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ECP-copa · Nov 8, 2023 · f071fd1 · f071fd1
1 parent c643d5c
commit f071fd1
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Showing 6 changed files with 59 additions and 52 deletions.
diff --git a/core/src/Cabana_LinkedCellList.hpp b/core/src/Cabana_LinkedCellList.hpp
@@ -198,7 +198,7 @@ class LinkedCellList
     */
     KOKKOS_INLINE_FUNCTION
     Scalar minDistanceToPoint( const Scalar x, const Scalar y, const Scalar z,
-                             const int i, const int j, const int k ) const
+                               const int i, const int j, const int k ) const
     {
         return _grid.minDistanceToPoint( x, y, z, i, j, k );
     }
@@ -264,20 +264,18 @@ class LinkedCellList
         _grid.ijkBinIndex( cell, i, j, k );
 
         kmin = ( k - _cell_range > 0 ) ? k - _cell_range : 0;
-        kmax =
-            ( k + _cell_range + 1 < _grid._nz ) ? k + _cell_range + 1 : _grid._nz;
+        kmax = ( k + _cell_range + 1 < _grid._nz ) ? k + _cell_range + 1
+                                                   : _grid._nz;
 
         jmin = ( j - _cell_range > 0 ) ? j - _cell_range : 0;
-        jmax =
-            ( j + _cell_range + 1 < _grid._ny ) ? j + _cell_range + 1 : _grid._ny;
+        jmax = ( j + _cell_range + 1 < _grid._ny ) ? j + _cell_range + 1
+                                                   : _grid._ny;
 
         imin = ( i - _cell_range > 0 ) ? i - _cell_range : 0;
-        imax =
-           ( i + _cell_range + 1 < _grid._nx ) ? i + _cell_range + 1 : _grid._nx;
+        imax = ( i + _cell_range + 1 < _grid._nx ) ? i + _cell_range + 1
+                                                   : _grid._nx;
     }
 
-
-
     /*!
       \brief Get the 1d bin data.
       \return The 1d bin data.
@@ -456,7 +454,7 @@ class LinkedCellList
     //! Cutoff squared.
     Scalar _rsqr;
     //! Background grid.
-//    Impl::CartesianGrid<double> grid;
+    //    Impl::CartesianGrid<double> grid;
     //! Maximum cells per dimension.
     int _max_cells_dir;
     //! Maximum total cells.
@@ -641,7 +639,7 @@ class NeighborList<LinkedCellList<DeviceType, ScalarType>>
         int total_count = 0;
         int imin, imax, jmin, jmax, kmin, kmax;
         list.getCells( cell( particle_index ), imin, imax, jmin, jmax, kmin,
-                          kmax );
+                       kmax );
 
         // Loop over the cell stencil.
         for ( int i = imin; i < imax; ++i )

diff --git a/core/src/Cabana_Parallel.hpp b/core/src/Cabana_Parallel.hpp
@@ -254,7 +254,8 @@ inline void neighbor_parallel_for(
     const Kokkos::RangePolicy<ExecParameters...>& exec_policy,
     const FunctorType& functor, const NeighborListType& list,
     const FirstNeighborsTag, const SerialOpTag, const std::string& str = "",
-    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ), int>::type* = 0 )
+    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ),
+                            int>::type* = 0 )
 {
     Kokkos::Profiling::pushRegion( "Cabana::neighbor_parallel_for" );
 
@@ -319,7 +320,8 @@ inline void neighbor_parallel_for(
     const Kokkos::RangePolicy<ExecParameters...>& exec_policy,
     const FunctorType& functor, const NeighborListType& list,
     const SecondNeighborsTag, const SerialOpTag, const std::string& str = "",
-    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ), int>::type* = 0 )
+    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ),
+                            int>::type* = 0 )
 {
     Kokkos::Profiling::pushRegion( "Cabana::neighbor_parallel_for" );
 
@@ -391,7 +393,8 @@ inline void neighbor_parallel_for(
     const Kokkos::RangePolicy<ExecParameters...>& exec_policy,
     const FunctorType& functor, const NeighborListType& list,
     const FirstNeighborsTag, const TeamOpTag, const std::string& str = "",
-    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ), int>::type* = 0 )
+    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ),
+                            int>::type* = 0 )
 {
     Kokkos::Profiling::pushRegion( "Cabana::neighbor_parallel_for" );
 
@@ -464,7 +467,8 @@ inline void neighbor_parallel_for(
     const Kokkos::RangePolicy<ExecParameters...>& exec_policy,
     const FunctorType& functor, const NeighborListType& list,
     const SecondNeighborsTag, const TeamOpTag, const std::string& str = "",
-    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ), int>::type* = 0 )
+    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ),
+                            int>::type* = 0 )
 {
     Kokkos::Profiling::pushRegion( "Cabana::neighbor_parallel_for" );
 
@@ -544,7 +548,8 @@ inline void neighbor_parallel_for(
     const FunctorType& functor, const NeighborListType& list,
     const SecondNeighborsTag, const TeamVectorOpTag,
     const std::string& str = "",
-    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ), int>::type* = 0 )
+    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ),
+                            int>::type* = 0 )
 {
     Kokkos::Profiling::pushRegion( "Cabana::neighbor_parallel_for" );
 
@@ -648,7 +653,8 @@ inline void neighbor_parallel_reduce(
     const FunctorType& functor, const NeighborListType& list,
     const FirstNeighborsTag, const SerialOpTag, ReduceType& reduce_val,
     const std::string& str = "",
-    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ), int>::type* = 0 )
+    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ),
+                            int>::type* = 0 )
 {
     Kokkos::Profiling::pushRegion( "Cabana::neighbor_parallel_reduce" );
 
@@ -719,7 +725,8 @@ inline void neighbor_parallel_reduce(
     const FunctorType& functor, const NeighborListType& list,
     const SecondNeighborsTag, const SerialOpTag, ReduceType& reduce_val,
     const std::string& str = "",
-    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ), int>::type* = 0 )
+    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ),
+                            int>::type* = 0 )
 {
     Kokkos::Profiling::pushRegion( "Cabana::neighbor_parallel_reduce" );
 
@@ -797,7 +804,8 @@ inline void neighbor_parallel_reduce(
     const FunctorType& functor, const NeighborListType& list,
     const FirstNeighborsTag, const TeamOpTag, ReduceType& reduce_val,
     const std::string& str = "",
-    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ), int>::type* = 0 )
+    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ),
+                            int>::type* = 0 )
 {
     Kokkos::Profiling::pushRegion( "Cabana::neighbor_parallel_reduce" );
 
@@ -879,7 +887,8 @@ inline void neighbor_parallel_reduce(
     const FunctorType& functor, const NeighborListType& list,
     const SecondNeighborsTag, const TeamOpTag, ReduceType& reduce_val,
     const std::string& str = "",
-    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ), int>::type* = 0 )
+    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ),
+                            int>::type* = 0 )
 {
     Kokkos::Profiling::pushRegion( "Cabana::neighbor_parallel_reduce" );
 
@@ -966,7 +975,8 @@ inline void neighbor_parallel_reduce(
     const FunctorType& functor, const NeighborListType& list,
     const SecondNeighborsTag, const TeamVectorOpTag, ReduceType& reduce_val,
     const std::string& str = "",
-    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ), int>::type* = 0 )
+    typename std::enable_if<( !is_linked_cell_list<NeighborListType>::value ),
+                            int>::type* = 0 )
 {
     Kokkos::Profiling::pushRegion( "Cabana::neighbor_parallel_reduce" );
 
@@ -1136,8 +1146,7 @@ struct LinkedCellParallelFor
 
     LinkedCellParallelFor( std::string label, Policy exec_policy,
                            Functor functor, const LinkedCellType& list,
-                           ViewType cells,
-                           const index_type begin = 0 )
+                           ViewType cells, const index_type begin = 0 )
         : _exec_policy( exec_policy )
         , _functor( functor )
         , _list( list )
@@ -1264,9 +1273,9 @@ template <class FunctorType, class LinkedCellType, class... ExecParameters>
 inline void neighbor_parallel_for(
     const Kokkos::RangePolicy<ExecParameters...>& exec_policy,
     const FunctorType& functor, const LinkedCellType& list,
-    const FirstNeighborsTag, const SerialOpTag,
-    const std::string& str = "",
-    typename std::enable_if<( is_linked_cell_list<LinkedCellType>::value ), int>::type* = 0 )
+    const FirstNeighborsTag, const SerialOpTag, const std::string& str = "",
+    typename std::enable_if<( is_linked_cell_list<LinkedCellType>::value ),
+                            int>::type* = 0 )
 {
     using work_tag = typename Kokkos::RangePolicy<ExecParameters...>::work_tag;
     using execution_space =
@@ -1332,9 +1341,9 @@ template <class FunctorType, class LinkedCellType, class... ExecParameters>
 inline void neighbor_parallel_for(
     const Kokkos::RangePolicy<ExecParameters...>& exec_policy,
     const FunctorType& functor, const LinkedCellType& list,
-    const FirstNeighborsTag, const TeamOpTag,
-    const std::string& str = "" ,
-    typename std::enable_if<( is_linked_cell_list<LinkedCellType>::value ), int>::type* = 0 )
+    const FirstNeighborsTag, const TeamOpTag, const std::string& str = "",
+    typename std::enable_if<( is_linked_cell_list<LinkedCellType>::value ),
+                            int>::type* = 0 )
 {
     using work_tag = typename Kokkos::RangePolicy<ExecParameters...>::work_tag;
     using execution_space =

diff --git a/core/src/Cabana_VerletList.hpp b/core/src/Cabana_VerletList.hpp
@@ -180,10 +180,9 @@ struct VerletListBuilder
         // treated as candidates for neighbors.
         double grid_size = cell_size_ratio * neighborhood_radius;
         PositionValueType grid_delta[3] = { grid_size, grid_size, grid_size };
-        linked_cell_list = LinkedCellList<memory_space, PositionValueType>( position, grid_delta,
-                                                         grid_min, grid_max,
-                                                         neighborhood_radius,
-                                                         cell_size_ratio );
+        linked_cell_list = LinkedCellList<memory_space, PositionValueType>(
+            position, grid_delta, grid_min, grid_max, neighborhood_radius,
+            cell_size_ratio );
         bin_data_1d = linked_cell_list.binningData();
 
         // We will use the square of the distance for neighbor determination.

diff --git a/core/unit_test/tstLinkedCellList.hpp b/core/unit_test/tstLinkedCellList.hpp
@@ -100,8 +100,9 @@ struct LCLTestData
     }
 };
 
-void copyListToHost( LCLTestData& test_data,
-                     const Cabana::LinkedCellList<TEST_MEMSPACE, double> cell_list )
+void copyListToHost(
+    LCLTestData& test_data,
+    const Cabana::LinkedCellList<TEST_MEMSPACE, double> cell_list )
 {
     // Copy data to the host for testing.
     auto np = test_data.num_p;
@@ -260,7 +261,8 @@ void testLinkedList()
         auto begin = test_data.begin;
         auto end = test_data.end;
         Cabana::LinkedCellList<TEST_MEMSPACE, double> cell_list(
-            pos, begin, end, grid_delta, grid_min, grid_max, test_data.grid_delta[0] );
+            pos, begin, end, grid_delta, grid_min, grid_max,
+            test_data.grid_delta[0] );
         Cabana::permute( cell_list, test_data.aosoa );
 
         copyListToHost( test_data, cell_list );
@@ -271,8 +273,8 @@ void testLinkedList()
 
     // Now bin and permute all of the particles.
     {
-        Cabana::LinkedCellList<TEST_MEMSPACE, double> cell_list( pos, grid_delta,
-                                                         grid_min, grid_max, test_data.grid_delta[0] );
+        Cabana::LinkedCellList<TEST_MEMSPACE, double> cell_list(
+            pos, grid_delta, grid_min, grid_max, test_data.grid_delta[0] );
         Cabana::permute( cell_list, test_data.aosoa );
 
         copyListToHost( test_data, cell_list );
@@ -307,8 +309,8 @@ void testLinkedListSlice()
     }
     // Now bin and permute all of the particles.
     {
-        Cabana::LinkedCellList<TEST_MEMSPACE, double> cell_list( pos, grid_delta,
-                                                         grid_min, grid_max, grid_delta[0] );
+        Cabana::LinkedCellList<TEST_MEMSPACE, double> cell_list(
+            pos, grid_delta, grid_min, grid_max, grid_delta[0] );
         Cabana::permute( cell_list, pos );
 
         copyListToHost( test_data, cell_list );
@@ -330,8 +332,7 @@ void testLinkedListSlice()
 //---------------------------------------------------------------------------//
 // linked_list_parallel
 //---------------------------------------------------------------------------//
-template <class ListType, class TestListType,
-          class PositionType>
+template <class ListType, class TestListType, class PositionType>
 void checkLinkedCellParallel( const ListType& nlist,
                               const TestListType& N2_list_copy,
                               const int num_particle,
@@ -389,11 +390,11 @@ void checkLinkedCellParallel( const ListType& nlist,
     };
     Kokkos::RangePolicy<TEST_EXECSPACE> policy( 0, num_particle );
     Cabana::neighbor_parallel_for( policy, serial_count_op, nlist,
-                                     Cabana::FirstNeighborsTag(),
-                                     Cabana::SerialOpTag(), "test_1st_serial" );
+                                   Cabana::FirstNeighborsTag(),
+                                   Cabana::SerialOpTag(), "test_1st_serial" );
     Cabana::neighbor_parallel_for( policy, team_count_op, nlist,
-                                     Cabana::FirstNeighborsTag(),
-                                     Cabana::TeamOpTag(), "test_1st_team" );
+                                   Cabana::FirstNeighborsTag(),
+                                   Cabana::TeamOpTag(), "test_1st_team" );
     Kokkos::fence();
 
     checkFirstNeighborParallelFor( N2_list_copy, serial_result, team_result,
@@ -420,9 +421,9 @@ void testLinkedCellParallel()
         positions, grid_delta, test_data.grid_min, test_data.grid_max,
         test_data.test_radius, test_data.cell_size_ratio );
 
-//    Cabana::LinkedCellStencil<double> stencil(
-//        test_data.test_radius, test_data.cell_size_ratio, test_data.grid_min,
-//        test_data.grid_max );
+    //    Cabana::LinkedCellStencil<double> stencil(
+    //        test_data.test_radius, test_data.cell_size_ratio,
+    //        test_data.grid_min, test_data.grid_max );
 
     checkLinkedCellParallel( nlist, test_data.N2_list_copy,
                              test_data.num_particle, positions,

diff --git a/core/unit_test/tstNeighborList.hpp b/core/unit_test/tstNeighborList.hpp
@@ -325,7 +325,7 @@ void testModifyNeighbors()
 //---------------------------------------------------------------------------//
 // TESTS
 //---------------------------------------------------------------------------//
-//TEST( TEST_CATEGORY, linked_cell_stencil_test ) { testLinkedCellStencil(); }
+// TEST( TEST_CATEGORY, linked_cell_stencil_test ) { testLinkedCellStencil(); }
 
 //---------------------------------------------------------------------------//
 TEST( TEST_CATEGORY, verlet_list_full_test )

diff --git a/example/core_tutorial/08_linked_cell_list/linked_cell_list_example.cpp b/example/core_tutorial/08_linked_cell_list/linked_cell_list_example.cpp
@@ -109,8 +109,8 @@ void linkedCellListExample()
                                                     grid_delta,
                                                     grid_min, grid_max );
      */
-    Cabana::LinkedCellList<MemorySpace, double> cell_list( positions, grid_delta,
-                                                   grid_min, grid_max, grid_delta[0] );
+    Cabana::LinkedCellList<MemorySpace, double> cell_list(
+        positions, grid_delta, grid_min, grid_max, grid_delta[0] );
 
     /*
       Now permute the AoSoA (i.e. reorder the data) using the linked cell list.