From 24dfbb47512b03f2b370e7499f2adff746f4038a Mon Sep 17 00:00:00 2001 From: "Automatic Deployment (GitHub Action)" Date: Fri, 7 Feb 2025 18:17:26 +0000 Subject: [PATCH] Documentation Update --- doxygen/Cabana__VerletList_8hpp_source.html | 1576 +++++++++-------- .../classCabana_1_1VerletList-members.html | 3 + doxygen/classCabana_1_1VerletList.html | 106 +- doxygen/doxygen_crawl.html | 3 + doxygen/search/all_16.js | 2 +- doxygen/search/all_2.js | 2 +- doxygen/search/functions_1.js | 2 +- doxygen/search/functions_15.js | 2 +- 8 files changed, 985 insertions(+), 711 deletions(-) diff --git a/doxygen/Cabana__VerletList_8hpp_source.html b/doxygen/Cabana__VerletList_8hpp_source.html index 72323e1fd..f89f3c752 100644 --- a/doxygen/Cabana__VerletList_8hpp_source.html +++ b/doxygen/Cabana__VerletList_8hpp_source.html @@ -210,734 +210,898 @@
123//---------------------------------------------------------------------------//
124// Verlet List Builder
125//---------------------------------------------------------------------------//
-
126template <class DeviceType, class PositionType, class RandomAccessPositionType,
+
126template <class DeviceType, class RandomAccessPositionType, class RadiusType,
127 class AlgorithmTag, class LayoutTag, class BuildOpTag>
128struct VerletListBuilder
129{
130 // Types.
131 using device = DeviceType;
-
132 using PositionValueType = typename PositionType::value_type;
+
132 using PositionValueType = typename RandomAccessPositionType::value_type;
133 using memory_space = typename device::memory_space;
134 using execution_space = typename device::execution_space;
135
136 // List data.
137 VerletListData<memory_space, LayoutTag> _data;
-
138
-
139 // Neighbor cutoff.
-
140 PositionValueType rsqr;
-
141
-
142 // Positions.
-
143 RandomAccessPositionType _position;
-
144 std::size_t pid_begin, pid_end;
-
145
-
146 // Binning Data.
-
147 BinningData<memory_space> bin_data_1d;
-
148 LinkedCellList<memory_space, PositionValueType> linked_cell_list;
-
149
-
150 // Check to count or refill.
-
151 bool refill;
-
152 bool count;
-
153
-
154 // Maximum allocated neighbors per particle
-
155 std::size_t alloc_n;
-
156
-
157 // Constructor.
-
158 VerletListBuilder( PositionType positions, const std::size_t begin,
-
159 const std::size_t end,
-
160 const PositionValueType neighborhood_radius,
-
161 const PositionValueType cell_size_ratio,
-
162 const PositionValueType grid_min[3],
-
163 const PositionValueType grid_max[3],
-
164 const std::size_t max_neigh )
-
165 : pid_begin( begin )
-
166 , pid_end( end )
-
167 , alloc_n( max_neigh )
-
168 {
-
169 count = true;
-
170 refill = false;
-
171
-
172 // Create the count view.
-
173 _data.counts = Kokkos::View<int*, memory_space>( "num_neighbors",
-
174 size( positions ) );
-
175
-
176 // Make a guess for the number of neighbors per particle for 2D lists.
-
177 initCounts( LayoutTag() );
-
178
-
179 // Shallow copy for random access read-only memory.
-
180 _position = positions;
-
181
-
182 // Bin the particles in the grid. Don't actually sort them but make a
-
183 // permutation vector. Note that we are binning all particles here and
-
184 // not just the requested range. This is because all particles are
-
185 // treated as candidates for neighbors.
-
186 double grid_size = cell_size_ratio * neighborhood_radius;
-
187 PositionValueType grid_delta[3] = { grid_size, grid_size, grid_size };
-
188 linked_cell_list = createLinkedCellList<memory_space>(
-
189 _position, grid_delta, grid_min, grid_max, neighborhood_radius,
-
190 cell_size_ratio );
-
191 bin_data_1d = linked_cell_list.binningData();
-
192
-
193 // We will use the square of the distance for neighbor determination.
-
194 rsqr = neighborhood_radius * neighborhood_radius;
-
195 }
+
138 // Background squared neighbor cutoff.
+
139 PositionValueType rsqr;
+
140 // Fixed or per-particle neighbor radius.
+
141 RadiusType radius;
+
142
+
143 // Positions.
+
144 RandomAccessPositionType _position;
+
145 std::size_t pid_begin, pid_end;
+
146
+
147 // Binning Data.
+
148 BinningData<memory_space> bin_data_1d;
+
149 LinkedCellList<memory_space, PositionValueType> linked_cell_list;
+
150
+
151 // Check to count or refill.
+
152 bool refill;
+
153 bool count;
+
154
+
155 // Maximum allocated neighbors per particle
+
156 std::size_t alloc_n;
+
157
+
158 // Constructor with a single cutoff radius.
+
159 template <class PositionType>
+
160 VerletListBuilder( PositionType positions, const std::size_t begin,
+
161 const std::size_t end,
+
162 const RadiusType neighborhood_radius,
+
163 const PositionValueType cell_size_ratio,
+
164 const PositionValueType grid_min[3],
+
165 const PositionValueType grid_max[3],
+
166 const std::size_t max_neigh )
+
167 : pid_begin( begin )
+
168 , pid_end( end )
+
169 , alloc_n( max_neigh )
+
170 {
+
171 init( positions, neighborhood_radius, cell_size_ratio, grid_min,
+
172 grid_max );
+
173 // This value is not currently used, but set to be consistent with the
+
174 // variable cutoff case below.
+
175 radius = neighborhood_radius;
+
176 }
+
177
+
178 // Constructor with a background radius (used for the LinkedCellList) and a
+
179 // per-particle radius.
+
180 template <class PositionType>
+
181 VerletListBuilder( PositionType positions, const std::size_t begin,
+
182 const std::size_t end,
+
183 const PositionValueType background_radius,
+
184 const RadiusType neighborhood_radius,
+
185 const PositionValueType cell_size_ratio,
+
186 const PositionValueType grid_min[3],
+
187 const PositionValueType grid_max[3],
+
188 const std::size_t max_neigh )
+
189 : pid_begin( begin )
+
190 , pid_end( end )
+
191 , alloc_n( max_neigh )
+
192 {
+
193 assert( positions.size() == neighborhood_radius.size() );
+
194 init( positions, background_radius, cell_size_ratio, grid_min,
+
195 grid_max );
196
-
197 // Neighbor count team operator (only used for CSR lists).
-
198 struct CountNeighborsTag
-
199 {
-
200 };
-
201 using CountNeighborsPolicy =
-
202 Kokkos::TeamPolicy<execution_space, CountNeighborsTag,
-
203 Kokkos::IndexType<int>,
-
204 Kokkos::Schedule<Kokkos::Dynamic>>;
-
205
-
206 KOKKOS_INLINE_FUNCTION
-
207 void
-
208 operator()( const CountNeighborsTag&,
-
209 const typename CountNeighborsPolicy::member_type& team ) const
-
210 {
-
211 // The league rank of the team is the cardinal cell index we are
-
212 // working on.
-
213 int cell = team.league_rank();
-
214
-
215 // Get the stencil for this cell.
-
216 int imin, imax, jmin, jmax, kmin, kmax;
-
217 linked_cell_list.getStencilCells( cell, imin, imax, jmin, jmax, kmin,
-
218 kmax );
+
197 // Store a shallow copy (not squared).
+
198 // TODO: for cases where the radii never change, this could be better
+
199 // optimized with a deep copy of the squared radius instead.
+
200 radius = neighborhood_radius;
+
201 }
+
202
+
203 template <class PositionType>
+
204 void init( PositionType positions,
+
205 const PositionValueType neighborhood_radius,
+
206 const PositionValueType cell_size_ratio,
+
207 const PositionValueType grid_min[3],
+
208 const PositionValueType grid_max[3] )
+
209 {
+
210 count = true;
+
211 refill = false;
+
212
+
213 // Create the count view.
+
214 _data.counts = Kokkos::View<int*, memory_space>( "num_neighbors",
+
215 size( positions ) );
+
216
+
217 // Make a guess for the number of neighbors per particle for 2D lists.
+
218 initCounts( LayoutTag() );
219
-
220 // Operate on the particles in the bin.
-
221 std::size_t b_offset = bin_data_1d.binOffset( cell );
-
222 Kokkos::parallel_for(
-
223 Kokkos::TeamThreadRange( team, 0, bin_data_1d.binSize( cell ) ),
-
224 [&]( const int bi )
-
225 {
-
226 // Get the true particle id. The binned particle index is the
-
227 // league rank of the team.
-
228 std::size_t pid = linked_cell_list.permutation( bi + b_offset );
-
229
-
230 if ( ( pid >= pid_begin ) && ( pid < pid_end ) )
-
231 {
-
232 // Cache the particle coordinates.
-
233 double x_p = _position( pid, 0 );
-
234 double y_p = _position( pid, 1 );
-
235 double z_p = _position( pid, 2 );
-
236
-
237 // Loop over the cell stencil.
-
238 int stencil_count = 0;
-
239 for ( int i = imin; i < imax; ++i )
-
240 for ( int j = jmin; j < jmax; ++j )
-
241 for ( int k = kmin; k < kmax; ++k )
-
242 {
-
243 // See if we should actually check this box for
-
244 // neighbors.
-
245 if ( linked_cell_list.cellStencil()
-
246 .grid.minDistanceToPoint(
-
247 x_p, y_p, z_p, i, j, k ) <= rsqr )
-
248 {
-
249 std::size_t n_offset =
-
250 linked_cell_list.binOffset( i, j, k );
-
251 std::size_t num_n =
-
252 linked_cell_list.binSize( i, j, k );
-
253
-
254 // Check the particles in this bin to see if
-
255 // they are neighbors. If they are add to
-
256 // the count for this bin.
-
257 int cell_count = 0;
-
258 neighbor_reduce( team, pid, x_p, y_p, z_p,
-
259 n_offset, num_n,
-
260 cell_count, BuildOpTag() );
-
261 stencil_count += cell_count;
-
262 }
-
263 }
-
264 Kokkos::single( Kokkos::PerThread( team ), [&]()
-
265 { _data.counts( pid ) = stencil_count; } );
-
266 }
-
267 } );
-
268 }
-
269
-
270 // Neighbor count team vector loop (only used for CSR lists).
-
271 KOKKOS_INLINE_FUNCTION void
-
272 neighbor_reduce( const typename CountNeighborsPolicy::member_type& team,
-
273 const std::size_t pid, const double x_p, const double y_p,
-
274 const double z_p, const int n_offset, const int num_n,
-
275 int& cell_count, TeamVectorOpTag ) const
-
276 {
-
277 Kokkos::parallel_reduce(
-
278 Kokkos::ThreadVectorRange( team, num_n ),
-
279 [&]( const int n, int& local_count ) {
-
280 neighbor_kernel( pid, x_p, y_p, z_p, n_offset, n, local_count );
-
281 },
-
282 cell_count );
-
283 }
-
284
-
285 // Neighbor count serial loop (only used for CSR lists).
-
286 KOKKOS_INLINE_FUNCTION
-
287 void neighbor_reduce( const typename CountNeighborsPolicy::member_type,
-
288 const std::size_t pid, const double x_p,
-
289 const double y_p, const double z_p,
-
290 const int n_offset, const int num_n, int& cell_count,
-
291 TeamOpTag ) const
-
292 {
-
293 for ( int n = 0; n < num_n; n++ )
-
294 neighbor_kernel( pid, x_p, y_p, z_p, n_offset, n, cell_count );
-
295 }
-
296
-
297 // Neighbor count kernel
-
298 KOKKOS_INLINE_FUNCTION
-
299 void neighbor_kernel( const int pid, const double x_p, const double y_p,
-
300 const double z_p, const int n_offset, const int n,
-
301 int& local_count ) const
-
302 {
-
303 // Get the true id of the candidate neighbor.
-
304 std::size_t nid = linked_cell_list.permutation( n_offset + n );
-
305
-
306 // Cache the candidate neighbor particle coordinates.
-
307 double x_n = _position( nid, 0 );
-
308 double y_n = _position( nid, 1 );
-
309 double z_n = _position( nid, 2 );
-
310
-
311 // If this could be a valid neighbor, continue.
-
312 if ( NeighborDiscriminator<AlgorithmTag>::isValid(
-
313 pid, x_p, y_p, z_p, nid, x_n, y_n, z_n ) )
-
314 {
-
315 // Calculate the distance between the particle and its candidate
-
316 // neighbor.
-
317 PositionValueType dx = x_p - x_n;
-
318 PositionValueType dy = y_p - y_n;
-
319 PositionValueType dz = z_p - z_n;
-
320 PositionValueType dist_sqr = dx * dx + dy * dy + dz * dz;
-
321
-
322 // If within the cutoff add to the count.
-
323 if ( dist_sqr <= rsqr )
-
324 local_count += 1;
-
325 }
-
326 }
-
327
-
328 // Process the CSR counts by computing offsets and allocating the neighbor
-
329 // list.
-
330 template <class KokkosMemorySpace>
-
331 struct OffsetScanOp
-
332 {
-
333 using kokkos_mem_space = KokkosMemorySpace;
-
334 Kokkos::View<int*, kokkos_mem_space> counts;
-
335 Kokkos::View<int*, kokkos_mem_space> offsets;
-
336 KOKKOS_INLINE_FUNCTION
-
337 void operator()( const int i, int& update, const bool final_pass ) const
-
338 {
-
339 if ( final_pass )
-
340 offsets( i ) = update;
-
341 update += counts( i );
-
342 }
-
343 };
-
344
-
345 void initCounts( VerletLayoutCSR ) {}
-
346
-
347 void initCounts( VerletLayout2D )
-
348 {
-
349 if ( alloc_n > 0 )
-
350 {
-
351 count = false;
-
352
-
353 _data.neighbors = Kokkos::View<int**, memory_space>(
-
354 Kokkos::ViewAllocateWithoutInitializing( "neighbors" ),
-
355 _data.counts.size(), alloc_n );
-
356 }
-
357 }
+
220 // Shallow copy for random access read-only memory.
+
221 _position = positions;
+
222
+
223 // Bin the particles in the grid. Don't actually sort them but make a
+
224 // permutation vector. Note that we are binning all particles here and
+
225 // not just the requested range. This is because all particles are
+
226 // treated as candidates for neighbors.
+
227 double grid_size = cell_size_ratio * neighborhood_radius;
+
228 PositionValueType grid_delta[3] = { grid_size, grid_size, grid_size };
+
229 linked_cell_list = createLinkedCellList<memory_space>(
+
230 _position, grid_delta, grid_min, grid_max, neighborhood_radius,
+
231 cell_size_ratio );
+
232 bin_data_1d = linked_cell_list.binningData();
+
233
+
234 // We will use the square of the distance for neighbor determination.
+
235 rsqr = neighborhood_radius * neighborhood_radius;
+
236 }
+
237
+
238 KOKKOS_INLINE_FUNCTION auto cutoff( [[maybe_unused]] const int p ) const
+
239 {
+
240 // Square the radius on the fly if using a per-particle field to avoid a
+
241 // deep copy.
+
242 if constexpr ( is_slice<RadiusType>::value ||
+
243 Kokkos::is_view<RadiusType>::value )
+
244 return radius( p ) * radius( p );
+
245 // This value is already squared.
+
246 else
+
247 return rsqr;
+
248 }
+
249
+
250 // Neighbor count team operator (only used for CSR lists).
+
251 struct CountNeighborsTag
+
252 {
+
253 };
+
254 using CountNeighborsPolicy =
+
255 Kokkos::TeamPolicy<execution_space, CountNeighborsTag,
+
256 Kokkos::IndexType<int>,
+
257 Kokkos::Schedule<Kokkos::Dynamic>>;
+
258
+
259 KOKKOS_INLINE_FUNCTION
+
260 void
+
261 operator()( const CountNeighborsTag&,
+
262 const typename CountNeighborsPolicy::member_type& team ) const
+
263 {
+
264 // The league rank of the team is the cardinal cell index we are
+
265 // working on.
+
266 int cell = team.league_rank();
+
267
+
268 // Get the stencil for this cell.
+
269 int imin, imax, jmin, jmax, kmin, kmax;
+
270 linked_cell_list.getStencilCells( cell, imin, imax, jmin, jmax, kmin,
+
271 kmax );
+
272
+
273 // Operate on the particles in the bin.
+
274 std::size_t b_offset = bin_data_1d.binOffset( cell );
+
275 Kokkos::parallel_for(
+
276 Kokkos::TeamThreadRange( team, 0, bin_data_1d.binSize( cell ) ),
+
277 [&]( const int bi )
+
278 {
+
279 // Get the true particle id. The binned particle index is the
+
280 // league rank of the team.
+
281 std::size_t pid = linked_cell_list.permutation( bi + b_offset );
+
282
+
283 if ( ( pid >= pid_begin ) && ( pid < pid_end ) )
+
284 {
+
285 // Cache the particle coordinates.
+
286 double x_p = _position( pid, 0 );
+
287 double y_p = _position( pid, 1 );
+
288 double z_p = _position( pid, 2 );
+
289
+
290 // Loop over the cell stencil.
+
291 int stencil_count = 0;
+
292 for ( int i = imin; i < imax; ++i )
+
293 for ( int j = jmin; j < jmax; ++j )
+
294 for ( int k = kmin; k < kmax; ++k )
+
295 {
+
296 // See if we should actually check this box for
+
297 // neighbors.
+
298 if ( linked_cell_list.cellStencil()
+
299 .grid.minDistanceToPoint(
+
300 x_p, y_p, z_p, i, j, k ) <= rsqr )
+
301 {
+
302 std::size_t n_offset =
+
303 linked_cell_list.binOffset( i, j, k );
+
304 std::size_t num_n =
+
305 linked_cell_list.binSize( i, j, k );
+
306
+
307 // Check the particles in this bin to see if
+
308 // they are neighbors. If they are add to
+
309 // the count for this bin.
+
310 int cell_count = 0;
+
311 neighbor_reduce( team, pid, x_p, y_p, z_p,
+
312 n_offset, num_n,
+
313 cell_count, BuildOpTag() );
+
314 stencil_count += cell_count;
+
315 }
+
316 }
+
317 Kokkos::single( Kokkos::PerThread( team ), [&]()
+
318 { _data.counts( pid ) = stencil_count; } );
+
319 }
+
320 } );
+
321 }
+
322
+
323 // Neighbor count team vector loop (only used for CSR lists).
+
324 KOKKOS_INLINE_FUNCTION void
+
325 neighbor_reduce( const typename CountNeighborsPolicy::member_type& team,
+
326 const std::size_t pid, const double x_p, const double y_p,
+
327 const double z_p, const int n_offset, const int num_n,
+
328 int& cell_count, TeamVectorOpTag ) const
+
329 {
+
330 Kokkos::parallel_reduce(
+
331 Kokkos::ThreadVectorRange( team, num_n ),
+
332 [&]( const int n, int& local_count ) {
+
333 neighbor_kernel( pid, x_p, y_p, z_p, n_offset, n, local_count );
+
334 },
+
335 cell_count );
+
336 }
+
337
+
338 // Neighbor count serial loop (only used for CSR lists).
+
339 KOKKOS_INLINE_FUNCTION
+
340 void neighbor_reduce( const typename CountNeighborsPolicy::member_type,
+
341 const std::size_t pid, const double x_p,
+
342 const double y_p, const double z_p,
+
343 const int n_offset, const int num_n, int& cell_count,
+
344 TeamOpTag ) const
+
345 {
+
346 for ( int n = 0; n < num_n; n++ )
+
347 neighbor_kernel( pid, x_p, y_p, z_p, n_offset, n, cell_count );
+
348 }
+
349
+
350 // Neighbor count kernel
+
351 KOKKOS_INLINE_FUNCTION
+
352 void neighbor_kernel( const int pid, const double x_p, const double y_p,
+
353 const double z_p, const int n_offset, const int n,
+
354 int& local_count ) const
+
355 {
+
356 // Get the true id of the candidate neighbor.
+
357 std::size_t nid = linked_cell_list.permutation( n_offset + n );
358
-
359 void processCounts( VerletLayoutCSR )
-
360 {
-
361 // Allocate offsets.
-
362 _data.offsets = Kokkos::View<int*, memory_space>(
-
363 Kokkos::ViewAllocateWithoutInitializing( "neighbor_offsets" ),
-
364 _data.counts.size() );
-
365
-
366 // Calculate offsets from counts and the total number of counts.
-
367 OffsetScanOp<memory_space> offset_op;
-
368 offset_op.counts = _data.counts;
-
369 offset_op.offsets = _data.offsets;
-
370 int total_num_neighbor;
-
371 Kokkos::RangePolicy<execution_space> range_policy(
-
372 0, _data.counts.extent( 0 ) );
-
373 Kokkos::parallel_scan( "Cabana::VerletListBuilder::offset_scan",
-
374 range_policy, offset_op, total_num_neighbor );
-
375 Kokkos::fence();
-
376
-
377 // Allocate the neighbor list.
-
378 _data.neighbors = Kokkos::View<int*, memory_space>(
-
379 Kokkos::ViewAllocateWithoutInitializing( "neighbors" ),
-
380 total_num_neighbor );
-
381
-
382 // Reset the counts. We count again when we fill.
-
383 Kokkos::deep_copy( _data.counts, 0 );
-
384 }
-
385
-
386 // Process 2D counts by computing the maximum number of neighbors and
-
387 // reallocating the 2D data structure if needed.
-
388 void processCounts( VerletLayout2D )
-
389 {
-
390 // Calculate the maximum number of neighbors.
-
391 auto counts = _data.counts;
-
392 int max;
-
393 Kokkos::Max<int> max_reduce( max );
-
394 Kokkos::parallel_reduce(
-
395 "Cabana::VerletListBuilder::reduce_max",
-
396 Kokkos::RangePolicy<execution_space>( 0, _data.counts.size() ),
-
397 KOKKOS_LAMBDA( const int i, int& value ) {
-
398 if ( counts( i ) > value )
-
399 value = counts( i );
-
400 },
-
401 max_reduce );
-
402 Kokkos::fence();
-
403 _data.max_n = static_cast<std::size_t>( max );
-
404
-
405 // Reallocate the neighbor list if previous size is exceeded.
-
406 if ( count or _data.max_n > _data.neighbors.extent( 1 ) )
-
407 {
-
408 refill = true;
-
409 Kokkos::deep_copy( _data.counts, 0 );
-
410 _data.neighbors = Kokkos::View<int**, memory_space>(
-
411 Kokkos::ViewAllocateWithoutInitializing( "neighbors" ),
-
412 _data.counts.size(), _data.max_n );
-
413 }
-
414 }
-
415
-
416 // Neighbor count team operator.
-
417 struct FillNeighborsTag
-
418 {
-
419 };
-
420 using FillNeighborsPolicy =
-
421 Kokkos::TeamPolicy<execution_space, FillNeighborsTag,
-
422 Kokkos::IndexType<int>,
-
423 Kokkos::Schedule<Kokkos::Dynamic>>;
-
424 KOKKOS_INLINE_FUNCTION
-
425 void
-
426 operator()( const FillNeighborsTag&,
-
427 const typename FillNeighborsPolicy::member_type& team ) const
-
428 {
-
429 // The league rank of the team is the cardinal cell index we are
-
430 // working on.
-
431 int cell = team.league_rank();
-
432
-
433 // Get the stencil for this cell.
-
434 int imin, imax, jmin, jmax, kmin, kmax;
-
435 linked_cell_list.getStencilCells( cell, imin, imax, jmin, jmax, kmin,
-
436 kmax );
-
437
-
438 // Operate on the particles in the bin.
-
439 std::size_t b_offset = bin_data_1d.binOffset( cell );
-
440 Kokkos::parallel_for(
-
441 Kokkos::TeamThreadRange( team, 0, bin_data_1d.binSize( cell ) ),
-
442 [&]( const int bi )
-
443 {
-
444 // Get the true particle id. The binned particle index is the
-
445 // league rank of the team.
-
446 std::size_t pid = linked_cell_list.permutation( bi + b_offset );
-
447
-
448 if ( ( pid >= pid_begin ) && ( pid < pid_end ) )
-
449 {
-
450 // Cache the particle coordinates.
-
451 double x_p = _position( pid, 0 );
-
452 double y_p = _position( pid, 1 );
-
453 double z_p = _position( pid, 2 );
-
454
-
455 // Loop over the cell stencil.
-
456 for ( int i = imin; i < imax; ++i )
-
457 for ( int j = jmin; j < jmax; ++j )
-
458 for ( int k = kmin; k < kmax; ++k )
-
459 {
-
460 // See if we should actually check this box for
-
461 // neighbors.
-
462 if ( linked_cell_list.cellStencil()
-
463 .grid.minDistanceToPoint(
-
464 x_p, y_p, z_p, i, j, k ) <= rsqr )
-
465 {
-
466 // Check the particles in this bin to see if
-
467 // they are neighbors.
-
468 std::size_t n_offset =
-
469 linked_cell_list.binOffset( i, j, k );
-
470 int num_n =
-
471 linked_cell_list.binSize( i, j, k );
-
472 neighbor_for( team, pid, x_p, y_p, z_p,
-
473 n_offset, num_n,
-
474 BuildOpTag() );
-
475 }
-
476 }
-
477 }
-
478 } );
-
479 }
-
480
-
481 // Neighbor fill team vector loop.
-
482 KOKKOS_INLINE_FUNCTION void
-
483 neighbor_for( const typename FillNeighborsPolicy::member_type& team,
-
484 const std::size_t pid, const double x_p, const double y_p,
-
485 const double z_p, const int n_offset, const int num_n,
-
486 TeamVectorOpTag ) const
-
487 {
-
488 Kokkos::parallel_for(
-
489 Kokkos::ThreadVectorRange( team, num_n ), [&]( const int n )
-
490 { neighbor_kernel( pid, x_p, y_p, z_p, n_offset, n ); } );
-
491 }
-
492
-
493 // Neighbor fill serial loop.
-
494 KOKKOS_INLINE_FUNCTION
-
495 void neighbor_for( const typename FillNeighborsPolicy::member_type team,
-
496 const std::size_t pid, const double x_p,
-
497 const double y_p, const double z_p, const int n_offset,
-
498 const int num_n, TeamOpTag ) const
-
499 {
-
500 for ( int n = 0; n < num_n; n++ )
-
501 Kokkos::single(
-
502 Kokkos::PerThread( team ),
-
503 [&]() { neighbor_kernel( pid, x_p, y_p, z_p, n_offset, n ); } );
-
504 }
-
505
-
506 // Neighbor fill kernel.
-
507 KOKKOS_INLINE_FUNCTION
-
508 void neighbor_kernel( const int pid, const double x_p, const double y_p,
-
509 const double z_p, const int n_offset,
-
510 const int n ) const
-
511 {
-
512 // Get the true id of the candidate neighbor.
-
513 std::size_t nid = linked_cell_list.permutation( n_offset + n );
-
514
-
515 // Cache the candidate neighbor particle coordinates.
-
516 double x_n = _position( nid, 0 );
-
517 double y_n = _position( nid, 1 );
-
518 double z_n = _position( nid, 2 );
-
519
-
520 // If this could be a valid neighbor, continue.
-
521 if ( NeighborDiscriminator<AlgorithmTag>::isValid(
-
522 pid, x_p, y_p, z_p, nid, x_n, y_n, z_n ) )
-
523 {
-
524 // Calculate the distance between the particle and its candidate
-
525 // neighbor.
-
526 PositionValueType dx = x_p - x_n;
-
527 PositionValueType dy = y_p - y_n;
-
528 PositionValueType dz = z_p - z_n;
-
529 PositionValueType dist_sqr = dx * dx + dy * dy + dz * dz;
-
530
-
531 // If within the cutoff increment the neighbor count and add as a
-
532 // neighbor at that index.
-
533 if ( dist_sqr <= rsqr )
-
534 {
-
535 _data.addNeighbor( pid, nid );
-
536 }
-
537 }
-
538 }
-
539};
-
540
-
541// Builder creation functions. This is only necessary to define the different
-
542// random access types.
-
543template <class DeviceType, class PositionType, class AlgorithmTag,
-
544 class LayoutTag, class BuildOpTag>
-
545auto createVerletListBuilder(
-
546 PositionType x, const std::size_t begin, const std::size_t end,
-
547 const typename PositionType::value_type radius,
-
548 const typename PositionType::value_type cell_size_ratio,
-
549 const typename PositionType::value_type grid_min[3],
-
550 const typename PositionType::value_type grid_max[3],
-
551 const std::size_t max_neigh,
-
552 typename std::enable_if<( is_slice<PositionType>::value ), int>::type* = 0 )
-
553{
-
554 using RandomAccessPositionType = typename PositionType::random_access_slice;
-
555 return VerletListBuilder<DeviceType, PositionType, RandomAccessPositionType,
-
556 AlgorithmTag, LayoutTag, BuildOpTag>(
-
557 x, begin, end, radius, cell_size_ratio, grid_min, grid_max, max_neigh );
-
558}
-
559
-
560template <class DeviceType, class PositionType, class AlgorithmTag,
-
561 class LayoutTag, class BuildOpTag>
-
562auto createVerletListBuilder(
-
563 PositionType x, const std::size_t begin, const std::size_t end,
-
564 const typename PositionType::value_type radius,
-
565 const typename PositionType::value_type cell_size_ratio,
-
566 const typename PositionType::value_type grid_min[3],
-
567 const typename PositionType::value_type grid_max[3],
-
568 const std::size_t max_neigh,
-
569 typename std::enable_if<( Kokkos::is_view<PositionType>::value ),
-
570 int>::type* = 0 )
-
571{
-
572 using RandomAccessPositionType =
-
573 Kokkos::View<typename PositionType::value_type**, DeviceType,
-
574 Kokkos::MemoryTraits<Kokkos::RandomAccess>>;
-
575 return VerletListBuilder<DeviceType, PositionType, RandomAccessPositionType,
-
576 AlgorithmTag, LayoutTag, BuildOpTag>(
-
577 x, begin, end, radius, cell_size_ratio, grid_min, grid_max, max_neigh );
-
578}
-
579
-
580//---------------------------------------------------------------------------//
-
581
-
583} // end namespace Impl
-
584
-
585//---------------------------------------------------------------------------//
-
603template <class MemorySpace, class AlgorithmTag, class LayoutTag,
-
604 class BuildTag = TeamVectorOpTag>
-
-
605class VerletList
+
359 // Cache the candidate neighbor particle coordinates.
+
360 double x_n = _position( nid, 0 );
+
361 double y_n = _position( nid, 1 );
+
362 double z_n = _position( nid, 2 );
+
363
+
364 // If this could be a valid neighbor, continue.
+
365 if ( NeighborDiscriminator<AlgorithmTag>::isValid(
+
366 pid, x_p, y_p, z_p, nid, x_n, y_n, z_n ) )
+
367 {
+
368 // Calculate the distance between the particle and its candidate
+
369 // neighbor.
+
370 PositionValueType dx = x_p - x_n;
+
371 PositionValueType dy = y_p - y_n;
+
372 PositionValueType dz = z_p - z_n;
+
373 PositionValueType dist_sqr = dx * dx + dy * dy + dz * dz;
+
374
+
375 // If within the cutoff add to the count.
+
376 if ( dist_sqr <= cutoff( pid ) )
+
377 local_count += 1;
+
378 }
+
379 }
+
380
+
381 // Process the CSR counts by computing offsets and allocating the neighbor
+
382 // list.
+
383 template <class KokkosMemorySpace>
+
384 struct OffsetScanOp
+
385 {
+
386 using kokkos_mem_space = KokkosMemorySpace;
+
387 Kokkos::View<int*, kokkos_mem_space> counts;
+
388 Kokkos::View<int*, kokkos_mem_space> offsets;
+
389 KOKKOS_INLINE_FUNCTION
+
390 void operator()( const int i, int& update, const bool final_pass ) const
+
391 {
+
392 if ( final_pass )
+
393 offsets( i ) = update;
+
394 update += counts( i );
+
395 }
+
396 };
+
397
+
398 void initCounts( VerletLayoutCSR ) {}
+
399
+
400 void initCounts( VerletLayout2D )
+
401 {
+
402 if ( alloc_n > 0 )
+
403 {
+
404 count = false;
+
405
+
406 _data.neighbors = Kokkos::View<int**, memory_space>(
+
407 Kokkos::ViewAllocateWithoutInitializing( "neighbors" ),
+
408 _data.counts.size(), alloc_n );
+
409 }
+
410 }
+
411
+
412 void processCounts( VerletLayoutCSR )
+
413 {
+
414 // Allocate offsets.
+
415 _data.offsets = Kokkos::View<int*, memory_space>(
+
416 Kokkos::ViewAllocateWithoutInitializing( "neighbor_offsets" ),
+
417 _data.counts.size() );
+
418
+
419 // Calculate offsets from counts and the total number of counts.
+
420 OffsetScanOp<memory_space> offset_op;
+
421 offset_op.counts = _data.counts;
+
422 offset_op.offsets = _data.offsets;
+
423 int total_num_neighbor;
+
424 Kokkos::RangePolicy<execution_space> range_policy(
+
425 0, _data.counts.extent( 0 ) );
+
426 Kokkos::parallel_scan( "Cabana::VerletListBuilder::offset_scan",
+
427 range_policy, offset_op, total_num_neighbor );
+
428 Kokkos::fence();
+
429
+
430 // Allocate the neighbor list.
+
431 _data.neighbors = Kokkos::View<int*, memory_space>(
+
432 Kokkos::ViewAllocateWithoutInitializing( "neighbors" ),
+
433 total_num_neighbor );
+
434
+
435 // Reset the counts. We count again when we fill.
+
436 Kokkos::deep_copy( _data.counts, 0 );
+
437 }
+
438
+
439 // Process 2D counts by computing the maximum number of neighbors and
+
440 // reallocating the 2D data structure if needed.
+
441 void processCounts( VerletLayout2D )
+
442 {
+
443 // Calculate the maximum number of neighbors.
+
444 auto counts = _data.counts;
+
445 int max;
+
446 Kokkos::Max<int> max_reduce( max );
+
447 Kokkos::parallel_reduce(
+
448 "Cabana::VerletListBuilder::reduce_max",
+
449 Kokkos::RangePolicy<execution_space>( 0, _data.counts.size() ),
+
450 KOKKOS_LAMBDA( const int i, int& value ) {
+
451 if ( counts( i ) > value )
+
452 value = counts( i );
+
453 },
+
454 max_reduce );
+
455 Kokkos::fence();
+
456 _data.max_n = static_cast<std::size_t>( max );
+
457
+
458 // Reallocate the neighbor list if previous size is exceeded.
+
459 if ( count or _data.max_n > _data.neighbors.extent( 1 ) )
+
460 {
+
461 refill = true;
+
462 Kokkos::deep_copy( _data.counts, 0 );
+
463 _data.neighbors = Kokkos::View<int**, memory_space>(
+
464 Kokkos::ViewAllocateWithoutInitializing( "neighbors" ),
+
465 _data.counts.size(), _data.max_n );
+
466 }
+
467 }
+
468
+
469 // Neighbor count team operator.
+
470 struct FillNeighborsTag
+
471 {
+
472 };
+
473 using FillNeighborsPolicy =
+
474 Kokkos::TeamPolicy<execution_space, FillNeighborsTag,
+
475 Kokkos::IndexType<int>,
+
476 Kokkos::Schedule<Kokkos::Dynamic>>;
+
477 KOKKOS_INLINE_FUNCTION
+
478 void
+
479 operator()( const FillNeighborsTag&,
+
480 const typename FillNeighborsPolicy::member_type& team ) const
+
481 {
+
482 // The league rank of the team is the cardinal cell index we are
+
483 // working on.
+
484 int cell = team.league_rank();
+
485
+
486 // Get the stencil for this cell.
+
487 int imin, imax, jmin, jmax, kmin, kmax;
+
488 linked_cell_list.getStencilCells( cell, imin, imax, jmin, jmax, kmin,
+
489 kmax );
+
490
+
491 // Operate on the particles in the bin.
+
492 std::size_t b_offset = bin_data_1d.binOffset( cell );
+
493 Kokkos::parallel_for(
+
494 Kokkos::TeamThreadRange( team, 0, bin_data_1d.binSize( cell ) ),
+
495 [&]( const int bi )
+
496 {
+
497 // Get the true particle id. The binned particle index is the
+
498 // league rank of the team.
+
499 std::size_t pid = linked_cell_list.permutation( bi + b_offset );
+
500
+
501 if ( ( pid >= pid_begin ) && ( pid < pid_end ) )
+
502 {
+
503 // Cache the particle coordinates.
+
504 double x_p = _position( pid, 0 );
+
505 double y_p = _position( pid, 1 );
+
506 double z_p = _position( pid, 2 );
+
507
+
508 // Loop over the cell stencil.
+
509 for ( int i = imin; i < imax; ++i )
+
510 for ( int j = jmin; j < jmax; ++j )
+
511 for ( int k = kmin; k < kmax; ++k )
+
512 {
+
513 // See if we should actually check this box for
+
514 // neighbors.
+
515 if ( linked_cell_list.cellStencil()
+
516 .grid.minDistanceToPoint(
+
517 x_p, y_p, z_p, i, j, k ) <= rsqr )
+
518 {
+
519 // Check the particles in this bin to see if
+
520 // they are neighbors.
+
521 std::size_t n_offset =
+
522 linked_cell_list.binOffset( i, j, k );
+
523 int num_n =
+
524 linked_cell_list.binSize( i, j, k );
+
525 neighbor_for( team, pid, x_p, y_p, z_p,
+
526 n_offset, num_n,
+
527 BuildOpTag() );
+
528 }
+
529 }
+
530 }
+
531 } );
+
532 }
+
533
+
534 // Neighbor fill team vector loop.
+
535 KOKKOS_INLINE_FUNCTION void
+
536 neighbor_for( const typename FillNeighborsPolicy::member_type& team,
+
537 const std::size_t pid, const double x_p, const double y_p,
+
538 const double z_p, const int n_offset, const int num_n,
+
539 TeamVectorOpTag ) const
+
540 {
+
541 Kokkos::parallel_for(
+
542 Kokkos::ThreadVectorRange( team, num_n ), [&]( const int n )
+
543 { neighbor_kernel( pid, x_p, y_p, z_p, n_offset, n ); } );
+
544 }
+
545
+
546 // Neighbor fill serial loop.
+
547 KOKKOS_INLINE_FUNCTION
+
548 void neighbor_for( const typename FillNeighborsPolicy::member_type team,
+
549 const std::size_t pid, const double x_p,
+
550 const double y_p, const double z_p, const int n_offset,
+
551 const int num_n, TeamOpTag ) const
+
552 {
+
553 for ( int n = 0; n < num_n; n++ )
+
554 Kokkos::single(
+
555 Kokkos::PerThread( team ),
+
556 [&]() { neighbor_kernel( pid, x_p, y_p, z_p, n_offset, n ); } );
+
557 }
+
558
+
559 // Neighbor fill kernel.
+
560 KOKKOS_INLINE_FUNCTION
+
561 void neighbor_kernel( const int pid, const double x_p, const double y_p,
+
562 const double z_p, const int n_offset,
+
563 const int n ) const
+
564 {
+
565 // Get the true id of the candidate neighbor.
+
566 std::size_t nid = linked_cell_list.permutation( n_offset + n );
+
567
+
568 // Cache the candidate neighbor particle coordinates.
+
569 double x_n = _position( nid, 0 );
+
570 double y_n = _position( nid, 1 );
+
571 double z_n = _position( nid, 2 );
+
572
+
573 // If this could be a valid neighbor, continue.
+
574 if ( NeighborDiscriminator<AlgorithmTag>::isValid(
+
575 pid, x_p, y_p, z_p, nid, x_n, y_n, z_n ) )
+
576 {
+
577 // Calculate the distance between the particle and its candidate
+
578 // neighbor.
+
579 PositionValueType dx = x_p - x_n;
+
580 PositionValueType dy = y_p - y_n;
+
581 PositionValueType dz = z_p - z_n;
+
582 PositionValueType dist_sqr = dx * dx + dy * dy + dz * dz;
+
583
+
584 // If within the cutoff increment the neighbor count and add as a
+
585 // neighbor at that index.
+
586 if ( dist_sqr <= cutoff( pid ) )
+
587 {
+
588 _data.addNeighbor( pid, nid );
+
589 }
+
590 }
+
591 }
+
592};
+
593
+
594// Builder creation functions. This is only necessary to define the different
+
595// random access types.
+
596template <class DeviceType, class AlgorithmTag, class LayoutTag,
+
597 class BuildOpTag, class PositionType>
+
598auto createVerletListBuilder(
+
599 PositionType x, const std::size_t begin, const std::size_t end,
+
600 const typename PositionType::value_type radius,
+
601 const typename PositionType::value_type cell_size_ratio,
+
602 const typename PositionType::value_type grid_min[3],
+
603 const typename PositionType::value_type grid_max[3],
+
604 const std::size_t max_neigh,
+
605 typename std::enable_if<( is_slice<PositionType>::value ), int>::type* = 0 )
606{
-
607 public:
-
608 static_assert( Kokkos::is_memory_space<MemorySpace>::value, "" );
-
609
-
611 using memory_space = MemorySpace;
-
612
-
614 using execution_space = typename memory_space::execution_space;
-
615
-
617 VerletListData<memory_space, LayoutTag> _data;
-
618
-
622 VerletList() {}
-
623
-
658 template <class PositionType>
-
-
659 VerletList(
-
660 PositionType x, const std::size_t begin, const std::size_t end,
-
661 const typename PositionType::value_type neighborhood_radius,
-
662 const typename PositionType::value_type cell_size_ratio,
-
663 const typename PositionType::value_type grid_min[3],
-
664 const typename PositionType::value_type grid_max[3],
-
665 const std::size_t max_neigh = 0,
-
666 typename std::enable_if<( is_slice<PositionType>::value ||
-
667 Kokkos::is_view<PositionType>::value ),
-
668 int>::type* = 0 )
-
669 {
-
670 build( x, begin, end, neighborhood_radius, cell_size_ratio, grid_min,
-
671 grid_max, max_neigh );
-
672 }
-
-
673
-
678 template <class PositionType>
-
679 void
-
-
680 build( PositionType x, const std::size_t begin, const std::size_t end,
-
681 const typename PositionType::value_type neighborhood_radius,
-
682 const typename PositionType::value_type cell_size_ratio,
-
683 const typename PositionType::value_type grid_min[3],
-
684 const typename PositionType::value_type grid_max[3],
-
685 const std::size_t max_neigh = 0,
-
686 typename std::enable_if<( is_slice<PositionType>::value ||
-
687 Kokkos::is_view<PositionType>::value ),
-
688 int>::type* = 0 )
-
689 {
-
690 // Use the default execution space.
-
691 build( execution_space{}, x, begin, end, neighborhood_radius,
-
692 cell_size_ratio, grid_min, grid_max, max_neigh );
-
693 }
-
-
698 template <class PositionType, class ExecutionSpace>
-
699 void
-
-
700 build( ExecutionSpace, PositionType x, const std::size_t begin,
-
701 const std::size_t end,
-
702 const typename PositionType::value_type neighborhood_radius,
-
703 const typename PositionType::value_type cell_size_ratio,
-
704 const typename PositionType::value_type grid_min[3],
-
705 const typename PositionType::value_type grid_max[3],
-
706 const std::size_t max_neigh = 0,
-
707 typename std::enable_if<( is_slice<PositionType>::value ||
-
708 Kokkos::is_view<PositionType>::value ),
-
709 int>::type* = 0 )
-
710 {
-
711 Kokkos::Profiling::ScopedRegion region( "Cabana::VerletList::build" );
-
712
-
713 static_assert( is_accessible_from<memory_space, ExecutionSpace>{}, "" );
+
607 using RandomAccessPositionType = typename PositionType::random_access_slice;
+
608 return VerletListBuilder<DeviceType, RandomAccessPositionType,
+
609 typename PositionType::value_type, AlgorithmTag,
+
610 LayoutTag, BuildOpTag>(
+
611 x, begin, end, radius, cell_size_ratio, grid_min, grid_max, max_neigh );
+
612}
+
613
+
614template <class DeviceType, class AlgorithmTag, class LayoutTag,
+
615 class BuildOpTag, class PositionType>
+
616auto createVerletListBuilder(
+
617 PositionType x, const std::size_t begin, const std::size_t end,
+
618 const typename PositionType::value_type radius,
+
619 const typename PositionType::value_type cell_size_ratio,
+
620 const typename PositionType::value_type grid_min[3],
+
621 const typename PositionType::value_type grid_max[3],
+
622 const std::size_t max_neigh,
+
623 typename std::enable_if<( Kokkos::is_view<PositionType>::value ),
+
624 int>::type* = 0 )
+
625{
+
626 using RandomAccessPositionType =
+
627 Kokkos::View<typename PositionType::value_type**, DeviceType,
+
628 Kokkos::MemoryTraits<Kokkos::RandomAccess>>;
+
629 return VerletListBuilder<DeviceType, RandomAccessPositionType,
+
630 typename PositionType::value_type, AlgorithmTag,
+
631 LayoutTag, BuildOpTag>(
+
632 x, begin, end, radius, cell_size_ratio, grid_min, grid_max, max_neigh );
+
633}
+
634
+
635template <class DeviceType, class AlgorithmTag, class LayoutTag,
+
636 class BuildOpTag, class PositionType, class RadiusType>
+
637auto createVerletListBuilder(
+
638 PositionType x, const std::size_t begin, const std::size_t end,
+
639 const typename PositionType::value_type background_radius,
+
640 const RadiusType radius,
+
641 const typename PositionType::value_type cell_size_ratio,
+
642 const typename PositionType::value_type grid_min[3],
+
643 const typename PositionType::value_type grid_max[3],
+
644 const std::size_t max_neigh,
+
645 typename std::enable_if<( is_slice<PositionType>::value ), int>::type* = 0 )
+
646{
+
647 using RandomAccessPositionType = typename PositionType::random_access_slice;
+
648 return VerletListBuilder<DeviceType, RandomAccessPositionType, RadiusType,
+
649 AlgorithmTag, LayoutTag, BuildOpTag>(
+
650 x, begin, end, background_radius, radius, cell_size_ratio, grid_min,
+
651 grid_max, max_neigh );
+
652}
+
653
+
654template <class DeviceType, class AlgorithmTag, class LayoutTag,
+
655 class BuildOpTag, class PositionType, class RadiusType>
+
656auto createVerletListBuilder(
+
657 PositionType x, const std::size_t begin, const std::size_t end,
+
658 const typename PositionType::value_type background_radius,
+
659 const RadiusType radius,
+
660 const typename PositionType::value_type cell_size_ratio,
+
661 const typename PositionType::value_type grid_min[3],
+
662 const typename PositionType::value_type grid_max[3],
+
663 const std::size_t max_neigh,
+
664 typename std::enable_if<( Kokkos::is_view<PositionType>::value ),
+
665 int>::type* = 0 )
+
666{
+
667 using RandomAccessPositionType =
+
668 Kokkos::View<typename PositionType::value_type**, DeviceType,
+
669 Kokkos::MemoryTraits<Kokkos::RandomAccess>>;
+
670 return VerletListBuilder<DeviceType, RandomAccessPositionType, RadiusType,
+
671 AlgorithmTag, LayoutTag, BuildOpTag>(
+
672 x, begin, end, background_radius, radius, cell_size_ratio, grid_min,
+
673 grid_max, max_neigh );
+
674}
+
675
+
676//---------------------------------------------------------------------------//
+
677
+
679} // end namespace Impl
+
680
+
681//---------------------------------------------------------------------------//
+
699template <class MemorySpace, class AlgorithmTag, class LayoutTag,
+
700 class BuildTag = TeamVectorOpTag>
+
+
701class VerletList
+
702{
+
703 public:
+
704 static_assert( Kokkos::is_memory_space<MemorySpace>::value, "" );
+
705
+
707 using memory_space = MemorySpace;
+
708
+
710 using execution_space = typename memory_space::execution_space;
+
711
+
713 VerletListData<memory_space, LayoutTag> _data;
714
-
715 assert( end >= begin );
-
716 assert( end <= size( x ) );
-
717
-
718 using device_type = Kokkos::Device<ExecutionSpace, memory_space>;
+
718 VerletList() {}
719
-
720 // Create a builder functor.
-
721 auto builder =
-
722 Impl::createVerletListBuilder<device_type, PositionType,
-
723 AlgorithmTag, LayoutTag, BuildTag>(
-
724 x, begin, end, neighborhood_radius, cell_size_ratio, grid_min,
-
725 grid_max, max_neigh );
-
726
-
727 // For each particle in the range check each neighboring bin for
-
728 // neighbor particles. Bins are at least the size of the neighborhood
-
729 // radius so the bin in which the particle resides and any surrounding
-
730 // bins are guaranteed to contain the neighboring particles.
-
731 // For CSR lists, we count, then fill neighbors. For 2D lists, we
-
732 // count and fill at the same time, unless the array size is exceeded,
-
733 // at which point only counting is continued to reallocate and refill.
-
734 typename decltype( builder )::FillNeighborsPolicy fill_policy(
-
735 builder.bin_data_1d.numBin(), Kokkos::AUTO, 4 );
-
736 if ( builder.count )
-
737 {
-
738 typename decltype( builder )::CountNeighborsPolicy count_policy(
-
739 builder.bin_data_1d.numBin(), Kokkos::AUTO, 4 );
-
740 Kokkos::parallel_for( "Cabana::VerletList::count_neighbors",
-
741 count_policy, builder );
-
742 }
-
743 else
-
744 {
-
745 builder.processCounts( LayoutTag() );
-
746 Kokkos::parallel_for( "Cabana::VerletList::fill_neighbors",
-
747 fill_policy, builder );
-
748 }
-
749 Kokkos::fence();
-
750
-
751 // Process the counts by computing offsets and allocating the neighbor
-
752 // list, if needed.
-
753 builder.processCounts( LayoutTag() );
-
754
-
755 // For each particle in the range fill (or refill) its part of the
-
756 // neighbor list.
-
757 if ( builder.count or builder.refill )
-
758 {
-
759 Kokkos::parallel_for( "Cabana::VerletList::fill_neighbors",
-
760 fill_policy, builder );
-
761 Kokkos::fence();
-
762 }
-
763
-
764 // Get the data from the builder.
-
765 _data = builder._data;
-
766 }
-
-
767
-
769 KOKKOS_INLINE_FUNCTION
-
-
770 void setNeighbor( const std::size_t particle_index,
-
771 const std::size_t neighbor_index,
-
772 const int new_index ) const
-
773 {
-
774 _data.setNeighbor( particle_index, neighbor_index, new_index );
-
775 }
-
-
776};
-
-
777
-
778//---------------------------------------------------------------------------//
-
779// Neighbor list interface implementation.
-
780//---------------------------------------------------------------------------//
-
782template <class MemorySpace, class AlgorithmTag, class BuildTag>
-
-
783class NeighborList<
-
784 VerletList<MemorySpace, AlgorithmTag, VerletLayoutCSR, BuildTag>>
-
785{
-
786 public:
-
788 using memory_space = MemorySpace;
-
790 using list_type =
-
791 VerletList<MemorySpace, AlgorithmTag, VerletLayoutCSR, BuildTag>;
-
792
-
794 KOKKOS_INLINE_FUNCTION
-
-
795 static std::size_t totalNeighbor( const list_type& list )
-
796 {
-
797 // Size of the allocated memory gives total neighbors.
-
798 return list._data.neighbors.extent( 0 );
-
799 }
-
-
800
-
802 KOKKOS_INLINE_FUNCTION
-
-
803 static std::size_t maxNeighbor( const list_type& list )
-
804 {
-
805 std::size_t num_p = list._data.counts.size();
-
806 return Impl::maxNeighbor( list, num_p );
-
807 }
-
-
808
-
810 KOKKOS_INLINE_FUNCTION
-
-
811 static std::size_t numNeighbor( const list_type& list,
-
812 const std::size_t particle_index )
-
813 {
-
814 return list._data.counts( particle_index );
-
815 }
-
-
816
-
819 KOKKOS_INLINE_FUNCTION
-
-
820 static std::size_t getNeighbor( const list_type& list,
-
821 const std::size_t particle_index,
-
822 const std::size_t neighbor_index )
-
823 {
-
824 return list._data.neighbors( list._data.offsets( particle_index ) +
-
825 neighbor_index );
-
826 }
-
-
827};
-
-
828
-
829//---------------------------------------------------------------------------//
-
831template <class MemorySpace, class AlgorithmTag, class BuildTag>
-
-
832class NeighborList<
-
833 VerletList<MemorySpace, AlgorithmTag, VerletLayout2D, BuildTag>>
-
834{
-
835 public:
-
837 using memory_space = MemorySpace;
-
839 using list_type =
-
840 VerletList<MemorySpace, AlgorithmTag, VerletLayout2D, BuildTag>;
-
841
-
843 KOKKOS_INLINE_FUNCTION
-
-
844 static std::size_t totalNeighbor( const list_type& list )
-
845 {
-
846 std::size_t num_p = list._data.counts.size();
-
847 return Impl::totalNeighbor( list, num_p );
-
848 }
-
-
849
-
851 KOKKOS_INLINE_FUNCTION
-
-
852 static std::size_t maxNeighbor( const list_type& list )
-
853 {
-
854 // Stored during neighbor search.
-
855 return list._data.max_n;
-
856 }
-
-
857
-
859 KOKKOS_INLINE_FUNCTION
-
-
860 static std::size_t numNeighbor( const list_type& list,
-
861 const std::size_t particle_index )
-
862 {
-
863 return list._data.counts( particle_index );
-
864 }
-
-
865
-
868 KOKKOS_INLINE_FUNCTION
-
-
869 static std::size_t getNeighbor( const list_type& list,
-
870 const std::size_t particle_index,
-
871 const std::size_t neighbor_index )
-
872 {
-
873 return list._data.neighbors( particle_index, neighbor_index );
-
874 }
-
-
875};
-
-
876
-
877//---------------------------------------------------------------------------//
-
878
-
879} // end namespace Cabana
-
880
-
881#endif // end CABANA_VERLETLIST_HPP
+
754 template <class PositionType>
+
+
755 VerletList(
+
756 PositionType x, const std::size_t begin, const std::size_t end,
+
757 const typename PositionType::value_type neighborhood_radius,
+
758 const typename PositionType::value_type cell_size_ratio,
+
759 const typename PositionType::value_type grid_min[3],
+
760 const typename PositionType::value_type grid_max[3],
+
761 const std::size_t max_neigh = 0,
+
762 typename std::enable_if<( is_slice<PositionType>::value ||
+
763 Kokkos::is_view<PositionType>::value ),
+
764 int>::type* = 0 )
+
765 {
+
766 build( x, begin, end, neighborhood_radius, cell_size_ratio, grid_min,
+
767 grid_max, max_neigh );
+
768 }
+
+
769
+
806 template <class PositionSlice, class RadiusSlice>
+
+
807 VerletList( PositionSlice x, const std::size_t begin, const std::size_t end,
+
808 const typename PositionSlice::value_type background_radius,
+
809 RadiusSlice neighborhood_radius,
+
810 const typename PositionSlice::value_type cell_size_ratio,
+
811 const typename PositionSlice::value_type grid_min[3],
+
812 const typename PositionSlice::value_type grid_max[3],
+
813 const std::size_t max_neigh = 0,
+
814 typename std::enable_if<( is_slice<PositionSlice>::value ),
+
815 int>::type* = 0 )
+
816 {
+
817 build( x, begin, end, background_radius, neighborhood_radius,
+
818 cell_size_ratio, grid_min, grid_max, max_neigh );
+
819 }
+
+
820
+
825 template <class PositionType>
+
826 void
+
+
827 build( PositionType x, const std::size_t begin, const std::size_t end,
+
828 const typename PositionType::value_type neighborhood_radius,
+
829 const typename PositionType::value_type cell_size_ratio,
+
830 const typename PositionType::value_type grid_min[3],
+
831 const typename PositionType::value_type grid_max[3],
+
832 const std::size_t max_neigh = 0,
+
833 typename std::enable_if<( is_slice<PositionType>::value ||
+
834 Kokkos::is_view<PositionType>::value ),
+
835 int>::type* = 0 )
+
836 {
+
837 // Use the default execution space.
+
838 build( execution_space{}, x, begin, end, neighborhood_radius,
+
839 cell_size_ratio, grid_min, grid_max, max_neigh );
+
840 }
+
+
845 template <class PositionType, class ExecutionSpace>
+
846 void
+
+
847 build( ExecutionSpace, PositionType x, const std::size_t begin,
+
848 const std::size_t end,
+
849 const typename PositionType::value_type neighborhood_radius,
+
850 const typename PositionType::value_type cell_size_ratio,
+
851 const typename PositionType::value_type grid_min[3],
+
852 const typename PositionType::value_type grid_max[3],
+
853 const std::size_t max_neigh = 0,
+
854 typename std::enable_if<( is_slice<PositionType>::value ||
+
855 Kokkos::is_view<PositionType>::value ),
+
856 int>::type* = 0 )
+
857 {
+
858 Kokkos::Profiling::ScopedRegion region( "Cabana::VerletList::build" );
+
859
+
860 static_assert( is_accessible_from<memory_space, ExecutionSpace>{}, "" );
+
861
+
862 assert( end >= begin );
+
863 assert( end <= size( x ) );
+
864
+
865 using device_type = Kokkos::Device<ExecutionSpace, memory_space>;
+
866 // Create a builder functor.
+
867 auto builder = Impl::createVerletListBuilder<device_type, AlgorithmTag,
+
868 LayoutTag, BuildTag>(
+
869 x, begin, end, neighborhood_radius, cell_size_ratio, grid_min,
+
870 grid_max, max_neigh );
+
871 buildImpl( builder );
+
872 }
+
+
873
+
878 template <class PositionSlice, class RadiusSlice>
+
+
879 void build( PositionSlice x, const std::size_t begin, const std::size_t end,
+
880 const typename PositionSlice::value_type background_radius,
+
881 RadiusSlice neighborhood_radius,
+
882 const typename PositionSlice::value_type cell_size_ratio,
+
883 const typename PositionSlice::value_type grid_min[3],
+
884 const typename PositionSlice::value_type grid_max[3],
+
885 const std::size_t max_neigh = 0 )
+
886 {
+
887 // Use the default execution space.
+
888 build( execution_space{}, x, begin, end, background_radius,
+
889 neighborhood_radius, cell_size_ratio, grid_min, grid_max,
+
890 max_neigh );
+
891 }
+
+
896 template <class PositionSlice, class RadiusSlice, class ExecutionSpace>
+
+
897 void build( ExecutionSpace, PositionSlice x, const std::size_t begin,
+
898 const std::size_t end,
+
899 const typename PositionSlice::value_type background_radius,
+
900 RadiusSlice neighborhood_radius,
+
901 const typename PositionSlice::value_type cell_size_ratio,
+
902 const typename PositionSlice::value_type grid_min[3],
+
903 const typename PositionSlice::value_type grid_max[3],
+
904 const std::size_t max_neigh = 0 )
+
905 {
+
906 Kokkos::Profiling::ScopedRegion region( "Cabana::VerletList::build" );
+
907
+
908 static_assert( is_accessible_from<memory_space, ExecutionSpace>{}, "" );
+
909
+
910 assert( end >= begin );
+
911 assert( end <= x.size() );
+
912
+
913 // Create a builder functor.
+
914 using device_type = Kokkos::Device<ExecutionSpace, memory_space>;
+
915 auto builder = Impl::createVerletListBuilder<device_type, AlgorithmTag,
+
916 LayoutTag, BuildTag>(
+
917 x, begin, end, background_radius, neighborhood_radius,
+
918 cell_size_ratio, grid_min, grid_max, max_neigh );
+
919 buildImpl( builder );
+
920 }
+
+
921
+
923 template <class BuilderType>
+
924 void buildImpl( BuilderType builder )
+
925 {
+
926 // For each particle in the range check each neighboring bin for
+
927 // neighbor particles. Bins are at least the size of the
+
928 // neighborhood radius so the bin in which the particle resides and
+
929 // any surrounding bins are guaranteed to contain the neighboring
+
930 // particles. For CSR lists, we count, then fill neighbors. For 2D
+
931 // lists, we count and fill at the same time, unless the array size
+
932 // is exceeded, at which point only counting is continued to
+
933 // reallocate and refill.
+
934 typename BuilderType::FillNeighborsPolicy fill_policy(
+
935 builder.bin_data_1d.numBin(), Kokkos::AUTO, 4 );
+
936 if ( builder.count )
+
937 {
+
938 typename BuilderType::CountNeighborsPolicy count_policy(
+
939 builder.bin_data_1d.numBin(), Kokkos::AUTO, 4 );
+
940 Kokkos::parallel_for( "Cabana::VerletList::count_neighbors",
+
941 count_policy, builder );
+
942 }
+
943 else
+
944 {
+
945 builder.processCounts( LayoutTag() );
+
946 Kokkos::parallel_for( "Cabana::VerletList::fill_neighbors",
+
947 fill_policy, builder );
+
948 }
+
949 Kokkos::fence();
+
950
+
951 // Process the counts by computing offsets and allocating the neighbor
+
952 // list, if needed.
+
953 builder.processCounts( LayoutTag() );
+
954
+
955 // For each particle in the range fill (or refill) its part of the
+
956 // neighbor list.
+
957 if ( builder.count or builder.refill )
+
958 {
+
959 Kokkos::parallel_for( "Cabana::VerletList::fill_neighbors",
+
960 fill_policy, builder );
+
961 Kokkos::fence();
+
962 }
+
963
+
964 // Get the data from the builder.
+
965 _data = builder._data;
+
966 }
+
968
+
970 KOKKOS_INLINE_FUNCTION
+
+
971 void setNeighbor( const std::size_t particle_index,
+
972 const std::size_t neighbor_index,
+
973 const int new_index ) const
+
974 {
+
975 _data.setNeighbor( particle_index, neighbor_index, new_index );
+
976 }
+
+
977};
+
+
978
+
979//---------------------------------------------------------------------------//
+
980// Neighbor list interface implementation.
+
981//---------------------------------------------------------------------------//
+
983template <class MemorySpace, class AlgorithmTag, class BuildTag>
+
+
984class NeighborList<
+
985 VerletList<MemorySpace, AlgorithmTag, VerletLayoutCSR, BuildTag>>
+
986{
+
987 public:
+
989 using memory_space = MemorySpace;
+
991 using list_type =
+
992 VerletList<MemorySpace, AlgorithmTag, VerletLayoutCSR, BuildTag>;
+
993
+
995 KOKKOS_INLINE_FUNCTION
+
+
996 static std::size_t totalNeighbor( const list_type& list )
+
997 {
+
998 // Size of the allocated memory gives total neighbors.
+
999 return list._data.neighbors.extent( 0 );
+
1000 }
+
+
1001
+
1003 KOKKOS_INLINE_FUNCTION
+
+
1004 static std::size_t maxNeighbor( const list_type& list )
+
1005 {
+
1006 std::size_t num_p = list._data.counts.size();
+
1007 return Impl::maxNeighbor( list, num_p );
+
1008 }
+
+
1009
+
1011 KOKKOS_INLINE_FUNCTION
+
+
1012 static std::size_t numNeighbor( const list_type& list,
+
1013 const std::size_t particle_index )
+
1014 {
+
1015 return list._data.counts( particle_index );
+
1016 }
+
+
1017
+
1020 KOKKOS_INLINE_FUNCTION
+
+
1021 static std::size_t getNeighbor( const list_type& list,
+
1022 const std::size_t particle_index,
+
1023 const std::size_t neighbor_index )
+
1024 {
+
1025 return list._data.neighbors( list._data.offsets( particle_index ) +
+
1026 neighbor_index );
+
1027 }
+
+
1028};
+
+
1029
+
1030//---------------------------------------------------------------------------//
+
1032template <class MemorySpace, class AlgorithmTag, class BuildTag>
+
+
1033class NeighborList<
+
1034 VerletList<MemorySpace, AlgorithmTag, VerletLayout2D, BuildTag>>
+
1035{
+
1036 public:
+
1038 using memory_space = MemorySpace;
+
1040 using list_type =
+
1041 VerletList<MemorySpace, AlgorithmTag, VerletLayout2D, BuildTag>;
+
1042
+
1044 KOKKOS_INLINE_FUNCTION
+
+
1045 static std::size_t totalNeighbor( const list_type& list )
+
1046 {
+
1047 std::size_t num_p = list._data.counts.size();
+
1048 return Impl::totalNeighbor( list, num_p );
+
1049 }
+
+
1050
+
1052 KOKKOS_INLINE_FUNCTION
+
+
1053 static std::size_t maxNeighbor( const list_type& list )
+
1054 {
+
1055 // Stored during neighbor search.
+
1056 return list._data.max_n;
+
1057 }
+
+
1058
+
1060 KOKKOS_INLINE_FUNCTION
+
+
1061 static std::size_t numNeighbor( const list_type& list,
+
1062 const std::size_t particle_index )
+
1063 {
+
1064 return list._data.counts( particle_index );
+
1065 }
+
+
1066
+
1069 KOKKOS_INLINE_FUNCTION
+
+
1070 static std::size_t getNeighbor( const list_type& list,
+
1071 const std::size_t particle_index,
+
1072 const std::size_t neighbor_index )
+
1073 {
+
1074 return list._data.neighbors( particle_index, neighbor_index );
+
1075 }
+
+
1076};
+
+
1077
+
1078//---------------------------------------------------------------------------//
+
1079
+
1080} // end namespace Cabana
+
1081
+
1082#endif // end CABANA_VERLETLIST_HPP
Cabana::Grid::ArrayOp::update
std::enable_if_t< 3==Array_t::num_space_dim, void > update(Array_t &a, const typename Array_t::value_type alpha, const Array_t &b, const typename Array_t::value_type beta, DecompositionTag tag)
Update two vectors such that a = alpha * a + beta * b. 3D specialization.
Definition Cabana_Grid_Array.hpp:595
Cabana::Grid::G2P::value
KOKKOS_INLINE_FUNCTION std::enable_if_t< 3==SplineDataType::num_space_dim, void > value(const ViewType &view, const SplineDataType &sd, PointDataType &result, typename std::enable_if<(std::rank< PointDataType >::value==0), void * >::type=0)
Interpolate a scalar value to a point. 3D specialization.
Definition Cabana_Grid_Interpolation.hpp:56
Cabana_LinkedCellList.hpp
Linked cell list binning (spatial sorting) and neighbor iteration.
Cabana_NeighborList.hpp
Neighbor list interface.
Cabana_Parallel.hpp
SIMD and neighbor extension of Kokkos parallel iteration.
-
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayout2D, BuildTag > >::getNeighbor
static KOKKOS_INLINE_FUNCTION std::size_t getNeighbor(const list_type &list, const std::size_t particle_index, const std::size_t neighbor_index)
Definition Cabana_VerletList.hpp:869
-
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayout2D, BuildTag > >::memory_space
MemorySpace memory_space
Kokkos memory space.
Definition Cabana_VerletList.hpp:837
-
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayout2D, BuildTag > >::numNeighbor
static KOKKOS_INLINE_FUNCTION std::size_t numNeighbor(const list_type &list, const std::size_t particle_index)
Get the number of neighbors for a given particle index.
Definition Cabana_VerletList.hpp:860
-
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayout2D, BuildTag > >::totalNeighbor
static KOKKOS_INLINE_FUNCTION std::size_t totalNeighbor(const list_type &list)
Get the total number of neighbors across all particles.
Definition Cabana_VerletList.hpp:844
-
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayout2D, BuildTag > >::maxNeighbor
static KOKKOS_INLINE_FUNCTION std::size_t maxNeighbor(const list_type &list)
Get the maximum number of neighbors per particle.
Definition Cabana_VerletList.hpp:852
-
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayoutCSR, BuildTag > >::numNeighbor
static KOKKOS_INLINE_FUNCTION std::size_t numNeighbor(const list_type &list, const std::size_t particle_index)
Get the number of neighbors for a given particle index.
Definition Cabana_VerletList.hpp:811
-
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayoutCSR, BuildTag > >::maxNeighbor
static KOKKOS_INLINE_FUNCTION std::size_t maxNeighbor(const list_type &list)
Get the maximum number of neighbors across all particles.
Definition Cabana_VerletList.hpp:803
-
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayoutCSR, BuildTag > >::totalNeighbor
static KOKKOS_INLINE_FUNCTION std::size_t totalNeighbor(const list_type &list)
Get the total number of neighbors across all particles.
Definition Cabana_VerletList.hpp:795
-
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayoutCSR, BuildTag > >::getNeighbor
static KOKKOS_INLINE_FUNCTION std::size_t getNeighbor(const list_type &list, const std::size_t particle_index, const std::size_t neighbor_index)
Definition Cabana_VerletList.hpp:820
-
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayoutCSR, BuildTag > >::memory_space
MemorySpace memory_space
Kokkos memory space.
Definition Cabana_VerletList.hpp:788
+
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayout2D, BuildTag > >::getNeighbor
static KOKKOS_INLINE_FUNCTION std::size_t getNeighbor(const list_type &list, const std::size_t particle_index, const std::size_t neighbor_index)
Definition Cabana_VerletList.hpp:1070
+
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayout2D, BuildTag > >::memory_space
MemorySpace memory_space
Kokkos memory space.
Definition Cabana_VerletList.hpp:1038
+
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayout2D, BuildTag > >::numNeighbor
static KOKKOS_INLINE_FUNCTION std::size_t numNeighbor(const list_type &list, const std::size_t particle_index)
Get the number of neighbors for a given particle index.
Definition Cabana_VerletList.hpp:1061
+
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayout2D, BuildTag > >::totalNeighbor
static KOKKOS_INLINE_FUNCTION std::size_t totalNeighbor(const list_type &list)
Get the total number of neighbors across all particles.
Definition Cabana_VerletList.hpp:1045
+
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayout2D, BuildTag > >::maxNeighbor
static KOKKOS_INLINE_FUNCTION std::size_t maxNeighbor(const list_type &list)
Get the maximum number of neighbors per particle.
Definition Cabana_VerletList.hpp:1053
+
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayoutCSR, BuildTag > >::numNeighbor
static KOKKOS_INLINE_FUNCTION std::size_t numNeighbor(const list_type &list, const std::size_t particle_index)
Get the number of neighbors for a given particle index.
Definition Cabana_VerletList.hpp:1012
+
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayoutCSR, BuildTag > >::maxNeighbor
static KOKKOS_INLINE_FUNCTION std::size_t maxNeighbor(const list_type &list)
Get the maximum number of neighbors across all particles.
Definition Cabana_VerletList.hpp:1004
+
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayoutCSR, BuildTag > >::totalNeighbor
static KOKKOS_INLINE_FUNCTION std::size_t totalNeighbor(const list_type &list)
Get the total number of neighbors across all particles.
Definition Cabana_VerletList.hpp:996
+
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayoutCSR, BuildTag > >::getNeighbor
static KOKKOS_INLINE_FUNCTION std::size_t getNeighbor(const list_type &list, const std::size_t particle_index, const std::size_t neighbor_index)
Definition Cabana_VerletList.hpp:1021
+
Cabana::NeighborList< VerletList< MemorySpace, AlgorithmTag, VerletLayoutCSR, BuildTag > >::memory_space
MemorySpace memory_space
Kokkos memory space.
Definition Cabana_VerletList.hpp:989
Cabana::NeighborList
Neighbor list interface. Provides an interface callable at the functor level that gives access to nei...
Definition Cabana_NeighborList.hpp:114
-
Cabana::VerletList
Neighbor list implementation based on binning particles on a 3d Cartesian grid with cells of the same...
Definition Cabana_VerletList.hpp:606
-
Cabana::VerletList::_data
VerletListData< memory_space, LayoutTag > _data
Verlet list data.
Definition Cabana_VerletList.hpp:617
-
Cabana::VerletList::VerletList
VerletList(PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[3], const typename PositionType::value_type grid_max[3], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value||Kokkos::is_view< PositionType >::value), int >::type *=0)
VerletList constructor. Given a list of particle positions and a neighborhood radius calculate the ne...
Definition Cabana_VerletList.hpp:659
-
Cabana::VerletList::setNeighbor
KOKKOS_INLINE_FUNCTION void setNeighbor(const std::size_t particle_index, const std::size_t neighbor_index, const int new_index) const
Modify a neighbor in the list; for example, mark it as a broken bond.
Definition Cabana_VerletList.hpp:770
-
Cabana::VerletList::execution_space
typename memory_space::execution_space execution_space
Kokkos default execution space for this memory space.
Definition Cabana_VerletList.hpp:614
-
Cabana::VerletList::build
void build(ExecutionSpace, PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[3], const typename PositionType::value_type grid_max[3], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value||Kokkos::is_view< PositionType >::value), int >::type *=0)
Given a list of particle positions and a neighborhood radius calculate the neighbor list.
Definition Cabana_VerletList.hpp:700
-
Cabana::VerletList::memory_space
MemorySpace memory_space
Kokkos memory space in which the neighbor list data resides.
Definition Cabana_VerletList.hpp:611
-
Cabana::VerletList::VerletList
VerletList()
Default constructor.
Definition Cabana_VerletList.hpp:622
-
Cabana::VerletList::build
void build(PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[3], const typename PositionType::value_type grid_max[3], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value||Kokkos::is_view< PositionType >::value), int >::type *=0)
Given a list of particle positions and a neighborhood radius calculate the neighbor list.
Definition Cabana_VerletList.hpp:680
+
Cabana::VerletList
Neighbor list implementation based on binning particles on a 3d Cartesian grid with cells of the same...
Definition Cabana_VerletList.hpp:702
+
Cabana::VerletList::build
void build(PositionSlice x, const std::size_t begin, const std::size_t end, const typename PositionSlice::value_type background_radius, RadiusSlice neighborhood_radius, const typename PositionSlice::value_type cell_size_ratio, const typename PositionSlice::value_type grid_min[3], const typename PositionSlice::value_type grid_max[3], const std::size_t max_neigh=0)
Given a list of particle positions and a neighborhood radius calculate the neighbor list.
Definition Cabana_VerletList.hpp:879
+
Cabana::VerletList::_data
VerletListData< memory_space, LayoutTag > _data
Verlet list data.
Definition Cabana_VerletList.hpp:713
+
Cabana::VerletList::VerletList
VerletList(PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[3], const typename PositionType::value_type grid_max[3], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value||Kokkos::is_view< PositionType >::value), int >::type *=0)
VerletList constructor. Given a list of particle positions and a neighborhood radius calculate the ne...
Definition Cabana_VerletList.hpp:755
+
Cabana::VerletList::setNeighbor
KOKKOS_INLINE_FUNCTION void setNeighbor(const std::size_t particle_index, const std::size_t neighbor_index, const int new_index) const
Modify a neighbor in the list; for example, mark it as a broken bond.
Definition Cabana_VerletList.hpp:971
+
Cabana::VerletList::execution_space
typename memory_space::execution_space execution_space
Kokkos default execution space for this memory space.
Definition Cabana_VerletList.hpp:710
+
Cabana::VerletList::build
void build(ExecutionSpace, PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[3], const typename PositionType::value_type grid_max[3], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value||Kokkos::is_view< PositionType >::value), int >::type *=0)
Given a list of particle positions and a neighborhood radius calculate the neighbor list.
Definition Cabana_VerletList.hpp:847
+
Cabana::VerletList::memory_space
MemorySpace memory_space
Kokkos memory space in which the neighbor list data resides.
Definition Cabana_VerletList.hpp:707
+
Cabana::VerletList::VerletList
VerletList()
Default constructor.
Definition Cabana_VerletList.hpp:718
+
Cabana::VerletList::build
void build(ExecutionSpace, PositionSlice x, const std::size_t begin, const std::size_t end, const typename PositionSlice::value_type background_radius, RadiusSlice neighborhood_radius, const typename PositionSlice::value_type cell_size_ratio, const typename PositionSlice::value_type grid_min[3], const typename PositionSlice::value_type grid_max[3], const std::size_t max_neigh=0)
Given a list of particle positions and a neighborhood radius calculate the neighbor list.
Definition Cabana_VerletList.hpp:897
+
Cabana::VerletList::VerletList
VerletList(PositionSlice x, const std::size_t begin, const std::size_t end, const typename PositionSlice::value_type background_radius, RadiusSlice neighborhood_radius, const typename PositionSlice::value_type cell_size_ratio, const typename PositionSlice::value_type grid_min[3], const typename PositionSlice::value_type grid_max[3], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionSlice >::value), int >::type *=0)
VerletList constructor. Given a list of particle positions and a neighborhood radius calculate the ne...
Definition Cabana_VerletList.hpp:807
+
Cabana::VerletList::build
void build(PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[3], const typename PositionType::value_type grid_max[3], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value||Kokkos::is_view< PositionType >::value), int >::type *=0)
Given a list of particle positions and a neighborhood radius calculate the neighbor list.
Definition Cabana_VerletList.hpp:827
Cabana
Core: particle data structures and algorithms.
Definition Cabana_AoSoA.hpp:36
Cabana::size
auto size(SliceType slice, typename std::enable_if< is_slice< SliceType >::value, int >::type *=0)
Check slice size (differs from Kokkos View).
Definition Cabana_Slice.hpp:1012
Cabana::VerletLayout2D
2D array neighbor list layout.
Definition Cabana_VerletList.hpp:40
diff --git a/doxygen/classCabana_1_1VerletList-members.html b/doxygen/classCabana_1_1VerletList-members.html index 30769bd19..25c27314c 100644 --- a/doxygen/classCabana_1_1VerletList-members.html +++ b/doxygen/classCabana_1_1VerletList-members.html @@ -97,11 +97,14 @@ _dataCabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag > build(PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[3], const typename PositionType::value_type grid_max[3], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value||Kokkos::is_view< PositionType >::value), int >::type *=0)Cabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag >inline build(ExecutionSpace, PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[3], const typename PositionType::value_type grid_max[3], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value||Kokkos::is_view< PositionType >::value), int >::type *=0)Cabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag >inline + build(PositionSlice x, const std::size_t begin, const std::size_t end, const typename PositionSlice::value_type background_radius, RadiusSlice neighborhood_radius, const typename PositionSlice::value_type cell_size_ratio, const typename PositionSlice::value_type grid_min[3], const typename PositionSlice::value_type grid_max[3], const std::size_t max_neigh=0)Cabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag >inline + build(ExecutionSpace, PositionSlice x, const std::size_t begin, const std::size_t end, const typename PositionSlice::value_type background_radius, RadiusSlice neighborhood_radius, const typename PositionSlice::value_type cell_size_ratio, const typename PositionSlice::value_type grid_min[3], const typename PositionSlice::value_type grid_max[3], const std::size_t max_neigh=0)Cabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag >inline execution_space typedefCabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag > memory_space typedefCabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag > setNeighbor(const std::size_t particle_index, const std::size_t neighbor_index, const int new_index) constCabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag >inline VerletList()Cabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag >inline VerletList(PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[3], const typename PositionType::value_type grid_max[3], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value||Kokkos::is_view< PositionType >::value), int >::type *=0)Cabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag >inline + VerletList(PositionSlice x, const std::size_t begin, const std::size_t end, const typename PositionSlice::value_type background_radius, RadiusSlice neighborhood_radius, const typename PositionSlice::value_type cell_size_ratio, const typename PositionSlice::value_type grid_min[3], const typename PositionSlice::value_type grid_max[3], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionSlice >::value), int >::type *=0)Cabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag >inline
diff --git a/doxygen/classCabana_1_1VerletList.html b/doxygen/classCabana_1_1VerletList.html index 28c6d697c..421bfcd3f 100644 --- a/doxygen/classCabana_1_1VerletList.html +++ b/doxygen/classCabana_1_1VerletList.html @@ -133,6 +133,10 @@  VerletList (PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[3], const typename PositionType::value_type grid_max[3], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value||Kokkos::is_view< PositionType >::value), int >::type *=0)  VerletList constructor. Given a list of particle positions and a neighborhood radius calculate the neighbor list.
  +template<class PositionSlice , class RadiusSlice > + VerletList (PositionSlice x, const std::size_t begin, const std::size_t end, const typename PositionSlice::value_type background_radius, RadiusSlice neighborhood_radius, const typename PositionSlice::value_type cell_size_ratio, const typename PositionSlice::value_type grid_min[3], const typename PositionSlice::value_type grid_max[3], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionSlice >::value), int >::type *=0) + VerletList constructor. Given a list of particle positions and a neighborhood radius calculate the neighbor list.
+  template<class PositionType > void build (PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[3], const typename PositionType::value_type grid_max[3], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value||Kokkos::is_view< PositionType >::value), int >::type *=0) @@ -143,6 +147,16 @@ void build (ExecutionSpace, PositionType x, const std::size_t begin, const std::size_t end, const typename PositionType::value_type neighborhood_radius, const typename PositionType::value_type cell_size_ratio, const typename PositionType::value_type grid_min[3], const typename PositionType::value_type grid_max[3], const std::size_t max_neigh=0, typename std::enable_if<(is_slice< PositionType >::value||Kokkos::is_view< PositionType >::value), int >::type *=0)  Given a list of particle positions and a neighborhood radius calculate the neighbor list.
  + +template<class PositionSlice , class RadiusSlice > +void build (PositionSlice x, const std::size_t begin, const std::size_t end, const typename PositionSlice::value_type background_radius, RadiusSlice neighborhood_radius, const typename PositionSlice::value_type cell_size_ratio, const typename PositionSlice::value_type grid_min[3], const typename PositionSlice::value_type grid_max[3], const std::size_t max_neigh=0) + Given a list of particle positions and a neighborhood radius calculate the neighbor list.
+  + +template<class PositionSlice , class RadiusSlice , class ExecutionSpace > +void build (ExecutionSpace, PositionSlice x, const std::size_t begin, const std::size_t end, const typename PositionSlice::value_type background_radius, RadiusSlice neighborhood_radius, const typename PositionSlice::value_type cell_size_ratio, const typename PositionSlice::value_type grid_min[3], const typename PositionSlice::value_type grid_max[3], const std::size_t max_neigh=0) + Given a list of particle positions and a neighborhood radius calculate the neighbor list.
+  KOKKOS_INLINE_FUNCTION void setNeighbor (const std::size_t particle_index, const std::size_t neighbor_index, const int new_index) const  Modify a neighbor in the list; for example, mark it as a broken bond.
@@ -170,7 +184,7 @@

Neighbor list implementation most appropriate for somewhat regularly distributed particles due to the use of a Cartesian grid.

Constructor & Destructor Documentation

-

◆ VerletList()

+

◆ VerletList() [1/2]

@@ -251,6 +265,96 @@

+

◆ VerletList() [2/2]

+ +
+
+
+template<class MemorySpace , class AlgorithmTag , class LayoutTag , class BuildTag = TeamVectorOpTag>
+
+template<class PositionSlice , class RadiusSlice >
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Cabana::VerletList< MemorySpace, AlgorithmTag, LayoutTag, BuildTag >::VerletList (PositionSlice x,
const std::size_t begin,
const std::size_t end,
const typename PositionSlice::value_type background_radius,
RadiusSlice neighborhood_radius,
const typename PositionSlice::value_type cell_size_ratio,
const typename PositionSlice::value_type grid_min[3],
const typename PositionSlice::value_type grid_max[3],
const std::size_t max_neigh = 0,
typename std::enable_if<(is_slice< PositionSlice >::value), int >::type * = 0 )
+ 		+inline
+
+ +

VerletList constructor. Given a list of particle positions and a neighborhood radius calculate the neighbor list.

+
Parameters
+ + + + + + + + + + +
xThe slice containing the particle positions
beginThe beginning particle index to compute neighbors for.
endThe end particle index to compute neighbors for.
background_radiusThe radius of the neighborhood used for the background grid cells in each dimension.
neighborhood_radiusThe radius of the neighborhood per particle. Particles within this radius are considered neighbors.
cell_size_ratioThe ratio of the cell size in the Cartesian grid to the neighborhood radius. For example, if the cell size ratio is 0.5 then the cells will be half the size of the neighborhood radius in each dimension.
grid_minThe minimum value of the grid containing the particles in each dimension.
grid_maxThe maximum value of the grid containing the particles in each dimension.
max_neighOptional maximum number of neighbors per particle to pre-allocate the neighbor list. Potentially avoids recounting with 2D layout only.
+
+
+

Particles outside of the neighborhood radius will not be considered neighbors. Only compute the neighbors of those that are within the given range. All particles are candidates for being a neighbor, regardless of whether or not they are in the range.

+
The documentation for this class was generated from the following file: