GMSH workflow #885
GMSH workflow #885
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added GMSH workflow
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Thanks @celyneira for this great contribution! As you can see on this link the documentation didn't compile properly:
https://festim--885.org.readthedocs.build/en/885/userguide/mesh.html#meshes-from-gmsh
I've added a bunch of comments with corrections.
You can alos check that the docs compile correctly locally by following the Documentation Guide
docs/source/userguide/mesh.rst
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| The Python API of GMSH can be used to create meshes that are useable in FESTIM. Here we will walk through its usage when creating a monoblock subsection consisting of tungsten surrounding a tube of CuCrZr | ||
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| <img width="948" alt="Screenshot 2024-09-11 at 17 09 10" src="https://github.com/user-attachments/assets/1ec52a67-840d-4ef8-a741-a79f0e2c1cc3"> |
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For images, please add them to the images folder and then add them to the documentation like this:
.. thumbnail:: ../images/path_to_your_image.png
:width: 400
:align: center
docs/source/userguide/mesh.rst
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| ``` | ||
| import gmsh as gmsh | ||
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| gmsh.initialize() | ||
| gmsh.model.add("mesh") | ||
| ``` |
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For code blocks, please use the same syntax as elsewhere in this file:
.. code-block:: python
your code goes here with an indent
This is not needed for inline code.
docs/source/userguide/mesh.rst
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| gmsh.model.addPhysicalGroup(2, [7, 10], front_id, name = "front") | ||
| gmsh.model.addPhysicalGroup(2, [6, 9], back_id, name = "back") | ||
| gmsh.model.addPhysicalGroup(2, [1], left_id, name = "left") | ||
| gmsh.model.addPhysicalGroup(2, [3], right_id, name = "right") | ||
| gmsh.model.addPhysicalGroup(2, [4], top_id, name = "top") | ||
| gmsh.model.addPhysicalGroup(2, [2], bottom_id, name = "bottom") | ||
| gmsh.model.addPhysicalGroup(2, [5], outer_cylinder_surface_id, name = "outer_cylinder") | ||
| gmsh.model.addPhysicalGroup(2, [8], inner_cylinder_surface_id, name = "inner_cylinder") | ||
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| gmsh.model.addPhysicalGroup(3,[1], tungsten_id, name = "tungsten") | ||
| gmsh.model.addPhysicalGroup(3, [2], cucrzr_id, name = "cucrzr") |
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can we also tag the interfaces?
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the inner and outer cylinder surfaces are the interfaces but i've renamed them for clarity
docs/source/userguide/mesh.rst
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| ``` | ||
| We have now created our mesh! | ||
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| However, for use in FESTIM, our mesh now has to be converted into XDMF files, and the surfaces and volume IDs extracted. |
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We could have a subsection heading here. The guide could be divided in two: 1) meshing the geometry 2) converting with meshio
docs/source/userguide/mesh.rst
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| import festim as F | ||
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| model = F.Simulation() | ||
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| model.mesh = F.MeshFromXDMF(volume_file ="volume_mesh.xdmf", boundary_file = "surface_mesh.xdmf") | ||
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| model.materials = [F.Material(id=1, D_0=1, E_D=0), | ||
| F.Material(id=2, D_0=5, E_D=0)] | ||
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| model.T = F.Temperature(800) | ||
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| model.boundary_conditions = [F.DirichletBC(surfaces = [top_id], value = 1, field = 0), | ||
| F.DirichletBC(surfaces = [inner_cylinder_surface_id], value = 0, field = 0)] | ||
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| model.exports = [F.XDMFExport("solute")] | ||
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| model.settings = F.Settings( | ||
| absolute_tolerance=1e-10, | ||
| relative_tolerance=1e-10, | ||
| transient=False, | ||
| ) | ||
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| model.initialise() | ||
| model.run() | ||
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can you format this code using black please?
| Meshes from GMSH | ||
| ---------------- |
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This can actually go replace the GMSH section instead
| - Points | ||
| - Lines | ||
| - Wires / Curve Loops | ||
| - whether we use curve loops or wires depends on whether we use the `.occ` or `.geo` geometry kernels. `.occ` allows for direct construction of more complex features such as cylinders, whereas using `.geo` requires explicit user definition of all the points, surfaces and volumes that would make up the cylinder. | ||
| - Surfaces | ||
| - Surface Loops | ||
| - Volumes |
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In the docs this doesn't seem to compile correctly, maybe it needs a blank line before the first bullet
| Meshing the geometry with GMSH | ||
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ||
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| Firstly, GMSH must be imported and initialised. |
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Can we add a .. note:: on how to install GMSH?
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| A FESTIM simulation can then be run: | ||
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| .. code-block:: bash |
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| .. code-block:: bash | |
| .. code-block:: python |
added GMSH workflow
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