*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
&ls, &n_nonlin_vsite, &rlist_1x1);
/* Set the pair-list buffer size in ir */
- verletbuf_get_list_setup(FALSE, &ls);
+ verletbuf_get_list_setup(FALSE, FALSE, &ls);
calc_verlet_buffer_size(mtop, det(box), ir, buffer_temp,
&ls, &n_nonlin_vsite, &ir->rlist);
ls.cluster_size_i, ls.cluster_size_j,
ir->rlist, ir->rlist-max(ir->rvdw, ir->rcoulomb));
+ printf("Note that mdrun will redetermine rlist based on the actual pair-list setup\n");
+
if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
{
gmx_fatal(FARGS, "The pair-list cut-off (%g nm) is longer than half the shortest box vector or longer than the smallest box diagonal element (%g nm). Increase the box size or decrease nstlist or increase verlet-buffer-tolerance.", ir->rlistlong, sqrt(max_cutoff2(ir->ePBC, box)));
"with [TT]-cpi[tt]. If you wish to change the ensemble or things",
"like output frequency, then supplying the checkpoint file to",
"[THISMODULE] with [TT]-t[tt] along with a new [TT].mdp[tt] file",
- "with [TT]-f[tt] is the recommended procedure.[PAR]",
+ "with [TT]-f[tt] is the recommended procedure. Actually preserving",
+ "the ensemble (if possible) still requires passing the checkpoint",
+ "file to [gmx-mdrun] [TT]-cpi[tt].[PAR]",
"By default, all bonded interactions which have constant energy due to",
"virtual site constructions will be removed. If this constant energy is",
t_inputrec *ir;
int natoms, nvsite, comb, mt;
t_params *plist;
- t_state state;
+ t_state *state;
matrix box;
real max_spacing, fudgeQQ;
double reppow;
{
gmx_fatal(FARGS, "%s does not exist", fn);
}
+ snew(state, 1);
new_status(fn, opt2fn_null("-pp", NFILE, fnm), opt2fn("-c", NFILE, fnm),
- opts, ir, bZero, bGenVel, bVerbose, &state,
+ opts, ir, bZero, bGenVel, bVerbose, state,
atype, sys, &nmi, &mi, plist, &comb, &reppow, &fudgeQQ,
opts->bMorse,
wi);
/* Check velocity for virtual sites and shells */
if (bGenVel)
{
- check_vel(sys, state.v);
+ check_vel(sys, state->v);
}
/* check for shells and inpurecs */
}
do_index(mdparin, ftp2fn_null(efNDX, NFILE, fnm),
sys, bVerbose, ir,
- bGenVel ? state.v : NULL,
+ bGenVel ? state->v : NULL,
wi);
if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 &&
}
else
{
- buffer_temp = calc_temp(sys, ir, state.v);
+ buffer_temp = calc_temp(sys, ir, state->v);
}
if (buffer_temp > 0)
{
warning_note(wi, warn_buf);
}
- set_verlet_buffer(sys, ir, buffer_temp, state.box, wi);
+ set_verlet_buffer(sys, ir, buffer_temp, state->box, wi);
}
}
}
/* Init the temperature coupling state */
- init_gtc_state(&state, ir->opts.ngtc, 0, ir->opts.nhchainlength); /* need to add nnhpres here? */
+ init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength); /* need to add nnhpres here? */
if (bVerbose)
{
fprintf(stderr, "getting data from old trajectory ...\n");
}
cont_status(ftp2fn(efTRN, NFILE, fnm), ftp2fn_null(efEDR, NFILE, fnm),
- bNeedVel, bGenVel, fr_time, ir, &state, sys, oenv);
+ bNeedVel, bGenVel, fr_time, ir, state, sys, oenv);
}
if (ir->ePBC == epbcXY && ir->nwall != 2)
{
- clear_rvec(state.box[ZZ]);
+ clear_rvec(state->box[ZZ]);
}
if (ir->cutoff_scheme != ecutsVERLET && ir->rlist > 0)
{
set_warning_line(wi, mdparin, -1);
- check_chargegroup_radii(sys, ir, state.x, wi);
+ check_chargegroup_radii(sys, ir, state->x, wi);
}
if (EEL_FULL(ir->coulombtype) || EVDW_PME(ir->vdwtype))
{
/* Calculate the optimal grid dimensions */
- copy_mat(state.box, box);
+ copy_mat(state->box, box);
if (ir->ePBC == epbcXY && ir->nwall == 2)
{
svmul(ir->wall_ewald_zfac, box[ZZ], box[ZZ]);
potentially conflict if not handled correctly. */
if (ir->efep != efepNO)
{
- state.fep_state = ir->fepvals->init_fep_state;
+ state->fep_state = ir->fepvals->init_fep_state;
for (i = 0; i < efptNR; i++)
{
/* init_lambda trumps state definitions*/
if (ir->fepvals->init_lambda >= 0)
{
- state.lambda[i] = ir->fepvals->init_lambda;
+ state->lambda[i] = ir->fepvals->init_lambda;
}
else
{
}
else
{
- state.lambda[i] = ir->fepvals->all_lambda[i][state.fep_state];
+ state->lambda[i] = ir->fepvals->all_lambda[i][state->fep_state];
}
}
}
if (ir->ePull != epullNO)
{
- set_pull_init(ir, sys, state.x, state.box, state.lambda[efptMASS], oenv, opts->pull_start);
+ set_pull_init(ir, sys, state->x, state->box, state->lambda[efptMASS], oenv, opts->pull_start);
}
if (ir->bRot)
{
- set_reference_positions(ir->rot, state.x, state.box,
+ set_reference_positions(ir->rot, state->x, state->box,
opt2fn("-ref", NFILE, fnm), opt2bSet("-ref", NFILE, fnm),
wi);
}
if (EEL_PME(ir->coulombtype))
{
- float ratio = pme_load_estimate(sys, ir, state.box);
+ float ratio = pme_load_estimate(sys, ir, state->box);
fprintf(stderr, "Estimate for the relative computational load of the PME mesh part: %.2f\n", ratio);
/* With free energy we might need to do PME both for the A and B state
* charges. This will double the cost, but the optimal performance will
}
done_warning(wi, FARGS);
- write_tpx_state(ftp2fn(efTPX, NFILE, fnm), ir, &state, sys);
+ write_tpx_state(ftp2fn(efTPX, NFILE, fnm), ir, state, sys);
/* Output IMD group, if bIMD is TRUE */
- write_IMDgroup_to_file(ir->bIMD, ir, &state, sys, NFILE, fnm);
+ write_IMDgroup_to_file(ir->bIMD, ir, state, sys, NFILE, fnm);
+ done_state(state);
+ sfree(state);
done_atomtype(atype);
done_mtop(sys, TRUE);
done_inputrec_strings();
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff