Merge branch 'reorganize_part_classes'

Improve structure of the code.
Better separation between the class definitions on one hand and the imports of the mesh and the subdomain data on the other hand.

.gitignore

@@ -8,4 +8,5 @@
 demo/loc_E12_u.pdf
 *.pyc.*
 *.egg-info/
-ho_homog/.idea
\ No newline at end of file
+ho_homog/.idea
+.idea/HO_homog.iml

demo/demo_pantograph_mesh.py

@@ -153,7 +153,7 @@ msh.set_periodicity_pairs(micro_bndry[1], micro_bndry[3])
 logger.info("Periodicity constraint : Done")
 
 logger.info("Cleaning model")
-factory.remove([(1, l.tag) for l in macro_ll.sides])
+factory.remove([(1, s.tag) for s in macro_ll.sides])
 factory.synchronize()
 factory.removeAllDuplicates()
 factory.synchronize()
@@ -164,4 +164,3 @@ geo.PhysicalGroup.set_group_mesh(1)
 gmsh.model.mesh.generate(2)
 gmsh.write(str(mesh_file))
 run(f"gmsh {str(mesh_file)} &", shell=True, check=True)
-gmsh.fltk.run()

ho_homog/geometry/__init__.py

@@ -79,7 +79,7 @@ from .transformations import plane_reflection, point_reflection, rotation, trans
 
 DEFAULT_GMSH_OPTIONS = {
     "General.Terminal": 1,
-    "General.Verbosity": 5,
+    "General.Verbosity": 3,
     "Geometry.AutoCoherence": 0,
     "Mesh.ColorCarousel": 2,
     # * 0=by element type, 1=by elementary entity, 2=by physical entity,3=by partition

ho_homog/homog2d.py

@@ -61,7 +61,7 @@ class Fenics2DHomogenization(object):
 
         """
         self.rve = fenics_2d_rve
-        self.topo_dim = topo_dim = fenics_2d_rve.mesh_dim
+        self.topo_dim = topo_dim = fenics_2d_rve.dim
         try:
             bottom_left_corner = fenics_2d_rve.bottom_left_corner
         except AttributeError:

ho_homog/homog_beam.py

@@ -58,7 +58,7 @@ class FenicsHomogenizationBeam(object):
 
         """
         self.rve = fenics_2d_rve
-        self.topo_dim = topo_dim = fenics_2d_rve.mesh_dim
+        self.topo_dim = topo_dim = fenics_2d_rve.dim
         self.pbc = periodicity.PeriodicDomain.pbc_dual_base(
             fenics_2d_rve.gen_vect, "X", topo_dim
         ) # * Périodicité selon X seulement

ho_homog/mesh_generate/__init__.py

@@ -451,7 +451,6 @@ def Gmsh2DPartFromRVE(cell: Gmsh2DRVE, nb_cells, part_name=None):
         tag = cell.phy_surf[i].tag + 1000
         name = cell.phy_surf[i].name
         phy_surfaces.append(geo.PhysicalGroup(all_surfaces, 2, name, tag))
-    # gmsh.fltk.run()
     for gp in cell.phy_surf:
         gp.remove_gmsh()
     factory.synchronize()

ho_homog/toolbox_FEniCS.py

@@ -37,7 +37,7 @@ DOLFIN_LU_METHODS = {
 SUPPORTED_MESH_SUFFIX = (".xml", ".xdmf")
 
 
-def get_MeshFunction_val(msh_fctn):
+def get_mesh_function_value(msh_fctn):
     """
     Get information about the set of values that a given MeshFunction outputs.
 
@@ -56,7 +56,7 @@ def get_MeshFunction_val(msh_fctn):
 
     val = np.unique(msh_fctn.array())
     nb = len(val)
-    return (nb, val)
+    return nb, val
 
 
 def facet_plot2d(
@@ -116,13 +116,21 @@ def function_from_xdmf(function_space, function_name="", xdmf_path=""):
     If multiple functions are requested: #TODO : test
     the first argument must be a list of tuples (FunctionSpace, function name)
     the second argument must be empty.
-    Ex: function_from_xdmf([(V,"u"),(W,"eps")], xdmf_path=checkpoint_path)
 
     Returns
     -------
     dolfin.Function, list of dolfin.Function
         New function(s) that is(are) identical to the previously saved function(s).
+
+    Example
+    --------
+    >>> import dolfin as fe
+    >>> mesh = xdmf_mesh("mesh.xdmf")
+    >>> V = fe.VectorFunctionSpace(mesh, "CG", 2)
+    >>> W = fe.VectorFunctionSpace(mesh, "DG", 1)
+    >>> function_from_xdmf([(V,"u"),(W,"eps")], xdmf_path="checkpoint.xdmf")
     """
+
     if isinstance(function_space, list):
         all_f = list()
         with fe.XDMFFile(str(xdmf_path)) as f_in:
@@ -181,8 +189,6 @@ def function_errornorm(u, v, norm_type="L2", enable_diff_fspace=False):
 
 def local_project(v, fspace, solver_method: str = "", **kwargs):
     """
-    Info : https://comet-fenics.readthedocs.io/en/latest/tips_and_tricks.html#efficient-projection-on-dg-or-quadrature-spaces #noqa
-
     Parameters
     ----------
     v : [type]
@@ -207,14 +213,20 @@ def local_project(v, fspace, solver_method: str = "", **kwargs):
     Returns
     -------
     Function
+
+    Notes
+    -----
+    Source for this code:
+    https://comet-fenics.readthedocs.io/en/latest/tips_and_tricks.html#efficient-projection-on-dg-or-quadrature-spaces
+
     """
     metadata = kwargs.get("metadata", {})
-    dX = kwargs.get("dx", fe.dx(metadata=metadata))
+    dx = kwargs.get("dx", fe.dx(metadata=metadata))
 
     dv = fe.TrialFunction(fspace)
     v_ = fe.TestFunction(fspace)
-    a_proj = fe.inner(dv, v_) * dX
-    b_proj = fe.inner(v, v_) * dX
+    a_proj = fe.inner(dv, v_) * dx
+    b_proj = fe.inner(v, v_) * dx
 
     if solver_method == "LU":
         solver = fe.LocalSolver(
@@ -249,87 +261,138 @@ def _wrap_in_list(obj, name, types=type):
         lst = [obj]
     for obj in lst:
         if not isinstance(obj, types):
-            raise TypeError(
-                "expected a (list of) %s as '%s' argument" % (str(types), name)
-            )
+            raise TypeError(f"expected a (list of) {types} as {name} argument")
     return lst
 
 
-def xdmf_mesh(mesh_file, import_subdomains=False, facet_file="", physical_file=""):
+def xdmf_mesh(mesh_file):
     """Create a FeniCS mesh from a mesh file with xdmf format.
 
     Parameters
     ----------
     mesh_file : str or Path
         Path of the file mesh (xdmf file)
-    import_subdomains : bool, optional
-        True if information about subdomains have to be imported.
-        The paths of the auxiliary files that contains information about subdomains
-        can be indicated with facet_file and physical_file.
-        The paths used by default are :
-            - "<mesh path>_facet_region.xdmf" and
-            - "<mesh path>_physical_region.xdmf" (for subdomains)
+
+    Returns
+    -------
+    dolfin.Mesh
+    """
+    if not isinstance(mesh_file, PurePath):
+        mesh_file = Path(mesh_file)
+    if not mesh_file.suffix == ".xdmf":
+        raise TypeError("Wrong suffix for the path to the mesh.")
+    mesh = fe.Mesh()
+    with fe.XDMFFile(str(mesh_file)) as f_in:
+        f_in.read(mesh)
+    return mesh
+
+
+_warning_message_ = "The {} file is missing for the mesh {}."
+
+
+def import_subdomain_data_xml(mesh, mesh_file):
+    """ Import data from the _physical_region.xml and _facet_region.xml files
+    that result from the mesh conversion to .xml with dolfin-convert
+
+    Parameters
+    ----------
+    mesh: dolfin.Mesh
+        mesh already imported from the `.xml` file (mesh_path)
+    mesh_file : pathlib.Path
+        Path to the mesh file (.xml).
+        The files that contain the data about the subdomains and the facet regions
+        are assumed to be in the same folder, with the names:
+        `[mesh_name]_physical_region.xml` and `[mesh_name]_facet_region.xml`.
+    """
+    name = mesh_file.stem
+    subdo_path = mesh_file.with_name(name + "_physical_region.xml")
+    facet_path = mesh_file.with_name(name + "_facet_region.xml")
+
+    if subdo_path.exists():
+        subdomains = fe.MeshFunction("size_t", mesh, subdo_path.as_posix())
+        subdo_val = get_mesh_function_value(subdomains)
+        logger.info(f"{subdo_val[0]} physical regions imported. Tags : {subdo_val[1]}")
+    else:
+
+        logger.warning(_warning_message_.format("_physical_region.xml", mesh_file.name))
+
+        subdomains = None
+
+    if facet_path.exists():
+        facets = fe.MeshFunction("size_t", mesh, facet_path.as_posix())
+        facets_val = get_mesh_function_value(facets)
+        logger.info(f"{facets_val[0]} facet regions imported. Tags : {facets_val[1]}")
+    else:
+        logger.warning(_warning_message_.format("_facet_region.xml", mesh_file.name))
+
+        facets = None
+    return subdomains, facets
+
+
+def import_subdomain_data_xdmf(mesh, mesh_file, facet_file="", physical_file=""):
+
+    """Import information about subdomains from .xdmf files from
+    obtained with the mesh conversion .msh -> .xdmf with meshio.
+
+    The paths of the auxiliary files that contains information about subdomains
+    can be indicated with facet_file and physical_file.
+    The paths used by default are :
+        - "<mesh path>_facet_region.xdmf" and
+        - "<mesh path>_physical_region.xdmf" (for subdomains)
+
+
+    Parameters
+    ----------
+    mesh: dolfin.Mesh
+        mesh already imported from the `.xdmf` file (mesh_path)
+    mesh_file : pathlib.Path
+        Path to the mesh file (.xdmf).
     facet_file : str or Path, optional
         Path to the mesh auxiliary file that contains subdomains data.
         Defaults to "" i.e. the default path will be used.
     physical_file : str or Path, optional
         Path to the mesh auxiliary file that contains facet regions data.
         Defaults to "" i.e. the default path will be used.
-
     Returns
     -------
-    Mesh / tuple
-        If subdomains are not requested :
-            - The Mesh instance
-        If subdomains are requested :
-            - The Mesh instance,
-            - The MeshFunction for subdomains if it exists else None,
-            - The MeshFunction for facets if it exists else None,
+    Tuple (length: 2)
+        - The MeshFunction for subdomains if it exists else None;
+        - The MeshFunction for facets if it exists else None.
 
     Source
     ------
     Gist meshtagging_mvc.py, June 2018, Michal Habera
     https://gist.github.com/michalhabera/bbe8a17f788192e53fd758a67cbf3bed
-    """
-    if not isinstance(mesh_file, PurePath):
-        mesh_file = Path(mesh_file)
-    if not mesh_file.suffix == ".xdmf":
-        raise TypeError("Wrong suffix for the path to the mesh.")
-    mesh = fe.Mesh()
-    with fe.XDMFFile(str(mesh_file)) as f_in:
-        f_in.read(mesh)
 
-    if not import_subdomains:
-        return mesh
+    """
 
     dim = mesh.geometric_dimension()
 
-    if not facet_file:
-        facet_file = mesh_file.with_name(f"{mesh_file.stem}_facet_region.xdmf")
-    else:
-        facet_file = Path(facet_file)
-        if not facet_file.suffix == ".xdmf":
-            raise TypeError("Wrong suffix for the path to facet regions.")
     if not physical_file:
         physical_file = mesh_file.with_name(f"{mesh_file.stem}_physical_region.xdmf")
+    if not facet_file:
+        facet_file = mesh_file.with_name(f"{mesh_file.stem}_facet_region.xdmf")
+    physical_file, facet_file = Path(physical_file), Path(facet_file)
+    for p, n in zip((physical_file, facet_file), ("subdomains", "facet regions")):
+        if not p.suffix == ".xdmf":
+            raise TypeError(f"Wrong suffix for the path to {n}.")
+
+    subdomains, facets = None, None
+    if physical_file.exists():
+        cell_vc = fe.MeshValueCollection("size_t", mesh, dim)
+        with fe.XDMFFile(str(physical_file)) as f_in:
+            f_in.read(cell_vc, "cell_data")
+        subdomains = fe.cpp.mesh.MeshFunctionSizet(mesh, cell_vc)
     else:
-        physical_file = Path(physical_file)
-        if not physical_file.suffix == ".xdmf":
-            raise TypeError("Wrong suffix for the path to subdomains.")
+        logger.warning(
+            _warning_message_.format("_physical_region.xdmf", mesh_file.name)
+        )
 
-    if not facet_file.exists():
-        facet_regions = None
-    else:
+    if facet_file.exists():
         facet_vc = fe.MeshValueCollection("size_t", mesh, dim - 1)
         with fe.XDMFFile(str(facet_file)) as f_in:
             f_in.read(facet_vc, "facet_data")
-        facet_regions = fe.cpp.mesh.MeshFunctionSizet(mesh, facet_vc)
-    if not physical_file.exists():
-        subdomains = None
+        facets = fe.cpp.mesh.MeshFunctionSizet(mesh, facet_vc)
     else:
-        cell_vc = fe.MeshValueCollection("size_t", mesh, dim - 1)
-        with fe.XDMFFile(str(physical_file)) as f_in:
-            f_in.read(cell_vc, "cell_data")
-        subdomains = fe.cpp.mesh.MeshFunctionSizet(mesh, cell_vc)
-
-    return mesh, subdomains, facet_regions
+        logger.warning(_warning_message_.format("_facet_region.xdmf", mesh_file.name))
+    return subdomains, facets

ho_homog/toolbox_gmsh.py

@@ -88,7 +88,7 @@ def conversion_to_xdmf(i_path, o_path, cell_reg, facet_reg, dim, subdomains=Fals
         raise NotImplementedError("3D meshes are not supported yet.")
         # * INFO :
     else:
-        ValueError
+        raise ValueError
 
     meshio.write(o_path, geo_only)
 

requirements.txt

+dolfin~=2019.1.0
+gmsh~=4.6.0.post3
+meshio~=4.3.1
+h5py~=3.1.0
+matplotlib~=3.3.3
+numpy~=1.19.4
+sympy~=1.1.1
+pytest~=6.2.1
+setuptools~=39.0.1
+

setup.py

@@ -6,7 +6,9 @@ Created on 21/03/2019
 
 sources : http://sametmax.com/vive-setup-cfg-et-mort-a-pyproject-toml/,
 http://sametmax.com/creer-un-setup-py-et-mettre-sa-bibliotheque-python-en-ligne-sur-pypi/
+
+https://docs.pytest.org/en/stable/goodpractices.html
 """
 
 from setuptools import setup
-setup()
\ No newline at end of file
+setup()

test/__init__.py

-# coding: utf8
-"""
-Created on 12/07/2019
-@author: baptiste
-
-Give the individual tests import contex.
-Source : https://docs.python-guide.org/writing/structure/#structure-of-the-repository
-"""
-
-
-import site
-from pathlib import Path
-
-
-cur_dir = Path(__file__).resolve().parent
-repository_dir = cur_dir.parent
-site.addsitedir(repository_dir)
-
-import ho_homog

test/context.py

-# coding: utf8
-"""
-Created on 12/07/2019
-@author: baptiste
-
-Give the individual tests import contex.
-Source : https://docs.python-guide.org/writing/structure/#structure-of-the-repository
-"""
-
-
-import site
-from pathlib import Path
-import sys, os
-
-sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
-
-# cur_dir = Path(__file__).resolve().parent
-# repository_dir = cur_dir.parent
-# site.addsitedir(repository_dir)
-
-import ho_homog

test/full_scale_pb_test.py

@@ -6,7 +6,7 @@ Created on 08/04/2019
 
 import logging
 import dolfin as fe
-from context.ho_homog import full_scale_pb as homog_full
+from ho_homog import full_scale_pb as fsp
 from pathlib import Path
 from pytest import approx
 
@@ -71,7 +71,7 @@ def test_reconstruction_vectors():
             strain_fspace,
         ),
     }
-    reconstr_sol = homog_full.reconstruction(
+    reconstr_sol = fsp.reconstruction(
         localization_tensors, macro_fields, function_spaces, trunc_order=1
     )
     results_file_path = Path(__file__).with_name("test_reconstruction.xdmf")
@@ -164,7 +164,7 @@ def test_reconstruction_with_constraint():
         fe.Expression("0.5*x[0] + x[1] + 0.5*x[1] + 1.*x[0]", degree=2), scalar_fspace
     )
 
-    reconstr_sol = homog_full.reconstruction(
+    reconstr_sol = fsp.reconstruction(
         localization_tensors,
         macro_fields,
         function_spaces,
@@ -191,7 +191,7 @@ def test_reconstruction_with_constraint():
 
 
 def test_select_solver():
-    "The solver Mumps is selected."
+    """The solver Mumps is selected."""
     logger = logging.getLogger("test_reconstruction")
     nb_x = nb_y = 20
     L_x = 2
@@ -239,7 +239,7 @@ def test_select_solver():
         fe.Expression("0.5*x[0] + x[1] + 0.5*x[1] + 1.*x[0]", degree=2), scalar_fspace
     )
 
-    reconstr_sol = homog_full.reconstruction(
+    reconstr_sol = fsp.reconstruction(
         localization_tensors,
         macro_fields,
         function_spaces,

test/geometry_test.py

@@ -5,18 +5,17 @@ Created on Mon Oct 15 11:00:18 2018
 @author: Baptiste
 """
 
-import os
-from .context import ho_homog
-import math
-import numpy as np
-import matplotlib.pyplot as plt
 import copy
 import logging
+import math
+import os
 from logging.handlers import RotatingFileHandler
 
 import gmsh
+import matplotlib.pyplot as plt
+import numpy as np
 
-geo = ho_homog.geometry
+import ho_homog.geometry as geo
 
 # nice shortcuts
 model = gmsh.model
@@ -435,46 +434,21 @@ def test_ll_modif():
     gmsh.model.add(name)
 
     t = math.tan(math.pi / 6)
-    vertcs_lists = []
-    vertcs_lists.append(
-        [
-            geo.Point(np.array(c), 0.05)
-            for c in [
-                (0, 0),
-                (2, 0),
-                (2 - SR2, 0 + SR2),
-                (2, 2),
-                (2 - 1, 2 + t),
-                (0, 2),
-            ]
-        ]
-    )  # angles : pi/4, pi/2 and 2*pi/3
-    vertcs_lists.append(
-        [
-            geo.Point(np.array(c), 0.05)
-            for c in [
-                (3, 0),
-                (5, 0),
-                (5 - SR2, 0 + SR2),
-                (5, 2),
-                (5 - 1, 2 + t),
-                (3, 2),
-            ]
-        ]
-    )
-    vertcs_lists.append(
-        [
-            geo.Point(np.array(c), 0.05)
-            for c in [
-                (6, 0),
-                (8, 0),
-                (8 - SR2, 0 + SR2),
-                (8, 2),
-                (8 - 1, 2 + t),
-                (6, 2),
-            ]
-        ]
-    )
+    vertcs_lists = [None, None, None]
+
+    vertcs_lists[0] = [
+        geo.Point(np.array(c), 0.05)
+        for c in [(0, 0), (2, 0), (2 - SR2, 0 + SR2), (2, 2), (2 - 1, 2 + t), (0, 2),]
+    ]  # angles : pi/4, pi/2 and 2*pi/3
+    vertcs_lists[1] = [
+        geo.Point(np.array(c), 0.05)
+        for c in [(3, 0), (5, 0), (5 - SR2, 0 + SR2), (5, 2), (5 - 1, 2 + t), (3, 2),]
+    ]
+    vertcs_lists[2] = [
+        geo.Point(np.array(c), 0.05)
+        for c in [(6, 0), (8, 0), (8 - SR2, 0 + SR2), (8, 2), (8 - 1, 2 + t), (6, 2),]
+    ]
+    vertcs_lists = [v_list_1, v_list_2, v_list_3]
 
     lls = [geo.LineLoop(vl, explicit=False) for vl in vertcs_lists]
     plt.figure()
@@ -567,8 +541,8 @@ def test_gather_line():
         gp_l = geo.PhysicalGroup(l_list, 1, n)
         gp_l.add_gmsh()
         gps.append(gp_l)
-        for l in l_list:
-            l.plot2D(col)
+        for ln in l_list:
+            ln.plot2D(col)
     factory.synchronize()
 
     gmsh.option.setNumber("Mesh.SaveAll", 1)
@@ -863,11 +837,6 @@ if __name__ == "__main__":
     # test_mesh_only_phy_groups()
 
     # * Bloc de fin
-    gmsh.fltk.run()
+    # gmsh.fltk.run()
     plt.show()
     # * Il faut fermer toutes les fenêtres avant de passer à la GUI gmsh. (pertinent en mode non interactive) #noqa
-    # gmsh.fltk.run()
-    # ! A revoir, ça génère des "kernel died" dans Spyder, pas idéal
-    # # gmsh.fltk.initialize()
-    # gmsh.finalize()
-    # plt.show()

test/homog2d_test.py

@@ -5,27 +5,28 @@ Created on 09/01/2019
 
 """
 
-import numpy as np
-import gmsh
-import meshio
-from ho_homog import geometry, homog2d, materials, mesh_generate_2D, part
-from pytest import approx
 import logging
 import time
+
 import dolfin as fe
+import gmsh
+import meshio
+import numpy as np
+from pytest import approx
+
+from ho_homog import geometry, homog2d, materials, mesh_generate, part
 
 logger = logging.getLogger("Test_homog2d")
 logger.setLevel(logging.DEBUG)
 formatter = logging.Formatter(
-    '%(asctime)s :: %(levelname)s :: %(name)s :: %(message)s',
-    "%H:%M:%S")
+    "%(asctime)s :: %(levelname)s :: %(name)s :: %(message)s", "%H:%M:%S"
+)
 stream_handler = logging.StreamHandler()
 stream_handler.setLevel(logging.DEBUG)
 stream_handler.setFormatter(formatter)
 logger.addHandler(stream_handler)
 
-np.set_printoptions(suppress=False, floatmode='fixed', precision=8,
-                    linewidth=150)
+np.set_printoptions(suppress=False, floatmode="fixed", precision=8, linewidth=150)
 
 
 def test_homog_EGG_pantograph_1x1(generate_mesh=False):
@@ -33,15 +34,16 @@ def test_homog_EGG_pantograph_1x1(generate_mesh=False):
     start = time.time()
     if generate_mesh:
         geometry.init_geo_tools()
-        geometry.set_gmsh_option('Mesh.MshFileVersion', 4.1)
+        geometry.set_gmsh_option("Mesh.MshFileVersion", 4.1)
         a = 1
-        b, k = a, a/3
+        b, k = a, a / 3
         r = 0.02
-        panto_test = mesh_generate_2D.Gmsh2DRVE.pantograph(
-            a, b, k, r, nb_cells=(1, 1), soft_mat=False, name='panto_rve_1x1')
-        lc_ratio = 1/6
-        lc_min_max = (lc_ratio*r*a, lc_ratio*a)
-        panto_test.main_mesh_refinement((2*r*a, a), lc_min_max, False)
+        panto_test = mesh_generate.pantograph.pantograph_RVE(
+            a, b, k, r, nb_cells=(1, 1), soft_mat=False, name="panto_rve_1x1"
+        )
+        lc_ratio = 1 / 6
+        lc_min_max = (lc_ratio * r * a, lc_ratio * a)
+        panto_test.main_mesh_refinement((2 * r * a, a), lc_min_max, False)
         panto_test.mesh_generate()
         gmsh.model.mesh.renumberNodes()
         gmsh.model.mesh.renumberElements()
@@ -49,44 +51,45 @@ def test_homog_EGG_pantograph_1x1(generate_mesh=False):
         mesh = meshio.read("panto_rve_1x1.msh")
         mesh.points = mesh.points[:, :2]
         geo_only = meshio.Mesh(
-            points=mesh.points,
-            cells={"triangle": mesh.cells["triangle"]})
+            points=mesh.points, cells={"triangle": mesh.cells["triangle"]}
+        )
         meshio.write("panto_rve_1x1.xdmf", geo_only)
         geometry.reset()
 
-    E, nu = 1., 0.3
-    material = materials.Material(E, nu, 'cp')
-    gen_vect = np.array([[4., 0.], [0., 8.]])
-    rve = part.Fenics2DRVE.file_2_Fenics_2DRVE(
-        "panto_rve_1x1.xdmf", gen_vect, material)
+    E, nu = 1.0, 0.3
+    material = materials.Material(E, nu, "cp")
+    gen_vect = np.array([[4.0, 0.0], [0.0, 8.0]])
+    rve = part.Fenics2DRVE.rve_from_file("panto_rve_1x1.xdmf", gen_vect, material)
 
     hom_model = homog2d.Fenics2DHomogenization(rve)
-    *localzt_dicts, constit_tensors = hom_model.homogenizationScheme('EGG')
+    *localzt_dicts, constit_tensors = hom_model.homogenizationScheme("EGG")
 
     Chom_ref = np.array(
-        [[2.58608139e-04, 3.45496903e-04, 5.16572422e-12],
-         [3.45496903e-04, 3.81860676e-02, 6.48384646e-11],
-         [5.16572422e-12, 6.48384646e-11, 3.27924466e-04]])
+        [
+            [2.58608139e-04, 3.45496903e-04, 5.16572422e-12],
+            [3.45496903e-04, 3.81860676e-02, 6.48384646e-11],
+            [5.16572422e-12, 6.48384646e-11, 3.27924466e-04],
+        ]
+    )
 
     D_ref = np.array(
-        [[3.72630940e-02,  2.20371444e-02,  1.00603288e-09,
-            -1.51425656e-11,  6.18921191e-10, -1.39407898e-03],
-         [2.20371444e-02, -4.32257286e-03,  3.52427076e-09,
-            3.08504101e-09,  2.91393310e-09,  1.24155443e-02],
-         [1.00603288e-09,  3.52427076e-09,  1.30706023e-01,
-            1.59177545e-02, -9.94987221e-03, -6.34655280e-10],
-         [-1.51425656e-11, 3.08504101e-09,  1.59177545e-02,
-            1.58014087e-01,  1.28902572e-01,  1.06773326e-09],
-         [6.18921191e-10,  2.91393310e-09, -9.94987221e-03,
-            1.28902572e-01,  1.16274758e-01,  7.79908277e-10],
-         [-1.39407898e-03, 1.24155443e-02, -6.34655280e-10,
-            1.06773326e-09,  7.79908277e-10,  6.38090435e-05]]
+        [
+            [3.7266e-02, 2.2039e-02, 4.6218e-10, 1.5420e-10, 1.2646e-09, -1.3939e-03],
+            [2.2039e-02, -4.3185e-03, -3.4719e-11, 2.7544e-10, 7.0720e-10, 1.2415e-02],
+            [4.6218e-10, -3.4719e-11, 1.3071e-01, 1.5918e-02, -9.9492e-03, -2.9101e-10],
+            [1.5420e-10, 2.7544e-10, 1.5918e-02, 1.5802e-01, 1.2891e-01, 1.5962e-09],
+            [1.2646e-09, 7.0720e-10, -9.9492e-03, 1.2891e-01, 1.1628e-01, 1.3358e-09],
+            [-1.3939e-03, 1.2415e-02, -2.9101e-10, 1.5962e-09, 1.3358e-09, 6.3893e-05],
+        ]
     )
 
-    Chom = constit_tensors['E']['E']
-    G = constit_tensors['E']['EGGbis']
-    D = (constit_tensors['EG']['EG']
-         - np.vstack((G[:, :6], G[:, 6:])) - np.vstack((G[:, :6], G[:, 6:])).T)
+    Chom = constit_tensors["E"]["E"]
+    G = constit_tensors["E"]["EGGbis"]
+    D = (
+        constit_tensors["EG"]["EG"]
+        - np.vstack((G[:, :6], G[:, 6:]))
+        - np.vstack((G[:, :6], G[:, 6:])).T
+    )
     logger.debug(f"Chom : \n {Chom}")
     logger.debug(f"D : \n {D}")
     logger.debug(f"Duration : {time.time() - start}")
@@ -111,14 +114,15 @@ def test_homogeneous_pantograph(generate_mesh=False, save_results=False):
     start = time.time()
     if generate_mesh:
         geometry.init_geo_tools()
-        geometry.set_gmsh_option('Mesh.MshFileVersion', 4.1)
+        geometry.set_gmsh_option("Mesh.MshFileVersion", 4.1)
         a = 1
-        b, k, r = a, a/3, 0.1*a
-        geo_model = mesh_generate_2D.Gmsh2DRVE.pantograph(
-            a, b, k, r, soft_mat=True, name='homogeneous_panto')
+        b, k, r = a, a / 3, 0.1 * a
+        geo_model = mesh_generate.pantograph.pantograph_RVE(
+            a, b, k, r, soft_mat=True, name="homogeneous_panto"
+        )
         lc_ratio = 1
-        lc_min_max = (lc_ratio*r, lc_ratio)
-        d_min_max = (2*r, a)
+        lc_min_max = (lc_ratio * r, lc_ratio)
+        d_min_max = (2 * r, a)
         geo_model.main_mesh_refinement(d_min_max, lc_min_max, False)
         geo_model.soft_mesh_refinement(d_min_max, lc_min_max, False)
         geo_model.mesh_generate()
@@ -128,41 +132,46 @@ def test_homogeneous_pantograph(generate_mesh=False, save_results=False):
         mesh = meshio.read("homogeneous_panto.msh")