}
-static void do_single_flood(FILE* edo,
- const rvec x[],
- rvec force[],
- t_edpar* edi,
- int64_t step,
- const matrix box,
- const t_commrec* cr,
- gmx_bool bNS) /* Are we in a neighbor searching step? */
+static void do_single_flood(FILE* edo,
+ gmx::ArrayRef<const gmx::RVec> coords,
+ gmx::ArrayRef<gmx::RVec> force,
+ t_edpar* edi,
+ int64_t step,
+ const matrix box,
+ const t_commrec* cr,
+ gmx_bool bNS) /* Are we in a neighbor searching step? */
{
int i;
matrix rotmat; /* rotation matrix */
buf->shifts_xcoll,
buf->extra_shifts_xcoll,
bNS,
- x,
+ as_rvec_array(coords.data()),
edi->sav.nr,
edi->sav.nr_loc,
edi->sav.anrs_loc,
buf->shifts_xc_ref,
buf->extra_shifts_xc_ref,
bNS,
- x,
+ as_rvec_array(coords.data()),
edi->sref.nr,
edi->sref.nr_loc,
edi->sref.anrs_loc,
/* Main flooding routine, called from do_force */
-void do_flood(const t_commrec* cr,
- const t_inputrec& ir,
- const rvec x[],
- rvec force[],
- gmx_edsam* ed,
- const matrix box,
- int64_t step,
- bool bNS)
+void do_flood(const t_commrec* cr,
+ const t_inputrec& ir,
+ gmx::ArrayRef<const gmx::RVec> coords,
+ gmx::ArrayRef<gmx::RVec> force,
+ gmx_edsam* ed,
+ const matrix box,
+ int64_t step,
+ bool bNS)
{
/* Write time to edo, when required. Output the time anyhow since we need
* it in the output file for ED constraints. */
/* Call flooding for one matrix */
if (edi.flood.vecs.neig)
{
- do_single_flood(ed->edo, x, force, &edi, step, box, cr, bNS);
+ do_single_flood(ed->edo, coords, force, &edi, step, box, cr, bNS);
}
}
}
const gmx_output_env_t* oenv,
const t_commrec* cr)
{
- auto edHandle = std::make_unique<gmx::EssentialDynamics>();
- auto ed = edHandle->getLegacyED();
+ auto edHandle = std::make_unique<gmx::EssentialDynamics>();
+ auto* ed = edHandle->getLegacyED();
/* We want to perform ED (this switch might later be upgraded to EssentialDynamicsType::Flooding) */
ed->eEDtype = EssentialDynamicsType::EDSampling;
{
if (edi->fitmas)
{
- edi->sref.m[i] = mtopGetAtomMass(&mtop, edi->sref.anrs[i], &molb);
+ edi->sref.m[i] = mtopGetAtomMass(mtop, edi->sref.anrs[i], &molb);
}
else
{
snew(edi->sav.m, edi->sav.nr);
for (i = 0; i < edi->sav.nr; i++)
{
- edi->sav.m[i] = mtopGetAtomMass(&mtop, edi->sav.anrs[i], &molb);
+ edi->sav.m[i] = mtopGetAtomMass(mtop, edi->sav.anrs[i], &molb);
if (edi->pcamas)
{
edi->sav.sqrtm[i] = sqrt(edi->sav.m[i]);
/* Gets the rms deviation of the positions to the structure s */
/* fit_to_structure has to be called before calling this routine! */
-static real rmsd_from_structure(rvec* x, /* The positions under consideration */
+static real rmsd_from_structure(rvec* x, /* The positions under consideration */
struct gmx_edx* s) /* The structure from which the rmsd shall be computed */
{
real rmsd = 0.0;
"gmx grompp and the related .mdp options may change also.");
/* Open input and output files, allocate space for ED data structure */
- auto edHandle = ed_open(mtop.natoms, oh, ediFileName, edoFileName, startingBehavior, oenv, cr);
- auto ed = edHandle->getLegacyED();
+ auto edHandle = ed_open(mtop.natoms, oh, ediFileName, edoFileName, startingBehavior, oenv, cr);
+ auto* ed = edHandle->getLegacyED();
GMX_RELEASE_ASSERT(constr != nullptr, "Must have valid constraints object");
constr->saveEdsamPointer(ed);
} /* end of MASTER only section */
- if (PAR(cr))
+ if (haveDDAtomOrdering(*cr))
{
- /* Broadcast the essential dynamics / flooding data to all nodes */
+ /* Broadcast the essential dynamics / flooding data to all nodes.
+ * In a single-rank case, only the necessary memory allocation is done. */
broadcast_ed_data(cr, ed);
}
else
{
- /* In the single-CPU case, point the local atom numbers pointers to the global
+ /* In the non-DD case, point the local atom numbers pointers to the global
* one, so that we can use the same notation in serial and parallel case: */
/* Loop over all ED data sets (usually only one, though) */
for (auto edi = ed->edpar.begin(); edi != ed->edpar.end(); ++edi)
}
-void do_edsam(const t_inputrec* ir, int64_t step, const t_commrec* cr, rvec xs[], rvec v[], const matrix box, gmx_edsam* ed)
+void do_edsam(const t_inputrec* ir,
+ int64_t step,
+ const t_commrec* cr,
+ gmx::ArrayRef<gmx::RVec> coords,
+ gmx::ArrayRef<gmx::RVec> velocities,
+ const matrix box,
+ gmx_edsam* ed)
{
int i, edinr, iupdate = 500;
matrix rotmat; /* rotation matrix */
buf->shifts_xcoll,
buf->extra_shifts_xcoll,
PAR(cr) ? buf->bUpdateShifts : TRUE,
- xs,
+ as_rvec_array(coords.data()),
edi.sav.nr,
edi.sav.nr_loc,
edi.sav.anrs_loc,
buf->shifts_xc_ref,
buf->extra_shifts_xc_ref,
PAR(cr) ? buf->bUpdateShifts : TRUE,
- xs,
+ as_rvec_array(coords.data()),
edi.sref.nr,
edi.sref.nr_loc,
edi.sref.anrs_loc,
box, buf->xcoll[edi.sav.c_ind[i]], buf->shifts_xcoll[edi.sav.c_ind[i]], x_unsh);
/* dx is the ED correction to the positions: */
- rvec_sub(x_unsh, xs[edi.sav.anrs_loc[i]], dx);
+ rvec_sub(x_unsh, coords[edi.sav.anrs_loc[i]], dx);
- if (v != nullptr)
+ if (!velocities.empty())
{
/* dv is the ED correction to the velocity: */
svmul(dt_1, dx, dv);
/* apply the velocity correction: */
- rvec_inc(v[edi.sav.anrs_loc[i]], dv);
+ rvec_inc(velocities[edi.sav.anrs_loc[i]], dv);
}
/* Finally apply the position correction due to ED: */
- copy_rvec(x_unsh, xs[edi.sav.anrs_loc[i]]);
+ copy_rvec(x_unsh, coords[edi.sav.anrs_loc[i]]);
}
}
} /* END of if ( bNeedDoEdsam(edi) ) */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff