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rAKA/python/akantu/__init__.py
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__init__.py
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__copyright__ = (
"Copyright (©) 2018-2023 EPFL (Ecole Polytechnique Fédérale de Lausanne)"
"Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)"
)
__license__ = "LGPLv3"
import warnings as _aka_warn
import scipy.sparse as _aka_sparse
import numpy as _aka_np
from . import py11_akantu as _py11_akantu
private_keys = set(dir(_py11_akantu)) - set(dir())
for k in private_keys:
globals()[k] = getattr(_py11_akantu, k)
if _py11_akantu.has_mpi():
try:
from mpi4py import MPI # noqa: F401
except Exception:
pass
def initialize(*args, **kwargs):
raise RuntimeError("No need to call initialize,"
" use parseInput to read an input file")
def finalize(*args, **kwargs):
_aka_warn.warn("No need to call finalize", DeprecationWarning)
class AkantuSparseMatrix (_aka_sparse.coo_matrix):
def __init__(self, aka_sparse):
self.aka_sparse = aka_sparse
matrix_type = self.aka_sparse.getMatrixType()
sz = self.aka_sparse.size()
row = self.aka_sparse.getIRN()[:, 0] - 1
col = self.aka_sparse.getJCN()[:, 0] - 1
data = self.aka_sparse.getA()[:, 0]
row = row.copy()
col = col.copy()
data = data.copy()
if matrix_type == _py11_akantu._symmetric:
non_diags = (row != col)
row_sup = col[non_diags]
col_sup = row[non_diags]
data_sup = data[non_diags]
col = _aka_np.concatenate((col, col_sup))
row = _aka_np.concatenate((row, row_sup))
data = _aka_np.concatenate((data, data_sup))
_aka_sparse.coo_matrix.__init__(
self, (data, (row, col)), shape=(sz, sz), dtype=data.dtype)
def convertGmshToAkantuMesh(gmsh):
_msh_to_akantu_element_types = [
_py11_akantu._not_defined,
_py11_akantu._segment_2,
_py11_akantu._triangle_3,
_py11_akantu._quadrangle_4,
_py11_akantu._tetrahedron_4,
_py11_akantu._hexahedron_8,
_py11_akantu._pentahedron_6,
_py11_akantu._not_defined,
_py11_akantu._segment_3,
_py11_akantu._triangle_6,
_py11_akantu._not_defined,
_py11_akantu._tetrahedron_10,
_py11_akantu._not_defined,
_py11_akantu._not_defined,
_py11_akantu._not_defined,
_py11_akantu._point_1,
_py11_akantu._quadrangle_8,
_py11_akantu._hexahedron_20,
_py11_akantu._pentahedron_15,
]
gmsh_mesh = gmsh.model.mesh
types = gmsh_mesh.get_element_types()
dim = -1
for el_type in types:
props = gmsh_mesh.get_element_properties(el_type)
dim = max(dim, props[1])
aka_mesh = _py11_akantu.Mesh(dim)
accessor = _py11_akantu.MeshAccessor(aka_mesh)
gmsh_nodes = gmsh_mesh.get_nodes()
nb_nodes = gmsh_nodes[0].shape[0]
accessor.resizeNodes(nb_nodes)
aka_nodes = aka_mesh.getNodes()
gmsh_aka_nodes = {}
for i in range(nb_nodes):
aka_nodes[i, :] = gmsh_nodes[1][i*3:i*3+dim]
gmsh_aka_nodes[gmsh_nodes[0][i]] = i
gmsh_aka_elements = {}
for el_type in types:
aka_type = _msh_to_akantu_element_types[el_type];
gmsh_aka_elements[aka_type] = {}
tags, gmsh_conn = gmsh_mesh.get_elements_by_type(el_type)
aka_mesh.addConnectivityType(aka_type)
accessor.resizeConnectivity(tags.shape[0], aka_type)
conn = aka_mesh.getConnectivity(aka_type)
for element, tag in enumerate(tags):
gmsh_aka_elements[aka_type][tag] = element
nnodes_per_el = conn.shape[1]
for node in range(nnodes_per_el):
conn[element, node] = gmsh_aka_nodes[
gmsh_conn[element * nnodes_per_el + node]]
for group in gmsh.model.get_physical_groups():
name = gmsh.model.get_physical_name(*group)
types = gmsh_mesh.get_element_types(*group)
aka_group = aka_mesh.createElementGroup(name,
spatial_dimension=group[0],
replace_group=True)
entities = gmsh.model.get_entities_for_physical_group(*group)
for el_type in types:
aka_type = _msh_to_akantu_element_types[el_type]
for entity in entities:
elements = gmsh_mesh.get_elements_by_type(el_type, tag=entity)
for el in elements[0]:
aka_group.add(
_py11_akantu.Element(aka_type,
gmsh_aka_elements[aka_type][el],
_py11_akantu._not_ghost), # noqa
True, False)
aka_group.optimize()
accessor.makeReady()
return aka_mesh
FromStress = _py11_akantu.FromHigherDim
FromTraction = _py11_akantu.FromSameDim
_py11_akantu.__initialize()
__version__ = _py11_akantu.getVersion()
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