 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3522 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3523 "This may lead to artifacts.\n"
3524 "In most cases one should use one group for the whole system.");
3527 /* Now we have filled the freeze struct, so we can calculate NRDF */
3528 calc_nrdf(mtop, ir, gnames);
3534 /* Must check per group! */
3535 for (i = 0; (i < ir->opts.ngtc); i++)
3537 ntot += ir->opts.nrdf[i];
3539 if (ntot != (DIM*natoms))
3541 fac = sqrt(ntot/(DIM*natoms));
3544 fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
3545 "and removal of center of mass motion\n", fac);
3547 for (i = 0; (i < natoms); i++)
3549 svmul(fac, v[i], v[i]);
3554 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3555 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3556 restnm, egrptpALL_GENREST, bVerbose, wi);
3557 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3558 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3559 restnm, egrptpALL_GENREST, bVerbose, wi);
3560 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3561 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3562 restnm, egrptpONE, bVerbose, wi);
3563 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3564 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3565 restnm, egrptpALL_GENREST, bVerbose, wi);
3567 /* QMMM input processing */
3568 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3569 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3570 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3571 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3573 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3574 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3576 /* group rest, if any, is always MM! */
3577 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3578 restnm, egrptpALL_GENREST, bVerbose, wi);
3579 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3580 ir->opts.ngQM = nQMg;
3581 snew(ir->opts.QMmethod, nr);
3582 snew(ir->opts.QMbasis, nr);
3583 for (i = 0; i < nr; i++)
3585 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3586 * converted to the corresponding enum in names.c
3588 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3590 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3594 nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
3595 nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
3596 nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
3597 snew(ir->opts.QMmult, nr);
3598 snew(ir->opts.QMcharge, nr);
3599 snew(ir->opts.bSH, nr);
3601 for (i = 0; i < nr; i++)
3603 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3604 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3605 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3608 nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
3609 nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
3610 snew(ir->opts.CASelectrons, nr);
3611 snew(ir->opts.CASorbitals, nr);
3612 for (i = 0; i < nr; i++)
3614 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3615 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3617 /* special optimization options */
3619 nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
3620 nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
3621 snew(ir->opts.bOPT, nr);
3622 snew(ir->opts.bTS, nr);
3623 for (i = 0; i < nr; i++)
3625 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3626 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3628 nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
3629 nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
3630 nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
3631 snew(ir->opts.SAon, nr);
3632 snew(ir->opts.SAoff, nr);
3633 snew(ir->opts.SAsteps, nr);
3635 for (i = 0; i < nr; i++)
3637 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3638 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3639 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3641 /* end of QMMM input */
3645 for (i = 0; (i < egcNR); i++)
3647 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3648 for (j = 0; (j < groups->grps[i].nr); j++)
3650 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3652 fprintf(stderr, "\n");
3656 nr = groups->grps[egcENER].nr;
3657 snew(ir->opts.egp_flags, nr*nr);
3659 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3660 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3662 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3664 if (bExcl && EEL_FULL(ir->coulombtype))
3666 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3669 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3670 if (bTable && !(ir->vdwtype == evdwUSER) &&
3671 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3672 !(ir->coulombtype == eelPMEUSERSWITCH))
3674 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3677 decode_cos(is->efield_x, &(ir->ex[XX]));
3678 decode_cos(is->efield_xt, &(ir->et[XX]));
3679 decode_cos(is->efield_y, &(ir->ex[YY]));
3680 decode_cos(is->efield_yt, &(ir->et[YY]));
3681 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3682 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3686 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3689 for (i = 0; (i < grps->nr); i++)
3701 static void check_disre(gmx_mtop_t *mtop)
3703 gmx_ffparams_t *ffparams;
3704 t_functype *functype;
3706 int i, ndouble, ftype;
3707 int label, old_label;
3709 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3711 ffparams = &mtop->ffparams;
3712 functype = ffparams->functype;
3713 ip = ffparams->iparams;
3716 for (i = 0; i < ffparams->ntypes; i++)
3718 ftype = functype[i];
3719 if (ftype == F_DISRES)
3721 label = ip[i].disres.label;
3722 if (label == old_label)
3724 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3732 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3733 "probably the parameters for multiple pairs in one restraint "
3734 "are not identical\n", ndouble);
3739 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3740 gmx_bool posres_only,
3744 gmx_mtop_ilistloop_t iloop;
3754 for (d = 0; d < DIM; d++)
3756 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3758 /* Check for freeze groups */
3759 for (g = 0; g < ir->opts.ngfrz; g++)
3761 for (d = 0; d < DIM; d++)
3763 if (ir->opts.nFreeze[g][d] != 0)
3771 /* Check for position restraints */
3772 iloop = gmx_mtop_ilistloop_init(sys);
3773 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3776 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3778 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3780 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3781 for (d = 0; d < DIM; d++)
3783 if (pr->posres.fcA[d] != 0)
3789 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3791 /* Check for flat-bottom posres */
3792 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3793 if (pr->fbposres.k != 0)
3795 switch (pr->fbposres.geom)
3797 case efbposresSPHERE:
3798 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3800 case efbposresCYLINDER:
3801 AbsRef[XX] = AbsRef[YY] = 1;
3803 case efbposresX: /* d=XX */
3804 case efbposresY: /* d=YY */
3805 case efbposresZ: /* d=ZZ */
3806 d = pr->fbposres.geom - efbposresX;
3810 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3811 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3819 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3823 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3824 gmx_bool *bC6ParametersWorkWithGeometricRules,
3825 gmx_bool *bC6ParametersWorkWithLBRules,
3826 gmx_bool *bLBRulesPossible)
3828 int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
3831 double geometricdiff, LBdiff;
3832 double c6i, c6j, c12i, c12j;
3833 double c6, c6_geometric, c6_LB;
3834 double sigmai, sigmaj, epsi, epsj;
3835 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3838 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3839 * force-field floating point parameters.
3842 ptr = getenv("GMX_LJCOMB_TOL");
3847 sscanf(ptr, "%lf", &dbl);
3851 *bC6ParametersWorkWithLBRules = TRUE;
3852 *bC6ParametersWorkWithGeometricRules = TRUE;
3853 bCanDoLBRules = TRUE;
3854 bCanDoGeometricRules = TRUE;
3855 ntypes = mtop->ffparams.atnr;
3856 snew(typecount, ntypes);
3857 gmx_mtop_count_atomtypes(mtop, state, typecount);
3858 geometricdiff = LBdiff = 0.0;
3859 *bLBRulesPossible = TRUE;
3860 for (tpi = 0; tpi < ntypes; ++tpi)
3862 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3863 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3864 for (tpj = tpi; tpj < ntypes; ++tpj)
3866 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3867 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3868 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3869 c6_geometric = sqrt(c6i * c6j);
3870 if (!gmx_numzero(c6_geometric))
3872 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3874 sigmai = pow(c12i / c6i, 1.0/6.0);
3875 sigmaj = pow(c12j / c6j, 1.0/6.0);
3876 epsi = c6i * c6i /(4.0 * c12i);
3877 epsj = c6j * c6j /(4.0 * c12j);
3878 c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
3882 *bLBRulesPossible = FALSE;
3883 c6_LB = c6_geometric;
3885 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3888 if (FALSE == bCanDoLBRules)
3890 *bC6ParametersWorkWithLBRules = FALSE;
3893 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3895 if (FALSE == bCanDoGeometricRules)
3897 *bC6ParametersWorkWithGeometricRules = FALSE;
3905 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3909 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3911 check_combination_rule_differences(mtop, 0,
3912 &bC6ParametersWorkWithGeometricRules,
3913 &bC6ParametersWorkWithLBRules,
3915 if (ir->ljpme_combination_rule == eljpmeLB)
3917 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
3919 warning(wi, "You are using arithmetic-geometric combination rules "
3920 "in LJ-PME, but your non-bonded C6 parameters do not "
3921 "follow these rules.");
3926 if (FALSE == bC6ParametersWorkWithGeometricRules)
3928 if (ir->eDispCorr != edispcNO)
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. Dispersion correction will correct total energy "
3935 "and/or pressure for isotropic systems, but not forces or surface tensions.");
3939 warning_note(wi, "You are using geometric combination rules in "
3940 "LJ-PME, but your non-bonded C6 parameters do "
3941 "not follow these rules. "
3942 "This will introduce very small errors in the forces and energies in "
3943 "your simulations. If your system is homogeneous, consider using dispersion correction "
3944 "for the total energy and pressure.");
3950 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
3954 int i, m, c, nmol, npct;
3955 gmx_bool bCharge, bAcc;
3956 real gdt_max, *mgrp, mt;
3958 gmx_mtop_atomloop_block_t aloopb;
3959 gmx_mtop_atomloop_all_t aloop;
3962 char warn_buf[STRLEN];
3964 set_warning_line(wi, mdparin, -1);
3966 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
3967 ir->comm_mode == ecmNO &&
3968 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
3969 !ETC_ANDERSEN(ir->etc))
3971 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");
3974 /* Check for pressure coupling with absolute position restraints */
3975 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
3977 absolute_reference(ir, sys, TRUE, AbsRef);
3979 for (m = 0; m < DIM; m++)
3981 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
3983 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
3991 aloopb = gmx_mtop_atomloop_block_init(sys);
3992 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
3994 if (atom->q != 0 || atom->qB != 0)
4002 if (EEL_FULL(ir->coulombtype))
4005 "You are using full electrostatics treatment %s for a system without charges.\n"
4006 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4007 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4008 warning(wi, err_buf);
4013 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4016 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4017 "You might want to consider using %s electrostatics.\n",
4019 warning_note(wi, err_buf);
4023 /* Check if combination rules used in LJ-PME are the same as in the force field */
4024 if (EVDW_PME(ir->vdwtype))
4026 check_combination_rules(ir, sys, wi);
4029 /* Generalized reaction field */
4030 if (ir->opts.ngtc == 0)
4032 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4034 CHECK(ir->coulombtype == eelGRF);
4038 sprintf(err_buf, "When using coulombtype = %s"
4039 " ref-t for temperature coupling should be > 0",
4041 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4044 if (ir->eI == eiSD1 &&
4045 (gmx_mtop_ftype_count(sys, F_CONSTR) > 0 ||
4046 gmx_mtop_ftype_count(sys, F_SETTLE) > 0))
4048 sprintf(warn_buf, "With constraints integrator %s is less accurate, consider using %s instead", ei_names[ir->eI], ei_names[eiSD2]);
4049 warning_note(wi, warn_buf);
4053 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4055 for (m = 0; (m < DIM); m++)
4057 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4066 snew(mgrp, sys->groups.grps[egcACC].nr);
4067 aloop = gmx_mtop_atomloop_all_init(sys);
4068 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4070 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4073 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4075 for (m = 0; (m < DIM); m++)
4077 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4081 for (m = 0; (m < DIM); m++)
4083 if (fabs(acc[m]) > 1e-6)
4085 const char *dim[DIM] = { "X", "Y", "Z" };
4087 "Net Acceleration in %s direction, will %s be corrected\n",
4088 dim[m], ir->nstcomm != 0 ? "" : "not");
4089 if (ir->nstcomm != 0 && m < ndof_com(ir))
4092 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4094 ir->opts.acc[i][m] -= acc[m];
4102 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4103 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4105 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4108 if (ir->ePull != epullNO)
4110 gmx_bool bPullAbsoluteRef;
4112 bPullAbsoluteRef = FALSE;
4113 for (i = 0; i < ir->pull->ncoord; i++)
4115 bPullAbsoluteRef = bPullAbsoluteRef ||
4116 ir->pull->coord[i].group[0] == 0 ||
4117 ir->pull->coord[i].group[1] == 0;
4119 if (bPullAbsoluteRef)
4121 absolute_reference(ir, sys, FALSE, AbsRef);
4122 for (m = 0; m < DIM; m++)
4124 if (ir->pull->dim[m] && !AbsRef[m])
4126 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.");
4132 if (ir->pull->eGeom == epullgDIRPBC)
4134 for (i = 0; i < 3; i++)
4136 for (m = 0; m <= i; m++)
4138 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4139 ir->deform[i][m] != 0)
4141 for (c = 0; c < ir->pull->ncoord; c++)
4143 if (ir->pull->coord[c].vec[m] != 0)
4145 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->eGeom), 'x'+m);
4157 void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr, warninp_t wi)
4161 char warn_buf[STRLEN];
4164 ptr = check_box(ir->ePBC, box);
4167 warning_error(wi, ptr);
4170 if (bConstr && ir->eConstrAlg == econtSHAKE)
4172 if (ir->shake_tol <= 0.0)
4174 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4176 warning_error(wi, warn_buf);
4179 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
4181 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
4182 if (ir->epc == epcNO)
4184 warning(wi, warn_buf);
4188 warning_error(wi, warn_buf);
4193 if ( (ir->eConstrAlg == econtLINCS) && bConstr)
4195 /* If we have Lincs constraints: */
4196 if (ir->eI == eiMD && ir->etc == etcNO &&
4197 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4199 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4200 warning_note(wi, warn_buf);
4203 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4205 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4206 warning_note(wi, warn_buf);
4208 if (ir->epc == epcMTTK)
4210 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4214 if (bConstr && ir->epc == epcMTTK)
4216 warning_note(wi, "MTTK with constraints is deprecated, and will be removed in GROMACS 5.1");
4219 if (ir->LincsWarnAngle > 90.0)
4221 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4222 warning(wi, warn_buf);
4223 ir->LincsWarnAngle = 90.0;
4226 if (ir->ePBC != epbcNONE)
4228 if (ir->nstlist == 0)
4230 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4232 bTWIN = (ir->rlistlong > ir->rlist);
4233 if (ir->ns_type == ensGRID)
4235 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
4237 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",
4238 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
4239 warning_error(wi, warn_buf);
4244 min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
4245 if (2*ir->rlistlong >= min_size)
4247 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4248 warning_error(wi, warn_buf);
4251 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4258 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4262 real rvdw1, rvdw2, rcoul1, rcoul2;
4263 char warn_buf[STRLEN];
4265 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4269 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4274 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4280 if (rvdw1 + rvdw2 > ir->rlist ||
4281 rcoul1 + rcoul2 > ir->rlist)
4284 "The sum of the two largest charge group radii (%f) "
4285 "is larger than rlist (%f)\n",
4286 max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4287 warning(wi, warn_buf);
4291 /* Here we do not use the zero at cut-off macro,
4292 * since user defined interactions might purposely
4293 * not be zero at the cut-off.
4295 if (ir_vdw_is_zero_at_cutoff(ir) &&
4296 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
4298 sprintf(warn_buf, "The sum of the two largest charge group "
4299 "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
4300 "With exact cut-offs, better performance can be "
4301 "obtained with cutoff-scheme = %s, because it "
4302 "does not use charge groups at all.",
4304 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4305 ir->rlistlong, ir->rvdw,
4306 ecutscheme_names[ecutsVERLET]);
4309 warning(wi, warn_buf);
4313 warning_note(wi, warn_buf);
4316 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4317 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
4319 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
4320 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4322 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4323 ir->rlistlong, ir->rcoulomb,
4324 ecutscheme_names[ecutsVERLET]);
4327 warning(wi, warn_buf);
4331 warning_note(wi, warn_buf);