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geometry

Abstract Base Interface for Geometry and Mesh Operations.

This module provides the base interface for implementing geometry and mesh handling capabilities in both 2D and 3D. It defines the essential structure for mesh operations including reading, generation, and manipulation.

Key functionalities
  • Abstract interface for mesh reading operations
  • Common mesh generation method definitions
  • VTK file generation specifications
  • Test point extraction framework
  • Mesh type and generation method standardization
The module serves as a foundation for
  • Both 2D and 3D mesh implementations
  • Various element type support
  • Multiple mesh generation approaches
  • Consistent mesh handling interface
Key classes
  • Geometry: Abstract base class for all geometry implementations
Dependencies
  • numpy: For numerical operations
  • meshio: For mesh input/output operations
  • gmsh: For mesh generation capabilities
  • matplotlib: For visualization
  • pyDOE: For sampling methods
  • abc: For abstract base class functionality
Note

This module provides only the interface definitions. Concrete implementations must be provided by derived classes for specific dimensional and element type requirements.

Geometry

Abstract base class for geometry and mesh operations.

This class defines the interface that all geometry implementations must follow, providing the basic structure for mesh handling operations in both 2D and 3D contexts.

Attributes:

Name Type Description
mesh_type

Type of mesh elements (e.g., 'quadrilateral', 'triangle')
mesh_generation_method

Method for mesh generation ('internal'/'external')
Example

class Geometry2D(Geometry): ... def init(self, mesh_type='quadrilateral', ... method='internal'): ... super().init(mesh_type, method) ... ... def read_mesh(self, mesh_file, boundary_level, ... sampling_method, refine_level): ... # Implementation ... pass ... ... def generate_vtk_for_test(self): ... # Implementation ... pass ... ... def get_test_points(self): ... # Implementation ... return points

Note

This is an abstract base class. Concrete implementations must override: - read_mesh() - generate_vtk_for_test() - get_test_points()

Each implementation should provide appropriate mesh handling for its specific dimensional and element type requirements.

Source code in scirex/core/sciml/geometry/geometry.py 
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class Geometry:
    """Abstract base class for geometry and mesh operations.

    This class defines the interface that all geometry implementations must
    follow, providing the basic structure for mesh handling operations in
    both 2D and 3D contexts.

    Attributes:
        mesh_type: Type of mesh elements (e.g., 'quadrilateral', 'triangle')
        mesh_generation_method: Method for mesh generation ('internal'/'external')

    Example:
        >>> class Geometry2D(Geometry):
        ...     def __init__(self, mesh_type='quadrilateral',
        ...                  method='internal'):
        ...         super().__init__(mesh_type, method)
        ...
        ...     def read_mesh(self, mesh_file, boundary_level,
        ...                   sampling_method, refine_level):
        ...         # Implementation
        ...         pass
        ...
        ...     def generate_vtk_for_test(self):
        ...         # Implementation
        ...         pass
        ...
        ...     def get_test_points(self):
        ...         # Implementation
        ...         return points

    Note:
        This is an abstract base class. Concrete implementations must override:
        - read_mesh()
        - generate_vtk_for_test()
        - get_test_points()

        Each implementation should provide appropriate mesh handling for its
        specific dimensional and element type requirements.
    """

    def __init__(self, mesh_type: str, mesh_generation_method: str):
        """
        Constructor for the Geometry class.

        Args:
            mesh_type: Type of mesh elements (e.g., 'quadrilateral', 'triangle')
            mesh_generation_method: Method for mesh generation ('internal'/'external')

        Returns:
            None
        """
        self.mesh_type = mesh_type
        self.mesh_generation_method = mesh_generation_method

    @abstractmethod
    def read_mesh(
        self,
        mesh_file: str,
        boundary_point_refinement_level: int,
        bd_sampling_method: str,
        refinement_level: int,
    ):
        """
        Abstract method to read mesh from Gmsh. This method should be implemented by the derived classes.

        Args:
            mesh_file (str): Path to the mesh file
            boundary_point_refinement_level (int): Level of refinement for boundary points
            bd_sampling_method (str): Sampling method for boundary points
            refinement_level (int): Level of mesh refinement

        Returns:
            None
        """

    @abstractmethod
    def generate_vtk_for_test(self):
        """
        Generates a VTK from Mesh file (External) or using gmsh (for Internal).

        Args:
        None

        Returns:
        None
        """

    @abstractmethod
    def get_test_points(self):
        """
        This function is used to extract the test points from the given mesh

        Args:
            None

        Returns:
            points (np.ndarray): Test points extracted from the mesh
        """

__init__(mesh_type, mesh_generation_method)

Constructor for the Geometry class.

Parameters:

Name Type Description Default
mesh_type str

Type of mesh elements (e.g., 'quadrilateral', 'triangle')

 required
mesh_generation_method str

Method for mesh generation ('internal'/'external')

 required

Returns:

Type Description

None
Source code in scirex/core/sciml/geometry/geometry.py 
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def __init__(self, mesh_type: str, mesh_generation_method: str):
    """
    Constructor for the Geometry class.

    Args:
        mesh_type: Type of mesh elements (e.g., 'quadrilateral', 'triangle')
        mesh_generation_method: Method for mesh generation ('internal'/'external')

    Returns:
        None
    """
    self.mesh_type = mesh_type
    self.mesh_generation_method = mesh_generation_method

generate_vtk_for_test() abstractmethod

Generates a VTK from Mesh file (External) or using gmsh (for Internal).

Args: None

Returns: None

Source code in scirex/core/sciml/geometry/geometry.py 
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@abstractmethod
def generate_vtk_for_test(self):
    """
    Generates a VTK from Mesh file (External) or using gmsh (for Internal).

    Args:
    None

    Returns:
    None
    """

get_test_points() abstractmethod

This function is used to extract the test points from the given mesh

Returns:

Name Type Description
points ndarray

Test points extracted from the mesh
Source code in scirex/core/sciml/geometry/geometry.py 
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@abstractmethod
def get_test_points(self):
    """
    This function is used to extract the test points from the given mesh

    Args:
        None

    Returns:
        points (np.ndarray): Test points extracted from the mesh
    """

read_mesh(mesh_file, boundary_point_refinement_level, bd_sampling_method, refinement_level) abstractmethod

Abstract method to read mesh from Gmsh. This method should be implemented by the derived classes.

Parameters:

Name Type Description Default
mesh_file str

Path to the mesh file

 required
boundary_point_refinement_level int

Level of refinement for boundary points

 required
bd_sampling_method str

Sampling method for boundary points

 required
refinement_level int

Level of mesh refinement

 required

Returns:

Type Description

None
Source code in scirex/core/sciml/geometry/geometry.py 
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@abstractmethod
def read_mesh(
    self,
    mesh_file: str,
    boundary_point_refinement_level: int,
    bd_sampling_method: str,
    refinement_level: int,
):
    """
    Abstract method to read mesh from Gmsh. This method should be implemented by the derived classes.

    Args:
        mesh_file (str): Path to the mesh file
        boundary_point_refinement_level (int): Level of refinement for boundary points
        bd_sampling_method (str): Sampling method for boundary points
        refinement_level (int): Level of mesh refinement

    Returns:
        None
    """