Rename atomGroups in gmx_domdec_t to atomGrouping

This is to avoid a name conflict with the atom group indices
(which index into atomGrouping).

Change-Id: Ieebb47e86ff6d84a79ff58cbb68f42b109e4658b

diff --git a/src/gromacs/domdec/distribute.cpp b/src/gromacs/domdec/distribute.cpp
index c333fdc6a22358e54c509d2d6f775d5b8b91cad4..3072799e84349112ee92243f3738c8e45c00ac92 100644 (file)
--- a/src/gromacs/domdec/distribute.cpp
+++ b/src/gromacs/domdec/distribute.cpp
@@ -494,10 +494,10 @@ static void distributeAtomGroups(FILE *fplog, gmx_domdec_t *dd,
 
     /* Determine the home charge group sizes */
     const t_block &globalAtomGroups = dd->comm->cgs_gl;
-    dd->atomGroups_.clear();
+    dd->atomGrouping_.clear();
     for (int i = 0; i < dd->ncg_home; i++)
     {
-        dd->atomGroups_.appendBlock(globalAtomGroups.blockSize(dd->globalAtomGroupIndices[i]));
+        dd->atomGrouping_.appendBlock(globalAtomGroups.blockSize(dd->globalAtomGroupIndices[i]));
     }
 
     if (debug)

diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp
index c848e10944cd2fcdc8989db475d17815b11b3c2c..a5b29edc469b458a61e69464a81e87701fa6f81b 100644 (file)
--- a/src/gromacs/domdec/domdec.cpp
+++ b/src/gromacs/domdec/domdec.cpp
@@ -354,7 +354,7 @@ void dd_move_x(gmx_domdec_t             *dd,
 
     comm = dd->comm;
 
-    const RangePartitioning &atomGroups = dd->atomGroups();
+    const RangePartitioning &atomGrouping = dd->atomGrouping();
 
     nzone   = 1;
     nat_tot = comm->atomRanges.numHomeAtoms();
@@ -376,7 +376,7 @@ void dd_move_x(gmx_domdec_t             *dd,
             {
                 for (int g : ind.index)
                 {
-                    for (int j : atomGroups.block(g))
+                    for (int j : atomGrouping.block(g))
                     {
                         sendBuffer[n] = x[j];
                         n++;
@@ -387,7 +387,7 @@ void dd_move_x(gmx_domdec_t             *dd,
             {
                 for (int g : ind.index)
                 {
-                    for (int j : atomGroups.block(g))
+                    for (int j : atomGrouping.block(g))
                     {
                         /* We need to shift the coordinates */
                         for (int d = 0; d < DIM; d++)
@@ -402,7 +402,7 @@ void dd_move_x(gmx_domdec_t             *dd,
             {
                 for (int g : ind.index)
                 {
-                    for (int j : atomGroups.block(g))
+                    for (int j : atomGrouping.block(g))
                     {
                         /* Shift x */
                         sendBuffer[n][XX] = x[j][XX] + shift[XX];
@@ -467,7 +467,7 @@ void dd_move_f(gmx_domdec_t             *dd,
 
     comm = dd->comm;
 
-    const RangePartitioning &atomGroups = dd->atomGroups();
+    const RangePartitioning &atomGrouping = dd->atomGrouping();
 
     nzone   = comm->zones.n/2;
     nat_tot = comm->atomRanges.end(DDAtomRanges::Type::Zones);
@@ -523,7 +523,7 @@ void dd_move_f(gmx_domdec_t             *dd,
             {
                 for (int g : ind.index)
                 {
-                    for (int j : atomGroups.block(g))
+                    for (int j : atomGrouping.block(g))
                     {
                         for (int d = 0; d < DIM; d++)
                         {
@@ -540,7 +540,7 @@ void dd_move_f(gmx_domdec_t             *dd,
                 assert(NULL != fshift);
                 for (int g : ind.index)
                 {
-                    for (int j : atomGroups.block(g))
+                    for (int j : atomGrouping.block(g))
                     {
                         for (int d = 0; d < DIM; d++)
                         {
@@ -559,7 +559,7 @@ void dd_move_f(gmx_domdec_t             *dd,
             {
                 for (int g : ind.index)
                 {
-                    for (int j : atomGroups.block(g))
+                    for (int j : atomGrouping.block(g))
                     {
                         /* Rotate the force */
                         f[j][XX] += receiveBuffer[n][XX];
@@ -605,7 +605,7 @@ void dd_atom_spread_real(gmx_domdec_t *dd, real v[])
 
     comm = dd->comm;
 
-    const RangePartitioning &atomGroups = dd->atomGroups();
+    const RangePartitioning &atomGrouping = dd->atomGrouping();
 
     nzone   = 1;
     nat_tot = comm->atomRanges.numHomeAtoms();
@@ -623,7 +623,7 @@ void dd_atom_spread_real(gmx_domdec_t *dd, real v[])
             int                       n          = 0;
             for (int g : ind.index)
             {
-                for (int j : atomGroups.block(g))
+                for (int j : atomGrouping.block(g))
                 {
                     sendBuffer[n++] = v[j];
                 }
@@ -668,7 +668,7 @@ void dd_atom_sum_real(gmx_domdec_t *dd, real v[])
 
     comm = dd->comm;
 
-    const gmx::RangePartitioning &atomGroups = dd->atomGroups();
+    const gmx::RangePartitioning &atomGrouping = dd->atomGrouping();
 
     nzone   = comm->zones.n/2;
     nat_tot = comm->atomRanges.end(DDAtomRanges::Type::Zones);
@@ -713,7 +713,7 @@ void dd_atom_sum_real(gmx_domdec_t *dd, real v[])
             int n = 0;
             for (int g : ind.index)
             {
-                for (int j : atomGroups.block(g))
+                for (int j : atomGrouping.block(g))
                 {
                     v[j] += receiveBuffer[n];
                     n++;
@@ -1126,7 +1126,7 @@ void write_dd_pdb(const char *fn, gmx_int64_t step, const char *title,
         if (i < dd->comm->atomRanges.end(DDAtomRanges::Type::Zones))
         {
             c = 0;
-            while (i >= dd->atomGroups().subRange(0, dd->comm->zones.cg_range[c + 1]).end())
+            while (i >= dd->atomGrouping().subRange(0, dd->comm->zones.cg_range[c + 1]).end())
             {
                 c++;
             }
@@ -1498,10 +1498,10 @@ static void restoreAtomGroups(gmx_domdec_t *dd,
     gmx::ArrayRef<const int>  atomGroupsState        = state->cg_gl;
 
     std::vector<int>         &globalAtomGroupIndices = dd->globalAtomGroupIndices;
-    gmx::RangePartitioning   &atomGroups             = dd->atomGroups_;
+    gmx::RangePartitioning   &atomGrouping           = dd->atomGrouping_;
 
     globalAtomGroupIndices.resize(atomGroupsState.size());
-    atomGroups.clear();
+    atomGrouping.clear();
 
     /* Copy back the global charge group indices from state
      * and rebuild the local charge group to atom index.
@@ -1511,11 +1511,11 @@ static void restoreAtomGroups(gmx_domdec_t *dd,
         const int atomGroupGlobal  = atomGroupsState[i];
         const int groupSize        = gcgs_index[atomGroupGlobal + 1] - gcgs_index[atomGroupGlobal];
         globalAtomGroupIndices[i]  = atomGroupGlobal;
-        atomGroups.appendBlock(groupSize);
+        atomGrouping.appendBlock(groupSize);
     }
 
     dd->ncg_home = atomGroupsState.size();
-    dd->comm->atomRanges.setEnd(DDAtomRanges::Type::Home, atomGroups.fullRange().end());
+    dd->comm->atomRanges.setEnd(DDAtomRanges::Type::Home, atomGrouping.fullRange().end());
 
     set_zones_ncg_home(dd);
 }
@@ -1564,7 +1564,7 @@ static void make_dd_indices(gmx_domdec_t *dd,
     }
 
     /* Make the local to global and global to local atom index */
-    int a = dd->atomGroups().subRange(cg_start, cg_start).begin();
+    int a = dd->atomGrouping().subRange(cg_start, cg_start).begin();
     globalAtomIndices.resize(a);
     for (int zone = 0; zone < numZones; zone++)
     {
@@ -5361,7 +5361,7 @@ static void setup_dd_communication(gmx_domdec_t *dd,
                         /* Get the cg's for this pulse in this zone */
                         get_zone_pulse_cgs(dd, zonei, zone, cg0_th, cg1_th,
                                            dd->globalAtomGroupIndices,
-                                           dd->atomGroups(),
+                                           dd->atomGrouping(),
                                            dim, dim_ind, dim0, dim1, dim2,
                                            r_comm2, r_bcomm2,
                                            box, distanceIsTriclinic,
@@ -5476,7 +5476,7 @@ static void setup_dd_communication(gmx_domdec_t *dd,
                         cg_gl                              = dd->globalAtomGroupIndices[pos_cg];
                         fr->cginfo[pos_cg]                 = ddcginfo(cginfo_mb, cg_gl);
                         nrcg                               = GET_CGINFO_NATOMS(fr->cginfo[pos_cg]);
-                        dd->atomGroups_.appendBlock(nrcg);
+                        dd->atomGrouping_.appendBlock(nrcg);
                         if (bBondComm)
                         {
                             /* Update the charge group presence,
@@ -5497,7 +5497,7 @@ static void setup_dd_communication(gmx_domdec_t *dd,
             else
             {
                 /* This part of the code is never executed with bBondComm. */
-                std::vector<int> &atomGroupsIndex = dd->atomGroups_.rawIndex();
+                std::vector<int> &atomGroupsIndex = dd->atomGrouping_.rawIndex();
                 atomGroupsIndex.resize(numAtomGroupsNew + 1);
 
                 merge_cg_buffers(nzone, cd, p, zone_cg_range,
@@ -5512,7 +5512,7 @@ static void setup_dd_communication(gmx_domdec_t *dd,
         if (!cd->receiveInPlace)
         {
             /* Store the atom block for easy copying of communication buffers */
-            make_cell2at_index(cd, nzone, zone_cg_range[nzone], dd->atomGroups());
+            make_cell2at_index(cd, nzone, zone_cg_range[nzone], dd->atomGrouping());
         }
         nzone += nzone;
     }
@@ -6055,13 +6055,13 @@ static void dd_sort_state(gmx_domdec_t *dd, rvec *cgcm, t_forcerec *fr, t_state
             gmx_incons("unimplemented");
     }
 
-    const gmx::RangePartitioning &atomGroups = dd->atomGroups();
+    const gmx::RangePartitioning &atomGrouping = dd->atomGrouping();
 
     /* We alloc with the old size, since cgindex is still old */
-    GMX_ASSERT(atomGroups.numBlocks() == dd->ncg_home, "atomGroups and dd should be consistent");
-    DDBufferAccess<gmx::RVec>     rvecBuffer(dd->comm->rvecBuffer, atomGroups.fullRange().end());
+    GMX_ASSERT(atomGrouping.numBlocks() == dd->ncg_home, "atomGroups and dd should be consistent");
+    DDBufferAccess<gmx::RVec>     rvecBuffer(dd->comm->rvecBuffer, atomGrouping.fullRange().end());
 
-    const gmx::RangePartitioning *atomGroupsPtr = (dd->comm->bCGs ? &atomGroups : nullptr);
+    const gmx::RangePartitioning *atomGroupsPtr = (dd->comm->bCGs ? &atomGrouping : nullptr);
 
     /* Set the new home atom/charge group count */
     dd->ncg_home = sort->sorted.size();
@@ -6109,16 +6109,16 @@ static void dd_sort_state(gmx_domdec_t *dd, rvec *cgcm, t_forcerec *fr, t_state
         gmx::RangePartitioning ordered;
         for (const gmx_cgsort_t &entry : cgsort)
         {
-            ordered.appendBlock(atomGroups.block(entry.ind).size());
+            ordered.appendBlock(atomGrouping.block(entry.ind).size());
         }
-        dd->atomGroups_ = ordered;
+        dd->atomGrouping_ = ordered;
     }
     else
     {
-        dd->atomGroups_.setAllBlocksSizeOne(dd->ncg_home);
+        dd->atomGrouping_.setAllBlocksSizeOne(dd->ncg_home);
     }
     /* Set the home atom number */
-    dd->comm->atomRanges.setEnd(DDAtomRanges::Type::Home, dd->atomGroups().fullRange().end());
+    dd->comm->atomRanges.setEnd(DDAtomRanges::Type::Home, dd->atomGrouping().fullRange().end());
 
     if (fr->cutoff_scheme == ecutsVERLET)
     {

diff --git a/src/gromacs/domdec/domdec_constraints.cpp b/src/gromacs/domdec/domdec_constraints.cpp
index 30d678329fbf07535150d28fa4a560d078ffb9e7..fcb2070e3338062683f24ea197eb503dddb0aa27 100644 (file)
--- a/src/gromacs/domdec/domdec_constraints.cpp
+++ b/src/gromacs/domdec/domdec_constraints.cpp
@@ -256,7 +256,7 @@ static void atoms_to_settles(gmx_domdec_t *dd,
     {
         if (GET_CGINFO_SETTLE(cginfo[cg]))
         {
-            for (int a : dd->atomGroups().block(cg))
+            for (int a : dd->atomGrouping().block(cg))
             {
                 int a_gl = dd->globalAtomIndices[a];
                 int a_mol;
@@ -350,7 +350,7 @@ static void atoms_to_constraints(gmx_domdec_t *dd,
     {
         if (GET_CGINFO_CONSTR(cginfo[cg]))
         {
-            for (int a : dd->atomGroups().block(cg))
+            for (int a : dd->atomGrouping().block(cg))
             {
                 int a_gl = dd->globalAtomIndices[a];
                 int molnr, a_mol;

diff --git a/src/gromacs/domdec/domdec_struct.h b/src/gromacs/domdec/domdec_struct.h
index b1af3b6d82210671364ea440d79cd39c9e46c8c9..53df6018bb2ad235e84f0b76cdfdda6fdc70cbe2 100644 (file)
--- a/src/gromacs/domdec/domdec_struct.h
+++ b/src/gromacs/domdec/domdec_struct.h
@@ -184,10 +184,10 @@ struct gmx_domdec_t {
     /* Global atom group indices for the home and all non-home groups */
     std::vector<int>              globalAtomGroupIndices;
     /* The atom groups for the home and all non-home groups, todo: make private */
-    gmx::RangePartitioning        atomGroups_;
-    const gmx::RangePartitioning &atomGroups() const
+    gmx::RangePartitioning        atomGrouping_;
+    const gmx::RangePartitioning &atomGrouping() const
     {
-        return atomGroups_;
+        return atomGrouping_;
     }
     /* Local atom to local atom-group index, only used for checking bondeds */
     std::vector<int> localAtomGroupFromAtom;

diff --git a/src/gromacs/domdec/domdec_topology.cpp b/src/gromacs/domdec/domdec_topology.cpp
index 2745f17ab53fa265c3db34d338002d0aeba3654b..6bb38470b5c3a2239929f086982e1e86068fc0c3 100644 (file)
--- a/src/gromacs/domdec/domdec_topology.cpp
+++ b/src/gromacs/domdec/domdec_topology.cpp
@@ -1096,13 +1096,13 @@ static void add_vsite(gmx_ga2la_t *ga2la, const int *index, const int *rtil,
 /*! \brief Build the index that maps each local atom to its local atom group */
 static void makeLocalAtomGroupsFromAtoms(gmx_domdec_t *dd)
 {
-    const gmx::RangePartitioning &atomGroups = dd->atomGroups();
+    const gmx::RangePartitioning &atomGrouping = dd->atomGrouping();
 
     dd->localAtomGroupFromAtom.clear();
 
     for (size_t g = 0; g < dd->globalAtomGroupIndices.size(); g++)
     {
-        for (int gmx_unused a : atomGroups.block(g))
+        for (int gmx_unused a : atomGrouping.block(g))
         {
             dd->localAtomGroupFromAtom.push_back(g);
         }
@@ -1601,8 +1601,8 @@ static void set_no_exclusions_zone(const gmx_domdec_t       *dd,
                                    int                       iz,
                                    t_blocka                 *lexcls)
 {
-    const auto zone = dd->atomGroups().subRange(zones->cg_range[iz],
-                                                zones->cg_range[iz + 1]);
+    const auto zone = dd->atomGrouping().subRange(zones->cg_range[iz],
+                                                  zones->cg_range[iz + 1]);
 
     for (int a : zone)
     {
@@ -1633,13 +1633,13 @@ static int make_exclusions_zone_cg(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
 
     ga2la = dd->ga2la;
 
-    const auto jRange = dd->atomGroups().subRange(zones->izone[iz].jcg0,
-                                                  zones->izone[iz].jcg1);
+    const auto jRange = dd->atomGrouping().subRange(zones->izone[iz].jcg0,
+                                                    zones->izone[iz].jcg1);
 
     n_excl_at_max = dd->reverse_top->n_excl_at_max;
 
     /* We set the end index, but note that we might not start at zero here */
-    lexcls->nr = dd->atomGroups().subRange(0, cg_end).size();
+    lexcls->nr = dd->atomGrouping().subRange(0, cg_end).size();
 
     int n     = lexcls->nra;
     int count = 0;
@@ -1650,7 +1650,7 @@ static int make_exclusions_zone_cg(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
             lexcls->nalloc_a = over_alloc_large(n + (cg_end - cg_start)*n_excl_at_max);
             srenew(lexcls->a, lexcls->nalloc_a);
         }
-        const auto atomGroup = dd->atomGroups().block(cg);
+        const auto atomGroup = dd->atomGrouping().block(cg);
         if (GET_CGINFO_EXCL_INTER(cginfo[cg]) ||
             !GET_CGINFO_EXCL_INTRA(cginfo[cg]))
         {
@@ -1767,8 +1767,8 @@ static void make_exclusions_zone(gmx_domdec_t *dd,
 
     ga2la = dd->ga2la;
 
-    const auto jRange = dd->atomGroups().subRange(zones->izone[iz].jcg0,
-                                                  zones->izone[iz].jcg1);
+    const auto jRange = dd->atomGrouping().subRange(zones->izone[iz].jcg0,
+                                                    zones->izone[iz].jcg1);
 
     n_excl_at_max = dd->reverse_top->n_excl_at_max;
 
@@ -1845,7 +1845,7 @@ static void check_alloc_index(t_blocka *ba, int nindex_max)
 static void check_exclusions_alloc(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
                                    t_blocka *lexcls)
 {
-    int nr = dd->atomGroups().subRange(0, zones->izone[zones->nizone - 1].cg1).size();
+    int nr = dd->atomGrouping().subRange(0, zones->izone[zones->nizone - 1].cg1).size();
 
     check_alloc_index(lexcls, nr);
 
@@ -1860,8 +1860,8 @@ static void finish_local_exclusions(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
                                     t_blocka *lexcls)
 {
     const auto nonhomeIzonesAtomRange =
-        dd->atomGroups().subRange(zones->izone[0].cg1,
-                                  zones->izone[zones->nizone - 1].cg1);
+        dd->atomGrouping().subRange(zones->izone[0].cg1,
+                                    zones->izone[zones->nizone - 1].cg1);
 
     if (dd->n_intercg_excl == 0)
     {
@@ -2007,7 +2007,7 @@ static int make_local_bondeds_excls(gmx_domdec_t *dd,
                                       idef_t,
                                       vsite_pbc, vsite_pbc_nalloc,
                                       izone,
-                                      dd->atomGroups().subRange(cg0t, cg1t));
+                                      dd->atomGrouping().subRange(cg0t, cg1t));
 
                 if (izone < nzone_excl)
                 {
@@ -2022,7 +2022,7 @@ static int make_local_bondeds_excls(gmx_domdec_t *dd,
                         excl_t->nra = 0;
                     }
 
-                    if (dd->atomGroups().allBlocksHaveSizeOne() &&
+                    if (dd->atomGrouping().allBlocksHaveSizeOne() &&
                         !rt->bExclRequired)
                     {
                         /* No charge groups and no distance check required */
@@ -2092,7 +2092,7 @@ static int make_local_bondeds_excls(gmx_domdec_t *dd,
 void dd_make_local_cgs(gmx_domdec_t *dd, t_block *lcgs)
 {
     lcgs->nr    = dd->globalAtomGroupIndices.size();
-    lcgs->index = dd->atomGroups_.rawIndex().data();
+    lcgs->index = dd->atomGrouping_.rawIndex().data();
 }
 
 void dd_make_local_top(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,

diff --git a/src/gromacs/domdec/redistribute.cpp b/src/gromacs/domdec/redistribute.cpp
index 54f1e5b033d481341d47ccd5ee418210957b64c7..a29e79111ecded0208499ec3fcb9b090cc890c23 100644 (file)
--- a/src/gromacs/domdec/redistribute.cpp
+++ b/src/gromacs/domdec/redistribute.cpp
@@ -248,14 +248,14 @@ static void print_cg_move(FILE *fplog,
     {
         fprintf(fplog, "%s %d moved more than the distance allowed by the domain decomposition (%f) in direction %c\n",
                 dd->comm->bCGs ? "The charge group starting at atom" : "Atom",
-                ddglatnr(dd, dd->atomGroups().block(cg).begin()), limitd, dim2char(dim));
+                ddglatnr(dd, dd->atomGrouping().block(cg).begin()), limitd, dim2char(dim));
     }
     else
     {
         /* We don't have a limiting distance available: don't print it */
         fprintf(fplog, "%s %d moved more than the distance allowed by the domain decomposition in direction %c\n",
                 dd->comm->bCGs ? "The charge group starting at atom" : "Atom",
-                ddglatnr(dd, dd->atomGroups().block(cg).begin()), dim2char(dim));
+                ddglatnr(dd, dd->atomGrouping().block(cg).begin()), dim2char(dim));
     }
     fprintf(fplog, "distance out of cell %f\n",
             dir == 1 ? pos_d - comm->cell_x1[dim] : pos_d - comm->cell_x0[dim]);
@@ -590,7 +590,7 @@ void dd_redistribute_cg(FILE *fplog, gmx_int64_t step,
 
     make_tric_corr_matrix(npbcdim, state->box, tcm);
 
-    const gmx::RangePartitioning &atomGroups = dd->atomGroups();
+    const gmx::RangePartitioning &atomGrouping = dd->atomGrouping();
 
     nthread = gmx_omp_nthreads_get(emntDomdec);
 
@@ -604,7 +604,7 @@ void dd_redistribute_cg(FILE *fplog, gmx_int64_t step,
         {
             calc_cg_move(fplog, step, dd, state, tric_dir, tcm,
                          cell_x0, cell_x1, limitd, limit0, limit1,
-                         atomGroups,
+                         atomGrouping,
                          ( thread   *dd->ncg_home)/nthread,
                          ((thread+1)*dd->ncg_home)/nthread,
                          fr->cutoff_scheme == ecutsGROUP ? cg_cm : as_rvec_array(state->x.data()),
@@ -634,7 +634,7 @@ void dd_redistribute_cg(FILE *fplog, gmx_int64_t step,
              * and the place where the charge group should go
              * in the next 6 bits. This saves some communication volume.
              */
-            nrcg = atomGroups.block(cg).size();
+            nrcg = atomGrouping.block(cg).size();
             cggl_flag[ncg[mc]*DD_CGIBS+1] = nrcg | flag;
             ncg[mc] += 1;
             nat[mc] += nrcg;
@@ -677,7 +677,7 @@ void dd_redistribute_cg(FILE *fplog, gmx_int64_t step,
              * but that could give rise to rounding issues.
              */
             home_pos_cg =
-                compact_and_copy_vec_cg(dd->ncg_home, move, dd->atomGroups(),
+                compact_and_copy_vec_cg(dd->ncg_home, move, dd->atomGrouping(),
                                         nvec, cg_cm, comm, bCompact);
             break;
         case ecutsVERLET:
@@ -686,7 +686,7 @@ void dd_redistribute_cg(FILE *fplog, gmx_int64_t step,
              * many conditionals for both for with and without charge groups.
              */
             home_pos_cg =
-                compact_and_copy_vec_cg(dd->ncg_home, move, dd->atomGroups(),
+                compact_and_copy_vec_cg(dd->ncg_home, move, dd->atomGrouping(),
                                         nvec, as_rvec_array(state->x.data()), comm, FALSE);
             if (bCompact)
             {
@@ -700,18 +700,18 @@ void dd_redistribute_cg(FILE *fplog, gmx_int64_t step,
 
     vec         = 0;
     home_pos_at =
-        compact_and_copy_vec_at(dd->ncg_home, move, dd->atomGroups(),
+        compact_and_copy_vec_at(dd->ncg_home, move, dd->atomGrouping(),
                                 nvec, vec++, as_rvec_array(state->x.data()),
                                 comm, bCompact);
     if (bV)
     {
-        compact_and_copy_vec_at(dd->ncg_home, move, dd->atomGroups(),
+        compact_and_copy_vec_at(dd->ncg_home, move, dd->atomGrouping(),
                                 nvec, vec++, as_rvec_array(state->v.data()),
                                 comm, bCompact);
     }
     if (bCGP)
     {
-        compact_and_copy_vec_at(dd->ncg_home, move, dd->atomGroups(),
+        compact_and_copy_vec_at(dd->ncg_home, move, dd->atomGrouping(),
                                 nvec, vec++, as_rvec_array(state->cg_p.data()),
                                 comm, bCompact);
     }
@@ -719,7 +719,7 @@ void dd_redistribute_cg(FILE *fplog, gmx_int64_t step,
     if (bCompact)
     {
         compact_ind(dd->ncg_home, move,
-                    dd->globalAtomGroupIndices, &dd->atomGroups_, dd->globalAtomIndices,
+                    dd->globalAtomGroupIndices, &dd->atomGrouping_, dd->globalAtomIndices,
                     dd->ga2la, comm->bLocalCG,
                     fr->cginfo);
     }
@@ -735,14 +735,14 @@ void dd_redistribute_cg(FILE *fplog, gmx_int64_t step,
         }
 
         clear_and_mark_ind(dd->ncg_home, move,
-                           dd->globalAtomGroupIndices, dd->atomGroups(), dd->globalAtomIndices,
+                           dd->globalAtomGroupIndices, dd->atomGrouping(), dd->globalAtomIndices,
                            dd->ga2la, comm->bLocalCG,
                            moved);
     }
 
     /* Now we can remove the excess global atom-group indices from the list */
     dd->globalAtomGroupIndices.resize(home_pos_cg);
-    dd->atomGroups_.reduceNumBlocks(home_pos_cg);
+    dd->atomGrouping_.reduceNumBlocks(home_pos_cg);
 
     /* We reuse the intBuffer without reacquiring since we are in the same scope */
     DDBufferAccess<int> &flagBuffer = moveBuffer;
@@ -904,7 +904,7 @@ void dd_redistribute_cg(FILE *fplog, gmx_int64_t step,
                 /* Set the global charge group index and size */
                 const int globalAtomGroupIndex = flagBuffer.buffer[cg*DD_CGIBS];
                 dd->globalAtomGroupIndices.push_back(globalAtomGroupIndex);
-                dd->atomGroups_.appendBlock(nrcg);
+                dd->atomGrouping_.appendBlock(nrcg);
                 /* Copy the state from the buffer */
                 if (fr->cutoff_scheme == ecutsGROUP)
                 {

diff --git a/src/gromacs/mdlib/wnblist.cpp b/src/gromacs/mdlib/wnblist.cpp
index 525cd73d9f081f39c1c7ec2546656846d49233aa..6f45539d9e6728052a49acf926a5a6bfcb6db457 100644 (file)
--- a/src/gromacs/mdlib/wnblist.cpp
+++ b/src/gromacs/mdlib/wnblist.cpp
@@ -75,7 +75,7 @@ static void write_nblist(FILE *out, gmx_domdec_t *dd, t_nblist *nblist, int nDNL
 
             for (zi = 0; zi < dd_zones->n; zi++)
             {
-                ca1[zi] = dd->atomGroups().block(dd_zones->cg_range[zi + 1]).begin();
+                ca1[zi] = dd->atomGrouping().block(dd_zones->cg_range[zi + 1]).begin();
             }
             i = 0;
             for (zi = 0; zi < dd_zones->nizone && zi < dd_zones->n; zi++)