GITRmProject - gmsh_automated_scripts

Hi User! As part of the effort to automate the workflow of DiMES local impurity transport simulations at DIII-D using the GITRm transport code, we propose a tool that generates meshes for simple DiMES geometries using the gmsh Python API. This user-friendly tool allows anyone to easily simulate their preferred DiMES setup without the need to manually draw and mesh the geometry each time.

Dependecies

This package was tested using pyhton version >= 3.10, gmsh version 4.13.1 and requires the math package

Build

This package was built using poetry , if you don't know what poetry is please check out: https://python-poetry.org/. Also, a short tutorial on how to use poetry with conda or mamba is provided in the wiki: https://github.com/DIII-D/GITRmProject/wiki/Use-gmsh-scripts--with-poetry

Documentation

The package consists of two files encoding all functions needed to run generate_dimes_mesh(input_dict,**kwargs)

generate_dimes_mesh(input_dict,**kwargs) automatically generates the DiMES mesh for a given input.

PARAMETERS: (KEYWORDS DESCRIPTION IS AFTER kwargs)

• input_dict: A dictionary containing the geometries of the dots to be simulated, where each dot is defined by a unique label followed by its properties.

• kwargs: Additional keyword arguments. Supported keywords include:

  • x_center_dimes: The X-coordinate of the center of the DiMES base (float, default: 0).
  • y_center_dimes: The Y-coordinate of the center of the DiMES base (float, default: 0).
  • z_top_dimes: The Z-coordinate of the center of the DiMES base (float, default: 0).
  • r_dimes: The radius of the DiMES base (float, default: 2.5).
  • x_center: The X-coordinate of the plasma volume base surface center (float, default: 0).
  • y_center: The Y-coordinate of the plasma volume base surface center (float, default: 0).
  • z_center: The Z-coordinate of the plasma volume base surface center (float, default: 0).
  • l_radial: The extent of plasma volume in the radial direction (half-length, float, default: 8).
  • l_toroidal: The extent of plasma volume in the toroidal direction (half-length, float, default: 8).
  • l_vertical: The extentof plasma volume in the vertical direction (float, default: 8).
  • ax: The X-component of the rotation axis (float, default: 0).
  • ay: The Y-component of the rotation axis (float, default: -1).
  • az: The Z-component of the rotation axis (float, default: 0).
  • msh_dim: The dimension of the mesh, which can be 1D, 2D, or 3D (int, default: 3).
  • filename: The name of the mesh file to be generated (string, default: "test.msh").
  • save_msh: A flag indicating whether to save the mesh (bool, default: False).
  • GUI_geo: A flag to use a GUI for visualizing the geometry before meshing (bool, default: False).
  • GUI_msh: A flag to use a GUI for visualizing both geometry and mesh (bool, default: True).
  • no_dots: A flag to remove all coatings (bool, default: False).

GEOMETRY KEYWORDS:

The DiMES geometry can take one of the following shapes:

• disk (DiMES head flushed with lower divertor)
• cylinder (DiMES head protruding in the plasma but top face still parallel to divertor)
• truncated cylinder (DiMES head tilted)

On top of the DiMES head different coatings can be added as discussed later.

The DiMES geometry is defined by its center and radius:

• x_center_dimes: The X-coordinate of the center of the DiMES base (float).
• y_center_dimes: The Y-coordinate of the center of the DiMES base (float).
• z_top_dimes: The Z-coordinate of the center of the DiMES base (float).
• r_dimes: The radius of the DiMES base (float).
• theta_dimes: Tilting angle
• ax, ay ,az: components of rotation' direction (gmsh rotates objects using Rodrigues formula)'

Right now only the following 4 directions are allowed:

ax = ± 1, ay = 0, az = 0
ax = 0, ay = ± 1, az = 0

Plasma Volume:

The DiMES geometry is enclosed within a volume known as plasma_volume, representing the plasma background. This volume is a symmetrical box extending in three directions:

• x_center: The X-coordinate of the plasma volume center (float).
• y_center: The Y-coordinate of the plasma volume center (float).
• z_center: The Z-coordinate of the plasma volume center (float).

The plasma volume extends symmetrically in these directions:

• l_radial: Twice the radial extent of the volume (float).
• l_toroidal: Twice the toroidal extent of the volume (float).
• l_vertical: The vertical extent of the volume (float).

Dots (Material Coatings):

On the DiMES top surface, dots represent the material coatings. Two geometries are currently supported:

• circle
• rectangle

Each dot's position and dimensions are specified within an input_dict dictionary. The user must manually create this dictionary, where each dot is defined by a unique label followed by values that describe its geometry, shape, and position.

Each dot can be tilted around the same rotation axis as DiMES, identified by its components (ax, ay, az) and the angle theta_dot (deg).

theta_dot can be set in the input_dict, as shown later.

NOTE: tilting both DiMES head and dots can result in wrong geometry and mesh generation! Try to avoid it.

Right now only the following 4 directions are allowed:

ax = ± 1, ay = 0, az = 0
ax = 0, ay = ± 1, az = 0

Example Input Dictionary:

This example illustrates the structure for two dots: one circle and one rectangle.

Names = ["Dot_1", "Dot_2"]

input_dict = {
    Names[0]: {
        "shape": "circle",
        "x": 0,
        "y": 0.75,
        "radius": 0.05  # Radius for the circle
        "theta_dot": 10
    },
    Names[1]: {
        "shape": "rectangle",
        "x": -0.5,
        "y": -0.25,
        "width": 1,    # Width of the rectangle
        "height": 0.5  # Height of the rectangle
        "theta_dot": 5
    }
    # Additional dots can be added as needed
}

Each dot has the following properties:

• x: The X-coordinate of the dot’s position on the DiMES top surface (float).
• y: The Y-coordinate of the dot’s position on the DiMES top surface (float).

For "Dot_1" (shape: "circle"), the x and y coordinates represent the center of the circle, and the radius defines its size.

For "Dot_2" (shape: "rectangle"), the x and y coordinates denote the lower-left corner of the rectangle, while the following values define its size:

• width: The width of the rectangle (float).
• height: The height of the rectangle (float).

Rotation:

The entire DiMES top surface and dots can be rotated by an angle theta_dimes (in degrees) relative to a direction defined by the unit vector components:

• ax: The X-component of the rotation axis (float).
• ay: The Y-component of the rotation axis (float).
• az: The Z-component of the rotation axis (float).

Right now only the following 4 directions are allowed:

ax = ± 1, ay = 0, az = 0
ax = 0, ay = ± 1, az = 0

if you pick other directions the code will produce an error. If requested, the feature of rotating around any direction will be added in future releases.

To make a DiMES head with no coatings you can simply set the no_dots flag:

• no_dots: A flag to remove all coatings (bool, default: False).

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MESH KEYWORDS:

Before generating the mesh, users can configure several options:

• msh_dim: The dimension of the mesh. It can be 1D, 2D, or 3D (int).

• filename: The name of the generated mesh file (e.g., "test.msh"; string).

• save_msh: A flag indicating whether to save the mesh file.

  • True: Save the mesh file.
  • False: Do not save the mesh file.

• GUI_geo: A flag to visualize the geometry before meshing using a graphical interface.

  • True: Use the GUI for geometry visualization.
  • False: Do not use the GUI.

• GUI_msh: A flag to visualize both the geometry and mesh using a graphical interface.

  • True: Use the GUI for both geometry and mesh visualization.
  • False: Do not use the GUI.