//! Sets the cginfo structures.
static void dd_set_cginfo(gmx::ArrayRef<const int> index_gl, int cg0, int cg1,
- t_forcerec *fr, char *bLocalCG)
+ t_forcerec *fr)
{
if (fr != nullptr)
{
cginfo[cg] = ddcginfo(cginfo_mb, index_gl[cg]);
}
}
-
- if (bLocalCG != nullptr)
- {
- for (int cg = cg0; cg < cg1; cg++)
- {
- bLocalCG[index_gl[cg]] = TRUE;
- }
- }
}
//! Makes the mappings between global and local atom indices during DD repartioning.
}
}
-//! Checks the charge-group assignements.
-static int check_bLocalCG(gmx_domdec_t *dd, int ncg_sys, const char *bLocalCG,
- const char *where)
-{
- int nerr = 0;
- if (bLocalCG == nullptr)
- {
- return nerr;
- }
- for (size_t i = 0; i < dd->globalAtomGroupIndices.size(); i++)
- {
- if (!bLocalCG[dd->globalAtomGroupIndices[i]])
- {
- fprintf(stderr,
- "DD rank %d, %s: atom group %zu, global atom group %d is not marked in bLocalCG (ncg_home %d)\n", dd->rank, where, i + 1, dd->globalAtomGroupIndices[i] + 1, dd->ncg_home);
- nerr++;
- }
- }
- size_t ngl = 0;
- for (int i = 0; i < ncg_sys; i++)
- {
- if (bLocalCG[i])
- {
- ngl++;
- }
- }
- if (ngl != dd->globalAtomGroupIndices.size())
- {
- fprintf(stderr, "DD rank %d, %s: In bLocalCG %zu atom groups are marked as local, whereas there are %zu\n", dd->rank, where, ngl, dd->globalAtomGroupIndices.size());
- nerr++;
- }
-
- return nerr;
-}
-
//! Checks whether global and local atom indices are consistent.
-static void check_index_consistency(gmx_domdec_t *dd,
- int natoms_sys, int ncg_sys,
- const char *where)
+static void check_index_consistency(const gmx_domdec_t *dd,
+ int natoms_sys,
+ const char *where)
{
int nerr = 0;
}
}
- nerr += check_bLocalCG(dd, ncg_sys, dd->comm->bLocalCG, where);
-
if (nerr > 0)
{
gmx_fatal(FARGS, "DD rank %d, %s: %d atom(group) index inconsistencies",
}
}
-//! Clear all DD global state indices, starting from \p atomGroupStart and \p atomStart
+//! Clear all DD global state indices
static void clearDDStateIndices(gmx_domdec_t *dd,
- int atomGroupStart,
- int atomStart)
+ const bool keepLocalAtomIndices)
{
gmx_ga2la_t &ga2la = *dd->ga2la;
- if (atomStart == 0)
+ if (!keepLocalAtomIndices)
{
/* Clear the whole list without the overhead of searching */
ga2la.clear();
}
}
- char *bLocalCG = dd->comm->bLocalCG;
- if (bLocalCG)
- {
- for (size_t atomGroup = atomGroupStart; atomGroup < dd->globalAtomGroupIndices.size(); atomGroup++)
- {
- bLocalCG[dd->globalAtomGroupIndices[atomGroup]] = FALSE;
- }
- }
-
dd_clear_local_vsite_indices(dd);
if (dd->constraints)
}
//! Returns whether a link is missing.
-static gmx_bool missing_link(t_blocka *link, int cg_gl, const char *bLocalCG)
+static gmx_bool missing_link(const t_blocka &link,
+ const int globalAtomIndex,
+ const gmx_ga2la_t &ga2la)
{
- int i;
- gmx_bool bMiss;
-
- bMiss = FALSE;
- for (i = link->index[cg_gl]; i < link->index[cg_gl+1]; i++)
+ for (int i = link.index[globalAtomIndex]; i < link.index[globalAtomIndex + 1]; i++)
{
- if (!bLocalCG[link->a[i]])
+ if (!ga2la.findHome(link.a[i]))
{
- bMiss = TRUE;
+ return true;
}
}
- return bMiss;
+ return false;
}
//! Domain corners for communication, a maximum of 4 i-zones see a j domain
(bDist2B && r2 < r_bcomm2)) &&
(!bBondComm ||
(GET_CGINFO_BOND_INTER(cginfo[cg]) &&
- missing_link(comm->cglink, globalAtomGroupIndices[cg],
- comm->bLocalCG)))))
+ missing_link(*comm->bondedLinks, globalAtomGroupIndices[cg],
+ *dd->ga2la)))))
{
/* Store the local and global atom group indices and position */
localAtomGroups->push_back(cg);
{
int dim_ind, dim, dim0, dim1, dim2, dimd, nat_tot;
int nzone, nzone_send, zone, zonei, cg0, cg1;
- int c, i, cg, cg_gl;
+ int c;
int *zone_cg_range, pos_cg;
gmx_domdec_comm_t *comm;
gmx_domdec_zones_t *zones;
/* Check if we need to compute triclinic distances along this dim */
bool distanceIsTriclinic = false;
- for (i = 0; i <= dim_ind; i++)
+ for (int i = 0; i <= dim_ind; i++)
{
if (ddbox->tric_dir[dd->dim[i]])
{
sf2_round[dimd] = 1;
if (ddbox->tric_dir[dimd])
{
- for (i = dd->dim[dimd]+1; i < DIM; i++)
+ for (int i = dd->dim[dimd] + 1; i < DIM; i++)
{
/* If we are shifted in dimension i
* and the cell plane is tilted forward
zone = (p == 0 ? 0 : nzone - 1);
while (zone < nzone)
{
- for (cg = 0; cg < ind->nrecv[zone]; cg++)
+ for (int i = 0; i < ind->nrecv[zone]; i++)
{
- cg_gl = dd->globalAtomGroupIndices[pos_cg];
- fr->cginfo[pos_cg] = ddcginfo(cginfo_mb, cg_gl);
- if (bBondComm)
- {
- /* Update the charge group presence,
- * so we can use it in the next pass of the loop.
- */
- comm->bLocalCG[cg_gl] = TRUE;
- }
+ int globalAtomIndex = dd->globalAtomGroupIndices[pos_cg];
+ fr->cginfo[pos_cg] = ddcginfo(cginfo_mb, globalAtomIndex);
pos_cg++;
}
if (p == 0)
*/
dd_set_cginfo(dd->globalAtomGroupIndices,
dd->ncg_home, dd->globalAtomGroupIndices.size(),
- nullptr, comm->bLocalCG);
+ nullptr);
}
if (debug)
if (bMasterState)
{
/* Clear the old state */
- clearDDStateIndices(dd, 0, 0);
+ clearDDStateIndices(dd, false);
ncgindex_set = 0;
auto xGlobal = positionsFromStatePointer(state_global);
inc_nrnb(nrnb, eNR_CGCM, comm->atomRanges.numHomeAtoms());
- dd_set_cginfo(dd->globalAtomGroupIndices, 0, dd->ncg_home, fr, comm->bLocalCG);
+ dd_set_cginfo(dd->globalAtomGroupIndices, 0, dd->ncg_home, fr);
}
else if (state_local->ddp_count != dd->ddp_count)
{
}
/* Clear the old state */
- clearDDStateIndices(dd, 0, 0);
+ clearDDStateIndices(dd, false);
/* Restore the atom group indices from state_local */
restoreAtomGroups(dd, state_local);
inc_nrnb(nrnb, eNR_CGCM, comm->atomRanges.numHomeAtoms());
- dd_set_cginfo(dd->globalAtomGroupIndices, 0, dd->ncg_home, fr, comm->bLocalCG);
+ dd_set_cginfo(dd->globalAtomGroupIndices, 0, dd->ncg_home, fr);
set_ddbox(*dd, bMasterState, state_local->box,
true, state_local->x, &ddbox);
/* We have the full state, only redistribute the cgs */
/* Clear the non-home indices */
- clearDDStateIndices(dd, dd->ncg_home, comm->atomRanges.numHomeAtoms());
+ clearDDStateIndices(dd, true);
ncgindex_set = 0;
/* To avoid global communication, we do not recompute the extent
if (comm->ddSettings.DD_debug > 0)
{
/* Set the env var GMX_DD_DEBUG if you suspect corrupted indices */
- check_index_consistency(dd, top_global.natoms, ncg_mtop(&top_global),
- "after partitioning");
+ check_index_consistency(dd, top_global.natoms, "after partitioning");
}
wallcycle_stop(wcycle, ewcDOMDEC);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff