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Original commit for this change: 0b6c4d15

The periodicity vectors must correspond to the columns of the matrix `cell_vect` provided.

[ ] Improve reconstruction
[ ] Cleaning in `part.py`
[ ] Doc for PeriodicDomain

Situation : when two 1D entities of the microstructure boundary have the same endpoints but only one is actually on the border of the unit cell. The second 1D entity can be an circular arc.
E.g.  `pantograph_RVE(1, 1, 1/3, junction_r=r, offset=(0.05, 0.0))`

Remove all the physical groups from the model except those representing the part.
Reason ? Delete the physical groups that may be used when defining the RVE for splitting/cutting the RVE into several parts.

Gmsh2DPartFromRVE : This function can now be used even when the RVE contains several domains.
pantograph_E11only_RVE : Modified to avoid creating a geometry  with junctions two times thinner on the horizontal borders.

Removing of the corresponding staticmethod from the Gmsh2DRVE class

New cells : only pantographic effect, no shear floppy mode

+ Split generate_mesh_2D
+ Offset functions (WIP)

Change name of boolean operations;
Correction name of plot functions;

Limitations (for the moment) : macro domain must be parallelogram /  parallelepiped with axes aligned with cell periodicity directions; no offset between the origins of the RVE and part coordinate systems.
Test, only for 2D geometry, and demo for pantograph (generate mesh, full scale solving, homogenization then comparison);
+ Black;
+ Activate/Deactivate physical group visibility in gmsh model;
+ Function for mesh conversion .msh -> .xmdf or .xml.

EGG scheme, pantograph microstructure, 1×1 RVE.
Support import of xdmf mesh for RVE definition.

Trailing spaces / empty lines / spaces/try-except conventions + change behavior of gemetry reset function.

Reorganizing and simplifying the logging.  One logger per homog file and only 2 handlers which are associated to the root logger.

fields attribute of is now set to a default value during the initialization of a Gmsh2DRVE instance.

Weak material domain of the RVE is now obtained by a boolean cutting operation and not an intersection anymore.\n
Static method to get the boundary of a group of surfaces seen as a single entity.\n
Mesh refinement methods have been consequently corrected. \n

The static method gmsh_2_Fenics_2DRVE that create FEniCS objetcs from gmsh objects has been completed. \nBasic tests with plots. \nIn addition to the mesh, physical regions and facets regions are imported.

Option Mesh.SaveAll has to be set to 1, otherwise the conversion with dolfin-convert fails.
New set_gmsh_option() function for more consistent changes of gmsh options.

Test of this function succeeded.

pantograph, auxetic squares and pantograph of beams.