ddfem 1.0.9__py3-none-any.whl → 1.0.11__py3-none-any.whl

ddfem/examples/beam.py

@@ -1,14 +1,10 @@
 import numpy as np
 import pygmsh
-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
 
@@ -45,31 +41,42 @@ def getDomain(initialRefine, version, adaptLevels=0, epsFactor=4.5, *args, **kwa
         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:
+
+        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(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)
+
+    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":
         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)
 
             rec = geom.add_rectangle([0, 0, 0], 1, 0.15)
 
             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,
             )
 
@@ -86,12 +93,11 @@ def getDomain(initialRefine, version, adaptLevels=0, epsFactor=4.5, *args, **kwa
 
     elif version == "gmsh_adaptive":
         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.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,
             )
 
@@ -111,37 +117,24 @@ def getDomain(initialRefine, version, adaptLevels=0, epsFactor=4.5, *args, **kwa
     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,
+            factor=radius,
+            refinements=refinements,
+            adaptLevels=adaptLevels,
+        )
+        h_min = h_max * 0.5 ** (refinements / 2)
+        omega.epsilon = get_eps(h_min)
+    else:
+        gridView = GridView(domain)
 
     domain = DomainDune(omega, gridView)
-    # domain.adapt(level=adaptLevels)
 
-    print(f"h={h * 0.5 ** (adaptLevels / 2)}, epsilon={epsilon.value}")
+    print(
+        f"h_max={h_max}, h_min={h_min * 0.5 ** (adaptLevels / 2)}, epsilon={omega.epsilon.value}"
+    )
 
     return gridView, domain

ddfem/examples/chemical_reaction.py

@@ -37,7 +37,7 @@ def crModel():
 
         def setup(u_h, DDMPotentialModel, psi_h):
             ChemModel.u_h_n = u_h.copy(name="u_h_n")
-            ChemModel.u_h_n.interpolate(zero(ChemModel.dimRange))
+            ChemModel.u_h_n.clear()
 
             ChemModel.dpsi_h = lambda x: DDMPotentialModel.sigma(
                 0, x, psi_h, grad(psi_h)

ddfem/examples/five_circle_flat.py

@@ -15,14 +15,12 @@ pip install dune-fem
     """
     )
 
-from dune.fem.function import gridFunction
-from dune.fem.space import lagrange
 from dune.grid import cartesianDomain
 from dune.ufl import Constant, Space
 from ufl import SpatialCoordinate, sqrt
 
-from ddfem import geometry as gm
 from ddfem import GridView
+from ddfem import geometry as gm
 from ddfem.geometry.domain_dune import DomainDune
 
 
@@ -75,7 +73,7 @@ def getDomain(
 
     h_max = h * 3
     h_min = h / 2
-    radius = 5
+    radius = 4
 
     x = SpatialCoordinate(Space(2))
     sdf = omega(x)
@@ -84,28 +82,40 @@ 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:
+
+        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
 
-    omega.epsilon = get_eps(h)
+        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)
+
+    omega.epsilon = get_eps(h_min)
 
     if version == "cartesian":
-        domain = cartesianDomain(*domain_range, initial_gridsize)
+        omega.epsilon = get_eps(h)
+        # domain = cartesianDomain(*domain_range, initial_gridsize)
+        domain = [*domain_range, initial_gridsize]
 
     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
+            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]
 
@@ -136,8 +146,8 @@ 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
+            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],
@@ -158,18 +168,22 @@ def getDomain(
     else:
         raise ValueError("invalid mesh type")
 
-    if not version == "dune_adaptive":
-        gridView = GridView(domain)
-    else:
+    if version == "dune_adaptive":
         refinements = int(2 * np.log2(h_max / h_min))
-        gridView = GridView(domain,omega,
-                      factor=radius,
-                      refinements=refinements,
-                      adaptLevels=adaptLevels)
+        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.value = get_eps(h_min)
+        omega.epsilon = get_eps(h_min)
+    else:
+        gridView = GridView(domain)
 
-    domain = DomainDune(omega, gridView)
+    domain = DomainDune(omega, gridView, filterTolerance=10 * omega.epsilon.value)
 
     print(
         f"h_max={h_max}, h_min={h_min * 0.5 ** (adaptLevels / 2)}, epsilon={omega.epsilon.value}"

ddfem/examples/linear_elasticity.py

@@ -1,5 +1,5 @@
 from dune.ufl import Constant
-from ufl import Identity, as_vector, div, grad, sym, tr, zero
+from ufl import Identity, as_vector, inner, sqrt, sym, tr
 
 from ddfem.boundary import BndFlux_v, BndValue
 
@@ -28,6 +28,10 @@ def leModel():
         def S_i(t, x, U, DU):
             return as_vector([0.0, -Model.rho * Model.g])
 
+        def von_Mises(U, DU):
+            s = Model.sigma(U, DU) - (1.0 / 3) * tr(Model.sigma(U, DU)) * Identity(2)
+            return sqrt(3.0 / 2 * inner(s, s))
+
         valD = lambda t, x, U: Model.vd
 
         valN = lambda t, x, U, DU, n: Model.vn

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