Demo script : Mesh import from xdmf

Including subdomains and with plots.
+ minor corrections linked to the msh_conversion function.

demo/demo_import_mesh_xdmf.py

+# coding: utf-8
+"""
+Created on 01/07/2019
+@author: baptiste
+
+1- Conversion of a mesh file MSH format (version 4) -> XDMF format,
+2- Import of the mesh from the XDMF file,
+3- Show facet regions and subdomains with matplotlib.
+"""
+
+import logging
+
+import gmsh
+import matplotlib.pyplot as plt
+import dolfin as fe
+from ho_homog import geometry, mesh_generate_2D, toolbox_FEniCS, toolbox_gmsh
+
+# * Logging
+logger = logging.getLogger(__name__)  # http://sametmax.com/ecrire-des-logs-en-python/
+logger.setLevel(logging.INFO)
+
+formatter = logging.Formatter("%(asctime)s :: %(levelname)s :: %(message)s", "%H:%M")
+stream_handler = logging.StreamHandler()
+stream_handler.setLevel(logging.INFO)
+stream_handler.setFormatter(formatter)
+logger.addHandler(stream_handler)
+
+geometry.init_geo_tools()
+geometry.set_gmsh_option("Mesh.MshFileVersion", 4.1)
+
+logger.info("Generating the geometry model")
+a = 1
+b, k = a, a / 3
+r = 0.01 * a
+rve_geo = mesh_generate_2D.Gmsh2DRVE.pantograph(a, b, k, r, soft_mat=True, name="panto")
+
+logger.info("Generating the mesh")
+lc_ratio = 1 / 3.0
+d_min_max = (2 * r, a)
+lc_min_max = (lc_ratio * r, lc_ratio * a)
+rve_geo.main_mesh_refinement(d_min_max, lc_min_max, False)
+rve_geo.soft_mesh_refinement(d_min_max, lc_min_max, False)
+rve_geo.mesh_generate()
+
+logger.info("Saving mesh with MSH 4 format")
+gmsh.model.mesh.renumberNodes()
+gmsh.model.mesh.renumberElements()
+gmsh.write(str(rve_geo.mesh_abs_path))
+
+logger.info("Mesh conversion MSH -> XDMF")
+mesh_path, *_ = toolbox_gmsh.msh_conversion(
+    rve_geo.mesh_abs_path, ".xdmf", subdomains=True
+)
+
+logger.info("Import of mesh and partitions as MeshFunction instances")
+mesh, subdomains, facet_regions = toolbox_FEniCS.xdmf_mesh(mesh_path, True)
+
+
+plt.figure()
+fe.plot(mesh, title="Mesh only")
+plt.figure()
+subdo_plt = fe.plot(subdomains, title="Subdomains")
+plt.colorbar(subdo_plt)
+
+nb_val, facets_val = toolbox_FEniCS.get_MeshFunction_val(facet_regions)
+facets_val = facets_val[facets_val != 18446744073709551615]
+facets_val = facets_val[facets_val != 0]
+print(facets_val)
+delta = max(facets_val) - max(facets_val)
+cmap = plt.cm.get_cmap("viridis", max(facets_val) - min(facets_val)+1)
+fig, ax = plt.subplots()
+facets_plt = toolbox_FEniCS.facet_plot2d(
+    facet_regions, mesh, cmap=cmap, exclude_val=(0, 18446744073709551615)
+)
+ax.set_title("Facet regions")
+cbar = fig.colorbar(facets_plt[0], ticks=list(facets_val))
+cbar.ax.set_xticklabels(list(facets_val))
+
+plt.show()

demo/demo_pantograph_compare_same_mesh.py

@@ -86,7 +86,7 @@ gmsh.logger.stop()
 gmsh.model.mesh.renumberNodes()
 gmsh.model.mesh.renumberElements()
 gmsh.write(str(rve_geo.mesh_abs_path))
-rve_path, *_ = msh_conversion(rve_geo.mesh_abs_path, ".xdmf")
+rve_path, = msh_conversion(rve_geo.mesh_abs_path, ".xdmf")
 
 
 # * Step 3 : Build the mesh of the part from the mesh of the RVE
@@ -94,7 +94,7 @@ gmsh.logger.start()
 part_geo = mesh_generate_2D.Gmsh2DPartFromRVE(rve_geo, (75, 1))
 process_gmsh_log(gmsh.logger.get())
 gmsh.logger.stop()
-part_path, *_ = msh_conversion(part_geo.mesh_abs_path, ".xdmf")
+part_path, = msh_conversion(part_geo.mesh_abs_path, ".xdmf")
 
 # * Step 4 : Defining the material properties
 E, nu = 1.0, 0.3

ho_homog/toolbox_FEniCS.py

@@ -292,7 +292,7 @@ def xdmf_mesh(mesh_file, import_subdomains=False, facet_file="", physical_file="
         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_function = fe.cpp.mesh.MeshFunctionSizet(mesh, facet_vc)
+        facet_regions = fe.cpp.mesh.MeshFunctionSizet(mesh, facet_vc)
     if not physical_file.exists():
         subdomains = None
     else:

ho_homog/toolbox_gmsh.py

@@ -44,7 +44,7 @@ def process_gmsh_log(gmsh_log: list, detect_error=True):
 
 
 def msh_conversion(
-    mesh, format_: str = ".xdmf", output_dir=None, subdomain: bool = False, dim: int = 2
+    mesh, format_: str = ".xdmf", output_dir=None, subdomains: bool = False, dim: int = 2
 ):
     """
     Convert a ".msh" mesh generated with Gmsh to a format suitable for FEniCS.
@@ -62,7 +62,7 @@ def msh_conversion(
         Path of the directory where the converted mesh file must be written.
         If None, the converted file is written in the same directory
         as the input file. (default: None)
-    subdomain : bool, optional
+    subdomains : bool, optional
         If True, extra files are created to store information about subdomains.
         (default: False)
     dim: int, optional
@@ -118,7 +118,7 @@ def msh_conversion(
         else:
             ValueError
         meshio.write(str(mesh_path), geo_only)
-        if subdomain:
+        if subdomains:
             cell_function = meshio.Mesh(
                 points=mesh.points,
                 cells={cell: mesh.cells[cell]},
@@ -131,11 +131,11 @@ def msh_conversion(
                 cell_data={face: {"facet_data": mesh.cell_data[face]["gmsh:physical"]}},
             )
             meshio.write(str(facet_region), facet_function)
-    if subdomain:
+    if subdomains:
         return (
             mesh_path,
-            physical_region if physical_region.exist() else None,
-            facet_region if facet_region.exist() else None,
+            physical_region if physical_region.exists() else None,
+            facet_region if facet_region.exists() else None,
         )
     else:
         return mesh_path