def _get_submesh_by_partition_id(partition_id, mesh):
"""
Getter for a submesh, derived from the given mesh, but only possesses elements, nodes and groups, which belong
to the given partition.
Parameters
----------
partition_id : int
ID of the partition
mesh : Mesh
partitioned Mesh-object
"""
submesh = Mesh(mesh.dimension)
ele_ids = mesh.get_elementids_by_tags(['partition_id'], partition_id)
nodes_df, el_df = mesh.get_submesh_by_elementids(ele_ids)
ele_groups = mesh.get_groups_dict_by_elementids(el_df.index.tolist())
node_groups = mesh.get_groups_dict_by_nodeids(nodes_df.index.tolist())
submesh.nodes_df = deepcopy(nodes_df)
submesh._el_df = deepcopy(el_df)
submesh.merge_into_groups(ele_groups)
submesh.merge_into_groups(node_groups)
submesh._update_iconnectivity()
return submesh
def test_constructor(self):
from amfe.mesh import Mesh
mesh = Mesh(dimension=2)
self.assertEqual(mesh.dimension, 2)
mesh = Mesh(dimension=3)
self.assertEqual(mesh.dimension, 3)
with self.assertRaises(ValueError) as err:
mesh = Mesh(dimension=1)
def __init__(self, l, h, n_ele_l, n_ele_h, x_start=0.0, y_start=0.0):
self.l = l
self.h = h
self.n_ele_l = n_ele_l
self.n_ele_h = n_ele_h
self.delta_h_x = self.l / self.n_ele_l
self.delta_h_y = self.h / self.n_ele_h
self.x_start = x_start
self.y_start = y_start
self._mesh = Mesh(2)
def setUp(self):
from amfe.mesh import Mesh
self.testmesh = Mesh(dimension=2)
'''
Testmesh: Partition:
9---10--11 11--12
9---10--11--12 | *3* | |*4*|
| | | | | | | |
| | | | 4---3---6 6---7
4---3---6---7
| |\ | /| 4---3---6 6---7
| | \| / | | *1* | |*2*|
1---2---5---8 | | | |
1---2---5 5---8
'''
nodes = np.array([[0.0, 0.0], [1.0, 0.0], [1.0, 1.0], [0.0, 1.0], [2.0, 0.0], [2.0, 1.0], [3.0, 1.0], [3.0, 0.0], [0.0, 2.0], [1.0, 2.0], [2.0, 2.0], [3.0, 2.0]], dtype=np.float)
connectivity = [np.array([5, 6, 3], dtype=np.int), np.array([3, 2, 5], dtype=np.int),
np.array([1, 2, 3, 4], dtype=np.int), np.array([5, 7, 8], dtype=np.int), np.array([6, 7, 5], dtype=np.int),
np.array([3, 4, 9, 10], dtype=np.int), np.array([6, 7, 11, 12], dtype=np.int), np.array([3, 6, 10, 11], dtype=np.int),
# boundary elements
np.array([4, 1], dtype=np.int), np.array([4, 9], dtype=np.int), np.array([7, 8], dtype=np.int), np.array([7, 12], dtype=np.int)]
self._connectivity = connectivity
data = {'shape': ['Tri3', 'Tri3', 'Quad4', 'Tri3', 'Tri3', 'Quad4', 'Quad4', 'Quad4', 'straight_line', 'straight_line', 'straight_line', 'straight_line'],
'is_boundary': [False, False, False, False, False, False, False, False, True, True, True, True],
'connectivity': connectivity,
'no_of_mesh_partitions': [4, 3, 2, 3, 4, 2, 4, 4, 2, 2, 2, 2],
'partition_id': [1, 1, 1, 2, 2, 3, 4, 3, 1, 3, 2, 4],
'partitions_neighbors': [(2, 3, 4), (2, 3), 3, (1, 4), (1, 3, 4), 1, (1, 2, 3), (1, 2, 4), 3, 1, 4, 2]
}
indices = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
el_df = pd.DataFrame(data, index=indices)
x = nodes[:, 0]
y = nodes[:, 1]
nodeids = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
nodes_df = pd.DataFrame({'x': x, 'y': y}, index=nodeids)
groups = {'left': {'elements': [3], 'nodes': []},
'right': {'elements': [1, 2], 'nodes': [2, 3, 5, 6]},
'left_boundary': {'elements': [9, 10], 'nodes': [1, 4]},
'right_boundary': {'elements': [11, 12], 'nodes': [7, 8]}
}
self.testmesh.nodes_df = nodes_df
self.testmesh.groups = groups
self.testmesh._el_df = el_df
def setUp(self):
self.testmesh = Mesh(dimension=2)
nodes = np.array([[0.0, 0.0], [1.0, 0.0], [1.0, 1.0], [0.0, 1.0], [2.0, 0.0], [2.0, 1.0]], dtype=np.float)
connectivity = [np.array([5, 6, 3], dtype=np.int), np.array([3, 2, 5], dtype=np.int),
np.array([1, 2, 3, 4], dtype=np.int),
# boundary elements
np.array([4, 1], dtype=np.int), np.array([5, 6], dtype=np.int)]
shapes = ['Tri3', 'Tri3', 'Quad4', 'straight_line', 'straight_line']
data = {'shape': shapes,
'is_boundary': [False, False, False, True, True],
'connectivity': connectivity}
indices = [1, 2, 3, 4, 5]
el_df = pd.DataFrame(data, index=indices)
x = nodes[:, 0]
y = nodes[:, 1]
nodeids = [1, 2, 3, 4, 5, 6]
self._nodeids = nodeids
self._nodes = nodes
self._eleids = indices
self._connectivity = connectivity
self._connectivity = connectivity
self._shapes = shapes
nodes_df = pd.DataFrame({'x': x, 'y': y}, index=nodeids)
groups = {'left': {'elements': [3], 'nodes': []},
'right': {'elements': [1, 2], 'nodes': [2, 3, 5, 6]},
'left_boundary': {'elements': [4], 'nodes': []},
'right_boundary': {'elements': [5], 'nodes': [1, 2]}
}
self.testmesh.nodes_df = nodes_df
self.testmesh.groups = groups
self.testmesh._el_df = el_df
self.testmesh3d = deepcopy(self.testmesh)
nodes3d = np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0],
[1.0, 1.0, 0.0], [0.0, 1.0, 0.0],
[2.0, 0.0, 1.0], [2.0, 1.0, 1.0]], dtype=np.float)
self.testmesh3d.dimension = 3
x = nodes3d[:, 0]
y = nodes3d[:, 1]
z = nodes3d[:, 2]
nodes_df3d = pd.DataFrame({'x': x, 'y': y, 'z': z}, index=nodeids)
self.testmesh3d.nodes_df = nodes_df3d
def __init__(self, verbose=False):
super().__init__()
self._verbose = verbose
self._mesh = Mesh()
self._dimension = None
self._no_of_nodes = None
self._no_of_elements = None
self._nodes = np.empty((0, 4), dtype=float)
self._currentnodeid = 0
self._groups = dict()
self._tags = dict()
# df information
self._el_df_indices = list()
self._el_df_eleshapes = list()
self._el_df_connectivity = list()
self._el_df_is_boundary = list()
return
def __init__(self, mesh=Mesh()):
super().__init__(mesh)
self.rayleigh_damping = None
self._assembly = StructuralAssembly()
self._M_constr = None
self._D_constr = None
self._C_csr = None
self._M_csr = None
self._f_glob_int = None
self._f_glob_ext = None
self._stresses = None
self._strains = None
def __init__(self, mesh=Mesh()):
super().__init__()
self._mesh = mesh
self._mapping = StandardMapping()
self._ele_obj_df = pd.DataFrame(
[], columns=['physics', 'fk_mesh', 'ele_obj', 'fk_mapping'])
self._ele_obj_df['fk_mapping'] = self._ele_obj_df['fk_mapping'].astype(
int)
self._ele_obj_df['fk_mesh'] = self._ele_obj_df['fk_mesh'].astype(int)
self._neumann = NeumannManager()
self._assembly = Assembly()
self._constraints = ConstraintManager()
class TestPartitionedMesh(TestCase):
def setUp(self):
from amfe.mesh import Mesh
self.testmesh = Mesh(dimension=2)
'''
Testmesh: Partition:
9---10--11 11--12
9---10--11--12 | *3* | |*4*|
| | | | | | | |
| | | | 4---3---6 6---7
4---3---6---7
| |\ | /| 4---3---6 6---7
| | \| / | | *1* | |*2*|
1---2---5---8 | | | |
1---2---5 5---8
'''
nodes = np.array([[0.0, 0.0], [1.0, 0.0], [1.0, 1.0], [0.0, 1.0],
[2.0, 0.0], [2.0, 1.0], [3.0, 1.0], [3.0, 0.0],
[0.0, 2.0], [1.0, 2.0], [2.0, 2.0], [3.0, 2.0]],
dtype=np.float)
connectivity = [
np.array([5, 6, 3], dtype=np.int),
np.array([3, 2, 5], dtype=np.int),
np.array([1, 2, 3, 4], dtype=np.int),
np.array([5, 7, 8], dtype=np.int),
np.array([6, 7, 5], dtype=np.int),
np.array([3, 4, 9, 10], dtype=np.int),
np.array([6, 7, 11, 12], dtype=np.int),
np.array([3, 6, 10, 11], dtype=np.int),
# boundary elements
np.array([4, 1], dtype=np.int),
np.array([4, 9], dtype=np.int),
np.array([7, 8], dtype=np.int),
np.array([7, 12], dtype=np.int)
]
self._connectivity = connectivity
data = {
'shape': [
'Tri3', 'Tri3', 'Quad4', 'Tri3', 'Tri3', 'Quad4', 'Quad4',
'Quad4', 'straight_line', 'straight_line', 'straight_line',
'straight_line'
],
'is_boundary': [
False, False, False, False, False, False, False, False, True,
True, True, True
],
'connectivity':
connectivity,
'no_of_mesh_partitions': [4, 3, 2, 3, 4, 2, 4, 4, 2, 2, 2, 2],
'partition_id': [1, 1, 1, 2, 2, 3, 4, 3, 1, 3, 2, 4],
'partitions_neighbors': [(2, 3, 4), (2, 3), 3, (1, 4), (1, 3, 4),
1, (1, 2, 3), (1, 2, 4), 3, 1, 4, 2]
}
indices = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
el_df = pd.DataFrame(data, index=indices)
x = nodes[:, 0]
y = nodes[:, 1]
nodeids = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
nodes_df = pd.DataFrame({'x': x, 'y': y}, index=nodeids)
groups = {
'left': {
'elements': [3],
'nodes': []
},
'right': {
'elements': [1, 2],
'nodes': [2, 3, 5, 6]
},
'left_boundary': {
'elements': [9, 10],
'nodes': [1, 4]
},
'right_boundary': {
'elements': [11, 12],
'nodes': [7, 8]
}
}
self.testmesh.nodes_df = nodes_df
self.testmesh.groups = groups
self.testmesh._el_df = el_df
def test_get_uniques_by_tag(self):
partition_ids_desired = [1, 2, 3, 4]
partition_ids_actual = self.testmesh.get_uniques_by_tag('partition_id')
assert_array_equal(partition_ids_actual, partition_ids_desired)
def test_get_submesh_by_elementids(self):
nodes_coord_desired = np.array(
[[2.0, 0.0], [2.0, 1.0], [3.0, 1.0], [3.0, 0.0]], dtype=np.float)
x = nodes_coord_desired[:, 0]
y = nodes_coord_desired[:, 1]
nodeids = [5, 6, 7, 8]
nodes_desired = pd.DataFrame({'x': x, 'y': y}, index=nodeids)
connectivity_desired = [
np.array([5, 7, 8], dtype=np.int),
np.array([6, 7, 5], dtype=np.int),
np.array([7, 8], dtype=np.int)
]
data = {
'shape': ['Tri3', 'Tri3', 'straight_line'],
'is_boundary': [False, False, True],
'connectivity': connectivity_desired,
'no_of_mesh_partitions': [3, 4, 2],
'partition_id': [2, 2, 2],
'partitions_neighbors': [(1, 4), (1, 3, 4), 4]
}
indices = [4, 5, 11]
elements_desired = pd.DataFrame(data, index=indices)
nodes, elements = self.testmesh.get_submesh_by_elementids([4, 5, 11])
assert_frame_equal(nodes, nodes_desired)
assert_frame_equal(elements, elements_desired)
def test_update_connectivity_with_new_node(self):
connectivity_desired = np.array([
np.array([5, 6, 3], dtype=np.int),
np.array([3, 2, 5], dtype=np.int),
np.array([1, 2, 3, 4], dtype=np.int),
np.array([5, 13, 8], dtype=np.int),
np.array([6, 7, 5], dtype=np.int),
np.array([3, 4, 9, 10], dtype=np.int),
np.array([6, 13, 11, 12], dtype=np.int),
np.array([3, 6, 10, 11], dtype=np.int),
# boundary elements
np.array([4, 1], dtype=np.int),
np.array([4, 9], dtype=np.int),
np.array([7, 8], dtype=np.int),
np.array([7, 12], dtype=np.int)
])
self.testmesh.update_connectivity_with_new_node(7, 13, [4, 7])
connectivity_actual = self.testmesh.get_connectivity_by_elementids(
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12])
for i in range(connectivity_desired.shape[0]):
assert_array_equal(connectivity_actual[i], connectivity_desired[i])
def test_get_elementids_by_tags(self):
desired = np.array([1, 2, 4, 5, 7, 8], dtype=int)
actual = self.testmesh.get_elementids_by_tags('no_of_mesh_partitions',
2, True)
assert_array_equal(desired, actual)
def test_get_value_by_elementid_and_tag(self):
neighbors_desired = [2, 3]
neighbors_actual = self.testmesh.get_value_by_elementid_and_tag(
2, 'partitions_neighbors')
assert_array_equal(neighbors_actual, neighbors_desired)
def test_add_element(self):
mesh = Mesh(2)
for nodeid, coords in zip(self._nodeids, self._nodes):
mesh.add_node(coords, nodeid)
conn_desired = np.array([5, 6, 3], dtype=np.int)
shape_desired = 'Tri3'
new_id = mesh.add_element(shape_desired, conn_desired)
shape_actual = mesh.get_ele_shapes_by_elementids([new_id])[0]
conn_actual = mesh.get_connectivity_by_elementids([new_id])[0]
self.assertEqual(shape_actual, shape_desired)
assert_array_equal(conn_actual, conn_desired)
conn_desired = np.array([4, 1], dtype=np.int)
shape_desired = 'straight_line'
new_id = mesh.add_element(shape_desired, conn_desired)
shape_actual = mesh.get_ele_shapes_by_elementids([new_id])[0]
conn_actual = mesh.get_connectivity_by_elementids([new_id])[0]
self.assertEqual(shape_actual, shape_desired)
assert_array_equal(conn_actual, conn_desired)
conn_desired = np.array([3, 2, 5], dtype=np.int)
shape_desired = 'Tri3'
new_id = mesh.add_element(shape_desired,
np.array([3, 2, 5], dtype=np.int), 5)
shape_actual = mesh.get_ele_shapes_by_elementids([new_id])[0]
conn_actual = mesh.get_connectivity_by_elementids([new_id])[0]
self.assertEqual(shape_actual, shape_desired)
assert_array_equal(conn_actual, conn_desired)
self.assertEqual(new_id, 5)
with self.assertRaises(ValueError):
mesh.add_element('Quad4', np.array([1, 2, 3, 4], dtype=np.int), 5)
conn_desired = np.array([1, 2, 3, 4], dtype=np.int)
shape_desired = 'Quad4'
new_id = mesh.add_element('Quad4',
np.array([1, 2, 3, 4], dtype=np.int),
5,
overwrite=True)
shape_actual = mesh.get_ele_shapes_by_elementids([new_id])[0]
conn_actual = mesh.get_connectivity_by_elementids([new_id])[0]
self.assertEqual(shape_actual, shape_desired)
assert_array_equal(conn_actual, conn_desired)
self.assertEqual(new_id, 5)
# Test wrong dtype
new_id = mesh.add_element('Quad4',
np.array([1, 2, 3, 4], dtype=np.float), 6)
shape_actual = mesh.get_ele_shapes_by_elementids([new_id])[0]
conn_actual = mesh.get_connectivity_by_elementids([new_id])[0]
self.assertEqual(shape_actual, shape_desired)
assert_array_equal(conn_actual, conn_desired)
self.assertEqual(new_id, 6)
# Test with tuple instead of array
new_id = mesh.add_element('Quad4', (1, 2, 3, 4), 7)
shape_actual = mesh.get_ele_shapes_by_elementids([new_id])[0]
conn_actual = mesh.get_connectivity_by_elementids([new_id])[0]
self.assertEqual(shape_actual, shape_desired)
assert_array_equal(conn_actual, conn_desired)
self.assertEqual(new_id, 7)
# Test wrong shape
with self.assertRaises(ValueError):
mesh.add_element('wrong_shape', np.array([1, 2, 3, 4],
dtype=np.int), 8)
def test_add_node(self):
# Test 3D mesh
mesh = Mesh(3)
# test with tuple
coords = (0.0, 1.0, 2.0)
new_id = mesh.add_node(coords)
coords_actual = mesh.nodes_df.loc[new_id, ['x', 'y', 'z']]
assert_array_equal(coords_actual, np.array(coords, dtype=float))
# test with array
coords = np.array([5, 6, 3], dtype=float)
new_id = mesh.add_node(coords)
coords_actual = mesh.nodes_df.loc[new_id, ['x', 'y', 'z']]
assert_array_equal(coords_actual, np.array(coords, dtype=float))
# test with dict and id
coords = {'x': 5.0, 'y': 6.0, 'z': 3}
new_id = mesh.add_node(coords, 8)
coords_actual = mesh.nodes_df.loc[new_id, ['x', 'y', 'z']]
assert_array_equal(coords_actual, np.array([5, 6, 3], dtype=float))
self.assertEqual(new_id, 8)
# test raise error no overwrite
coords = np.array([10, 4, 2], dtype=float)
with self.assertRaises(ValueError):
new_id = mesh.add_node(coords, 8)
# test overwrite and with int array
coords = np.array([10, 4, 2], dtype=int)
new_id = mesh.add_node(coords, 8, overwrite=True)
coords_actual = mesh.nodes_df.loc[new_id, ['x', 'y', 'z']]
assert_array_equal(coords_actual, np.array(coords, dtype=float))
self.assertEqual(new_id, 8)
# Test 2D mesh
mesh = Mesh(2)
# test with tuple
coords = (0.0, 1.0, 2.0)
new_id = mesh.add_node(coords)
coords_actual = mesh.nodes_df.loc[new_id, ['x', 'y']]
assert_array_equal(coords_actual, np.array(coords[0:2], dtype=float))
# test with array
coords = np.array([5, 6, 3], dtype=float)
new_id = mesh.add_node(coords)
coords_actual = mesh.nodes_df.loc[new_id, ['x', 'y']]
assert_array_equal(coords_actual, np.array(coords[0:2], dtype=float))
# test with dict and id
coords = {'x': 5.0, 'y': 6.0, 'z': 3}
new_id = mesh.add_node(coords, 8)
coords_actual = mesh.nodes_df.loc[new_id, ['x', 'y']]
assert_array_equal(coords_actual, np.array([5, 6], dtype=float))
self.assertEqual(new_id, 8)
# test raise error no overwrite
coords = np.array([10, 4, 2], dtype=float)
with self.assertRaises(ValueError):
new_id = mesh.add_node(coords, 8)
# test overwrite and with int array
coords = np.array([10, 4, 2], dtype=int)
new_id = mesh.add_node(coords, 8, overwrite=True)
coords_actual = mesh.nodes_df.loc[new_id, ['x', 'y']]
assert_array_equal(coords_actual, np.array(coords[0:2], dtype=float))
self.assertEqual(new_id, 8)
class TestMesh(TestCase):
def setUp(self):
self.testmesh = Mesh(dimension=2)
nodes = np.array([[0.0, 0.0], [1.0, 0.0], [1.0, 1.0], [0.0, 1.0],
[2.0, 0.0], [2.0, 1.0]],
dtype=np.float)
connectivity = [
np.array([5, 6, 3], dtype=np.int),
np.array([3, 2, 5], dtype=np.int),
np.array([1, 2, 3, 4], dtype=np.int),
# boundary elements
np.array([4, 1], dtype=np.int),
np.array([5, 6], dtype=np.int)
]
shapes = ['Tri3', 'Tri3', 'Quad4', 'straight_line', 'straight_line']
data = {
'shape': shapes,
'is_boundary': [False, False, False, True, True],
'connectivity': connectivity
}
indices = [1, 2, 3, 4, 5]
el_df = pd.DataFrame(data, index=indices)
x = nodes[:, 0]
y = nodes[:, 1]
nodeids = [1, 2, 3, 4, 5, 6]
self._nodeids = nodeids
self._nodes = nodes
self._eleids = indices
self._connectivity = connectivity
self._connectivity = connectivity
self._shapes = shapes
nodes_df = pd.DataFrame({'x': x, 'y': y}, index=nodeids)
groups = {
'left': {
'elements': [3],
'nodes': []
},
'right': {
'elements': [1, 2],
'nodes': [2, 3, 5, 6]
},
'left_boundary': {
'elements': [4],
'nodes': []
},
'right_boundary': {
'elements': [5],
'nodes': [1, 2]
}
}
self.testmesh.nodes_df = nodes_df
self.testmesh.groups = groups
self.testmesh._el_df = el_df
self.testmesh3d = deepcopy(self.testmesh)
nodes3d = np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [1.0, 1.0, 0.0],
[0.0, 1.0, 0.0], [2.0, 0.0, 1.0], [2.0, 1.0, 1.0]],
dtype=np.float)
self.testmesh3d.dimension = 3
x = nodes3d[:, 0]
y = nodes3d[:, 1]
z = nodes3d[:, 2]
nodes_df3d = pd.DataFrame({'x': x, 'y': y, 'z': z}, index=nodeids)
self.testmesh3d.nodes_df = nodes_df3d
def tearDown(self):
pass
def test_constructor(self):
from amfe.mesh import Mesh
mesh = Mesh(dimension=2)
self.assertEqual(mesh.dimension, 2)
mesh = Mesh(dimension=3)
self.assertEqual(mesh.dimension, 3)
with self.assertRaises(ValueError) as err:
mesh = Mesh(dimension=1)
def test_element_ids(self):
assert_array_equal(self.testmesh.element_ids, self._eleids)
def test_no_of_properties(self):
self.assertEqual(self.testmesh.no_of_nodes, 6)
self.assertEqual(self.testmesh.no_of_elements, 3)
self.assertEqual(self.testmesh.no_of_boundary_elements, 2)
self.assertEqual(self.testmesh.dimension, 2)
def test_nodes_voigt(self):
desired = np.array(
[0.0, 0.0, 1.0, 0.0, 1.0, 1.0, 0.0, 1.0, 2.0, 0.0, 2.0, 1.0],
dtype=np.float)
assert_equal(self.testmesh.nodes_voigt, desired)
def test_connectivity(self):
desireds = np.array(self._connectivity)
actuals = self.testmesh.connectivity
for actual, desired in zip(actuals, desireds):
assert_array_equal(actual, desired)
def test_create_group(self):
elementids = [1, 4, 6, 8]
nodeids = np.array([100, 400], dtype=int)
desired = {'elements': [1, 4, 6, 8], 'nodes': [100, 400]}
self.testmesh.create_group('mygroup', nodeids, elementids)
actual_nodes = set(self.testmesh.groups['mygroup']['nodes'])
desired_nodes = set(desired['nodes'])
actual_elements = set(self.testmesh.groups['mygroup']['elements'])
desired_elements = set(desired['elements'])
self.assertEqual(actual_nodes, desired_nodes)
self.assertEqual(actual_elements, desired_elements)
with self.assertRaises(ValueError):
self.testmesh.create_group('right', nodeids, elementids)
self.testmesh.create_group('mygroup2', elementids=(4, 8, 1, 6))
actual_nodes = set(self.testmesh.groups['mygroup2']['nodes'])
desired_nodes = set()
actual_elements = set(self.testmesh.groups['mygroup2']['elements'])
desired_elements = set(desired['elements'])
self.assertEqual(actual_nodes, desired_nodes)
self.assertEqual(actual_elements, desired_elements)
def test_get_connectivity_by_elementids(self):
desireds = [
np.array([5, 6, 3], dtype=int),
np.array([4, 1], dtype=int)
]
for actual, desired in zip(
self.testmesh.get_connectivity_by_elementids([1, 4]),
desireds):
assert_array_equal(actual, desired)
def test_get_elementidxs_by_group(self):
actual = self.testmesh.get_elementidxs_by_groups(['right'])
desired = np.array([0, 1], dtype=int)
assert_array_equal(actual, desired)
def test_get_elementidxs_by_elementids(self):
actual = self.testmesh.get_elementidxs_by_elementids([4, 1])
desired = np.array([3, 0], dtype=int)
assert_array_equal(actual, desired)
def test_get_elementids_by_elementidxs(self):
actual = self.testmesh.get_elementids_by_elementidxs([3, 0])
desired = np.array([4, 1], dtype=int)
assert_array_equal(actual, desired)
def test_get_elementids_by_nodeids(self):
actual = self.testmesh.get_elementids_by_nodeids([1])
desired = np.array([3, 4], dtype=int)
assert_array_equal(actual, desired)
actual = self.testmesh.get_elementids_by_nodeids([3, 1])
desired = np.array([1, 2, 3, 4], dtype=int)
assert_array_equal(actual, desired)
actual = self.testmesh.get_elementids_by_nodeids((3, 1))
assert_array_equal(actual, desired)
actual = self.testmesh.get_elementids_by_nodeids(np.array([3, 1]))
assert_array_equal(actual, desired)
actual = self.testmesh.get_elementids_by_nodeids([0])
desired = np.array([], dtype=int)
assert_array_equal(actual, desired)
def test_get_elementidxs_by_groups(self):
actual = self.testmesh.get_elementidxs_by_groups(
['right', 'left_boundary'])
desired = np.array([0, 1, 3], dtype=int)
assert_array_equal(actual, desired)
def test_get_elementids_by_groups(self):
actual = self.testmesh.get_elementids_by_groups(
['right', 'left_boundary'])
desired = np.array([1, 2, 4], dtype=int)
assert_array_equal(actual, desired)
with self.assertRaises(ValueError):
self.testmesh.get_elementids_by_groups(['wrong'])
def test_get_nodeid_by_coordinates(self):
# 2d case
x, y = 2.0, 0.0
desired = 5
actual = self.testmesh.get_nodeid_by_coordinates(x, y)
self.assertEqual(actual, desired)
# 3d Case
z = 1.0
actual = self.testmesh3d.get_nodeid_by_coordinates(x, y, z)
self.assertEqual(actual, desired)
# big tolerance
x = 500.0
epsilon = np.inf
actual = self.testmesh.get_nodeid_by_coordinates(x, y, epsilon=epsilon)
self.assertEqual(actual, desired)
actual = self.testmesh3d.get_nodeid_by_coordinates(x,
y,
z,
epsilon=epsilon)
self.assertEqual(actual, desired)
# zero return
x = 500.0
desired = None
actual = self.testmesh.get_nodeid_by_coordinates(x, y)
self.assertEqual(actual, desired)
actual = self.testmesh3d.get_nodeid_by_coordinates(x, y, z)
self.assertEqual(actual, desired)
def test_get_nodeids_by_x_coordinates(self):
x = 2.0
epsilon = 0.1
desired = {5, 6}
actual = set(self.testmesh.get_nodeids_by_x_coordinates(x, epsilon))
self.assertEqual(actual, desired)
epsilon = 1.1
desired = {2, 3, 5, 6}
actual = set(self.testmesh.get_nodeids_by_x_coordinates(x, epsilon))
self.assertEqual(actual, desired)
def test_get_nodeids_by_lesser_equal_x_coordinates(self):
x = 1.0
epsilon = 0.1
desired = {1, 2, 3, 4}
actual = set(
self.testmesh.get_nodeids_by_lesser_equal_x_coordinates(
x, epsilon))
self.assertEqual(actual, desired)
x = 0.9
actual = set(
self.testmesh.get_nodeids_by_lesser_equal_x_coordinates(
x, epsilon))
self.assertEqual(actual, desired)
epsilon = 0.01
desired = {1, 4}
actual = set(
self.testmesh.get_nodeids_by_lesser_equal_x_coordinates(
x, epsilon))
self.assertEqual(actual, desired)
def test_get_nodeids_by_greater_equal_x_coordinates(self):
x = 1.0
epsilon = 0.1
desired = {2, 3, 5, 6}
actual = set(
self.testmesh.get_nodeids_by_greater_equal_x_coordinates(
x, epsilon))
self.assertEqual(actual, desired)
x = 1.1
actual = set(
self.testmesh.get_nodeids_by_greater_equal_x_coordinates(
x, epsilon))
self.assertEqual(actual, desired)
epsilon = 0.01
desired = {5, 6}
actual = set(
self.testmesh.get_nodeids_by_greater_equal_x_coordinates(
x, epsilon))
self.assertEqual(actual, desired)
def test_get_nodeids_by_group(self):
actual = self.testmesh.get_nodeids_by_groups(['left'])
desired = np.array([1, 2, 3, 4], dtype=np.int)
assert_equal(actual, desired)
actual = set(self.testmesh.get_nodeids_by_groups(['right_boundary']))
desired = set(np.array([1, 2, 5, 6]))
assert_equal(actual, desired)
actual = set(self.testmesh.get_nodeids_by_groups(['left_boundary']))
desired = set(np.array([1, 4], dtype=int))
assert_equal(actual, desired)
def test_get_ele_shapes_by_idxs(self):
actual = self.testmesh.get_ele_shapes_by_elementidxs([1, 4, 2])
desired = np.array(['Tri3', 'straight_line', 'Quad4'], dtype=object)
assert_equal(actual, desired)
def test_get_ele_shapes_by_ids(self):
actual = self.testmesh.get_ele_shapes_by_ids([2, 5, 3])
desired = np.array(['Tri3', 'straight_line', 'Quad4'], dtype=object)
assert_equal(actual, desired)
def test_get_nodeidxs_by_all(self):
actual = self.testmesh.get_nodeidxs_by_all()
desired = np.array([0, 1, 2, 3, 4, 5], dtype=np.int)
assert_equal(actual, desired)
def test_get_nodeidxs_by_nodeids(self):
actual = self.testmesh.get_nodeidxs_by_nodeids(np.array([1, 2, 5, 6]))
desired = np.array([0, 1, 4, 5])
assert_equal(actual, desired)
def test_get_nodeids_by_nodeidxs(self):
actual = self.testmesh.get_nodeids_by_nodeidxs([3, 5, 2])
desired = [4, 6, 3]
assert_equal(actual, desired)
actual = self.testmesh.get_nodeids_by_nodeidxs([3])
desired = [4]
assert_equal(actual, desired)
def test_get_nodeids_by_elementids(self):
actual = self.testmesh.get_nodeids_by_elementids(
np.array([2, 3], dtype=int))
desired = np.array([1, 2, 3, 4, 5], dtype=int)
assert_array_equal(actual, desired)
# test zero list:
actual = self.testmesh.get_nodeids_by_elementids(
np.array([], dtype=int))
desired = np.array([], dtype=int)
assert_array_equal(actual, desired)
def test_insert_tag(self):
current_col_num = len(self.testmesh.el_df.columns)
tag_to_add = 'partition_id'
self.testmesh.insert_tag(tag_to_add)
new_col_num = len(self.testmesh.el_df.columns)
assert_equal(current_col_num + 1, new_col_num)
self.assertTrue(tag_to_add in self.testmesh.el_df.columns)
def test_remove_tag(self):
tag_name = self.testmesh.el_df.columns[1]
current_col_num = len(self.testmesh.el_df.columns)
self.testmesh.remove_tag(tag_name)
new_col_num = len(self.testmesh.el_df.columns)
assert_equal(current_col_num, new_col_num + 1)
self.assertFalse(tag_name in self.testmesh.el_df.columns)
def test_change_tag_values_by_dict(self):
desired_list_1 = [4, 5]
desired_list_2 = [1, 2, 3]
tag_value_dict = {}
tag_value_dict['False'] = desired_list_1
tag_value_dict['True'] = desired_list_2
self.testmesh._change_tag_values_by_dict('is_boundary', tag_value_dict)
actual_list_1 = self.testmesh.el_df[self.testmesh.el_df['is_boundary']
== 'False'].index.tolist()
actual_list_2 = self.testmesh.el_df[self.testmesh.el_df['is_boundary']
== 'True'].index.tolist()
assert_equal(actual_list_1, desired_list_1)
assert_equal(actual_list_2, desired_list_2)
def test_replace_tag_values(self):
current_key = 'Tri3'
new_key = 'Tri6'
tag_name = 'shape'
desired = [1, 2]
self.testmesh.replace_tag_values(tag_name, current_key, new_key)
actual = self.testmesh.el_df[self.testmesh.el_df[tag_name] ==
new_key].index.tolist()
assert_equal(desired, actual)
def test_get_elementids_by_tags(self):
desired = np.array([1, 2], dtype=int)
actual = self.testmesh.get_elementids_by_tags(['shape', 'is_boundary'],
['Tri3', False])
assert_array_equal(desired, actual)
def test_get_nodeids_by_tag(self):
desired = np.array([1, 4, 5, 6], dtype=int)
actual = self.testmesh.get_nodeids_by_tags('shape', 'straight_line')
assert_array_equal(desired, actual)
def test_get_elementidxs_by_tags(self):
desired = np.array([0, 1], dtype=int)
actual = self.testmesh.get_elementidxs_by_tags('shape', 'Tri3')
assert_equal(desired, actual)
def test_get_iconnectivity_by_elementids(self):
desired = np.array([
np.array([0, 1, 2, 3], dtype=int),
np.array([4, 5, 2], dtype=int)
])
actual = self.testmesh.get_iconnectivity_by_elementids(
np.array([3, 1], dtype=int))
for actual_arr, desired_arr in zip(actual, desired):
assert_array_equal(desired_arr, actual_arr)
# Ask a second time to test lazy evaluation:
actual = self.testmesh.get_iconnectivity_by_elementids(
np.array([3, 1], dtype=int))
for actual_arr, desired_arr in zip(actual, desired):
assert_array_equal(desired_arr, actual_arr)
def test_get_groups_by_elementids(self):
groups_actual = self.testmesh.get_groups_by_elementids([1, 2, 4])
groups_desired = ['right', 'left_boundary']
assert_equal(groups_actual, groups_desired)
self.testmesh.groups = {
'left': {
'elements': [3],
'nodes': []
},
'right': {
'elements': [1, 2],
'nodes': [2, 3, 5, 6]
},
'left_boundary': {
'elements': [4],
'nodes': []
},
'right_boundary': {
'elements': [5, 2],
'nodes': [1, 2]
}
}
groups_actual = self.testmesh.get_groups_by_elementids([1, 2, 4])
groups_desired = ['right', 'left_boundary', 'right_boundary']
assert_equal(groups_actual, groups_desired)
def test_get_groups_by_nodeids(self):
groups_actual = self.testmesh.get_groups_by_nodeids([1, 2, 6])
groups_desired = ['right', 'right_boundary']
assert_equal(groups_actual, groups_desired)
def test_get_groups_dict_by_elementids(self):
groups_actual = self.testmesh.get_groups_dict_by_elementids([1, 2, 4])
groups_desired = {
'right': {
'elements': [1, 2]
},
'left_boundary': {
'elements': [4]
}
}
assert_equal(groups_actual, groups_desired)
self.testmesh.groups = {
'left': {
'elements': [3],
'nodes': []
},
'right': {
'elements': [1, 2],
'nodes': [2, 3, 5, 6]
},
'left_boundary': {
'elements': [4],
'nodes': []
},
'right_boundary': {
'elements': [5, 2],
'nodes': [1, 2]
}
}
groups_actual = self.testmesh.get_groups_dict_by_elementids([1, 2, 4])
groups_desired = {
'right': {
'elements': [1, 2]
},
'left_boundary': {
'elements': [4]
},
'right_boundary': {
'elements': [2]
}
}
assert_equal(groups_actual, groups_desired)
def test_get_groups_dict_by_nodeids(self):
groups_actual = self.testmesh.get_groups_dict_by_nodeids([1, 2, 6])
groups_desired = {
'right': {
'nodes': [2, 6]
},
'right_boundary': {
'nodes': [1, 2]
}
}
assert_equal(groups_actual, groups_desired)
def test_merge_into_groups(self):
add_groups = {
'left': {
'elements': [3],
'nodes': [1, 4]
},
'right': {
'elements': [1, 2]
},
'left_boundary': {
'elements': [4],
'nodes': []
},
'right_boundary': {
'elements': [5, 2],
'nodes': []
},
'new_node_group': {
'nodes': [1, 2, 3, 4]
}
}
self.testmesh.merge_into_groups(add_groups)
groups_desired = {
'left': {
'elements': [3],
'nodes': [1, 4]
},
'right': {
'elements': [1, 2],
'nodes': [2, 3, 5, 6]
},
'left_boundary': {
'elements': [4],
'nodes': []
},
'right_boundary': {
'elements': [5, 2],
'nodes': [1, 2]
},
'new_node_group': {
'elements': [],
'nodes': [1, 2, 3, 4]
}
}
for group_desired in groups_desired:
for secondary_group in ['elements', 'nodes']:
assert_equal(
set(self.testmesh.groups[group_desired][secondary_group]),
set(groups_desired[group_desired][secondary_group]))
self.assertEqual(len(self.testmesh.groups), len(groups_desired))
def test_add_node(self):
# Test 3D mesh
mesh = Mesh(3)
# test with tuple
coords = (0.0, 1.0, 2.0)
new_id = mesh.add_node(coords)
coords_actual = mesh.nodes_df.loc[new_id, ['x', 'y', 'z']]
assert_array_equal(coords_actual, np.array(coords, dtype=float))
# test with array
coords = np.array([5, 6, 3], dtype=float)
new_id = mesh.add_node(coords)
coords_actual = mesh.nodes_df.loc[new_id, ['x', 'y', 'z']]
assert_array_equal(coords_actual, np.array(coords, dtype=float))
# test with dict and id
coords = {'x': 5.0, 'y': 6.0, 'z': 3}
new_id = mesh.add_node(coords, 8)
coords_actual = mesh.nodes_df.loc[new_id, ['x', 'y', 'z']]
assert_array_equal(coords_actual, np.array([5, 6, 3], dtype=float))
self.assertEqual(new_id, 8)
# test raise error no overwrite
coords = np.array([10, 4, 2], dtype=float)
with self.assertRaises(ValueError):
new_id = mesh.add_node(coords, 8)
# test overwrite and with int array
coords = np.array([10, 4, 2], dtype=int)
new_id = mesh.add_node(coords, 8, overwrite=True)
coords_actual = mesh.nodes_df.loc[new_id, ['x', 'y', 'z']]
assert_array_equal(coords_actual, np.array(coords, dtype=float))
self.assertEqual(new_id, 8)
# Test 2D mesh
mesh = Mesh(2)
# test with tuple
coords = (0.0, 1.0, 2.0)
new_id = mesh.add_node(coords)
coords_actual = mesh.nodes_df.loc[new_id, ['x', 'y']]
assert_array_equal(coords_actual, np.array(coords[0:2], dtype=float))
# test with array
coords = np.array([5, 6, 3], dtype=float)
new_id = mesh.add_node(coords)
coords_actual = mesh.nodes_df.loc[new_id, ['x', 'y']]
assert_array_equal(coords_actual, np.array(coords[0:2], dtype=float))
# test with dict and id
coords = {'x': 5.0, 'y': 6.0, 'z': 3}
new_id = mesh.add_node(coords, 8)
coords_actual = mesh.nodes_df.loc[new_id, ['x', 'y']]
assert_array_equal(coords_actual, np.array([5, 6], dtype=float))
self.assertEqual(new_id, 8)
# test raise error no overwrite
coords = np.array([10, 4, 2], dtype=float)
with self.assertRaises(ValueError):
new_id = mesh.add_node(coords, 8)
# test overwrite and with int array
coords = np.array([10, 4, 2], dtype=int)
new_id = mesh.add_node(coords, 8, overwrite=True)
coords_actual = mesh.nodes_df.loc[new_id, ['x', 'y']]
assert_array_equal(coords_actual, np.array(coords[0:2], dtype=float))
self.assertEqual(new_id, 8)
def test_add_element(self):
mesh = Mesh(2)
for nodeid, coords in zip(self._nodeids, self._nodes):
mesh.add_node(coords, nodeid)
conn_desired = np.array([5, 6, 3], dtype=np.int)
shape_desired = 'Tri3'
new_id = mesh.add_element(shape_desired, conn_desired)
shape_actual = mesh.get_ele_shapes_by_elementids([new_id])[0]
conn_actual = mesh.get_connectivity_by_elementids([new_id])[0]
self.assertEqual(shape_actual, shape_desired)
assert_array_equal(conn_actual, conn_desired)
conn_desired = np.array([4, 1], dtype=np.int)
shape_desired = 'straight_line'
new_id = mesh.add_element(shape_desired, conn_desired)
shape_actual = mesh.get_ele_shapes_by_elementids([new_id])[0]
conn_actual = mesh.get_connectivity_by_elementids([new_id])[0]
self.assertEqual(shape_actual, shape_desired)
assert_array_equal(conn_actual, conn_desired)
conn_desired = np.array([3, 2, 5], dtype=np.int)
shape_desired = 'Tri3'
new_id = mesh.add_element(shape_desired,
np.array([3, 2, 5], dtype=np.int), 5)
shape_actual = mesh.get_ele_shapes_by_elementids([new_id])[0]
conn_actual = mesh.get_connectivity_by_elementids([new_id])[0]
self.assertEqual(shape_actual, shape_desired)
assert_array_equal(conn_actual, conn_desired)
self.assertEqual(new_id, 5)
with self.assertRaises(ValueError):
mesh.add_element('Quad4', np.array([1, 2, 3, 4], dtype=np.int), 5)
conn_desired = np.array([1, 2, 3, 4], dtype=np.int)
shape_desired = 'Quad4'
new_id = mesh.add_element('Quad4',
np.array([1, 2, 3, 4], dtype=np.int),
5,
overwrite=True)
shape_actual = mesh.get_ele_shapes_by_elementids([new_id])[0]
conn_actual = mesh.get_connectivity_by_elementids([new_id])[0]
self.assertEqual(shape_actual, shape_desired)
assert_array_equal(conn_actual, conn_desired)
self.assertEqual(new_id, 5)
# Test wrong dtype
new_id = mesh.add_element('Quad4',
np.array([1, 2, 3, 4], dtype=np.float), 6)
shape_actual = mesh.get_ele_shapes_by_elementids([new_id])[0]
conn_actual = mesh.get_connectivity_by_elementids([new_id])[0]
self.assertEqual(shape_actual, shape_desired)
assert_array_equal(conn_actual, conn_desired)
self.assertEqual(new_id, 6)
# Test with tuple instead of array
new_id = mesh.add_element('Quad4', (1, 2, 3, 4), 7)
shape_actual = mesh.get_ele_shapes_by_elementids([new_id])[0]
conn_actual = mesh.get_connectivity_by_elementids([new_id])[0]
self.assertEqual(shape_actual, shape_desired)
assert_array_equal(conn_actual, conn_desired)
self.assertEqual(new_id, 7)
# Test wrong shape
with self.assertRaises(ValueError):
mesh.add_element('wrong_shape', np.array([1, 2, 3, 4],
dtype=np.int), 8)
def test_copy_node_by_id(self):
nodes_df_old = deepcopy(self.testmesh.nodes_df)
nodes_df_desired = pd.DataFrame(
{
'x': [0.0, 1.0, 1.0, 0.0, 2.0, 2.0, 1.0],
'y': [0.0, 0.0, 1.0, 1.0, 0.0, 1.0, 1.0]
},
index=[1, 2, 3, 4, 5, 6, 7])
self.testmesh.copy_node_by_id(3)
assert_frame_equal(self.testmesh.nodes_df, nodes_df_desired)
def test_iconnectivity(self):
actual = self.testmesh.iconnectivity
desired = [
np.array([4, 5, 2], dtype=np.int),
np.array([2, 1, 4], dtype=np.int),
np.array([0, 1, 2, 3], dtype=np.int),
# boundary elements
np.array([3, 0], dtype=np.int),
np.array([4, 5], dtype=np.int)
]
for actual_arr, desired_arr in zip(actual, desired):
assert_array_equal(desired_arr, actual_arr)
def test_str(self):
print(self.testmesh)
def create_amfe_obj():
# Define input file path
meshobj = Mesh(dimension=2)
nodes = np.array([
[1.345600000e-02, 3.561675700e-02], [5.206839561e-01, 3.740820950e-02],
[3.851982918e-02, 5.460016703e-01], [5.457667372e-01, 5.477935420e-01],
[1.027911912e+00, 3.919966200e-02], [6.358365836e-02, 1.056386584e+00],
[1.040469476e+00, 5.445628213e-01], [5.582746582e-01, 1.053154002e+00],
[1.052965658e+00, 1.049921420e+00], [1.535139868e+00, 4.099111450e-02],
[1.547697432e+00, 5.463542738e-01], [1.547656658e+00, 1.046688838e+00],
[2.042367825e+00, 4.278256700e-02], [2.042357741e+00, 5.431194119e-01],
[2.042347658e+00, 1.043456257e+00]
],
dtype=float)
connectivity = [
np.array([13, 15, 9, 14, 12, 11], dtype=int),
np.array([9, 6, 5, 8, 4, 7], dtype=int),
np.array([9, 5, 13, 7, 10, 11], dtype=int),
np.array([1, 5, 6, 2, 4, 3], dtype=int),
np.array([5, 13, 10], dtype=int),
np.array([1, 5, 2], dtype=int),
np.array([6, 1, 3], dtype=int),
np.array([9, 6, 8], dtype=int),
np.array([13, 15, 14], dtype=int),
np.array([15, 9, 12], dtype=int)
]
data = {
'shape': [
'Tri6', 'Tri6', 'Tri6', 'Tri6', 'quadratic_line', 'quadratic_line',
'quadratic_line', 'quadratic_line', 'quadratic_line',
'quadratic_line'
],
'connectivity':
connectivity,
'is_boundary':
[False, False, False, False, True, True, True, True, True, True]
}
indices = list(np.arange(1, 11))
meshobj.el_df = pd.DataFrame(data, index=indices)
meshobj.groups = {
'left': {
'nodes': [],
'elements': [2, 4]
},
'right': {
'nodes': [],
'elements': [1, 3]
},
'left_boundary': {
'nodes': [],
'elements': [7]
},
'right_boundary': {
'nodes': [],
'elements': [9]
},
'top_boundary': {
'nodes': [],
'elements': [8, 10]
},
'left_dirichlet': {
'nodes': [1, 3, 6],
'elements': []
}
}
nodeids = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]
meshobj.nodes_df = pd.DataFrame({
'x': nodes[:, 0],
'y': nodes[:, 1]
},
index=nodeids)
return meshobj
class AmfeMeshConverter(MeshConverter):
"""
Converter for AMfe meshes.
Examples
--------
Convert GiD json file to AMfe mesh:
>>> from amfe.io.mesh.reader import GidJsonMeshReader
>>> from amfe.io.mesh.writer import AmfeMeshConverter
>>> filename = '/path/to/your/file.json'
>>> converter = AmfeMeshConverter()
>>> reader = GidJsonMeshReader(filename)
>>> reader.parse(converter)
>>> converter.return_mesh()
"""
def __init__(self, verbose=False):
super().__init__()
self._verbose = verbose
self._mesh = Mesh()
self._dimension = None
self._no_of_nodes = None
self._no_of_elements = None
self._nodes = np.empty((0, 4), dtype=float)
self._currentnodeid = 0
self._groups = dict()
self._tags = dict()
# df information
self._el_df_indices = list()
self._el_df_eleshapes = list()
self._el_df_connectivity = list()
self._el_df_is_boundary = list()
return
def build_no_of_nodes(self, no):
# This function is only used for preallocation
# It is not necessary to call, but useful if information about no_of_nodes exists
self._no_of_nodes = no
if self._nodes.shape[0] == 0:
self._nodes = np.zeros((no, 4), dtype=float)
return
def build_no_of_elements(self, no):
# This function is not used
# If someone wants to improve performance he/she can add preallocation functionality for elements
self._no_of_elements = no
# preallocation...
return
def build_mesh_dimension(self, dim):
self._dimension = dim
return
def build_node(self, idx, x, y, z):
# amfeid is the row-index in nodes array
amfeid = self._currentnodeid
# Check if preallocation has been done so far
if self._no_of_nodes is not None:
# write node in preallocated array
self._nodes[amfeid, :] = [idx, x, y, z]
else:
# append node if array is not preallocated with full node dimension
self._nodes = np.append(self._nodes,
np.array([idx, x, y, z],
dtype=float,
ndmin=2),
axis=0)
self._currentnodeid += 1
return
def build_element(self, idx, etype, nodes):
# update df information
self._el_df_connectivity.append(np.array(nodes, dtype=int))
self._el_df_indices.append(idx)
self._el_df_eleshapes.append(etype)
return
def build_group(self, name, nodeids=None, elementids=None):
# append group information
group = {name: {'nodes': nodeids, 'elements': elementids}}
self._groups.update(group)
return
def build_tag(self, tag_dict):
# append tag information
self._tags.update(tag_dict)
return None
def return_mesh(self):
# Check dimension of model
if self._dimension is None:
if not VOLUME_ELEMENTS_3D.intersection(set(self._el_df_eleshapes)):
# No 3D element in eleshapes, thus:
self._dimension = 2
else:
self._dimension = 3
# If dimension = 2 cut the z coordinate
x = self._nodes[:, 1]
y = self._nodes[:, 2]
if self._dimension == 2:
self._mesh.nodes_df = pd.DataFrame({
'x': x,
'y': y
},
index=np.array(self._nodes[:,
0],
dtype=int))
else:
z = self._nodes[:, 3]
self._mesh.nodes_df = pd.DataFrame({
'x': x,
'y': y,
'z': z
},
index=np.array(self._nodes[:,
0],
dtype=int))
# divide in boundary and volume elements
if self._dimension == 3:
volume_element_set = VOLUME_ELEMENTS_3D
boundary_element_set = BOUNDARY_ELEMENTS_3D
elif self._dimension == 2:
volume_element_set = VOLUME_ELEMENTS_2D
boundary_element_set = BOUNDARY_ELEMENTS_2D
else:
raise ValueError('Dimension must be 2 or 3')
# write properties
self._mesh.dimension = self._dimension
self._el_df_is_boundary = len(self._el_df_connectivity) * [False]
for index, shape in enumerate(self._el_df_eleshapes):
if shape in boundary_element_set:
self._el_df_is_boundary[index] = True
data = {
'shape': self._el_df_eleshapes,
'is_boundary': self._el_df_is_boundary,
'connectivity': self._el_df_connectivity
}
self._mesh.el_df = pd.DataFrame(data, index=self._el_df_indices)
self._mesh.groups = self._groups
for tag_name, tag_dict in self._tags.items():
self._mesh.insert_tag(tag_name, tag_dict)
return self._mesh
class RectangleMesh2D:
def __init__(self, l, h, n_ele_l, n_ele_h, x_start=0.0, y_start=0.0):
self.l = l
self.h = h
self.n_ele_l = n_ele_l
self.n_ele_h = n_ele_h
self.delta_h_x = self.l / self.n_ele_l
self.delta_h_y = self.h / self.n_ele_h
self.x_start = x_start
self.y_start = y_start
self._mesh = Mesh(2)
@property
def mesh(self):
return self._mesh
def generate_mesh(self):
self._create_nodes()
self._create_elements()
def _create_nodes(self):
for i_node_y in np.arange(self.n_ele_h+1):
for i_node_x in np.arange(self.n_ele_l+1):
self._mesh.add_node([self.x_start + i_node_x * self.delta_h_x, self.y_start + i_node_y * self.delta_h_y])
def _create_elements(self):
for i_ele_y in np.arange(self.n_ele_h):
for i_ele_x in np.arange(self.n_ele_l):
node1 = self._mesh.get_nodeid_by_coordinates(self.x_start + i_ele_x * self.delta_h_x,
self.y_start + i_ele_y * self.delta_h_y)
node2 = self._mesh.get_nodeid_by_coordinates(self.x_start + (i_ele_x + 1) * self.delta_h_x,
self.y_start + i_ele_y * self.delta_h_y)
node3 = self._mesh.get_nodeid_by_coordinates(self.x_start + (i_ele_x + 1) * self.delta_h_x,
self.y_start + (i_ele_y + 1) * self.delta_h_y)
node4 = self._mesh.get_nodeid_by_coordinates(self.x_start + i_ele_x * self.delta_h_x,
self.y_start + (i_ele_y + 1) * self.delta_h_y)
connectivity = np.array([node1, node2, node3, node4])
self._mesh.add_element('Quad4', connectivity)
def add_boundary(self, edge, group_name=None):
if edge is 'left':
nodes = self._mesh.get_nodeids_by_coordinate_axis(self.x_start, 'x', 1e-6)
elif edge is 'right':
nodes = self._mesh.get_nodeids_by_coordinate_axis(self.x_start+self.l, 'x', 1e-6)
elif edge is 'bottom':
nodes = self._mesh.get_nodeids_by_coordinate_axis(self.y_start, 'y', 1e-6)
elif edge is 'top':
nodes = self._mesh.get_nodeids_by_coordinate_axis(self.y_start + self.h, 'y', 1e-6)
else:
raise ValueError('Unknown edge-type')
for idx in range(nodes.size-1):
eleid = self._mesh.add_element('straight_line', np.array([nodes[idx], nodes[idx+1]]))
if group_name is not None and len(self._mesh.get_groups_by_elementids([eleid])) == 0:
if group_name in self._mesh.groups:
self._mesh.add_element_to_groups(eleid, [group_name])
else:
self._mesh.create_group(group_name, (), [eleid])
def set_checkerboard_groups(self, segment_length, segment_height, segment_groups):
n_seg_x = int(round(self.l/segment_length))
n_seg_y = int(round(self.h/segment_height))
segments = dict()
seg = 0
for seg_y in range(n_seg_y):
for seg_x in range(n_seg_x):
if seg_y % 2 == 0:
group_name = segment_groups[seg_x % len(segment_groups)]
else:
group_name = segment_groups[(seg_x+1) % len(segment_groups)]
segments[seg] = {'nodes': {'lowerleft': np.array([seg_x * segment_length, seg_y * segment_height]),
'lowerright': np.array([(seg_x + 1) * segment_length, seg_y * segment_height]),
'upperleft': np.array([seg_x * segment_length, (seg_y + 1) * segment_height]),
'upperright': np.array([(seg_x + 1) * segment_length, (seg_y + 1) * segment_height])},
'group': group_name
}
seg += 1
def check_node_in_segment(P1, P2, P3, P4, node):
edge_x = P2 - P1
edge_y = P4 - P1
constraint_x = (np.dot(edge_x, P1) <= np.dot(edge_x, node) <= np.dot(edge_x, P2))
constraint_y = (np.dot(edge_y, P1) <= np.dot(edge_y, node) <= np.dot(edge_y, P4))
return constraint_x and constraint_y
eleids = self._mesh.get_elementids_by_tags(['shape'], ['Quad4'])
for eleid in eleids:
nodes = self._mesh.get_nodeids_by_elementids([eleid])
for idx, seg in segments.items():
seg_nodes = seg['nodes']
ele_in_segment = True
for node in nodes:
node_pos = np.array([self._mesh.nodes_df.at[node,'x'], self._mesh.nodes_df.at[node,'y']])
if not check_node_in_segment(seg_nodes['lowerleft'], seg_nodes['lowerright'],
seg_nodes['upperright'], seg_nodes['upperleft'], node_pos):
ele_in_segment = False
break
if ele_in_segment:
if seg['group'] in self._mesh.groups:
self._mesh.add_element_to_groups(eleid, [seg['group']])
else:
self._mesh.create_group(seg['group'], (), [eleid])
break
def set_homogeneous_group(self, groupname):
self._mesh.create_group(groupname, (), self._mesh.get_elementids_by_tags(['shape'], ['Quad4']))