2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team,
6 * check out http://www.gromacs.org for more information.
7 * Copyright (c) 2012,2013, by the GROMACS development team, led by
8 * David van der Spoel, Berk Hess, Erik Lindahl, and including many
9 * others, as listed in the AUTHORS file in the top-level source
10 * directory and at http://www.gromacs.org.
12 * GROMACS is free software; you can redistribute it and/or
13 * modify it under the terms of the GNU Lesser General Public License
14 * as published by the Free Software Foundation; either version 2.1
15 * of the License, or (at your option) any later version.
17 * GROMACS is distributed in the hope that it will be useful,
18 * but WITHOUT ANY WARRANTY; without even the implied warranty of
19 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20 * Lesser General Public License for more details.
22 * You should have received a copy of the GNU Lesser General Public
23 * License along with GROMACS; if not, see
24 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
25 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
27 * If you want to redistribute modifications to GROMACS, please
28 * consider that scientific software is very special. Version
29 * control is crucial - bugs must be traceable. We will be happy to
30 * consider code for inclusion in the official distribution, but
31 * derived work must not be called official GROMACS. Details are found
32 * in the README & COPYING files - if they are missing, get the
33 * official version at http://www.gromacs.org.
35 * To help us fund GROMACS development, we humbly ask that you cite
36 * the research papers on the package. Check out http://www.gromacs.org.
50 #include "gmx_fatal.h"
63 #include "mtop_util.h"
64 #include "chargegroup.h"
69 #define MAXLAMBDAS 1024
71 /* Resource parameters
72 * Do not change any of these until you read the instruction
73 * in readinp.h. Some cpp's do not take spaces after the backslash
74 * (like the c-shell), which will give you a very weird compiler
78 static char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN],
79 acc[STRLEN], accgrps[STRLEN], freeze[STRLEN], frdim[STRLEN],
80 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], xtc_grps[STRLEN],
81 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
82 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN];
83 static char fep_lambda[efptNR][STRLEN];
84 static char lambda_weights[STRLEN];
85 static char **pull_grp;
86 static char **rot_grp;
87 static char anneal[STRLEN], anneal_npoints[STRLEN],
88 anneal_time[STRLEN], anneal_temp[STRLEN];
89 static char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
90 bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
91 SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
92 static char efield_x[STRLEN], efield_xt[STRLEN], efield_y[STRLEN],
93 efield_yt[STRLEN], efield_z[STRLEN], efield_zt[STRLEN];
96 egrptpALL, /* All particles have to be a member of a group. */
97 egrptpALL_GENREST, /* A rest group with name is generated for particles *
98 * that are not part of any group. */
99 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
100 * for the rest group. */
101 egrptpONE /* Merge all selected groups into one group, *
102 * make a rest group for the remaining particles. */
106 void init_ir(t_inputrec *ir, t_gromppopts *opts)
108 snew(opts->include, STRLEN);
109 snew(opts->define, STRLEN);
110 snew(ir->fepvals, 1);
111 snew(ir->expandedvals, 1);
112 snew(ir->simtempvals, 1);
115 static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
120 for (i = 0; i < ntemps; i++)
122 /* simple linear scaling -- allows more control */
123 if (simtemp->eSimTempScale == esimtempLINEAR)
125 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*temperature_lambdas[i];
127 else if (simtemp->eSimTempScale == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
129 simtemp->temperatures[i] = simtemp->simtemp_low * pow(simtemp->simtemp_high/simtemp->simtemp_low, (1.0*i)/(ntemps-1));
131 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
133 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*((exp(temperature_lambdas[i])-1)/(exp(1.0)-1));
138 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
139 gmx_fatal(FARGS, errorstr);
146 static void _low_check(gmx_bool b, char *s, warninp_t wi)
150 warning_error(wi, s);
154 static void check_nst(const char *desc_nst, int nst,
155 const char *desc_p, int *p,
160 if (*p > 0 && *p % nst != 0)
162 /* Round up to the next multiple of nst */
163 *p = ((*p)/nst + 1)*nst;
164 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n",
165 desc_p, desc_nst, desc_p, *p);
170 static gmx_bool ir_NVE(const t_inputrec *ir)
172 return ((ir->eI == eiMD || EI_VV(ir->eI)) && ir->etc == etcNO);
175 static int lcd(int n1, int n2)
180 for (i = 2; (i <= n1 && i <= n2); i++)
182 if (n1 % i == 0 && n2 % i == 0)
191 static void process_interaction_modifier(const t_inputrec *ir, int *eintmod)
193 if (*eintmod == eintmodPOTSHIFT_VERLET)
195 if (ir->cutoff_scheme == ecutsVERLET)
197 *eintmod = eintmodPOTSHIFT;
201 *eintmod = eintmodNONE;
206 void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
208 /* Check internal consistency */
210 /* Strange macro: first one fills the err_buf, and then one can check
211 * the condition, which will print the message and increase the error
214 #define CHECK(b) _low_check(b, err_buf, wi)
215 char err_buf[256], warn_buf[STRLEN];
221 t_lambda *fep = ir->fepvals;
222 t_expanded *expand = ir->expandedvals;
224 set_warning_line(wi, mdparin, -1);
226 /* BASIC CUT-OFF STUFF */
227 if (ir->rcoulomb < 0)
229 warning_error(wi, "rcoulomb should be >= 0");
233 warning_error(wi, "rvdw should be >= 0");
236 !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_drift > 0))
238 warning_error(wi, "rlist should be >= 0");
241 process_interaction_modifier(ir, &ir->coulomb_modifier);
242 process_interaction_modifier(ir, &ir->vdw_modifier);
244 if (ir->cutoff_scheme == ecutsGROUP)
246 /* BASIC CUT-OFF STUFF */
247 if (ir->rlist == 0 ||
248 !((EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > ir->rlist) ||
249 (EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && ir->rvdw > ir->rlist)))
251 /* No switched potential and/or no twin-range:
252 * we can set the long-range cut-off to the maximum of the other cut-offs.
254 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
256 else if (ir->rlistlong < 0)
258 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
259 sprintf(warn_buf, "rlistlong was not set, setting it to %g (no buffer)",
261 warning(wi, warn_buf);
263 if (ir->rlistlong == 0 && ir->ePBC != epbcNONE)
265 warning_error(wi, "Can not have an infinite cut-off with PBC");
267 if (ir->rlistlong > 0 && (ir->rlist == 0 || ir->rlistlong < ir->rlist))
269 warning_error(wi, "rlistlong can not be shorter than rlist");
271 if (IR_TWINRANGE(*ir) && ir->nstlist <= 0)
273 warning_error(wi, "Can not have nstlist<=0 with twin-range interactions");
277 if (ir->rlistlong == ir->rlist)
281 else if (ir->rlistlong > ir->rlist && ir->nstcalclr == 0)
283 warning_error(wi, "With different cutoffs for electrostatics and VdW, nstcalclr must be -1 or a positive number");
286 if (ir->cutoff_scheme == ecutsVERLET)
290 /* Normal Verlet type neighbor-list, currently only limited feature support */
291 if (inputrec2nboundeddim(ir) < 3)
293 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
295 if (ir->rcoulomb != ir->rvdw)
297 warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported");
299 if (ir->vdwtype != evdwCUT)
301 warning_error(wi, "With Verlet lists only cut-off LJ interactions are supported");
303 if (!(ir->coulombtype == eelCUT ||
304 (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC) ||
305 EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
307 warning_error(wi, "With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
310 if (ir->nstlist <= 0)
312 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
315 if (ir->nstlist < 10)
317 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.");
320 rc_max = max(ir->rvdw, ir->rcoulomb);
322 if (ir->verletbuf_drift <= 0)
324 if (ir->verletbuf_drift == 0)
326 warning_error(wi, "Can not have an energy drift of exactly 0");
329 if (ir->rlist < rc_max)
331 warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
334 if (ir->rlist == rc_max && ir->nstlist > 1)
336 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.");
341 if (ir->rlist > rc_max)
343 warning_note(wi, "You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-drift > 0. Will set rlist using verlet-buffer-drift.");
346 if (ir->nstlist == 1)
348 /* No buffer required */
353 if (EI_DYNAMICS(ir->eI))
355 if (EI_MD(ir->eI) && ir->etc == etcNO)
357 warning_error(wi, "Temperature coupling is required for calculating rlist using the energy drift with verlet-buffer-drift > 0. Either use temperature coupling or set rlist yourself together with verlet-buffer-drift = -1.");
360 if (inputrec2nboundeddim(ir) < 3)
362 warning_error(wi, "The box volume is required for calculating rlist from the energy drift with verlet-buffer-drift > 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-drift = -1.");
364 /* Set rlist temporarily so we can continue processing */
369 /* Set the buffer to 5% of the cut-off */
370 ir->rlist = 1.05*rc_max;
375 /* No twin-range calculations with Verlet lists */
376 ir->rlistlong = ir->rlist;
379 if (ir->nstcalclr == -1)
381 /* if rlist=rlistlong, this will later be changed to nstcalclr=0 */
382 ir->nstcalclr = ir->nstlist;
384 else if (ir->nstcalclr > 0)
386 if (ir->nstlist > 0 && (ir->nstlist % ir->nstcalclr != 0))
388 warning_error(wi, "nstlist must be evenly divisible by nstcalclr. Use nstcalclr = -1 to automatically follow nstlist");
391 else if (ir->nstcalclr < -1)
393 warning_error(wi, "nstcalclr must be a positive number (divisor of nstcalclr), or -1 to follow nstlist.");
396 if (EEL_PME(ir->coulombtype) && ir->rcoulomb > ir->rvdw && ir->nstcalclr > 1)
398 warning_error(wi, "When used with PME, the long-range component of twin-range interactions must be updated every step (nstcalclr)");
401 /* GENERAL INTEGRATOR STUFF */
402 if (!(ir->eI == eiMD || EI_VV(ir->eI)))
406 if (ir->eI == eiVVAK)
408 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]);
409 warning_note(wi, warn_buf);
411 if (!EI_DYNAMICS(ir->eI))
415 if (EI_DYNAMICS(ir->eI))
417 if (ir->nstcalcenergy < 0)
419 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
420 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
422 /* nstcalcenergy larger than nstener does not make sense.
423 * We ideally want nstcalcenergy=nstener.
427 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
431 ir->nstcalcenergy = ir->nstenergy;
435 else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
436 (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
437 (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
440 const char *nsten = "nstenergy";
441 const char *nstdh = "nstdhdl";
442 const char *min_name = nsten;
443 int min_nst = ir->nstenergy;
445 /* find the smallest of ( nstenergy, nstdhdl ) */
446 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
447 (ir->fepvals->nstdhdl < ir->nstenergy) )
449 min_nst = ir->fepvals->nstdhdl;
452 /* If the user sets nstenergy small, we should respect that */
454 "Setting nstcalcenergy (%d) equal to %s (%d)",
455 ir->nstcalcenergy, min_name, min_nst);
456 warning_note(wi, warn_buf);
457 ir->nstcalcenergy = min_nst;
460 if (ir->epc != epcNO)
462 if (ir->nstpcouple < 0)
464 ir->nstpcouple = ir_optimal_nstpcouple(ir);
467 if (IR_TWINRANGE(*ir))
469 check_nst("nstlist", ir->nstlist,
470 "nstcalcenergy", &ir->nstcalcenergy, wi);
471 if (ir->epc != epcNO)
473 check_nst("nstlist", ir->nstlist,
474 "nstpcouple", &ir->nstpcouple, wi);
478 if (ir->nstcalcenergy > 0)
480 if (ir->efep != efepNO)
482 /* nstdhdl should be a multiple of nstcalcenergy */
483 check_nst("nstcalcenergy", ir->nstcalcenergy,
484 "nstdhdl", &ir->fepvals->nstdhdl, wi);
485 /* nstexpanded should be a multiple of nstcalcenergy */
486 check_nst("nstcalcenergy", ir->nstcalcenergy,
487 "nstexpanded", &ir->expandedvals->nstexpanded, wi);
489 /* for storing exact averages nstenergy should be
490 * a multiple of nstcalcenergy
492 check_nst("nstcalcenergy", ir->nstcalcenergy,
493 "nstenergy", &ir->nstenergy, wi);
498 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
499 ir->bContinuation && ir->ld_seed != -1)
501 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)");
507 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
508 CHECK(ir->ePBC != epbcXYZ);
509 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
510 CHECK(ir->ns_type != ensGRID);
511 sprintf(err_buf, "with TPI nstlist should be larger than zero");
512 CHECK(ir->nstlist <= 0);
513 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
514 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
518 if ( (opts->nshake > 0) && (opts->bMorse) )
521 "Using morse bond-potentials while constraining bonds is useless");
522 warning(wi, warn_buf);
525 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
526 ir->bContinuation && ir->ld_seed != -1)
528 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)");
530 /* verify simulated tempering options */
534 gmx_bool bAllTempZero = TRUE;
535 for (i = 0; i < fep->n_lambda; i++)
537 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]);
538 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
539 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
541 bAllTempZero = FALSE;
544 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
545 CHECK(bAllTempZero == TRUE);
547 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
548 CHECK(ir->eI != eiVV);
550 /* check compatability of the temperature coupling with simulated tempering */
552 if (ir->etc == etcNOSEHOOVER)
554 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
555 warning_note(wi, warn_buf);
558 /* check that the temperatures make sense */
560 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);
561 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
563 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
564 CHECK(ir->simtempvals->simtemp_high <= 0);
566 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
567 CHECK(ir->simtempvals->simtemp_low <= 0);
570 /* verify free energy options */
572 if (ir->efep != efepNO)
575 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
577 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
579 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
580 (int)fep->sc_r_power);
581 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
583 sprintf(err_buf, "Can't use postive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
584 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
586 sprintf(err_buf, "Can't use postive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
587 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
589 sprintf(err_buf, "Free-energy not implemented for Ewald");
590 CHECK(ir->coulombtype == eelEWALD);
592 /* check validty of lambda inputs */
593 if (fep->n_lambda == 0)
595 /* Clear output in case of no states:*/
596 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
597 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
601 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
602 CHECK((fep->init_fep_state >= fep->n_lambda));
605 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
606 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
608 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",
609 fep->init_lambda, fep->init_fep_state);
610 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
614 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
618 for (i = 0; i < efptNR; i++)
620 if (fep->separate_dvdl[i])
625 if (n_lambda_terms > 1)
627 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.");
628 warning(wi, warn_buf);
631 if (n_lambda_terms < 2 && fep->n_lambda > 0)
634 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
638 for (j = 0; j < efptNR; j++)
640 for (i = 0; i < fep->n_lambda; i++)
642 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]);
643 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
647 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
649 for (i = 0; i < fep->n_lambda; i++)
651 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],
652 fep->all_lambda[efptCOUL][i]);
653 CHECK((fep->sc_alpha > 0) &&
654 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
655 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
656 ((fep->all_lambda[efptVDW][i] > 0.0) &&
657 (fep->all_lambda[efptVDW][i] < 1.0))));
661 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
663 real sigma, lambda, r_sc;
666 /* Maximum estimate for A and B charges equal with lambda power 1 */
668 r_sc = pow(lambda*fep->sc_alpha*pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
669 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.",
671 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
672 warning_note(wi, warn_buf);
675 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
676 be treated differently, but that's the next step */
678 for (i = 0; i < efptNR; i++)
680 for (j = 0; j < fep->n_lambda; j++)
682 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
683 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
688 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
691 expand = ir->expandedvals;
693 /* checking equilibration of weights inputs for validity */
695 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
696 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
697 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
699 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
700 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
701 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
703 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
704 expand->equil_steps, elmceq_names[elmceqSTEPS]);
705 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
707 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
708 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
709 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
711 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
712 expand->equil_ratio, elmceq_names[elmceqRATIO]);
713 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
715 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
716 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
717 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
719 sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
720 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
721 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
723 sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
724 expand->equil_steps, elmceq_names[elmceqSTEPS]);
725 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
727 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
728 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
729 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
731 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
732 expand->equil_ratio, elmceq_names[elmceqRATIO]);
733 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
735 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
736 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
737 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
739 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
740 CHECK((expand->lmc_repeats <= 0));
741 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
742 CHECK((expand->minvarmin <= 0));
743 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
744 CHECK((expand->c_range < 0));
745 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
746 fep->init_fep_state, expand->lmc_forced_nstart);
747 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
748 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
749 CHECK((expand->lmc_forced_nstart < 0));
750 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
751 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
753 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
754 CHECK((expand->init_wl_delta < 0));
755 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
756 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
757 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
758 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
760 /* if there is no temperature control, we need to specify an MC temperature */
761 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
762 if (expand->nstTij > 0)
764 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
765 expand->nstTij, ir->nstlog);
766 CHECK((mod(expand->nstTij, ir->nstlog) != 0));
771 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
772 CHECK(ir->nwall && ir->ePBC != epbcXY);
775 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
777 if (ir->ePBC == epbcNONE)
779 if (ir->epc != epcNO)
781 warning(wi, "Turning off pressure coupling for vacuum system");
787 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
788 epbc_names[ir->ePBC]);
789 CHECK(ir->epc != epcNO);
791 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
792 CHECK(EEL_FULL(ir->coulombtype));
794 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
795 epbc_names[ir->ePBC]);
796 CHECK(ir->eDispCorr != edispcNO);
799 if (ir->rlist == 0.0)
801 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
802 "with coulombtype = %s or coulombtype = %s\n"
803 "without periodic boundary conditions (pbc = %s) and\n"
804 "rcoulomb and rvdw set to zero",
805 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
806 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
807 (ir->ePBC != epbcNONE) ||
808 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
812 warning_error(wi, "Can not have heuristic neighborlist updates without cut-off");
816 warning_note(wi, "Simulating without cut-offs is usually (slightly) faster with nstlist=0, nstype=simple and particle decomposition");
821 if (ir->nstcomm == 0)
823 ir->comm_mode = ecmNO;
825 if (ir->comm_mode != ecmNO)
829 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");
830 ir->nstcomm = abs(ir->nstcomm);
833 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
835 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
836 ir->nstcomm = ir->nstcalcenergy;
839 if (ir->comm_mode == ecmANGULAR)
841 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
842 CHECK(ir->bPeriodicMols);
843 if (ir->ePBC != epbcNONE)
845 warning(wi, "Removing the rotation around the center of mass in a periodic system (this is not a problem when you have only one molecule).");
850 if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
852 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.");
855 sprintf(err_buf, "Twin-range neighbour searching (NS) with simple NS"
856 " algorithm not implemented");
857 CHECK(((ir->rcoulomb > ir->rlist) || (ir->rvdw > ir->rlist))
858 && (ir->ns_type == ensSIMPLE));
860 /* TEMPERATURE COUPLING */
861 if (ir->etc == etcYES)
863 ir->etc = etcBERENDSEN;
864 warning_note(wi, "Old option for temperature coupling given: "
865 "changing \"yes\" to \"Berendsen\"\n");
868 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
870 if (ir->opts.nhchainlength < 1)
872 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
873 ir->opts.nhchainlength = 1;
874 warning(wi, warn_buf);
877 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
879 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
880 ir->opts.nhchainlength = 1;
885 ir->opts.nhchainlength = 0;
888 if (ir->eI == eiVVAK)
890 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
892 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
895 if (ETC_ANDERSEN(ir->etc))
897 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
898 CHECK(!(EI_VV(ir->eI)));
900 for (i = 0; i < ir->opts.ngtc; i++)
902 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
903 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
904 sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
905 i, ir->opts.tau_t[i]);
906 CHECK(ir->opts.tau_t[i] < 0);
908 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
910 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]);
911 warning_note(wi, warn_buf);
914 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]);
915 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
917 for (i = 0; i < ir->opts.ngtc; i++)
919 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
920 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);
921 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
924 if (ir->etc == etcBERENDSEN)
926 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
927 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
928 warning_note(wi, warn_buf);
931 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
932 && ir->epc == epcBERENDSEN)
934 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
935 "true ensemble for the thermostat");
936 warning(wi, warn_buf);
939 /* PRESSURE COUPLING */
940 if (ir->epc == epcISOTROPIC)
942 ir->epc = epcBERENDSEN;
943 warning_note(wi, "Old option for pressure coupling given: "
944 "changing \"Isotropic\" to \"Berendsen\"\n");
947 if (ir->epc != epcNO)
949 dt_pcoupl = ir->nstpcouple*ir->delta_t;
951 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
952 CHECK(ir->tau_p <= 0);
954 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc))
956 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
957 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
958 warning(wi, warn_buf);
961 sprintf(err_buf, "compressibility must be > 0 when using pressure"
962 " coupling %s\n", EPCOUPLTYPE(ir->epc));
963 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
964 ir->compress[ZZ][ZZ] < 0 ||
965 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
966 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
968 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
971 "You are generating velocities so I am assuming you "
972 "are equilibrating a system. You are using "
973 "%s pressure coupling, but this can be "
974 "unstable for equilibration. If your system crashes, try "
975 "equilibrating first with Berendsen pressure coupling. If "
976 "you are not equilibrating the system, you can probably "
977 "ignore this warning.",
978 epcoupl_names[ir->epc]);
979 warning(wi, warn_buf);
987 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
989 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.");
995 /* More checks are in triple check (grompp.c) */
997 if (ir->coulombtype == eelSWITCH)
999 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1000 "artifacts, advice: use coulombtype = %s",
1001 eel_names[ir->coulombtype],
1002 eel_names[eelRF_ZERO]);
1003 warning(wi, warn_buf);
1006 if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
1008 sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
1009 warning_note(wi, warn_buf);
1012 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1014 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);
1015 warning(wi, warn_buf);
1016 ir->epsilon_rf = ir->epsilon_r;
1017 ir->epsilon_r = 1.0;
1020 if (getenv("GALACTIC_DYNAMICS") == NULL)
1022 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1023 CHECK(ir->epsilon_r < 0);
1026 if (EEL_RF(ir->coulombtype))
1028 /* reaction field (at the cut-off) */
1030 if (ir->coulombtype == eelRF_ZERO)
1032 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1033 eel_names[ir->coulombtype]);
1034 CHECK(ir->epsilon_rf != 0);
1035 ir->epsilon_rf = 0.0;
1038 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1039 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1040 (ir->epsilon_r == 0));
1041 if (ir->epsilon_rf == ir->epsilon_r)
1043 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1044 eel_names[ir->coulombtype]);
1045 warning(wi, warn_buf);
1048 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1049 * means the interaction is zero outside rcoulomb, but it helps to
1050 * provide accurate energy conservation.
1052 if (EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype))
1054 if (EEL_SWITCHED(ir->coulombtype))
1057 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1058 eel_names[ir->coulombtype]);
1059 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1062 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1064 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1066 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1067 eel_names[ir->coulombtype]);
1068 CHECK(ir->rlist > ir->rcoulomb);
1072 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1073 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1076 "The switch/shift interaction settings are just for compatibility; you will get better "
1077 "performance from applying potential modifiers to your interactions!\n");
1078 warning_note(wi, warn_buf);
1081 if (EEL_FULL(ir->coulombtype))
1083 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1084 ir->coulombtype == eelPMEUSERSWITCH)
1086 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1087 eel_names[ir->coulombtype]);
1088 CHECK(ir->rcoulomb > ir->rlist);
1090 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1092 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1095 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
1096 "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
1097 "a potential modifier.", eel_names[ir->coulombtype]);
1098 if (ir->nstcalclr == 1)
1100 CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
1104 CHECK(ir->rcoulomb != ir->rlist);
1110 if (EEL_PME(ir->coulombtype))
1112 if (ir->pme_order < 3)
1114 warning_error(wi, "pme-order can not be smaller than 3");
1118 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1120 if (ir->ewald_geometry == eewg3D)
1122 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1123 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1124 warning(wi, warn_buf);
1126 /* This check avoids extra pbc coding for exclusion corrections */
1127 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1128 CHECK(ir->wall_ewald_zfac < 2);
1131 if (EVDW_SWITCHED(ir->vdwtype))
1133 sprintf(err_buf, "With vdwtype = %s rvdw-switch must be < rvdw. Or, better - use a potential modifier.",
1134 evdw_names[ir->vdwtype]);
1135 CHECK(ir->rvdw_switch >= ir->rvdw);
1137 else if (ir->vdwtype == evdwCUT)
1139 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1141 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1142 CHECK(ir->rlist > ir->rvdw);
1145 if (ir->cutoff_scheme == ecutsGROUP)
1147 if (EEL_IS_ZERO_AT_CUTOFF(ir->coulombtype)
1148 && (ir->rlistlong <= ir->rcoulomb))
1150 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
1151 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1152 warning_note(wi, warn_buf);
1154 if (EVDW_SWITCHED(ir->vdwtype) && (ir->rlistlong <= ir->rvdw))
1156 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
1157 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1158 warning_note(wi, warn_buf);
1162 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1164 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.");
1167 if (ir->nstlist == -1)
1169 sprintf(err_buf, "With nstlist=-1 rvdw and rcoulomb should be smaller than rlist to account for diffusion and possibly charge-group radii");
1170 CHECK(ir->rvdw >= ir->rlist || ir->rcoulomb >= ir->rlist);
1172 sprintf(err_buf, "nstlist can not be smaller than -1");
1173 CHECK(ir->nstlist < -1);
1175 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1178 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1181 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1183 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1186 /* ENERGY CONSERVATION */
1187 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1189 if (!EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1191 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1192 evdw_names[evdwSHIFT]);
1193 warning_note(wi, warn_buf);
1195 if (!EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > 0 && ir->coulomb_modifier == eintmodNONE)
1197 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1198 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1199 warning_note(wi, warn_buf);
1203 /* IMPLICIT SOLVENT */
1204 if (ir->coulombtype == eelGB_NOTUSED)
1206 ir->coulombtype = eelCUT;
1207 ir->implicit_solvent = eisGBSA;
1208 fprintf(stderr, "Note: Old option for generalized born electrostatics given:\n"
1209 "Changing coulombtype from \"generalized-born\" to \"cut-off\" and instead\n"
1210 "setting implicit-solvent value to \"GBSA\" in input section.\n");
1213 if (ir->sa_algorithm == esaSTILL)
1215 sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
1216 CHECK(ir->sa_algorithm == esaSTILL);
1219 if (ir->implicit_solvent == eisGBSA)
1221 sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
1222 CHECK(ir->rgbradii != ir->rlist);
1224 if (ir->coulombtype != eelCUT)
1226 sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
1227 CHECK(ir->coulombtype != eelCUT);
1229 if (ir->vdwtype != evdwCUT)
1231 sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
1232 CHECK(ir->vdwtype != evdwCUT);
1234 if (ir->nstgbradii < 1)
1236 sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
1237 warning_note(wi, warn_buf);
1240 if (ir->sa_algorithm == esaNO)
1242 sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
1243 warning_note(wi, warn_buf);
1245 if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
1247 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");
1248 warning_note(wi, warn_buf);
1250 if (ir->gb_algorithm == egbSTILL)
1252 ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
1256 ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
1259 if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
1261 sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
1262 CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
1269 if (ir->cutoff_scheme != ecutsGROUP)
1271 warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
1275 warning_error(wi, "AdresS simulation supports only stochastic dynamics");
1277 if (ir->epc != epcNO)
1279 warning_error(wi, "AdresS simulation does not support pressure coupling");
1281 if (EEL_FULL(ir->coulombtype))
1283 warning_error(wi, "AdresS simulation does not support long-range electrostatics");
1288 /* count the number of text elemets separated by whitespace in a string.
1289 str = the input string
1290 maxptr = the maximum number of allowed elements
1291 ptr = the output array of pointers to the first character of each element
1292 returns: the number of elements. */
1293 int str_nelem(const char *str, int maxptr, char *ptr[])
1298 copy0 = strdup(str);
1301 while (*copy != '\0')
1305 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1313 while ((*copy != '\0') && !isspace(*copy))
1332 /* interpret a number of doubles from a string and put them in an array,
1333 after allocating space for them.
1334 str = the input string
1335 n = the (pre-allocated) number of doubles read
1336 r = the output array of doubles. */
1337 static void parse_n_real(char *str, int *n, real **r)
1342 *n = str_nelem(str, MAXPTR, ptr);
1345 for (i = 0; i < *n; i++)
1347 (*r)[i] = strtod(ptr[i], NULL);
1351 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
1354 int i, j, max_n_lambda, nweights, nfep[efptNR];
1355 t_lambda *fep = ir->fepvals;
1356 t_expanded *expand = ir->expandedvals;
1357 real **count_fep_lambdas;
1358 gmx_bool bOneLambda = TRUE;
1360 snew(count_fep_lambdas, efptNR);
1362 /* FEP input processing */
1363 /* first, identify the number of lambda values for each type.
1364 All that are nonzero must have the same number */
1366 for (i = 0; i < efptNR; i++)
1368 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
1371 /* now, determine the number of components. All must be either zero, or equal. */
1374 for (i = 0; i < efptNR; i++)
1376 if (nfep[i] > max_n_lambda)
1378 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1379 must have the same number if its not zero.*/
1384 for (i = 0; i < efptNR; i++)
1388 ir->fepvals->separate_dvdl[i] = FALSE;
1390 else if (nfep[i] == max_n_lambda)
1392 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1393 respect to the temperature currently */
1395 ir->fepvals->separate_dvdl[i] = TRUE;
1400 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1401 nfep[i], efpt_names[i], max_n_lambda);
1404 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1405 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1407 /* the number of lambdas is the number we've read in, which is either zero
1408 or the same for all */
1409 fep->n_lambda = max_n_lambda;
1411 /* allocate space for the array of lambda values */
1412 snew(fep->all_lambda, efptNR);
1413 /* if init_lambda is defined, we need to set lambda */
1414 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1416 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1418 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1419 for (i = 0; i < efptNR; i++)
1421 snew(fep->all_lambda[i], fep->n_lambda);
1422 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1425 for (j = 0; j < fep->n_lambda; j++)
1427 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1429 sfree(count_fep_lambdas[i]);
1432 sfree(count_fep_lambdas);
1434 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1435 bookkeeping -- for now, init_lambda */
1437 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1439 for (i = 0; i < fep->n_lambda; i++)
1441 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1445 /* check to see if only a single component lambda is defined, and soft core is defined.
1446 In this case, turn on coulomb soft core */
1448 if (max_n_lambda == 0)
1454 for (i = 0; i < efptNR; i++)
1456 if ((nfep[i] != 0) && (i != efptFEP))
1462 if ((bOneLambda) && (fep->sc_alpha > 0))
1464 fep->bScCoul = TRUE;
1467 /* Fill in the others with the efptFEP if they are not explicitly
1468 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1469 they are all zero. */
1471 for (i = 0; i < efptNR; i++)
1473 if ((nfep[i] == 0) && (i != efptFEP))
1475 for (j = 0; j < fep->n_lambda; j++)
1477 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1483 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1484 if (fep->sc_r_power == 48)
1486 if (fep->sc_alpha > 0.1)
1488 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1492 expand = ir->expandedvals;
1493 /* now read in the weights */
1494 parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
1497 expand->bInit_weights = FALSE;
1498 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1500 else if (nweights != fep->n_lambda)
1502 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1503 nweights, fep->n_lambda);
1507 expand->bInit_weights = TRUE;
1509 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1511 expand->nstexpanded = fep->nstdhdl;
1512 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1514 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1516 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1517 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1518 2*tau_t just to be careful so it's not to frequent */
1523 static void do_simtemp_params(t_inputrec *ir)
1526 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1527 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1532 static void do_wall_params(t_inputrec *ir,
1533 char *wall_atomtype, char *wall_density,
1537 char *names[MAXPTR];
1540 opts->wall_atomtype[0] = NULL;
1541 opts->wall_atomtype[1] = NULL;
1543 ir->wall_atomtype[0] = -1;
1544 ir->wall_atomtype[1] = -1;
1545 ir->wall_density[0] = 0;
1546 ir->wall_density[1] = 0;
1550 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1551 if (nstr != ir->nwall)
1553 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1556 for (i = 0; i < ir->nwall; i++)
1558 opts->wall_atomtype[i] = strdup(names[i]);
1561 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1563 nstr = str_nelem(wall_density, MAXPTR, names);
1564 if (nstr != ir->nwall)
1566 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1568 for (i = 0; i < ir->nwall; i++)
1570 sscanf(names[i], "%lf", &dbl);
1573 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1575 ir->wall_density[i] = dbl;
1581 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1589 srenew(groups->grpname, groups->ngrpname+nwall);
1590 grps = &(groups->grps[egcENER]);
1591 srenew(grps->nm_ind, grps->nr+nwall);
1592 for (i = 0; i < nwall; i++)
1594 sprintf(str, "wall%d", i);
1595 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1596 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1601 void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1602 t_expanded *expand, warninp_t wi)
1604 int ninp, nerror = 0;
1610 /* read expanded ensemble parameters */
1611 CCTYPE ("expanded ensemble variables");
1612 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1613 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1614 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1615 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1616 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1617 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1618 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1619 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1620 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1621 CCTYPE("Seed for Monte Carlo in lambda space");
1622 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1623 RTYPE ("mc-temperature", expand->mc_temp, -1);
1624 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1625 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1626 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1627 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1628 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1629 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1630 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1631 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1632 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1633 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1634 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
1642 void get_ir(const char *mdparin, const char *mdparout,
1643 t_inputrec *ir, t_gromppopts *opts,
1647 double dumdub[2][6];
1651 char warn_buf[STRLEN];
1652 t_lambda *fep = ir->fepvals;
1653 t_expanded *expand = ir->expandedvals;
1655 inp = read_inpfile(mdparin, &ninp, NULL, wi);
1657 snew(dumstr[0], STRLEN);
1658 snew(dumstr[1], STRLEN);
1660 /* remove the following deprecated commands */
1663 REM_TYPE("domain-decomposition");
1664 REM_TYPE("andersen-seed");
1666 REM_TYPE("dihre-fc");
1667 REM_TYPE("dihre-tau");
1668 REM_TYPE("nstdihreout");
1669 REM_TYPE("nstcheckpoint");
1671 /* replace the following commands with the clearer new versions*/
1672 REPL_TYPE("unconstrained-start", "continuation");
1673 REPL_TYPE("foreign-lambda", "fep-lambdas");
1675 CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
1676 CTYPE ("Preprocessor information: use cpp syntax.");
1677 CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
1678 STYPE ("include", opts->include, NULL);
1679 CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1680 STYPE ("define", opts->define, NULL);
1682 CCTYPE ("RUN CONTROL PARAMETERS");
1683 EETYPE("integrator", ir->eI, ei_names);
1684 CTYPE ("Start time and timestep in ps");
1685 RTYPE ("tinit", ir->init_t, 0.0);
1686 RTYPE ("dt", ir->delta_t, 0.001);
1687 STEPTYPE ("nsteps", ir->nsteps, 0);
1688 CTYPE ("For exact run continuation or redoing part of a run");
1689 STEPTYPE ("init-step", ir->init_step, 0);
1690 CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
1691 ITYPE ("simulation-part", ir->simulation_part, 1);
1692 CTYPE ("mode for center of mass motion removal");
1693 EETYPE("comm-mode", ir->comm_mode, ecm_names);
1694 CTYPE ("number of steps for center of mass motion removal");
1695 ITYPE ("nstcomm", ir->nstcomm, 100);
1696 CTYPE ("group(s) for center of mass motion removal");
1697 STYPE ("comm-grps", vcm, NULL);
1699 CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
1700 CTYPE ("Friction coefficient (amu/ps) and random seed");
1701 RTYPE ("bd-fric", ir->bd_fric, 0.0);
1702 ITYPE ("ld-seed", ir->ld_seed, 1993);
1705 CCTYPE ("ENERGY MINIMIZATION OPTIONS");
1706 CTYPE ("Force tolerance and initial step-size");
1707 RTYPE ("emtol", ir->em_tol, 10.0);
1708 RTYPE ("emstep", ir->em_stepsize, 0.01);
1709 CTYPE ("Max number of iterations in relax-shells");
1710 ITYPE ("niter", ir->niter, 20);
1711 CTYPE ("Step size (ps^2) for minimization of flexible constraints");
1712 RTYPE ("fcstep", ir->fc_stepsize, 0);
1713 CTYPE ("Frequency of steepest descents steps when doing CG");
1714 ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
1715 ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
1717 CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
1718 RTYPE ("rtpi", ir->rtpi, 0.05);
1720 /* Output options */
1721 CCTYPE ("OUTPUT CONTROL OPTIONS");
1722 CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
1723 ITYPE ("nstxout", ir->nstxout, 0);
1724 ITYPE ("nstvout", ir->nstvout, 0);
1725 ITYPE ("nstfout", ir->nstfout, 0);
1726 ir->nstcheckpoint = 1000;
1727 CTYPE ("Output frequency for energies to log file and energy file");
1728 ITYPE ("nstlog", ir->nstlog, 1000);
1729 ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
1730 ITYPE ("nstenergy", ir->nstenergy, 1000);
1731 CTYPE ("Output frequency and precision for .xtc file");
1732 ITYPE ("nstxtcout", ir->nstxtcout, 0);
1733 RTYPE ("xtc-precision", ir->xtcprec, 1000.0);
1734 CTYPE ("This selects the subset of atoms for the .xtc file. You can");
1735 CTYPE ("select multiple groups. By default all atoms will be written.");
1736 STYPE ("xtc-grps", xtc_grps, NULL);
1737 CTYPE ("Selection of energy groups");
1738 STYPE ("energygrps", energy, NULL);
1740 /* Neighbor searching */
1741 CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
1742 CTYPE ("cut-off scheme (group: using charge groups, Verlet: particle based cut-offs)");
1743 EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
1744 CTYPE ("nblist update frequency");
1745 ITYPE ("nstlist", ir->nstlist, 10);
1746 CTYPE ("ns algorithm (simple or grid)");
1747 EETYPE("ns-type", ir->ns_type, ens_names);
1748 /* set ndelta to the optimal value of 2 */
1750 CTYPE ("Periodic boundary conditions: xyz, no, xy");
1751 EETYPE("pbc", ir->ePBC, epbc_names);
1752 EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
1753 CTYPE ("Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom,");
1754 CTYPE ("a value of -1 means: use rlist");
1755 RTYPE("verlet-buffer-drift", ir->verletbuf_drift, 0.005);
1756 CTYPE ("nblist cut-off");
1757 RTYPE ("rlist", ir->rlist, 1.0);
1758 CTYPE ("long-range cut-off for switched potentials");
1759 RTYPE ("rlistlong", ir->rlistlong, -1);
1760 ITYPE ("nstcalclr", ir->nstcalclr, -1);
1762 /* Electrostatics */
1763 CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
1764 CTYPE ("Method for doing electrostatics");
1765 EETYPE("coulombtype", ir->coulombtype, eel_names);
1766 EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
1767 CTYPE ("cut-off lengths");
1768 RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
1769 RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
1770 CTYPE ("Relative dielectric constant for the medium and the reaction field");
1771 RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
1772 RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
1773 CTYPE ("Method for doing Van der Waals");
1774 EETYPE("vdw-type", ir->vdwtype, evdw_names);
1775 EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
1776 CTYPE ("cut-off lengths");
1777 RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
1778 RTYPE ("rvdw", ir->rvdw, 1.0);
1779 CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
1780 EETYPE("DispCorr", ir->eDispCorr, edispc_names);
1781 CTYPE ("Extension of the potential lookup tables beyond the cut-off");
1782 RTYPE ("table-extension", ir->tabext, 1.0);
1783 CTYPE ("Separate tables between energy group pairs");
1784 STYPE ("energygrp-table", egptable, NULL);
1785 CTYPE ("Spacing for the PME/PPPM FFT grid");
1786 RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
1787 CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
1788 ITYPE ("fourier-nx", ir->nkx, 0);
1789 ITYPE ("fourier-ny", ir->nky, 0);
1790 ITYPE ("fourier-nz", ir->nkz, 0);
1791 CTYPE ("EWALD/PME/PPPM parameters");
1792 ITYPE ("pme-order", ir->pme_order, 4);
1793 RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
1794 EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
1795 RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
1796 EETYPE("optimize-fft", ir->bOptFFT, yesno_names);
1798 CCTYPE("IMPLICIT SOLVENT ALGORITHM");
1799 EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
1801 CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
1802 CTYPE ("Algorithm for calculating Born radii");
1803 EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
1804 CTYPE ("Frequency of calculating the Born radii inside rlist");
1805 ITYPE ("nstgbradii", ir->nstgbradii, 1);
1806 CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
1807 CTYPE ("between rlist and rgbradii is updated every nstlist steps");
1808 RTYPE ("rgbradii", ir->rgbradii, 1.0);
1809 CTYPE ("Dielectric coefficient of the implicit solvent");
1810 RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
1811 CTYPE ("Salt concentration in M for Generalized Born models");
1812 RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
1813 CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
1814 RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
1815 RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
1816 RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
1817 RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
1818 EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
1819 CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
1820 CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
1821 RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
1823 /* Coupling stuff */
1824 CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
1825 CTYPE ("Temperature coupling");
1826 EETYPE("tcoupl", ir->etc, etcoupl_names);
1827 ITYPE ("nsttcouple", ir->nsttcouple, -1);
1828 ITYPE("nh-chain-length", ir->opts.nhchainlength, NHCHAINLENGTH);
1829 EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
1830 CTYPE ("Groups to couple separately");
1831 STYPE ("tc-grps", tcgrps, NULL);
1832 CTYPE ("Time constant (ps) and reference temperature (K)");
1833 STYPE ("tau-t", tau_t, NULL);
1834 STYPE ("ref-t", ref_t, NULL);
1835 CTYPE ("pressure coupling");
1836 EETYPE("pcoupl", ir->epc, epcoupl_names);
1837 EETYPE("pcoupltype", ir->epct, epcoupltype_names);
1838 ITYPE ("nstpcouple", ir->nstpcouple, -1);
1839 CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
1840 RTYPE ("tau-p", ir->tau_p, 1.0);
1841 STYPE ("compressibility", dumstr[0], NULL);
1842 STYPE ("ref-p", dumstr[1], NULL);
1843 CTYPE ("Scaling of reference coordinates, No, All or COM");
1844 EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
1847 CCTYPE ("OPTIONS FOR QMMM calculations");
1848 EETYPE("QMMM", ir->bQMMM, yesno_names);
1849 CTYPE ("Groups treated Quantum Mechanically");
1850 STYPE ("QMMM-grps", QMMM, NULL);
1851 CTYPE ("QM method");
1852 STYPE("QMmethod", QMmethod, NULL);
1853 CTYPE ("QMMM scheme");
1854 EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
1855 CTYPE ("QM basisset");
1856 STYPE("QMbasis", QMbasis, NULL);
1857 CTYPE ("QM charge");
1858 STYPE ("QMcharge", QMcharge, NULL);
1859 CTYPE ("QM multiplicity");
1860 STYPE ("QMmult", QMmult, NULL);
1861 CTYPE ("Surface Hopping");
1862 STYPE ("SH", bSH, NULL);
1863 CTYPE ("CAS space options");
1864 STYPE ("CASorbitals", CASorbitals, NULL);
1865 STYPE ("CASelectrons", CASelectrons, NULL);
1866 STYPE ("SAon", SAon, NULL);
1867 STYPE ("SAoff", SAoff, NULL);
1868 STYPE ("SAsteps", SAsteps, NULL);
1869 CTYPE ("Scale factor for MM charges");
1870 RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
1871 CTYPE ("Optimization of QM subsystem");
1872 STYPE ("bOPT", bOPT, NULL);
1873 STYPE ("bTS", bTS, NULL);
1875 /* Simulated annealing */
1876 CCTYPE("SIMULATED ANNEALING");
1877 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
1878 STYPE ("annealing", anneal, NULL);
1879 CTYPE ("Number of time points to use for specifying annealing in each group");
1880 STYPE ("annealing-npoints", anneal_npoints, NULL);
1881 CTYPE ("List of times at the annealing points for each group");
1882 STYPE ("annealing-time", anneal_time, NULL);
1883 CTYPE ("Temp. at each annealing point, for each group.");
1884 STYPE ("annealing-temp", anneal_temp, NULL);
1887 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
1888 EETYPE("gen-vel", opts->bGenVel, yesno_names);
1889 RTYPE ("gen-temp", opts->tempi, 300.0);
1890 ITYPE ("gen-seed", opts->seed, 173529);
1893 CCTYPE ("OPTIONS FOR BONDS");
1894 EETYPE("constraints", opts->nshake, constraints);
1895 CTYPE ("Type of constraint algorithm");
1896 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
1897 CTYPE ("Do not constrain the start configuration");
1898 EETYPE("continuation", ir->bContinuation, yesno_names);
1899 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
1900 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
1901 CTYPE ("Relative tolerance of shake");
1902 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
1903 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
1904 ITYPE ("lincs-order", ir->nProjOrder, 4);
1905 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
1906 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
1907 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
1908 ITYPE ("lincs-iter", ir->nLincsIter, 1);
1909 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
1910 CTYPE ("rotates over more degrees than");
1911 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
1912 CTYPE ("Convert harmonic bonds to morse potentials");
1913 EETYPE("morse", opts->bMorse, yesno_names);
1915 /* Energy group exclusions */
1916 CCTYPE ("ENERGY GROUP EXCLUSIONS");
1917 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
1918 STYPE ("energygrp-excl", egpexcl, NULL);
1922 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
1923 ITYPE ("nwall", ir->nwall, 0);
1924 EETYPE("wall-type", ir->wall_type, ewt_names);
1925 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
1926 STYPE ("wall-atomtype", wall_atomtype, NULL);
1927 STYPE ("wall-density", wall_density, NULL);
1928 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
1931 CCTYPE("COM PULLING");
1932 CTYPE("Pull type: no, umbrella, constraint or constant-force");
1933 EETYPE("pull", ir->ePull, epull_names);
1934 if (ir->ePull != epullNO)
1937 pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
1940 /* Enforced rotation */
1941 CCTYPE("ENFORCED ROTATION");
1942 CTYPE("Enforced rotation: No or Yes");
1943 EETYPE("rotation", ir->bRot, yesno_names);
1947 rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
1951 CCTYPE("NMR refinement stuff");
1952 CTYPE ("Distance restraints type: No, Simple or Ensemble");
1953 EETYPE("disre", ir->eDisre, edisre_names);
1954 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
1955 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
1956 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
1957 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
1958 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
1959 RTYPE ("disre-tau", ir->dr_tau, 0.0);
1960 CTYPE ("Output frequency for pair distances to energy file");
1961 ITYPE ("nstdisreout", ir->nstdisreout, 100);
1962 CTYPE ("Orientation restraints: No or Yes");
1963 EETYPE("orire", opts->bOrire, yesno_names);
1964 CTYPE ("Orientation restraints force constant and tau for time averaging");
1965 RTYPE ("orire-fc", ir->orires_fc, 0.0);
1966 RTYPE ("orire-tau", ir->orires_tau, 0.0);
1967 STYPE ("orire-fitgrp", orirefitgrp, NULL);
1968 CTYPE ("Output frequency for trace(SD) and S to energy file");
1969 ITYPE ("nstorireout", ir->nstorireout, 100);
1971 /* free energy variables */
1972 CCTYPE ("Free energy variables");
1973 EETYPE("free-energy", ir->efep, efep_names);
1974 STYPE ("couple-moltype", couple_moltype, NULL);
1975 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
1976 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
1977 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
1979 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
1981 it was not entered */
1982 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
1983 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
1984 ITYPE ("nstdhdl", fep->nstdhdl, 50);
1985 STYPE ("fep-lambdas", fep_lambda[efptFEP], NULL);
1986 STYPE ("mass-lambdas", fep_lambda[efptMASS], NULL);
1987 STYPE ("coul-lambdas", fep_lambda[efptCOUL], NULL);
1988 STYPE ("vdw-lambdas", fep_lambda[efptVDW], NULL);
1989 STYPE ("bonded-lambdas", fep_lambda[efptBONDED], NULL);
1990 STYPE ("restraint-lambdas", fep_lambda[efptRESTRAINT], NULL);
1991 STYPE ("temperature-lambdas", fep_lambda[efptTEMPERATURE], NULL);
1992 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
1993 STYPE ("init-lambda-weights", lambda_weights, NULL);
1994 EETYPE("dhdl-print-energy", fep->bPrintEnergy, yesno_names);
1995 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
1996 ITYPE ("sc-power", fep->sc_power, 1);
1997 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
1998 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
1999 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2000 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2001 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2002 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2003 separate_dhdl_file_names);
2004 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2005 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2006 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2008 /* Non-equilibrium MD stuff */
2009 CCTYPE("Non-equilibrium MD stuff");
2010 STYPE ("acc-grps", accgrps, NULL);
2011 STYPE ("accelerate", acc, NULL);
2012 STYPE ("freezegrps", freeze, NULL);
2013 STYPE ("freezedim", frdim, NULL);
2014 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2015 STYPE ("deform", deform, NULL);
2017 /* simulated tempering variables */
2018 CCTYPE("simulated tempering variables");
2019 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2020 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2021 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2022 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2024 /* expanded ensemble variables */
2025 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2027 read_expandedparams(&ninp, &inp, expand, wi);
2030 /* Electric fields */
2031 CCTYPE("Electric fields");
2032 CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
2033 CTYPE ("and a phase angle (real)");
2034 STYPE ("E-x", efield_x, NULL);
2035 STYPE ("E-xt", efield_xt, NULL);
2036 STYPE ("E-y", efield_y, NULL);
2037 STYPE ("E-yt", efield_yt, NULL);
2038 STYPE ("E-z", efield_z, NULL);
2039 STYPE ("E-zt", efield_zt, NULL);
2041 /* AdResS defined thingies */
2042 CCTYPE ("AdResS parameters");
2043 EETYPE("adress", ir->bAdress, yesno_names);
2046 snew(ir->adress, 1);
2047 read_adressparams(&ninp, &inp, ir->adress, wi);
2050 /* User defined thingies */
2051 CCTYPE ("User defined thingies");
2052 STYPE ("user1-grps", user1, NULL);
2053 STYPE ("user2-grps", user2, NULL);
2054 ITYPE ("userint1", ir->userint1, 0);
2055 ITYPE ("userint2", ir->userint2, 0);
2056 ITYPE ("userint3", ir->userint3, 0);
2057 ITYPE ("userint4", ir->userint4, 0);
2058 RTYPE ("userreal1", ir->userreal1, 0);
2059 RTYPE ("userreal2", ir->userreal2, 0);
2060 RTYPE ("userreal3", ir->userreal3, 0);
2061 RTYPE ("userreal4", ir->userreal4, 0);
2064 write_inpfile(mdparout, ninp, inp, FALSE, wi);
2065 for (i = 0; (i < ninp); i++)
2068 sfree(inp[i].value);
2072 /* Process options if necessary */
2073 for (m = 0; m < 2; m++)
2075 for (i = 0; i < 2*DIM; i++)
2084 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2086 warning_error(wi, "Pressure coupling not enough values (I need 1)");
2088 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2090 case epctSEMIISOTROPIC:
2091 case epctSURFACETENSION:
2092 if (sscanf(dumstr[m], "%lf%lf",
2093 &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2095 warning_error(wi, "Pressure coupling not enough values (I need 2)");
2097 dumdub[m][YY] = dumdub[m][XX];
2099 case epctANISOTROPIC:
2100 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2101 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2102 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2104 warning_error(wi, "Pressure coupling not enough values (I need 6)");
2108 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2109 epcoupltype_names[ir->epct]);
2113 clear_mat(ir->ref_p);
2114 clear_mat(ir->compress);
2115 for (i = 0; i < DIM; i++)
2117 ir->ref_p[i][i] = dumdub[1][i];
2118 ir->compress[i][i] = dumdub[0][i];
2120 if (ir->epct == epctANISOTROPIC)
2122 ir->ref_p[XX][YY] = dumdub[1][3];
2123 ir->ref_p[XX][ZZ] = dumdub[1][4];
2124 ir->ref_p[YY][ZZ] = dumdub[1][5];
2125 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2127 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2129 ir->compress[XX][YY] = dumdub[0][3];
2130 ir->compress[XX][ZZ] = dumdub[0][4];
2131 ir->compress[YY][ZZ] = dumdub[0][5];
2132 for (i = 0; i < DIM; i++)
2134 for (m = 0; m < i; m++)
2136 ir->ref_p[i][m] = ir->ref_p[m][i];
2137 ir->compress[i][m] = ir->compress[m][i];
2142 if (ir->comm_mode == ecmNO)
2147 opts->couple_moltype = NULL;
2148 if (strlen(couple_moltype) > 0)
2150 if (ir->efep != efepNO)
2152 opts->couple_moltype = strdup(couple_moltype);
2153 if (opts->couple_lam0 == opts->couple_lam1)
2155 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2157 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2158 opts->couple_lam1 == ecouplamNONE))
2160 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2165 warning(wi, "Can not couple a molecule with free_energy = no");
2168 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2169 if (ir->efep != efepNO)
2171 if (fep->delta_lambda > 0)
2173 ir->efep = efepSLOWGROWTH;
2179 fep->bPrintEnergy = TRUE;
2180 /* always print out the energy to dhdl if we are doing expanded ensemble, since we need the total energy
2181 if the temperature is changing. */
2184 if ((ir->efep != efepNO) || ir->bSimTemp)
2186 ir->bExpanded = FALSE;
2187 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2189 ir->bExpanded = TRUE;
2191 do_fep_params(ir, fep_lambda, lambda_weights);
2192 if (ir->bSimTemp) /* done after fep params */
2194 do_simtemp_params(ir);
2199 ir->fepvals->n_lambda = 0;
2202 /* WALL PARAMETERS */
2204 do_wall_params(ir, wall_atomtype, wall_density, opts);
2206 /* ORIENTATION RESTRAINT PARAMETERS */
2208 if (opts->bOrire && str_nelem(orirefitgrp, MAXPTR, NULL) != 1)
2210 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2213 /* DEFORMATION PARAMETERS */
2215 clear_mat(ir->deform);
2216 for (i = 0; i < 6; i++)
2220 m = sscanf(deform, "%lf %lf %lf %lf %lf %lf",
2221 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2222 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2223 for (i = 0; i < 3; i++)
2225 ir->deform[i][i] = dumdub[0][i];
2227 ir->deform[YY][XX] = dumdub[0][3];
2228 ir->deform[ZZ][XX] = dumdub[0][4];
2229 ir->deform[ZZ][YY] = dumdub[0][5];
2230 if (ir->epc != epcNO)
2232 for (i = 0; i < 3; i++)
2234 for (j = 0; j <= i; j++)
2236 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2238 warning_error(wi, "A box element has deform set and compressibility > 0");
2242 for (i = 0; i < 3; i++)
2244 for (j = 0; j < i; j++)
2246 if (ir->deform[i][j] != 0)
2248 for (m = j; m < DIM; m++)
2250 if (ir->compress[m][j] != 0)
2252 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.");
2253 warning(wi, warn_buf);
2265 static int search_QMstring(char *s, int ng, const char *gn[])
2267 /* same as normal search_string, but this one searches QM strings */
2270 for (i = 0; (i < ng); i++)
2272 if (gmx_strcasecmp(s, gn[i]) == 0)
2278 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2282 } /* search_QMstring */
2285 int search_string(char *s, int ng, char *gn[])
2289 for (i = 0; (i < ng); i++)
2291 if (gmx_strcasecmp(s, gn[i]) == 0)
2298 "Group %s referenced in the .mdp file was not found in the index file.\n"
2299 "Group names must match either [moleculetype] names or custom index group\n"
2300 "names, in which case you must supply an index file to the '-n' option\n"
2307 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2308 t_blocka *block, char *gnames[],
2309 int gtype, int restnm,
2310 int grptp, gmx_bool bVerbose,
2313 unsigned short *cbuf;
2314 t_grps *grps = &(groups->grps[gtype]);
2315 int i, j, gid, aj, ognr, ntot = 0;
2318 char warn_buf[STRLEN];
2322 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2325 title = gtypes[gtype];
2328 /* Mark all id's as not set */
2329 for (i = 0; (i < natoms); i++)
2334 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2335 for (i = 0; (i < ng); i++)
2337 /* Lookup the group name in the block structure */
2338 gid = search_string(ptrs[i], block->nr, gnames);
2339 if ((grptp != egrptpONE) || (i == 0))
2341 grps->nm_ind[grps->nr++] = gid;
2345 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2348 /* Now go over the atoms in the group */
2349 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2354 /* Range checking */
2355 if ((aj < 0) || (aj >= natoms))
2357 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2359 /* Lookup up the old group number */
2363 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2364 aj+1, title, ognr+1, i+1);
2368 /* Store the group number in buffer */
2369 if (grptp == egrptpONE)
2382 /* Now check whether we have done all atoms */
2386 if (grptp == egrptpALL)
2388 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2389 natoms-ntot, title);
2391 else if (grptp == egrptpPART)
2393 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2394 natoms-ntot, title);
2395 warning_note(wi, warn_buf);
2397 /* Assign all atoms currently unassigned to a rest group */
2398 for (j = 0; (j < natoms); j++)
2400 if (cbuf[j] == NOGID)
2406 if (grptp != egrptpPART)
2411 "Making dummy/rest group for %s containing %d elements\n",
2412 title, natoms-ntot);
2414 /* Add group name "rest" */
2415 grps->nm_ind[grps->nr] = restnm;
2417 /* Assign the rest name to all atoms not currently assigned to a group */
2418 for (j = 0; (j < natoms); j++)
2420 if (cbuf[j] == NOGID)
2429 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2431 /* All atoms are part of one (or no) group, no index required */
2432 groups->ngrpnr[gtype] = 0;
2433 groups->grpnr[gtype] = NULL;
2437 groups->ngrpnr[gtype] = natoms;
2438 snew(groups->grpnr[gtype], natoms);
2439 for (j = 0; (j < natoms); j++)
2441 groups->grpnr[gtype][j] = cbuf[j];
2447 return (bRest && grptp == egrptpPART);
2450 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2453 gmx_groups_t *groups;
2455 int natoms, ai, aj, i, j, d, g, imin, jmin, nc;
2457 int *nrdf2, *na_vcm, na_tot;
2458 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2459 gmx_mtop_atomloop_all_t aloop;
2461 int mb, mol, ftype, as;
2462 gmx_molblock_t *molb;
2463 gmx_moltype_t *molt;
2466 * First calc 3xnr-atoms for each group
2467 * then subtract half a degree of freedom for each constraint
2469 * Only atoms and nuclei contribute to the degrees of freedom...
2474 groups = &mtop->groups;
2475 natoms = mtop->natoms;
2477 /* Allocate one more for a possible rest group */
2478 /* We need to sum degrees of freedom into doubles,
2479 * since floats give too low nrdf's above 3 million atoms.
2481 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2482 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2483 snew(na_vcm, groups->grps[egcVCM].nr+1);
2485 for (i = 0; i < groups->grps[egcTC].nr; i++)
2489 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2494 snew(nrdf2, natoms);
2495 aloop = gmx_mtop_atomloop_all_init(mtop);
2496 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2499 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2501 g = ggrpnr(groups, egcFREEZE, i);
2502 /* Double count nrdf for particle i */
2503 for (d = 0; d < DIM; d++)
2505 if (opts->nFreeze[g][d] == 0)
2510 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2511 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2516 for (mb = 0; mb < mtop->nmolblock; mb++)
2518 molb = &mtop->molblock[mb];
2519 molt = &mtop->moltype[molb->type];
2520 atom = molt->atoms.atom;
2521 for (mol = 0; mol < molb->nmol; mol++)
2523 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2525 ia = molt->ilist[ftype].iatoms;
2526 for (i = 0; i < molt->ilist[ftype].nr; )
2528 /* Subtract degrees of freedom for the constraints,
2529 * if the particles still have degrees of freedom left.
2530 * If one of the particles is a vsite or a shell, then all
2531 * constraint motion will go there, but since they do not
2532 * contribute to the constraints the degrees of freedom do not
2537 if (((atom[ia[1]].ptype == eptNucleus) ||
2538 (atom[ia[1]].ptype == eptAtom)) &&
2539 ((atom[ia[2]].ptype == eptNucleus) ||
2540 (atom[ia[2]].ptype == eptAtom)))
2558 imin = min(imin, nrdf2[ai]);
2559 jmin = min(jmin, nrdf2[aj]);
2562 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2563 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2564 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2565 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2567 ia += interaction_function[ftype].nratoms+1;
2568 i += interaction_function[ftype].nratoms+1;
2571 ia = molt->ilist[F_SETTLE].iatoms;
2572 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2574 /* Subtract 1 dof from every atom in the SETTLE */
2575 for (j = 0; j < 3; j++)
2578 imin = min(2, nrdf2[ai]);
2580 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2581 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2586 as += molt->atoms.nr;
2590 if (ir->ePull == epullCONSTRAINT)
2592 /* Correct nrdf for the COM constraints.
2593 * We correct using the TC and VCM group of the first atom
2594 * in the reference and pull group. If atoms in one pull group
2595 * belong to different TC or VCM groups it is anyhow difficult
2596 * to determine the optimal nrdf assignment.
2599 if (pull->eGeom == epullgPOS)
2602 for (i = 0; i < DIM; i++)
2614 for (i = 0; i < pull->ngrp; i++)
2617 if (pull->grp[0].nat > 0)
2619 /* Subtract 1/2 dof from the reference group */
2620 ai = pull->grp[0].ind[0];
2621 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] > 1)
2623 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5;
2624 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5;
2628 /* Subtract 1/2 dof from the pulled group */
2629 ai = pull->grp[1+i].ind[0];
2630 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2631 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2632 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2634 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)]]);
2639 if (ir->nstcomm != 0)
2641 /* Subtract 3 from the number of degrees of freedom in each vcm group
2642 * when com translation is removed and 6 when rotation is removed
2645 switch (ir->comm_mode)
2648 n_sub = ndof_com(ir);
2655 gmx_incons("Checking comm_mode");
2658 for (i = 0; i < groups->grps[egcTC].nr; i++)
2660 /* Count the number of atoms of TC group i for every VCM group */
2661 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2666 for (ai = 0; ai < natoms; ai++)
2668 if (ggrpnr(groups, egcTC, ai) == i)
2670 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2674 /* Correct for VCM removal according to the fraction of each VCM
2675 * group present in this TC group.
2677 nrdf_uc = nrdf_tc[i];
2680 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2684 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2686 if (nrdf_vcm[j] > n_sub)
2688 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2689 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2693 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2694 j, nrdf_vcm[j], nrdf_tc[i]);
2699 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2701 opts->nrdf[i] = nrdf_tc[i];
2702 if (opts->nrdf[i] < 0)
2707 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2708 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
2717 static void decode_cos(char *s, t_cosines *cosine, gmx_bool bTime)
2720 char format[STRLEN], f1[STRLEN];
2732 sscanf(t, "%d", &(cosine->n));
2739 snew(cosine->a, cosine->n);
2740 snew(cosine->phi, cosine->n);
2742 sprintf(format, "%%*d");
2743 for (i = 0; (i < cosine->n); i++)
2746 strcat(f1, "%lf%lf");
2747 if (sscanf(t, f1, &a, &phi) < 2)
2749 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
2752 cosine->phi[i] = phi;
2753 strcat(format, "%*lf%*lf");
2760 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
2761 const char *option, const char *val, int flag)
2763 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
2764 * But since this is much larger than STRLEN, such a line can not be parsed.
2765 * The real maximum is the number of names that fit in a string: STRLEN/2.
2767 #define EGP_MAX (STRLEN/2)
2768 int nelem, i, j, k, nr;
2769 char *names[EGP_MAX];
2773 gnames = groups->grpname;
2775 nelem = str_nelem(val, EGP_MAX, names);
2778 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
2780 nr = groups->grps[egcENER].nr;
2782 for (i = 0; i < nelem/2; i++)
2786 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
2792 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
2793 names[2*i], option);
2797 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
2803 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
2804 names[2*i+1], option);
2806 if ((j < nr) && (k < nr))
2808 ir->opts.egp_flags[nr*j+k] |= flag;
2809 ir->opts.egp_flags[nr*k+j] |= flag;
2817 void do_index(const char* mdparin, const char *ndx,
2820 t_inputrec *ir, rvec *v,
2824 gmx_groups_t *groups;
2828 char warnbuf[STRLEN], **gnames;
2829 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
2832 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
2833 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
2834 int i, j, k, restnm;
2836 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
2837 int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
2838 nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
2839 char warn_buf[STRLEN];
2843 fprintf(stderr, "processing index file...\n");
2849 snew(grps->index, 1);
2851 atoms_all = gmx_mtop_global_atoms(mtop);
2852 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
2853 free_t_atoms(&atoms_all, FALSE);
2857 grps = init_index(ndx, &gnames);
2860 groups = &mtop->groups;
2861 natoms = mtop->natoms;
2862 symtab = &mtop->symtab;
2864 snew(groups->grpname, grps->nr+1);
2866 for (i = 0; (i < grps->nr); i++)
2868 groups->grpname[i] = put_symtab(symtab, gnames[i]);
2870 groups->grpname[i] = put_symtab(symtab, "rest");
2872 srenew(gnames, grps->nr+1);
2873 gnames[restnm] = *(groups->grpname[i]);
2874 groups->ngrpname = grps->nr+1;
2876 set_warning_line(wi, mdparin, -1);
2878 ntau_t = str_nelem(tau_t, MAXPTR, ptr1);
2879 nref_t = str_nelem(ref_t, MAXPTR, ptr2);
2880 ntcg = str_nelem(tcgrps, MAXPTR, ptr3);
2881 if ((ntau_t != ntcg) || (nref_t != ntcg))
2883 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
2884 "%d tau-t values", ntcg, nref_t, ntau_t);
2887 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
2888 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
2889 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
2890 nr = groups->grps[egcTC].nr;
2892 snew(ir->opts.nrdf, nr);
2893 snew(ir->opts.tau_t, nr);
2894 snew(ir->opts.ref_t, nr);
2895 if (ir->eI == eiBD && ir->bd_fric == 0)
2897 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
2904 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
2908 for (i = 0; (i < nr); i++)
2910 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
2911 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
2913 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
2914 warning_error(wi, warn_buf);
2917 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
2919 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.");
2922 if (ir->opts.tau_t[i] >= 0)
2924 tau_min = min(tau_min, ir->opts.tau_t[i]);
2927 if (ir->etc != etcNO && ir->nsttcouple == -1)
2929 ir->nsttcouple = ir_optimal_nsttcouple(ir);
2934 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
2936 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");
2938 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
2940 if (ir->nstpcouple != ir->nsttcouple)
2942 int mincouple = min(ir->nstpcouple, ir->nsttcouple);
2943 ir->nstpcouple = ir->nsttcouple = mincouple;
2944 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);
2945 warning_note(wi, warn_buf);
2949 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
2950 primarily for testing purposes, and does not work with temperature coupling other than 1 */
2952 if (ETC_ANDERSEN(ir->etc))
2954 if (ir->nsttcouple != 1)
2957 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");
2958 warning_note(wi, warn_buf);
2961 nstcmin = tcouple_min_integration_steps(ir->etc);
2964 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
2966 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
2967 ETCOUPLTYPE(ir->etc),
2969 ir->nsttcouple*ir->delta_t);
2970 warning(wi, warn_buf);
2973 for (i = 0; (i < nr); i++)
2975 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
2976 if (ir->opts.ref_t[i] < 0)
2978 gmx_fatal(FARGS, "ref-t for group %d negative", i);
2981 /* set the lambda mc temperature to the md integrator temperature (which should be defined
2982 if we are in this conditional) if mc_temp is negative */
2983 if (ir->expandedvals->mc_temp < 0)
2985 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
2989 /* Simulated annealing for each group. There are nr groups */
2990 nSA = str_nelem(anneal, MAXPTR, ptr1);
2991 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
2995 if (nSA > 0 && nSA != nr)
2997 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3001 snew(ir->opts.annealing, nr);
3002 snew(ir->opts.anneal_npoints, nr);
3003 snew(ir->opts.anneal_time, nr);
3004 snew(ir->opts.anneal_temp, nr);
3005 for (i = 0; i < nr; i++)
3007 ir->opts.annealing[i] = eannNO;
3008 ir->opts.anneal_npoints[i] = 0;
3009 ir->opts.anneal_time[i] = NULL;
3010 ir->opts.anneal_temp[i] = NULL;
3015 for (i = 0; i < nr; i++)
3017 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3019 ir->opts.annealing[i] = eannNO;
3021 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3023 ir->opts.annealing[i] = eannSINGLE;
3026 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3028 ir->opts.annealing[i] = eannPERIODIC;
3034 /* Read the other fields too */
3035 nSA_points = str_nelem(anneal_npoints, MAXPTR, ptr1);
3036 if (nSA_points != nSA)
3038 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3040 for (k = 0, i = 0; i < nr; i++)
3042 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3043 if (ir->opts.anneal_npoints[i] == 1)
3045 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3047 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3048 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3049 k += ir->opts.anneal_npoints[i];
3052 nSA_time = str_nelem(anneal_time, MAXPTR, ptr1);
3055 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3057 nSA_temp = str_nelem(anneal_temp, MAXPTR, ptr2);
3060 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3063 for (i = 0, k = 0; i < nr; i++)
3066 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3068 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3069 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3072 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3074 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3080 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3082 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3083 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3086 if (ir->opts.anneal_temp[i][j] < 0)
3088 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3093 /* Print out some summary information, to make sure we got it right */
3094 for (i = 0, k = 0; i < nr; i++)
3096 if (ir->opts.annealing[i] != eannNO)
3098 j = groups->grps[egcTC].nm_ind[i];
3099 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3100 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3101 ir->opts.anneal_npoints[i]);
3102 fprintf(stderr, "Time (ps) Temperature (K)\n");
3103 /* All terms except the last one */
3104 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3106 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3109 /* Finally the last one */
3110 j = ir->opts.anneal_npoints[i]-1;
3111 if (ir->opts.annealing[i] == eannSINGLE)
3113 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3117 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3118 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3120 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3129 if (ir->ePull != epullNO)
3131 make_pull_groups(ir->pull, pull_grp, grps, gnames);
3136 make_rotation_groups(ir->rot, rot_grp, grps, gnames);
3139 nacc = str_nelem(acc, MAXPTR, ptr1);
3140 nacg = str_nelem(accgrps, MAXPTR, ptr2);
3141 if (nacg*DIM != nacc)
3143 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3146 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3147 restnm, egrptpALL_GENREST, bVerbose, wi);
3148 nr = groups->grps[egcACC].nr;
3149 snew(ir->opts.acc, nr);
3150 ir->opts.ngacc = nr;
3152 for (i = k = 0; (i < nacg); i++)
3154 for (j = 0; (j < DIM); j++, k++)
3156 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3159 for (; (i < nr); i++)
3161 for (j = 0; (j < DIM); j++)
3163 ir->opts.acc[i][j] = 0;
3167 nfrdim = str_nelem(frdim, MAXPTR, ptr1);
3168 nfreeze = str_nelem(freeze, MAXPTR, ptr2);
3169 if (nfrdim != DIM*nfreeze)
3171 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3174 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3175 restnm, egrptpALL_GENREST, bVerbose, wi);
3176 nr = groups->grps[egcFREEZE].nr;
3177 ir->opts.ngfrz = nr;
3178 snew(ir->opts.nFreeze, nr);
3179 for (i = k = 0; (i < nfreeze); i++)
3181 for (j = 0; (j < DIM); j++, k++)
3183 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3184 if (!ir->opts.nFreeze[i][j])
3186 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3188 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3189 "(not %s)", ptr1[k]);
3190 warning(wi, warn_buf);
3195 for (; (i < nr); i++)
3197 for (j = 0; (j < DIM); j++)
3199 ir->opts.nFreeze[i][j] = 0;
3203 nenergy = str_nelem(energy, MAXPTR, ptr1);
3204 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3205 restnm, egrptpALL_GENREST, bVerbose, wi);
3206 add_wall_energrps(groups, ir->nwall, symtab);
3207 ir->opts.ngener = groups->grps[egcENER].nr;
3208 nvcm = str_nelem(vcm, MAXPTR, ptr1);
3210 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3211 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3214 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3215 "This may lead to artifacts.\n"
3216 "In most cases one should use one group for the whole system.");
3219 /* Now we have filled the freeze struct, so we can calculate NRDF */
3220 calc_nrdf(mtop, ir, gnames);
3226 /* Must check per group! */
3227 for (i = 0; (i < ir->opts.ngtc); i++)
3229 ntot += ir->opts.nrdf[i];
3231 if (ntot != (DIM*natoms))
3233 fac = sqrt(ntot/(DIM*natoms));
3236 fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
3237 "and removal of center of mass motion\n", fac);
3239 for (i = 0; (i < natoms); i++)
3241 svmul(fac, v[i], v[i]);
3246 nuser = str_nelem(user1, MAXPTR, ptr1);
3247 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3248 restnm, egrptpALL_GENREST, bVerbose, wi);
3249 nuser = str_nelem(user2, MAXPTR, ptr1);
3250 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3251 restnm, egrptpALL_GENREST, bVerbose, wi);
3252 nuser = str_nelem(xtc_grps, MAXPTR, ptr1);
3253 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcXTC,
3254 restnm, egrptpONE, bVerbose, wi);
3255 nofg = str_nelem(orirefitgrp, MAXPTR, ptr1);
3256 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3257 restnm, egrptpALL_GENREST, bVerbose, wi);
3259 /* QMMM input processing */
3260 nQMg = str_nelem(QMMM, MAXPTR, ptr1);
3261 nQMmethod = str_nelem(QMmethod, MAXPTR, ptr2);
3262 nQMbasis = str_nelem(QMbasis, MAXPTR, ptr3);
3263 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3265 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3266 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3268 /* group rest, if any, is always MM! */
3269 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3270 restnm, egrptpALL_GENREST, bVerbose, wi);
3271 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3272 ir->opts.ngQM = nQMg;
3273 snew(ir->opts.QMmethod, nr);
3274 snew(ir->opts.QMbasis, nr);
3275 for (i = 0; i < nr; i++)
3277 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3278 * converted to the corresponding enum in names.c
3280 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3282 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3286 nQMmult = str_nelem(QMmult, MAXPTR, ptr1);
3287 nQMcharge = str_nelem(QMcharge, MAXPTR, ptr2);
3288 nbSH = str_nelem(bSH, MAXPTR, ptr3);
3289 snew(ir->opts.QMmult, nr);
3290 snew(ir->opts.QMcharge, nr);
3291 snew(ir->opts.bSH, nr);
3293 for (i = 0; i < nr; i++)
3295 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3296 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3297 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3300 nCASelec = str_nelem(CASelectrons, MAXPTR, ptr1);
3301 nCASorb = str_nelem(CASorbitals, MAXPTR, ptr2);
3302 snew(ir->opts.CASelectrons, nr);
3303 snew(ir->opts.CASorbitals, nr);
3304 for (i = 0; i < nr; i++)
3306 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3307 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3309 /* special optimization options */
3311 nbOPT = str_nelem(bOPT, MAXPTR, ptr1);
3312 nbTS = str_nelem(bTS, MAXPTR, ptr2);
3313 snew(ir->opts.bOPT, nr);
3314 snew(ir->opts.bTS, nr);
3315 for (i = 0; i < nr; i++)
3317 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3318 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3320 nSAon = str_nelem(SAon, MAXPTR, ptr1);
3321 nSAoff = str_nelem(SAoff, MAXPTR, ptr2);
3322 nSAsteps = str_nelem(SAsteps, MAXPTR, ptr3);
3323 snew(ir->opts.SAon, nr);
3324 snew(ir->opts.SAoff, nr);
3325 snew(ir->opts.SAsteps, nr);
3327 for (i = 0; i < nr; i++)
3329 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3330 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3331 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3333 /* end of QMMM input */
3337 for (i = 0; (i < egcNR); i++)
3339 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3340 for (j = 0; (j < groups->grps[i].nr); j++)
3342 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3344 fprintf(stderr, "\n");
3348 nr = groups->grps[egcENER].nr;
3349 snew(ir->opts.egp_flags, nr*nr);
3351 bExcl = do_egp_flag(ir, groups, "energygrp-excl", egpexcl, EGP_EXCL);
3352 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3354 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3356 if (bExcl && EEL_FULL(ir->coulombtype))
3358 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3361 bTable = do_egp_flag(ir, groups, "energygrp-table", egptable, EGP_TABLE);
3362 if (bTable && !(ir->vdwtype == evdwUSER) &&
3363 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3364 !(ir->coulombtype == eelPMEUSERSWITCH))
3366 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3369 decode_cos(efield_x, &(ir->ex[XX]), FALSE);
3370 decode_cos(efield_xt, &(ir->et[XX]), TRUE);
3371 decode_cos(efield_y, &(ir->ex[YY]), FALSE);
3372 decode_cos(efield_yt, &(ir->et[YY]), TRUE);
3373 decode_cos(efield_z, &(ir->ex[ZZ]), FALSE);
3374 decode_cos(efield_zt, &(ir->et[ZZ]), TRUE);
3378 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3381 for (i = 0; (i < grps->nr); i++)
3393 static void check_disre(gmx_mtop_t *mtop)
3395 gmx_ffparams_t *ffparams;
3396 t_functype *functype;
3398 int i, ndouble, ftype;
3399 int label, old_label;
3401 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3403 ffparams = &mtop->ffparams;
3404 functype = ffparams->functype;
3405 ip = ffparams->iparams;
3408 for (i = 0; i < ffparams->ntypes; i++)
3410 ftype = functype[i];
3411 if (ftype == F_DISRES)
3413 label = ip[i].disres.label;
3414 if (label == old_label)
3416 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3424 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3425 "probably the parameters for multiple pairs in one restraint "
3426 "are not identical\n", ndouble);
3431 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3432 gmx_bool posres_only,
3436 gmx_mtop_ilistloop_t iloop;
3446 for (d = 0; d < DIM; d++)
3448 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3450 /* Check for freeze groups */
3451 for (g = 0; g < ir->opts.ngfrz; g++)
3453 for (d = 0; d < DIM; d++)
3455 if (ir->opts.nFreeze[g][d] != 0)
3463 /* Check for position restraints */
3464 iloop = gmx_mtop_ilistloop_init(sys);
3465 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3468 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3470 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3472 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3473 for (d = 0; d < DIM; d++)
3475 if (pr->posres.fcA[d] != 0)
3484 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3487 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
3491 int i, m, g, nmol, npct;
3492 gmx_bool bCharge, bAcc;
3493 real gdt_max, *mgrp, mt;
3495 gmx_mtop_atomloop_block_t aloopb;
3496 gmx_mtop_atomloop_all_t aloop;
3499 char warn_buf[STRLEN];
3501 set_warning_line(wi, mdparin, -1);
3503 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
3504 ir->comm_mode == ecmNO &&
3505 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10))
3507 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");
3510 /* Check for pressure coupling with absolute position restraints */
3511 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
3513 absolute_reference(ir, sys, TRUE, AbsRef);
3515 for (m = 0; m < DIM; m++)
3517 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
3519 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
3527 aloopb = gmx_mtop_atomloop_block_init(sys);
3528 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
3530 if (atom->q != 0 || atom->qB != 0)
3538 if (EEL_FULL(ir->coulombtype))
3541 "You are using full electrostatics treatment %s for a system without charges.\n"
3542 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
3543 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
3544 warning(wi, err_buf);
3549 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
3552 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
3553 "You might want to consider using %s electrostatics.\n",
3555 warning_note(wi, err_buf);
3559 /* Generalized reaction field */
3560 if (ir->opts.ngtc == 0)
3562 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
3564 CHECK(ir->coulombtype == eelGRF);
3568 sprintf(err_buf, "When using coulombtype = %s"
3569 " ref-t for temperature coupling should be > 0",
3571 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
3574 if (ir->eI == eiSD1 &&
3575 (gmx_mtop_ftype_count(sys, F_CONSTR) > 0 ||
3576 gmx_mtop_ftype_count(sys, F_SETTLE) > 0))
3578 sprintf(warn_buf, "With constraints integrator %s is less accurate, consider using %s instead", ei_names[ir->eI], ei_names[eiSD2]);
3579 warning_note(wi, warn_buf);
3583 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
3585 for (m = 0; (m < DIM); m++)
3587 if (fabs(ir->opts.acc[i][m]) > 1e-6)
3596 snew(mgrp, sys->groups.grps[egcACC].nr);
3597 aloop = gmx_mtop_atomloop_all_init(sys);
3598 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
3600 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
3603 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
3605 for (m = 0; (m < DIM); m++)
3607 acc[m] += ir->opts.acc[i][m]*mgrp[i];
3611 for (m = 0; (m < DIM); m++)
3613 if (fabs(acc[m]) > 1e-6)
3615 const char *dim[DIM] = { "X", "Y", "Z" };
3617 "Net Acceleration in %s direction, will %s be corrected\n",
3618 dim[m], ir->nstcomm != 0 ? "" : "not");
3619 if (ir->nstcomm != 0 && m < ndof_com(ir))
3622 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
3624 ir->opts.acc[i][m] -= acc[m];
3632 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
3633 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
3635 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
3638 if (ir->ePull != epullNO)
3640 if (ir->pull->grp[0].nat == 0)
3642 absolute_reference(ir, sys, FALSE, AbsRef);
3643 for (m = 0; m < DIM; m++)
3645 if (ir->pull->dim[m] && !AbsRef[m])
3647 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.");
3653 if (ir->pull->eGeom == epullgDIRPBC)
3655 for (i = 0; i < 3; i++)
3657 for (m = 0; m <= i; m++)
3659 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
3660 ir->deform[i][m] != 0)
3662 for (g = 1; g < ir->pull->ngrp; g++)
3664 if (ir->pull->grp[g].vec[m] != 0)
3666 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->eGeom), 'x'+m);
3678 void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr, warninp_t wi)
3682 char warn_buf[STRLEN];
3685 ptr = check_box(ir->ePBC, box);
3688 warning_error(wi, ptr);
3691 if (bConstr && ir->eConstrAlg == econtSHAKE)
3693 if (ir->shake_tol <= 0.0)
3695 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
3697 warning_error(wi, warn_buf);
3700 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
3702 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
3703 if (ir->epc == epcNO)
3705 warning(wi, warn_buf);
3709 warning_error(wi, warn_buf);
3714 if ( (ir->eConstrAlg == econtLINCS) && bConstr)
3716 /* If we have Lincs constraints: */
3717 if (ir->eI == eiMD && ir->etc == etcNO &&
3718 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
3720 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
3721 warning_note(wi, warn_buf);
3724 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
3726 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
3727 warning_note(wi, warn_buf);
3729 if (ir->epc == epcMTTK)
3731 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
3735 if (ir->LincsWarnAngle > 90.0)
3737 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
3738 warning(wi, warn_buf);
3739 ir->LincsWarnAngle = 90.0;
3742 if (ir->ePBC != epbcNONE)
3744 if (ir->nstlist == 0)
3746 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
3748 bTWIN = (ir->rlistlong > ir->rlist);
3749 if (ir->ns_type == ensGRID)
3751 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
3753 sprintf(warn_buf, "ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease %s.\n",
3754 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
3755 warning_error(wi, warn_buf);
3760 min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
3761 if (2*ir->rlistlong >= min_size)
3763 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
3764 warning_error(wi, warn_buf);
3767 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
3774 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
3778 real rvdw1, rvdw2, rcoul1, rcoul2;
3779 char warn_buf[STRLEN];
3781 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
3785 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
3790 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
3796 if (rvdw1 + rvdw2 > ir->rlist ||
3797 rcoul1 + rcoul2 > ir->rlist)
3799 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than rlist (%f)\n", max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
3800 warning(wi, warn_buf);
3804 /* Here we do not use the zero at cut-off macro,
3805 * since user defined interactions might purposely
3806 * not be zero at the cut-off.
3808 if (EVDW_IS_ZERO_AT_CUTOFF(ir->vdwtype) &&
3809 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
3811 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rvdw (%f)\n",
3813 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
3814 ir->rlistlong, ir->rvdw);
3817 warning(wi, warn_buf);
3821 warning_note(wi, warn_buf);
3824 if (EEL_IS_ZERO_AT_CUTOFF(ir->coulombtype) &&
3825 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
3827 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f)\n",
3829 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
3830 ir->rlistlong, ir->rcoulomb);
3833 warning(wi, warn_buf);
3837 warning_note(wi, warn_buf);