ddfem 1.0.10__py3-none-any.whl → 1.0.11__py3-none-any.whl

ddfem/examples/triple_circle.py

@@ -15,15 +15,11 @@ pip install dune-fem
     """
     )
 
-from dune.alugrid import aluConformGrid as leafGridView
-from dune.fem import adapt, mark, markNeighbors
-from dune.fem.function import gridFunction
-from dune.fem.space import lagrange
-from dune.fem.view import adaptiveLeafGridView
 from dune.grid import cartesianDomain
 from dune.ufl import Constant, Space
 from ufl import SpatialCoordinate, sqrt
 
+from ddfem import GridView
 from ddfem import geometry as gm
 from ddfem.geometry.domain_dune import DomainDune
 
@@ -61,7 +57,7 @@ def getDomain(
 
     h_max = h * 3
     h_min = h / 2
-    radius = 5
+    radius = 4
 
     x = SpatialCoordinate(Space(2))
     sdf = omega(x)
@@ -70,51 +66,61 @@ def getDomain(
         r_min = epsilon.value
         r_max = radius * epsilon.value
         dist = np.abs(sdf((x, y)))
-        if dist <= r_min:
-            return geom.characteristic_length_min
-        elif dist >= r_max:
-            return geom.characteristic_length_max
-        else:
-            # Linear
-            m = (geom.characteristic_length_max - geom.characteristic_length_min) / (
-                r_max - r_min
-            )
-            return m * (dist - r_min) + geom.characteristic_length_min
 
-    if version == "cartesian":
-        domain = cartesianDomain(*domain_range, initial_gridsize)
-        epsilon = get_eps(h)
+        gmax = geom.characteristic_length_max
+        gmin = geom.characteristic_length_min
 
-    elif version == "fitted":
-        if pygmsh is None:
-            raise AttributeError("'fitted' requires install pygmsh")
-        with pygmsh.occ.Geometry() as geom:
-            geom.characteristic_length_max = h_max
-            geom.characteristic_length_min = h_min
-            epsilon = get_eps(h_min)
+        if False:
+            # Linear
+            if dist <= r_min:
+                return gmin
+            elif dist >= r_max:
+                return gmax
+            else:
+                m = (gmax - gmin) / (r_max - r_min)
+                return m * (dist - r_min) + gmin
 
-            disks = [geom.add_disk([c[1][0], c[1][1], 0.0], c[0]) for c in balls]
+        else:
+            # Exponential
+            R = int(2 * np.log2(gmax / gmin))
+            j = max(0, min(R, (dist * R) / r_max - 0.5))
+            # j = max(0, min(R, np.floor(dist * R / r_max)))
+            return gmax * 0.5 ** ((R - j) / 2)
 
-            ds = geom.boolean_union([disks[0], disks[1]])
-            shape = geom.boolean_intersection([ds, disks[2]])
-            if inverted:
-                rectangle = geom.add_rectangle(
-                    [domain_range[0][0], domain_range[0][1], 0.0],
-                    domain_range[1][0] - domain_range[0][0],
-                    domain_range[1][1] - domain_range[0][1],
-                )
-                geom.boolean_difference(rectangle, shape)
+    omega.epsilon = get_eps(h_min)
+    if version == "cartesian":
+        omega.epsilon = get_eps(h)
+        domain = cartesianDomain(*domain_range, initial_gridsize)
 
-            geom.set_mesh_size_callback(
-                lambda dim, tag, x, y, z, lc: spacing(x, y, epsilon),
-                ignore_other_mesh_sizes=True,
-            )
-            mesh = geom.generate_mesh()
-            points, cells = mesh.points, mesh.cells_dict
-            domain = {
-                "vertices": points[:, :2].astype(float),
-                "simplices": cells["triangle"].astype(int),
-            }
+    # elif version == "fitted":
+    #     if pygmsh is None:
+    #         raise AttributeError("'fitted' requires install pygmsh")
+    #     with pygmsh.occ.Geometry() as geom:
+    #         geom.characteristic_length_max = h_max / sqrt(2)
+    #         geom.characteristic_length_min = h_min / sqrt(2)
+
+    #         disks = [geom.add_disk([c[1][0], c[1][1], 0.0], c[0]) for c in balls]
+
+    #         ds = geom.boolean_union([disks[0], disks[1]])
+    #         shape = geom.boolean_intersection([ds, disks[2]])
+    #         if inverted:
+    #             rectangle = geom.add_rectangle(
+    #                 [domain_range[0][0], domain_range[0][1], 0.0],
+    #                 domain_range[1][0] - domain_range[0][0],
+    #                 domain_range[1][1] - domain_range[0][1],
+    #             )
+    #             geom.boolean_difference(rectangle, shape)
+
+    #         geom.set_mesh_size_callback(
+    #             lambda dim, tag, x, y, z, lc: spacing(x, y, omega.epsilon),
+    #             ignore_other_mesh_sizes=True,
+    #         )
+    #         mesh = geom.generate_mesh()
+    #         points, cells = mesh.points, mesh.cells_dict
+    #         domain = {
+    #             "vertices": points[:, :2].astype(float),
+    #             "simplices": cells["triangle"].astype(int),
+    #         }
 
     elif version == "dune_adaptive":
         gridsize = [int(j * h / h_max) for j in initial_gridsize]
@@ -124,9 +130,8 @@ def getDomain(
         if pygmsh is None:
             raise AttributeError("'gmsh_adaptive' requires install pygmsh")
         with pygmsh.occ.Geometry() as geom:
-            geom.characteristic_length_max = h_max
-            geom.characteristic_length_min = h_min
-            epsilon = get_eps(h_min)
+            geom.characteristic_length_max = h_max / sqrt(2)
+            geom.characteristic_length_min = h_min / sqrt(2)
 
             geom.add_rectangle(
                 [domain_range[0][0], domain_range[0][1], 0.0],
@@ -135,7 +140,7 @@ def getDomain(
             )
 
             geom.set_mesh_size_callback(
-                lambda dim, tag, x, y, z, lc: spacing(x, y, epsilon),
+                lambda dim, tag, x, y, z, lc: spacing(x, y, omega.epsilon),
                 ignore_other_mesh_sizes=True,
             )
             mesh = geom.generate_mesh()
@@ -145,13 +150,12 @@ def getDomain(
                 "simplices": cells["triangle"].astype(int),
             }
 
-    elif version == "gmsh_embedded":
+    elif version == "gmsh_embedded" or version == "fitted":
         if pygmsh is None:
             raise AttributeError("'fitted' requires install pygmsh")
         with pygmsh.occ.Geometry() as geom:
-            geom.characteristic_length_max = h_max
-            geom.characteristic_length_min = h_min
-            epsilon = get_eps(h_min)
+            geom.characteristic_length_max = h_max / sqrt(2)
+            geom.characteristic_length_min = h_min / sqrt(2)
 
             disks = [geom.add_disk([c[1][0], c[1][1], 0.0], c[0]) for c in balls]
 
@@ -165,53 +169,52 @@ def getDomain(
 
             geom.boolean_fragments(rectangle, shape)
 
+            geom.add_physical(shape, label="fitted_domain")
+
             geom.set_mesh_size_callback(
-                lambda dim, tag, x, y, z, lc: spacing(x, y, epsilon),
+                lambda dim, tag, x, y, z, lc: spacing(x, y, omega.epsilon),
                 ignore_other_mesh_sizes=True,
             )
             mesh = geom.generate_mesh()
             points, cells = mesh.points, mesh.cells_dict
+
+            if version == "fitted":
+                fitted_domain_indices = mesh.cell_sets_dict["fitted_domain"]["triangle"]
+                mesh_cells = cells["triangle"][fitted_domain_indices].astype(int)
+            else:
+                mesh_cells = cells["triangle"].astype(int)
+
             domain = {
                 "vertices": points[:, :2].astype(float),
-                "simplices": cells["triangle"].astype(int),
+                "simplices": mesh_cells,
             }
 
     else:
         raise ValueError("invalid mesh type")
 
-    gridView = adaptiveLeafGridView(leafGridView(domain))
-
     if version == "dune_adaptive":
-        omega.epsilon = get_eps(h_min)
-        omega.epsilon.value *= radius
-        epsilon_value = omega.epsilon.value
-
-        marker = mark
-
         refinements = int(2 * np.log2(h_max / h_min))
-
-        region = gridFunction(
-            omega.phi(x) * (1 - omega.phi(x)), gridView=gridView
-        )  # interface
-
-        for j in range(1, refinements + 1):
-
-            omega.epsilon.value = epsilon_value * j / refinements
-            marker(region, 0.00247262315663, maxLevel=refinements)  # 1 epsilon
-
-            adapt(gridView.hierarchicalGrid)
-
-        h_min = h_max * 0.5 ** (j / 2)
-        epsilon = get_eps(h_min)
-
-    omega.epsilon = epsilon
-    domain = omega
+        gridView = GridView(
+            domain,
+            omega,
+            filterTolerance=10 * omega.epsilon.value,
+            factor=radius,
+            refinements=refinements,
+            adaptLevels=adaptLevels,
+        )
+        h_min = h_max * 0.5 ** (refinements / 2)
+        omega.epsilon = get_eps(h_min)
+    else:
+        gridView = GridView(
+            domain,
+            omega,
+            filterTolerance=10 * omega.epsilon.value,
+        )
 
     domain = DomainDune(omega, gridView)
-    domain.adapt(level=adaptLevels)
 
     print(
-        f"h_max={h_max}, h_min={h_min * 0.5 ** (adaptLevels / 2)}, epsilon={epsilon.value}"
+        f"h_max={h_max}, h_min={h_min * 0.5 ** (adaptLevels / 2)}, epsilon={omega.epsilon.value}"
     )
 
     return gridView, domain

ddfem/examples/triple_circle_beam.py

@@ -7,6 +7,10 @@ except ImportError:
 
 try:
     import dune
+    from dune.fem import adapt, mark, markNeighbors
+    from dune.fem.function import gridFunction
+    from dune.fem.view import adaptiveLeafGridView, filteredGridView
+    from dune.alugrid import aluConformGrid as leafGridView
 except ImportError:
     print(
         """
@@ -15,16 +19,12 @@ pip install dune-fem
     """
     )
 
-from dune.alugrid import aluConformGrid as leafGridView
-from dune.fem import adapt, mark, markNeighbors
-from dune.fem.function import gridFunction
-from dune.fem.space import lagrange
-from dune.fem.utility import gridWidth
-from dune.fem.view import adaptiveLeafGridView
+
 from dune.grid import cartesianDomain
 from dune.ufl import Constant, Space
-from ufl import SpatialCoordinate, as_vector, sqrt
+from ufl import SpatialCoordinate, sqrt
 
+from ddfem import GridView
 from ddfem import geometry as gm
 from ddfem.geometry.domain_dune import DomainDune
 
@@ -37,16 +37,17 @@ def getDomain(initialRefine, version, adaptLevels=0, epsFactor=4.5, dirichlet=Tr
 
     if dirichlet:
         domain_range = [
-            [-0.8 + shiftx, -0.8 + shifty, 0.1],  # -0.5
-            [0.8 + shiftx, 0.8 + shifty, 3.3],  #  3.2
+            [-0.75 + shiftx, -0.75 + shifty, 0.1],  # -0.5
+            [0.75 + shiftx, 0.75 + shifty, 3.3],  #  3.2
         ]
-        initial_gridsize = [60, 60, 60]
+        # initial_gridsize = [60, 60, 60]
+        initial_gridsize = [25, 25, 25]
     else:
         domain_range = [
-            [-0.8 + shiftx, -0.8 + shifty, 0.0 - 0.5],
-            [0.8 + shiftx, 0.8 + shifty, 3.2 + 0.5],
+            [-0.75 + shiftx, -0.75 + shifty, 0.0 - 0.25],
+            [0.75 + shiftx, 0.75 + shifty, 3.2 + 0.25],
         ]
-        initial_gridsize = [60, 60, 80]
+        initial_gridsize = [25, 25, 40]
     initial_gridsize = [i * 2**initialRefine for i in initial_gridsize]
     h = sqrt(
         ((domain_range[1][0] - domain_range[0][0]) / initial_gridsize[0]) ** 2
@@ -69,16 +70,16 @@ def getDomain(initialRefine, version, adaptLevels=0, epsFactor=4.5, dirichlet=Tr
 
     face_2d.name = "beam"
 
-    if dirichlet:
+    if dirichlet and not version == "fitted":
         length = 4
     else:
         length = 3.2
     omega = face_2d.extrude(length, True)
     omega.name = "full"
 
-    h_max = h * 3
-    h_min = h / 2
-    radius = 3
+    h_max = h * 4
+    h_min = h / 3
+    radius = 0.5    # 3
 
     x = SpatialCoordinate(Space(3))
     sdf = omega(x)
@@ -87,28 +88,39 @@ def getDomain(initialRefine, version, adaptLevels=0, epsFactor=4.5, dirichlet=Tr
         r_min = epsilon.value
         r_max = radius * epsilon.value
         dist = np.abs(sdf((x, y, z)))
-        if dist <= r_min:
-            return geom.characteristic_length_min
-        elif dist >= r_max:
-            return geom.characteristic_length_max
-        else:
+
+        gmax = geom.characteristic_length_max
+        gmin = geom.characteristic_length_min
+
+        if False:
             # Linear
-            m = (geom.characteristic_length_max - geom.characteristic_length_min) / (
-                r_max - r_min
-            )
-            return m * (dist - r_min) + geom.characteristic_length_min
+            if dist <= r_min:
+                return gmin
+            elif dist >= r_max:
+                return gmax
+            else:
+                m = (gmax - gmin) / (r_max - r_min)
+                return m * (dist - r_min) + gmin
+
+        else:
+            # Exponential
+            R = int(3 * np.log2(gmax / gmin))
+            j = max(0, min(R, (dist * R) / r_max - 0.5))
+            # j = max(0, min(R, np.floor(dist * R / r_max)))
+            return gmax * 0.5 ** ((R - j) / 3)
+
+    omega.epsilon = get_eps(h_min)
 
     if version == "cartesian":
+        omega.epsilon = get_eps(h)
         domain = cartesianDomain(*domain_range, initial_gridsize)
-        epsilon = get_eps(h)
 
     elif version == "fitted":
         if pygmsh is None:
             raise AttributeError("'fitted' requires install pygmsh")
         with pygmsh.occ.Geometry() as geom:
-            geom.characteristic_length_max = h_max
-            geom.characteristic_length_min = h_min
-            epsilon = get_eps(h_min)
+            geom.characteristic_length_max = h_max / sqrt(2)
+            geom.characteristic_length_min = h_min / sqrt(2)
 
             disks = [geom.add_disk([c[1][0], c[1][1], 0.0], c[0]) for c in balls]
 
@@ -117,7 +129,7 @@ def getDomain(initialRefine, version, adaptLevels=0, epsFactor=4.5, dirichlet=Tr
             geom.extrude(shape, [0, 0, length])
 
             geom.set_mesh_size_callback(
-                lambda dim, tag, x, y, z, lc: spacing(x, y, z, epsilon),
+                lambda dim, tag, x, y, z, lc: spacing(x, y, z, omega.epsilon),
                 ignore_other_mesh_sizes=True,
             )
             mesh = geom.generate_mesh()
@@ -135,9 +147,8 @@ def getDomain(initialRefine, version, adaptLevels=0, epsFactor=4.5, dirichlet=Tr
         if pygmsh is None:
             raise AttributeError("'gmsh_adaptive' requires install pygmsh")
         with pygmsh.occ.Geometry() as geom:
-            geom.characteristic_length_max = h_max
-            geom.characteristic_length_min = h_min
-            epsilon = get_eps(h_min)
+            geom.characteristic_length_max = h_max / sqrt(2)
+            geom.characteristic_length_min = h_min / sqrt(2)
 
             geom.add_box(
                 [0.0, 0.0, 0.0],
@@ -149,7 +160,7 @@ def getDomain(initialRefine, version, adaptLevels=0, epsFactor=4.5, dirichlet=Tr
             )
 
             geom.set_mesh_size_callback(
-                lambda dim, tag, x, y, z, lc: spacing(x, y, z, epsilon),
+                lambda dim, tag, x, y, z, lc: spacing(x, y, z, omega.epsilon),
                 ignore_other_mesh_sizes=True,
             )
             mesh = geom.generate_mesh()
@@ -161,48 +172,47 @@ def getDomain(initialRefine, version, adaptLevels=0, epsFactor=4.5, dirichlet=Tr
     else:
         raise ValueError("invalid mesh type")
 
-    gridView = adaptiveLeafGridView(leafGridView(domain))
-    # return gridView, None
-
     if version == "dune_adaptive":
-        # omega.epsilon = get_eps(h)
+        refinements = int(3 * np.log2(h_max / h_min))
+        gridView = GridView(
+            domain,
+            omega,
+            factor=radius,
+            refinements=refinements,
+            adaptLevels=adaptLevels,
+            filterTolerance=0.08,
+
+        )
+        h_min = h_max * 0.5 ** (refinements/3+1)
+        omega.epsilon.value = get_eps(h_min).value
+        """
+        gridView = adaptiveLeafGridView(leafGridView(domain))
         omega.epsilon = get_eps(h_min)
         omega.epsilon.value *= radius
         epsilon_value = omega.epsilon.value
-
         marker = mark
-
         refinements = int(3 * np.log2(h_max / h_min))
         region = gridFunction(
             omega.phi(x) * (1 - omega.phi(x)), gridView=gridView
         )  # interface
-
-        for j in range(1, refinements + 1):
-            print("refining:", j, gridView.size(2), flush=True)
-            if gridView.size(2) > 5e5:
-                assert j == refinements
-                j -= 1
-                break
+        for j in range(1, refinements-1):
+            print("refining:", j, gridView.size(3), flush=True)
+            # if gridView.size(3) > 1e5:
+            #     break
             omega.epsilon.value = epsilon_value * j / refinements
             marker(region, 0.00247262315663, maxLevel=refinements)  # epsilon
             adapt(gridView.hierarchicalGrid)
-
-            # markNeighbors(region, 0.1, maxLevel=refinements)
-            # marker(region, 0.2, maxLevel=refinements)
-            # adapt(gridView.hierarchicalGrid)
-            # omega.epsilon.value = omega.epsilon.value * 2**(-1/3)
-
-        h_min = h_max * 0.5 ** (j / 3)
-        epsilon = get_eps(h_min)
-
-    omega.epsilon = epsilon
-    domain = omega
+        h_min = h_max * 0.5 ** (refinements/3)
+        omega.epsilon.value = get_eps(h_min).value
+        gridView = filteredGridView(gridView, lambda e:1, 1, useFilteredIndexSet=True)
+        """
+    else:
+        gridView = GridView(domain)
 
     domain = DomainDune(omega, gridView)
-    # domain.adapt(level=adaptLevels)
 
     print(
-        f"h_max={h_max}, h_min={h_min * 0.5 ** (adaptLevels / 3)}, epsilon={epsilon.value}"
+        f"h_max={h_max}, h_min={h_min * 0.5 ** (adaptLevels / 2)}, epsilon={omega.epsilon.value}"
     )
 
     return gridView, domain

ddfem-1.0.11.dist-info/METADATA

@@ -0,0 +1,78 @@
+Metadata-Version: 2.4
+Name: ddfem
+Version: 1.0.11
+Summary: Diffuse domain finite element solver
+Author-email: Luke Benfield <luke.benfield@warwick.ac.uk>, Andreas Dedner <a.s.dedner@warwick.ac.uk>
+License-Expression: MIT
+Project-URL: Homepage, https://gitlab.dune-project.org/dune-fem/ddfem
+Project-URL: Issues, https://gitlab.dune-project.org/dune-fem/ddfem/-/issues
+Project-URL: Documentation, https://ddfem.readthedocs.io/en/latest/index.html
+Project-URL: Repository, https://gitlab.dune-project.org/dune-fem/ddfem.git
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: fenics-ufl==2022.2.0
+Requires-Dist: numpy
+Requires-Dist: setuptools<79.1
+Provides-Extra: dune
+Requires-Dist: dune-fem==2.11.dev20250709; extra == "dune"
+Requires-Dist: dune_alugrid==2.11.dev20250709; extra == "dune"
+Requires-Dist: dune_common==2.11.dev20250709; extra == "dune"
+Requires-Dist: dune_fem-dg==2.11.dev20250709; extra == "dune"
+Requires-Dist: dune_geometry==2.11.dev20250709; extra == "dune"
+Requires-Dist: dune_grid==2.11.dev20250709; extra == "dune"
+Requires-Dist: dune_istl==2.11.dev20250709; extra == "dune"
+Requires-Dist: dune_localfunctions==2.11.dev20250709; extra == "dune"
+Requires-Dist: pygmsh; extra == "dune"
+Provides-Extra: doc
+Requires-Dist: jupyter; extra == "doc"
+Requires-Dist: jupytext; extra == "doc"
+Requires-Dist: nbsphinx; extra == "doc"
+Requires-Dist: sphinx_rtd_theme; extra == "doc"
+Requires-Dist: twine; extra == "doc"
+Requires-Dist: build; extra == "doc"
+Provides-Extra: dev
+Requires-Dist: ddfem[doc,dune]; extra == "dev"
+Dynamic: license-file
+
+# Diffuse Domain Finite Element Methods
+
+[ddfem][0] is a Python package that simplifies the transformation
+of a wide range of PDEs using the Diffuse Domain Method.
+While the original PDE will often be defined on a complex domain,
+after the transformation it can be solved on simple e.g. square domain.
+The original geometry is embedded in the simpler domain using
+a phase-field function representation.
+We provide implementations for different versions of the Diffuse Domain Method
+making it easy to compare and chose the most suitable version for the problem at hand.
+Adding new versions is also straightforward.
+Furthermore, we provide a new approach
+to combine multiple boundary conditions
+of different types on distinct boundary segments.
+
+The geometry subpackage provides several simple signed distance functions (SDF),
+and operators to allow an easy definition of the complex domain.
+
+We have designed the package to have a wide compatibility with existing finite element solvers,
+as all transformations are performed using the Unified Form Language,
+[UFL][2] and do not require any other external packages. 
+
+While not required, we recommend using [Dune-Fem][1]
+as it enables some optimisations for form compiling,
+and can improve the mesh by utilising the different grid views.
+We have used this package to test the package and
+for all examples used throughout this tutorial.
+
+## Getting started
+
+How to install the package using `pip` is discussed in our [tutorial][4].
+
+Enjoy - and let us know of any [issues][3] you encountered 
+
+[0]: https://ddfem.readthedocs.io/en/latest/index.html
+[1]: https://www.dune-project.org/modules/dune-fem/
+[2]: https://github.com/FEniCS/ufl
+[3]: https://gitlab.dune-project.org/dune-fem/ddfem/-/issues
+[4]: https://ddfem.readthedocs.io/en/latest/installation.html