*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016,2017, 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.
unsigned long Flags,
gmx_walltime_accounting_t walltime_accounting)
{
- gmx_mdoutf_t outf = NULL;
+ gmx_mdoutf_t outf = nullptr;
gmx_int64_t step, step_rel;
double elapsed_time;
double t, t0, lam0[efptNR];
t_vcm *vcm;
matrix parrinellorahmanMu, M;
t_trxframe rerun_fr;
- gmx_repl_ex_t repl_ex = NULL;
+ gmx_repl_ex_t repl_ex = nullptr;
int nchkpt = 1;
gmx_localtop_t *top;
- t_mdebin *mdebin = NULL;
+ t_mdebin *mdebin = nullptr;
gmx_enerdata_t *enerd;
PaddedRVecVector f {};
gmx_global_stat_t gstat;
- gmx_update_t *upd = NULL;
- t_graph *graph = NULL;
+ gmx_update_t *upd = nullptr;
+ t_graph *graph = nullptr;
gmx_groups_t *groups;
gmx_ekindata_t *ekind;
gmx_shellfc_t *shellfc;
gmx_bool bResetCountersHalfMaxH = FALSE;
gmx_bool bTemp, bPres, bTrotter;
real dvdl_constr;
- rvec *cbuf = NULL;
+ rvec *cbuf = nullptr;
int cbuf_nalloc = 0;
matrix lastbox;
int lamnew = 0;
/* PME load balancing data for GPU kernels */
- pme_load_balancing_t *pme_loadbal = NULL;
+ pme_load_balancing_t *pme_loadbal = nullptr;
gmx_bool bPMETune = FALSE;
gmx_bool bPMETunePrinting = FALSE;
state_global, top_global, ir,
state, &f, mdatoms, top, fr,
vsite, constr,
- nrnb, NULL, FALSE);
+ nrnb, nullptr, FALSE);
shouldCheckNumberOfBondedInteractions = true;
update_realloc(upd, state->natoms);
}
if (vsite)
{
/* Construct the virtual sites for the initial configuration */
- construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, NULL,
+ construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, nullptr,
top->idef.iparams, top->idef.il,
fr->ePBC, fr->bMolPBC, cr, state->box);
}
bSumEkinhOld = FALSE;
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
- NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
constr, &nullSignaller, state->box,
&totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags
| (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
perhaps loses some logic?*/
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
- NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
constr, &nullSignaller, state->box,
- NULL, &bSumEkinhOld,
+ nullptr, &bSumEkinhOld,
cglo_flags &~(CGLO_STOPCM | CGLO_PRESSURE));
}
{
/* PME grid + cut-off optimization with GPUs or PME nodes */
pme_loadbal_do(pme_loadbal, cr,
- (bVerbose && MASTER(cr)) ? stderr : NULL,
+ (bVerbose && MASTER(cr)) ? stderr : nullptr,
fplog, mdlog,
ir, fr, state,
wcycle,
* the full step kinetic energy and possibly for T-coupling.*/
/* This may not be quite working correctly yet . . . . */
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
- wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
+ wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
constr, &nullSignaller, state->box,
&totalNumberOfBondedInteractions, &bSumEkinhOld,
CGLO_GSTAT | CGLO_TEMPERATURE | CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS);
if (EI_VV(ir->eI) && !startingFromCheckpoint && !bRerunMD)
/* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
{
- rvec *vbuf = NULL;
+ rvec *vbuf = nullptr;
wallcycle_start(wcycle, ewcUPDATE);
if (ir->eI == eiVV && bInitStep)
if (!bRerunMD || rerun_fr.bV || bForceUpdate) /* Why is rerun_fr.bV here? Unclear. */
{
wallcycle_stop(wcycle, ewcUPDATE);
- update_constraints(fplog, step, NULL, ir, mdatoms,
+ update_constraints(fplog, step, nullptr, ir, mdatoms,
state, fr->bMolPBC, graph, &f,
&top->idef, shake_vir,
cr, nrnb, wcycle, upd, constr,
if (inputrecNvtTrotter(ir) && ir->eI == eiVV)
{
/* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
- enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, NULL, (ir->eI == eiVV), FALSE);
+ enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, nullptr, (ir->eI == eiVV), FALSE);
enerd->term[F_EKIN] = trace(ekind->ekin);
}
}
* the full step kinetic energy and possibly for T-coupling.*/
/* This may not be quite working correctly yet . . . . */
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
- wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
+ wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
constr, &nullSignaller, state->box,
- NULL, &bSumEkinhOld,
+ nullptr, &bSumEkinhOld,
CGLO_GSTAT | CGLO_TEMPERATURE);
wallcycle_start(wcycle, ewcUPDATE);
}
/* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
if (constr && bIfRandomize)
{
- update_constraints(fplog, step, NULL, ir, mdatoms,
+ update_constraints(fplog, step, nullptr, ir, mdatoms,
state, fr->bMolPBC, graph, &f,
&top->idef, tmp_vir,
cr, nrnb, wcycle, upd, constr,
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
constr, &nullSignaller, lastbox,
- NULL, &bSumEkinhOld,
+ nullptr, &bSumEkinhOld,
(bGStat ? CGLO_GSTAT : 0) | CGLO_TEMPERATURE
);
wallcycle_start(wcycle, ewcUPDATE);
* to numerical errors, or are they important
* physically? I'm thinking they are just errors, but not completely sure.
* For now, will call without actually constraining, constr=NULL*/
- update_constraints(fplog, step, NULL, ir, mdatoms,
+ update_constraints(fplog, step, nullptr, ir, mdatoms,
state, fr->bMolPBC, graph, &f,
&top->idef, tmp_vir,
- cr, nrnb, wcycle, upd, NULL,
+ cr, nrnb, wcycle, upd, nullptr,
FALSE, bCalcVir);
}
if (EI_VV(ir->eI))
unshift_self(graph, state->box, as_rvec_array(state->x.data()));
}
- if (vsite != NULL)
+ if (vsite != nullptr)
{
wallcycle_start(wcycle, ewcVSITECONSTR);
- if (graph != NULL)
+ if (graph != nullptr)
{
shift_self(graph, state->box, as_rvec_array(state->x.data()));
}
top->idef.iparams, top->idef.il,
fr->ePBC, fr->bMolPBC, cr, state->box);
- if (graph != NULL)
+ if (graph != nullptr)
{
unshift_self(graph, state->box, as_rvec_array(state->x.data()));
}
if (fplog && do_log && bDoExpanded)
{
/* only needed if doing expanded ensemble */
- PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals, ir->bSimTemp ? ir->simtempvals : NULL,
+ PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals, ir->bSimTemp ? ir->simtempvals : nullptr,
state_global->dfhist, state->fep_state, ir->nstlog, step);
}
if (bCalcEner)
gmx_bool do_dr = do_per_step(step, ir->nstdisreout);
gmx_bool do_or = do_per_step(step, ir->nstorireout);
- print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : NULL,
+ print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : nullptr,
step, t,
eprNORMAL, mdebin, fcd, groups, &(ir->opts));
/* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
- if ( (membed != NULL) && (!bLastStep) )
+ if ( (membed != nullptr) && (!bLastStep) )
{
rescale_membed(step_rel, membed, as_rvec_array(state_global->x.data()));
}
"mdrun -resetstep.", step);
}
reset_all_counters(fplog, mdlog, cr, step, &step_rel, ir, wcycle, nrnb, walltime_accounting,
- use_GPU(fr->nbv) ? fr->nbv : NULL);
+ use_GPU(fr->nbv) ? fr->nbv : nullptr);
wcycle_set_reset_counters(wcycle, -1);
if (!(cr->duty & DUTY_PME))
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff