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 * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
45 #include "gromacs/gmxpreprocess/toputil.h"
46 #include "gromacs/legacyheaders/chargegroup.h"
47 #include "gromacs/legacyheaders/inputrec.h"
48 #include "gromacs/legacyheaders/macros.h"
49 #include "gromacs/legacyheaders/names.h"
50 #include "gromacs/legacyheaders/network.h"
51 #include "gromacs/legacyheaders/readinp.h"
52 #include "gromacs/legacyheaders/typedefs.h"
53 #include "gromacs/legacyheaders/warninp.h"
54 #include "gromacs/math/units.h"
55 #include "gromacs/math/vec.h"
56 #include "gromacs/mdlib/calc_verletbuf.h"
57 #include "gromacs/pbcutil/pbc.h"
58 #include "gromacs/topology/block.h"
59 #include "gromacs/topology/index.h"
60 #include "gromacs/topology/mtop_util.h"
61 #include "gromacs/topology/symtab.h"
62 #include "gromacs/utility/cstringutil.h"
63 #include "gromacs/utility/fatalerror.h"
64 #include "gromacs/utility/smalloc.h"
69 /* Resource parameters
70 * Do not change any of these until you read the instruction
71 * in readinp.h. Some cpp's do not take spaces after the backslash
72 * (like the c-shell), which will give you a very weird compiler
76 typedef struct t_inputrec_strings
78 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], x_compressed_groups[STRLEN],
81 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
82 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN],
84 char fep_lambda[efptNR][STRLEN];
85 char lambda_weights[STRLEN];
88 char anneal[STRLEN], anneal_npoints[STRLEN],
89 anneal_time[STRLEN], anneal_temp[STRLEN];
90 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
91 bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
92 SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
93 char efield_x[STRLEN], efield_xt[STRLEN], efield_y[STRLEN],
94 efield_yt[STRLEN], efield_z[STRLEN], efield_zt[STRLEN];
96 } gmx_inputrec_strings;
98 static gmx_inputrec_strings *is = NULL;
100 void init_inputrec_strings()
104 gmx_incons("Attempted to call init_inputrec_strings before calling done_inputrec_strings. Only one inputrec (i.e. .mdp file) can be parsed at a time.");
109 void done_inputrec_strings()
115 static char swapgrp[STRLEN], splitgrp0[STRLEN], splitgrp1[STRLEN], solgrp[STRLEN];
118 egrptpALL, /* All particles have to be a member of a group. */
119 egrptpALL_GENREST, /* A rest group with name is generated for particles *
120 * that are not part of any group. */
121 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
122 * for the rest group. */
123 egrptpONE /* Merge all selected groups into one group, *
124 * make a rest group for the remaining particles. */
127 static const char *constraints[eshNR+1] = {
128 "none", "h-bonds", "all-bonds", "h-angles", "all-angles", NULL
131 static const char *couple_lam[ecouplamNR+1] = {
132 "vdw-q", "vdw", "q", "none", NULL
135 void init_ir(t_inputrec *ir, t_gromppopts *opts)
137 snew(opts->include, STRLEN);
138 snew(opts->define, STRLEN);
139 snew(ir->fepvals, 1);
140 snew(ir->expandedvals, 1);
141 snew(ir->simtempvals, 1);
144 static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
149 for (i = 0; i < ntemps; i++)
151 /* simple linear scaling -- allows more control */
152 if (simtemp->eSimTempScale == esimtempLINEAR)
154 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*temperature_lambdas[i];
156 else if (simtemp->eSimTempScale == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
158 simtemp->temperatures[i] = simtemp->simtemp_low * pow(simtemp->simtemp_high/simtemp->simtemp_low, (1.0*i)/(ntemps-1));
160 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
162 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*(gmx_expm1(temperature_lambdas[i])/gmx_expm1(1.0));
167 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
168 gmx_fatal(FARGS, errorstr);
175 static void _low_check(gmx_bool b, char *s, warninp_t wi)
179 warning_error(wi, s);
183 static void check_nst(const char *desc_nst, int nst,
184 const char *desc_p, int *p,
189 if (*p > 0 && *p % nst != 0)
191 /* Round up to the next multiple of nst */
192 *p = ((*p)/nst + 1)*nst;
193 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n",
194 desc_p, desc_nst, desc_p, *p);
199 static gmx_bool ir_NVE(const t_inputrec *ir)
201 return ((ir->eI == eiMD || EI_VV(ir->eI)) && ir->etc == etcNO);
204 static int lcd(int n1, int n2)
209 for (i = 2; (i <= n1 && i <= n2); i++)
211 if (n1 % i == 0 && n2 % i == 0)
220 static void process_interaction_modifier(const t_inputrec *ir, int *eintmod)
222 if (*eintmod == eintmodPOTSHIFT_VERLET)
224 if (ir->cutoff_scheme == ecutsVERLET)
226 *eintmod = eintmodPOTSHIFT;
230 *eintmod = eintmodNONE;
235 void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
237 /* Check internal consistency.
238 * NOTE: index groups are not set here yet, don't check things
239 * like temperature coupling group options here, but in triple_check
242 /* Strange macro: first one fills the err_buf, and then one can check
243 * the condition, which will print the message and increase the error
246 #define CHECK(b) _low_check(b, err_buf, wi)
247 char err_buf[256], warn_buf[STRLEN];
253 t_lambda *fep = ir->fepvals;
254 t_expanded *expand = ir->expandedvals;
256 set_warning_line(wi, mdparin, -1);
258 /* BASIC CUT-OFF STUFF */
259 if (ir->rcoulomb < 0)
261 warning_error(wi, "rcoulomb should be >= 0");
265 warning_error(wi, "rvdw should be >= 0");
268 !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
270 warning_error(wi, "rlist should be >= 0");
272 sprintf(err_buf, "nstlist can not be smaller than 0. (If you were trying to use the heuristic neighbour-list update scheme for efficient buffering for improved energy conservation, please use the Verlet cut-off scheme instead.)");
273 CHECK(ir->nstlist < 0);
275 process_interaction_modifier(ir, &ir->coulomb_modifier);
276 process_interaction_modifier(ir, &ir->vdw_modifier);
278 if (ir->cutoff_scheme == ecutsGROUP)
281 "The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future "
282 "release when all interaction forms are supported for the verlet scheme. The verlet "
283 "scheme already scales better, and it is compatible with GPUs and other accelerators.");
285 /* BASIC CUT-OFF STUFF */
286 if (ir->rlist == 0 ||
287 !((ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > ir->rlist) ||
288 (ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > ir->rlist)))
290 /* No switched potential and/or no twin-range:
291 * we can set the long-range cut-off to the maximum of the other cut-offs.
293 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
295 else if (ir->rlistlong < 0)
297 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
298 sprintf(warn_buf, "rlistlong was not set, setting it to %g (no buffer)",
300 warning(wi, warn_buf);
302 if (ir->rlistlong == 0 && ir->ePBC != epbcNONE)
304 warning_error(wi, "Can not have an infinite cut-off with PBC");
306 if (ir->rlistlong > 0 && (ir->rlist == 0 || ir->rlistlong < ir->rlist))
308 warning_error(wi, "rlistlong can not be shorter than rlist");
310 if (IR_TWINRANGE(*ir) && ir->nstlist == 0)
312 warning_error(wi, "Can not have nstlist == 0 with twin-range interactions");
316 if (ir->rlistlong == ir->rlist)
320 else if (ir->rlistlong > ir->rlist && ir->nstcalclr == 0)
322 warning_error(wi, "With different cutoffs for electrostatics and VdW, nstcalclr must be -1 or a positive number");
325 if (ir->cutoff_scheme == ecutsVERLET)
329 /* Normal Verlet type neighbor-list, currently only limited feature support */
330 if (inputrec2nboundeddim(ir) < 3)
332 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
334 if (ir->rcoulomb != ir->rvdw)
336 warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported");
338 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
340 if (ir->vdw_modifier == eintmodNONE ||
341 ir->vdw_modifier == eintmodPOTSHIFT)
343 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
345 sprintf(warn_buf, "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], evdw_names[evdwCUT], eintmod_names[ir->vdw_modifier]);
346 warning_note(wi, warn_buf);
348 ir->vdwtype = evdwCUT;
352 sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
353 warning_error(wi, warn_buf);
357 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
359 warning_error(wi, "With Verlet lists only cut-off and PME LJ interactions are supported");
361 if (!(ir->coulombtype == eelCUT ||
362 (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC) ||
363 EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
365 warning_error(wi, "With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
367 if (!(ir->coulomb_modifier == eintmodNONE ||
368 ir->coulomb_modifier == eintmodPOTSHIFT))
370 sprintf(warn_buf, "coulomb_modifier=%s is not supported with the Verlet cut-off scheme", eintmod_names[ir->coulomb_modifier]);
371 warning_error(wi, warn_buf);
374 if (ir->implicit_solvent != eisNO)
376 warning_error(wi, "Implicit solvent is not (yet) supported with the with Verlet lists.");
379 if (ir->nstlist <= 0)
381 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
384 if (ir->nstlist < 10)
386 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.");
389 rc_max = max(ir->rvdw, ir->rcoulomb);
391 if (ir->verletbuf_tol <= 0)
393 if (ir->verletbuf_tol == 0)
395 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
398 if (ir->rlist < rc_max)
400 warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
403 if (ir->rlist == rc_max && ir->nstlist > 1)
405 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.");
410 if (ir->rlist > rc_max)
412 warning_note(wi, "You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance.");
415 if (ir->nstlist == 1)
417 /* No buffer required */
422 if (EI_DYNAMICS(ir->eI))
424 if (inputrec2nboundeddim(ir) < 3)
426 warning_error(wi, "The box volume is required for calculating rlist from the energy drift with verlet-buffer-tolerance > 0. You are using at least one unbounded dimension, so no volume can be computed. Either use a finite box, or set rlist yourself together with verlet-buffer-tolerance = -1.");
428 /* Set rlist temporarily so we can continue processing */
433 /* Set the buffer to 5% of the cut-off */
434 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
439 /* No twin-range calculations with Verlet lists */
440 ir->rlistlong = ir->rlist;
443 if (ir->nstcalclr == -1)
445 /* if rlist=rlistlong, this will later be changed to nstcalclr=0 */
446 ir->nstcalclr = ir->nstlist;
448 else if (ir->nstcalclr > 0)
450 if (ir->nstlist > 0 && (ir->nstlist % ir->nstcalclr != 0))
452 warning_error(wi, "nstlist must be evenly divisible by nstcalclr. Use nstcalclr = -1 to automatically follow nstlist");
455 else if (ir->nstcalclr < -1)
457 warning_error(wi, "nstcalclr must be a positive number (divisor of nstcalclr), or -1 to follow nstlist.");
460 if (EEL_PME(ir->coulombtype) && ir->rcoulomb > ir->rlist && ir->nstcalclr > 1)
462 warning_error(wi, "When used with PME, the long-range component of twin-range interactions must be updated every step (nstcalclr)");
465 /* GENERAL INTEGRATOR STUFF */
466 if (!(ir->eI == eiMD || EI_VV(ir->eI)))
470 if (ir->eI == eiVVAK)
472 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]);
473 warning_note(wi, warn_buf);
475 if (!EI_DYNAMICS(ir->eI))
479 if (EI_DYNAMICS(ir->eI))
481 if (ir->nstcalcenergy < 0)
483 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
484 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
486 /* nstcalcenergy larger than nstener does not make sense.
487 * We ideally want nstcalcenergy=nstener.
491 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
495 ir->nstcalcenergy = ir->nstenergy;
499 else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
500 (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
501 (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
504 const char *nsten = "nstenergy";
505 const char *nstdh = "nstdhdl";
506 const char *min_name = nsten;
507 int min_nst = ir->nstenergy;
509 /* find the smallest of ( nstenergy, nstdhdl ) */
510 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
511 (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
513 min_nst = ir->fepvals->nstdhdl;
516 /* If the user sets nstenergy small, we should respect that */
518 "Setting nstcalcenergy (%d) equal to %s (%d)",
519 ir->nstcalcenergy, min_name, min_nst);
520 warning_note(wi, warn_buf);
521 ir->nstcalcenergy = min_nst;
524 if (ir->epc != epcNO)
526 if (ir->nstpcouple < 0)
528 ir->nstpcouple = ir_optimal_nstpcouple(ir);
531 if (IR_TWINRANGE(*ir))
533 check_nst("nstcalclr", ir->nstcalclr,
534 "nstcalcenergy", &ir->nstcalcenergy, wi);
535 if (ir->epc != epcNO)
537 check_nst("nstlist", ir->nstlist,
538 "nstpcouple", &ir->nstpcouple, wi);
542 if (ir->nstcalcenergy > 0)
544 if (ir->efep != efepNO)
546 /* nstdhdl should be a multiple of nstcalcenergy */
547 check_nst("nstcalcenergy", ir->nstcalcenergy,
548 "nstdhdl", &ir->fepvals->nstdhdl, wi);
549 /* nstexpanded should be a multiple of nstcalcenergy */
550 check_nst("nstcalcenergy", ir->nstcalcenergy,
551 "nstexpanded", &ir->expandedvals->nstexpanded, wi);
553 /* for storing exact averages nstenergy should be
554 * a multiple of nstcalcenergy
556 check_nst("nstcalcenergy", ir->nstcalcenergy,
557 "nstenergy", &ir->nstenergy, wi);
561 if (ir->nsteps == 0 && !ir->bContinuation)
563 warning_note(wi, "For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates.");
567 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
568 ir->bContinuation && ir->ld_seed != -1)
570 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)");
576 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
577 CHECK(ir->ePBC != epbcXYZ);
578 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
579 CHECK(ir->ns_type != ensGRID);
580 sprintf(err_buf, "with TPI nstlist should be larger than zero");
581 CHECK(ir->nstlist <= 0);
582 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
583 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
584 sprintf(err_buf, "TPI does not work (yet) with the Verlet cut-off scheme");
585 CHECK(ir->cutoff_scheme == ecutsVERLET);
589 if ( (opts->nshake > 0) && (opts->bMorse) )
592 "Using morse bond-potentials while constraining bonds is useless");
593 warning(wi, warn_buf);
596 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
597 ir->bContinuation && ir->ld_seed != -1)
599 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)");
601 /* verify simulated tempering options */
605 gmx_bool bAllTempZero = TRUE;
606 for (i = 0; i < fep->n_lambda; i++)
608 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]);
609 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
610 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
612 bAllTempZero = FALSE;
615 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
616 CHECK(bAllTempZero == TRUE);
618 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
619 CHECK(ir->eI != eiVV);
621 /* check compatability of the temperature coupling with simulated tempering */
623 if (ir->etc == etcNOSEHOOVER)
625 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
626 warning_note(wi, warn_buf);
629 /* check that the temperatures make sense */
631 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);
632 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
634 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
635 CHECK(ir->simtempvals->simtemp_high <= 0);
637 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
638 CHECK(ir->simtempvals->simtemp_low <= 0);
641 /* verify free energy options */
643 if (ir->efep != efepNO)
646 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
648 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
650 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
651 (int)fep->sc_r_power);
652 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
654 sprintf(err_buf, "Can't use postive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
655 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
657 sprintf(err_buf, "Can't use postive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
658 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
660 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
661 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
663 sprintf(err_buf, "Free-energy not implemented for Ewald");
664 CHECK(ir->coulombtype == eelEWALD);
666 /* check validty of lambda inputs */
667 if (fep->n_lambda == 0)
669 /* Clear output in case of no states:*/
670 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
671 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
675 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
676 CHECK((fep->init_fep_state >= fep->n_lambda));
679 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
680 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
682 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",
683 fep->init_lambda, fep->init_fep_state);
684 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
688 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
692 for (i = 0; i < efptNR; i++)
694 if (fep->separate_dvdl[i])
699 if (n_lambda_terms > 1)
701 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.");
702 warning(wi, warn_buf);
705 if (n_lambda_terms < 2 && fep->n_lambda > 0)
708 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
712 for (j = 0; j < efptNR; j++)
714 for (i = 0; i < fep->n_lambda; i++)
716 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]);
717 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
721 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
723 for (i = 0; i < fep->n_lambda; i++)
725 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],
726 fep->all_lambda[efptCOUL][i]);
727 CHECK((fep->sc_alpha > 0) &&
728 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
729 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
730 ((fep->all_lambda[efptVDW][i] > 0.0) &&
731 (fep->all_lambda[efptVDW][i] < 1.0))));
735 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
737 real sigma, lambda, r_sc;
740 /* Maximum estimate for A and B charges equal with lambda power 1 */
742 r_sc = pow(lambda*fep->sc_alpha*pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
743 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.",
745 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
746 warning_note(wi, warn_buf);
749 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
750 be treated differently, but that's the next step */
752 for (i = 0; i < efptNR; i++)
754 for (j = 0; j < fep->n_lambda; j++)
756 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
757 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
761 if (IR_TWINRANGE(*ir))
763 sprintf(err_buf, "nstdhdl must be divisible by nstcalclr");
764 CHECK(ir->fepvals->nstdhdl > 0 &&
765 ir->fepvals->nstdhdl % ir->nstcalclr != 0);
767 if (ir->efep == efepEXPANDED)
769 sprintf(err_buf, "nstexpanded must be divisible by nstcalclr");
770 CHECK(ir->expandedvals->nstexpanded % ir->nstcalclr != 0);
775 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
778 expand = ir->expandedvals;
780 /* checking equilibration of weights inputs for validity */
782 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
783 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
784 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
786 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
787 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
788 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
790 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
791 expand->equil_steps, elmceq_names[elmceqSTEPS]);
792 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
794 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
795 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
796 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
798 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
799 expand->equil_ratio, elmceq_names[elmceqRATIO]);
800 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
802 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
803 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
804 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
806 sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
807 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
808 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
810 sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
811 expand->equil_steps, elmceq_names[elmceqSTEPS]);
812 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
814 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
815 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
816 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
818 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
819 expand->equil_ratio, elmceq_names[elmceqRATIO]);
820 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
822 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
823 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
824 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
826 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
827 CHECK((expand->lmc_repeats <= 0));
828 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
829 CHECK((expand->minvarmin <= 0));
830 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
831 CHECK((expand->c_range < 0));
832 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
833 fep->init_fep_state, expand->lmc_forced_nstart);
834 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
835 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
836 CHECK((expand->lmc_forced_nstart < 0));
837 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
838 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
840 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
841 CHECK((expand->init_wl_delta < 0));
842 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
843 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
844 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
845 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
847 /* if there is no temperature control, we need to specify an MC temperature */
848 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
849 if (expand->nstTij > 0)
851 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
852 expand->nstTij, ir->nstlog);
853 CHECK((mod(expand->nstTij, ir->nstlog) != 0));
858 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
859 CHECK(ir->nwall && ir->ePBC != epbcXY);
862 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
864 if (ir->ePBC == epbcNONE)
866 if (ir->epc != epcNO)
868 warning(wi, "Turning off pressure coupling for vacuum system");
874 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
875 epbc_names[ir->ePBC]);
876 CHECK(ir->epc != epcNO);
878 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
879 CHECK(EEL_FULL(ir->coulombtype));
881 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
882 epbc_names[ir->ePBC]);
883 CHECK(ir->eDispCorr != edispcNO);
886 if (ir->rlist == 0.0)
888 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
889 "with coulombtype = %s or coulombtype = %s\n"
890 "without periodic boundary conditions (pbc = %s) and\n"
891 "rcoulomb and rvdw set to zero",
892 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
893 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
894 (ir->ePBC != epbcNONE) ||
895 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
899 warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
904 if (ir->nstcomm == 0)
906 ir->comm_mode = ecmNO;
908 if (ir->comm_mode != ecmNO)
912 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");
913 ir->nstcomm = abs(ir->nstcomm);
916 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
918 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
919 ir->nstcomm = ir->nstcalcenergy;
922 if (ir->comm_mode == ecmANGULAR)
924 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
925 CHECK(ir->bPeriodicMols);
926 if (ir->ePBC != epbcNONE)
928 warning(wi, "Removing the rotation around the center of mass in a periodic system, this can lead to artifacts. Only use this on a single (cluster of) molecules. This cluster should not cross periodic boundaries.");
933 if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
935 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.");
938 sprintf(err_buf, "Twin-range neighbour searching (NS) with simple NS"
939 " algorithm not implemented");
940 CHECK(((ir->rcoulomb > ir->rlist) || (ir->rvdw > ir->rlist))
941 && (ir->ns_type == ensSIMPLE));
943 /* TEMPERATURE COUPLING */
944 if (ir->etc == etcYES)
946 ir->etc = etcBERENDSEN;
947 warning_note(wi, "Old option for temperature coupling given: "
948 "changing \"yes\" to \"Berendsen\"\n");
951 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
953 if (ir->opts.nhchainlength < 1)
955 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
956 ir->opts.nhchainlength = 1;
957 warning(wi, warn_buf);
960 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
962 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
963 ir->opts.nhchainlength = 1;
968 ir->opts.nhchainlength = 0;
971 if (ir->eI == eiVVAK)
973 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
975 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
978 if (ETC_ANDERSEN(ir->etc))
980 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
981 CHECK(!(EI_VV(ir->eI)));
983 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
985 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]);
986 warning_note(wi, warn_buf);
989 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]);
990 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
993 if (ir->etc == etcBERENDSEN)
995 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
996 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
997 warning_note(wi, warn_buf);
1000 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
1001 && ir->epc == epcBERENDSEN)
1003 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
1004 "true ensemble for the thermostat");
1005 warning(wi, warn_buf);
1008 /* PRESSURE COUPLING */
1009 if (ir->epc == epcISOTROPIC)
1011 ir->epc = epcBERENDSEN;
1012 warning_note(wi, "Old option for pressure coupling given: "
1013 "changing \"Isotropic\" to \"Berendsen\"\n");
1016 if (ir->epc != epcNO)
1018 dt_pcoupl = ir->nstpcouple*ir->delta_t;
1020 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1021 CHECK(ir->tau_p <= 0);
1023 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10*GMX_REAL_EPS)
1025 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
1026 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1027 warning(wi, warn_buf);
1030 sprintf(err_buf, "compressibility must be > 0 when using pressure"
1031 " coupling %s\n", EPCOUPLTYPE(ir->epc));
1032 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
1033 ir->compress[ZZ][ZZ] < 0 ||
1034 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
1035 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
1037 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1040 "You are generating velocities so I am assuming you "
1041 "are equilibrating a system. You are using "
1042 "%s pressure coupling, but this can be "
1043 "unstable for equilibration. If your system crashes, try "
1044 "equilibrating first with Berendsen pressure coupling. If "
1045 "you are not equilibrating the system, you can probably "
1046 "ignore this warning.",
1047 epcoupl_names[ir->epc]);
1048 warning(wi, warn_buf);
1054 if (ir->epc > epcNO)
1056 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1058 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.");
1064 if (ir->epc == epcMTTK)
1066 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1070 /* ELECTROSTATICS */
1071 /* More checks are in triple check (grompp.c) */
1073 if (ir->coulombtype == eelSWITCH)
1075 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1076 "artifacts, advice: use coulombtype = %s",
1077 eel_names[ir->coulombtype],
1078 eel_names[eelRF_ZERO]);
1079 warning(wi, warn_buf);
1082 if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
1084 sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
1085 warning_note(wi, warn_buf);
1088 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1090 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);
1091 warning(wi, warn_buf);
1092 ir->epsilon_rf = ir->epsilon_r;
1093 ir->epsilon_r = 1.0;
1096 if (ir->epsilon_r == 0)
1099 "It is pointless to use long-range or Generalized Born electrostatics with infinite relative permittivity."
1100 "Since you are effectively turning of electrostatics, a plain cutoff will be much faster.");
1101 CHECK(EEL_FULL(ir->coulombtype) || ir->implicit_solvent == eisGBSA);
1104 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == NULL)
1106 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1107 CHECK(ir->epsilon_r < 0);
1110 if (EEL_RF(ir->coulombtype))
1112 /* reaction field (at the cut-off) */
1114 if (ir->coulombtype == eelRF_ZERO)
1116 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1117 eel_names[ir->coulombtype]);
1118 CHECK(ir->epsilon_rf != 0);
1119 ir->epsilon_rf = 0.0;
1122 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1123 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1124 (ir->epsilon_r == 0));
1125 if (ir->epsilon_rf == ir->epsilon_r)
1127 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1128 eel_names[ir->coulombtype]);
1129 warning(wi, warn_buf);
1132 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1133 * means the interaction is zero outside rcoulomb, but it helps to
1134 * provide accurate energy conservation.
1136 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1138 if (ir_coulomb_switched(ir))
1141 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1142 eel_names[ir->coulombtype]);
1143 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1146 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1148 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1150 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1151 eel_names[ir->coulombtype]);
1152 CHECK(ir->rlist > ir->rcoulomb);
1156 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1159 "Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier.");
1160 CHECK( ir->coulomb_modifier != eintmodNONE);
1162 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1165 "Explicit switch/shift vdw interactions cannot be used in combination with a secondary vdw-modifier.");
1166 CHECK( ir->vdw_modifier != eintmodNONE);
1169 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1170 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1173 "The switch/shift interaction settings are just for compatibility; you will get better "
1174 "performance from applying potential modifiers to your interactions!\n");
1175 warning_note(wi, warn_buf);
1178 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1180 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1182 real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
1183 sprintf(warn_buf, "The switching range should be 5%% or less (currently %.2f%% using a switching range of %4f-%4f) for accurate electrostatic energies, energy conservation will be good regardless, since ewald_rtol = %g.",
1184 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1185 warning(wi, warn_buf);
1189 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1191 if (ir->rvdw_switch == 0)
1193 sprintf(warn_buf, "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones potential. This suggests it was not set in the mdp, which can lead to large energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw switching range.");
1194 warning(wi, warn_buf);
1198 if (EEL_FULL(ir->coulombtype))
1200 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1201 ir->coulombtype == eelPMEUSERSWITCH)
1203 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1204 eel_names[ir->coulombtype]);
1205 CHECK(ir->rcoulomb > ir->rlist);
1207 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1209 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1212 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
1213 "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
1214 "a potential modifier.", eel_names[ir->coulombtype]);
1215 if (ir->nstcalclr == 1)
1217 CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
1221 CHECK(ir->rcoulomb != ir->rlist);
1227 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1229 if (ir->pme_order < 3)
1231 warning_error(wi, "pme-order can not be smaller than 3");
1235 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1237 if (ir->ewald_geometry == eewg3D)
1239 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1240 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1241 warning(wi, warn_buf);
1243 /* This check avoids extra pbc coding for exclusion corrections */
1244 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1245 CHECK(ir->wall_ewald_zfac < 2);
1247 if ((ir->ewald_geometry == eewg3DC) && (ir->ePBC != epbcXY) &&
1248 EEL_FULL(ir->coulombtype))
1250 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1251 eel_names[ir->coulombtype], eewg_names[eewg3DC], epbc_names[epbcXY]);
1252 warning(wi, warn_buf);
1254 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1256 if (ir->cutoff_scheme == ecutsVERLET)
1258 sprintf(warn_buf, "Since molecules/charge groups are broken using the Verlet scheme, you can not use a dipole correction to the %s electrostatics.",
1259 eel_names[ir->coulombtype]);
1260 warning(wi, warn_buf);
1264 sprintf(warn_buf, "Dipole corrections to %s electrostatics only work if all charge groups that can cross PBC boundaries are dipoles. If this is not the case set epsilon_surface to 0",
1265 eel_names[ir->coulombtype]);
1266 warning_note(wi, warn_buf);
1270 if (ir_vdw_switched(ir))
1272 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1273 CHECK(ir->rvdw_switch >= ir->rvdw);
1275 if (ir->rvdw_switch < 0.5*ir->rvdw)
1277 sprintf(warn_buf, "You are applying a switch function to vdw forces or potentials from %g to %g nm, which is more than half the interaction range, whereas switch functions are intended to act only close to the cut-off.",
1278 ir->rvdw_switch, ir->rvdw);
1279 warning_note(wi, warn_buf);
1282 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1284 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1286 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1287 CHECK(ir->rlist > ir->rvdw);
1291 if (ir->vdwtype == evdwPME)
1293 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1295 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s a\
1297 evdw_names[ir->vdwtype],
1298 eintmod_names[eintmodPOTSHIFT],
1299 eintmod_names[eintmodNONE]);
1303 if (ir->cutoff_scheme == ecutsGROUP)
1305 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1306 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)))
1308 warning_note(wi, "With exact cut-offs, rlist should be "
1309 "larger than rcoulomb and rvdw, so that there "
1310 "is a buffer region for particle motion "
1311 "between neighborsearch steps");
1314 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlistlong <= ir->rcoulomb)
1316 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
1317 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1318 warning_note(wi, warn_buf);
1320 if (ir_vdw_switched(ir) && (ir->rlistlong <= ir->rvdw))
1322 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
1323 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1324 warning_note(wi, warn_buf);
1328 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1330 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.");
1333 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1336 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1339 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1341 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1344 /* ENERGY CONSERVATION */
1345 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1347 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1349 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1350 evdw_names[evdwSHIFT]);
1351 warning_note(wi, warn_buf);
1353 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1355 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1356 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1357 warning_note(wi, warn_buf);
1361 if (EI_VV(ir->eI) && IR_TWINRANGE(*ir) && ir->nstlist > 1)
1363 sprintf(warn_buf, "Twin-range multiple time stepping does not work with integrator %s.", ei_names[ir->eI]);
1364 warning_error(wi, warn_buf);
1367 /* IMPLICIT SOLVENT */
1368 if (ir->coulombtype == eelGB_NOTUSED)
1370 sprintf(warn_buf, "Invalid option %s for coulombtype",
1371 eel_names[ir->coulombtype]);
1372 warning_error(wi, warn_buf);
1375 if (ir->sa_algorithm == esaSTILL)
1377 sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
1378 CHECK(ir->sa_algorithm == esaSTILL);
1381 if (ir->implicit_solvent == eisGBSA)
1383 sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
1384 CHECK(ir->rgbradii != ir->rlist);
1386 if (ir->coulombtype != eelCUT)
1388 sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
1389 CHECK(ir->coulombtype != eelCUT);
1391 if (ir->vdwtype != evdwCUT)
1393 sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
1394 CHECK(ir->vdwtype != evdwCUT);
1396 if (ir->nstgbradii < 1)
1398 sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
1399 warning_note(wi, warn_buf);
1402 if (ir->sa_algorithm == esaNO)
1404 sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
1405 warning_note(wi, warn_buf);
1407 if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
1409 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");
1410 warning_note(wi, warn_buf);
1412 if (ir->gb_algorithm == egbSTILL)
1414 ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
1418 ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
1421 if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
1423 sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
1424 CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
1431 if (ir->cutoff_scheme != ecutsGROUP)
1433 warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
1437 warning_error(wi, "AdresS simulation supports only stochastic dynamics");
1439 if (ir->epc != epcNO)
1441 warning_error(wi, "AdresS simulation does not support pressure coupling");
1443 if (EEL_FULL(ir->coulombtype))
1445 warning_error(wi, "AdresS simulation does not support long-range electrostatics");
1450 /* count the number of text elemets separated by whitespace in a string.
1451 str = the input string
1452 maxptr = the maximum number of allowed elements
1453 ptr = the output array of pointers to the first character of each element
1454 returns: the number of elements. */
1455 int str_nelem(const char *str, int maxptr, char *ptr[])
1460 copy0 = gmx_strdup(str);
1463 while (*copy != '\0')
1467 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1475 while ((*copy != '\0') && !isspace(*copy))
1494 /* interpret a number of doubles from a string and put them in an array,
1495 after allocating space for them.
1496 str = the input string
1497 n = the (pre-allocated) number of doubles read
1498 r = the output array of doubles. */
1499 static void parse_n_real(char *str, int *n, real **r)
1504 *n = str_nelem(str, MAXPTR, ptr);
1507 for (i = 0; i < *n; i++)
1509 (*r)[i] = strtod(ptr[i], NULL);
1513 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
1516 int i, j, max_n_lambda, nweights, nfep[efptNR];
1517 t_lambda *fep = ir->fepvals;
1518 t_expanded *expand = ir->expandedvals;
1519 real **count_fep_lambdas;
1520 gmx_bool bOneLambda = TRUE;
1522 snew(count_fep_lambdas, efptNR);
1524 /* FEP input processing */
1525 /* first, identify the number of lambda values for each type.
1526 All that are nonzero must have the same number */
1528 for (i = 0; i < efptNR; i++)
1530 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
1533 /* now, determine the number of components. All must be either zero, or equal. */
1536 for (i = 0; i < efptNR; i++)
1538 if (nfep[i] > max_n_lambda)
1540 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1541 must have the same number if its not zero.*/
1546 for (i = 0; i < efptNR; i++)
1550 ir->fepvals->separate_dvdl[i] = FALSE;
1552 else if (nfep[i] == max_n_lambda)
1554 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1555 respect to the temperature currently */
1557 ir->fepvals->separate_dvdl[i] = TRUE;
1562 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1563 nfep[i], efpt_names[i], max_n_lambda);
1566 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1567 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1569 /* the number of lambdas is the number we've read in, which is either zero
1570 or the same for all */
1571 fep->n_lambda = max_n_lambda;
1573 /* allocate space for the array of lambda values */
1574 snew(fep->all_lambda, efptNR);
1575 /* if init_lambda is defined, we need to set lambda */
1576 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1578 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1580 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1581 for (i = 0; i < efptNR; i++)
1583 snew(fep->all_lambda[i], fep->n_lambda);
1584 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1587 for (j = 0; j < fep->n_lambda; j++)
1589 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1591 sfree(count_fep_lambdas[i]);
1594 sfree(count_fep_lambdas);
1596 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1597 bookkeeping -- for now, init_lambda */
1599 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1601 for (i = 0; i < fep->n_lambda; i++)
1603 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1607 /* check to see if only a single component lambda is defined, and soft core is defined.
1608 In this case, turn on coulomb soft core */
1610 if (max_n_lambda == 0)
1616 for (i = 0; i < efptNR; i++)
1618 if ((nfep[i] != 0) && (i != efptFEP))
1624 if ((bOneLambda) && (fep->sc_alpha > 0))
1626 fep->bScCoul = TRUE;
1629 /* Fill in the others with the efptFEP if they are not explicitly
1630 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1631 they are all zero. */
1633 for (i = 0; i < efptNR; i++)
1635 if ((nfep[i] == 0) && (i != efptFEP))
1637 for (j = 0; j < fep->n_lambda; j++)
1639 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1645 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1646 if (fep->sc_r_power == 48)
1648 if (fep->sc_alpha > 0.1)
1650 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1654 expand = ir->expandedvals;
1655 /* now read in the weights */
1656 parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
1659 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1661 else if (nweights != fep->n_lambda)
1663 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1664 nweights, fep->n_lambda);
1666 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1668 expand->nstexpanded = fep->nstdhdl;
1669 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1671 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1673 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1674 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1675 2*tau_t just to be careful so it's not to frequent */
1680 static void do_simtemp_params(t_inputrec *ir)
1683 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1684 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1689 static void do_wall_params(t_inputrec *ir,
1690 char *wall_atomtype, char *wall_density,
1694 char *names[MAXPTR];
1697 opts->wall_atomtype[0] = NULL;
1698 opts->wall_atomtype[1] = NULL;
1700 ir->wall_atomtype[0] = -1;
1701 ir->wall_atomtype[1] = -1;
1702 ir->wall_density[0] = 0;
1703 ir->wall_density[1] = 0;
1707 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1708 if (nstr != ir->nwall)
1710 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1713 for (i = 0; i < ir->nwall; i++)
1715 opts->wall_atomtype[i] = gmx_strdup(names[i]);
1718 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1720 nstr = str_nelem(wall_density, MAXPTR, names);
1721 if (nstr != ir->nwall)
1723 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1725 for (i = 0; i < ir->nwall; i++)
1727 sscanf(names[i], "%lf", &dbl);
1730 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1732 ir->wall_density[i] = dbl;
1738 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1746 srenew(groups->grpname, groups->ngrpname+nwall);
1747 grps = &(groups->grps[egcENER]);
1748 srenew(grps->nm_ind, grps->nr+nwall);
1749 for (i = 0; i < nwall; i++)
1751 sprintf(str, "wall%d", i);
1752 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1753 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1758 void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1759 t_expanded *expand, warninp_t wi)
1761 int ninp, nerror = 0;
1767 /* read expanded ensemble parameters */
1768 CCTYPE ("expanded ensemble variables");
1769 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1770 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1771 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1772 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1773 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1774 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1775 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1776 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1777 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1778 CCTYPE("Seed for Monte Carlo in lambda space");
1779 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1780 RTYPE ("mc-temperature", expand->mc_temp, -1);
1781 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1782 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1783 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1784 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1785 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1786 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1787 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1788 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1789 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1790 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1791 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
1799 /*! \brief Return whether an end state with the given coupling-lambda
1800 * value describes fully-interacting VDW.
1802 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1803 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1805 static gmx_bool couple_lambda_has_vdw_on(int couple_lambda_value)
1807 return (couple_lambda_value == ecouplamVDW ||
1808 couple_lambda_value == ecouplamVDWQ);
1811 void get_ir(const char *mdparin, const char *mdparout,
1812 t_inputrec *ir, t_gromppopts *opts,
1816 double dumdub[2][6];
1820 char warn_buf[STRLEN];
1821 t_lambda *fep = ir->fepvals;
1822 t_expanded *expand = ir->expandedvals;
1824 init_inputrec_strings();
1825 inp = read_inpfile(mdparin, &ninp, wi);
1827 snew(dumstr[0], STRLEN);
1828 snew(dumstr[1], STRLEN);
1830 if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
1833 "%s did not specify a value for the .mdp option "
1834 "\"cutoff-scheme\". Probably it was first intended for use "
1835 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1836 "introduced, but the group scheme was still the default. "
1837 "The default is now the Verlet scheme, so you will observe "
1838 "different behaviour.", mdparin);
1839 warning_note(wi, warn_buf);
1842 /* ignore the following deprecated commands */
1845 REM_TYPE("domain-decomposition");
1846 REM_TYPE("andersen-seed");
1848 REM_TYPE("dihre-fc");
1849 REM_TYPE("dihre-tau");
1850 REM_TYPE("nstdihreout");
1851 REM_TYPE("nstcheckpoint");
1852 REM_TYPE("optimize-fft");
1854 /* replace the following commands with the clearer new versions*/
1855 REPL_TYPE("unconstrained-start", "continuation");
1856 REPL_TYPE("foreign-lambda", "fep-lambdas");
1857 REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
1858 REPL_TYPE("nstxtcout", "nstxout-compressed");
1859 REPL_TYPE("xtc-grps", "compressed-x-grps");
1860 REPL_TYPE("xtc-precision", "compressed-x-precision");
1862 CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
1863 CTYPE ("Preprocessor information: use cpp syntax.");
1864 CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
1865 STYPE ("include", opts->include, NULL);
1866 CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1867 STYPE ("define", opts->define, NULL);
1869 CCTYPE ("RUN CONTROL PARAMETERS");
1870 EETYPE("integrator", ir->eI, ei_names);
1871 CTYPE ("Start time and timestep in ps");
1872 RTYPE ("tinit", ir->init_t, 0.0);
1873 RTYPE ("dt", ir->delta_t, 0.001);
1874 STEPTYPE ("nsteps", ir->nsteps, 0);
1875 CTYPE ("For exact run continuation or redoing part of a run");
1876 STEPTYPE ("init-step", ir->init_step, 0);
1877 CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
1878 ITYPE ("simulation-part", ir->simulation_part, 1);
1879 CTYPE ("mode for center of mass motion removal");
1880 EETYPE("comm-mode", ir->comm_mode, ecm_names);
1881 CTYPE ("number of steps for center of mass motion removal");
1882 ITYPE ("nstcomm", ir->nstcomm, 100);
1883 CTYPE ("group(s) for center of mass motion removal");
1884 STYPE ("comm-grps", is->vcm, NULL);
1886 CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
1887 CTYPE ("Friction coefficient (amu/ps) and random seed");
1888 RTYPE ("bd-fric", ir->bd_fric, 0.0);
1889 STEPTYPE ("ld-seed", ir->ld_seed, -1);
1892 CCTYPE ("ENERGY MINIMIZATION OPTIONS");
1893 CTYPE ("Force tolerance and initial step-size");
1894 RTYPE ("emtol", ir->em_tol, 10.0);
1895 RTYPE ("emstep", ir->em_stepsize, 0.01);
1896 CTYPE ("Max number of iterations in relax-shells");
1897 ITYPE ("niter", ir->niter, 20);
1898 CTYPE ("Step size (ps^2) for minimization of flexible constraints");
1899 RTYPE ("fcstep", ir->fc_stepsize, 0);
1900 CTYPE ("Frequency of steepest descents steps when doing CG");
1901 ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
1902 ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
1904 CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
1905 RTYPE ("rtpi", ir->rtpi, 0.05);
1907 /* Output options */
1908 CCTYPE ("OUTPUT CONTROL OPTIONS");
1909 CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
1910 ITYPE ("nstxout", ir->nstxout, 0);
1911 ITYPE ("nstvout", ir->nstvout, 0);
1912 ITYPE ("nstfout", ir->nstfout, 0);
1913 CTYPE ("Output frequency for energies to log file and energy file");
1914 ITYPE ("nstlog", ir->nstlog, 1000);
1915 ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
1916 ITYPE ("nstenergy", ir->nstenergy, 1000);
1917 CTYPE ("Output frequency and precision for .xtc file");
1918 ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
1919 RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
1920 CTYPE ("This selects the subset of atoms for the compressed");
1921 CTYPE ("trajectory file. You can select multiple groups. By");
1922 CTYPE ("default, all atoms will be written.");
1923 STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
1924 CTYPE ("Selection of energy groups");
1925 STYPE ("energygrps", is->energy, NULL);
1927 /* Neighbor searching */
1928 CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
1929 CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1930 EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
1931 CTYPE ("nblist update frequency");
1932 ITYPE ("nstlist", ir->nstlist, 10);
1933 CTYPE ("ns algorithm (simple or grid)");
1934 EETYPE("ns-type", ir->ns_type, ens_names);
1935 CTYPE ("Periodic boundary conditions: xyz, no, xy");
1936 EETYPE("pbc", ir->ePBC, epbc_names);
1937 EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
1938 CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1939 CTYPE ("a value of -1 means: use rlist");
1940 RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
1941 CTYPE ("nblist cut-off");
1942 RTYPE ("rlist", ir->rlist, 1.0);
1943 CTYPE ("long-range cut-off for switched potentials");
1944 RTYPE ("rlistlong", ir->rlistlong, -1);
1945 ITYPE ("nstcalclr", ir->nstcalclr, -1);
1947 /* Electrostatics */
1948 CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
1949 CTYPE ("Method for doing electrostatics");
1950 EETYPE("coulombtype", ir->coulombtype, eel_names);
1951 EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
1952 CTYPE ("cut-off lengths");
1953 RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
1954 RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
1955 CTYPE ("Relative dielectric constant for the medium and the reaction field");
1956 RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
1957 RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
1958 CTYPE ("Method for doing Van der Waals");
1959 EETYPE("vdw-type", ir->vdwtype, evdw_names);
1960 EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
1961 CTYPE ("cut-off lengths");
1962 RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
1963 RTYPE ("rvdw", ir->rvdw, 1.0);
1964 CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
1965 EETYPE("DispCorr", ir->eDispCorr, edispc_names);
1966 CTYPE ("Extension of the potential lookup tables beyond the cut-off");
1967 RTYPE ("table-extension", ir->tabext, 1.0);
1968 CTYPE ("Separate tables between energy group pairs");
1969 STYPE ("energygrp-table", is->egptable, NULL);
1970 CTYPE ("Spacing for the PME/PPPM FFT grid");
1971 RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
1972 CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
1973 ITYPE ("fourier-nx", ir->nkx, 0);
1974 ITYPE ("fourier-ny", ir->nky, 0);
1975 ITYPE ("fourier-nz", ir->nkz, 0);
1976 CTYPE ("EWALD/PME/PPPM parameters");
1977 ITYPE ("pme-order", ir->pme_order, 4);
1978 RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
1979 RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
1980 EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
1981 EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
1982 RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
1984 CCTYPE("IMPLICIT SOLVENT ALGORITHM");
1985 EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
1987 CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
1988 CTYPE ("Algorithm for calculating Born radii");
1989 EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
1990 CTYPE ("Frequency of calculating the Born radii inside rlist");
1991 ITYPE ("nstgbradii", ir->nstgbradii, 1);
1992 CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
1993 CTYPE ("between rlist and rgbradii is updated every nstlist steps");
1994 RTYPE ("rgbradii", ir->rgbradii, 1.0);
1995 CTYPE ("Dielectric coefficient of the implicit solvent");
1996 RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
1997 CTYPE ("Salt concentration in M for Generalized Born models");
1998 RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
1999 CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
2000 RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
2001 RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
2002 RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
2003 RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
2004 EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
2005 CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
2006 CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
2007 RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
2009 /* Coupling stuff */
2010 CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
2011 CTYPE ("Temperature coupling");
2012 EETYPE("tcoupl", ir->etc, etcoupl_names);
2013 ITYPE ("nsttcouple", ir->nsttcouple, -1);
2014 ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
2015 EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
2016 CTYPE ("Groups to couple separately");
2017 STYPE ("tc-grps", is->tcgrps, NULL);
2018 CTYPE ("Time constant (ps) and reference temperature (K)");
2019 STYPE ("tau-t", is->tau_t, NULL);
2020 STYPE ("ref-t", is->ref_t, NULL);
2021 CTYPE ("pressure coupling");
2022 EETYPE("pcoupl", ir->epc, epcoupl_names);
2023 EETYPE("pcoupltype", ir->epct, epcoupltype_names);
2024 ITYPE ("nstpcouple", ir->nstpcouple, -1);
2025 CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
2026 RTYPE ("tau-p", ir->tau_p, 1.0);
2027 STYPE ("compressibility", dumstr[0], NULL);
2028 STYPE ("ref-p", dumstr[1], NULL);
2029 CTYPE ("Scaling of reference coordinates, No, All or COM");
2030 EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
2033 CCTYPE ("OPTIONS FOR QMMM calculations");
2034 EETYPE("QMMM", ir->bQMMM, yesno_names);
2035 CTYPE ("Groups treated Quantum Mechanically");
2036 STYPE ("QMMM-grps", is->QMMM, NULL);
2037 CTYPE ("QM method");
2038 STYPE("QMmethod", is->QMmethod, NULL);
2039 CTYPE ("QMMM scheme");
2040 EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
2041 CTYPE ("QM basisset");
2042 STYPE("QMbasis", is->QMbasis, NULL);
2043 CTYPE ("QM charge");
2044 STYPE ("QMcharge", is->QMcharge, NULL);
2045 CTYPE ("QM multiplicity");
2046 STYPE ("QMmult", is->QMmult, NULL);
2047 CTYPE ("Surface Hopping");
2048 STYPE ("SH", is->bSH, NULL);
2049 CTYPE ("CAS space options");
2050 STYPE ("CASorbitals", is->CASorbitals, NULL);
2051 STYPE ("CASelectrons", is->CASelectrons, NULL);
2052 STYPE ("SAon", is->SAon, NULL);
2053 STYPE ("SAoff", is->SAoff, NULL);
2054 STYPE ("SAsteps", is->SAsteps, NULL);
2055 CTYPE ("Scale factor for MM charges");
2056 RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
2057 CTYPE ("Optimization of QM subsystem");
2058 STYPE ("bOPT", is->bOPT, NULL);
2059 STYPE ("bTS", is->bTS, NULL);
2061 /* Simulated annealing */
2062 CCTYPE("SIMULATED ANNEALING");
2063 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
2064 STYPE ("annealing", is->anneal, NULL);
2065 CTYPE ("Number of time points to use for specifying annealing in each group");
2066 STYPE ("annealing-npoints", is->anneal_npoints, NULL);
2067 CTYPE ("List of times at the annealing points for each group");
2068 STYPE ("annealing-time", is->anneal_time, NULL);
2069 CTYPE ("Temp. at each annealing point, for each group.");
2070 STYPE ("annealing-temp", is->anneal_temp, NULL);
2073 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
2074 EETYPE("gen-vel", opts->bGenVel, yesno_names);
2075 RTYPE ("gen-temp", opts->tempi, 300.0);
2076 ITYPE ("gen-seed", opts->seed, -1);
2079 CCTYPE ("OPTIONS FOR BONDS");
2080 EETYPE("constraints", opts->nshake, constraints);
2081 CTYPE ("Type of constraint algorithm");
2082 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
2083 CTYPE ("Do not constrain the start configuration");
2084 EETYPE("continuation", ir->bContinuation, yesno_names);
2085 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
2086 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
2087 CTYPE ("Relative tolerance of shake");
2088 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
2089 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
2090 ITYPE ("lincs-order", ir->nProjOrder, 4);
2091 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
2092 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
2093 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
2094 ITYPE ("lincs-iter", ir->nLincsIter, 1);
2095 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
2096 CTYPE ("rotates over more degrees than");
2097 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
2098 CTYPE ("Convert harmonic bonds to morse potentials");
2099 EETYPE("morse", opts->bMorse, yesno_names);
2101 /* Energy group exclusions */
2102 CCTYPE ("ENERGY GROUP EXCLUSIONS");
2103 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
2104 STYPE ("energygrp-excl", is->egpexcl, NULL);
2108 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2109 ITYPE ("nwall", ir->nwall, 0);
2110 EETYPE("wall-type", ir->wall_type, ewt_names);
2111 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
2112 STYPE ("wall-atomtype", is->wall_atomtype, NULL);
2113 STYPE ("wall-density", is->wall_density, NULL);
2114 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
2117 CCTYPE("COM PULLING");
2118 EETYPE("pull", ir->bPull, yesno_names);
2122 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, wi);
2125 /* Enforced rotation */
2126 CCTYPE("ENFORCED ROTATION");
2127 CTYPE("Enforced rotation: No or Yes");
2128 EETYPE("rotation", ir->bRot, yesno_names);
2132 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2135 /* Interactive MD */
2137 CCTYPE("Group to display and/or manipulate in interactive MD session");
2138 STYPE ("IMD-group", is->imd_grp, NULL);
2139 if (is->imd_grp[0] != '\0')
2146 CCTYPE("NMR refinement stuff");
2147 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2148 EETYPE("disre", ir->eDisre, edisre_names);
2149 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2150 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2151 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2152 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2153 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2154 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2155 CTYPE ("Output frequency for pair distances to energy file");
2156 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2157 CTYPE ("Orientation restraints: No or Yes");
2158 EETYPE("orire", opts->bOrire, yesno_names);
2159 CTYPE ("Orientation restraints force constant and tau for time averaging");
2160 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2161 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2162 STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
2163 CTYPE ("Output frequency for trace(SD) and S to energy file");
2164 ITYPE ("nstorireout", ir->nstorireout, 100);
2166 /* free energy variables */
2167 CCTYPE ("Free energy variables");
2168 EETYPE("free-energy", ir->efep, efep_names);
2169 STYPE ("couple-moltype", is->couple_moltype, NULL);
2170 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2171 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2172 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2174 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2176 it was not entered */
2177 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2178 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2179 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2180 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
2181 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
2182 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
2183 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
2184 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
2185 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
2186 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
2187 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2188 STYPE ("init-lambda-weights", is->lambda_weights, NULL);
2189 EETYPE("dhdl-print-energy", fep->edHdLPrintEnergy, edHdLPrintEnergy_names);
2190 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2191 ITYPE ("sc-power", fep->sc_power, 1);
2192 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2193 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2194 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2195 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2196 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2197 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2198 separate_dhdl_file_names);
2199 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2200 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2201 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2203 /* Non-equilibrium MD stuff */
2204 CCTYPE("Non-equilibrium MD stuff");
2205 STYPE ("acc-grps", is->accgrps, NULL);
2206 STYPE ("accelerate", is->acc, NULL);
2207 STYPE ("freezegrps", is->freeze, NULL);
2208 STYPE ("freezedim", is->frdim, NULL);
2209 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2210 STYPE ("deform", is->deform, NULL);
2212 /* simulated tempering variables */
2213 CCTYPE("simulated tempering variables");
2214 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2215 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2216 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2217 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2219 /* expanded ensemble variables */
2220 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2222 read_expandedparams(&ninp, &inp, expand, wi);
2225 /* Electric fields */
2226 CCTYPE("Electric fields");
2227 CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
2228 CTYPE ("and a phase angle (real)");
2229 STYPE ("E-x", is->efield_x, NULL);
2230 CTYPE ("Time dependent (pulsed) electric field. Format is omega, time for pulse");
2231 CTYPE ("peak, and sigma (width) for pulse. Sigma = 0 removes pulse, leaving");
2232 CTYPE ("the field to be a cosine function.");
2233 STYPE ("E-xt", is->efield_xt, NULL);
2234 STYPE ("E-y", is->efield_y, NULL);
2235 STYPE ("E-yt", is->efield_yt, NULL);
2236 STYPE ("E-z", is->efield_z, NULL);
2237 STYPE ("E-zt", is->efield_zt, NULL);
2239 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2240 CTYPE("Swap positions along direction: no, X, Y, Z");
2241 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2242 if (ir->eSwapCoords != eswapNO)
2245 CTYPE("Swap attempt frequency");
2246 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2247 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2248 STYPE("split-group0", splitgrp0, NULL);
2249 STYPE("split-group1", splitgrp1, NULL);
2250 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2251 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2252 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2254 CTYPE("Group name of ions that can be exchanged with solvent molecules");
2255 STYPE("swap-group", swapgrp, NULL);
2256 CTYPE("Group name of solvent molecules");
2257 STYPE("solvent-group", solgrp, NULL);
2259 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2260 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2261 CTYPE("however, if correctly defined, the ion permeation events are counted per channel");
2262 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2263 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2264 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2265 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2266 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2267 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2269 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2270 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2271 CTYPE("Requested number of anions and cations for each of the two compartments");
2272 CTYPE("-1 means fix the numbers as found in time step 0");
2273 ITYPE("anionsA", ir->swap->nanions[0], -1);
2274 ITYPE("cationsA", ir->swap->ncations[0], -1);
2275 ITYPE("anionsB", ir->swap->nanions[1], -1);
2276 ITYPE("cationsB", ir->swap->ncations[1], -1);
2277 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2278 RTYPE("threshold", ir->swap->threshold, 1.0);
2281 /* AdResS defined thingies */
2282 CCTYPE ("AdResS parameters");
2283 EETYPE("adress", ir->bAdress, yesno_names);
2286 snew(ir->adress, 1);
2287 read_adressparams(&ninp, &inp, ir->adress, wi);
2290 /* User defined thingies */
2291 CCTYPE ("User defined thingies");
2292 STYPE ("user1-grps", is->user1, NULL);
2293 STYPE ("user2-grps", is->user2, NULL);
2294 ITYPE ("userint1", ir->userint1, 0);
2295 ITYPE ("userint2", ir->userint2, 0);
2296 ITYPE ("userint3", ir->userint3, 0);
2297 ITYPE ("userint4", ir->userint4, 0);
2298 RTYPE ("userreal1", ir->userreal1, 0);
2299 RTYPE ("userreal2", ir->userreal2, 0);
2300 RTYPE ("userreal3", ir->userreal3, 0);
2301 RTYPE ("userreal4", ir->userreal4, 0);
2304 write_inpfile(mdparout, ninp, inp, FALSE, wi);
2305 for (i = 0; (i < ninp); i++)
2308 sfree(inp[i].value);
2312 /* Process options if necessary */
2313 for (m = 0; m < 2; m++)
2315 for (i = 0; i < 2*DIM; i++)
2324 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2326 warning_error(wi, "Pressure coupling not enough values (I need 1)");
2328 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2330 case epctSEMIISOTROPIC:
2331 case epctSURFACETENSION:
2332 if (sscanf(dumstr[m], "%lf%lf",
2333 &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2335 warning_error(wi, "Pressure coupling not enough values (I need 2)");
2337 dumdub[m][YY] = dumdub[m][XX];
2339 case epctANISOTROPIC:
2340 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2341 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2342 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2344 warning_error(wi, "Pressure coupling not enough values (I need 6)");
2348 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2349 epcoupltype_names[ir->epct]);
2353 clear_mat(ir->ref_p);
2354 clear_mat(ir->compress);
2355 for (i = 0; i < DIM; i++)
2357 ir->ref_p[i][i] = dumdub[1][i];
2358 ir->compress[i][i] = dumdub[0][i];
2360 if (ir->epct == epctANISOTROPIC)
2362 ir->ref_p[XX][YY] = dumdub[1][3];
2363 ir->ref_p[XX][ZZ] = dumdub[1][4];
2364 ir->ref_p[YY][ZZ] = dumdub[1][5];
2365 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2367 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2369 ir->compress[XX][YY] = dumdub[0][3];
2370 ir->compress[XX][ZZ] = dumdub[0][4];
2371 ir->compress[YY][ZZ] = dumdub[0][5];
2372 for (i = 0; i < DIM; i++)
2374 for (m = 0; m < i; m++)
2376 ir->ref_p[i][m] = ir->ref_p[m][i];
2377 ir->compress[i][m] = ir->compress[m][i];
2382 if (ir->comm_mode == ecmNO)
2387 opts->couple_moltype = NULL;
2388 if (strlen(is->couple_moltype) > 0)
2390 if (ir->efep != efepNO)
2392 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2393 if (opts->couple_lam0 == opts->couple_lam1)
2395 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2397 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2398 opts->couple_lam1 == ecouplamNONE))
2400 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2405 warning_note(wi, "Free energy is turned off, so we will not decouple the molecule listed in your input.");
2408 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2409 if (ir->efep != efepNO)
2411 if (fep->delta_lambda > 0)
2413 ir->efep = efepSLOWGROWTH;
2417 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2419 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2420 warning_note(wi, "Old option for dhdl-print-energy given: "
2421 "changing \"yes\" to \"total\"\n");
2424 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2426 /* always print out the energy to dhdl if we are doing
2427 expanded ensemble, since we need the total energy for
2428 analysis if the temperature is changing. In some
2429 conditions one may only want the potential energy, so
2430 we will allow that if the appropriate mdp setting has
2431 been enabled. Otherwise, total it is:
2433 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2436 if ((ir->efep != efepNO) || ir->bSimTemp)
2438 ir->bExpanded = FALSE;
2439 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2441 ir->bExpanded = TRUE;
2443 do_fep_params(ir, is->fep_lambda, is->lambda_weights);
2444 if (ir->bSimTemp) /* done after fep params */
2446 do_simtemp_params(ir);
2449 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2450 * setup and not on the old way of specifying the free-energy setup,
2451 * we should check for using soft-core when not needed, since that
2452 * can complicate the sampling significantly.
2453 * Note that we only check for the automated coupling setup.
2454 * If the (advanced) user does FEP through manual topology changes,
2455 * this check will not be triggered.
2457 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 &&
2458 ir->fepvals->sc_alpha != 0 &&
2459 (couple_lambda_has_vdw_on(opts->couple_lam0) &&
2460 couple_lambda_has_vdw_on(opts->couple_lam1)))
2462 warning(wi, "You are using soft-core interactions while the Van der Waals interactions are not decoupled (note that the sc-coul option is only active when using lambda states). Although this will not lead to errors, you will need much more sampling than without soft-core interactions. Consider using sc-alpha=0.");
2467 ir->fepvals->n_lambda = 0;
2470 /* WALL PARAMETERS */
2472 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2474 /* ORIENTATION RESTRAINT PARAMETERS */
2476 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
2478 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2481 /* DEFORMATION PARAMETERS */
2483 clear_mat(ir->deform);
2484 for (i = 0; i < 6; i++)
2488 m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
2489 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2490 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2491 for (i = 0; i < 3; i++)
2493 ir->deform[i][i] = dumdub[0][i];
2495 ir->deform[YY][XX] = dumdub[0][3];
2496 ir->deform[ZZ][XX] = dumdub[0][4];
2497 ir->deform[ZZ][YY] = dumdub[0][5];
2498 if (ir->epc != epcNO)
2500 for (i = 0; i < 3; i++)
2502 for (j = 0; j <= i; j++)
2504 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2506 warning_error(wi, "A box element has deform set and compressibility > 0");
2510 for (i = 0; i < 3; i++)
2512 for (j = 0; j < i; j++)
2514 if (ir->deform[i][j] != 0)
2516 for (m = j; m < DIM; m++)
2518 if (ir->compress[m][j] != 0)
2520 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.");
2521 warning(wi, warn_buf);
2529 /* Ion/water position swapping checks */
2530 if (ir->eSwapCoords != eswapNO)
2532 if (ir->swap->nstswap < 1)
2534 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2536 if (ir->swap->nAverage < 1)
2538 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2540 if (ir->swap->threshold < 1.0)
2542 warning_error(wi, "Ion count threshold must be at least 1.\n");
2550 static int search_QMstring(const char *s, int ng, const char *gn[])
2552 /* same as normal search_string, but this one searches QM strings */
2555 for (i = 0; (i < ng); i++)
2557 if (gmx_strcasecmp(s, gn[i]) == 0)
2563 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2567 } /* search_QMstring */
2569 /* We would like gn to be const as well, but C doesn't allow this */
2570 /* TODO this is utility functionality (search for the index of a
2571 string in a collection), so should be refactored and located more
2573 int search_string(const char *s, int ng, char *gn[])
2577 for (i = 0; (i < ng); i++)
2579 if (gmx_strcasecmp(s, gn[i]) == 0)
2586 "Group %s referenced in the .mdp file was not found in the index file.\n"
2587 "Group names must match either [moleculetype] names or custom index group\n"
2588 "names, in which case you must supply an index file to the '-n' option\n"
2595 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2596 t_blocka *block, char *gnames[],
2597 int gtype, int restnm,
2598 int grptp, gmx_bool bVerbose,
2601 unsigned short *cbuf;
2602 t_grps *grps = &(groups->grps[gtype]);
2603 int i, j, gid, aj, ognr, ntot = 0;
2606 char warn_buf[STRLEN];
2610 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2613 title = gtypes[gtype];
2616 /* Mark all id's as not set */
2617 for (i = 0; (i < natoms); i++)
2622 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2623 for (i = 0; (i < ng); i++)
2625 /* Lookup the group name in the block structure */
2626 gid = search_string(ptrs[i], block->nr, gnames);
2627 if ((grptp != egrptpONE) || (i == 0))
2629 grps->nm_ind[grps->nr++] = gid;
2633 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2636 /* Now go over the atoms in the group */
2637 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2642 /* Range checking */
2643 if ((aj < 0) || (aj >= natoms))
2645 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2647 /* Lookup up the old group number */
2651 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2652 aj+1, title, ognr+1, i+1);
2656 /* Store the group number in buffer */
2657 if (grptp == egrptpONE)
2670 /* Now check whether we have done all atoms */
2674 if (grptp == egrptpALL)
2676 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2677 natoms-ntot, title);
2679 else if (grptp == egrptpPART)
2681 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2682 natoms-ntot, title);
2683 warning_note(wi, warn_buf);
2685 /* Assign all atoms currently unassigned to a rest group */
2686 for (j = 0; (j < natoms); j++)
2688 if (cbuf[j] == NOGID)
2694 if (grptp != egrptpPART)
2699 "Making dummy/rest group for %s containing %d elements\n",
2700 title, natoms-ntot);
2702 /* Add group name "rest" */
2703 grps->nm_ind[grps->nr] = restnm;
2705 /* Assign the rest name to all atoms not currently assigned to a group */
2706 for (j = 0; (j < natoms); j++)
2708 if (cbuf[j] == NOGID)
2717 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2719 /* All atoms are part of one (or no) group, no index required */
2720 groups->ngrpnr[gtype] = 0;
2721 groups->grpnr[gtype] = NULL;
2725 groups->ngrpnr[gtype] = natoms;
2726 snew(groups->grpnr[gtype], natoms);
2727 for (j = 0; (j < natoms); j++)
2729 groups->grpnr[gtype][j] = cbuf[j];
2735 return (bRest && grptp == egrptpPART);
2738 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2741 gmx_groups_t *groups;
2742 pull_params_t *pull;
2743 int natoms, ai, aj, i, j, d, g, imin, jmin;
2745 int *nrdf2, *na_vcm, na_tot;
2746 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2747 gmx_mtop_atomloop_all_t aloop;
2749 int mb, mol, ftype, as;
2750 gmx_molblock_t *molb;
2751 gmx_moltype_t *molt;
2754 * First calc 3xnr-atoms for each group
2755 * then subtract half a degree of freedom for each constraint
2757 * Only atoms and nuclei contribute to the degrees of freedom...
2762 groups = &mtop->groups;
2763 natoms = mtop->natoms;
2765 /* Allocate one more for a possible rest group */
2766 /* We need to sum degrees of freedom into doubles,
2767 * since floats give too low nrdf's above 3 million atoms.
2769 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2770 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2771 snew(na_vcm, groups->grps[egcVCM].nr+1);
2773 for (i = 0; i < groups->grps[egcTC].nr; i++)
2777 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2782 snew(nrdf2, natoms);
2783 aloop = gmx_mtop_atomloop_all_init(mtop);
2784 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2787 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2789 g = ggrpnr(groups, egcFREEZE, i);
2790 /* Double count nrdf for particle i */
2791 for (d = 0; d < DIM; d++)
2793 if (opts->nFreeze[g][d] == 0)
2798 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2799 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2804 for (mb = 0; mb < mtop->nmolblock; mb++)
2806 molb = &mtop->molblock[mb];
2807 molt = &mtop->moltype[molb->type];
2808 atom = molt->atoms.atom;
2809 for (mol = 0; mol < molb->nmol; mol++)
2811 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2813 ia = molt->ilist[ftype].iatoms;
2814 for (i = 0; i < molt->ilist[ftype].nr; )
2816 /* Subtract degrees of freedom for the constraints,
2817 * if the particles still have degrees of freedom left.
2818 * If one of the particles is a vsite or a shell, then all
2819 * constraint motion will go there, but since they do not
2820 * contribute to the constraints the degrees of freedom do not
2825 if (((atom[ia[1]].ptype == eptNucleus) ||
2826 (atom[ia[1]].ptype == eptAtom)) &&
2827 ((atom[ia[2]].ptype == eptNucleus) ||
2828 (atom[ia[2]].ptype == eptAtom)))
2846 imin = min(imin, nrdf2[ai]);
2847 jmin = min(jmin, nrdf2[aj]);
2850 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2851 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2852 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2853 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2855 ia += interaction_function[ftype].nratoms+1;
2856 i += interaction_function[ftype].nratoms+1;
2859 ia = molt->ilist[F_SETTLE].iatoms;
2860 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2862 /* Subtract 1 dof from every atom in the SETTLE */
2863 for (j = 0; j < 3; j++)
2866 imin = min(2, nrdf2[ai]);
2868 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2869 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2874 as += molt->atoms.nr;
2880 /* Correct nrdf for the COM constraints.
2881 * We correct using the TC and VCM group of the first atom
2882 * in the reference and pull group. If atoms in one pull group
2883 * belong to different TC or VCM groups it is anyhow difficult
2884 * to determine the optimal nrdf assignment.
2888 for (i = 0; i < pull->ncoord; i++)
2890 if (pull->coord[i].eType != epullCONSTRAINT)
2897 for (j = 0; j < 2; j++)
2899 const t_pull_group *pgrp;
2901 pgrp = &pull->group[pull->coord[i].group[j]];
2905 /* Subtract 1/2 dof from each group */
2907 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2908 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2909 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2911 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)]]);
2916 /* We need to subtract the whole DOF from group j=1 */
2923 if (ir->nstcomm != 0)
2925 /* Subtract 3 from the number of degrees of freedom in each vcm group
2926 * when com translation is removed and 6 when rotation is removed
2929 switch (ir->comm_mode)
2932 n_sub = ndof_com(ir);
2939 gmx_incons("Checking comm_mode");
2942 for (i = 0; i < groups->grps[egcTC].nr; i++)
2944 /* Count the number of atoms of TC group i for every VCM group */
2945 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2950 for (ai = 0; ai < natoms; ai++)
2952 if (ggrpnr(groups, egcTC, ai) == i)
2954 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2958 /* Correct for VCM removal according to the fraction of each VCM
2959 * group present in this TC group.
2961 nrdf_uc = nrdf_tc[i];
2964 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2968 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2970 if (nrdf_vcm[j] > n_sub)
2972 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2973 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2977 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2978 j, nrdf_vcm[j], nrdf_tc[i]);
2983 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2985 opts->nrdf[i] = nrdf_tc[i];
2986 if (opts->nrdf[i] < 0)
2991 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2992 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
3001 static void decode_cos(char *s, t_cosines *cosine)
3004 char format[STRLEN], f1[STRLEN];
3016 sscanf(t, "%d", &(cosine->n));
3023 snew(cosine->a, cosine->n);
3024 snew(cosine->phi, cosine->n);
3026 sprintf(format, "%%*d");
3027 for (i = 0; (i < cosine->n); i++)
3030 strcat(f1, "%lf%lf");
3031 if (sscanf(t, f1, &a, &phi) < 2)
3033 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
3036 cosine->phi[i] = phi;
3037 strcat(format, "%*lf%*lf");
3044 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
3045 const char *option, const char *val, int flag)
3047 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3048 * But since this is much larger than STRLEN, such a line can not be parsed.
3049 * The real maximum is the number of names that fit in a string: STRLEN/2.
3051 #define EGP_MAX (STRLEN/2)
3052 int nelem, i, j, k, nr;
3053 char *names[EGP_MAX];
3057 gnames = groups->grpname;
3059 nelem = str_nelem(val, EGP_MAX, names);
3062 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3064 nr = groups->grps[egcENER].nr;
3066 for (i = 0; i < nelem/2; i++)
3070 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
3076 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3077 names[2*i], option);
3081 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
3087 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3088 names[2*i+1], option);
3090 if ((j < nr) && (k < nr))
3092 ir->opts.egp_flags[nr*j+k] |= flag;
3093 ir->opts.egp_flags[nr*k+j] |= flag;
3102 static void make_swap_groups(
3111 int ig = -1, i = 0, j;
3115 /* Just a quick check here, more thorough checks are in mdrun */
3116 if (strcmp(splitg0name, splitg1name) == 0)
3118 gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
3121 /* First get the swap group index atoms */
3122 ig = search_string(swapgname, grps->nr, gnames);
3123 swap->nat = grps->index[ig+1] - grps->index[ig];
3126 fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
3127 snew(swap->ind, swap->nat);
3128 for (i = 0; i < swap->nat; i++)
3130 swap->ind[i] = grps->a[grps->index[ig]+i];
3135 gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
3138 /* Now do so for the split groups */
3139 for (j = 0; j < 2; j++)
3143 splitg = splitg0name;
3147 splitg = splitg1name;
3150 ig = search_string(splitg, grps->nr, gnames);
3151 swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
3152 if (swap->nat_split[j] > 0)
3154 fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
3155 j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
3156 snew(swap->ind_split[j], swap->nat_split[j]);
3157 for (i = 0; i < swap->nat_split[j]; i++)
3159 swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
3164 gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
3168 /* Now get the solvent group index atoms */
3169 ig = search_string(solgname, grps->nr, gnames);
3170 swap->nat_sol = grps->index[ig+1] - grps->index[ig];
3171 if (swap->nat_sol > 0)
3173 fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
3174 snew(swap->ind_sol, swap->nat_sol);
3175 for (i = 0; i < swap->nat_sol; i++)
3177 swap->ind_sol[i] = grps->a[grps->index[ig]+i];
3182 gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
3187 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3192 ig = search_string(IMDgname, grps->nr, gnames);
3193 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3195 if (IMDgroup->nat > 0)
3197 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3198 IMDgname, IMDgroup->nat);
3199 snew(IMDgroup->ind, IMDgroup->nat);
3200 for (i = 0; i < IMDgroup->nat; i++)
3202 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3208 void do_index(const char* mdparin, const char *ndx,
3211 t_inputrec *ir, rvec *v,
3215 gmx_groups_t *groups;
3219 char warnbuf[STRLEN], **gnames;
3220 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3223 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3224 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3225 int i, j, k, restnm;
3227 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3228 int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
3229 nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
3230 char warn_buf[STRLEN];
3234 fprintf(stderr, "processing index file...\n");
3240 snew(grps->index, 1);
3242 atoms_all = gmx_mtop_global_atoms(mtop);
3243 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3244 free_t_atoms(&atoms_all, FALSE);
3248 grps = init_index(ndx, &gnames);
3251 groups = &mtop->groups;
3252 natoms = mtop->natoms;
3253 symtab = &mtop->symtab;
3255 snew(groups->grpname, grps->nr+1);
3257 for (i = 0; (i < grps->nr); i++)
3259 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3261 groups->grpname[i] = put_symtab(symtab, "rest");
3263 srenew(gnames, grps->nr+1);
3264 gnames[restnm] = *(groups->grpname[i]);
3265 groups->ngrpname = grps->nr+1;
3267 set_warning_line(wi, mdparin, -1);
3269 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3270 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3271 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3272 if ((ntau_t != ntcg) || (nref_t != ntcg))
3274 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3275 "%d tau-t values", ntcg, nref_t, ntau_t);
3278 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3279 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3280 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3281 nr = groups->grps[egcTC].nr;
3283 snew(ir->opts.nrdf, nr);
3284 snew(ir->opts.tau_t, nr);
3285 snew(ir->opts.ref_t, nr);
3286 if (ir->eI == eiBD && ir->bd_fric == 0)
3288 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3295 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3299 for (i = 0; (i < nr); i++)
3301 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
3302 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
3304 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3305 warning_error(wi, warn_buf);
3308 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3310 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.");
3313 if (ir->opts.tau_t[i] >= 0)
3315 tau_min = min(tau_min, ir->opts.tau_t[i]);
3318 if (ir->etc != etcNO && ir->nsttcouple == -1)
3320 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3325 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3327 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");
3329 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
3331 if (ir->nstpcouple != ir->nsttcouple)
3333 int mincouple = min(ir->nstpcouple, ir->nsttcouple);
3334 ir->nstpcouple = ir->nsttcouple = mincouple;
3335 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);
3336 warning_note(wi, warn_buf);
3340 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3341 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3343 if (ETC_ANDERSEN(ir->etc))
3345 if (ir->nsttcouple != 1)
3348 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");
3349 warning_note(wi, warn_buf);
3352 nstcmin = tcouple_min_integration_steps(ir->etc);
3355 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin - 10*GMX_REAL_EPS)
3357 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3358 ETCOUPLTYPE(ir->etc),
3360 ir->nsttcouple*ir->delta_t);
3361 warning(wi, warn_buf);
3364 for (i = 0; (i < nr); i++)
3366 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
3367 if (ir->opts.ref_t[i] < 0)
3369 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3372 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3373 if we are in this conditional) if mc_temp is negative */
3374 if (ir->expandedvals->mc_temp < 0)
3376 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3380 /* Simulated annealing for each group. There are nr groups */
3381 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3382 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3386 if (nSA > 0 && nSA != nr)
3388 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3392 snew(ir->opts.annealing, nr);
3393 snew(ir->opts.anneal_npoints, nr);
3394 snew(ir->opts.anneal_time, nr);
3395 snew(ir->opts.anneal_temp, nr);
3396 for (i = 0; i < nr; i++)
3398 ir->opts.annealing[i] = eannNO;
3399 ir->opts.anneal_npoints[i] = 0;
3400 ir->opts.anneal_time[i] = NULL;
3401 ir->opts.anneal_temp[i] = NULL;
3406 for (i = 0; i < nr; i++)
3408 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3410 ir->opts.annealing[i] = eannNO;
3412 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3414 ir->opts.annealing[i] = eannSINGLE;
3417 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3419 ir->opts.annealing[i] = eannPERIODIC;
3425 /* Read the other fields too */
3426 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3427 if (nSA_points != nSA)
3429 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3431 for (k = 0, i = 0; i < nr; i++)
3433 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3434 if (ir->opts.anneal_npoints[i] == 1)
3436 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3438 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3439 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3440 k += ir->opts.anneal_npoints[i];
3443 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3446 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3448 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3451 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3454 for (i = 0, k = 0; i < nr; i++)
3457 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3459 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3460 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3463 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3465 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3471 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3473 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3474 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3477 if (ir->opts.anneal_temp[i][j] < 0)
3479 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3484 /* Print out some summary information, to make sure we got it right */
3485 for (i = 0, k = 0; i < nr; i++)
3487 if (ir->opts.annealing[i] != eannNO)
3489 j = groups->grps[egcTC].nm_ind[i];
3490 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3491 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3492 ir->opts.anneal_npoints[i]);
3493 fprintf(stderr, "Time (ps) Temperature (K)\n");
3494 /* All terms except the last one */
3495 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3497 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3500 /* Finally the last one */
3501 j = ir->opts.anneal_npoints[i]-1;
3502 if (ir->opts.annealing[i] == eannSINGLE)
3504 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3508 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3509 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3511 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3522 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3524 make_pull_coords(ir->pull);
3529 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3532 if (ir->eSwapCoords != eswapNO)
3534 make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
3537 /* Make indices for IMD session */
3540 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3543 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3544 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3545 if (nacg*DIM != nacc)
3547 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3550 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3551 restnm, egrptpALL_GENREST, bVerbose, wi);
3552 nr = groups->grps[egcACC].nr;
3553 snew(ir->opts.acc, nr);
3554 ir->opts.ngacc = nr;
3556 for (i = k = 0; (i < nacg); i++)
3558 for (j = 0; (j < DIM); j++, k++)
3560 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3563 for (; (i < nr); i++)
3565 for (j = 0; (j < DIM); j++)
3567 ir->opts.acc[i][j] = 0;
3571 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3572 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3573 if (nfrdim != DIM*nfreeze)
3575 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3578 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3579 restnm, egrptpALL_GENREST, bVerbose, wi);
3580 nr = groups->grps[egcFREEZE].nr;
3581 ir->opts.ngfrz = nr;
3582 snew(ir->opts.nFreeze, nr);
3583 for (i = k = 0; (i < nfreeze); i++)
3585 for (j = 0; (j < DIM); j++, k++)
3587 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3588 if (!ir->opts.nFreeze[i][j])
3590 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3592 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3593 "(not %s)", ptr1[k]);
3594 warning(wi, warn_buf);
3599 for (; (i < nr); i++)
3601 for (j = 0; (j < DIM); j++)
3603 ir->opts.nFreeze[i][j] = 0;
3607 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3608 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3609 restnm, egrptpALL_GENREST, bVerbose, wi);
3610 add_wall_energrps(groups, ir->nwall, symtab);
3611 ir->opts.ngener = groups->grps[egcENER].nr;
3612 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3614 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3615 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3618 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3619 "This may lead to artifacts.\n"
3620 "In most cases one should use one group for the whole system.");
3623 /* Now we have filled the freeze struct, so we can calculate NRDF */
3624 calc_nrdf(mtop, ir, gnames);
3630 /* Must check per group! */
3631 for (i = 0; (i < ir->opts.ngtc); i++)
3633 ntot += ir->opts.nrdf[i];
3635 if (ntot != (DIM*natoms))
3637 fac = sqrt(ntot/(DIM*natoms));
3640 fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
3641 "and removal of center of mass motion\n", fac);
3643 for (i = 0; (i < natoms); i++)
3645 svmul(fac, v[i], v[i]);
3650 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3651 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3652 restnm, egrptpALL_GENREST, bVerbose, wi);
3653 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3654 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3655 restnm, egrptpALL_GENREST, bVerbose, wi);
3656 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3657 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3658 restnm, egrptpONE, bVerbose, wi);
3659 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3660 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3661 restnm, egrptpALL_GENREST, bVerbose, wi);
3663 /* QMMM input processing */
3664 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3665 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3666 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3667 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3669 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3670 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3672 /* group rest, if any, is always MM! */
3673 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3674 restnm, egrptpALL_GENREST, bVerbose, wi);
3675 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3676 ir->opts.ngQM = nQMg;
3677 snew(ir->opts.QMmethod, nr);
3678 snew(ir->opts.QMbasis, nr);
3679 for (i = 0; i < nr; i++)
3681 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3682 * converted to the corresponding enum in names.c
3684 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3686 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3690 nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
3691 nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
3692 nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
3693 snew(ir->opts.QMmult, nr);
3694 snew(ir->opts.QMcharge, nr);
3695 snew(ir->opts.bSH, nr);
3697 for (i = 0; i < nr; i++)
3699 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3700 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3701 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3704 nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
3705 nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
3706 snew(ir->opts.CASelectrons, nr);
3707 snew(ir->opts.CASorbitals, nr);
3708 for (i = 0; i < nr; i++)
3710 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3711 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3713 /* special optimization options */
3715 nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
3716 nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
3717 snew(ir->opts.bOPT, nr);
3718 snew(ir->opts.bTS, nr);
3719 for (i = 0; i < nr; i++)
3721 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3722 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3724 nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
3725 nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
3726 nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
3727 snew(ir->opts.SAon, nr);
3728 snew(ir->opts.SAoff, nr);
3729 snew(ir->opts.SAsteps, nr);
3731 for (i = 0; i < nr; i++)
3733 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3734 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3735 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3737 /* end of QMMM input */
3741 for (i = 0; (i < egcNR); i++)
3743 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3744 for (j = 0; (j < groups->grps[i].nr); j++)
3746 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3748 fprintf(stderr, "\n");
3752 nr = groups->grps[egcENER].nr;
3753 snew(ir->opts.egp_flags, nr*nr);
3755 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3756 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3758 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3760 if (bExcl && EEL_FULL(ir->coulombtype))
3762 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3765 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3766 if (bTable && !(ir->vdwtype == evdwUSER) &&
3767 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3768 !(ir->coulombtype == eelPMEUSERSWITCH))
3770 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3773 decode_cos(is->efield_x, &(ir->ex[XX]));
3774 decode_cos(is->efield_xt, &(ir->et[XX]));
3775 decode_cos(is->efield_y, &(ir->ex[YY]));
3776 decode_cos(is->efield_yt, &(ir->et[YY]));
3777 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3778 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3782 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3785 for (i = 0; (i < grps->nr); i++)
3797 static void check_disre(gmx_mtop_t *mtop)
3799 gmx_ffparams_t *ffparams;
3800 t_functype *functype;
3802 int i, ndouble, ftype;
3803 int label, old_label;
3805 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3807 ffparams = &mtop->ffparams;
3808 functype = ffparams->functype;
3809 ip = ffparams->iparams;
3812 for (i = 0; i < ffparams->ntypes; i++)
3814 ftype = functype[i];
3815 if (ftype == F_DISRES)
3817 label = ip[i].disres.label;
3818 if (label == old_label)
3820 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3828 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3829 "probably the parameters for multiple pairs in one restraint "
3830 "are not identical\n", ndouble);
3835 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3836 gmx_bool posres_only,
3840 gmx_mtop_ilistloop_t iloop;
3850 for (d = 0; d < DIM; d++)
3852 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3854 /* Check for freeze groups */
3855 for (g = 0; g < ir->opts.ngfrz; g++)
3857 for (d = 0; d < DIM; d++)
3859 if (ir->opts.nFreeze[g][d] != 0)
3867 /* Check for position restraints */
3868 iloop = gmx_mtop_ilistloop_init(sys);
3869 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3872 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3874 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3876 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3877 for (d = 0; d < DIM; d++)
3879 if (pr->posres.fcA[d] != 0)
3885 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3887 /* Check for flat-bottom posres */
3888 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3889 if (pr->fbposres.k != 0)
3891 switch (pr->fbposres.geom)
3893 case efbposresSPHERE:
3894 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3896 case efbposresCYLINDERX:
3897 AbsRef[YY] = AbsRef[ZZ] = 1;
3899 case efbposresCYLINDERY:
3900 AbsRef[XX] = AbsRef[ZZ] = 1;
3902 case efbposresCYLINDER:
3903 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3904 case efbposresCYLINDERZ:
3905 AbsRef[XX] = AbsRef[YY] = 1;
3907 case efbposresX: /* d=XX */
3908 case efbposresY: /* d=YY */
3909 case efbposresZ: /* d=ZZ */
3910 d = pr->fbposres.geom - efbposresX;
3914 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3915 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3923 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3927 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3928 gmx_bool *bC6ParametersWorkWithGeometricRules,
3929 gmx_bool *bC6ParametersWorkWithLBRules,
3930 gmx_bool *bLBRulesPossible)
3932 int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
3935 double geometricdiff, LBdiff;
3936 double c6i, c6j, c12i, c12j;
3937 double c6, c6_geometric, c6_LB;
3938 double sigmai, sigmaj, epsi, epsj;
3939 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3942 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3943 * force-field floating point parameters.
3946 ptr = getenv("GMX_LJCOMB_TOL");
3951 sscanf(ptr, "%lf", &dbl);
3955 *bC6ParametersWorkWithLBRules = TRUE;
3956 *bC6ParametersWorkWithGeometricRules = TRUE;
3957 bCanDoLBRules = TRUE;
3958 bCanDoGeometricRules = TRUE;
3959 ntypes = mtop->ffparams.atnr;
3960 snew(typecount, ntypes);
3961 gmx_mtop_count_atomtypes(mtop, state, typecount);
3962 geometricdiff = LBdiff = 0.0;
3963 *bLBRulesPossible = TRUE;
3964 for (tpi = 0; tpi < ntypes; ++tpi)
3966 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3967 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3968 for (tpj = tpi; tpj < ntypes; ++tpj)
3970 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3971 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3972 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3973 c6_geometric = sqrt(c6i * c6j);
3974 if (!gmx_numzero(c6_geometric))
3976 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3978 sigmai = pow(c12i / c6i, 1.0/6.0);
3979 sigmaj = pow(c12j / c6j, 1.0/6.0);
3980 epsi = c6i * c6i /(4.0 * c12i);
3981 epsj = c6j * c6j /(4.0 * c12j);
3982 c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
3986 *bLBRulesPossible = FALSE;
3987 c6_LB = c6_geometric;
3989 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3992 if (FALSE == bCanDoLBRules)
3994 *bC6ParametersWorkWithLBRules = FALSE;
3997 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3999 if (FALSE == bCanDoGeometricRules)
4001 *bC6ParametersWorkWithGeometricRules = FALSE;
4009 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
4013 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4015 check_combination_rule_differences(mtop, 0,
4016 &bC6ParametersWorkWithGeometricRules,
4017 &bC6ParametersWorkWithLBRules,
4019 if (ir->ljpme_combination_rule == eljpmeLB)
4021 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
4023 warning(wi, "You are using arithmetic-geometric combination rules "
4024 "in LJ-PME, but your non-bonded C6 parameters do not "
4025 "follow these rules.");
4030 if (FALSE == bC6ParametersWorkWithGeometricRules)
4032 if (ir->eDispCorr != edispcNO)
4034 warning_note(wi, "You are using geometric combination rules in "
4035 "LJ-PME, but your non-bonded C6 parameters do "
4036 "not follow these rules. "
4037 "This will introduce very small errors in the forces and energies in "
4038 "your simulations. Dispersion correction will correct total energy "
4039 "and/or pressure for isotropic systems, but not forces or surface tensions.");
4043 warning_note(wi, "You are using geometric combination rules in "
4044 "LJ-PME, but your non-bonded C6 parameters do "
4045 "not follow these rules. "
4046 "This will introduce very small errors in the forces and energies in "
4047 "your simulations. If your system is homogeneous, consider using dispersion correction "
4048 "for the total energy and pressure.");
4054 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
4057 char err_buf[STRLEN];
4058 int i, m, c, nmol, npct;
4059 gmx_bool bCharge, bAcc;
4060 real gdt_max, *mgrp, mt;
4062 gmx_mtop_atomloop_block_t aloopb;
4063 gmx_mtop_atomloop_all_t aloop;
4066 char warn_buf[STRLEN];
4068 set_warning_line(wi, mdparin, -1);
4070 if (ir->cutoff_scheme == ecutsVERLET &&
4071 ir->verletbuf_tol > 0 &&
4073 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
4074 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4076 /* Check if a too small Verlet buffer might potentially
4077 * cause more drift than the thermostat can couple off.
4079 /* Temperature error fraction for warning and suggestion */
4080 const real T_error_warn = 0.002;
4081 const real T_error_suggest = 0.001;
4082 /* For safety: 2 DOF per atom (typical with constraints) */
4083 const real nrdf_at = 2;
4084 real T, tau, max_T_error;
4089 for (i = 0; i < ir->opts.ngtc; i++)
4091 T = max(T, ir->opts.ref_t[i]);
4092 tau = max(tau, ir->opts.tau_t[i]);
4096 /* This is a worst case estimate of the temperature error,
4097 * assuming perfect buffer estimation and no cancelation
4098 * of errors. The factor 0.5 is because energy distributes
4099 * equally over Ekin and Epot.
4101 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4102 if (max_T_error > T_error_warn)
4104 sprintf(warn_buf, "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to %.0e or decrease tau_t.",
4105 ir->verletbuf_tol, T, tau,
4107 100*T_error_suggest,
4108 ir->verletbuf_tol*T_error_suggest/max_T_error);
4109 warning(wi, warn_buf);
4114 if (ETC_ANDERSEN(ir->etc))
4118 for (i = 0; i < ir->opts.ngtc; i++)
4120 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4121 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4122 sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
4123 i, ir->opts.tau_t[i]);
4124 CHECK(ir->opts.tau_t[i] < 0);
4127 for (i = 0; i < ir->opts.ngtc; i++)
4129 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
4130 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);
4131 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
4135 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4136 ir->comm_mode == ecmNO &&
4137 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4138 !ETC_ANDERSEN(ir->etc))
4140 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");
4143 /* Check for pressure coupling with absolute position restraints */
4144 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4146 absolute_reference(ir, sys, TRUE, AbsRef);
4148 for (m = 0; m < DIM; m++)
4150 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4152 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4160 aloopb = gmx_mtop_atomloop_block_init(sys);
4161 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4163 if (atom->q != 0 || atom->qB != 0)
4171 if (EEL_FULL(ir->coulombtype))
4174 "You are using full electrostatics treatment %s for a system without charges.\n"
4175 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4176 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4177 warning(wi, err_buf);
4182 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4185 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4186 "You might want to consider using %s electrostatics.\n",
4188 warning_note(wi, err_buf);
4192 /* Check if combination rules used in LJ-PME are the same as in the force field */
4193 if (EVDW_PME(ir->vdwtype))
4195 check_combination_rules(ir, sys, wi);
4198 /* Generalized reaction field */
4199 if (ir->opts.ngtc == 0)
4201 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4203 CHECK(ir->coulombtype == eelGRF);
4207 sprintf(err_buf, "When using coulombtype = %s"
4208 " ref-t for temperature coupling should be > 0",
4210 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4213 if (ir->eI == eiSD2)
4215 sprintf(warn_buf, "The stochastic dynamics integrator %s is deprecated, since\n"
4216 "it is slower than integrator %s and is slightly less accurate\n"
4217 "with constraints. Use the %s integrator.",
4218 ei_names[ir->eI], ei_names[eiSD1], ei_names[eiSD1]);
4219 warning_note(wi, warn_buf);
4223 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4225 for (m = 0; (m < DIM); m++)
4227 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4236 snew(mgrp, sys->groups.grps[egcACC].nr);
4237 aloop = gmx_mtop_atomloop_all_init(sys);
4238 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4240 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4243 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4245 for (m = 0; (m < DIM); m++)
4247 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4251 for (m = 0; (m < DIM); m++)
4253 if (fabs(acc[m]) > 1e-6)
4255 const char *dim[DIM] = { "X", "Y", "Z" };
4257 "Net Acceleration in %s direction, will %s be corrected\n",
4258 dim[m], ir->nstcomm != 0 ? "" : "not");
4259 if (ir->nstcomm != 0 && m < ndof_com(ir))
4262 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4264 ir->opts.acc[i][m] -= acc[m];
4272 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4273 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4275 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4283 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4285 if (ir->pull->coord[i].group[0] == 0 ||
4286 ir->pull->coord[i].group[1] == 0)
4288 absolute_reference(ir, sys, FALSE, AbsRef);
4289 for (m = 0; m < DIM; m++)
4291 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4293 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.");
4301 for (i = 0; i < 3; i++)
4303 for (m = 0; m <= i; m++)
4305 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4306 ir->deform[i][m] != 0)
4308 for (c = 0; c < ir->pull->ncoord; c++)
4310 if (ir->pull->coord[c].eGeom == epullgDIRPBC &&
4311 ir->pull->coord[c].vec[m] != 0)
4313 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->coord[c].eGeom), 'x'+m);
4324 void double_check(t_inputrec *ir, matrix box,
4325 gmx_bool bHasNormalConstraints,
4326 gmx_bool bHasAnyConstraints,
4331 char warn_buf[STRLEN];
4334 ptr = check_box(ir->ePBC, box);
4337 warning_error(wi, ptr);
4340 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4342 if (ir->shake_tol <= 0.0)
4344 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4346 warning_error(wi, warn_buf);
4349 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
4351 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
4352 if (ir->epc == epcNO)
4354 warning(wi, warn_buf);
4358 warning_error(wi, warn_buf);
4363 if ( (ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4365 /* If we have Lincs constraints: */
4366 if (ir->eI == eiMD && ir->etc == etcNO &&
4367 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4369 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4370 warning_note(wi, warn_buf);
4373 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4375 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4376 warning_note(wi, warn_buf);
4378 if (ir->epc == epcMTTK)
4380 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4384 if (bHasAnyConstraints && ir->epc == epcMTTK)
4386 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4389 if (ir->LincsWarnAngle > 90.0)
4391 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4392 warning(wi, warn_buf);
4393 ir->LincsWarnAngle = 90.0;
4396 if (ir->ePBC != epbcNONE)
4398 if (ir->nstlist == 0)
4400 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4402 bTWIN = (ir->rlistlong > ir->rlist);
4403 if (ir->ns_type == ensGRID)
4405 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
4407 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",
4408 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
4409 warning_error(wi, warn_buf);
4414 min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
4415 if (2*ir->rlistlong >= min_size)
4417 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4418 warning_error(wi, warn_buf);
4421 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4428 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4432 real rvdw1, rvdw2, rcoul1, rcoul2;
4433 char warn_buf[STRLEN];
4435 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4439 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4444 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4450 if (rvdw1 + rvdw2 > ir->rlist ||
4451 rcoul1 + rcoul2 > ir->rlist)
4454 "The sum of the two largest charge group radii (%f) "
4455 "is larger than rlist (%f)\n",
4456 max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4457 warning(wi, warn_buf);
4461 /* Here we do not use the zero at cut-off macro,
4462 * since user defined interactions might purposely
4463 * not be zero at the cut-off.
4465 if (ir_vdw_is_zero_at_cutoff(ir) &&
4466 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
4468 sprintf(warn_buf, "The sum of the two largest charge group "
4469 "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
4470 "With exact cut-offs, better performance can be "
4471 "obtained with cutoff-scheme = %s, because it "
4472 "does not use charge groups at all.",
4474 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4475 ir->rlistlong, ir->rvdw,
4476 ecutscheme_names[ecutsVERLET]);
4479 warning(wi, warn_buf);
4483 warning_note(wi, warn_buf);
4486 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4487 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
4489 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
4490 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4492 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4493 ir->rlistlong, ir->rcoulomb,
4494 ecutscheme_names[ecutsVERLET]);
4497 warning(wi, warn_buf);
4501 warning_note(wi, warn_buf);