Merge pull request #14 from GeoStat-Framework/remove_pygmesh

remove pygmsh support

Author: MuellerSeb

CHANGELOG.md

@@ -3,6 +3,15 @@
 All notable changes to **ogs5py** will be documented in this file.
 
 
+## [1.2.1] - 2020-05-15
+
+### Enhancements
+* `MSH.import_mesh` can handle `meshio.Mesh` as input now [#13](https://github.com/GeoStat-Framework/ogs5py/pull/13)
+
+### Changes
+* `pygmsh` support was removed. You can't use pygmsh Geometry objects to generate meshes anymore. Please generate beforehand and import the generated mesh. Other generators are using `gmsh` directly now. [#13](https://github.com/GeoStat-Framework/ogs5py/pull/13)
+
+
 ## [1.2.0] - 2020-05-15
 
 ### Enhancements
@@ -169,7 +178,8 @@ All notable changes to **ogs5py** will be documented in this file.
 First release of ogs5py.
 
 
-[Unreleased]: https://github.com/GeoStat-Framework/ogs5py/compare/v1.2.0...HEAD
+[Unreleased]: https://github.com/GeoStat-Framework/ogs5py/compare/v1.2.1...HEAD
+[1.2.1]: https://github.com/GeoStat-Framework/ogs5py/compare/v1.2.0...v1.2.1
 [1.2.0]: https://github.com/GeoStat-Framework/ogs5py/compare/v1.1.1...v1.2.0
 [1.1.1]: https://github.com/GeoStat-Framework/ogs5py/compare/v1.1.0...v1.1.1
 [1.1.0]: https://github.com/GeoStat-Framework/ogs5py/compare/v1.0.5...v1.1.0

docs/source/tutorial_03_gmsh.rst

@@ -2,38 +2,43 @@ Tutorial 2: Interaction with pygmsh
 ===================================
 
 In this example we are generating different meshes with the aid of
-`pygmsh <https://github.com/nschloe/pygmsh>`_..
+`pygmsh <https://github.com/nschloe/pygmsh>`_ and `gmsh <https://gmsh.info>`_
 
 .. code-block:: python
 
     import numpy as np
-    from ogs5py import OGS
     import pygmsh
 
-    geom = pygmsh.built_in.Geometry()
-    poly = geom.add_polygon([
-        [ 0.0,  0.5, 0.0],
-        [-0.1,  0.1, 0.0],
-        [-0.5,  0.0, 0.0],
-        [-0.1, -0.1, 0.0],
-        [ 0.0, -0.5, 0.0],
-        [ 0.1, -0.1, 0.0],
-        [ 0.5,  0.0, 0.0],
-        [ 0.1,  0.1, 0.0]
-        ],
-        lcar=0.05
-    )
-    axis = [0, 0, 1]
-    geom.extrude(
-        poly,
-        translation_axis=axis,
-        rotation_axis=axis,
-        point_on_axis=[0, 0, 0],
-        angle=2.0 / 6.0 * np.pi
-    )
-    model = OGS()  # dummy model
+    from ogs5py import OGS
+
+    with pygmsh.geo.Geometry() as geom:
+        poly = geom.add_polygon(
+            [
+                [+0.0, +0.5],
+                [-0.1, +0.1],
+                [-0.5, +0.0],
+                [-0.1, -0.1],
+                [+0.0, -0.5],
+                [+0.1, -0.1],
+                [+0.5, +0.0],
+                [+0.1, +0.1],
+            ],
+            mesh_size=0.05,
+        )
+
+        geom.twist(
+            poly,
+            translation_axis=[0, 0, 1],
+            rotation_axis=[0, 0, 1],
+            point_on_axis=[0, 0, 0],
+            angle=np.pi / 3,
+        )
+
+        mesh = geom.generate_mesh()
+
+    model = OGS()
     # generate example above
-    model.msh.generate("gmsh", geo_object=geom)
+    model.msh.import_mesh(mesh, import_dim=3)
     model.msh.show()
     # generate a predefined grid adapter in 2D
     model.msh.generate("grid_adapter2D", in_mat=1, out_mat=0, fill=True)

examples/03_pygmsh_generated.py

@@ -4,31 +4,34 @@
 
 from ogs5py import OGS
 
-geom = pygmsh.built_in.Geometry()
-poly = geom.add_polygon(
-    [
-        [0.0, 0.5, 0.0],
-        [-0.1, 0.1, 0.0],
-        [-0.5, 0.0, 0.0],
-        [-0.1, -0.1, 0.0],
-        [0.0, -0.5, 0.0],
-        [0.1, -0.1, 0.0],
-        [0.5, 0.0, 0.0],
-        [0.1, 0.1, 0.0],
-    ],
-    lcar=0.05,
-)
-axis = [0, 0, 1]
-geom.extrude(
-    poly,
-    translation_axis=axis,
-    rotation_axis=axis,
-    point_on_axis=[0, 0, 0],
-    angle=2.0 / 6.0 * np.pi,
-)
+with pygmsh.geo.Geometry() as geom:
+    poly = geom.add_polygon(
+        [
+            [+0.0, +0.5],
+            [-0.1, +0.1],
+            [-0.5, +0.0],
+            [-0.1, -0.1],
+            [+0.0, -0.5],
+            [+0.1, -0.1],
+            [+0.5, +0.0],
+            [+0.1, +0.1],
+        ],
+        mesh_size=0.05,
+    )
+
+    geom.twist(
+        poly,
+        translation_axis=[0, 0, 1],
+        rotation_axis=[0, 0, 1],
+        point_on_axis=[0, 0, 0],
+        angle=np.pi / 3,
+    )
+
+    mesh = geom.generate_mesh()
+
 model = OGS()
 # generate example above
-model.msh.generate("gmsh", geo_object=geom)
+model.msh.import_mesh(mesh, import_dim=3)
 model.msh.show()
 # generate a predefined grid adapter in 2D
 model.msh.generate("grid_adapter2D", in_mat=1, out_mat=0, fill=True)

ogs5py/fileclasses/msh/core.py

@@ -773,8 +773,8 @@ def import_mesh(self, filepath, **kwargs):
 
         Parameters
         ----------
-        filepath : string
-            path to the mesh file to import
+        filepath : string or meshio.Mesh instance
+            mesh to import
         file_format : str, optional
             Here you can specify the fileformat. If 'None' it will be
             determined by file extension. Default: None

ogs5py/fileclasses/msh/generator.py

@@ -1,5 +1,4 @@
 # -*- coding: utf-8 -*-
-# -*- coding: utf-8 -*-
 """
 Generators for the ogs MESH file.
 
@@ -585,13 +584,12 @@ def block_adapter3D(xy_dim=10.0, z_dim=5.0, in_res=1.0):
 
 def gmsh(geo_object, import_dim=(1, 2, 3)):
     """
-    Generate mesh from pygmsh Geometry instance, gmsh code or gmsh .geo file.
+    Generate mesh from gmsh code or gmsh .geo file.
 
     Parameters
     ----------
-    geo_object : str or list of str or Geometry instance from pygmsh
-        Either path to the gmsh .geo file, list of codelines for a .geo file
-        or a pygmsh Geometry instance from pygmsh.
+    geo_object : str or list of str
+        Either path to the gmsh .geo file or list of codelines for a .geo file.
     import_dim : iterable of int or single int, optional
         State which elements should be imported by dimensionality.
         Default: (1, 2, 3)
@@ -621,11 +619,8 @@ def gmsh(geo_object, import_dim=(1, 2, 3)):
             element_id : dict
                 contains element ids for each element sorted by element types
     """
-    import pygmsh as pg
+    from ogs5py.fileclasses.msh.helpers import generate_mesh
 
-    if hasattr(geo_object, "get_code"):
-        geo = geo_object
-    else:
-        geo = gmsh_code(geo_object)
-    mesh = pg.generate_mesh(geo)
+    geo = gmsh_code(geo_object)
+    mesh = generate_mesh(geo)
     return convert_meshio(mesh, import_dim=import_dim)

ogs5py/fileclasses/msh/gmsh.py

@@ -4,33 +4,20 @@
 
 def gmsh_code(path_or_code):
     """Generate mesh with gmsh."""
-    try:
-        from pygmsh import Geometry
-    except ImportError:
-        from pygmsh.built_in import Geometry
-
-    geo = Geometry()
     if isinstance(path_or_code, list):
-        code = map(str, path_or_code)
+        code = list(map(str, path_or_code))
     else:
         try:
             with open(path_or_code, "r") as gmsh_f:
                 code = gmsh_f.readlines()
         except (OSError, IOError):
             print("gmsh_code: could not read file...")
-            return geo
-    geo.add_raw_code(code)
-    return geo
+            code = []
+    return code
 
 
 def gmsh_block_adapt3D(xy_dim=10.0, z_dim=5.0, in_res=1.0):
     """Generate the mesh adapter."""
-    try:
-        from pygmsh import Geometry
-    except ImportError:
-        from pygmsh.built_in import Geometry
-
-    geo = Geometry()
     code = [
         f"xydim = {xy_dim};",
         f"zdim = {z_dim};",
@@ -49,8 +36,7 @@ def gmsh_block_adapt3D(xy_dim=10.0, z_dim=5.0, in_res=1.0):
         "Plane Surface(1) = {1};",
         "Extrude{0,0,zdim}{Surface{1};Layers{1};Recombine;};",
     ]
-    geo.add_raw_code(code)
-    return geo
+    return code
 
 
 def gmsh_grid_adapt3D(
@@ -64,12 +50,6 @@ def gmsh_grid_adapt3D(
     z_pos=0.0,
 ):
     """Generate the mesh adapter."""
-    try:
-        from pygmsh import Geometry
-    except ImportError:
-        from pygmsh.built_in import Geometry
-
-    geo = Geometry()
     code = [
         # "// layer thickness",
         f"dimz = {z_dim};",
@@ -199,8 +179,7 @@ def gmsh_grid_adapt3D(
         "Surface Loop(48) = {39, 28, 33, 35, 37, 31, 47, 41, 43, 45};",
         "Volume(49) = {48};",
     ]
-    geo.add_raw_code(code)
-    return geo
+    return code
 
 
 def gmsh_grid_adapt2D(
@@ -213,12 +192,6 @@ def gmsh_grid_adapt2D(
     z_pos=0.0,
 ):
     """Generate the 2D mesh adapter."""
-    try:
-        from pygmsh import Geometry
-    except ImportError:
-        from pygmsh.built_in import Geometry
-
-    geo = Geometry()
     code = [
         # "// size of the outer block",
         f"outx = {out_dim[0]};",
@@ -271,5 +244,4 @@ def gmsh_grid_adapt2D(
         "Transfinite Line{13, 15} = inx/grix + 1;",
         "Transfinite Line{14, 16} = iny/griy + 1;",
     ]
-    geo.add_raw_code(code)
-    return geo
+    return code