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49 #include "gromacs/fileio/readinp.h"
50 #include "gromacs/fileio/warninp.h"
51 #include "gromacs/gmxlib/chargegroup.h"
52 #include "gromacs/gmxlib/network.h"
53 #include "gromacs/gmxpreprocess/toputil.h"
54 #include "gromacs/math/functions.h"
55 #include "gromacs/math/units.h"
56 #include "gromacs/math/vec.h"
57 #include "gromacs/mdlib/calc_verletbuf.h"
58 #include "gromacs/mdtypes/inputrec.h"
59 #include "gromacs/mdtypes/md_enums.h"
60 #include "gromacs/mdtypes/pull-params.h"
61 #include "gromacs/pbcutil/pbc.h"
62 #include "gromacs/topology/block.h"
63 #include "gromacs/topology/ifunc.h"
64 #include "gromacs/topology/index.h"
65 #include "gromacs/topology/mtop_util.h"
66 #include "gromacs/topology/symtab.h"
67 #include "gromacs/topology/topology.h"
68 #include "gromacs/utility/cstringutil.h"
69 #include "gromacs/utility/fatalerror.h"
70 #include "gromacs/utility/smalloc.h"
75 /* Resource parameters
76 * Do not change any of these until you read the instruction
77 * in readinp.h. Some cpp's do not take spaces after the backslash
78 * (like the c-shell), which will give you a very weird compiler
82 typedef struct t_inputrec_strings
84 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN],
85 acc[STRLEN], accgrps[STRLEN], freeze[STRLEN], frdim[STRLEN],
86 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
87 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
88 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN],
90 char fep_lambda[efptNR][STRLEN];
91 char lambda_weights[STRLEN];
94 char anneal[STRLEN], anneal_npoints[STRLEN],
95 anneal_time[STRLEN], anneal_temp[STRLEN];
96 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
97 bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
98 SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
99 char efield_x[STRLEN], efield_xt[STRLEN], efield_y[STRLEN],
100 efield_yt[STRLEN], efield_z[STRLEN], efield_zt[STRLEN];
102 } gmx_inputrec_strings;
104 static gmx_inputrec_strings *is = NULL;
106 void init_inputrec_strings()
110 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.");
115 void done_inputrec_strings()
123 egrptpALL, /* All particles have to be a member of a group. */
124 egrptpALL_GENREST, /* A rest group with name is generated for particles *
125 * that are not part of any group. */
126 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
127 * for the rest group. */
128 egrptpONE /* Merge all selected groups into one group, *
129 * make a rest group for the remaining particles. */
132 static const char *constraints[eshNR+1] = {
133 "none", "h-bonds", "all-bonds", "h-angles", "all-angles", NULL
136 static const char *couple_lam[ecouplamNR+1] = {
137 "vdw-q", "vdw", "q", "none", NULL
140 void init_ir(t_inputrec *ir, t_gromppopts *opts)
142 snew(opts->include, STRLEN);
143 snew(opts->define, STRLEN);
144 snew(ir->fepvals, 1);
145 snew(ir->expandedvals, 1);
146 snew(ir->simtempvals, 1);
149 static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
154 for (i = 0; i < ntemps; i++)
156 /* simple linear scaling -- allows more control */
157 if (simtemp->eSimTempScale == esimtempLINEAR)
159 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*temperature_lambdas[i];
161 else if (simtemp->eSimTempScale == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
163 simtemp->temperatures[i] = simtemp->simtemp_low * std::pow(simtemp->simtemp_high/simtemp->simtemp_low, static_cast<real>((1.0*i)/(ntemps-1)));
165 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
167 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*(std::expm1(temperature_lambdas[i])/std::expm1(1.0));
172 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
173 gmx_fatal(FARGS, errorstr);
180 static void _low_check(gmx_bool b, const char *s, warninp_t wi)
184 warning_error(wi, s);
188 static void check_nst(const char *desc_nst, int nst,
189 const char *desc_p, int *p,
194 if (*p > 0 && *p % nst != 0)
196 /* Round up to the next multiple of nst */
197 *p = ((*p)/nst + 1)*nst;
198 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n",
199 desc_p, desc_nst, desc_p, *p);
204 static gmx_bool ir_NVE(const t_inputrec *ir)
206 return (EI_MD(ir->eI) && ir->etc == etcNO);
209 static int lcd(int n1, int n2)
214 for (i = 2; (i <= n1 && i <= n2); i++)
216 if (n1 % i == 0 && n2 % i == 0)
225 static void process_interaction_modifier(const t_inputrec *ir, int *eintmod)
227 if (*eintmod == eintmodPOTSHIFT_VERLET)
229 if (ir->cutoff_scheme == ecutsVERLET)
231 *eintmod = eintmodPOTSHIFT;
235 *eintmod = eintmodNONE;
240 void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
242 /* Check internal consistency.
243 * NOTE: index groups are not set here yet, don't check things
244 * like temperature coupling group options here, but in triple_check
247 /* Strange macro: first one fills the err_buf, and then one can check
248 * the condition, which will print the message and increase the error
251 #define CHECK(b) _low_check(b, err_buf, wi)
252 char err_buf[256], warn_buf[STRLEN];
255 t_lambda *fep = ir->fepvals;
256 t_expanded *expand = ir->expandedvals;
258 set_warning_line(wi, mdparin, -1);
260 if (ir->coulombtype == eelRF_NEC_UNSUPPORTED)
262 sprintf(warn_buf, "%s electrostatics is no longer supported",
263 eel_names[eelRF_NEC_UNSUPPORTED]);
264 warning_error(wi, warn_buf);
267 /* BASIC CUT-OFF STUFF */
268 if (ir->rcoulomb < 0)
270 warning_error(wi, "rcoulomb should be >= 0");
274 warning_error(wi, "rvdw should be >= 0");
277 !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
279 warning_error(wi, "rlist should be >= 0");
281 sprintf(err_buf, "nstlist can not be smaller than 0. (If you were trying to use the heuristic neighbour-list update scheme for efficient buffering for improved energy conservation, please use the Verlet cut-off scheme instead.)");
282 CHECK(ir->nstlist < 0);
284 process_interaction_modifier(ir, &ir->coulomb_modifier);
285 process_interaction_modifier(ir, &ir->vdw_modifier);
287 if (ir->cutoff_scheme == ecutsGROUP)
290 "The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future "
291 "release when all interaction forms are supported for the verlet scheme. The verlet "
292 "scheme already scales better, and it is compatible with GPUs and other accelerators.");
294 if (ir->rlist > 0 && ir->rlist < ir->rcoulomb)
296 gmx_fatal(FARGS, "rcoulomb must not be greater than rlist (twin-range schemes are not supported)");
298 if (ir->rlist > 0 && ir->rlist < ir->rvdw)
300 gmx_fatal(FARGS, "rvdw must not be greater than rlist (twin-range schemes are not supported)");
303 if (ir->rlist == 0 && ir->ePBC != epbcNONE)
305 warning_error(wi, "Can not have an infinite cut-off with PBC");
309 if (ir->cutoff_scheme == ecutsVERLET)
313 /* Normal Verlet type neighbor-list, currently only limited feature support */
314 if (inputrec2nboundeddim(ir) < 3)
316 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
318 if (ir->rcoulomb != ir->rvdw)
320 warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported");
322 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
324 if (ir->vdw_modifier == eintmodNONE ||
325 ir->vdw_modifier == eintmodPOTSHIFT)
327 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
329 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]);
330 warning_note(wi, warn_buf);
332 ir->vdwtype = evdwCUT;
336 sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
337 warning_error(wi, warn_buf);
341 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
343 warning_error(wi, "With Verlet lists only cut-off and PME LJ interactions are supported");
345 if (!(ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype) ||
346 EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
348 warning_error(wi, "With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
350 if (!(ir->coulomb_modifier == eintmodNONE ||
351 ir->coulomb_modifier == eintmodPOTSHIFT))
353 sprintf(warn_buf, "coulomb_modifier=%s is not supported with the Verlet cut-off scheme", eintmod_names[ir->coulomb_modifier]);
354 warning_error(wi, warn_buf);
357 if (ir->implicit_solvent != eisNO)
359 warning_error(wi, "Implicit solvent is not (yet) supported with the with Verlet lists.");
362 if (ir->nstlist <= 0)
364 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
367 if (ir->nstlist < 10)
369 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.");
372 rc_max = std::max(ir->rvdw, ir->rcoulomb);
374 if (ir->verletbuf_tol <= 0)
376 if (ir->verletbuf_tol == 0)
378 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
381 if (ir->rlist < rc_max)
383 warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
386 if (ir->rlist == rc_max && ir->nstlist > 1)
388 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.");
393 if (ir->rlist > rc_max)
395 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.");
398 if (ir->nstlist == 1)
400 /* No buffer required */
405 if (EI_DYNAMICS(ir->eI))
407 if (inputrec2nboundeddim(ir) < 3)
409 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.");
411 /* Set rlist temporarily so we can continue processing */
416 /* Set the buffer to 5% of the cut-off */
417 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
423 /* GENERAL INTEGRATOR STUFF */
426 if (ir->etc != etcNO)
428 if (EI_RANDOM(ir->eI))
430 sprintf(warn_buf, "Setting tcoupl from '%s' to 'no'. %s handles temperature coupling implicitly. See the documentation for more information on which parameters affect temperature for %s.", etcoupl_names[ir->etc], ei_names[ir->eI], ei_names[ir->eI]);
434 sprintf(warn_buf, "Setting tcoupl from '%s' to 'no'. Temperature coupling does not apply to %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
436 warning_note(wi, warn_buf);
440 if (ir->eI == eiVVAK)
442 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]);
443 warning_note(wi, warn_buf);
445 if (!EI_DYNAMICS(ir->eI))
447 if (ir->epc != epcNO)
449 sprintf(warn_buf, "Setting pcoupl from '%s' to 'no'. Pressure coupling does not apply to %s.", epcoupl_names[ir->epc], ei_names[ir->eI]);
450 warning_note(wi, warn_buf);
454 if (EI_DYNAMICS(ir->eI))
456 if (ir->nstcalcenergy < 0)
458 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
459 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
461 /* nstcalcenergy larger than nstener does not make sense.
462 * We ideally want nstcalcenergy=nstener.
466 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
470 ir->nstcalcenergy = ir->nstenergy;
474 else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
475 (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
476 (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
479 const char *nsten = "nstenergy";
480 const char *nstdh = "nstdhdl";
481 const char *min_name = nsten;
482 int min_nst = ir->nstenergy;
484 /* find the smallest of ( nstenergy, nstdhdl ) */
485 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
486 (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
488 min_nst = ir->fepvals->nstdhdl;
491 /* If the user sets nstenergy small, we should respect that */
493 "Setting nstcalcenergy (%d) equal to %s (%d)",
494 ir->nstcalcenergy, min_name, min_nst);
495 warning_note(wi, warn_buf);
496 ir->nstcalcenergy = min_nst;
499 if (ir->epc != epcNO)
501 if (ir->nstpcouple < 0)
503 ir->nstpcouple = ir_optimal_nstpcouple(ir);
507 if (ir->nstcalcenergy > 0)
509 if (ir->efep != efepNO)
511 /* nstdhdl should be a multiple of nstcalcenergy */
512 check_nst("nstcalcenergy", ir->nstcalcenergy,
513 "nstdhdl", &ir->fepvals->nstdhdl, wi);
514 /* nstexpanded should be a multiple of nstcalcenergy */
515 check_nst("nstcalcenergy", ir->nstcalcenergy,
516 "nstexpanded", &ir->expandedvals->nstexpanded, wi);
518 /* for storing exact averages nstenergy should be
519 * a multiple of nstcalcenergy
521 check_nst("nstcalcenergy", ir->nstcalcenergy,
522 "nstenergy", &ir->nstenergy, wi);
526 if (ir->nsteps == 0 && !ir->bContinuation)
528 warning_note(wi, "For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates.");
532 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
533 ir->bContinuation && ir->ld_seed != -1)
535 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)");
541 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
542 CHECK(ir->ePBC != epbcXYZ);
543 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
544 CHECK(ir->ns_type != ensGRID);
545 sprintf(err_buf, "with TPI nstlist should be larger than zero");
546 CHECK(ir->nstlist <= 0);
547 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
548 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
549 sprintf(err_buf, "TPI does not work (yet) with the Verlet cut-off scheme");
550 CHECK(ir->cutoff_scheme == ecutsVERLET);
554 if ( (opts->nshake > 0) && (opts->bMorse) )
557 "Using morse bond-potentials while constraining bonds is useless");
558 warning(wi, warn_buf);
561 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
562 ir->bContinuation && ir->ld_seed != -1)
564 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)");
566 /* verify simulated tempering options */
570 gmx_bool bAllTempZero = TRUE;
571 for (i = 0; i < fep->n_lambda; i++)
573 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]);
574 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
575 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
577 bAllTempZero = FALSE;
580 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
581 CHECK(bAllTempZero == TRUE);
583 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
584 CHECK(ir->eI != eiVV);
586 /* check compatability of the temperature coupling with simulated tempering */
588 if (ir->etc == etcNOSEHOOVER)
590 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
591 warning_note(wi, warn_buf);
594 /* check that the temperatures make sense */
596 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);
597 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
599 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
600 CHECK(ir->simtempvals->simtemp_high <= 0);
602 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
603 CHECK(ir->simtempvals->simtemp_low <= 0);
606 /* verify free energy options */
608 if (ir->efep != efepNO)
611 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
613 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
615 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
616 (int)fep->sc_r_power);
617 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
619 sprintf(err_buf, "Can't use positive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
620 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
622 sprintf(err_buf, "Can't use positive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
623 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
625 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
626 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
628 sprintf(err_buf, "Free-energy not implemented for Ewald");
629 CHECK(ir->coulombtype == eelEWALD);
631 /* check validty of lambda inputs */
632 if (fep->n_lambda == 0)
634 /* Clear output in case of no states:*/
635 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
636 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
640 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
641 CHECK((fep->init_fep_state >= fep->n_lambda));
644 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
645 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
647 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",
648 fep->init_lambda, fep->init_fep_state);
649 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
653 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
657 for (i = 0; i < efptNR; i++)
659 if (fep->separate_dvdl[i])
664 if (n_lambda_terms > 1)
666 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.");
667 warning(wi, warn_buf);
670 if (n_lambda_terms < 2 && fep->n_lambda > 0)
673 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
677 for (j = 0; j < efptNR; j++)
679 for (i = 0; i < fep->n_lambda; i++)
681 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]);
682 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
686 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
688 for (i = 0; i < fep->n_lambda; i++)
690 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],
691 fep->all_lambda[efptCOUL][i]);
692 CHECK((fep->sc_alpha > 0) &&
693 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
694 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
695 ((fep->all_lambda[efptVDW][i] > 0.0) &&
696 (fep->all_lambda[efptVDW][i] < 1.0))));
700 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
702 real sigma, lambda, r_sc;
705 /* Maximum estimate for A and B charges equal with lambda power 1 */
707 r_sc = std::pow(lambda*fep->sc_alpha*std::pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
708 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.",
710 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
711 warning_note(wi, warn_buf);
714 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
715 be treated differently, but that's the next step */
717 for (i = 0; i < efptNR; i++)
719 for (j = 0; j < fep->n_lambda; j++)
721 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
722 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
727 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
731 /* checking equilibration of weights inputs for validity */
733 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
734 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
735 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
737 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
738 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
739 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
741 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
742 expand->equil_steps, elmceq_names[elmceqSTEPS]);
743 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
745 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
746 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
747 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
749 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
750 expand->equil_ratio, elmceq_names[elmceqRATIO]);
751 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
753 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%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) must be a positive integer if lmc-weights-equil=%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) must be a positive integer if lmc-weights-equil=%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 (%f) must be > 0 if lmc-weights-equil=%s",
766 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
767 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
769 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
770 expand->equil_ratio, elmceq_names[elmceqRATIO]);
771 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
773 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
774 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
775 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
777 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
778 CHECK((expand->lmc_repeats <= 0));
779 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
780 CHECK((expand->minvarmin <= 0));
781 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
782 CHECK((expand->c_range < 0));
783 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
784 fep->init_fep_state, expand->lmc_forced_nstart);
785 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
786 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
787 CHECK((expand->lmc_forced_nstart < 0));
788 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
789 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
791 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
792 CHECK((expand->init_wl_delta < 0));
793 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
794 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
795 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
796 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
798 /* if there is no temperature control, we need to specify an MC temperature */
799 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
800 if (expand->nstTij > 0)
802 sprintf(err_buf, "nstlog must be non-zero");
803 CHECK(ir->nstlog != 0);
804 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
805 expand->nstTij, ir->nstlog);
806 CHECK((expand->nstTij % ir->nstlog) != 0);
811 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
812 CHECK(ir->nwall && ir->ePBC != epbcXY);
815 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
817 if (ir->ePBC == epbcNONE)
819 if (ir->epc != epcNO)
821 warning(wi, "Turning off pressure coupling for vacuum system");
827 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
828 epbc_names[ir->ePBC]);
829 CHECK(ir->epc != epcNO);
831 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
832 CHECK(EEL_FULL(ir->coulombtype));
834 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
835 epbc_names[ir->ePBC]);
836 CHECK(ir->eDispCorr != edispcNO);
839 if (ir->rlist == 0.0)
841 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
842 "with coulombtype = %s or coulombtype = %s\n"
843 "without periodic boundary conditions (pbc = %s) and\n"
844 "rcoulomb and rvdw set to zero",
845 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
846 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
847 (ir->ePBC != epbcNONE) ||
848 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
852 warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
857 if (ir->nstcomm == 0)
859 ir->comm_mode = ecmNO;
861 if (ir->comm_mode != ecmNO)
865 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");
866 ir->nstcomm = abs(ir->nstcomm);
869 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
871 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
872 ir->nstcomm = ir->nstcalcenergy;
875 if (ir->comm_mode == ecmANGULAR)
877 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
878 CHECK(ir->bPeriodicMols);
879 if (ir->ePBC != epbcNONE)
881 warning(wi, "Removing the rotation around the center of mass in a periodic system, this can lead to artifacts. Only use this on a single (cluster of) molecules. This cluster should not cross periodic boundaries.");
886 if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
888 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.");
891 /* TEMPERATURE COUPLING */
892 if (ir->etc == etcYES)
894 ir->etc = etcBERENDSEN;
895 warning_note(wi, "Old option for temperature coupling given: "
896 "changing \"yes\" to \"Berendsen\"\n");
899 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
901 if (ir->opts.nhchainlength < 1)
903 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
904 ir->opts.nhchainlength = 1;
905 warning(wi, warn_buf);
908 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
910 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
911 ir->opts.nhchainlength = 1;
916 ir->opts.nhchainlength = 0;
919 if (ir->eI == eiVVAK)
921 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
923 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
926 if (ETC_ANDERSEN(ir->etc))
928 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
929 CHECK(!(EI_VV(ir->eI)));
931 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
933 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]);
934 warning_note(wi, warn_buf);
937 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]);
938 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
941 if (ir->etc == etcBERENDSEN)
943 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
944 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
945 warning_note(wi, warn_buf);
948 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
949 && ir->epc == epcBERENDSEN)
951 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
952 "true ensemble for the thermostat");
953 warning(wi, warn_buf);
956 /* PRESSURE COUPLING */
957 if (ir->epc == epcISOTROPIC)
959 ir->epc = epcBERENDSEN;
960 warning_note(wi, "Old option for pressure coupling given: "
961 "changing \"Isotropic\" to \"Berendsen\"\n");
964 if (ir->epc != epcNO)
966 dt_pcoupl = ir->nstpcouple*ir->delta_t;
968 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
969 CHECK(ir->tau_p <= 0);
971 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10*GMX_REAL_EPS)
973 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
974 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
975 warning(wi, warn_buf);
978 sprintf(err_buf, "compressibility must be > 0 when using pressure"
979 " coupling %s\n", EPCOUPLTYPE(ir->epc));
980 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
981 ir->compress[ZZ][ZZ] < 0 ||
982 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
983 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
985 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
988 "You are generating velocities so I am assuming you "
989 "are equilibrating a system. You are using "
990 "%s pressure coupling, but this can be "
991 "unstable for equilibration. If your system crashes, try "
992 "equilibrating first with Berendsen pressure coupling. If "
993 "you are not equilibrating the system, you can probably "
994 "ignore this warning.",
995 epcoupl_names[ir->epc]);
996 warning(wi, warn_buf);
1002 if (ir->epc > epcNO)
1004 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1006 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.");
1012 if (ir->epc == epcMTTK)
1014 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1018 /* ELECTROSTATICS */
1019 /* More checks are in triple check (grompp.c) */
1021 if (ir->coulombtype == eelSWITCH)
1023 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1024 "artifacts, advice: use coulombtype = %s",
1025 eel_names[ir->coulombtype],
1026 eel_names[eelRF_ZERO]);
1027 warning(wi, warn_buf);
1030 if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
1032 sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
1033 warning_note(wi, warn_buf);
1036 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1038 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);
1039 warning(wi, warn_buf);
1040 ir->epsilon_rf = ir->epsilon_r;
1041 ir->epsilon_r = 1.0;
1044 if (ir->epsilon_r == 0)
1047 "It is pointless to use long-range or Generalized Born electrostatics with infinite relative permittivity."
1048 "Since you are effectively turning of electrostatics, a plain cutoff will be much faster.");
1049 CHECK(EEL_FULL(ir->coulombtype) || ir->implicit_solvent == eisGBSA);
1052 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == NULL)
1054 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1055 CHECK(ir->epsilon_r < 0);
1058 if (EEL_RF(ir->coulombtype))
1060 /* reaction field (at the cut-off) */
1062 if (ir->coulombtype == eelRF_ZERO && ir->epsilon_rf != 0)
1064 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1065 eel_names[ir->coulombtype]);
1066 warning(wi, warn_buf);
1067 ir->epsilon_rf = 0.0;
1070 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1071 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1072 (ir->epsilon_r == 0));
1073 if (ir->epsilon_rf == ir->epsilon_r)
1075 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1076 eel_names[ir->coulombtype]);
1077 warning(wi, warn_buf);
1080 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1081 * means the interaction is zero outside rcoulomb, but it helps to
1082 * provide accurate energy conservation.
1084 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1086 if (ir_coulomb_switched(ir))
1089 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1090 eel_names[ir->coulombtype]);
1091 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1094 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1096 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1098 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1099 eel_names[ir->coulombtype]);
1100 CHECK(ir->rlist > ir->rcoulomb);
1104 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1107 "Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier.");
1108 CHECK( ir->coulomb_modifier != eintmodNONE);
1110 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1113 "Explicit switch/shift vdw interactions cannot be used in combination with a secondary vdw-modifier.");
1114 CHECK( ir->vdw_modifier != eintmodNONE);
1117 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1118 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1121 "The switch/shift interaction settings are just for compatibility; you will get better "
1122 "performance from applying potential modifiers to your interactions!\n");
1123 warning_note(wi, warn_buf);
1126 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1128 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1130 real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
1131 sprintf(warn_buf, "The switching range should be 5%% or less (currently %.2f%% using a switching range of %4f-%4f) for accurate electrostatic energies, energy conservation will be good regardless, since ewald_rtol = %g.",
1132 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1133 warning(wi, warn_buf);
1137 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1139 if (ir->rvdw_switch == 0)
1141 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.");
1142 warning(wi, warn_buf);
1146 if (EEL_FULL(ir->coulombtype))
1148 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1149 ir->coulombtype == eelPMEUSERSWITCH)
1151 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1152 eel_names[ir->coulombtype]);
1153 CHECK(ir->rcoulomb > ir->rlist);
1155 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1157 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1160 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist.\n"
1161 "For optimal energy conservation,consider using\n"
1162 "a potential modifier.", eel_names[ir->coulombtype]);
1163 CHECK(ir->rcoulomb != ir->rlist);
1168 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1170 if (ir->pme_order < 3)
1172 warning_error(wi, "pme-order can not be smaller than 3");
1176 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1178 if (ir->ewald_geometry == eewg3D)
1180 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1181 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1182 warning(wi, warn_buf);
1184 /* This check avoids extra pbc coding for exclusion corrections */
1185 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1186 CHECK(ir->wall_ewald_zfac < 2);
1188 if ((ir->ewald_geometry == eewg3DC) && (ir->ePBC != epbcXY) &&
1189 EEL_FULL(ir->coulombtype))
1191 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1192 eel_names[ir->coulombtype], eewg_names[eewg3DC], epbc_names[epbcXY]);
1193 warning(wi, warn_buf);
1195 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1197 if (ir->cutoff_scheme == ecutsVERLET)
1199 sprintf(warn_buf, "Since molecules/charge groups are broken using the Verlet scheme, you can not use a dipole correction to the %s electrostatics.",
1200 eel_names[ir->coulombtype]);
1201 warning(wi, warn_buf);
1205 sprintf(warn_buf, "Dipole corrections to %s electrostatics only work if all charge groups that can cross PBC boundaries are dipoles. If this is not the case set epsilon_surface to 0",
1206 eel_names[ir->coulombtype]);
1207 warning_note(wi, warn_buf);
1211 if (ir_vdw_switched(ir))
1213 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1214 CHECK(ir->rvdw_switch >= ir->rvdw);
1216 if (ir->rvdw_switch < 0.5*ir->rvdw)
1218 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.",
1219 ir->rvdw_switch, ir->rvdw);
1220 warning_note(wi, warn_buf);
1223 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1225 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1227 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1228 CHECK(ir->rlist > ir->rvdw);
1232 if (ir->vdwtype == evdwPME)
1234 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1236 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s and %s",
1237 evdw_names[ir->vdwtype],
1238 eintmod_names[eintmodPOTSHIFT],
1239 eintmod_names[eintmodNONE]);
1243 if (ir->cutoff_scheme == ecutsGROUP)
1245 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1246 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)))
1248 warning_note(wi, "With exact cut-offs, rlist should be "
1249 "larger than rcoulomb and rvdw, so that there "
1250 "is a buffer region for particle motion "
1251 "between neighborsearch steps");
1254 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlist <= ir->rcoulomb)
1256 sprintf(warn_buf, "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb.");
1257 warning_note(wi, warn_buf);
1259 if (ir_vdw_switched(ir) && (ir->rlist <= ir->rvdw))
1261 sprintf(warn_buf, "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw.");
1262 warning_note(wi, warn_buf);
1266 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1268 warning_note(wi, "You have selected user tables with dispersion correction, the dispersion will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction between rvdw_switch and rvdw will not be double counted). Make sure that you really want dispersion correction to -C6/r^6.");
1271 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1274 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1277 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1279 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1282 /* ENERGY CONSERVATION */
1283 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1285 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1287 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1288 evdw_names[evdwSHIFT]);
1289 warning_note(wi, warn_buf);
1291 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1293 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1294 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1295 warning_note(wi, warn_buf);
1299 /* IMPLICIT SOLVENT */
1300 if (ir->coulombtype == eelGB_NOTUSED)
1302 sprintf(warn_buf, "Invalid option %s for coulombtype",
1303 eel_names[ir->coulombtype]);
1304 warning_error(wi, warn_buf);
1307 if (ir->sa_algorithm == esaSTILL)
1309 sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
1310 CHECK(ir->sa_algorithm == esaSTILL);
1313 if (ir->implicit_solvent == eisGBSA)
1315 sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
1316 CHECK(ir->rgbradii != ir->rlist);
1318 if (ir->coulombtype != eelCUT)
1320 sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
1321 CHECK(ir->coulombtype != eelCUT);
1323 if (ir->vdwtype != evdwCUT)
1325 sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
1326 CHECK(ir->vdwtype != evdwCUT);
1328 if (ir->nstgbradii < 1)
1330 sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
1331 warning_note(wi, warn_buf);
1334 if (ir->sa_algorithm == esaNO)
1336 sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
1337 warning_note(wi, warn_buf);
1339 if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
1341 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");
1342 warning_note(wi, warn_buf);
1344 if (ir->gb_algorithm == egbSTILL)
1346 ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
1350 ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
1353 if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
1355 sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
1356 CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
1363 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1367 /* count the number of text elemets separated by whitespace in a string.
1368 str = the input string
1369 maxptr = the maximum number of allowed elements
1370 ptr = the output array of pointers to the first character of each element
1371 returns: the number of elements. */
1372 int str_nelem(const char *str, int maxptr, char *ptr[])
1377 copy0 = gmx_strdup(str);
1380 while (*copy != '\0')
1384 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1392 while ((*copy != '\0') && !isspace(*copy))
1411 /* interpret a number of doubles from a string and put them in an array,
1412 after allocating space for them.
1413 str = the input string
1414 n = the (pre-allocated) number of doubles read
1415 r = the output array of doubles. */
1416 static void parse_n_real(char *str, int *n, real **r, warninp_t wi)
1421 char warn_buf[STRLEN];
1423 *n = str_nelem(str, MAXPTR, ptr);
1426 for (i = 0; i < *n; i++)
1428 (*r)[i] = strtod(ptr[i], &endptr);
1431 sprintf(warn_buf, "Invalid value %s in string in mdp file. Expected a real number.", ptr[i]);
1432 warning_error(wi, warn_buf);
1437 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN], warninp_t wi)
1440 int i, j, max_n_lambda, nweights, nfep[efptNR];
1441 t_lambda *fep = ir->fepvals;
1442 t_expanded *expand = ir->expandedvals;
1443 real **count_fep_lambdas;
1444 gmx_bool bOneLambda = TRUE;
1446 snew(count_fep_lambdas, efptNR);
1448 /* FEP input processing */
1449 /* first, identify the number of lambda values for each type.
1450 All that are nonzero must have the same number */
1452 for (i = 0; i < efptNR; i++)
1454 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]), wi);
1457 /* now, determine the number of components. All must be either zero, or equal. */
1460 for (i = 0; i < efptNR; i++)
1462 if (nfep[i] > max_n_lambda)
1464 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1465 must have the same number if its not zero.*/
1470 for (i = 0; i < efptNR; i++)
1474 ir->fepvals->separate_dvdl[i] = FALSE;
1476 else if (nfep[i] == max_n_lambda)
1478 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1479 respect to the temperature currently */
1481 ir->fepvals->separate_dvdl[i] = TRUE;
1486 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1487 nfep[i], efpt_names[i], max_n_lambda);
1490 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1491 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1493 /* the number of lambdas is the number we've read in, which is either zero
1494 or the same for all */
1495 fep->n_lambda = max_n_lambda;
1497 /* allocate space for the array of lambda values */
1498 snew(fep->all_lambda, efptNR);
1499 /* if init_lambda is defined, we need to set lambda */
1500 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1502 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1504 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1505 for (i = 0; i < efptNR; i++)
1507 snew(fep->all_lambda[i], fep->n_lambda);
1508 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1511 for (j = 0; j < fep->n_lambda; j++)
1513 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1515 sfree(count_fep_lambdas[i]);
1518 sfree(count_fep_lambdas);
1520 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1521 bookkeeping -- for now, init_lambda */
1523 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1525 for (i = 0; i < fep->n_lambda; i++)
1527 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1531 /* check to see if only a single component lambda is defined, and soft core is defined.
1532 In this case, turn on coulomb soft core */
1534 if (max_n_lambda == 0)
1540 for (i = 0; i < efptNR; i++)
1542 if ((nfep[i] != 0) && (i != efptFEP))
1548 if ((bOneLambda) && (fep->sc_alpha > 0))
1550 fep->bScCoul = TRUE;
1553 /* Fill in the others with the efptFEP if they are not explicitly
1554 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1555 they are all zero. */
1557 for (i = 0; i < efptNR; i++)
1559 if ((nfep[i] == 0) && (i != efptFEP))
1561 for (j = 0; j < fep->n_lambda; j++)
1563 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1569 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1570 if (fep->sc_r_power == 48)
1572 if (fep->sc_alpha > 0.1)
1574 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1578 /* now read in the weights */
1579 parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
1582 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1584 else if (nweights != fep->n_lambda)
1586 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1587 nweights, fep->n_lambda);
1589 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1591 expand->nstexpanded = fep->nstdhdl;
1592 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1594 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1596 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1597 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1598 2*tau_t just to be careful so it's not to frequent */
1603 static void do_simtemp_params(t_inputrec *ir)
1606 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1607 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1612 static void do_wall_params(t_inputrec *ir,
1613 char *wall_atomtype, char *wall_density,
1617 char *names[MAXPTR];
1620 opts->wall_atomtype[0] = NULL;
1621 opts->wall_atomtype[1] = NULL;
1623 ir->wall_atomtype[0] = -1;
1624 ir->wall_atomtype[1] = -1;
1625 ir->wall_density[0] = 0;
1626 ir->wall_density[1] = 0;
1630 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1631 if (nstr != ir->nwall)
1633 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1636 for (i = 0; i < ir->nwall; i++)
1638 opts->wall_atomtype[i] = gmx_strdup(names[i]);
1641 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1643 nstr = str_nelem(wall_density, MAXPTR, names);
1644 if (nstr != ir->nwall)
1646 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1648 for (i = 0; i < ir->nwall; i++)
1650 sscanf(names[i], "%lf", &dbl);
1653 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1655 ir->wall_density[i] = dbl;
1661 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1669 srenew(groups->grpname, groups->ngrpname+nwall);
1670 grps = &(groups->grps[egcENER]);
1671 srenew(grps->nm_ind, grps->nr+nwall);
1672 for (i = 0; i < nwall; i++)
1674 sprintf(str, "wall%d", i);
1675 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1676 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1681 void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1682 t_expanded *expand, warninp_t wi)
1690 /* read expanded ensemble parameters */
1691 CCTYPE ("expanded ensemble variables");
1692 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1693 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1694 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1695 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1696 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1697 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1698 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1699 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1700 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1701 CCTYPE("Seed for Monte Carlo in lambda space");
1702 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1703 RTYPE ("mc-temperature", expand->mc_temp, -1);
1704 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1705 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1706 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1707 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1708 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1709 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1710 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1711 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1712 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1713 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1714 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
1722 /*! \brief Return whether an end state with the given coupling-lambda
1723 * value describes fully-interacting VDW.
1725 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1726 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1728 static gmx_bool couple_lambda_has_vdw_on(int couple_lambda_value)
1730 return (couple_lambda_value == ecouplamVDW ||
1731 couple_lambda_value == ecouplamVDWQ);
1734 void get_ir(const char *mdparin, const char *mdparout,
1735 t_inputrec *ir, t_gromppopts *opts,
1739 double dumdub[2][6];
1743 char warn_buf[STRLEN];
1744 t_lambda *fep = ir->fepvals;
1745 t_expanded *expand = ir->expandedvals;
1747 init_inputrec_strings();
1748 inp = read_inpfile(mdparin, &ninp, wi);
1750 snew(dumstr[0], STRLEN);
1751 snew(dumstr[1], STRLEN);
1753 if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
1756 "%s did not specify a value for the .mdp option "
1757 "\"cutoff-scheme\". Probably it was first intended for use "
1758 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1759 "introduced, but the group scheme was still the default. "
1760 "The default is now the Verlet scheme, so you will observe "
1761 "different behaviour.", mdparin);
1762 warning_note(wi, warn_buf);
1765 /* ignore the following deprecated commands */
1768 REM_TYPE("domain-decomposition");
1769 REM_TYPE("andersen-seed");
1771 REM_TYPE("dihre-fc");
1772 REM_TYPE("dihre-tau");
1773 REM_TYPE("nstdihreout");
1774 REM_TYPE("nstcheckpoint");
1775 REM_TYPE("optimize-fft");
1776 REM_TYPE("adress_type");
1777 REM_TYPE("adress_const_wf");
1778 REM_TYPE("adress_ex_width");
1779 REM_TYPE("adress_hy_width");
1780 REM_TYPE("adress_ex_forcecap");
1781 REM_TYPE("adress_interface_correction");
1782 REM_TYPE("adress_site");
1783 REM_TYPE("adress_reference_coords");
1784 REM_TYPE("adress_tf_grp_names");
1785 REM_TYPE("adress_cg_grp_names");
1786 REM_TYPE("adress_do_hybridpairs");
1787 REM_TYPE("rlistlong");
1788 REM_TYPE("nstcalclr");
1789 REM_TYPE("pull-print-com2");
1791 /* replace the following commands with the clearer new versions*/
1792 REPL_TYPE("unconstrained-start", "continuation");
1793 REPL_TYPE("foreign-lambda", "fep-lambdas");
1794 REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
1795 REPL_TYPE("nstxtcout", "nstxout-compressed");
1796 REPL_TYPE("xtc-grps", "compressed-x-grps");
1797 REPL_TYPE("xtc-precision", "compressed-x-precision");
1798 REPL_TYPE("pull-print-com1", "pull-print-com");
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 CTYPE ("Output frequency for energies to log file and energy file");
1852 ITYPE ("nstlog", ir->nstlog, 1000);
1853 ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
1854 ITYPE ("nstenergy", ir->nstenergy, 1000);
1855 CTYPE ("Output frequency and precision for .xtc file");
1856 ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
1857 RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
1858 CTYPE ("This selects the subset of atoms for the compressed");
1859 CTYPE ("trajectory file. You can select multiple groups. By");
1860 CTYPE ("default, all atoms will be written.");
1861 STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
1862 CTYPE ("Selection of energy groups");
1863 STYPE ("energygrps", is->energy, NULL);
1865 /* Neighbor searching */
1866 CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
1867 CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1868 EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
1869 CTYPE ("nblist update frequency");
1870 ITYPE ("nstlist", ir->nstlist, 10);
1871 CTYPE ("ns algorithm (simple or grid)");
1872 EETYPE("ns-type", ir->ns_type, ens_names);
1873 CTYPE ("Periodic boundary conditions: xyz, no, xy");
1874 EETYPE("pbc", ir->ePBC, epbc_names);
1875 EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
1876 CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1877 CTYPE ("a value of -1 means: use rlist");
1878 RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
1879 CTYPE ("nblist cut-off");
1880 RTYPE ("rlist", ir->rlist, 1.0);
1881 CTYPE ("long-range cut-off for switched potentials");
1883 /* Electrostatics */
1884 CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
1885 CTYPE ("Method for doing electrostatics");
1886 EETYPE("coulombtype", ir->coulombtype, eel_names);
1887 EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
1888 CTYPE ("cut-off lengths");
1889 RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
1890 RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
1891 CTYPE ("Relative dielectric constant for the medium and the reaction field");
1892 RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
1893 RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
1894 CTYPE ("Method for doing Van der Waals");
1895 EETYPE("vdw-type", ir->vdwtype, evdw_names);
1896 EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
1897 CTYPE ("cut-off lengths");
1898 RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
1899 RTYPE ("rvdw", ir->rvdw, 1.0);
1900 CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
1901 EETYPE("DispCorr", ir->eDispCorr, edispc_names);
1902 CTYPE ("Extension of the potential lookup tables beyond the cut-off");
1903 RTYPE ("table-extension", ir->tabext, 1.0);
1904 CTYPE ("Separate tables between energy group pairs");
1905 STYPE ("energygrp-table", is->egptable, NULL);
1906 CTYPE ("Spacing for the PME/PPPM FFT grid");
1907 RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
1908 CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
1909 ITYPE ("fourier-nx", ir->nkx, 0);
1910 ITYPE ("fourier-ny", ir->nky, 0);
1911 ITYPE ("fourier-nz", ir->nkz, 0);
1912 CTYPE ("EWALD/PME/PPPM parameters");
1913 ITYPE ("pme-order", ir->pme_order, 4);
1914 RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
1915 RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
1916 EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
1917 EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
1918 RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
1920 CCTYPE("IMPLICIT SOLVENT ALGORITHM");
1921 EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
1923 CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
1924 CTYPE ("Algorithm for calculating Born radii");
1925 EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
1926 CTYPE ("Frequency of calculating the Born radii inside rlist");
1927 ITYPE ("nstgbradii", ir->nstgbradii, 1);
1928 CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
1929 CTYPE ("between rlist and rgbradii is updated every nstlist steps");
1930 RTYPE ("rgbradii", ir->rgbradii, 1.0);
1931 CTYPE ("Dielectric coefficient of the implicit solvent");
1932 RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
1933 CTYPE ("Salt concentration in M for Generalized Born models");
1934 RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
1935 CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
1936 RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
1937 RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
1938 RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
1939 RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
1940 EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
1941 CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
1942 CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
1943 RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
1945 /* Coupling stuff */
1946 CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
1947 CTYPE ("Temperature coupling");
1948 EETYPE("tcoupl", ir->etc, etcoupl_names);
1949 ITYPE ("nsttcouple", ir->nsttcouple, -1);
1950 ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
1951 EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
1952 CTYPE ("Groups to couple separately");
1953 STYPE ("tc-grps", is->tcgrps, NULL);
1954 CTYPE ("Time constant (ps) and reference temperature (K)");
1955 STYPE ("tau-t", is->tau_t, NULL);
1956 STYPE ("ref-t", is->ref_t, NULL);
1957 CTYPE ("pressure coupling");
1958 EETYPE("pcoupl", ir->epc, epcoupl_names);
1959 EETYPE("pcoupltype", ir->epct, epcoupltype_names);
1960 ITYPE ("nstpcouple", ir->nstpcouple, -1);
1961 CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
1962 RTYPE ("tau-p", ir->tau_p, 1.0);
1963 STYPE ("compressibility", dumstr[0], NULL);
1964 STYPE ("ref-p", dumstr[1], NULL);
1965 CTYPE ("Scaling of reference coordinates, No, All or COM");
1966 EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
1969 CCTYPE ("OPTIONS FOR QMMM calculations");
1970 EETYPE("QMMM", ir->bQMMM, yesno_names);
1971 CTYPE ("Groups treated Quantum Mechanically");
1972 STYPE ("QMMM-grps", is->QMMM, NULL);
1973 CTYPE ("QM method");
1974 STYPE("QMmethod", is->QMmethod, NULL);
1975 CTYPE ("QMMM scheme");
1976 EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
1977 CTYPE ("QM basisset");
1978 STYPE("QMbasis", is->QMbasis, NULL);
1979 CTYPE ("QM charge");
1980 STYPE ("QMcharge", is->QMcharge, NULL);
1981 CTYPE ("QM multiplicity");
1982 STYPE ("QMmult", is->QMmult, NULL);
1983 CTYPE ("Surface Hopping");
1984 STYPE ("SH", is->bSH, NULL);
1985 CTYPE ("CAS space options");
1986 STYPE ("CASorbitals", is->CASorbitals, NULL);
1987 STYPE ("CASelectrons", is->CASelectrons, NULL);
1988 STYPE ("SAon", is->SAon, NULL);
1989 STYPE ("SAoff", is->SAoff, NULL);
1990 STYPE ("SAsteps", is->SAsteps, NULL);
1991 CTYPE ("Scale factor for MM charges");
1992 RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
1993 CTYPE ("Optimization of QM subsystem");
1994 STYPE ("bOPT", is->bOPT, NULL);
1995 STYPE ("bTS", is->bTS, NULL);
1997 /* Simulated annealing */
1998 CCTYPE("SIMULATED ANNEALING");
1999 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
2000 STYPE ("annealing", is->anneal, NULL);
2001 CTYPE ("Number of time points to use for specifying annealing in each group");
2002 STYPE ("annealing-npoints", is->anneal_npoints, NULL);
2003 CTYPE ("List of times at the annealing points for each group");
2004 STYPE ("annealing-time", is->anneal_time, NULL);
2005 CTYPE ("Temp. at each annealing point, for each group.");
2006 STYPE ("annealing-temp", is->anneal_temp, NULL);
2009 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
2010 EETYPE("gen-vel", opts->bGenVel, yesno_names);
2011 RTYPE ("gen-temp", opts->tempi, 300.0);
2012 ITYPE ("gen-seed", opts->seed, -1);
2015 CCTYPE ("OPTIONS FOR BONDS");
2016 EETYPE("constraints", opts->nshake, constraints);
2017 CTYPE ("Type of constraint algorithm");
2018 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
2019 CTYPE ("Do not constrain the start configuration");
2020 EETYPE("continuation", ir->bContinuation, yesno_names);
2021 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
2022 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
2023 CTYPE ("Relative tolerance of shake");
2024 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
2025 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
2026 ITYPE ("lincs-order", ir->nProjOrder, 4);
2027 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
2028 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
2029 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
2030 ITYPE ("lincs-iter", ir->nLincsIter, 1);
2031 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
2032 CTYPE ("rotates over more degrees than");
2033 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
2034 CTYPE ("Convert harmonic bonds to morse potentials");
2035 EETYPE("morse", opts->bMorse, yesno_names);
2037 /* Energy group exclusions */
2038 CCTYPE ("ENERGY GROUP EXCLUSIONS");
2039 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
2040 STYPE ("energygrp-excl", is->egpexcl, NULL);
2044 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2045 ITYPE ("nwall", ir->nwall, 0);
2046 EETYPE("wall-type", ir->wall_type, ewt_names);
2047 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
2048 STYPE ("wall-atomtype", is->wall_atomtype, NULL);
2049 STYPE ("wall-density", is->wall_density, NULL);
2050 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
2053 CCTYPE("COM PULLING");
2054 EETYPE("pull", ir->bPull, yesno_names);
2058 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, wi);
2061 /* Enforced rotation */
2062 CCTYPE("ENFORCED ROTATION");
2063 CTYPE("Enforced rotation: No or Yes");
2064 EETYPE("rotation", ir->bRot, yesno_names);
2068 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2071 /* Interactive MD */
2073 CCTYPE("Group to display and/or manipulate in interactive MD session");
2074 STYPE ("IMD-group", is->imd_grp, NULL);
2075 if (is->imd_grp[0] != '\0')
2082 CCTYPE("NMR refinement stuff");
2083 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2084 EETYPE("disre", ir->eDisre, edisre_names);
2085 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2086 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2087 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2088 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2089 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2090 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2091 CTYPE ("Output frequency for pair distances to energy file");
2092 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2093 CTYPE ("Orientation restraints: No or Yes");
2094 EETYPE("orire", opts->bOrire, yesno_names);
2095 CTYPE ("Orientation restraints force constant and tau for time averaging");
2096 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2097 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2098 STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
2099 CTYPE ("Output frequency for trace(SD) and S to energy file");
2100 ITYPE ("nstorireout", ir->nstorireout, 100);
2102 /* free energy variables */
2103 CCTYPE ("Free energy variables");
2104 EETYPE("free-energy", ir->efep, efep_names);
2105 STYPE ("couple-moltype", is->couple_moltype, NULL);
2106 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2107 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2108 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2110 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2112 it was not entered */
2113 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2114 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2115 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2116 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
2117 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
2118 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
2119 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
2120 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
2121 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
2122 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
2123 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2124 STYPE ("init-lambda-weights", is->lambda_weights, NULL);
2125 EETYPE("dhdl-print-energy", fep->edHdLPrintEnergy, edHdLPrintEnergy_names);
2126 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2127 ITYPE ("sc-power", fep->sc_power, 1);
2128 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2129 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2130 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2131 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2132 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2133 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2134 separate_dhdl_file_names);
2135 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2136 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2137 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2139 /* Non-equilibrium MD stuff */
2140 CCTYPE("Non-equilibrium MD stuff");
2141 STYPE ("acc-grps", is->accgrps, NULL);
2142 STYPE ("accelerate", is->acc, NULL);
2143 STYPE ("freezegrps", is->freeze, NULL);
2144 STYPE ("freezedim", is->frdim, NULL);
2145 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2146 STYPE ("deform", is->deform, NULL);
2148 /* simulated tempering variables */
2149 CCTYPE("simulated tempering variables");
2150 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2151 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2152 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2153 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2155 /* expanded ensemble variables */
2156 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2158 read_expandedparams(&ninp, &inp, expand, wi);
2161 /* Electric fields */
2162 CCTYPE("Electric fields");
2163 CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
2164 CTYPE ("and a phase angle (real)");
2165 STYPE ("E-x", is->efield_x, NULL);
2166 CTYPE ("Time dependent (pulsed) electric field. Format is omega, time for pulse");
2167 CTYPE ("peak, and sigma (width) for pulse. Sigma = 0 removes pulse, leaving");
2168 CTYPE ("the field to be a cosine function.");
2169 STYPE ("E-xt", is->efield_xt, NULL);
2170 STYPE ("E-y", is->efield_y, NULL);
2171 STYPE ("E-yt", is->efield_yt, NULL);
2172 STYPE ("E-z", is->efield_z, NULL);
2173 STYPE ("E-zt", is->efield_zt, NULL);
2175 /* Ion/water position swapping ("computational electrophysiology") */
2176 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2177 CTYPE("Swap positions along direction: no, X, Y, Z");
2178 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2179 if (ir->eSwapCoords != eswapNO)
2186 CTYPE("Swap attempt frequency");
2187 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2188 CTYPE("Number of ion types to be controlled");
2189 ITYPE("iontypes", nIonTypes, 1);
2192 warning_error(wi, "You need to provide at least one ion type for position exchanges.");
2194 ir->swap->ngrp = nIonTypes + eSwapFixedGrpNR;
2195 snew(ir->swap->grp, ir->swap->ngrp);
2196 for (i = 0; i < ir->swap->ngrp; i++)
2198 snew(ir->swap->grp[i].molname, STRLEN);
2200 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2201 STYPE("split-group0", ir->swap->grp[eGrpSplit0].molname, NULL);
2202 STYPE("split-group1", ir->swap->grp[eGrpSplit1].molname, NULL);
2203 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2204 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2205 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2207 CTYPE("Name of solvent molecules");
2208 STYPE("solvent-group", ir->swap->grp[eGrpSolvent].molname, NULL);
2210 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2211 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2212 CTYPE("however, if correctly defined, the permeation events are recorded per channel");
2213 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2214 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2215 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2216 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2217 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2218 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2220 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2221 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2223 CTYPE("Names of the ion types that can be exchanged with solvent molecules,");
2224 CTYPE("and the requested number of ions of this type in compartments A and B");
2225 CTYPE("-1 means fix the numbers as found in step 0");
2226 for (i = 0; i < nIonTypes; i++)
2228 int ig = eSwapFixedGrpNR + i;
2230 sprintf(buf, "iontype%d-name", i);
2231 STYPE(buf, ir->swap->grp[ig].molname, NULL);
2232 sprintf(buf, "iontype%d-in-A", i);
2233 ITYPE(buf, ir->swap->grp[ig].nmolReq[0], -1);
2234 sprintf(buf, "iontype%d-in-B", i);
2235 ITYPE(buf, ir->swap->grp[ig].nmolReq[1], -1);
2238 CTYPE("By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers");
2239 CTYPE("at maximum distance (= bulk concentration) to the split group layers. However,");
2240 CTYPE("an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0");
2241 CTYPE("towards one of the compartment-partitioning layers (at +/- 1.0).");
2242 RTYPE("bulk-offsetA", ir->swap->bulkOffset[0], 0.0);
2243 RTYPE("bulk-offsetB", ir->swap->bulkOffset[1], 0.0);
2244 if (!(ir->swap->bulkOffset[0] > -1.0 && ir->swap->bulkOffset[0] < 1.0)
2245 || !(ir->swap->bulkOffset[1] > -1.0 && ir->swap->bulkOffset[1] < 1.0) )
2247 warning_error(wi, "Bulk layer offsets must be > -1.0 and < 1.0 !");
2250 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2251 RTYPE("threshold", ir->swap->threshold, 1.0);
2254 /* AdResS is no longer supported, but we need mdrun to be able to refuse to run old AdResS .tpr files */
2255 EETYPE("adress", ir->bAdress, yesno_names);
2257 /* User defined thingies */
2258 CCTYPE ("User defined thingies");
2259 STYPE ("user1-grps", is->user1, NULL);
2260 STYPE ("user2-grps", is->user2, NULL);
2261 ITYPE ("userint1", ir->userint1, 0);
2262 ITYPE ("userint2", ir->userint2, 0);
2263 ITYPE ("userint3", ir->userint3, 0);
2264 ITYPE ("userint4", ir->userint4, 0);
2265 RTYPE ("userreal1", ir->userreal1, 0);
2266 RTYPE ("userreal2", ir->userreal2, 0);
2267 RTYPE ("userreal3", ir->userreal3, 0);
2268 RTYPE ("userreal4", ir->userreal4, 0);
2271 write_inpfile(mdparout, ninp, inp, FALSE, wi);
2272 for (i = 0; (i < ninp); i++)
2275 sfree(inp[i].value);
2279 /* Process options if necessary */
2280 for (m = 0; m < 2; m++)
2282 for (i = 0; i < 2*DIM; i++)
2291 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2293 warning_error(wi, "Pressure coupling not enough values (I need 1)");
2295 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2297 case epctSEMIISOTROPIC:
2298 case epctSURFACETENSION:
2299 if (sscanf(dumstr[m], "%lf%lf",
2300 &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2302 warning_error(wi, "Pressure coupling not enough values (I need 2)");
2304 dumdub[m][YY] = dumdub[m][XX];
2306 case epctANISOTROPIC:
2307 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2308 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2309 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2311 warning_error(wi, "Pressure coupling not enough values (I need 6)");
2315 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2316 epcoupltype_names[ir->epct]);
2320 clear_mat(ir->ref_p);
2321 clear_mat(ir->compress);
2322 for (i = 0; i < DIM; i++)
2324 ir->ref_p[i][i] = dumdub[1][i];
2325 ir->compress[i][i] = dumdub[0][i];
2327 if (ir->epct == epctANISOTROPIC)
2329 ir->ref_p[XX][YY] = dumdub[1][3];
2330 ir->ref_p[XX][ZZ] = dumdub[1][4];
2331 ir->ref_p[YY][ZZ] = dumdub[1][5];
2332 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2334 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2336 ir->compress[XX][YY] = dumdub[0][3];
2337 ir->compress[XX][ZZ] = dumdub[0][4];
2338 ir->compress[YY][ZZ] = dumdub[0][5];
2339 for (i = 0; i < DIM; i++)
2341 for (m = 0; m < i; m++)
2343 ir->ref_p[i][m] = ir->ref_p[m][i];
2344 ir->compress[i][m] = ir->compress[m][i];
2349 if (ir->comm_mode == ecmNO)
2354 opts->couple_moltype = NULL;
2355 if (strlen(is->couple_moltype) > 0)
2357 if (ir->efep != efepNO)
2359 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2360 if (opts->couple_lam0 == opts->couple_lam1)
2362 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2364 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2365 opts->couple_lam1 == ecouplamNONE))
2367 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2372 warning_note(wi, "Free energy is turned off, so we will not decouple the molecule listed in your input.");
2375 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2376 if (ir->efep != efepNO)
2378 if (fep->delta_lambda > 0)
2380 ir->efep = efepSLOWGROWTH;
2384 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2386 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2387 warning_note(wi, "Old option for dhdl-print-energy given: "
2388 "changing \"yes\" to \"total\"\n");
2391 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2393 /* always print out the energy to dhdl if we are doing
2394 expanded ensemble, since we need the total energy for
2395 analysis if the temperature is changing. In some
2396 conditions one may only want the potential energy, so
2397 we will allow that if the appropriate mdp setting has
2398 been enabled. Otherwise, total it is:
2400 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2403 if ((ir->efep != efepNO) || ir->bSimTemp)
2405 ir->bExpanded = FALSE;
2406 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2408 ir->bExpanded = TRUE;
2410 do_fep_params(ir, is->fep_lambda, is->lambda_weights, wi);
2411 if (ir->bSimTemp) /* done after fep params */
2413 do_simtemp_params(ir);
2416 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2417 * setup and not on the old way of specifying the free-energy setup,
2418 * we should check for using soft-core when not needed, since that
2419 * can complicate the sampling significantly.
2420 * Note that we only check for the automated coupling setup.
2421 * If the (advanced) user does FEP through manual topology changes,
2422 * this check will not be triggered.
2424 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 &&
2425 ir->fepvals->sc_alpha != 0 &&
2426 (couple_lambda_has_vdw_on(opts->couple_lam0) &&
2427 couple_lambda_has_vdw_on(opts->couple_lam1)))
2429 warning(wi, "You are using soft-core interactions while the Van der Waals interactions are not decoupled (note that the sc-coul option is only active when using lambda states). Although this will not lead to errors, you will need much more sampling than without soft-core interactions. Consider using sc-alpha=0.");
2434 ir->fepvals->n_lambda = 0;
2437 /* WALL PARAMETERS */
2439 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2441 /* ORIENTATION RESTRAINT PARAMETERS */
2443 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
2445 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2448 /* DEFORMATION PARAMETERS */
2450 clear_mat(ir->deform);
2451 for (i = 0; i < 6; i++)
2455 sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
2456 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2457 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2458 for (i = 0; i < 3; i++)
2460 ir->deform[i][i] = dumdub[0][i];
2462 ir->deform[YY][XX] = dumdub[0][3];
2463 ir->deform[ZZ][XX] = dumdub[0][4];
2464 ir->deform[ZZ][YY] = dumdub[0][5];
2465 if (ir->epc != epcNO)
2467 for (i = 0; i < 3; i++)
2469 for (j = 0; j <= i; j++)
2471 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2473 warning_error(wi, "A box element has deform set and compressibility > 0");
2477 for (i = 0; i < 3; i++)
2479 for (j = 0; j < i; j++)
2481 if (ir->deform[i][j] != 0)
2483 for (m = j; m < DIM; m++)
2485 if (ir->compress[m][j] != 0)
2487 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.");
2488 warning(wi, warn_buf);
2496 /* Ion/water position swapping checks */
2497 if (ir->eSwapCoords != eswapNO)
2499 if (ir->swap->nstswap < 1)
2501 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2503 if (ir->swap->nAverage < 1)
2505 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2507 if (ir->swap->threshold < 1.0)
2509 warning_error(wi, "Ion count threshold must be at least 1.\n");
2517 static int search_QMstring(const char *s, int ng, const char *gn[])
2519 /* same as normal search_string, but this one searches QM strings */
2522 for (i = 0; (i < ng); i++)
2524 if (gmx_strcasecmp(s, gn[i]) == 0)
2530 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2534 } /* search_QMstring */
2536 /* We would like gn to be const as well, but C doesn't allow this */
2537 /* TODO this is utility functionality (search for the index of a
2538 string in a collection), so should be refactored and located more
2540 int search_string(const char *s, int ng, char *gn[])
2544 for (i = 0; (i < ng); i++)
2546 if (gmx_strcasecmp(s, gn[i]) == 0)
2553 "Group %s referenced in the .mdp file was not found in the index file.\n"
2554 "Group names must match either [moleculetype] names or custom index group\n"
2555 "names, in which case you must supply an index file to the '-n' option\n"
2562 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2563 t_blocka *block, char *gnames[],
2564 int gtype, int restnm,
2565 int grptp, gmx_bool bVerbose,
2568 unsigned short *cbuf;
2569 t_grps *grps = &(groups->grps[gtype]);
2570 int i, j, gid, aj, ognr, ntot = 0;
2573 char warn_buf[STRLEN];
2577 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2580 title = gtypes[gtype];
2583 /* Mark all id's as not set */
2584 for (i = 0; (i < natoms); i++)
2589 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2590 for (i = 0; (i < ng); i++)
2592 /* Lookup the group name in the block structure */
2593 gid = search_string(ptrs[i], block->nr, gnames);
2594 if ((grptp != egrptpONE) || (i == 0))
2596 grps->nm_ind[grps->nr++] = gid;
2600 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2603 /* Now go over the atoms in the group */
2604 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2609 /* Range checking */
2610 if ((aj < 0) || (aj >= natoms))
2612 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2614 /* Lookup up the old group number */
2618 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2619 aj+1, title, ognr+1, i+1);
2623 /* Store the group number in buffer */
2624 if (grptp == egrptpONE)
2637 /* Now check whether we have done all atoms */
2641 if (grptp == egrptpALL)
2643 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2644 natoms-ntot, title);
2646 else if (grptp == egrptpPART)
2648 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2649 natoms-ntot, title);
2650 warning_note(wi, warn_buf);
2652 /* Assign all atoms currently unassigned to a rest group */
2653 for (j = 0; (j < natoms); j++)
2655 if (cbuf[j] == NOGID)
2661 if (grptp != egrptpPART)
2666 "Making dummy/rest group for %s containing %d elements\n",
2667 title, natoms-ntot);
2669 /* Add group name "rest" */
2670 grps->nm_ind[grps->nr] = restnm;
2672 /* Assign the rest name to all atoms not currently assigned to a group */
2673 for (j = 0; (j < natoms); j++)
2675 if (cbuf[j] == NOGID)
2684 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2686 /* All atoms are part of one (or no) group, no index required */
2687 groups->ngrpnr[gtype] = 0;
2688 groups->grpnr[gtype] = NULL;
2692 groups->ngrpnr[gtype] = natoms;
2693 snew(groups->grpnr[gtype], natoms);
2694 for (j = 0; (j < natoms); j++)
2696 groups->grpnr[gtype][j] = cbuf[j];
2702 return (bRest && grptp == egrptpPART);
2705 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2708 gmx_groups_t *groups;
2709 pull_params_t *pull;
2710 int natoms, ai, aj, i, j, d, g, imin, jmin;
2712 int *nrdf2, *na_vcm, na_tot;
2713 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2714 gmx_mtop_atomloop_all_t aloop;
2716 int mb, mol, ftype, as;
2717 gmx_molblock_t *molb;
2718 gmx_moltype_t *molt;
2721 * First calc 3xnr-atoms for each group
2722 * then subtract half a degree of freedom for each constraint
2724 * Only atoms and nuclei contribute to the degrees of freedom...
2729 groups = &mtop->groups;
2730 natoms = mtop->natoms;
2732 /* Allocate one more for a possible rest group */
2733 /* We need to sum degrees of freedom into doubles,
2734 * since floats give too low nrdf's above 3 million atoms.
2736 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2737 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2738 snew(na_vcm, groups->grps[egcVCM].nr+1);
2740 for (i = 0; i < groups->grps[egcTC].nr; i++)
2744 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2749 snew(nrdf2, natoms);
2750 aloop = gmx_mtop_atomloop_all_init(mtop);
2751 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2754 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2756 g = ggrpnr(groups, egcFREEZE, i);
2757 /* Double count nrdf for particle i */
2758 for (d = 0; d < DIM; d++)
2760 if (opts->nFreeze[g][d] == 0)
2765 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2766 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2771 for (mb = 0; mb < mtop->nmolblock; mb++)
2773 molb = &mtop->molblock[mb];
2774 molt = &mtop->moltype[molb->type];
2775 atom = molt->atoms.atom;
2776 for (mol = 0; mol < molb->nmol; mol++)
2778 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2780 ia = molt->ilist[ftype].iatoms;
2781 for (i = 0; i < molt->ilist[ftype].nr; )
2783 /* Subtract degrees of freedom for the constraints,
2784 * if the particles still have degrees of freedom left.
2785 * If one of the particles is a vsite or a shell, then all
2786 * constraint motion will go there, but since they do not
2787 * contribute to the constraints the degrees of freedom do not
2792 if (((atom[ia[1]].ptype == eptNucleus) ||
2793 (atom[ia[1]].ptype == eptAtom)) &&
2794 ((atom[ia[2]].ptype == eptNucleus) ||
2795 (atom[ia[2]].ptype == eptAtom)))
2813 imin = std::min(imin, nrdf2[ai]);
2814 jmin = std::min(jmin, nrdf2[aj]);
2817 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2818 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2819 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2820 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2822 ia += interaction_function[ftype].nratoms+1;
2823 i += interaction_function[ftype].nratoms+1;
2826 ia = molt->ilist[F_SETTLE].iatoms;
2827 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2829 /* Subtract 1 dof from every atom in the SETTLE */
2830 for (j = 0; j < 3; j++)
2833 imin = std::min(2, nrdf2[ai]);
2835 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2836 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2841 as += molt->atoms.nr;
2847 /* Correct nrdf for the COM constraints.
2848 * We correct using the TC and VCM group of the first atom
2849 * in the reference and pull group. If atoms in one pull group
2850 * belong to different TC or VCM groups it is anyhow difficult
2851 * to determine the optimal nrdf assignment.
2855 for (i = 0; i < pull->ncoord; i++)
2857 if (pull->coord[i].eType != epullCONSTRAINT)
2864 for (j = 0; j < 2; j++)
2866 const t_pull_group *pgrp;
2868 pgrp = &pull->group[pull->coord[i].group[j]];
2872 /* Subtract 1/2 dof from each group */
2874 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2875 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2876 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2878 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)]]);
2883 /* We need to subtract the whole DOF from group j=1 */
2890 if (ir->nstcomm != 0)
2892 /* Subtract 3 from the number of degrees of freedom in each vcm group
2893 * when com translation is removed and 6 when rotation is removed
2896 switch (ir->comm_mode)
2899 n_sub = ndof_com(ir);
2905 gmx_incons("Checking comm_mode");
2908 for (i = 0; i < groups->grps[egcTC].nr; i++)
2910 /* Count the number of atoms of TC group i for every VCM group */
2911 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2916 for (ai = 0; ai < natoms; ai++)
2918 if (ggrpnr(groups, egcTC, ai) == i)
2920 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2924 /* Correct for VCM removal according to the fraction of each VCM
2925 * group present in this TC group.
2927 nrdf_uc = nrdf_tc[i];
2930 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2934 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2936 if (nrdf_vcm[j] > n_sub)
2938 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2939 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2943 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2944 j, nrdf_vcm[j], nrdf_tc[i]);
2949 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2951 opts->nrdf[i] = nrdf_tc[i];
2952 if (opts->nrdf[i] < 0)
2957 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2958 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
2967 static void decode_cos(char *s, t_cosines *cosine)
2970 char format[STRLEN], f1[STRLEN];
2982 sscanf(t, "%d", &(cosine->n));
2989 snew(cosine->a, cosine->n);
2990 snew(cosine->phi, cosine->n);
2992 sprintf(format, "%%*d");
2993 for (i = 0; (i < cosine->n); i++)
2996 strcat(f1, "%lf%lf");
2997 if (sscanf(t, f1, &a, &phi) < 2)
2999 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
3002 cosine->phi[i] = phi;
3003 strcat(format, "%*lf%*lf");
3010 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
3011 const char *option, const char *val, int flag)
3013 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3014 * But since this is much larger than STRLEN, such a line can not be parsed.
3015 * The real maximum is the number of names that fit in a string: STRLEN/2.
3017 #define EGP_MAX (STRLEN/2)
3018 int nelem, i, j, k, nr;
3019 char *names[EGP_MAX];
3023 gnames = groups->grpname;
3025 nelem = str_nelem(val, EGP_MAX, names);
3028 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3030 nr = groups->grps[egcENER].nr;
3032 for (i = 0; i < nelem/2; i++)
3036 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
3042 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3043 names[2*i], option);
3047 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
3053 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3054 names[2*i+1], option);
3056 if ((j < nr) && (k < nr))
3058 ir->opts.egp_flags[nr*j+k] |= flag;
3059 ir->opts.egp_flags[nr*k+j] |= flag;
3068 static void make_swap_groups(
3073 int ig = -1, i = 0, gind;
3077 /* Just a quick check here, more thorough checks are in mdrun */
3078 if (strcmp(swap->grp[eGrpSplit0].molname, swap->grp[eGrpSplit1].molname) == 0)
3080 gmx_fatal(FARGS, "The split groups can not both be '%s'.", swap->grp[eGrpSplit0].molname);
3083 /* Get the index atoms of the split0, split1, solvent, and swap groups */
3084 for (ig = 0; ig < swap->ngrp; ig++)
3086 swapg = &swap->grp[ig];
3087 gind = search_string(swap->grp[ig].molname, grps->nr, gnames);
3088 swapg->nat = grps->index[gind+1] - grps->index[gind];
3092 fprintf(stderr, "%s group '%s' contains %d atoms.\n",
3093 ig < 3 ? eSwapFixedGrp_names[ig] : "Swap",
3094 swap->grp[ig].molname, swapg->nat);
3095 snew(swapg->ind, swapg->nat);
3096 for (i = 0; i < swapg->nat; i++)
3098 swapg->ind[i] = grps->a[grps->index[gind]+i];
3103 gmx_fatal(FARGS, "Swap group %s does not contain any atoms.", swap->grp[ig].molname);
3109 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3114 ig = search_string(IMDgname, grps->nr, gnames);
3115 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3117 if (IMDgroup->nat > 0)
3119 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3120 IMDgname, IMDgroup->nat);
3121 snew(IMDgroup->ind, IMDgroup->nat);
3122 for (i = 0; i < IMDgroup->nat; i++)
3124 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3130 void do_index(const char* mdparin, const char *ndx,
3137 gmx_groups_t *groups;
3141 char warnbuf[STRLEN], **gnames;
3142 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3145 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3146 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3147 int i, j, k, restnm;
3148 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3149 int nQMmethod, nQMbasis, nQMg;
3150 char warn_buf[STRLEN];
3155 fprintf(stderr, "processing index file...\n");
3160 snew(grps->index, 1);
3162 atoms_all = gmx_mtop_global_atoms(mtop);
3163 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3164 done_atom(&atoms_all);
3168 grps = init_index(ndx, &gnames);
3171 groups = &mtop->groups;
3172 natoms = mtop->natoms;
3173 symtab = &mtop->symtab;
3175 snew(groups->grpname, grps->nr+1);
3177 for (i = 0; (i < grps->nr); i++)
3179 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3181 groups->grpname[i] = put_symtab(symtab, "rest");
3183 srenew(gnames, grps->nr+1);
3184 gnames[restnm] = *(groups->grpname[i]);
3185 groups->ngrpname = grps->nr+1;
3187 set_warning_line(wi, mdparin, -1);
3189 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3190 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3191 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3192 if ((ntau_t != ntcg) || (nref_t != ntcg))
3194 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3195 "%d tau-t values", ntcg, nref_t, ntau_t);
3198 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3199 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3200 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3201 nr = groups->grps[egcTC].nr;
3203 snew(ir->opts.nrdf, nr);
3204 snew(ir->opts.tau_t, nr);
3205 snew(ir->opts.ref_t, nr);
3206 if (ir->eI == eiBD && ir->bd_fric == 0)
3208 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3215 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3219 for (i = 0; (i < nr); i++)
3221 ir->opts.tau_t[i] = strtod(ptr1[i], &endptr);
3224 warning_error(wi, "Invalid value for mdp option tau-t. tau-t should only consist of real numbers separated by spaces.");
3226 if ((ir->eI == eiBD) && ir->opts.tau_t[i] <= 0)
3228 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3229 warning_error(wi, warn_buf);
3232 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3234 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.");
3237 if (ir->opts.tau_t[i] >= 0)
3239 tau_min = std::min(tau_min, ir->opts.tau_t[i]);
3242 if (ir->etc != etcNO && ir->nsttcouple == -1)
3244 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3249 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3251 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");
3253 if (ir->epc == epcMTTK)
3255 if (ir->etc != etcNOSEHOOVER)
3257 gmx_fatal(FARGS, "Cannot do MTTK pressure coupling without Nose-Hoover temperature control");
3261 if (ir->nstpcouple != ir->nsttcouple)
3263 int mincouple = std::min(ir->nstpcouple, ir->nsttcouple);
3264 ir->nstpcouple = ir->nsttcouple = mincouple;
3265 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);
3266 warning_note(wi, warn_buf);
3271 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3272 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3274 if (ETC_ANDERSEN(ir->etc))
3276 if (ir->nsttcouple != 1)
3279 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");
3280 warning_note(wi, warn_buf);
3283 nstcmin = tcouple_min_integration_steps(ir->etc);
3286 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin - 10*GMX_REAL_EPS)
3288 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3289 ETCOUPLTYPE(ir->etc),
3291 ir->nsttcouple*ir->delta_t);
3292 warning(wi, warn_buf);
3295 for (i = 0; (i < nr); i++)
3297 ir->opts.ref_t[i] = strtod(ptr2[i], &endptr);
3300 warning_error(wi, "Invalid value for mdp option ref-t. ref-t should only consist of real numbers separated by spaces.");
3302 if (ir->opts.ref_t[i] < 0)
3304 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3307 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3308 if we are in this conditional) if mc_temp is negative */
3309 if (ir->expandedvals->mc_temp < 0)
3311 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3315 /* Simulated annealing for each group. There are nr groups */
3316 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3317 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3321 if (nSA > 0 && nSA != nr)
3323 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3327 snew(ir->opts.annealing, nr);
3328 snew(ir->opts.anneal_npoints, nr);
3329 snew(ir->opts.anneal_time, nr);
3330 snew(ir->opts.anneal_temp, nr);
3331 for (i = 0; i < nr; i++)
3333 ir->opts.annealing[i] = eannNO;
3334 ir->opts.anneal_npoints[i] = 0;
3335 ir->opts.anneal_time[i] = NULL;
3336 ir->opts.anneal_temp[i] = NULL;
3341 for (i = 0; i < nr; i++)
3343 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3345 ir->opts.annealing[i] = eannNO;
3347 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3349 ir->opts.annealing[i] = eannSINGLE;
3352 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3354 ir->opts.annealing[i] = eannPERIODIC;
3360 /* Read the other fields too */
3361 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3362 if (nSA_points != nSA)
3364 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3366 for (k = 0, i = 0; i < nr; i++)
3368 ir->opts.anneal_npoints[i] = strtol(ptr1[i], &endptr, 10);
3371 warning_error(wi, "Invalid value for mdp option annealing-npoints. annealing should only consist of integers separated by spaces.");
3373 if (ir->opts.anneal_npoints[i] == 1)
3375 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3377 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3378 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3379 k += ir->opts.anneal_npoints[i];
3382 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3385 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3387 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3390 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3393 for (i = 0, k = 0; i < nr; i++)
3396 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3398 ir->opts.anneal_time[i][j] = strtod(ptr1[k], &endptr);
3401 warning_error(wi, "Invalid value for mdp option anneal-time. anneal-time should only consist of real numbers separated by spaces.");
3403 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], &endptr);
3406 warning_error(wi, "Invalid value for anneal-temp. anneal-temp should only consist of real numbers separated by spaces.");
3410 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3412 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3418 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3420 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3421 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3424 if (ir->opts.anneal_temp[i][j] < 0)
3426 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3431 /* Print out some summary information, to make sure we got it right */
3432 for (i = 0, k = 0; i < nr; i++)
3434 if (ir->opts.annealing[i] != eannNO)
3436 j = groups->grps[egcTC].nm_ind[i];
3437 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3438 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3439 ir->opts.anneal_npoints[i]);
3440 fprintf(stderr, "Time (ps) Temperature (K)\n");
3441 /* All terms except the last one */
3442 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3444 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3447 /* Finally the last one */
3448 j = ir->opts.anneal_npoints[i]-1;
3449 if (ir->opts.annealing[i] == eannSINGLE)
3451 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3455 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3456 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3458 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3469 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3471 make_pull_coords(ir->pull);
3476 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3479 if (ir->eSwapCoords != eswapNO)
3481 make_swap_groups(ir->swap, grps, gnames);
3484 /* Make indices for IMD session */
3487 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3490 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3491 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3492 if (nacg*DIM != nacc)
3494 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3497 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3498 restnm, egrptpALL_GENREST, bVerbose, wi);
3499 nr = groups->grps[egcACC].nr;
3500 snew(ir->opts.acc, nr);
3501 ir->opts.ngacc = nr;
3503 for (i = k = 0; (i < nacg); i++)
3505 for (j = 0; (j < DIM); j++, k++)
3507 ir->opts.acc[i][j] = strtod(ptr1[k], &endptr);
3510 warning_error(wi, "Invalid value for mdp option accelerate. accelerate should only consist of real numbers separated by spaces.");
3514 for (; (i < nr); i++)
3516 for (j = 0; (j < DIM); j++)
3518 ir->opts.acc[i][j] = 0;
3522 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3523 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3524 if (nfrdim != DIM*nfreeze)
3526 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3529 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3530 restnm, egrptpALL_GENREST, bVerbose, wi);
3531 nr = groups->grps[egcFREEZE].nr;
3532 ir->opts.ngfrz = nr;
3533 snew(ir->opts.nFreeze, nr);
3534 for (i = k = 0; (i < nfreeze); i++)
3536 for (j = 0; (j < DIM); j++, k++)
3538 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3539 if (!ir->opts.nFreeze[i][j])
3541 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3543 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3544 "(not %s)", ptr1[k]);
3545 warning(wi, warn_buf);
3550 for (; (i < nr); i++)
3552 for (j = 0; (j < DIM); j++)
3554 ir->opts.nFreeze[i][j] = 0;
3558 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3559 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3560 restnm, egrptpALL_GENREST, bVerbose, wi);
3561 add_wall_energrps(groups, ir->nwall, symtab);
3562 ir->opts.ngener = groups->grps[egcENER].nr;
3563 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3565 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3566 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3569 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3570 "This may lead to artifacts.\n"
3571 "In most cases one should use one group for the whole system.");
3574 /* Now we have filled the freeze struct, so we can calculate NRDF */
3575 calc_nrdf(mtop, ir, gnames);
3577 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3578 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3579 restnm, egrptpALL_GENREST, bVerbose, wi);
3580 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3581 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3582 restnm, egrptpALL_GENREST, bVerbose, wi);
3583 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3584 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3585 restnm, egrptpONE, bVerbose, wi);
3586 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3587 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3588 restnm, egrptpALL_GENREST, bVerbose, wi);
3590 /* QMMM input processing */
3591 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3592 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3593 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3594 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3596 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3597 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3599 /* group rest, if any, is always MM! */
3600 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3601 restnm, egrptpALL_GENREST, bVerbose, wi);
3602 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3603 ir->opts.ngQM = nQMg;
3604 snew(ir->opts.QMmethod, nr);
3605 snew(ir->opts.QMbasis, nr);
3606 for (i = 0; i < nr; i++)
3608 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3609 * converted to the corresponding enum in names.c
3611 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3613 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3617 str_nelem(is->QMmult, MAXPTR, ptr1);
3618 str_nelem(is->QMcharge, MAXPTR, ptr2);
3619 str_nelem(is->bSH, MAXPTR, ptr3);
3620 snew(ir->opts.QMmult, nr);
3621 snew(ir->opts.QMcharge, nr);
3622 snew(ir->opts.bSH, nr);
3624 for (i = 0; i < nr; i++)
3626 ir->opts.QMmult[i] = strtol(ptr1[i], &endptr, 10);
3629 warning_error(wi, "Invalid value for mdp option QMmult. QMmult should only consist of integers separated by spaces.");
3631 ir->opts.QMcharge[i] = strtol(ptr2[i], &endptr, 10);
3634 warning_error(wi, "Invalid value for mdp option QMcharge. QMcharge should only consist of integers separated by spaces.");
3636 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3639 str_nelem(is->CASelectrons, MAXPTR, ptr1);
3640 str_nelem(is->CASorbitals, MAXPTR, ptr2);
3641 snew(ir->opts.CASelectrons, nr);
3642 snew(ir->opts.CASorbitals, nr);
3643 for (i = 0; i < nr; i++)
3645 ir->opts.CASelectrons[i] = strtol(ptr1[i], &endptr, 10);
3648 warning_error(wi, "Invalid value for mdp option CASelectrons. CASelectrons should only consist of integers separated by spaces.");
3650 ir->opts.CASorbitals[i] = strtol(ptr2[i], &endptr, 10);
3653 warning_error(wi, "Invalid value for mdp option CASorbitals. CASorbitals should only consist of integers separated by spaces.");
3656 /* special optimization options */
3658 str_nelem(is->bOPT, MAXPTR, ptr1);
3659 str_nelem(is->bTS, MAXPTR, ptr2);
3660 snew(ir->opts.bOPT, nr);
3661 snew(ir->opts.bTS, nr);
3662 for (i = 0; i < nr; i++)
3664 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3665 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3667 str_nelem(is->SAon, MAXPTR, ptr1);
3668 str_nelem(is->SAoff, MAXPTR, ptr2);
3669 str_nelem(is->SAsteps, MAXPTR, ptr3);
3670 snew(ir->opts.SAon, nr);
3671 snew(ir->opts.SAoff, nr);
3672 snew(ir->opts.SAsteps, nr);
3674 for (i = 0; i < nr; i++)
3676 ir->opts.SAon[i] = strtod(ptr1[i], &endptr);
3679 warning_error(wi, "Invalid value for mdp option SAon. SAon should only consist of real numbers separated by spaces.");
3681 ir->opts.SAoff[i] = strtod(ptr2[i], &endptr);
3684 warning_error(wi, "Invalid value for mdp option SAoff. SAoff should only consist of real numbers separated by spaces.");
3686 ir->opts.SAsteps[i] = strtol(ptr3[i], &endptr, 10);
3689 warning_error(wi, "Invalid value for mdp option SAsteps. SAsteps should only consist of integers separated by spaces.");
3692 /* end of QMMM input */
3696 for (i = 0; (i < egcNR); i++)
3698 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3699 for (j = 0; (j < groups->grps[i].nr); j++)
3701 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3703 fprintf(stderr, "\n");
3707 nr = groups->grps[egcENER].nr;
3708 snew(ir->opts.egp_flags, nr*nr);
3710 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3711 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3713 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3715 if (bExcl && EEL_FULL(ir->coulombtype))
3717 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3720 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3721 if (bTable && !(ir->vdwtype == evdwUSER) &&
3722 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3723 !(ir->coulombtype == eelPMEUSERSWITCH))
3725 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3728 decode_cos(is->efield_x, &(ir->ex[XX]));
3729 decode_cos(is->efield_xt, &(ir->et[XX]));
3730 decode_cos(is->efield_y, &(ir->ex[YY]));
3731 decode_cos(is->efield_yt, &(ir->et[YY]));
3732 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3733 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3735 for (i = 0; (i < grps->nr); i++)
3747 static void check_disre(gmx_mtop_t *mtop)
3749 gmx_ffparams_t *ffparams;
3750 t_functype *functype;
3752 int i, ndouble, ftype;
3753 int label, old_label;
3755 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3757 ffparams = &mtop->ffparams;
3758 functype = ffparams->functype;
3759 ip = ffparams->iparams;
3762 for (i = 0; i < ffparams->ntypes; i++)
3764 ftype = functype[i];
3765 if (ftype == F_DISRES)
3767 label = ip[i].disres.label;
3768 if (label == old_label)
3770 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3778 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3779 "probably the parameters for multiple pairs in one restraint "
3780 "are not identical\n", ndouble);
3785 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3786 gmx_bool posres_only,
3790 gmx_mtop_ilistloop_t iloop;
3800 for (d = 0; d < DIM; d++)
3802 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3804 /* Check for freeze groups */
3805 for (g = 0; g < ir->opts.ngfrz; g++)
3807 for (d = 0; d < DIM; d++)
3809 if (ir->opts.nFreeze[g][d] != 0)
3817 /* Check for position restraints */
3818 iloop = gmx_mtop_ilistloop_init(sys);
3819 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3822 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3824 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3826 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3827 for (d = 0; d < DIM; d++)
3829 if (pr->posres.fcA[d] != 0)
3835 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3837 /* Check for flat-bottom posres */
3838 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3839 if (pr->fbposres.k != 0)
3841 switch (pr->fbposres.geom)
3843 case efbposresSPHERE:
3844 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3846 case efbposresCYLINDERX:
3847 AbsRef[YY] = AbsRef[ZZ] = 1;
3849 case efbposresCYLINDERY:
3850 AbsRef[XX] = AbsRef[ZZ] = 1;
3852 case efbposresCYLINDER:
3853 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3854 case efbposresCYLINDERZ:
3855 AbsRef[XX] = AbsRef[YY] = 1;
3857 case efbposresX: /* d=XX */
3858 case efbposresY: /* d=YY */
3859 case efbposresZ: /* d=ZZ */
3860 d = pr->fbposres.geom - efbposresX;
3864 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3865 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3873 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3877 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3878 gmx_bool *bC6ParametersWorkWithGeometricRules,
3879 gmx_bool *bC6ParametersWorkWithLBRules,
3880 gmx_bool *bLBRulesPossible)
3882 int ntypes, tpi, tpj;
3885 double c6i, c6j, c12i, c12j;
3886 double c6, c6_geometric, c6_LB;
3887 double sigmai, sigmaj, epsi, epsj;
3888 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3891 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3892 * force-field floating point parameters.
3895 ptr = getenv("GMX_LJCOMB_TOL");
3900 sscanf(ptr, "%lf", &dbl);
3904 *bC6ParametersWorkWithLBRules = TRUE;
3905 *bC6ParametersWorkWithGeometricRules = TRUE;
3906 bCanDoLBRules = TRUE;
3907 ntypes = mtop->ffparams.atnr;
3908 snew(typecount, ntypes);
3909 gmx_mtop_count_atomtypes(mtop, state, typecount);
3910 *bLBRulesPossible = TRUE;
3911 for (tpi = 0; tpi < ntypes; ++tpi)
3913 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3914 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3915 for (tpj = tpi; tpj < ntypes; ++tpj)
3917 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3918 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3919 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3920 c6_geometric = std::sqrt(c6i * c6j);
3921 if (!gmx_numzero(c6_geometric))
3923 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3925 sigmai = gmx::sixthroot(c12i / c6i);
3926 sigmaj = gmx::sixthroot(c12j / c6j);
3927 epsi = c6i * c6i /(4.0 * c12i);
3928 epsj = c6j * c6j /(4.0 * c12j);
3929 c6_LB = 4.0 * std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
3933 *bLBRulesPossible = FALSE;
3934 c6_LB = c6_geometric;
3936 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3939 if (FALSE == bCanDoLBRules)
3941 *bC6ParametersWorkWithLBRules = FALSE;
3944 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3946 if (FALSE == bCanDoGeometricRules)
3948 *bC6ParametersWorkWithGeometricRules = FALSE;
3956 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
3959 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
3961 check_combination_rule_differences(mtop, 0,
3962 &bC6ParametersWorkWithGeometricRules,
3963 &bC6ParametersWorkWithLBRules,
3965 if (ir->ljpme_combination_rule == eljpmeLB)
3967 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
3969 warning(wi, "You are using arithmetic-geometric combination rules "
3970 "in LJ-PME, but your non-bonded C6 parameters do not "
3971 "follow these rules.");
3976 if (FALSE == bC6ParametersWorkWithGeometricRules)
3978 if (ir->eDispCorr != edispcNO)
3980 warning_note(wi, "You are using geometric combination rules in "
3981 "LJ-PME, but your non-bonded C6 parameters do "
3982 "not follow these rules. "
3983 "This will introduce very small errors in the forces and energies in "
3984 "your simulations. Dispersion correction will correct total energy "
3985 "and/or pressure for isotropic systems, but not forces or surface tensions.");
3989 warning_note(wi, "You are using geometric combination rules in "
3990 "LJ-PME, but your non-bonded C6 parameters do "
3991 "not follow these rules. "
3992 "This will introduce very small errors in the forces and energies in "
3993 "your simulations. If your system is homogeneous, consider using dispersion correction "
3994 "for the total energy and pressure.");
4000 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
4003 char err_buf[STRLEN];
4005 gmx_bool bCharge, bAcc;
4008 gmx_mtop_atomloop_block_t aloopb;
4009 gmx_mtop_atomloop_all_t aloop;
4012 char warn_buf[STRLEN];
4014 set_warning_line(wi, mdparin, -1);
4016 if (ir->cutoff_scheme == ecutsVERLET &&
4017 ir->verletbuf_tol > 0 &&
4019 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
4020 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4022 /* Check if a too small Verlet buffer might potentially
4023 * cause more drift than the thermostat can couple off.
4025 /* Temperature error fraction for warning and suggestion */
4026 const real T_error_warn = 0.002;
4027 const real T_error_suggest = 0.001;
4028 /* For safety: 2 DOF per atom (typical with constraints) */
4029 const real nrdf_at = 2;
4030 real T, tau, max_T_error;
4035 for (i = 0; i < ir->opts.ngtc; i++)
4037 T = std::max(T, ir->opts.ref_t[i]);
4038 tau = std::max(tau, ir->opts.tau_t[i]);
4042 /* This is a worst case estimate of the temperature error,
4043 * assuming perfect buffer estimation and no cancelation
4044 * of errors. The factor 0.5 is because energy distributes
4045 * equally over Ekin and Epot.
4047 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4048 if (max_T_error > T_error_warn)
4050 sprintf(warn_buf, "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to %.0e or decrease tau_t.",
4051 ir->verletbuf_tol, T, tau,
4053 100*T_error_suggest,
4054 ir->verletbuf_tol*T_error_suggest/max_T_error);
4055 warning(wi, warn_buf);
4060 if (ETC_ANDERSEN(ir->etc))
4064 for (i = 0; i < ir->opts.ngtc; i++)
4066 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4067 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4068 sprintf(err_buf, "all tau_t must be positive using Andersen temperature control, tau_t[%d]=%10.6f",
4069 i, ir->opts.tau_t[i]);
4070 CHECK(ir->opts.tau_t[i] < 0);
4073 for (i = 0; i < ir->opts.ngtc; i++)
4075 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
4076 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);
4077 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
4081 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4082 ir->comm_mode == ecmNO &&
4083 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4084 !ETC_ANDERSEN(ir->etc))
4086 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");
4089 /* Check for pressure coupling with absolute position restraints */
4090 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4092 absolute_reference(ir, sys, TRUE, AbsRef);
4094 for (m = 0; m < DIM; m++)
4096 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4098 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4106 aloopb = gmx_mtop_atomloop_block_init(sys);
4107 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4109 if (atom->q != 0 || atom->qB != 0)
4117 if (EEL_FULL(ir->coulombtype))
4120 "You are using full electrostatics treatment %s for a system without charges.\n"
4121 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4122 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4123 warning(wi, err_buf);
4128 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4131 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4132 "You might want to consider using %s electrostatics.\n",
4134 warning_note(wi, err_buf);
4138 /* Check if combination rules used in LJ-PME are the same as in the force field */
4139 if (EVDW_PME(ir->vdwtype))
4141 check_combination_rules(ir, sys, wi);
4144 /* Generalized reaction field */
4145 if (ir->opts.ngtc == 0)
4147 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4149 CHECK(ir->coulombtype == eelGRF);
4153 sprintf(err_buf, "When using coulombtype = %s"
4154 " ref-t for temperature coupling should be > 0",
4156 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4160 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4162 for (m = 0; (m < DIM); m++)
4164 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4173 snew(mgrp, sys->groups.grps[egcACC].nr);
4174 aloop = gmx_mtop_atomloop_all_init(sys);
4175 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4177 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4180 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4182 for (m = 0; (m < DIM); m++)
4184 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4188 for (m = 0; (m < DIM); m++)
4190 if (fabs(acc[m]) > 1e-6)
4192 const char *dim[DIM] = { "X", "Y", "Z" };
4194 "Net Acceleration in %s direction, will %s be corrected\n",
4195 dim[m], ir->nstcomm != 0 ? "" : "not");
4196 if (ir->nstcomm != 0 && m < ndof_com(ir))
4199 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4201 ir->opts.acc[i][m] -= acc[m];
4209 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4210 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4212 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4220 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4222 if (ir->pull->coord[i].group[0] == 0 ||
4223 ir->pull->coord[i].group[1] == 0)
4225 absolute_reference(ir, sys, FALSE, AbsRef);
4226 for (m = 0; m < DIM; m++)
4228 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4230 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.");
4238 for (i = 0; i < 3; i++)
4240 for (m = 0; m <= i; m++)
4242 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4243 ir->deform[i][m] != 0)
4245 for (c = 0; c < ir->pull->ncoord; c++)
4247 if (ir->pull->coord[c].eGeom == epullgDIRPBC &&
4248 ir->pull->coord[c].vec[m] != 0)
4250 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->coord[c].eGeom), 'x'+m);
4261 void double_check(t_inputrec *ir, matrix box,
4262 gmx_bool bHasNormalConstraints,
4263 gmx_bool bHasAnyConstraints,
4267 char warn_buf[STRLEN];
4270 ptr = check_box(ir->ePBC, box);
4273 warning_error(wi, ptr);
4276 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4278 if (ir->shake_tol <= 0.0)
4280 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4282 warning_error(wi, warn_buf);
4286 if ( (ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4288 /* If we have Lincs constraints: */
4289 if (ir->eI == eiMD && ir->etc == etcNO &&
4290 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4292 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4293 warning_note(wi, warn_buf);
4296 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4298 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4299 warning_note(wi, warn_buf);
4301 if (ir->epc == epcMTTK)
4303 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4307 if (bHasAnyConstraints && ir->epc == epcMTTK)
4309 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4312 if (ir->LincsWarnAngle > 90.0)
4314 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4315 warning(wi, warn_buf);
4316 ir->LincsWarnAngle = 90.0;
4319 if (ir->ePBC != epbcNONE)
4321 if (ir->nstlist == 0)
4323 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4325 if (ir->ns_type == ensGRID)
4327 if (gmx::square(ir->rlist) >= max_cutoff2(ir->ePBC, box))
4329 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 rlist.\n");
4330 warning_error(wi, warn_buf);
4335 min_size = std::min(box[XX][XX], std::min(box[YY][YY], box[ZZ][ZZ]));
4336 if (2*ir->rlist >= min_size)
4338 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4339 warning_error(wi, warn_buf);
4342 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4349 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4353 real rvdw1, rvdw2, rcoul1, rcoul2;
4354 char warn_buf[STRLEN];
4356 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4360 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4365 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4371 if (rvdw1 + rvdw2 > ir->rlist ||
4372 rcoul1 + rcoul2 > ir->rlist)
4375 "The sum of the two largest charge group radii (%f) "
4376 "is larger than rlist (%f)\n",
4377 std::max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4378 warning(wi, warn_buf);
4382 /* Here we do not use the zero at cut-off macro,
4383 * since user defined interactions might purposely
4384 * not be zero at the cut-off.
4386 if (ir_vdw_is_zero_at_cutoff(ir) &&
4387 rvdw1 + rvdw2 > ir->rlist - ir->rvdw)
4389 sprintf(warn_buf, "The sum of the two largest charge group "
4390 "radii (%f) is larger than rlist (%f) - rvdw (%f).\n"
4391 "With exact cut-offs, better performance can be "
4392 "obtained with cutoff-scheme = %s, because it "
4393 "does not use charge groups at all.",
4395 ir->rlist, ir->rvdw,
4396 ecutscheme_names[ecutsVERLET]);
4399 warning(wi, warn_buf);
4403 warning_note(wi, warn_buf);
4406 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4407 rcoul1 + rcoul2 > ir->rlist - ir->rcoulomb)
4409 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than rlist (%f) - rcoulomb (%f).\n"
4410 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4412 ir->rlist, ir->rcoulomb,
4413 ecutscheme_names[ecutsVERLET]);
4416 warning(wi, warn_buf);
4420 warning_note(wi, warn_buf);