fe_mesh_t* fe_mesh_from_mesh(mesh_t* fv_mesh,
string_array_t* element_block_tags)
{
fe_mesh_t* fe_mesh = fe_mesh_new(fv_mesh->comm, fv_mesh->num_nodes);
if ((element_block_tags != NULL) && (element_block_tags->size > 1))
{
// Block-by-block construction.
for (int b = 0; b < element_block_tags->size; ++b)
{
char* tag_name = element_block_tags->data[b];
size_t num_elem;
int* block_tag = mesh_tag(fv_mesh->cell_tags, tag_name, &num_elem);
int* num_elem_faces = polymec_malloc(sizeof(int) * num_elem);
int elem_faces_size = 0;
for (int i = 0; i < num_elem; ++i)
{
int nef = fv_mesh->cell_face_offsets[block_tag[i]+1] - fv_mesh->cell_face_offsets[block_tag[i]];
num_elem_faces[i] = nef;
elem_faces_size += nef;
}
int* elem_faces = polymec_malloc(sizeof(int) * elem_faces_size);
int offset = 0;
for (int i = 0; i < num_elem; ++i)
{
for (int f = 0; f < num_elem_faces[i]; ++f, ++offset)
elem_faces[offset+f] = fv_mesh->cell_faces[fv_mesh->cell_face_offsets[block_tag[i]+f]];
}
fe_block_t* block = polyhedral_fe_block_new((int)num_elem, num_elem_faces, fv_mesh->cell_faces);
fe_mesh_add_block(fe_mesh, tag_name, block);
polymec_free(num_elem_faces);
polymec_free(elem_faces);
}
}
else
{
// One honking block.
int num_elem = fv_mesh->num_cells;
int* num_elem_faces = polymec_malloc(sizeof(int) * num_elem);
for (int i = 0; i < num_elem; ++i)
num_elem_faces[i] = fv_mesh->cell_face_offsets[i+1] - fv_mesh->cell_face_offsets[i];
fe_block_t* block = polyhedral_fe_block_new(num_elem, num_elem_faces, fv_mesh->cell_faces);
fe_mesh_add_block(fe_mesh, "block_1", block);
polymec_free(num_elem_faces);
}
// Copy coordinates.
memcpy(fe_mesh_node_positions(fe_mesh), fv_mesh->nodes, sizeof(point_t) * fv_mesh->num_nodes);
return fe_mesh;
}
void test_write_poly_exodus_file(void** state)
{
fe_mesh_t* mesh = fe_mesh_new(MPI_COMM_WORLD, 14);
int num_elem_faces[3] = {5, 5, 7};
int elem_face_indices[] = {0, 1, 2, 3, 4, 3, 5, 6, 7, 8, 7, 9, 10, 11, 12, 13, 14};
fe_block_t* block = polyhedral_fe_block_new(3, num_elem_faces, elem_face_indices);
fe_mesh_add_block(mesh, "nfaced_1", block);
int num_face_nodes[15] = {2, 2, 3, 3, 3, 2, 2, 3, 3, 4, 4, 3, 3, 3, 3};
int face_nodes[] = {4, 5, 7, 1, 0, 3, 5, 1, 3, 7, 7, 3, 0, 4, 0, 1, 5, 4, 4, 7, 6, 0,
2, 3, 6, 7, 3, 2, 6, 2, 0, 4, 7, 3, 13, 9, 11, 6, 10, 8, 12, 2, 6, 7,
11, 10, 10, 11, 9, 8, 8, 9, 13, 12, 12, 13, 3, 2};
fe_mesh_set_face_nodes(mesh, 15, num_face_nodes, face_nodes);
point_t* X = fe_mesh_node_positions(mesh);
X[ 0].x = 0.0; X[ 0].y = 0.0; X[ 0].z = 0.0;
X[ 1].x = 2.0; X[ 1].y = 0.0; X[ 1].z = 0.0;
X[ 2].x = 0.0; X[ 2].y = 2.0; X[ 2].z = 0.0;
X[ 3].x = 2.0; X[ 3].y = 2.0; X[ 3].z = 0.0;
X[ 4].x = 0.0; X[ 4].y = 0.0; X[ 4].z = 2.0;
X[ 5].x = 2.0; X[ 5].y = 0.0; X[ 5].z = 2.0;
X[ 6].x = 0.0; X[ 6].y = 2.0; X[ 6].z = 2.0;
X[ 7].x = 2.0; X[ 7].y = 2.0; X[ 7].z = 2.0;
X[ 8].x = 0.0; X[ 8].y = 3.5; X[ 8].z = 1.0;
X[ 9].x = 2.0; X[ 9].y = 3.5; X[ 9].z = 1.0;
X[10].x = 0.0; X[10].y = 3.0; X[10].z = 1.0;
X[11].x = 2.0; X[11].y = 3.0; X[11].z = 1.0;
X[12].x = 0.0; X[12].y = 3.0; X[12].z = 0.5;
X[13].x = 2.0; X[13].y = 3.0; X[13].z = 0.5;
exodus_file_t* file = exodus_file_new(MPI_COMM_WORLD, "test-nfaced-2.exo");
assert_true(file != NULL);
exodus_file_set_title(file, "This is a test");
exodus_file_write_mesh(file, mesh);
exodus_file_close(file);
fe_mesh_free(mesh);
}
void test_write_exodus_file(void** state)
{
fe_mesh_t* mesh = fe_mesh_new(MPI_COMM_WORLD, 22);
int elem1_node_indices[] = {0, 1, 2, 3, 4, 5, 6, 7};
fe_block_t* block = fe_block_new(1, FE_HEXAHEDRON, 8, elem1_node_indices);
fe_mesh_add_block(mesh, "block_1", block);
int elem2_node_indices[] = {8, 9, 10, 11};
block = fe_block_new(1, FE_TETRAHEDRON, 4, elem2_node_indices);
fe_mesh_add_block(mesh, "block_2", block);
int elem3_node_indices[] = {12, 13, 14, 15, 16, 17};
block = fe_block_new(1, FE_WEDGE, 6, elem3_node_indices);
fe_mesh_add_block(mesh, "block_3", block);
int elem4_node_indices[] = {18, 19, 20, 21};
block = fe_block_new(1, FE_TETRAHEDRON, 4, elem4_node_indices);
fe_mesh_add_block(mesh, "block_4", block);
point_t* X = fe_mesh_node_positions(mesh);
X[ 0].x = 0.0; X[ 0].y = 0.0; X[ 0].z = 0.0;
X[ 1].x = 10.0; X[ 1].y = 0.0; X[ 1].z = 0.0;
X[ 2].x = 10.0; X[ 2].y = 0.0; X[ 2].z = -10.0;
X[ 3].x = 1.0; X[ 3].y = 0.0; X[ 3].z = -10.0;
X[ 4].x = 0.0; X[ 4].y = 10.0; X[ 4].z = 0.0;
X[ 5].x = 10.0; X[ 5].y = 10.0; X[ 5].z = 0.0;
X[ 6].x = 10.0; X[ 6].y = 10.0; X[ 6].z = -10.0;
X[ 7].x = 1.0; X[ 7].y = 10.0; X[ 7].z = -10.0;
X[ 8].x = 0.0; X[ 8].y = 0.0; X[ 8].z = 0.0;
X[ 9].x = 1.0; X[ 9].y = 0.0; X[ 9].z = 5.0;
X[10].x = 10.0; X[10].y = 0.0; X[10].z = 2.0;
X[11].x = 7.0; X[11].y = 5.0; X[11].z = 3.0;
X[12].x = 3.0; X[12].y = 0.0; X[12].z = 6.0;
X[13].x = 6.0; X[13].y = 0.0; X[13].z = 0.0;
X[14].x = 0.0; X[14].y = 0.0; X[14].z = 0.0;
X[15].x = 3.0; X[15].y = 2.0; X[15].z = 6.0;
X[16].x = 6.0; X[16].y = 2.0; X[16].z = 2.5;
X[17].x = 2.0; X[17].y = 2.0; X[17].z = 0.0;
X[18].x = 2.7; X[18].y = 1.7; X[18].z = 2.7;
X[19].x = 6.0; X[19].y = 1.7; X[19].z = 3.3;
X[20].x = 5.7; X[20].y = 1.7; X[20].z = 1.7;
X[21].x = 3.7; X[21].y = 0.0; X[21].z = 2.3;
// Node sets.
int* ns1 = fe_mesh_create_node_set(mesh, "nset_1", 5);
ns1[0] = 1; ns1[1] = 2; ns1[2] = 3; ns1[3] = 4; ns1[4] = 5;
int* ns2 = fe_mesh_create_node_set(mesh, "nset_2", 3);
ns2[0] = 11; ns2[1] = 12; ns2[2] = 13;
// Side set.
int* ss1 = fe_mesh_create_side_set(mesh, "sset_1", 1);
ss1[0] = 0; ss1[1] = 5;
exodus_file_t* file = exodus_file_new(MPI_COMM_WORLD, "test-3d.exo");
assert_true(file != NULL);
exodus_file_set_title(file, "This is a test");
exodus_file_write_mesh(file, mesh);
exodus_file_close(file);
fe_mesh_free(mesh);
}
fe_mesh_t* exodus_file_read_mesh(exodus_file_t* file)
{
// Create the "host" FE mesh.
fe_mesh_t* mesh = fe_mesh_new(file->comm, file->num_nodes);
// Count up the number of polyhedral blocks.
int num_poly_blocks = 0;
for (int i = 0; i < file->num_elem_blocks; ++i)
{
int elem_block = file->elem_block_ids[i];
char elem_type_name[MAX_NAME_LENGTH+1];
int num_elem, num_nodes_per_elem, num_faces_per_elem;
ex_get_block(file->ex_id, EX_ELEM_BLOCK, elem_block,
elem_type_name, &num_elem,
&num_nodes_per_elem, NULL,
&num_faces_per_elem, NULL);
fe_mesh_element_t elem_type = get_element_type(elem_type_name);
if (elem_type == FE_POLYHEDRON)
++num_poly_blocks;
}
// If we have any polyhedral element blocks, we read a single face
// block that incorporates all of the polyhedral elements.
if (num_poly_blocks > 0)
{
// Dig up the face block corresponding to this element block.
char face_type[MAX_NAME_LENGTH+1];
int num_faces, num_nodes;
ex_get_block(file->ex_id, EX_FACE_BLOCK, file->face_block_ids[0], face_type, &num_faces,
&num_nodes, NULL, NULL, NULL);
if (string_ncasecmp(face_type, "nsided", 6) != 0)
{
fe_mesh_free(mesh);
ex_close(file->ex_id);
polymec_error("Invalid face type for polyhedral element block.");
}
// Find the number of nodes for each face in the block.
int* num_face_nodes = polymec_malloc(sizeof(int) * num_faces);
ex_get_entity_count_per_polyhedra(file->ex_id, EX_FACE_BLOCK,
file->face_block_ids[0],
num_face_nodes);
// Read face->node connectivity information.
int face_node_size = 0;
for (int i = 0; i < num_faces; ++i)
face_node_size += num_face_nodes[i];
int* face_nodes = polymec_malloc(sizeof(int) * face_node_size);
ex_get_conn(file->ex_id, EX_FACE_BLOCK, 1, face_nodes, NULL, NULL);
for (int i = 0; i < face_node_size; ++i)
face_nodes[i] -= 1;
fe_mesh_set_face_nodes(mesh, num_faces, num_face_nodes, face_nodes);
// Clean up.
polymec_free(num_face_nodes);
}
// Go over the element blocks and feel out the data.
for (int i = 0; i < file->num_elem_blocks; ++i)
{
int elem_block = file->elem_block_ids[i];
char elem_type_name[MAX_NAME_LENGTH+1];
int num_elem, num_nodes_per_elem, num_faces_per_elem;
ex_get_block(file->ex_id, EX_ELEM_BLOCK, elem_block,
elem_type_name, &num_elem,
&num_nodes_per_elem, NULL,
&num_faces_per_elem, NULL);
// Get the type of element for this block.
fe_mesh_element_t elem_type = get_element_type(elem_type_name);
fe_block_t* block = NULL;
char block_name[MAX_NAME_LENGTH+1];
if (elem_type == FE_POLYHEDRON)
{
// Find the number of faces for each element in the block.
int* num_elem_faces = polymec_malloc(sizeof(int) * num_elem);
ex_get_entity_count_per_polyhedra(file->ex_id, EX_ELEM_BLOCK, elem_block,
num_elem_faces);
// Get the element->face connectivity.
int elem_face_size = 0;
for (int j = 0; j < num_elem; ++j)
elem_face_size += num_elem_faces[j];
int* elem_faces = polymec_malloc(sizeof(int) * elem_face_size);
ex_get_conn(file->ex_id, EX_ELEM_BLOCK, elem_block, NULL, NULL, elem_faces);
// Subtract 1 from each element face.
for (int j = 0; j < elem_face_size; ++j)
elem_faces[j] -= 1;
// Create the element block.
block = polyhedral_fe_block_new(num_elem, num_elem_faces, elem_faces);
}
else if (elem_type != FE_INVALID)
{
// Get the element's nodal mapping.
int* node_conn = polymec_malloc(sizeof(int) * num_elem * num_nodes_per_elem);
ex_get_conn(file->ex_id, EX_ELEM_BLOCK, elem_block, node_conn, NULL, NULL);
// Subtract 1 from each element node.
for (int j = 0; j < num_elem * num_nodes_per_elem; ++j)
node_conn[j] -= 1;
// Build the element block.
block = fe_block_new(num_elem, elem_type, num_nodes_per_elem, node_conn);
}
else
{
fe_mesh_free(mesh);
ex_close(file->ex_id);
polymec_error("Block %d contains an invalid (3D) element type.", elem_block);
}
// Fish out the element block name if it has one, or make a default.
ex_get_name(file->ex_id, EX_ELEM_BLOCK, elem_block, block_name);
if (strlen(block_name) == 0)
sprintf(block_name, "block_%d", elem_block);
// Add the element block to the mesh.
fe_mesh_add_block(mesh, block_name, block);
}
// Fetch node positions and compute geometry.
real_t x[file->num_nodes], y[file->num_nodes], z[file->num_nodes];
ex_get_coord(file->ex_id, x, y, z);
point_t* X = fe_mesh_node_positions(mesh);
for (int n = 0; n < file->num_nodes; ++n)
{
X[n].x = x[n];
X[n].y = y[n];
X[n].z = z[n];
}
// Fetch sets of entities.
for (int i = 1; i <= file->num_elem_sets; ++i)
fetch_set(file, EX_ELEM_SET, i, mesh, fe_mesh_create_element_set);
for (int i = 1; i <= file->num_face_sets; ++i)
fetch_set(file, EX_FACE_SET, i, mesh, fe_mesh_create_face_set);
for (int i = 1; i <= file->num_edge_sets; ++i)
fetch_set(file, EX_EDGE_SET, i, mesh, fe_mesh_create_edge_set);
for (int i = 1; i <= file->num_node_sets; ++i)
fetch_set(file, EX_NODE_SET, i, mesh, fe_mesh_create_node_set);
for (int i = 1; i <= file->num_side_sets; ++i)
fetch_set(file, EX_SIDE_SET, i, mesh, fe_mesh_create_side_set);
return mesh;
}
