void test_read_poly_exodus_file(void** state)
{
exodus_file_t* file = exodus_file_open(MPI_COMM_WORLD, "test-nfaced.exo");
assert_true(file != NULL);
assert_true(strcmp(exodus_file_title(file), "This is a test") == 0);
fe_mesh_t* mesh = exodus_file_read_mesh(file);
assert_int_equal(14, fe_mesh_num_nodes(mesh));
assert_int_equal(1, fe_mesh_num_blocks(mesh));
assert_int_equal(3, fe_mesh_num_elements(mesh));
assert_int_equal(0, fe_mesh_num_element_sets(mesh));
assert_int_equal(0, fe_mesh_num_face_sets(mesh));
assert_int_equal(0, fe_mesh_num_edge_sets(mesh));
assert_int_equal(0, fe_mesh_num_node_sets(mesh));
assert_int_equal(0, fe_mesh_num_side_sets(mesh));
int elem_faces[10];
assert_int_equal(5, fe_mesh_num_element_faces(mesh, 0));
fe_mesh_get_element_faces(mesh, 0, elem_faces);
assert_int_equal(0, elem_faces[0]);
assert_int_equal(1, elem_faces[1]);
assert_int_equal(2, elem_faces[2]);
assert_int_equal(3, elem_faces[3]);
assert_int_equal(4, elem_faces[4]);
assert_int_equal(5, fe_mesh_num_element_faces(mesh, 1));
fe_mesh_get_element_faces(mesh, 1, elem_faces);
assert_int_equal(3, elem_faces[0]);
assert_int_equal(5, elem_faces[1]);
assert_int_equal(6, elem_faces[2]);
assert_int_equal(7, elem_faces[3]);
assert_int_equal(8, elem_faces[4]);
assert_int_equal(7, fe_mesh_num_element_faces(mesh, 2));
fe_mesh_get_element_faces(mesh, 2, elem_faces);
assert_int_equal(7, elem_faces[0]);
assert_int_equal(9, elem_faces[1]);
assert_int_equal(10, elem_faces[2]);
assert_int_equal(11, elem_faces[3]);
assert_int_equal(12, elem_faces[4]);
assert_int_equal(13, elem_faces[5]);
assert_int_equal(14, elem_faces[6]);
int pos = 0;
char* block_name;
fe_block_t* block;
assert_true(fe_mesh_next_block(mesh, &pos, &block_name, &block));
assert_true(strcmp(block_name, "nfaced_1") == 0);
assert_int_equal(5, fe_block_num_element_faces(block, 0));
fe_mesh_free(mesh);
exodus_file_close(file);
}
int fe_mesh_num_element_nodes(fe_mesh_t* mesh, int elem_index)
{
ASSERT(elem_index >= 0);
ASSERT(elem_index < fe_mesh_num_elements(mesh));
// Find the block that houses this element.
int b = 0;
if (mesh->blocks->size > 1)
{
while ((mesh->block_elem_offsets->data[b] < elem_index) &&
((b+1) <= mesh->block_elem_offsets->size)) ++b;
if (b == mesh->block_elem_offsets->size-1)
return -1;
}
// Now ask the block about the element.
fe_block_t* block = mesh->blocks->data[b];
int e = elem_index - mesh->block_elem_offsets->data[b];
return fe_block_num_element_nodes(block, e);
}
mesh_t* mesh_from_fe_mesh(fe_mesh_t* fe_mesh)
{
// Feel out the faces for the finite element mesh. Do we need to create
// them ourselves, or are they already all there?
int num_cells = fe_mesh_num_elements(fe_mesh);
int num_faces = fe_mesh_num_faces(fe_mesh);
int* cell_face_offsets = polymec_malloc(sizeof(int) * (num_cells + 1));
cell_face_offsets[0] = 0;
int* cell_faces = NULL;
int* face_node_offsets = NULL;
int* face_nodes = NULL;
if (num_faces == 0)
{
// Traverse the element blocks and figure out the number of faces per cell.
int pos = 0, elem_offset = 0;
char* block_name;
fe_block_t* block;
while (fe_mesh_next_block(fe_mesh, &pos, &block_name, &block))
{
int num_block_elem = fe_block_num_elements(block);
fe_mesh_element_t elem_type = fe_block_element_type(block);
int num_elem_faces = get_num_cell_faces(elem_type);
for (int i = 0; i < num_block_elem; ++i)
cell_face_offsets[elem_offset+i+1] = cell_face_offsets[elem_offset+i] + num_elem_faces;
elem_offset += num_block_elem;
}
// Now assemble the faces for each cell.
int_tuple_int_unordered_map_t* node_face_map = int_tuple_int_unordered_map_new();
cell_faces = polymec_malloc(sizeof(int) * cell_face_offsets[num_cells]);
// We build the face->node connectivity data on-the-fly.
int_array_t* face_node_offsets_array = int_array_new();
int_array_append(face_node_offsets_array, 0);
int_array_t* face_nodes_array = int_array_new();
pos = 0, elem_offset = 0;
while (fe_mesh_next_block(fe_mesh, &pos, &block_name, &block))
{
int num_block_elem = fe_block_num_elements(block);
fe_mesh_element_t elem_type = fe_block_element_type(block);
int num_elem_nodes = fe_block_num_element_nodes(block, 0);
int elem_nodes[num_elem_nodes];
for (int i = 0; i < num_block_elem; ++i)
{
fe_block_get_element_nodes(block, i, elem_nodes);
int offset = cell_face_offsets[elem_offset+i];
get_cell_faces(elem_type, elem_nodes, node_face_map,
&cell_faces[offset], face_node_offsets_array,
face_nodes_array);
}
elem_offset += num_block_elem;
}
// Record the total number of faces and discard the map.
num_faces = node_face_map->size;
int_tuple_int_unordered_map_free(node_face_map);
// Gift the contents of the arrays to our pointers.
face_node_offsets = face_node_offsets_array->data;
int_array_release_data_and_free(face_node_offsets_array);
face_nodes = face_nodes_array->data;
int_array_release_data_and_free(face_nodes_array);
}
else
{
// Fill in these arrays block by block.
int pos = 0;
char* block_name;
fe_block_t* block;
int block_cell_offset = 0;
while (fe_mesh_next_block(fe_mesh, &pos, &block_name, &block))
{
int num_block_elem = fe_block_num_elements(block);
for (int i = 0; i < num_block_elem; ++i)
cell_face_offsets[block_cell_offset+i] = cell_face_offsets[block_cell_offset+i-1] + block->elem_face_offsets[i];
block_cell_offset += num_block_elem;
}
cell_faces = polymec_malloc(sizeof(int) * cell_face_offsets[num_cells]);
pos = 0, block_cell_offset = 0;
while (fe_mesh_next_block(fe_mesh, &pos, &block_name, &block))
{
int num_block_elem = fe_block_num_elements(block);
memcpy(&cell_faces[cell_face_offsets[block_cell_offset]], block->elem_faces, sizeof(int) * block->elem_face_offsets[num_block_elem]);
block_cell_offset += num_block_elem;
}
// We just borrow these from the mesh. Theeenks!
face_node_offsets = fe_mesh->face_node_offsets;
face_nodes = fe_mesh->face_nodes;
}
ASSERT(cell_faces != NULL);
ASSERT(face_node_offsets != NULL);
ASSERT(face_nodes != NULL);
// Create the finite volume mesh and set up its cell->face and face->node
// connectivity.
int num_ghost_cells = 0; // FIXME!
mesh_t* mesh = mesh_new(fe_mesh_comm(fe_mesh),
num_cells, num_ghost_cells,
num_faces,
fe_mesh_num_nodes(fe_mesh));
memcpy(mesh->cell_face_offsets, cell_face_offsets, sizeof(int) * (mesh->num_cells+1));
memcpy(mesh->face_node_offsets, face_node_offsets, sizeof(int) * (mesh->num_faces+1));
mesh_reserve_connectivity_storage(mesh);
memcpy(mesh->cell_faces, cell_faces, sizeof(int) * (mesh->cell_face_offsets[mesh->num_cells]));
memcpy(mesh->face_nodes, face_nodes, sizeof(int) * (mesh->face_node_offsets[mesh->num_faces]));
// Set up face->cell connectivity.
for (int c = 0; c < mesh->num_cells; ++c)
{
for (int f = mesh->cell_face_offsets[c]; f < mesh->cell_face_offsets[c+1]; ++f)
{
int face = mesh->cell_faces[f];
if (mesh->face_cells[2*face] == -1)
mesh->face_cells[2*face] = c;
else
mesh->face_cells[2*face+1] = c;
}
}
// Set up face->edge connectivity and edge->node connectivity (if provided).
if (fe_mesh->face_edges != NULL)
{
memcpy(mesh->face_edge_offsets, fe_mesh->face_edge_offsets, sizeof(int) * (mesh->num_faces+1));
mesh->face_edges = polymec_malloc(sizeof(int) * fe_mesh->face_edge_offsets[mesh->num_faces]);
memcpy(mesh->face_edges, fe_mesh->face_edges, sizeof(int) * fe_mesh->face_edge_offsets[mesh->num_faces]);
}
else
{
// Construct edges if we didn't find them.
mesh_construct_edges(mesh);
}
// Copy the node positions into place.
memcpy(mesh->nodes, fe_mesh_node_positions(fe_mesh), sizeof(point_t) * mesh->num_nodes);
// Calculate geometry.
mesh_compute_geometry(mesh);
// Sets -> tags.
int pos = 0, *set;
size_t set_size;
char* set_name;
while (fe_mesh_next_element_set(fe_mesh, &pos, &set_name, &set, &set_size))
{
int* tag = mesh_create_tag(mesh->cell_tags, set_name, set_size);
memcpy(tag, set, sizeof(int) * set_size);
}
pos = 0;
while (fe_mesh_next_face_set(fe_mesh, &pos, &set_name, &set, &set_size))
{
int* tag = mesh_create_tag(mesh->face_tags, set_name, set_size);
memcpy(tag, set, sizeof(int) * set_size);
}
pos = 0;
while (fe_mesh_next_edge_set(fe_mesh, &pos, &set_name, &set, &set_size))
{
int* tag = mesh_create_tag(mesh->edge_tags, set_name, set_size);
memcpy(tag, set, sizeof(int) * set_size);
}
pos = 0;
while (fe_mesh_next_node_set(fe_mesh, &pos, &set_name, &set, &set_size))
{
int* tag = mesh_create_tag(mesh->node_tags, set_name, set_size);
memcpy(tag, set, sizeof(int) * set_size);
}
// Clean up.
polymec_free(cell_face_offsets);
polymec_free(cell_faces);
if (fe_mesh_num_faces(fe_mesh) == 0)
{
polymec_free(face_node_offsets);
polymec_free(face_nodes);
}
return mesh;
}
void test_read_exodus_file(void** state)
{
exodus_file_t* file = exodus_file_open(MPI_COMM_WORLD, "test-3d.exo");
assert_true(file != NULL);
assert_true(strcmp(exodus_file_title(file), "This is a test") == 0);
fe_mesh_t* mesh = exodus_file_read_mesh(file);
assert_int_equal(22, fe_mesh_num_nodes(mesh));
assert_int_equal(4, fe_mesh_num_blocks(mesh));
assert_int_equal(4, fe_mesh_num_elements(mesh));
assert_int_equal(0, fe_mesh_num_element_sets(mesh));
assert_int_equal(0, fe_mesh_num_face_sets(mesh));
assert_int_equal(0, fe_mesh_num_edge_sets(mesh));
assert_int_equal(2, fe_mesh_num_node_sets(mesh));
assert_int_equal(1, fe_mesh_num_side_sets(mesh));
int elem_nodes[10];
assert_int_equal(8, fe_mesh_num_element_nodes(mesh, 0));
fe_mesh_get_element_nodes(mesh, 0, elem_nodes);
assert_int_equal(0, elem_nodes[0]);
assert_int_equal(1, elem_nodes[1]);
assert_int_equal(2, elem_nodes[2]);
assert_int_equal(3, elem_nodes[3]);
assert_int_equal(4, elem_nodes[4]);
assert_int_equal(5, elem_nodes[5]);
assert_int_equal(6, elem_nodes[6]);
assert_int_equal(7, elem_nodes[7]);
assert_int_equal(4, fe_mesh_num_element_nodes(mesh, 1));
fe_mesh_get_element_nodes(mesh, 1, elem_nodes);
assert_int_equal(8, elem_nodes[0]);
assert_int_equal(9, elem_nodes[1]);
assert_int_equal(10, elem_nodes[2]);
assert_int_equal(11, elem_nodes[3]);
assert_int_equal(6, fe_mesh_num_element_nodes(mesh, 2));
fe_mesh_get_element_nodes(mesh, 2, elem_nodes);
assert_int_equal(12, elem_nodes[0]);
assert_int_equal(13, elem_nodes[1]);
assert_int_equal(14, elem_nodes[2]);
assert_int_equal(15, elem_nodes[3]);
assert_int_equal(16, elem_nodes[4]);
assert_int_equal(17, elem_nodes[5]);
assert_int_equal(4, fe_mesh_num_element_nodes(mesh, 3));
fe_mesh_get_element_nodes(mesh, 3, elem_nodes);
assert_int_equal(18, elem_nodes[0]);
assert_int_equal(19, elem_nodes[1]);
assert_int_equal(20, elem_nodes[2]);
assert_int_equal(21, elem_nodes[3]);
int pos = 0;
char* block_name;
fe_block_t* block;
assert_true(fe_mesh_next_block(mesh, &pos, &block_name, &block));
assert_true(strcmp(block_name, "block_1") == 0);
assert_true(fe_block_element_type(block) == FE_HEXAHEDRON);
assert_true(fe_mesh_next_block(mesh, &pos, &block_name, &block));
assert_true(strcmp(block_name, "block_2") == 0);
assert_true(fe_block_element_type(block) == FE_TETRAHEDRON);
assert_true(fe_mesh_next_block(mesh, &pos, &block_name, &block));
assert_true(strcmp(block_name, "block_3") == 0);
assert_true(fe_block_element_type(block) == FE_WEDGE);
assert_true(fe_mesh_next_block(mesh, &pos, &block_name, &block));
assert_true(strcmp(block_name, "block_4") == 0);
assert_true(fe_block_element_type(block) == FE_TETRAHEDRON);
// Node sets.
int* set, set_size;
char* set_name;
pos = 0;
int num_node_sets = 0;
while (fe_mesh_next_node_set(mesh, &pos, &set_name, &set, &set_size))
{
++num_node_sets;
assert_true((strcmp(set_name, "nset_1") == 0) ||
(strcmp(set_name, "nset_2") == 0));
if (strcmp(set_name, "nset_1") == 0)
{
assert_int_equal(5, set_size);
assert_int_equal(1, set[0]);
assert_int_equal(2, set[1]);
assert_int_equal(3, set[2]);
assert_int_equal(4, set[3]);
assert_int_equal(5, set[4]);
}
else
{
assert_int_equal(3, set_size);
assert_int_equal(11, set[0]);
assert_int_equal(12, set[1]);
assert_int_equal(13, set[2]);
}
}
assert_int_equal(2, num_node_sets);
fe_mesh_free(mesh);
exodus_file_close(file);
}
void exodus_file_write_mesh(exodus_file_t* file,
fe_mesh_t* mesh)
{
ASSERT(file->writing);
// See whether we have polyhedral blocks, and whether the non-polyhedral
// blocks have supported element types.
int num_blocks = fe_mesh_num_blocks(mesh);
bool is_polyhedral = false;
int pos = 0;
char* block_name;
fe_block_t* block;
while (fe_mesh_next_block(mesh, &pos, &block_name, &block))
{
fe_mesh_element_t elem_type = fe_block_element_type(block);
if (elem_type == FE_POLYHEDRON)
{
is_polyhedral = true;
break;
}
else if (elem_type != FE_INVALID)
{
// Check the number of nodes for the element.
if (!element_is_supported(elem_type, fe_block_num_element_nodes(block, 0)))
polymec_error("exodus_file_write_mesh: Element type in block %s has invalid number of nodes.", block_name);
}
else
polymec_error("exodus_file_write_mesh: Invalid element type for block %s.", block_name);
}
// Write out information about elements, faces, edges, nodes.
file->num_nodes = fe_mesh_num_nodes(mesh);
ex_init_params params;
strcpy(params.title, file->title);
params.num_dim = 3;
params.num_nodes = file->num_nodes;
int num_edges = fe_mesh_num_edges(mesh);
params.num_edge = num_edges;
params.num_edge_blk = 0;
int num_faces = fe_mesh_num_faces(mesh);
params.num_face = num_faces;
params.num_face_blk = (is_polyhedral) ? 1 : 0;
int num_elem = fe_mesh_num_elements(mesh);
params.num_elem = num_elem;
params.num_elem_blk = num_blocks;
params.num_elem_sets = file->num_elem_sets = fe_mesh_num_element_sets(mesh);
params.num_face_sets = file->num_face_sets = fe_mesh_num_face_sets(mesh);
params.num_edge_sets = file->num_edge_sets = fe_mesh_num_edge_sets(mesh);
params.num_node_sets = file->num_node_sets = fe_mesh_num_node_sets(mesh);
params.num_side_sets = file->num_side_sets = fe_mesh_num_side_sets(mesh);
params.num_elem_maps = 0;
params.num_face_maps = 0;
params.num_edge_maps = 0;
params.num_node_maps = 0;
ex_put_init_ext(file->ex_id, ¶ms);
// If we have any polyhedral element blocks, we write out a single face
// block that incorporates all of the polyhedral elements.
if (is_polyhedral)
{
// Generate face->node connectivity information.
int num_pfaces = fe_mesh_num_faces(mesh);
int face_node_size = 0;
int num_face_nodes[num_pfaces];
for (int f = 0; f < num_pfaces; ++f)
{
int num_nodes = fe_mesh_num_face_nodes(mesh, f);
num_face_nodes[f] = num_nodes;
face_node_size += num_nodes;
}
int* face_nodes = polymec_malloc(sizeof(int) * face_node_size);
int offset = 0;
for (int f = 0; f < num_pfaces; ++f)
{
fe_mesh_get_face_nodes(mesh, f, &face_nodes[offset]);
offset += num_face_nodes[f];
}
for (int i = 0; i < face_node_size; ++i)
face_nodes[i] += 1;
// Write an "nsided" face block.
ex_put_block(file->ex_id, EX_FACE_BLOCK, 1, "nsided",
num_pfaces, face_node_size, 0, 0, 0);
ex_put_name(file->ex_id, EX_FACE_BLOCK, 1, "face_block");
ex_put_conn(file->ex_id, EX_FACE_BLOCK, 1, face_nodes, NULL, NULL);
// Clean up.
polymec_free(face_nodes);
// Number of nodes per face.
ex_put_entity_count_per_polyhedra(file->ex_id, EX_FACE_BLOCK,
1, num_face_nodes);
}
// Go over the element blocks and write out the data.
pos = 0;
while (fe_mesh_next_block(mesh, &pos, &block_name, &block))
{
int elem_block = pos;
int num_e = fe_block_num_elements(block);
fe_mesh_element_t elem_type = fe_block_element_type(block);
if (elem_type == FE_POLYHEDRON)
{
// Count up the faces in the block and write the block information.
int tot_num_elem_faces = 0;
int faces_per_elem[num_e];
for (int i = 0; i < num_e; ++i)
{
faces_per_elem[i] = fe_block_num_element_faces(block, i);
tot_num_elem_faces += faces_per_elem[i];
}
ex_put_block(file->ex_id, EX_ELEM_BLOCK, elem_block, "nfaced",
num_e, 0, 0, tot_num_elem_faces, 0);
// Write elem->face connectivity information.
int elem_faces[tot_num_elem_faces], offset = 0;
for (int i = 0; i < num_e; ++i)
{
fe_block_get_element_faces(block, i, &elem_faces[offset]);
offset += faces_per_elem[i];
}
for (int i = 0; i < tot_num_elem_faces; ++i)
elem_faces[i] += 1;
ex_put_conn(file->ex_id, EX_ELEM_BLOCK, elem_block, NULL, NULL, elem_faces);
ex_put_entity_count_per_polyhedra(file->ex_id, EX_ELEM_BLOCK, elem_block, faces_per_elem);
}
else if (elem_type != FE_INVALID)
{
// Get element information.
char elem_type_name[MAX_NAME_LENGTH+1];
get_elem_name(elem_type, elem_type_name);
int num_nodes_per_elem = fe_block_num_element_nodes(block, 0);
// Write the block.
ex_put_block(file->ex_id, EX_ELEM_BLOCK, elem_block, elem_type_name,
num_e, num_nodes_per_elem, 0, 0, 0);
// Write the elem->node connectivity.
int elem_nodes[num_e* num_nodes_per_elem], offset = 0;
for (int i = 0; i < num_e; ++i)
{
fe_block_get_element_nodes(block, i, &elem_nodes[offset]);
offset += num_nodes_per_elem;
}
for (int i = 0; i < num_e* num_nodes_per_elem; ++i)
elem_nodes[i] += 1;
ex_put_conn(file->ex_id, EX_ELEM_BLOCK, elem_block, elem_nodes, NULL, NULL);
}
// Set the element block name.
ex_put_name(file->ex_id, EX_ELEM_BLOCK, elem_block, block_name);
}
// Set node positions.
real_t x[file->num_nodes], y[file->num_nodes], z[file->num_nodes];
point_t* X = fe_mesh_node_positions(mesh);
for (int n = 0; n < file->num_nodes; ++n)
{
x[n] = X[n].x;
y[n] = X[n].y;
z[n] = X[n].z;
}
ex_put_coord(file->ex_id, x, y, z);
char* coord_names[3] = {"x", "y", "z"};
ex_put_coord_names(file->ex_id, coord_names);
// Write sets of entities.
int *set, set_id = 0;
size_t set_size;
char* set_name;
pos = set_id = 0;
while (fe_mesh_next_element_set(mesh, &pos, &set_name, &set, &set_size))
write_set(file, EX_ELEM_SET, ++set_id, set_name, set, set_size);
pos = set_id = 0;
while (fe_mesh_next_face_set(mesh, &pos, &set_name, &set, &set_size))
write_set(file, EX_FACE_SET, ++set_id, set_name, set, set_size);
pos = set_id = 0;
while (fe_mesh_next_edge_set(mesh, &pos, &set_name, &set, &set_size))
write_set(file, EX_EDGE_SET, ++set_id, set_name, set, set_size);
pos = set_id = 0;
while (fe_mesh_next_node_set(mesh, &pos, &set_name, &set, &set_size))
write_set(file, EX_NODE_SET, ++set_id, set_name, set, set_size);
pos = set_id = 0;
while (fe_mesh_next_side_set(mesh, &pos, &set_name, &set, &set_size))
write_set(file, EX_SIDE_SET, ++set_id, set_name, set, set_size);
}