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BoxMeshFixture.hpp
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/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 2.0
// Copyright (2014) Sandia Corporation
//
// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
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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 */

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