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

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/geometry/primitive_base.py

@@ -250,7 +250,7 @@ class Scale(BaseOperator):
 
 
 class Rotate(BaseOperator):
-    """Rotates SDF, counterclockwise of orgin"""
+    """Rotates SDF, counterclockwise of origin"""
 
     def __init__(self, sdf1, angle, radians=True, *args, **kwargs):
         if not radians:

{ddfem-1.0.9.dist-info → ddfem-1.0.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ddfem
-Version: 1.0.9
+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
@@ -39,8 +39,40 @@ Dynamic: license-file
 
 # Diffuse Domain Finite Element Methods
 
-This is a package for solving complex PDEs based on the diffuse domain idea.
+[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.
 
-[Documentation][0]
+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

ddfem-1.0.11.dist-info/RECORD

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ddfem/data/2.11.dev20250709/boundary.modules

@@ -1,9 +0,0 @@
-yaspcoordinates_dim2_ctdouble
-hierarchicalgrid_966e2a5c8356c5b278ccd3acad180f0a
-referenceelements_de274310a0055100b832a0e8892b0258
-referenceelements_0fff57b283123cc055345ec95574c857
-referenceelements_f4457f35395151d83a965d4cf5fce70d
-femspace_90f0a9524a8cb701e8ee5027b7658a0e_0faf32f13b591f4f60f83c591507b9be
-localfunction_fc22d5adaf3b9563160dc2aec55e8ba1_19659fe2f2f74bcfb5d532f1a0d38be9
-localfunction_c5ebc4ae4b5d3bad6be770eb08c50d08_19659fe2f2f74bcfb5d532f1a0d38be9
-localfunction_e69118a51208cfab8a028711e966e76c_19659fe2f2f74bcfb5d532f1a0d38be9

ddfem/data/2.11.dev20250709/femspace_90f0a9524a8cb701e8ee5027b7658a0e_0faf32f13b591f4f60f83c591507b9be.cc

@@ -1,40 +0,0 @@
-#ifndef Guard_femspace_90f0a9524a8cb701e8ee5027b7658a0e_0faf32f13b591f4f60f83c591507b9be
-#define Guard_femspace_90f0a9524a8cb701e8ee5027b7658a0e_0faf32f13b591f4f60f83c591507b9be
-
-#include <config.h>
-
-#define USING_DUNE_PYTHON 1
-
-#define BACKENDNAME "as_numpy"
-#include <dune/fem/function/adaptivefunction.hh>
-#include <dune/fem/space/lagrange.hh>
-#include <dune/fempy/py/discretefunction.hh>
-#include <dune/fempy/py/space.hh>
-#include <dune/grid/io/file/dgfparser/dgfyasp.hh>
-#include <dune/grid/yaspgrid.hh>
-#include <dune/python/grid/hierarchical.hh>
-
-#include <dune/python/common/typeregistry.hh>
-#include <dune/python/pybind11/pybind11.h>
-#include <dune/python/pybind11/stl.h>
-
-PYBIND11_MODULE( femspace_90f0a9524a8cb701e8ee5027b7658a0e_0faf32f13b591f4f60f83c591507b9be, module )
-{
-  using pybind11::operator""_a;
-  pybind11::module cls0 = module;
-  {
-    using DuneType = Dune::Fem::DynamicLagrangeDiscreteFunctionSpace< Dune::Fem::FunctionSpace< double, double, 2, 1 >, Dune::FemPy::GridPart< Dune::YaspGrid< 2, Dune::EquidistantOffsetCoordinates< double, 2 > >::LeafGridView >, Dune::Fem::CodegenStorage>;
-    auto cls = Dune::Python::insertClass< DuneType, std::shared_ptr<DuneType> >( cls0, "Space",pybind11::dynamic_attr(), Dune::Python::GenerateTypeName("Dune::Fem::DynamicLagrangeDiscreteFunctionSpace< Dune::Fem::FunctionSpace< double, double, 2, 1 >, Dune::FemPy::GridPart< Dune::YaspGrid< 2, Dune::EquidistantOffsetCoordinates< double, 2 > >::LeafGridView >, Dune::Fem::CodegenStorage>"), Dune::Python::IncludeFiles{"dune/fem/function/adaptivefunction.hh","dune/fem/space/lagrange.hh","dune/fempy/py/discretefunction.hh","dune/fempy/py/space.hh","dune/grid/io/file/dgfparser/dgfyasp.hh","dune/grid/yaspgrid.hh","dune/python/grid/hierarchical.hh"}).first;
-    Dune::FemPy::registerSpace( cls0, cls );
-  }
-  using pybind11::operator""_a;
-  {
-    using DuneType = Dune::Fem::AdaptiveDiscreteFunction< Dune::Fem::DynamicLagrangeDiscreteFunctionSpace< Dune::Fem::FunctionSpace< double, double, 2, 1 >, Dune::FemPy::GridPart< Dune::YaspGrid< 2, Dune::EquidistantOffsetCoordinates< double, 2 > >::LeafGridView >, Dune::Fem::CodegenStorage> >;
-    auto cls = Dune::Python::insertClass< DuneType >( cls0, "DiscreteFunction",pybind11::buffer_protocol(),pybind11::dynamic_attr(), Dune::Python::GenerateTypeName("Dune::Fem::AdaptiveDiscreteFunction< Dune::Fem::DynamicLagrangeDiscreteFunctionSpace< Dune::Fem::FunctionSpace< double, double, 2, 1 >, Dune::FemPy::GridPart< Dune::YaspGrid< 2, Dune::EquidistantOffsetCoordinates< double, 2 > >::LeafGridView >, Dune::Fem::CodegenStorage> >"), Dune::Python::IncludeFiles{"dune/fem/function/adaptivefunction.hh","dune/fem/space/lagrange.hh","dune/fempy/py/discretefunction.hh","dune/fempy/py/space.hh","dune/grid/io/file/dgfparser/dgfyasp.hh","dune/grid/yaspgrid.hh","dune/python/grid/hierarchical.hh"}).first;
-    Dune::FemPy::registerDiscreteFunction( cls0, cls );
-    cls.def( pybind11::init( [] ( const std::string &name, const Dune::Fem::DynamicLagrangeDiscreteFunctionSpace< Dune::Fem::FunctionSpace< double, double, 2, 1 >, Dune::FemPy::GridPart< Dune::YaspGrid< 2, Dune::EquidistantOffsetCoordinates< double, 2 > >::LeafGridView >, Dune::Fem::CodegenStorage>&space, pybind11::array_t<double> dofVector ) {double *dof = static_cast< double* >( dofVector.request(false).ptr );
-        return new DuneType(name,space,dof);
-      } ), "name"_a, "space"_a, "dofVector"_a, pybind11::keep_alive< 1, 3 >(), pybind11::keep_alive< 1, 4 >() );
-  }
-}
-#endif

ddfem/data/2.11.dev20250709/geometry.modules

@@ -1,84 +0,0 @@
-yaspcoordinates_dim2_ctdouble
-hierarchicalgrid_966e2a5c8356c5b278ccd3acad180f0a
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-yaspcoordinates_dim3_ctdouble
-hierarchicalgrid_472c2c2d007bf5604887ab2f16b7eb13
-referenceelements_de274310a0055100b832a0e8892b0258
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ddfem/data/2.11.dev20250709/hierarchicalgrid_966e2a5c8356c5b278ccd3acad180f0a.cc

@@ -1,30 +0,0 @@
-#ifndef Guard_hierarchicalgrid_966e2a5c8356c5b278ccd3acad180f0a
-#define Guard_hierarchicalgrid_966e2a5c8356c5b278ccd3acad180f0a
-
-#include <config.h>
-
-#define USING_DUNE_PYTHON 1
-
-#include <dune/grid/io/file/dgfparser/dgfyasp.hh>
-#include <dune/grid/yaspgrid.hh>
-#include <dune/python/grid/hierarchical.hh>
-
-#include <dune/python/common/typeregistry.hh>
-#include <dune/python/pybind11/pybind11.h>
-#include <dune/python/pybind11/stl.h>
-
-PYBIND11_MODULE( hierarchicalgrid_966e2a5c8356c5b278ccd3acad180f0a, module )
-{
-  using pybind11::operator""_a;
-  pybind11::module cls0 = module;
-  {
-    using DuneType = Dune::YaspGrid< 2, Dune::EquidistantOffsetCoordinates< double, 2 > >;
-    auto cls = Dune::Python::insertClass< DuneType, std::shared_ptr<DuneType> >( cls0, "HierarchicalGrid",pybind11::dynamic_attr(), Dune::Python::GenerateTypeName("Dune::YaspGrid< 2, Dune::EquidistantOffsetCoordinates< double, 2 > >"), Dune::Python::IncludeFiles{"dune/grid/io/file/dgfparser/dgfyasp.hh","dune/grid/yaspgrid.hh","dune/python/grid/hierarchical.hh"}).first;
-    Dune::Python::registerHierarchicalGrid( cls0, cls );
-    cls.def( pybind11::init( [] ( const Dune::EquidistantOffsetCoordinates< double, 2 >& coordinates, std::array<bool, 2> periodic, int overlap ) {std::bitset<2> periodic_;
-        for (int i=0;i<2;++i) periodic_.set(i,periodic[i]);
-        return new DuneType(coordinates,periodic_,overlap);
-      } ), "coordinates"_a, "periodic"_a, "overlap"_a );
-  }
-}
-#endif