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 _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 __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 __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()
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 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)
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