Merge pull request #72 from sigma-epsilon/nightly

Nightly

pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "sigmaepsilon.mesh"
-version = "2.1.0"
+version = "2.2.0"
 description = "A Python package to build, manipulate and analyze polygonal meshes."
 classifiers=[
         "Development Status :: 5 - Production/Stable",

requirements.txt

@@ -3,4 +3,5 @@ sigmaepsilon.deepdict >=1.2.1, < 2.0.0
 sigmaepsilon.math >= 1.0.1
 fsspec >= 2023.1.0  # to use awkward.to_parquet
 sectionproperties >= 2.1.3
-meshio
+meshio
+triangle

src/sigmaepsilon/mesh/cellapproximator.py

@@ -44,17 +44,19 @@ def _approximator(
     if shp_source_inverse is None:
         assert isinstance(x_source, Iterable)
         shp_source = shp_fnc(x_source)  # (nP_source, nNE)
-        
+
         num_rows, num_columns = shp_source.shape
         rank = np.linalg.matrix_rank(shp_source)
-        square_and_full_rank = (num_rows == num_columns) and rank == num_columns == num_rows
+        square_and_full_rank = (
+            num_rows == num_columns
+        ) and rank == num_columns == num_rows
         if not square_and_full_rank:  # pragma: no cover
             warnings.warn(
                 "The approximation involves the calculation of a generalized inverse "
                 "which probably results in loss of precision.",
-                SigmaEpsilonPerformanceWarning
+                SigmaEpsilonPerformanceWarning,
             )
-        
+
         shp_source_inverse = generalized_inverse(shp_source)
 
     if not isinstance(values_source, ndarray):

src/sigmaepsilon/mesh/cells/__init__.py

@@ -7,7 +7,7 @@
 from .t3 import T3 as Tri
 from .q4 import Q4
 from .q4 import Q4 as Quad
-from.q8 import Q8
+from .q8 import Q8
 from .q9 import Q9
 from .t6 import T6
 from .h8 import H8

src/sigmaepsilon/mesh/cells/h27.py

@@ -1,21 +1,19 @@
 from typing import Tuple, List
+from functools import partial
+
 import numpy as np
 from numpy import ndarray
 import sympy as sy
 
-from sigmaepsilon.math.numint import gauss_points as gp
-
 from ..geometry import PolyCellGeometry3d
 from ..data.polycell import PolyCell
-from ..utils.utils import cells_coords
 from ..utils.cells.h27 import (
     shp_H27_multi,
     dshp_H27_multi,
-    volumes_H27,
     shape_function_matrix_H27_multi,
     monoms_H27,
 )
-from ..utils.cells.numint import Gauss_Legendre_Hex_Grid
+from ..utils.numint import Gauss_Legendre_Hex_Grid
 
 
 class H27(PolyCell):
@@ -56,7 +54,8 @@ class Geometry(PolyCellGeometry3d):
         shape_function_derivative_evaluator: dshp_H27_multi
         monomial_evaluator: monoms_H27
         quadrature = {
-            "full": Gauss_Legendre_Hex_Grid(3, 3, 3),
+            "full": partial(Gauss_Legendre_Hex_Grid, 3, 3, 3),
+            "geometry": "full",
         }
 
         @classmethod
@@ -155,17 +154,3 @@ def master_center(cls) -> ndarray:
             numpy.ndarray
             """
             return np.array([0.0, 0.0, 0.0])
-
-    def volumes(self) -> ndarray:
-        """
-        Returns the volumes of the cells.
-
-        Returns
-        -------
-        numpy.ndarray
-        """
-        coords = self.source_coords()
-        topo = self.topology().to_numpy()
-        ecoords = cells_coords(coords, topo)
-        qpos, qweight = gp(3, 3, 3)
-        return volumes_H27(ecoords, qpos, qweight)

src/sigmaepsilon/mesh/cells/h8.py

@@ -1,22 +1,19 @@
 from typing import Tuple, List
+from functools import partial
 
 from sympy import symbols
 import numpy as np
 from numpy import ndarray
 
-from sigmaepsilon.math.numint import gauss_points as gp
-
 from ..geometry import PolyCellGeometry3d
 from ..data.polycell import PolyCell
-from ..utils.utils import cells_coords
 from ..utils.cells.h8 import (
     shp_H8_multi,
     dshp_H8_multi,
-    volumes_H8,
     shape_function_matrix_H8_multi,
     monoms_H8,
 )
-from ..utils.cells.numint import Gauss_Legendre_Hex_Grid
+from ..utils.numint import Gauss_Legendre_Hex_Grid
 
 
 class H8(PolyCell):
@@ -46,7 +43,8 @@ class Geometry(PolyCellGeometry3d):
         shape_function_derivative_evaluator: dshp_H8_multi
         monomial_evaluator: monoms_H8
         quadrature = {
-            "full": Gauss_Legendre_Hex_Grid(2, 2, 2),
+            "full": partial(Gauss_Legendre_Hex_Grid, 2, 2, 2),
+            "geometry": "full",
         }
 
         @classmethod
@@ -104,17 +102,3 @@ def tetmap(cls) -> np.ndarray:
                 [[1, 2, 0, 5], [3, 0, 2, 7], [5, 4, 7, 0], [6, 5, 7, 2], [0, 2, 7, 5]],
                 dtype=int,
             )
-
-    def volumes(self) -> ndarray:
-        """
-        Returns the volumes of the cells.
-
-        Returns
-        -------
-        numpy.ndarray
-        """
-        coords = self.source_coords()
-        topo = self.topology().to_numpy()
-        ecoords = cells_coords(coords, topo)
-        qpos, qweight = gp(2, 2, 2)
-        return volumes_H8(ecoords, qpos, qweight)

src/sigmaepsilon/mesh/cells/l2.py

@@ -1,4 +1,6 @@
 # -*- coding: utf-8 -*-
+from functools import partial
+
 from ..geometry import PolyCellGeometry1d
 from ..data.polycell import PolyCell
 from ..utils.cells.l2 import (
@@ -7,7 +9,7 @@
     shape_function_matrix_L2_multi,
     monoms_L2,
 )
-from ..utils.cells.numint import Gauss_Legendre_Line_Grid
+from ..utils.numint import Gauss_Legendre_Line_Grid
 
 __all__ = ["L2"]
 
@@ -25,5 +27,6 @@ class Geometry(PolyCellGeometry1d):
         shape_function_derivative_evaluator: dshp_L2_multi
         monomial_evaluator: monoms_L2
         quadrature = {
-            "full": Gauss_Legendre_Line_Grid(2),
+            "full": partial(Gauss_Legendre_Line_Grid, 2),
+            "geometry": "full",
         }

src/sigmaepsilon/mesh/cells/l3.py

@@ -1,7 +1,9 @@
 # -*- coding: utf-8 -*-
+from functools import partial
+
 from ..geometry import PolyCellGeometry1d
 from ..data.polycell import PolyCell
-from ..utils.cells.numint import Gauss_Legendre_Line_Grid
+from ..utils.numint import Gauss_Legendre_Line_Grid
 from ..utils.cells.l3 import monoms_L3
 
 
@@ -18,5 +20,6 @@ class Geometry(PolyCellGeometry1d):
         vtk_cell_id = 21
         monomial_evaluator: monoms_L3
         quadrature = {
-            "full": Gauss_Legendre_Line_Grid(3),
+            "full": partial(Gauss_Legendre_Line_Grid, 3),
+            "geometry": "full",
         }

src/sigmaepsilon/mesh/cells/q4.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 from typing import Tuple, List
+
 import numpy as np
 from numpy import ndarray
 from sympy import symbols
@@ -12,7 +13,7 @@
     shape_function_matrix_Q4_multi,
     monoms_Q4,
 )
-from ..utils.cells.numint import Gauss_Legendre_Quad_4
+from ..utils.numint import Gauss_Legendre_Quad_4
 from ..utils.topology import Q4_to_T3
 
 
@@ -31,7 +32,8 @@ class Geometry(PolyCellGeometry2d):
         shape_function_derivative_evaluator: dshp_Q4_multi
         monomial_evaluator: monoms_Q4
         quadrature = {
-            "full": Gauss_Legendre_Quad_4(),
+            "full": Gauss_Legendre_Quad_4,
+            "geometry": "full",
         }
 
         @classmethod

src/sigmaepsilon/mesh/cells/q8.py

@@ -1,4 +1,5 @@
 from typing import Tuple, List
+
 import numpy as np
 from numpy import ndarray
 from sympy import symbols
@@ -11,7 +12,7 @@
     shape_function_matrix_Q8_multi,
     monoms_Q8,
 )
-from ..utils.cells.numint import Gauss_Legendre_Quad_9
+from ..utils.numint import Gauss_Legendre_Quad_9
 from ..utils.topology import Q8_to_T3, trimap_Q8
 
 
@@ -30,7 +31,8 @@ class Geometry(PolyCellGeometry2d):
         shape_function_derivative_evaluator: dshp_Q8_multi
         monomial_evaluator: monoms_Q8
         quadrature = {
-            "full": Gauss_Legendre_Quad_9(),
+            "full": Gauss_Legendre_Quad_9,
+            "geometry": "full",
         }
 
         @classmethod

src/sigmaepsilon/mesh/cells/q9.py

@@ -1,4 +1,5 @@
 from typing import Tuple, List
+
 import numpy as np
 from numpy import ndarray
 from sympy import symbols
@@ -11,7 +12,7 @@
     shape_function_matrix_Q9_multi,
     monoms_Q9,
 )
-from ..utils.cells.numint import Gauss_Legendre_Quad_9
+from ..utils.numint import Gauss_Legendre_Quad_9
 from ..utils.topology import Q4_to_T3, Q9_to_Q4
 
 
@@ -30,7 +31,8 @@ class Geometry(PolyCellGeometry2d):
         shape_function_derivative_evaluator: dshp_Q9_multi
         monomial_evaluator: monoms_Q9
         quadrature = {
-            "full": Gauss_Legendre_Quad_9(),
+            "full": Gauss_Legendre_Quad_9,
+            "geometry": "full",
         }
 
         @classmethod

src/sigmaepsilon/mesh/cells/t3.py

@@ -1,12 +1,13 @@
 # -*- coding: utf-8 -*-
 from typing import Tuple, List
+
 import numpy as np
 from numpy import ndarray
 from sympy import symbols
 
 from ..geometry import PolyCellGeometry2d
 from ..data.polycell import PolyCell
-from ..utils.cells.numint import Gauss_Legendre_Tri_1
+from ..utils.numint import Gauss_Legendre_Tri_1
 from ..utils.cells.t3 import (
     shp_T3_multi,
     dshp_T3_multi,
@@ -20,6 +21,17 @@
 class T3(PolyCell):
     """
     A class to handle 3-noded triangles.
+
+    Example
+    -------
+    >>> from sigmaepsilon.mesh import TriMesh, CartesianFrame, PointData, triangulate
+    >>> from sigmaepsilon.mesh.cells import T3 as CellData
+    >>> A = CartesianFrame(dim=3)
+    >>> coords, topo = triangulate(size=(800, 600), shape=(10, 10))
+    >>> pd = PointData(coords=coords, frame=A)
+    >>> cd = CellData(topo=topo)
+    >>> trimesh = TriMesh(pd, cd)
+    >>> trimesh.area()
     """
 
     label = "T3"
@@ -32,11 +44,16 @@ class Geometry(PolyCellGeometry2d):
         shape_function_derivative_evaluator: dshp_T3_multi
         monomial_evaluator: monoms_T3
         quadrature = {
-            "full": Gauss_Legendre_Tri_1(),
+            "full": Gauss_Legendre_Tri_1,
+            "geometry": "full",
         }
 
         @classmethod
         def trimap(cls) -> ndarray:
+            """
+            Returns a mapping used to transform the topology to triangles.
+            This is only implemented here for standardization.
+            """
             return np.array([[0, 1, 2]], dtype=int)
 
         @classmethod
@@ -58,36 +75,46 @@ def polybase(cls) -> Tuple[List]:
         @classmethod
         def master_coordinates(cls) -> ndarray:
             """
-            Returns local coordinates of the cell.
+            Returns local coordinates of the master cell relative to the origo
+            of the master cell.
 
             Returns
             -------
             numpy.ndarray
             """
-            return np.array([[0.0, 0.0], [1.0, 0.0], [0.0, 1.0]])
+            return np.array([[-1 / 3, -1 / 3], [2 / 3, -1 / 3], [-1 / 3, 2 / 3]])
 
         @classmethod
         def master_center(cls) -> ndarray:
             """
-            Returns the local coordinates of the center of the cell.
+            Returns the center of the master cell relative to the origo
+            of the master cell.
 
             Returns
             -------
             numpy.ndarray
             """
-            return np.array([[1 / 3, 1 / 3]])
+            return np.array([[0.0, 0.0]], dtype=float)
 
     def to_triangles(self) -> ndarray:
+        """
+        Returns the topology as triangles.
+        """
         return self.topology().to_numpy()
 
-    def areas(self, *args, **kwargs) -> ndarray:
+    def areas(self, *_, **__) -> ndarray:
+        """
+        Returns the areas of the cells as an 1d NumPy array.
+        """
         coords = self.container.source().coords()
         topo = self.topology().to_numpy()
         ec = points_of_cells(coords, topo, local_axes=self.frames)
         return area_tri_bulk(ec)
 
     @classmethod
-    def from_TriMesh(cls, *args, coords=None, topo=None, **kwargs):
+    def from_TriMesh(
+        cls, *args, coords: ndarray = None, topo: ndarray = None, **__
+    ) -> Tuple[ndarray, ndarray]:
         from sigmaepsilon.mesh.data.trimesh import TriMesh
 
         if len(args) > 0 and isinstance(args[0], TriMesh):