Change some domdec data members to RVec or IVec

Where a trivial change from rvec/ivec to RVec/IVec is possible,
that change has been made. The data member gmx_domdec_t.nc is
renamed to numCells to facilitate completing the todo about
changing this member to IVec. Some dead code is also removed
from the domdec module.

Change-Id: I1ef78c5ec198c60a1dd40a57ee5f87feb48bf490

diff --git a/src/gromacs/domdec/box.cpp b/src/gromacs/domdec/box.cpp
index 0e9f4e611bc9258494c3d6ba3be60f0d7d8bf1d4..80c7797bf610d32106ed7daecd8175cfa0627bcb 100644 (file)
--- a/src/gromacs/domdec/box.cpp
+++ b/src/gromacs/domdec/box.cpp
@@ -288,8 +288,8 @@ void set_ddbox(const gmx_domdec_t&            dd,
         gmx::ArrayRef<const gmx::RVec> xRef = constArrayRefFromArray(
                 x.data(), masterRankHasTheSystemState ? x.size() : dd.comm->atomRanges.numHomeAtoms());
 
-        low_set_ddbox(dd.unitCellInfo.npbcdim, dd.unitCellInfo.numBoundedDimensions, &dd.nc, box,
-                      calculateUnboundedSize, xRef,
+        low_set_ddbox(dd.unitCellInfo.npbcdim, dd.unitCellInfo.numBoundedDimensions, &dd.numCells,
+                      box, calculateUnboundedSize, xRef,
                       needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ddbox);
     }
 

diff --git a/src/gromacs/domdec/cellsizes.cpp b/src/gromacs/domdec/cellsizes.cpp
index 28078ffc54bfd45b2c663529cf18a3aad64b527e..4867f64330aebaac43ddc9c040398bae851ae8f0 100644 (file)
--- a/src/gromacs/domdec/cellsizes.cpp
+++ b/src/gromacs/domdec/cellsizes.cpp
@@ -70,7 +70,7 @@ static void set_pme_maxshift(gmx_domdec_t*      dd,
     int                sh;
 
     comm = dd->comm;
-    nc   = dd->nc[ddpme->dim];
+    nc   = dd->numCells[ddpme->dim];
     ns   = ddpme->nslab;
 
     if (!ddpme->dim_match)
@@ -137,13 +137,13 @@ static void check_box_size(const gmx_domdec_t* dd, const gmx_ddbox_t* ddbox)
         dim = dd->dim[d];
         if (dim < ddbox->nboundeddim
             && ddbox->box_size[dim] * ddbox->skew_fac[dim]
-                       < dd->nc[dim] * dd->comm->cellsize_limit * DD_CELL_MARGIN)
+                       < dd->numCells[dim] * dd->comm->cellsize_limit * DD_CELL_MARGIN)
         {
             gmx_fatal(
                     FARGS,
                     "The %c-size of the box (%f) times the triclinic skew factor (%f) is smaller "
                     "than the number of DD cells (%d) times the smallest allowed cell size (%f)\n",
-                    dim2char(dim), ddbox->box_size[dim], ddbox->skew_fac[dim], dd->nc[dim],
+                    dim2char(dim), ddbox->box_size[dim], ddbox->skew_fac[dim], dd->numCells[dim],
                     dd->comm->cellsize_limit);
         }
     }
@@ -221,14 +221,14 @@ set_dd_cell_sizes_slb(gmx_domdec_t* dd, const gmx_ddbox_t* ddbox, int setmode, i
     {
         cellsize_min[d] = ddbox->box_size[d] * ddbox->skew_fac[d];
         npulse[d]       = 1;
-        if (dd->nc[d] == 1 || comm->slb_frac[d] == nullptr)
+        if (dd->numCells[d] == 1 || comm->slb_frac[d] == nullptr)
         {
             /* Uniform grid */
-            real cell_dx = ddbox->box_size[d] / dd->nc[d];
+            real cell_dx = ddbox->box_size[d] / dd->numCells[d];
             switch (setmode)
             {
                 case setcellsizeslbMASTER:
-                    for (int j = 0; j < dd->nc[d] + 1; j++)
+                    for (int j = 0; j < dd->numCells[d] + 1; j++)
                     {
                         cell_x_master[d][j] = ddbox->box0[d] + j * cell_dx;
                     }
@@ -261,16 +261,16 @@ set_dd_cell_sizes_slb(gmx_domdec_t* dd, const gmx_ddbox_t* ddbox, int setmode, i
             }
             else
             {
-                cell_x_buffer.resize(dd->nc[d] + 1);
+                cell_x_buffer.resize(dd->numCells[d] + 1);
                 cell_x = cell_x_buffer;
             }
             cell_x[0] = ddbox->box0[d];
-            for (int j = 0; j < dd->nc[d]; j++)
+            for (int j = 0; j < dd->numCells[d]; j++)
             {
                 real cell_dx  = ddbox->box_size[d] * comm->slb_frac[d][j];
                 cell_x[j + 1] = cell_x[j] + cell_dx;
                 real cellsize = cell_dx * ddbox->skew_fac[d];
-                while (cellsize * npulse[d] < comm->systemInfo.cutoff && npulse[d] < dd->nc[d] - 1)
+                while (cellsize * npulse[d] < comm->systemInfo.cutoff && npulse[d] < dd->numCells[d] - 1)
                 {
                     npulse[d]++;
                 }
@@ -286,7 +286,7 @@ set_dd_cell_sizes_slb(gmx_domdec_t* dd, const gmx_ddbox_t* ddbox, int setmode, i
          * some of its own home charge groups back over the periodic boundary.
          * Double charge groups cause trouble with the global indices.
          */
-        if (d < ddbox->npbcdim && dd->nc[d] > 1 && npulse[d] >= dd->nc[d])
+        if (d < ddbox->npbcdim && dd->numCells[d] > 1 && npulse[d] >= dd->numCells[d])
         {
             char error_string[STRLEN];
 
@@ -295,7 +295,7 @@ set_dd_cell_sizes_slb(gmx_domdec_t* dd, const gmx_ddbox_t* ddbox, int setmode, i
                     "small for a cut-off of %f with %d domain decomposition cells, use 1 or more "
                     "than %d %s or increase the box size in this direction",
                     dim2char(d), ddbox->box_size[d], ddbox->skew_fac[d], comm->systemInfo.cutoff,
-                    dd->nc[d], dd->nc[d], dd->nnodes > dd->nc[d] ? "cells" : "ranks");
+                    dd->numCells[d], dd->numCells[d], dd->nnodes > dd->numCells[d] ? "cells" : "ranks");
 
             if (setmode == setcellsizeslbLOCAL)
             {
@@ -346,7 +346,7 @@ static void dd_cell_sizes_dlb_root_enforce_limits(gmx_domdec_t*      dd,
 
     comm = dd->comm;
 
-    const int ncd = dd->nc[dim];
+    const int ncd = dd->numCells[dim];
 
     const bool dimHasPbc = (dim < ddbox->npbcdim);
 
@@ -391,7 +391,7 @@ static void dd_cell_sizes_dlb_root_enforce_limits(gmx_domdec_t*      dd,
             if (!rowMaster->isCellMin[i])
             {
                 cell_size[i] *= fac;
-                if (!dimHasPbc && (i == 0 || i == dd->nc[dim] - 1))
+                if (!dimHasPbc && (i == 0 || i == dd->numCells[dim] - 1))
                 {
                     cellsize_limit_f_i = 0;
                 }
@@ -572,7 +572,7 @@ static void set_dd_cell_sizes_dlb_root(gmx_domdec_t*      dd,
     /* Convert the maximum change from the input percentage to a fraction */
     const real change_limit = comm->ddSettings.dlb_scale_lim * 0.01;
 
-    const int ncd = dd->nc[dim];
+    const int ncd = dd->numCells[dim];
 
     const bool bPBC = (dim < ddbox->npbcdim);
 
@@ -688,7 +688,7 @@ static void set_dd_cell_sizes_dlb_root(gmx_domdec_t*      dd,
                     rowMaster->cellFrac[i], rowMaster->cellFrac[i + 1]);
         }
 
-        if ((bPBC || (i != 0 && i != dd->nc[dim] - 1))
+        if ((bPBC || (i != 0 && i != dd->numCells[dim] - 1))
             && rowMaster->cellFrac[i + 1] - rowMaster->cellFrac[i] < cellsize_limit_f / DD_CELL_MARGIN)
         {
             char buf[22];
@@ -757,7 +757,7 @@ static void distribute_dd_cell_sizes_dlb(gmx_domdec_t*       dd,
     comm.cellsizesWithDlb[d].fracLower = cellFracRow[dd->ci[dim]];
     comm.cellsizesWithDlb[d].fracUpper = cellFracRow[dd->ci[dim] + 1];
     /* The whole array was communicated, so set the buffer position */
-    int pos = dd->nc[dim] + 1;
+    int pos = dd->numCells[dim] + 1;
     for (int d1 = 0; d1 <= d; d1++)
     {
         if (d1 < d)
@@ -860,7 +860,7 @@ static void set_dd_cell_sizes_dlb(gmx_domdec_t*      dd,
     /* Set the dimensions for which no DD is used */
     for (dim = 0; dim < DIM; dim++)
     {
-        if (dd->nc[dim] == 1)
+        if (dd->numCells[dim] == 1)
         {
             comm->cell_x0[dim] = 0;
             comm->cell_x1[dim] = ddbox->box_size[dim];

diff --git a/src/gromacs/domdec/distribute.cpp b/src/gromacs/domdec/distribute.cpp
index 50b17507ce8bdb23d9f3db9b18e816b4665c2cea..a681378a0514147c1271370e75683dbd7a4e3f32 100644 (file)
--- a/src/gromacs/domdec/distribute.cpp
+++ b/src/gromacs/domdec/distribute.cpp
@@ -310,7 +310,7 @@ static inline int computeAtomGroupDomainIndex(const gmx_domdec_t& dd,
         if (d < dd.unitCellInfo.npbcdim)
         {
             bool bScrew = (dd.unitCellInfo.haveScrewPBC && d == XX);
-            if (ddbox.tric_dir[d] && dd.nc[d] > 1)
+            if (ddbox.tric_dir[d] && dd.numCells[d] > 1)
             {
                 /* Use triclinic coordinates for this dimension */
                 for (int j = d + 1; j < DIM; j++)
@@ -359,13 +359,13 @@ static inline int computeAtomGroupDomainIndex(const gmx_domdec_t& dd,
         }
         /* This could be done more efficiently */
         ind[d] = 0;
-        while (ind[d] + 1 < dd.nc[d] && pos_d >= cellBoundaries[d][ind[d] + 1])
+        while (ind[d] + 1 < dd.numCells[d] && pos_d >= cellBoundaries[d][ind[d] + 1])
         {
             ind[d]++;
         }
     }
 
-    return dd_index(dd.nc, ind);
+    return dd_index(dd.numCells, ind);
 }
 
 

diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp
index 83bdef480341954040855b72c527206655376131..3f93013309faafb36a5989ed74febd712487ae1c 100644 (file)
--- a/src/gromacs/domdec/domdec.cpp
+++ b/src/gromacs/domdec/domdec.cpp
@@ -143,18 +143,6 @@ static const int ddNonbondedZonePairRanges[DD_MAXIZONE][3] = { { 0, 0, 8 },
                                                                { 2, 5, 6 },
                                                                { 3, 5, 7 } };
 
-
-/*
-   #define dd_index(n,i) ((((i)[ZZ]*(n)[YY] + (i)[YY])*(n)[XX]) + (i)[XX])
-
-   static void index2xyz(ivec nc,int ind,ivec xyz)
-   {
-   xyz[XX] = ind % nc[XX];
-   xyz[YY] = (ind / nc[XX]) % nc[YY];
-   xyz[ZZ] = ind / (nc[YY]*nc[XX]);
-   }
- */
-
 static void ddindex2xyz(const ivec nc, int ind, ivec xyz)
 {
     xyz[XX] = ind / (nc[YY] * nc[ZZ]);
@@ -167,7 +155,7 @@ static int ddcoord2ddnodeid(gmx_domdec_t* dd, ivec c)
     int ddnodeid = -1;
 
     const CartesianRankSetup& cartSetup = dd->comm->cartesianRankSetup;
-    const int                 ddindex   = dd_index(dd->nc, c);
+    const int                 ddindex   = dd_index(dd->numCells, c);
     if (cartSetup.bCartesianPP_PME)
     {
         ddnodeid = cartSetup.ddindex2ddnodeid[ddindex];
@@ -701,24 +689,11 @@ static int gmx_ddcoord2pmeindex(const t_commrec* cr, int x, int y, int z)
     ivec          coords;
     int           slab;
 
-    dd = cr->dd;
-    /*
-       if (dd->comm->bCartesian) {
-       gmx_ddindex2xyz(dd->nc,ddindex,coords);
-       dd_coords2pmecoords(dd,coords,coords_pme);
-       copy_ivec(dd->ntot,nc);
-       nc[dd->cartpmedim]         -= dd->nc[dd->cartpmedim];
-       coords_pme[dd->cartpmedim] -= dd->nc[dd->cartpmedim];
-
-       slab = (coords_pme[XX]*nc[YY] + coords_pme[YY])*nc[ZZ] + coords_pme[ZZ];
-       } else {
-       slab = (ddindex*cr->npmenodes + cr->npmenodes/2)/dd->nnodes;
-       }
-     */
+    dd         = cr->dd;
     coords[XX] = x;
     coords[YY] = y;
     coords[ZZ] = z;
-    slab       = ddindex2pmeindex(dd->comm->ddRankSetup, dd_index(dd->nc, coords));
+    slab       = ddindex2pmeindex(dd->comm->ddRankSetup, dd_index(dd->numCells, coords));
 
     return slab;
 }
@@ -737,7 +712,7 @@ static int ddcoord2simnodeid(const t_commrec* cr, int x, int y, int z)
     }
     else
     {
-        int ddindex = dd_index(cr->dd->nc, coords);
+        int ddindex = dd_index(cr->dd->numCells, coords);
         if (cartSetup.bCartesianPP)
         {
             nodeid = cartSetup.ddindex2simnodeid[ddindex];
@@ -884,7 +859,7 @@ static gmx_bool receive_vir_ener(const gmx_domdec_t* dd, gmx::ArrayRef<const int
             ivec coords;
             MPI_Cart_coords(cr->mpi_comm_mysim, cr->sim_nodeid, DIM, coords);
             coords[cartSetup.cartpmedim]++;
-            if (coords[cartSetup.cartpmedim] < dd->nc[cartSetup.cartpmedim])
+            if (coords[cartSetup.cartpmedim] < dd->numCells[cartSetup.cartpmedim])
             {
                 int rank;
                 MPI_Cart_rank(cr->mpi_comm_mysim, coords, &rank);
@@ -922,9 +897,9 @@ static void set_slb_pme_dim_f(gmx_domdec_t* dd, int dim, real** dim_f)
 
     comm = dd->comm;
 
-    snew(*dim_f, dd->nc[dim] + 1);
+    snew(*dim_f, dd->numCells[dim] + 1);
     (*dim_f)[0] = 0;
-    for (i = 1; i < dd->nc[dim]; i++)
+    for (i = 1; i < dd->numCells[dim]; i++)
     {
         if (comm->slb_frac[dim])
         {
@@ -932,10 +907,10 @@ static void set_slb_pme_dim_f(gmx_domdec_t* dd, int dim, real** dim_f)
         }
         else
         {
-            (*dim_f)[i] = static_cast<real>(i) / static_cast<real>(dd->nc[dim]);
+            (*dim_f)[i] = static_cast<real>(i) / static_cast<real>(dd->numCells[dim]);
         }
     }
-    (*dim_f)[dd->nc[dim]] = 1;
+    (*dim_f)[dd->numCells[dim]] = 1;
 }
 
 static void init_ddpme(gmx_domdec_t* dd, gmx_ddpme_t* ddpme, int dimind)
@@ -965,13 +940,13 @@ static void init_ddpme(gmx_domdec_t* dd, gmx_ddpme_t* ddpme, int dimind)
     snew(ddpme->pp_max, ddpme->nslab);
     for (int slab = 0; slab < ddpme->nslab; slab++)
     {
-        ddpme->pp_min[slab] = dd->nc[dd->dim[dimind]] - 1;
+        ddpme->pp_min[slab] = dd->numCells[dd->dim[dimind]] - 1;
         ddpme->pp_max[slab] = 0;
     }
     for (int i = 0; i < dd->nnodes; i++)
     {
         ivec xyz;
-        ddindex2xyz(dd->nc, i, xyz);
+        ddindex2xyz(dd->numCells, i, xyz);
         /* For y only use our y/z slab.
          * This assumes that the PME x grid size matches the DD grid size.
          */
@@ -1062,10 +1037,10 @@ static void make_load_communicator(gmx_domdec_t* dd, int dim_ind, ivec loc)
 
     dim = dd->dim[dim_ind];
     copy_ivec(loc, loc_c);
-    for (i = 0; i < dd->nc[dim]; i++)
+    for (i = 0; i < dd->numCells[dim]; i++)
     {
         loc_c[dim] = i;
-        rank       = dd_index(dd->nc, loc_c);
+        rank       = dd_index(dd->numCells, loc_c);
         if (rank == dd->rank)
         {
             /* This process is part of the group */
@@ -1087,13 +1062,13 @@ static void make_load_communicator(gmx_domdec_t* dd, int dim_ind, ivec loc)
 
                 RowMaster& rowMaster = *cellsizes.rowMaster;
                 rowMaster.cellFrac.resize(ddCellFractionBufferSize(dd, dim_ind));
-                rowMaster.oldCellFrac.resize(dd->nc[dim] + 1);
-                rowMaster.isCellMin.resize(dd->nc[dim]);
+                rowMaster.oldCellFrac.resize(dd->numCells[dim] + 1);
+                rowMaster.isCellMin.resize(dd->numCells[dim]);
                 if (dim_ind > 0)
                 {
-                    rowMaster.bounds.resize(dd->nc[dim]);
+                    rowMaster.bounds.resize(dd->numCells[dim]);
                 }
-                rowMaster.buf_ncd.resize(dd->nc[dim]);
+                rowMaster.buf_ncd.resize(dd->numCells[dim]);
             }
             else
             {
@@ -1103,7 +1078,7 @@ static void make_load_communicator(gmx_domdec_t* dd, int dim_ind, ivec loc)
         }
         if (dd->ci[dim] == dd->master_ci[dim])
         {
-            snew(dd->comm->load[dim_ind].load, dd->nc[dim] * DD_NLOAD_MAX);
+            snew(dd->comm->load[dim_ind].load, dd->numCells[dim] * DD_NLOAD_MAX);
         }
     }
 }
@@ -1186,7 +1161,7 @@ static void make_load_communicators(gmx_domdec_t gmx_unused* dd)
     if (dd->ndim > 1)
     {
         dim0 = dd->dim[0];
-        for (i = 0; i < dd->nc[dim0]; i++)
+        for (i = 0; i < dd->numCells[dim0]; i++)
         {
             loc[dim0] = i;
             make_load_communicator(dd, 1, loc);
@@ -1195,11 +1170,11 @@ static void make_load_communicators(gmx_domdec_t gmx_unused* dd)
     if (dd->ndim > 2)
     {
         dim0 = dd->dim[0];
-        for (i = 0; i < dd->nc[dim0]; i++)
+        for (i = 0; i < dd->numCells[dim0]; i++)
         {
             loc[dim0] = i;
             dim1      = dd->dim[1];
-            for (j = 0; j < dd->nc[dim1]; j++)
+            for (j = 0; j < dd->numCells[dim1]; j++)
             {
                 loc[dim1] = j;
                 make_load_communicator(dd, 2, loc);
@@ -1226,10 +1201,10 @@ static void setup_neighbor_relations(gmx_domdec_t* dd)
     {
         dim = dd->dim[d];
         copy_ivec(dd->ci, tmp);
-        tmp[dim]           = (tmp[dim] + 1) % dd->nc[dim];
+        tmp[dim]           = (tmp[dim] + 1) % dd->numCells[dim];
         dd->neighbor[d][0] = ddcoord2ddnodeid(dd, tmp);
         copy_ivec(dd->ci, tmp);
-        tmp[dim]           = (tmp[dim] - 1 + dd->nc[dim]) % dd->nc[dim];
+        tmp[dim]           = (tmp[dim] - 1 + dd->numCells[dim]) % dd->numCells[dim];
         dd->neighbor[d][1] = ddcoord2ddnodeid(dd, tmp);
         if (debug)
         {
@@ -1262,11 +1237,11 @@ static void setup_neighbor_relations(gmx_domdec_t* dd)
             s[d] = dd->ci[d] - zones->shift[i][d];
             if (s[d] < 0)
             {
-                s[d] += dd->nc[d];
+                s[d] += dd->numCells[d];
             }
-            else if (s[d] >= dd->nc[d])
+            else if (s[d] >= dd->numCells[d])
             {
-                s[d] -= dd->nc[d];
+                s[d] -= dd->numCells[d];
             }
         }
     }
@@ -1285,7 +1260,7 @@ static void setup_neighbor_relations(gmx_domdec_t* dd)
                                            std::min(ddNonbondedZonePairRanges[iZoneIndex][2], nzone));
         for (dim = 0; dim < DIM; dim++)
         {
-            if (dd->nc[dim] == 1)
+            if (dd->numCells[dim] == 1)
             {
                 /* All shifts should be allowed */
                 iZone.shift0[dim] = -1;
@@ -1338,8 +1313,8 @@ static void make_pp_communicator(const gmx::MDLogger& mdlog,
     {
         /* Set up cartesian communication for the particle-particle part */
         GMX_LOG(mdlog.info)
-                .appendTextFormatted("Will use a Cartesian communicator: %d x %d x %d", dd->nc[XX],
-                                     dd->nc[YY], dd->nc[ZZ]);
+                .appendTextFormatted("Will use a Cartesian communicator: %d x %d x %d",
+                                     dd->numCells[XX], dd->numCells[YY], dd->numCells[ZZ]);
 
         ivec periods;
         for (int i = 0; i < DIM; i++)
@@ -1347,7 +1322,8 @@ static void make_pp_communicator(const gmx::MDLogger& mdlog,
             periods[i] = TRUE;
         }
         MPI_Comm comm_cart;
-        MPI_Cart_create(cr->mpi_comm_mygroup, DIM, dd->nc, periods, static_cast<int>(reorder), &comm_cart);
+        MPI_Cart_create(cr->mpi_comm_mygroup, DIM, dd->numCells, periods, static_cast<int>(reorder),
+                        &comm_cart);
         /* We overwrite the old communicator with the new cartesian one */
         cr->mpi_comm_mygroup = comm_cart;
     }
@@ -1361,7 +1337,7 @@ static void make_pp_communicator(const gmx::MDLogger& mdlog,
          * and not the one after split, we need to make an index.
          */
         cartSetup.ddindex2ddnodeid.resize(dd->nnodes);
-        cartSetup.ddindex2ddnodeid[dd_index(dd->nc, dd->ci)] = dd->rank;
+        cartSetup.ddindex2ddnodeid[dd_index(dd->numCells, dd->ci)] = dd->rank;
         gmx_sumi(dd->nnodes, cartSetup.ddindex2ddnodeid.data(), cr);
         /* Get the rank of the DD master,
          * above we made sure that the master node is a PP node.
@@ -1397,7 +1373,7 @@ static void make_pp_communicator(const gmx::MDLogger& mdlog,
         std::vector<int> buf(dd->nnodes);
         if (thisRankHasDuty(cr, DUTY_PP))
         {
-            buf[dd_index(dd->nc, dd->ci)] = cr->sim_nodeid;
+            buf[dd_index(dd->numCells, dd->ci)] = cr->sim_nodeid;
         }
         /* Communicate the ddindex to simulation nodeid index */
         MPI_Allreduce(buf.data(), cartSetup.ddindex2simnodeid.data(), dd->nnodes, MPI_INT, MPI_SUM,
@@ -1410,7 +1386,7 @@ static void make_pp_communicator(const gmx::MDLogger& mdlog,
         {
             if (cartSetup.ddindex2simnodeid[i] == 0)
             {
-                ddindex2xyz(dd->nc, i, dd->master_ci);
+                ddindex2xyz(dd->numCells, i, dd->master_ci);
                 MPI_Cart_rank(dd->mpi_comm_all, dd->master_ci, &dd->masterrank);
             }
         }
@@ -1423,7 +1399,7 @@ static void make_pp_communicator(const gmx::MDLogger& mdlog,
     {
         /* No Cartesian communicators */
         /* We use the rank in dd->comm->all as DD index */
-        ddindex2xyz(dd->nc, dd->rank, dd->ci);
+        ddindex2xyz(dd->numCells, dd->rank, dd->ci);
         /* The simulation master nodeid is 0, so the DD master rank is also 0 */
         dd->masterrank = 0;
         clear_ivec(dd->master_ci);
@@ -1451,7 +1427,7 @@ static void receive_ddindex2simnodeid(gmx_domdec_t* dd, t_commrec* cr)
         std::vector<int> buf(dd->nnodes);
         if (thisRankHasDuty(cr, DUTY_PP))
         {
-            buf[dd_index(dd->nc, dd->ci)] = cr->sim_nodeid;
+            buf[dd_index(dd->numCells, dd->ci)] = cr->sim_nodeid;
         }
         /* Communicate the ddindex to simulation nodeid index */
         MPI_Allreduce(buf.data(), cartSetup.ddindex2simnodeid.data(), dd->nnodes, MPI_INT, MPI_SUM,
@@ -1699,7 +1675,7 @@ static void setupGroupCommunication(const gmx::MDLogger&     mdlog,
     /* We can not use DDMASTER(dd), because dd->masterrank is set later */
     if (MASTER(cr))
     {
-        dd->ma = std::make_unique<AtomDistribution>(dd->nc, numAtomsInSystem, numAtomsInSystem);
+        dd->ma = std::make_unique<AtomDistribution>(dd->numCells, numAtomsInSystem, numAtomsInSystem);
     }
 }
 
@@ -1782,7 +1758,7 @@ static int dd_getenv(const gmx::MDLogger& mdlog, const char* env_var, int def)
 
 static void check_dd_restrictions(const gmx_domdec_t* dd, const t_inputrec* ir, const gmx::MDLogger& mdlog)
 {
-    if (ir->ePBC == epbcSCREW && (dd->nc[XX] == 1 || dd->nc[YY] > 1 || dd->nc[ZZ] > 1))
+    if (ir->ePBC == epbcSCREW && (dd->numCells[XX] == 1 || dd->numCells[YY] > 1 || dd->numCells[ZZ] > 1))
     {
         gmx_fatal(FARGS, "With pbc=%s can only do domain decomposition in the x-direction",
                   epbc_names[ir->ePBC]);
@@ -2436,18 +2412,18 @@ static void set_dd_limits(const gmx::MDLogger& mdlog,
     }
 
     /* Set the DD setup given by ddGridSetup */
-    copy_ivec(ddGridSetup.numDomains, dd->nc);
+    copy_ivec(ddGridSetup.numDomains, dd->numCells);
     dd->ndim = ddGridSetup.numDDDimensions;
     copy_ivec(ddGridSetup.ddDimensions, dd->dim);
 
-    dd->nnodes = dd->nc[XX] * dd->nc[YY] * dd->nc[ZZ];
+    dd->nnodes = dd->numCells[XX] * dd->numCells[YY] * dd->numCells[ZZ];
 
     snew(comm->slb_frac, DIM);
     if (isDlbDisabled(comm))
     {
-        comm->slb_frac[XX] = get_slb_frac(mdlog, "x", dd->nc[XX], options.cellSizeX);
-        comm->slb_frac[YY] = get_slb_frac(mdlog, "y", dd->nc[YY], options.cellSizeY);
-        comm->slb_frac[ZZ] = get_slb_frac(mdlog, "z", dd->nc[ZZ], options.cellSizeZ);
+        comm->slb_frac[XX] = get_slb_frac(mdlog, "x", dd->numCells[XX], options.cellSizeX);
+        comm->slb_frac[YY] = get_slb_frac(mdlog, "y", dd->numCells[YY], options.cellSizeY);
+        comm->slb_frac[ZZ] = get_slb_frac(mdlog, "z", dd->numCells[ZZ], options.cellSizeZ);
     }
 
     /* Set the multi-body cut-off and cellsize limit for DLB */
@@ -2461,7 +2437,7 @@ static void set_dd_limits(const gmx::MDLogger& mdlog,
              * the minimum and the maximum,
              * since the extra communication cost is nearly zero.
              */
-            real acs           = average_cellsize_min(ddbox, dd->nc);
+            real acs           = average_cellsize_min(ddbox, dd->numCells);
             comm->cutoff_mbody = 0.5 * (systemInfo.minCutoffForMultiBody + acs);
             if (!isDlbDisabled(comm))
             {
@@ -2562,16 +2538,16 @@ static void writeSettings(gmx::TextWriter*   log,
         log->writeString("The allowed shrink of domain decomposition cells is:");
         for (d = 0; d < DIM; d++)
         {
-            if (dd->nc[d] > 1)
+            if (dd->numCells[d] > 1)
             {
-                if (d >= ddbox->npbcdim && dd->nc[d] == 2)
+                if (d >= ddbox->npbcdim && dd->numCells[d] == 2)
                 {
                     shrink = 0;
                 }
                 else
                 {
                     shrink = comm->cellsize_min_dlb[d]
-                             / (ddbox->box_size[d] * ddbox->skew_fac[d] / dd->nc[d]);
+                             / (ddbox->box_size[d] * ddbox->skew_fac[d] / dd->numCells[d]);
                 }
                 log->writeStringFormatted(" %c %.2f", dim2char(d), shrink);
             }
@@ -2590,7 +2566,7 @@ static void writeSettings(gmx::TextWriter*   log,
         log->writeString("The initial domain decomposition cell size is:");
         for (d = 0; d < DIM; d++)
         {
-            if (dd->nc[d] > 1)
+            if (dd->numCells[d] > 1)
             {
                 log->writeStringFormatted(" %c %.2f nm", dim2char(d), dd->comm->cellsize_min[d]);
             }
@@ -2722,7 +2698,7 @@ static void set_cell_limits_dlb(const gmx::MDLogger& mdlog,
     else
     {
         /* There is no cell size limit */
-        npulse = std::max(dd->nc[XX] - 1, std::max(dd->nc[YY] - 1, dd->nc[ZZ] - 1));
+        npulse = std::max(dd->numCells[XX] - 1, std::max(dd->numCells[YY] - 1, dd->numCells[ZZ] - 1));
     }
 
     if (!bNoCutOff && npulse > 1)
@@ -2734,7 +2710,7 @@ static void set_cell_limits_dlb(const gmx::MDLogger& mdlog,
             dim      = dd->dim[d];
             npulse_d = static_cast<int>(
                     1
-                    + dd->nc[dim] * comm->systemInfo.cutoff
+                    + dd->numCells[dim] * comm->systemInfo.cutoff
                               / (ddbox->box_size[dim] * ddbox->skew_fac[dim] * dlb_scale));
             npulse_d_max = std::max(npulse_d_max, npulse_d);
         }
@@ -2758,10 +2734,10 @@ static void set_cell_limits_dlb(const gmx::MDLogger& mdlog,
         }
         else
         {
-            comm->cd[d].np_dlb = std::min(npulse, dd->nc[dd->dim[d]] - 1);
+            comm->cd[d].np_dlb = std::min(npulse, dd->numCells[dd->dim[d]] - 1);
             comm->maxpulse     = std::max(comm->maxpulse, comm->cd[d].np_dlb);
         }
-        if (comm->cd[d].np_dlb < dd->nc[dd->dim[d]] - 1)
+        if (comm->cd[d].np_dlb < dd->numCells[dd->dim[d]] - 1)
         {
             comm->bVacDLBNoLimit = FALSE;
         }
@@ -2807,7 +2783,7 @@ gmx_bool dd_bonded_molpbc(const gmx_domdec_t* dd, int ePBC)
      * we do not need to take pbc into account for the bonded interactions.
      */
     return (ePBC != epbcNONE && dd->comm->systemInfo.haveInterDomainBondeds
-            && !(dd->nc[XX] > 1 && dd->nc[YY] > 1 && (dd->nc[ZZ] > 1 || ePBC == epbcXY)));
+            && !(dd->numCells[XX] > 1 && dd->numCells[YY] > 1 && (dd->numCells[ZZ] > 1 || ePBC == epbcXY)));
 }
 
 /*! \brief Sets grid size limits and PP-PME setup, prints settings to log */
@@ -2857,7 +2833,7 @@ static void set_ddgrid_parameters(const gmx::MDLogger& mdlog,
     }
     else
     {
-        vol_frac = (1 + comm_box_frac(dd->nc, comm->systemInfo.cutoff, *ddbox))
+        vol_frac = (1 + comm_box_frac(dd->numCells, comm->systemInfo.cutoff, *ddbox))
                    / static_cast<double>(dd->nnodes);
     }
     if (debug)
@@ -2966,8 +2942,8 @@ static bool canMake1DAnd1PulseDomainDecomposition(const DDSettings&
 
 bool is1DAnd1PulseDD(const gmx_domdec_t& dd)
 {
-    const int  maxDimensionSize             = std::max(dd.nc[XX], std::max(dd.nc[YY], dd.nc[ZZ]));
-    const int  productOfDimensionSizes      = dd.nc[XX] * dd.nc[YY] * dd.nc[ZZ];
+    const int maxDimensionSize = std::max(dd.numCells[XX], std::max(dd.numCells[YY], dd.numCells[ZZ]));
+    const int  productOfDimensionSizes      = dd.numCells[XX] * dd.numCells[YY] * dd.numCells[ZZ];
     const bool decompositionHasOneDimension = (maxDimensionSize == productOfDimensionSizes);
 
     const bool hasMax1Pulse =
@@ -3162,7 +3138,7 @@ static gmx_bool test_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<co
     {
         dim = dd->dim[d];
 
-        inv_cell_size = DD_CELL_MARGIN * dd->nc[dim] / ddbox.box_size[dim];
+        inv_cell_size = DD_CELL_MARGIN * dd->numCells[dim] / ddbox.box_size[dim];
         if (dd->unitCellInfo.ddBoxIsDynamic)
         {
             inv_cell_size *= DD_PRES_SCALE_MARGIN;

diff --git a/src/gromacs/domdec/domdec_internal.h b/src/gromacs/domdec/domdec_internal.h
index 1b62f894b093964c6f0d804a07d28e78f700f8b6..354f94352c1f9fcb91213a2dc6d217cd5fae79a6 100644 (file)
--- a/src/gromacs/domdec/domdec_internal.h
+++ b/src/gromacs/domdec/domdec_internal.h
@@ -778,7 +778,7 @@ static inline int dd_index(const ivec numDomains, const ivec domainCoordinates)
 /*! Returns the size of the buffer to hold fractional cell boundaries for DD dimension index dimIndex */
 static inline int ddCellFractionBufferSize(const gmx_domdec_t* dd, int dimIndex)
 {
-    return dd->nc[dd->dim[dimIndex]] + 1 + dimIndex * 2 + 1 + dimIndex;
+    return dd->numCells[dd->dim[dimIndex]] + 1 + dimIndex * 2 + 1 + dimIndex;
 }
 
 /*! \brief Maximum number of ranks for using send/recv for state scattering and gathering

diff --git a/src/gromacs/domdec/domdec_specatomcomm.cpp b/src/gromacs/domdec/domdec_specatomcomm.cpp
index 04faddad435aa3791c6a9662dc3e28ec5b3ec5e4..7c15e8ab3323fdd69f2e0f54085ea257a7e2c300 100644 (file)
--- a/src/gromacs/domdec/domdec_specatomcomm.cpp
+++ b/src/gromacs/domdec/domdec_specatomcomm.cpp
@@ -76,7 +76,7 @@ void dd_move_f_specat(gmx_domdec_t* dd, gmx_domdec_specat_comm_t* spac, rvec* f,
     for (int d = dd->ndim - 1; d >= 0; d--)
     {
         dim = dd->dim[d];
-        if (dd->nc[dim] > 2)
+        if (dd->numCells[dim] > 2)
         {
             /* Pulse the grid forward and backward */
             spas = spac->spas[d];
@@ -89,7 +89,8 @@ void dd_move_f_specat(gmx_domdec_t* dd, gmx_domdec_specat_comm_t* spac, rvec* f,
                               vbuf + spas[0].a.size(), spas[1].a.size());
             for (dir = 0; dir < 2; dir++)
             {
-                bPBC = ((dir == 0 && dd->ci[dim] == 0) || (dir == 1 && dd->ci[dim] == dd->nc[dim] - 1));
+                bPBC   = ((dir == 0 && dd->ci[dim] == 0)
+                        || (dir == 1 && dd->ci[dim] == dd->numCells[dim] - 1));
                 bScrew = (bPBC && dd->unitCellInfo.haveScrewPBC && dim == XX);
 
                 spas = &spac->spas[d][dir];
@@ -145,7 +146,7 @@ void dd_move_f_specat(gmx_domdec_t* dd, gmx_domdec_specat_comm_t* spac, rvec* f,
                        spas->a.size());
             /* Sum the buffer into the required forces */
             if (dd->unitCellInfo.haveScrewPBC && dim == XX
-                && (dd->ci[dim] == 0 || dd->ci[dim] == dd->nc[dim] - 1))
+                && (dd->ci[dim] == 0 || dd->ci[dim] == dd->numCells[dim] - 1))
             {
                 int i = 0;
                 for (int a : spas->a)
@@ -187,7 +188,7 @@ void dd_move_x_specat(gmx_domdec_t* dd, gmx_domdec_specat_comm_t* spac, const ma
     for (d = 0; d < dd->ndim; d++)
     {
         dim = dd->dim[d];
-        if (dd->nc[dim] > 2)
+        if (dd->numCells[dim] > 2)
         {
             /* Pulse the grid forward and backward */
             rvec* vbuf = as_rvec_array(spac->vbuf.data());
@@ -199,7 +200,7 @@ void dd_move_x_specat(gmx_domdec_t* dd, gmx_domdec_specat_comm_t* spac, const ma
                     bScrew = (dd->unitCellInfo.haveScrewPBC && dim == XX);
                     copy_rvec(box[dim], shift);
                 }
-                else if (dir == 1 && dd->ci[dim] == dd->nc[dim] - 1)
+                else if (dir == 1 && dd->ci[dim] == dd->numCells[dim] - 1)
                 {
                     bPBC   = TRUE;
                     bScrew = (dd->unitCellInfo.haveScrewPBC && dim == XX);
@@ -295,7 +296,7 @@ void dd_move_x_specat(gmx_domdec_t* dd, gmx_domdec_specat_comm_t* spac, const ma
             {
                 rvec* x = (v == 0 ? x0 : x1);
                 if (dd->unitCellInfo.haveScrewPBC && dim == XX
-                    && (dd->ci[XX] == 0 || dd->ci[XX] == dd->nc[XX] - 1))
+                    && (dd->ci[XX] == 0 || dd->ci[XX] == dd->numCells[XX] - 1))
                 {
                     /* Here we only perform the rotation, the rest of the pbc
                      * is handled in the constraint or viste routines.
@@ -379,7 +380,7 @@ int setup_specat_communication(gmx_domdec_t*             dd,
         /* Pulse the grid forward and backward */
         dim  = dd->dim[d];
         bPBC = (dim < dd->unitCellInfo.npbcdim);
-        if (dd->nc[dim] == 2)
+        if (dd->numCells[dim] == 2)
         {
             /* Only 2 cells, so we only need to communicate once */
             ndir = 1;
@@ -390,8 +391,8 @@ int setup_specat_communication(gmx_domdec_t*             dd,
         }
         for (int dir = 0; dir < ndir; dir++)
         {
-            if (!bPBC && dd->nc[dim] > 2
-                && ((dir == 0 && dd->ci[dim] == dd->nc[dim] - 1) || (dir == 1 && dd->ci[dim] == 0)))
+            if (!bPBC && dd->numCells[dim] > 2
+                && ((dir == 0 && dd->ci[dim] == dd->numCells[dim] - 1) || (dir == 1 && dd->ci[dim] == 0)))
             {
                 /* No pbc: the fist/last cell should not request atoms */
                 nsend_ptr = nsend_zero;
@@ -423,7 +424,7 @@ int setup_specat_communication(gmx_domdec_t*             dd,
     for (int d = 0; d < dd->ndim; d++)
     {
         /* Pulse the grid forward and backward */
-        if (dd->dim[d] >= dd->unitCellInfo.npbcdim || dd->nc[dd->dim[d]] > 2)
+        if (dd->dim[d] >= dd->unitCellInfo.npbcdim || dd->numCells[dd->dim[d]] > 2)
         {
             ndir = 2;
         }

diff --git a/src/gromacs/domdec/domdec_struct.h b/src/gromacs/domdec/domdec_struct.h
index 55a6a3e9690b253df20089df981867b88cbb3808..12a134c96c3b6ecf022e31506980ce38c81b2e60 100644 (file)
--- a/src/gromacs/domdec/domdec_struct.h
+++ b/src/gromacs/domdec/domdec_struct.h
@@ -94,21 +94,21 @@ struct DDPairInteractionRanges
     //! The j-atom range
     gmx::Range<int> jAtomRange;
     //! Minimum shifts to consider
-    ivec shift0 = {};
+    gmx::IVec shift0 = { 0, 0, 0 };
     //! Maximum shifts to consider
-    ivec shift1 = {};
+    gmx::IVec shift1 = { 0, 0, 0 };
 };
 
 typedef struct
 {
     /* Zone lower corner in triclinic coordinates         */
-    rvec x0 = {};
+    gmx::RVec x0 = { 0, 0, 0 };
     /* Zone upper corner in triclinic coordinates         */
-    rvec x1 = {};
+    gmx::RVec x1 = { 0, 0, 0 };
     /* Zone bounding box lower corner in Cartesian coords */
-    rvec bb_x0 = {};
+    gmx::RVec bb_x0 = { 0, 0, 0 };
     /* Zone bounding box upper corner in Cartesian coords */
-    rvec bb_x1 = {};
+    gmx::RVec bb_x1 = { 0, 0, 0 };
 } gmx_domdec_zone_size_t;
 
 struct gmx_domdec_zones_t
@@ -129,13 +129,13 @@ struct gmx_domdec_zones_t
 
 struct gmx_ddbox_t
 {
-    int  npbcdim;
-    int  nboundeddim;
-    rvec box0;
-    rvec box_size;
+    int       npbcdim;
+    int       nboundeddim;
+    gmx::RVec box0     = { 0, 0, 0 };
+    gmx::RVec box_size = { 0, 0, 0 };
     /* Tells if the box is skewed for each of the three cartesian directions */
-    ivec tric_dir;
-    rvec skew_fac;
+    gmx::IVec tric_dir = { 0, 0, 0 };
+    gmx::RVec skew_fac = { 0, 0, 0 };
     /* Orthogonal vectors for triclinic cells, Cartesian index */
     rvec v[DIM][DIM];
     /* Normal vectors for the cells walls */
@@ -170,10 +170,10 @@ struct gmx_domdec_t
     int      nnodes       = 0;
     MPI_Comm mpi_comm_all = MPI_COMM_NULL;
     /* The local DD cell index and rank */
-    ivec ci         = { 0, 0, 0 };
-    int  rank       = 0;
-    ivec master_ci  = { 0, 0, 0 };
-    int  masterrank = 0;
+    gmx::IVec ci         = { 0, 0, 0 };
+    int       rank       = 0;
+    gmx::IVec master_ci  = { 0, 0, 0 };
+    int       masterrank = 0;
     /* Communication with the PME only nodes */
     int                   pme_nodeid           = 0;
     gmx_bool              pme_receive_vir_ener = false;
@@ -185,9 +185,10 @@ struct gmx_domdec_t
     UnitCellInfo unitCellInfo;
 
     /* The communication setup, identical for each cell, cartesian index */
-    ivec nc   = { 0, 0, 0 };
-    int  ndim = 0;
-    ivec dim  = { 0, 0, 0 }; /* indexed by 0 to ndim */
+    //! Todo: refactor nbnxm to not rely on this sometimes being a nullptr so this can be IVec
+    ivec      numCells = { 0, 0, 0 };
+    int       ndim     = 0;
+    gmx::IVec dim      = { 0, 0, 0 }; /* indexed by 0 to ndim */
 
     /* Forward and backward neighboring cells, indexed by 0 to ndim */
     int neighbor[DIM][2] = { { 0, 0 }, { 0, 0 }, { 0, 0 } };

diff --git a/src/gromacs/domdec/domdec_topology.cpp b/src/gromacs/domdec/domdec_topology.cpp
index 502ae91eedc9f80ca05ce4657a76b7e385278c8c..a8424c8a6c1764fd28d2871cc017a10f56804fc4 100644 (file)
--- a/src/gromacs/domdec/domdec_topology.cpp
+++ b/src/gromacs/domdec/domdec_topology.cpp
@@ -1640,9 +1640,10 @@ void dd_make_local_top(gmx_domdec_t*       dd,
             /* Only need to check for dimensions where the part of the box
              * that is not communicated is smaller than the cut-off.
              */
-            if (d < npbcdim && dd->nc[d] > 1 && (dd->nc[d] - npulse[d]) * cellsize_min[d] < 2 * rc)
+            if (d < npbcdim && dd->numCells[d] > 1
+                && (dd->numCells[d] - npulse[d]) * cellsize_min[d] < 2 * rc)
             {
-                if (dd->nc[d] == 2)
+                if (dd->numCells[d] == 2)
                 {
                     rcheck[d] = TRUE;
                     bRCheckMB = TRUE;
@@ -1663,7 +1664,7 @@ void dd_make_local_top(gmx_domdec_t*       dd,
         {
             if (fr->bMolPBC)
             {
-                pbc_null = set_pbc_dd(&pbc, fr->ePBC, dd->nc, TRUE, box);
+                pbc_null = set_pbc_dd(&pbc, fr->ePBC, dd->numCells, TRUE, box);
             }
             else
             {

diff --git a/src/gromacs/domdec/dump.cpp b/src/gromacs/domdec/dump.cpp
index 28db18d212d455e594929bc1b897e8a22b34eaa2..e0e1a549e7c0b527911402facb53b54421943e72 100644 (file)
--- a/src/gromacs/domdec/dump.cpp
+++ b/src/gromacs/domdec/dump.cpp
@@ -87,7 +87,7 @@ void write_dd_grid_pdb(const char* fn, int64_t step, gmx_domdec_t* dd, matrix bo
                 }
                 else
                 {
-                    if (d < ddbox->npbcdim && dd->nc[d] > 1)
+                    if (d < ddbox->npbcdim && dd->numCells[d] > 1)
                     {
                         tric[d][i] = box[i][d] / box[i][i];
                     }

diff --git a/src/gromacs/domdec/partition.cpp b/src/gromacs/domdec/partition.cpp
index 2ff39b3a906010485c96926e7ec6438a2da7fa60..487514edae70a00b6e050768b0c5324499f2b096 100644 (file)
--- a/src/gromacs/domdec/partition.cpp
+++ b/src/gromacs/domdec/partition.cpp
@@ -209,7 +209,7 @@ static void dd_move_cellx(gmx_domdec_t* dd, const gmx_ddbox_t* ddbox, rvec cell_
         if (applyPbc)
         {
             /* Take the minimum to avoid double communication */
-            numPulsesMin = std::min(numPulses, dd->nc[dim] - 1 - numPulses);
+            numPulsesMin = std::min(numPulses, dd->numCells[dim] - 1 - numPulses);
         }
         else
         {
@@ -243,7 +243,7 @@ static void dd_move_cellx(gmx_domdec_t* dd, const gmx_ddbox_t* ddbox, rvec cell_
         for (int pulse = 0; pulse < numPulses; pulse++)
         {
             /* Communicate all the zone information backward */
-            bool receiveValidData = (applyPbc || dd->ci[dim] < dd->nc[dim] - 1);
+            bool receiveValidData = (applyPbc || dd->ci[dim] < dd->numCells[dim] - 1);
 
             static_assert(
                     sizeof(gmx_ddzone_t) == c_ddzoneNumReals * sizeof(real),
@@ -325,8 +325,8 @@ static void dd_move_cellx(gmx_domdec_t* dd, const gmx_ddbox_t* ddbox, rvec cell_
                  */
                 buf_s[i] = buf_r[i];
             }
-            if (((applyPbc || dd->ci[dim] + numPulses < dd->nc[dim]) && pulse == numPulses - 1)
-                || (!applyPbc && dd->ci[dim] + 1 + pulse == dd->nc[dim] - 1))
+            if (((applyPbc || dd->ci[dim] + numPulses < dd->numCells[dim]) && pulse == numPulses - 1)
+                || (!applyPbc && dd->ci[dim] + 1 + pulse == dd->numCells[dim] - 1))
             {
                 /* Store the extremes */
                 int pos = 0;
@@ -732,7 +732,7 @@ static void comm_dd_ns_cell_sizes(gmx_domdec_t* dd, gmx_ddbox_t* ddbox, rvec cel
         dim = dd->dim[dim_ind];
 
         /* Without PBC we don't have restrictions on the outer cells */
-        if (!(dim >= ddbox->npbcdim && (dd->ci[dim] == 0 || dd->ci[dim] == dd->nc[dim] - 1))
+        if (!(dim >= ddbox->npbcdim && (dd->ci[dim] == 0 || dd->ci[dim] == dd->numCells[dim] - 1))
             && isDlbOn(comm)
             && (comm->cell_x1[dim] - comm->cell_x0[dim]) * ddbox->skew_fac[dim] < comm->cellsize_min[dim])
         {
@@ -863,7 +863,7 @@ static void get_load_distribution(gmx_domdec_t* dd, gmx_wallcycle_t wcycle)
                 load->mdf      = 0;
                 load->pme      = 0;
                 int pos        = 0;
-                for (int i = 0; i < dd->nc[dim]; i++)
+                for (int i = 0; i < dd->numCells[dim]; i++)
                 {
                     load->sum += load->load[pos++];
                     load->max = std::max(load->max, load->load[pos]);
@@ -904,7 +904,7 @@ static void get_load_distribution(gmx_domdec_t* dd, gmx_wallcycle_t wcycle)
                 }
                 if (isDlbOn(comm) && rowMaster->dlbIsLimited)
                 {
-                    load->sum_m *= dd->nc[dim];
+                    load->sum_m *= dd->numCells[dim];
                     load->flags |= (1 << d);
                 }
             }
@@ -1258,7 +1258,7 @@ static void turn_on_dlb(const gmx::MDLogger& mdlog, gmx_domdec_t* dd, int64_t st
         {
             comm->load[d].sum_m = comm->load[d].sum;
 
-            int nc = dd->nc[dd->dim[d]];
+            int nc = dd->numCells[dd->dim[d]];
             for (int i = 0; i < nc; i++)
             {
                 rowMaster->cellFrac[i] = i / static_cast<real>(nc);

diff --git a/src/gromacs/domdec/redistribute.cpp b/src/gromacs/domdec/redistribute.cpp
index a747a26a1ccd6d67dc1b94ee97f9ca12c33d9e31..ba86477b598c5db0b46f25b3fa3c1c2ce7c7877f 100644 (file)
--- a/src/gromacs/domdec/redistribute.cpp
+++ b/src/gromacs/domdec/redistribute.cpp
@@ -299,7 +299,7 @@ static int computeMoveFlag(const gmx_domdec_t& dd, const ivec& dev)
             flag |= DD_FLAG_BW(d);
             if (firstMoveDimValue == -1)
             {
-                if (dd.nc[dim] > 2)
+                if (dd.numCells[dim] > 2)
                 {
                     firstMoveDimValue = d * 2 + 1;
                 }
@@ -344,7 +344,7 @@ static void calc_cg_move(FILE*              fplog,
         /* Do pbc and check DD cell boundary crossings */
         for (int d = DIM - 1; d >= 0; d--)
         {
-            if (dd->nc[d] > 1)
+            if (dd->numCells[d] > 1)
             {
                 bool bScrew = (dd->unitCellInfo.haveScrewPBC && d == XX);
                 /* Determine the location of this cg in lattice coordinates */
@@ -365,7 +365,7 @@ static void calc_cg_move(FILE*              fplog,
                                       cm_new, cm_new, pos_d);
                     }
                     dev[d] = 1;
-                    if (dd->ci[d] == dd->nc[d] - 1)
+                    if (dd->ci[d] == dd->numCells[d] - 1)
                     {
                         rvec_dec(cm_new, state->box[d]);
                         if (bScrew)
@@ -468,7 +468,7 @@ static void calcGroupMove(FILE*                     fplog,
         /* Do pbc and check DD cell boundary crossings */
         for (int d = DIM - 1; d >= 0; d--)
         {
-            if (dd->nc[d] > 1)
+            if (dd->numCells[d] > 1)
             {
                 /* Determine the location of this COG in lattice coordinates */
                 real pos_d = cog[d];
@@ -488,7 +488,7 @@ static void calcGroupMove(FILE*                     fplog,
                                       cogOld, cog, pos_d);
                     }
                     dev[d] = 1;
-                    if (dd->ci[d] == dd->nc[d] - 1)
+                    if (dd->ci[d] == dd->numCells[d] - 1)
                     {
                         rvec_dec(cog, state->box[d]);
                     }
@@ -584,7 +584,7 @@ void dd_redistribute_cg(FILE*                        fplog,
         {
             cell_x0[d] = comm->cell_x0[d];
         }
-        if (d >= npbcdim && dd->ci[d] == dd->nc[d] - 1)
+        if (d >= npbcdim && dd->ci[d] == dd->numCells[d] - 1)
         {
             cell_x1[d] = GMX_FLOAT_MAX;
         }
@@ -748,7 +748,7 @@ void dd_redistribute_cg(FILE*                        fplog,
         const int dim      = dd->dim[d];
         int       ncg_recv = 0;
         int       nvr      = 0;
-        for (int dir = 0; dir < (dd->nc[dim] == 2 ? 1 : 2); dir++)
+        for (int dir = 0; dir < (dd->numCells[dim] == 2 ? 1 : 2); dir++)
         {
             const int cdd = d * 2 + dir;
             /* Communicate the cg and atom counts */
@@ -787,7 +787,7 @@ void dd_redistribute_cg(FILE*                        fplog,
             int              flag = flagBuffer.buffer[cg * DD_CGIBS + 1];
             const gmx::RVec& cog  = rvecBuffer.buffer[buf_pos];
 
-            if (dim >= npbcdim && dd->nc[dim] > 2)
+            if (dim >= npbcdim && dd->numCells[dim] > 2)
             {
                 /* No pbc in this dim and more than one domain boundary.
                  * We do a separate check if a charge group didn't move too far.
@@ -819,7 +819,7 @@ void dd_redistribute_cg(FILE*                        fplog,
                          * so we do not need to handle boundary crossings.
                          * This also means we do not have to handle PBC here.
                          */
-                        if (!((dd->ci[dim2] == dd->nc[dim2] - 1 && (flag & DD_FLAG_FW(d2)))
+                        if (!((dd->ci[dim2] == dd->numCells[dim2] - 1 && (flag & DD_FLAG_FW(d2)))
                               || (dd->ci[dim2] == 0 && (flag & DD_FLAG_BW(d2)))))
                         {
                             /* Clear the two flags for this dimension */
@@ -842,7 +842,7 @@ void dd_redistribute_cg(FILE*                        fplog,
                              * to an adjacent cell because of the
                              * staggering.
                              */
-                            if (pos_d >= cell_x1[dim2] && dd->ci[dim2] != dd->nc[dim2] - 1)
+                            if (pos_d >= cell_x1[dim2] && dd->ci[dim2] != dd->numCells[dim2] - 1)
                             {
                                 flag |= DD_FLAG_FW(d2);
                             }
@@ -861,7 +861,7 @@ void dd_redistribute_cg(FILE*                        fplog,
                     }
                     else if (flag & DD_FLAG_BW(d2))
                     {
-                        if (dd->nc[dd->dim[d2]] > 2)
+                        if (dd->numCells[dd->dim[d2]] > 2)
                         {
                             mc = d2 * 2 + 1;
                         }

diff --git a/src/gromacs/mdlib/constr.cpp b/src/gromacs/mdlib/constr.cpp
index eccc21f1f07ba174969b664840d449d0fa5ff7e7..984c901e62508918eb4eeb85429c1594e2365ec1 100644 (file)
--- a/src/gromacs/mdlib/constr.cpp
+++ b/src/gromacs/mdlib/constr.cpp
@@ -431,7 +431,7 @@ bool Constraints::Impl::apply(bool               bLog,
          * by the constraint coordinate communication routine,
          * so that here we can use normal pbc.
          */
-        pbc_null = set_pbc_dd(&pbc, ir.ePBC, DOMAINDECOMP(cr) ? cr->dd->nc : nullptr, FALSE, box);
+        pbc_null = set_pbc_dd(&pbc, ir.ePBC, DOMAINDECOMP(cr) ? cr->dd->numCells : nullptr, FALSE, box);
     }
     else
     {

diff --git a/src/gromacs/mdlib/force.cpp b/src/gromacs/mdlib/force.cpp
index 8b36c27e8c51971d255494c600142101a6e9dcbe..3e7c359e0326f478548ef83dc85e7523e3af3729 100644 (file)
--- a/src/gromacs/mdlib/force.cpp
+++ b/src/gromacs/mdlib/force.cpp
@@ -177,7 +177,7 @@ void do_force_lowlevel(t_forcerec*                         fr,
             /* Since all atoms are in the rectangular or triclinic unit-cell,
              * only single box vector shifts (2 in x) are required.
              */
-            set_pbc_dd(&pbc, fr->ePBC, DOMAINDECOMP(cr) ? cr->dd->nc : nullptr, TRUE, box);
+            set_pbc_dd(&pbc, fr->ePBC, DOMAINDECOMP(cr) ? cr->dd->numCells : nullptr, TRUE, box);
         }
 
         do_force_listed(wcycle, box, ir->fepvals, cr, ms, idef, x, hist, forceOutputs, fr, &pbc,

diff --git a/src/gromacs/mdlib/mdoutf.cpp b/src/gromacs/mdlib/mdoutf.cpp
index 24215b1b33d1c9803982aa804d9a7e7018eeda87..085f30201c82f5a9afd109e49156afdc08e983a4 100644 (file)
--- a/src/gromacs/mdlib/mdoutf.cpp
+++ b/src/gromacs/mdlib/mdoutf.cpp
@@ -297,7 +297,7 @@ void mdoutf_write_to_trajectory_files(FILE*                    fplog,
             fflush_tng(of->tng_low_prec);
             ivec one_ivec = { 1, 1, 1 };
             write_checkpoint(of->fn_cpt, of->bKeepAndNumCPT, fplog, cr,
-                             DOMAINDECOMP(cr) ? cr->dd->nc : one_ivec,
+                             DOMAINDECOMP(cr) ? cr->dd->numCells : one_ivec,
                              DOMAINDECOMP(cr) ? cr->dd->nnodes : cr->nnodes, of->eIntegrator,
                              of->simulation_part, of->bExpanded, of->elamstats, step, t,
                              state_global, observablesHistory, *(of->mdModulesNotifier));

diff --git a/src/gromacs/mdlib/nsgrid.cpp b/src/gromacs/mdlib/nsgrid.cpp
index db14315e70b945f2d25470d01f10efc57e7ada22..461a4984ab3dbfd3d3b14e1a363ea070ef9af266 100644 (file)
--- a/src/gromacs/mdlib/nsgrid.cpp
+++ b/src/gromacs/mdlib/nsgrid.cpp
@@ -179,7 +179,7 @@ void get_nsgrid_boundaries(int           nboundeddim,
                 bdens0     = (*gr0)[d];
             }
             /* Check for a DD cell not at a higher edge */
-            if (dd != nullptr && gr1 != nullptr && dd->ci[d] < dd->nc[d] - 1)
+            if (dd != nullptr && gr1 != nullptr && dd->ci[d] < dd->numCells[d] - 1)
             {
                 grid_x1[d] = (*gr1)[d];
                 bdens1     = (*gr1)[d];
@@ -238,7 +238,7 @@ static void set_grid_sizes(matrix              box,
         grid->cell_offset[i] = izones_x0[i];
         size                 = izones_size[i];
 
-        bDD = (dd != nullptr) && (dd->nc[i] > 1);
+        bDD = (dd != nullptr) && (dd->numCells[i] > 1);
         if (!bDD)
         {
             bDDRect = FALSE;

diff --git a/src/gromacs/mdlib/qmmm.cpp b/src/gromacs/mdlib/qmmm.cpp
index 24b3c75d2adbb5f0268a941f659659b06c3c6b4a..078afe88cf21a603fbaac3850e6c4037b7fd42a3 100644 (file)
--- a/src/gromacs/mdlib/qmmm.cpp
+++ b/src/gromacs/mdlib/qmmm.cpp
@@ -614,7 +614,7 @@ void update_QMMMrec(const t_commrec* cr, const t_forcerec* fr, const rvec* x, co
     /*  init_pbc(box);  needs to be called first, see pbc.h */
     ivec null_ivec;
     clear_ivec(null_ivec);
-    set_pbc_dd(&pbc, fr->ePBC, DOMAINDECOMP(cr) ? cr->dd->nc : null_ivec, FALSE, box);
+    set_pbc_dd(&pbc, fr->ePBC, DOMAINDECOMP(cr) ? cr->dd->numCells : null_ivec, FALSE, box);
     /* only in standard (normal) QMMM we need the neighbouring MM
      * particles to provide a electric field of point charges for the QM
      * atoms.

diff --git a/src/gromacs/mdlib/vsite.cpp b/src/gromacs/mdlib/vsite.cpp
index 4a0fe17a00e9e3ad1e9945044ff596d533ddb5c9..152567de68ccfdf054ff995edeb5bc925cbfbe88 100644 (file)
--- a/src/gromacs/mdlib/vsite.cpp
+++ b/src/gromacs/mdlib/vsite.cpp
@@ -641,7 +641,7 @@ void construct_vsites(const gmx_vsite_t* vsite,
          */
         ivec null_ivec;
         clear_ivec(null_ivec);
-        pbc_null = set_pbc_dd(&pbc, ePBC, useDomdec ? cr->dd->nc : null_ivec, FALSE, box);
+        pbc_null = set_pbc_dd(&pbc, ePBC, useDomdec ? cr->dd->numCells : null_ivec, FALSE, box);
     }
     else
     {
@@ -1748,7 +1748,7 @@ void spread_vsite_f(const gmx_vsite_t* vsite,
         /* This is wasting some CPU time as we now do this multiple times
          * per MD step.
          */
-        pbc_null = set_pbc_dd(&pbc, ePBC, useDomdec ? cr->dd->nc : nullptr, FALSE, box);
+        pbc_null = set_pbc_dd(&pbc, ePBC, useDomdec ? cr->dd->numCells : nullptr, FALSE, box);
     }
     else
     {

diff --git a/src/gromacs/nbnxm/nbnxm_setup.cpp b/src/gromacs/nbnxm/nbnxm_setup.cpp
index 89a34776391caa3f252bb9100e5cdd2524c7ea80..686179accd91db4e7399a735afc04febf3499792 100644 (file)
--- a/src/gromacs/nbnxm/nbnxm_setup.cpp
+++ b/src/gromacs/nbnxm/nbnxm_setup.cpp
@@ -456,7 +456,7 @@ std::unique_ptr<nonbonded_verlet_t> init_nb_verlet(const gmx::MDLogger&     mdlo
                                                        minimumIlistCountForGpuBalancing);
 
     auto pairSearch = std::make_unique<PairSearch>(
-            ir->ePBC, EI_TPI(ir->eI), DOMAINDECOMP(cr) ? &cr->dd->nc : nullptr,
+            ir->ePBC, EI_TPI(ir->eI), DOMAINDECOMP(cr) ? &cr->dd->numCells : nullptr,
             DOMAINDECOMP(cr) ? domdec_zones(cr->dd) : nullptr, pairlistParams.pairlistType,
             bFEP_NonBonded, gmx_omp_nthreads_get(emntPairsearch), pinPolicy);