BoxMeshFixture.hpp
b5a1ba9bfademaster

BoxMeshFixture.hpp
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			#ifndef KOKKOS_BOXMESHFIXTURE_HPP
			#define KOKKOS_BOXMESHFIXTURE_HPP

			#include <cmath>
			#include <stdexcept>
			#include <sstream>

			#include <Kokkos_Core.hpp>
			#include <BoxMeshPartition.hpp>
			#include <FEMesh.hpp>
			#include <HexElement.hpp>

			//----------------------------------------------------------------------------

			struct FixtureElementHex8 {

			static const unsigned element_node_count = 8 ;

			HybridFEM::HexElement_TensorData< element_node_count > elem_data ;
			BoxBoundsLinear box_bounds ;

			FixtureElementHex8() : elem_data(), box_bounds() {}

			static void create_node_boxes_from_vertex_boxes(
			const BoxType & vertex_box_global ,
			const std::vector< BoxType > & vertex_box_parts ,
			BoxType & node_box_global ,
			std::vector< BoxType > & node_box_parts )
			{
			node_box_global = vertex_box_global ;
			node_box_parts = vertex_box_parts ;
			}

			void elem_to_node( const unsigned node_local , unsigned coord[] ) const
			{
			coord[0] += elem_data.eval_map[ node_local ][0] ;
			coord[1] += elem_data.eval_map[ node_local ][1] ;
			coord[2] += elem_data.eval_map[ node_local ][2] ;
			}
			};

			struct FixtureElementHex27 {
			static const unsigned element_node_count = 27 ;

			HybridFEM::HexElement_TensorData< element_node_count > elem_data ;
			BoxBoundsQuadratic box_bounds ;

			FixtureElementHex27() : elem_data(), box_bounds() {}

			static void create_node_boxes_from_vertex_boxes(
			const BoxType & vertex_box_global ,
			const std::vector< BoxType > & vertex_box_parts ,
			BoxType & node_box_global ,
			std::vector< BoxType > & node_box_parts )
			{
			node_box_global = vertex_box_global ;
			node_box_parts = vertex_box_parts ;

			node_box_global[0][1] = 2 * node_box_global[0][1] - 1 ;
			node_box_global[1][1] = 2 * node_box_global[1][1] - 1 ;
			node_box_global[2][1] = 2 * node_box_global[2][1] - 1 ;

			for ( unsigned i = 0 ; i < vertex_box_parts.size() ; ++i ) {
			node_box_parts[i][0][0] = 2 * node_box_parts[i][0][0] ;
			node_box_parts[i][1][0] = 2 * node_box_parts[i][1][0] ;
			node_box_parts[i][2][0] = 2 * node_box_parts[i][2][0] ;

			node_box_parts[i][0][1] =
			std::min( node_box_global[0][1] , 2 * node_box_parts[i][0][1] );
			node_box_parts[i][1][1] =
			std::min( node_box_global[1][1] , 2 * node_box_parts[i][1][1] );
			node_box_parts[i][2][1] =
			std::min( node_box_global[2][1] , 2 * node_box_parts[i][2][1] );
			}
			}

			void elem_to_node( const unsigned node_local , unsigned coord[] ) const
			{
			coord[0] = 2 * coord[0] + elem_data.eval_map[ node_local ][0] ;
			coord[1] = 2 * coord[1] + elem_data.eval_map[ node_local ][1] ;
			coord[2] = 2 * coord[2] + elem_data.eval_map[ node_local ][2] ;
			}
			};

			//----------------------------------------------------------------------------

			template< typename Scalar , class Device , class ElementSpec >
			struct BoxMeshFixture {

			typedef Scalar coordinate_scalar_type ;
			typedef Device execution_space ;

			static const unsigned element_node_count = ElementSpec::element_node_count ;

			typedef HybridFEM::FEMesh< coordinate_scalar_type ,
			element_node_count ,
			execution_space > FEMeshType ;

			typedef typename FEMeshType::node_coords_type node_coords_type ;
			typedef typename FEMeshType::elem_node_ids_type elem_node_ids_type ;
			typedef typename FEMeshType::node_elem_ids_type node_elem_ids_type ;


			static void verify(
			const typename FEMeshType::node_coords_type::HostMirror & node_coords ,
			const typename FEMeshType::elem_node_ids_type::HostMirror & elem_node_ids ,
			const typename FEMeshType::node_elem_ids_type::HostMirror & node_elem_ids )
			{
			typedef typename FEMeshType::size_type size_type ;
			//typedef typename node_coords_type::value_type coords_type ; // unused

			const size_type node_count_total = node_coords.dimension_0();
			const size_type elem_count_total = elem_node_ids.dimension_0();

			const ElementSpec element ;

			for ( size_type node_index = 0 ;
			node_index < node_count_total ; ++node_index ) {

			for ( size_type
			j = node_elem_ids.row_map[ node_index ] ;
			j < node_elem_ids.row_map[ node_index + 1 ] ; ++j ) {

			const size_type elem_index = node_elem_ids.entries(j,0);
			const size_type node_local = node_elem_ids.entries(j,1);
			const size_type en_id = elem_node_ids(elem_index,node_local);

			if ( node_index != en_id ) {
			std::ostringstream msg ;
			msg << "BoxMeshFixture node_elem_ids error"
			<< " : node_index(" << node_index
			<< ") entry(" << j
			<< ") elem_index(" << elem_index
			<< ") node_local(" << node_local
			<< ") elem_node_id(" << en_id
			<< ")" ;
			throw std::runtime_error( msg.str() );
			}
			}
			}

			for ( size_type elem_index = 0 ;
			elem_index < elem_count_total; ++elem_index ) {

			coordinate_scalar_type elem_node_coord[ element_node_count ][3] ;

			for ( size_type nn = 0 ; nn < element_node_count ; ++nn ) {
			const size_type node_index = elem_node_ids( elem_index , nn );

			for ( size_type nc = 0 ; nc < 3 ; ++nc ) {
			elem_node_coord[nn][nc] = node_coords( node_index , nc );
			}
			}


			for ( size_type nn = 0 ; nn < element_node_count ; ++nn ) {

			const unsigned ix = element.elem_data.eval_map[nn][0] ;
			const unsigned iy = element.elem_data.eval_map[nn][1] ;
			const unsigned iz = element.elem_data.eval_map[nn][2] ;

			if ( elem_node_coord[nn][0] != elem_node_coord[0][0] + ix \|\|
			elem_node_coord[nn][1] != elem_node_coord[0][1] + iy \|\|
			elem_node_coord[nn][2] != elem_node_coord[0][2] + iz ) {

			std::ostringstream msg ;
			msg << "BoxMeshFixture elem_node_coord mapping failure { "
			<< elem_node_coord[nn][0] << " "
			<< elem_node_coord[nn][1] << " "
			<< elem_node_coord[nn][2] << " } != { "
			<< elem_node_coord[ 0][0] + ix << " "
			<< elem_node_coord[ 0][1] + iy << " "
			<< elem_node_coord[ 0][2] + iz
			<< " }" ;
			throw std::runtime_error( msg.str() );
			}
			}
			}
			}

			//------------------------------------
			// Initialize element-node connectivity:
			// Order elements that only depend on owned nodes first.
			// These elements could be computed while waiting for
			// received node data.

			static void layout_elements_interior_exterior(
			const BoxType vertex_box_local_used ,
			const BoxType vertex_box_local_owned ,
			const BoxType node_box_local_used ,
			const std::vector<size_t> & node_used_id_map ,
			const ElementSpec element_fixture ,
			const size_t elem_count_interior ,
			const typename elem_node_ids_type::HostMirror elem_node_ids )
			{
			size_t elem_index_interior = 0 ;
			size_t elem_index_boundary = elem_count_interior ;

			for ( size_t iz = vertex_box_local_used[2][0] ;
			iz < vertex_box_local_used[2][1] - 1 ; ++iz ) {
			for ( size_t iy = vertex_box_local_used[1][0] ;
			iy < vertex_box_local_used[1][1] - 1 ; ++iy ) {
			for ( size_t ix = vertex_box_local_used[0][0] ;
			ix < vertex_box_local_used[0][1] - 1 ; ++ix ) {

			size_t elem_index ;

			// If lower and upper vertices are owned then element is interior
			if ( contain( vertex_box_local_owned, ix, iy, iz ) &&
			contain( vertex_box_local_owned, ix+1, iy+1, iz+1 ) ) {
			elem_index = elem_index_interior++ ;
			}
			else {
			elem_index = elem_index_boundary++ ;
			}

			for ( size_t nn = 0 ; nn < element_node_count ; ++nn ) {
			unsigned coord[3] = { static_cast<unsigned>(ix) , static_cast<unsigned>(iy) , static_cast<unsigned>(iz) };

			element_fixture.elem_to_node( nn , coord );

			const size_t node_local_id =
			box_map_id( node_box_local_used ,
			node_used_id_map ,
			coord[0] , coord[1] , coord[2] );

			elem_node_ids( elem_index , nn ) = node_local_id ;
			}
			}}}
			}

			//------------------------------------
			// Nested partitioning of elements by number of thread 'gangs'

			static void layout_elements_partitioned(
			const BoxType vertex_box_local_used ,
			const BoxType /vertex_box_local_owned/ ,
			const BoxType node_box_local_used ,
			const std::vector<size_t> & node_used_id_map ,
			const ElementSpec element_fixture ,
			const size_t thread_gang_count ,
			const typename elem_node_ids_type::HostMirror elem_node_ids )
			{
			std::vector< BoxType > element_box_gangs( thread_gang_count );

			BoxType element_box_local_used = vertex_box_local_used ;

			element_box_local_used[0][1] -= 1 ;
			element_box_local_used[1][1] -= 1 ;
			element_box_local_used[2][1] -= 1 ;

			box_partition_rcb( element_box_local_used , element_box_gangs );

			size_t elem_index = 0 ;

			for ( size_t ig = 0 ; ig < thread_gang_count ; ++ig ) {

			const BoxType box = element_box_gangs[ig] ;

			for ( size_t iz = box[2][0] ; iz < box[2][1] ; ++iz ) {
			for ( size_t iy = box[1][0] ; iy < box[1][1] ; ++iy ) {
			for ( size_t ix = box[0][0] ; ix < box[0][1] ; ++ix , ++elem_index ) {

			for ( size_t nn = 0 ; nn < element_node_count ; ++nn ) {
			unsigned coord[3] = { static_cast<unsigned>(ix) , static_cast<unsigned>(iy) , static_cast<unsigned>(iz) };

			element_fixture.elem_to_node( nn , coord );

			const size_t node_local_id =
			box_map_id( node_box_local_used ,
			node_used_id_map ,
			coord[0] , coord[1] , coord[2] );

			elem_node_ids( elem_index , nn ) = node_local_id ;
			}
			}}}
			}
			}

			//------------------------------------

			static FEMeshType create( const size_t proc_count ,
			const size_t proc_local ,
			const size_t gang_count ,
			const size_t elems_x ,
			const size_t elems_y ,
			const size_t elems_z ,
			const double x_coord_curve = 1 ,
			const double y_coord_curve = 1 ,
			const double z_coord_curve = 1 )
			{
			const size_t vertices_x = elems_x + 1 ;
			const size_t vertices_y = elems_y + 1 ;
			const size_t vertices_z = elems_z + 1 ;

			const BoxBoundsLinear vertex_box_bounds ;
			const ElementSpec element ;

			// Partition based upon vertices:

			BoxType vertex_box_global ;
			std::vector< BoxType > vertex_box_parts( proc_count );

			vertex_box_global[0][0] = 0 ; vertex_box_global[0][1] = vertices_x ;
			vertex_box_global[1][0] = 0 ; vertex_box_global[1][1] = vertices_y ;
			vertex_box_global[2][0] = 0 ; vertex_box_global[2][1] = vertices_z ;

			box_partition_rcb( vertex_box_global , vertex_box_parts );

			const BoxType vertex_box_local_owned = vertex_box_parts[ proc_local ];

			// Determine interior and used vertices:

			BoxType vertex_box_local_interior ;
			BoxType vertex_box_local_used ;

			vertex_box_bounds.apply( vertex_box_global ,
			vertex_box_local_owned ,
			vertex_box_local_interior ,
			vertex_box_local_used );

			// Element counts:

			const long local_elems_x =
			( vertex_box_local_used[0][1] - vertex_box_local_used[0][0] ) - 1 ;
			const long local_elems_y =
			( vertex_box_local_used[1][1] - vertex_box_local_used[1][0] ) - 1 ;
			const long local_elems_z =
			( vertex_box_local_used[2][1] - vertex_box_local_used[2][0] ) - 1 ;

			const size_t elem_count_total = std::max( long(0) , local_elems_x ) *
			std::max( long(0) , local_elems_y ) *
			std::max( long(0) , local_elems_z );

			const long interior_elems_x =
			( vertex_box_local_owned[0][1] - vertex_box_local_owned[0][0] ) - 1 ;
			const long interior_elems_y =
			( vertex_box_local_owned[1][1] - vertex_box_local_owned[1][0] ) - 1 ;
			const long interior_elems_z =
			( vertex_box_local_owned[2][1] - vertex_box_local_owned[2][0] ) - 1 ;

			const size_t elem_count_interior = std::max( long(0) , interior_elems_x ) *
			std::max( long(0) , interior_elems_y ) *
			std::max( long(0) , interior_elems_z );

			// Expand vertex boxes to node boxes:

			BoxType node_box_global ;
			BoxType node_box_local_used ;
			std::vector< BoxType > node_box_parts ;

			element.create_node_boxes_from_vertex_boxes(
			vertex_box_global , vertex_box_parts ,
			node_box_global , node_box_parts );

			// Node communication maps:

			size_t node_count_interior = 0 ;
			size_t node_count_owned = 0 ;
			size_t node_count_total = 0 ;
			std::vector<size_t> node_used_id_map ;
			std::vector<size_t> node_part_counts ;
			std::vector< std::vector<size_t> > node_send_map ;

			box_partition_maps( node_box_global ,
			node_box_parts ,
			element.box_bounds ,
			proc_local ,
			node_box_local_used ,
			node_used_id_map ,
			node_count_interior ,
			node_count_owned ,
			node_count_total ,
			node_part_counts ,
			node_send_map );

			size_t node_count_send = 0 ;
			for ( size_t i = 0 ; i < node_send_map.size() ; ++i ) {
			node_count_send += node_send_map[i].size();
			}

			size_t recv_msg_count = 0 ;
			size_t send_msg_count = 0 ;
			size_t send_count = 0 ;

			for ( size_t i = 1 ; i < proc_count ; ++i ) {
			if ( node_part_counts[i] ) ++recv_msg_count ;
			if ( node_send_map[i].size() ) {
			++send_msg_count ;
			send_count += node_send_map[i].size();
			}
			}

			// Finite element mesh:

			FEMeshType mesh ;

			if ( node_count_total ) {
			mesh.node_coords = node_coords_type( "node_coords", node_count_total );
			}

			if ( elem_count_total ) {
			mesh.elem_node_ids =
			elem_node_ids_type( "elem_node_ids", elem_count_total );
			}

			mesh.parallel_data_map.assign( node_count_interior ,
			node_count_owned ,
			node_count_total ,
			recv_msg_count ,
			send_msg_count ,
			send_count );

			typename node_coords_type::HostMirror node_coords =
			Kokkos::create_mirror( mesh.node_coords );

			typename elem_node_ids_type::HostMirror elem_node_ids =
			Kokkos::create_mirror( mesh.elem_node_ids );

			//------------------------------------
			// set node coordinates to grid location for subsequent verification

			for ( size_t iz = node_box_local_used[2][0] ;
			iz < node_box_local_used[2][1] ; ++iz ) {

			for ( size_t iy = node_box_local_used[1][0] ;
			iy < node_box_local_used[1][1] ; ++iy ) {

			for ( size_t ix = node_box_local_used[0][0] ;
			ix < node_box_local_used[0][1] ; ++ix ) {

			const size_t node_local_id =
			box_map_id( node_box_local_used , node_used_id_map , ix , iy , iz );

			node_coords( node_local_id , 0 ) = ix ;
			node_coords( node_local_id , 1 ) = iy ;
			node_coords( node_local_id , 2 ) = iz ;
			}}}

			//------------------------------------
			// Initialize element-node connectivity:

			if ( 1 < gang_count ) {
			layout_elements_partitioned( vertex_box_local_used ,
			vertex_box_local_owned ,
			node_box_local_used ,
			node_used_id_map ,
			element ,
			gang_count ,
			elem_node_ids );
			}
			else {
			layout_elements_interior_exterior( vertex_box_local_used ,
			vertex_box_local_owned ,
			node_box_local_used ,
			node_used_id_map ,
			element ,
			elem_count_interior ,
			elem_node_ids );
			}

			//------------------------------------
			// Populate node->element connectivity:

			std::vector<size_t> node_elem_work( node_count_total , (size_t) 0 );

			for ( size_t i = 0 ; i < elem_count_total ; ++i ) {
			for ( size_t n = 0 ; n < element_node_count ; ++n ) {
			++node_elem_work[ elem_node_ids(i,n) ];
			}
			}

			mesh.node_elem_ids =
			Kokkos::create_staticcrsgraph< node_elem_ids_type >( "node_elem_ids" , node_elem_work );

			typename node_elem_ids_type::HostMirror
			node_elem_ids = Kokkos::create_mirror( mesh.node_elem_ids );

			for ( size_t i = 0 ; i < node_count_total ; ++i ) {
			node_elem_work[i] = node_elem_ids.row_map[i];
			}

			// Looping in element order insures the list of elements
			// is sorted by element index.

			for ( size_t i = 0 ; i < elem_count_total ; ++i ) {
			for ( size_t n = 0 ; n < element_node_count ; ++n ) {
			const unsigned nid = elem_node_ids(i, n);
			const unsigned j = node_elem_work[nid] ; ++node_elem_work[nid] ;

			node_elem_ids.entries( j , 0 ) = i ;
			node_elem_ids.entries( j , 1 ) = n ;
			}
			}
			//------------------------------------
			// Verify setup with node coordinates matching grid indices.
			verify( node_coords , elem_node_ids , node_elem_ids );

			//------------------------------------
			// Scale node coordinates to problem extent with
			// nonlinear mapping.
			{
			const double problem_extent[3] =
			{ static_cast<double>( vertex_box_global[0][1] - 1 ) ,
			static_cast<double>( vertex_box_global[1][1] - 1 ) ,
			static_cast<double>( vertex_box_global[2][1] - 1 ) };

			const double grid_extent[3] =
			{ static_cast<double>( node_box_global[0][1] - 1 ) ,
			static_cast<double>( node_box_global[1][1] - 1 ) ,
			static_cast<double>( node_box_global[2][1] - 1 ) };

			for ( size_t i = 0 ; i < node_count_total ; ++i ) {
			const double x_unit = node_coords(i,0) / grid_extent[0] ;
			const double y_unit = node_coords(i,1) / grid_extent[1] ;
			const double z_unit = node_coords(i,2) / grid_extent[2] ;

			node_coords(i,0) = coordinate_scalar_type( problem_extent[0] * std::pow( x_unit , x_coord_curve ) );
			node_coords(i,1) = coordinate_scalar_type( problem_extent[1] * std::pow( y_unit , y_coord_curve ) );
			node_coords(i,2) = coordinate_scalar_type( problem_extent[2] * std::pow( z_unit , z_coord_curve ) );
			}
			}

			Kokkos::deep_copy( mesh.node_coords , node_coords );
			Kokkos::deep_copy( mesh.elem_node_ids , elem_node_ids );
			Kokkos::deep_copy( mesh.node_elem_ids.entries , node_elem_ids.entries );

			//------------------------------------
			// Communication lists:
			{
			recv_msg_count = 0 ;
			send_msg_count = 0 ;
			send_count = 0 ;

			for ( size_t i = 1 ; i < proc_count ; ++i ) {

			// Order sending starting with the local processor rank
			// to try to smooth out the amount of messages simultaneously
			// send to a particular processor.

			const int proc = ( proc_local + i ) % proc_count ;
			if ( node_part_counts[i] ) {
			mesh.parallel_data_map.host_recv(recv_msg_count,0) = proc ;
			mesh.parallel_data_map.host_recv(recv_msg_count,1) = node_part_counts[i] ;
			++recv_msg_count ;
			}
			if ( node_send_map[i].size() ) {
			mesh.parallel_data_map.host_send(send_msg_count,0) = proc ;
			mesh.parallel_data_map.host_send(send_msg_count,1) = node_send_map[i].size() ;
			for ( size_t j = 0 ; j < node_send_map[i].size() ; ++j , ++send_count ) {
			mesh.parallel_data_map.host_send_item(send_count) = node_send_map[i][j] - node_count_interior ;
			}
			++send_msg_count ;
			}
			}
			}

			return mesh ;
			}
			};

			//----------------------------------------------------------------------------
			//----------------------------------------------------------------------------

			#endif /* #ifndef KOKKOS_BOXMESHFIXTURE_HPP */

lammps/lib/kokkos/example/multi_fem/BoxMeshFixture.hppb5a1ba9bfademaster

BoxMeshFixture.hppView Options

lammps/lib/kokkos/example/multi_fem/BoxMeshFixture.hpp
b5a1ba9bfademaster

BoxMeshFixture.hpp
View Options