ddfem 1.0.8__tar.gz → 1.0.10__tar.gz

ddfem-1.0.10/PKG-INFO

@@ -0,0 +1,101 @@
+Metadata-Version: 2.4
+Name: ddfem
+Version: 1.0.10
+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
+
+This is a Python package that implements a framework for transforming PDEs defined on
+a complex domains using the Diffuse Domain Method to reformulate the problem on a simple domain.
+This method avoids traditional challenges by embedding the original geometry with a phase-field function representation.
+
+Our aim is to make the application of a variety of Diffuse Domain approaches more accessible and straightforward to use. We have designed the package to have a wide compatibility with existing finite element solvers, as all transformations are performed only using the Unified Form Language,
+[UFL][2].
+
+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. The `transfromers` subpackes implements a number of different diffuse domain approaches including some novel ones which we
+will describe in detail in an upcoming paper.
+
+While not required, we recommend using [Dune-Fem][1] as it enables some optimisations for form compiling and has been used for testing the package and for the examples throughout
+our [Documentation][0].
+
+## Getting started
+
+Using `pip` and a virtual environment is the easiest way to get started with`ddfem`:
+
+```bash
+pip install ddfem
+```
+
+will install the basic package. We have mainly tested it with `dune` as solver backend and provide some extra features when used with `dune`. Currently the code relies on a pre-release version and the best way to guarantee compatibility is to use
+
+```bash
+pip install ddfem[dune]
+```
+
+On most machine you will also need to run
+
+```bash
+pip install mpi4py
+```
+
+The main example `intro` file in our tutorial can be obtained easily by running
+
+```
+python -m ddfem
+```
+
+This step can take some time (so do it before a coffee break) since it precompiles all required modules. This is done in parallel using `4` processes by default. Change that by adding a parameter to the above call, e.g., to use `8` processes run
+
+```
+python -m ddfem 8
+```
+
+After this step has completed you should find the two files `intro.py` and `intro_nb.ipynb` in your folder.
+
+Enjoy - and let use 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
+

ddfem-1.0.10/README.md

@@ -0,0 +1,62 @@
+# Diffuse Domain Finite Element Methods
+
+This is a Python package that implements a framework for transforming PDEs defined on
+a complex domains using the Diffuse Domain Method to reformulate the problem on a simple domain.
+This method avoids traditional challenges by embedding the original geometry with a phase-field function representation.
+
+Our aim is to make the application of a variety of Diffuse Domain approaches more accessible and straightforward to use. We have designed the package to have a wide compatibility with existing finite element solvers, as all transformations are performed only using the Unified Form Language,
+[UFL][2].
+
+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. The `transfromers` subpackes implements a number of different diffuse domain approaches including some novel ones which we
+will describe in detail in an upcoming paper.
+
+While not required, we recommend using [Dune-Fem][1] as it enables some optimisations for form compiling and has been used for testing the package and for the examples throughout
+our [Documentation][0].
+
+## Getting started
+
+Using `pip` and a virtual environment is the easiest way to get started with`ddfem`:
+
+```bash
+pip install ddfem
+```
+
+will install the basic package. We have mainly tested it with `dune` as solver backend and provide some extra features when used with `dune`. Currently the code relies on a pre-release version and the best way to guarantee compatibility is to use
+
+```bash
+pip install ddfem[dune]
+```
+
+On most machine you will also need to run
+
+```bash
+pip install mpi4py
+```
+
+The main example `intro` file in our tutorial can be obtained easily by running
+
+```
+python -m ddfem
+```
+
+This step can take some time (so do it before a coffee break) since it precompiles all required modules. This is done in parallel using `4` processes by default. Change that by adding a parameter to the above call, e.g., to use `8` processes run
+
+```
+python -m ddfem 8
+```
+
+After this step has completed you should find the two files `intro.py` and `intro_nb.ipynb` in your folder.
+
+Enjoy - and let use 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
+

{ddfem-1.0.8 → ddfem-1.0.10}/ddfem/__init__.py

@@ -65,7 +65,7 @@ def GridView(domain, omega=None, *,
 def solve(uflModel, domain):
     # we use a Lagrange space
     from dune.fem.space import lagrange
-    # and the build-in solver
+    # and the built-in solver
     from dune.fem.scheme import galerkin
 
     gridView = GridView(domain)

{ddfem-1.0.8 → ddfem-1.0.10}/ddfem/__main__.py

@@ -1,4 +1,4 @@
-import sys, os
+import sys, os, urllib
 try:
     import dune
 except ImportError:
@@ -28,7 +28,7 @@ def main():
         from dune.generator import builder
 
         module = "intro"
-        workers = 8
+        workers = 4
         if len(sys.argv)>1:
             workers = int(sys.argv[1])
             if len(sys.argv)>2:
@@ -56,5 +56,24 @@ def main():
                 with open(filename,"r") as f:
                     executor.submit( builder.load, file.replace(".cc",""), f.read(), None )
 
+        # make sure things are safe on Mac
+        # https://docs.python.org/3/library/urllib.request.html
+        os.environ["no_proxy"] = "*"
+
+        url = "https://gitlab.dune-project.org/dune-fem/ddfem/-/raw/improveDocBuild/doc/XXX?ref_type=heads"
+        if module == "all":
+            modules = ["boundary","examples","intro",
+                       "transformers", "geometry"]
+        else:
+            modules = [module]
+        for filebase in modules:
+            a = urllib.request.urlretrieve(
+                 url.replace("XXX",f"{filebase}.py"),
+                 filename=f"{filebase}.py")
+            b = urllib.request.urlretrieve(
+                 url.replace("XXX",f"{filebase}_nb.ipynb"),
+                 filename=f"{filebase}_nb.ipynb"
+                 )
+
 if __name__ == "__main__":
     main()

{ddfem-1.0.8 → ddfem-1.0.10}/ddfem/data/2.11.dev20250709/boundary.modules

@@ -5,5 +5,5 @@ referenceelements_0fff57b283123cc055345ec95574c857
 referenceelements_f4457f35395151d83a965d4cf5fce70d
 femspace_90f0a9524a8cb701e8ee5027b7658a0e_0faf32f13b591f4f60f83c591507b9be
 localfunction_fc22d5adaf3b9563160dc2aec55e8ba1_19659fe2f2f74bcfb5d532f1a0d38be9
-localfunction_c5ebc4ae4b5d3bad6be770eb08c50d08_19659fe2f2f74bcfb5d532f1a0d38be9
+localfunction_c3d0902cf8bb4b86b62a2293de2b74e9_19659fe2f2f74bcfb5d532f1a0d38be9
 localfunction_e69118a51208cfab8a028711e966e76c_19659fe2f2f74bcfb5d532f1a0d38be9

ddfem-1.0.10/ddfem/data/2.11.dev20250709/hierarchicalgrid_472c2c2d007bf5604887ab2f16b7eb13.cc

@@ -0,0 +1,30 @@
+#ifndef Guard_hierarchicalgrid_472c2c2d007bf5604887ab2f16b7eb13
+#define Guard_hierarchicalgrid_472c2c2d007bf5604887ab2f16b7eb13
+
+#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_472c2c2d007bf5604887ab2f16b7eb13, module )
+{
+  using pybind11::operator""_a;
+  pybind11::module cls0 = module;
+  {
+    using DuneType = Dune::YaspGrid< 3, Dune::EquidistantOffsetCoordinates< double, 3 > >;
+    auto cls = Dune::Python::insertClass< DuneType, std::shared_ptr<DuneType> >( cls0, "HierarchicalGrid",pybind11::dynamic_attr(), Dune::Python::GenerateTypeName("Dune::YaspGrid< 3, Dune::EquidistantOffsetCoordinates< double, 3 > >"), 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, 3 >& coordinates, std::array<bool, 3> periodic, int overlap ) {std::bitset<3> periodic_;
+        for (int i=0;i<3;++i) periodic_.set(i,periodic[i]);
+        return new DuneType(coordinates,periodic_,overlap);
+      } ), "coordinates"_a, "periodic"_a, "overlap"_a );
+  }
+}
+#endif