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Closes pyccel#476: * Do not restrict the maximum Python version to 3.12 in `pyproject.toml` * Require `Cython >= 3` to avoid `h5py` installation crash w/ Python 3.13 * Require `sympde == 0.19.2` which supports Python 3.13 * Run unit tests with Python 3.13 too
Currently, Psydac can not be used on Apple M4 computers since the `PSYDAC_BACKEND_GPYCCEL['flags']` is not set correctly. This change sets the flag for `Apple MX (etc.)` to `apple-mX`, which should work so long as the naming scheme stays unchanged. In addition, the regular expression used to find the GFortran version is now defined in a raw string instead of a standard Python UTF8 string. This avoids a `SyntaxWarning: invalid escape sequence`. --------- Co-authored-by: Yaman Güçlü <yaman.guclu@gmail.com>
* Use raw strings for docstrings with LaTeX to avoid UTF8 syntax warnings on escape sequences; * Use CSC matrices to avoid SciPy sparse solver warning. We do not address the NumPy warnings which arise in our MPI unit tests (see pyccel#353).
…yccel#484) Main changes -------------- * Rename the method `dot` of the base class `VectorSpace` as `inner`, and make it an abstract method (which must be implemented by the subclasses). * Rename the method `dot` of the base class `Vector` as `inner`. This is a concrete method which calls `self.space.inner` and does not need to be overridden by the subclasses. * Add `inner` methods to the classes `StencilVector`, `BlockVectorSpace`, and `DenseVectorSpace`. These methods override the abstract method of the base class as required, and are derived from the former functions `Stencil.dot`, `BlockVector.dot`, and `DenseVector.dot`, which have been removed (see next point). * Remove the property `dtype` and the method `dot` (now `inner`) from the classes `StencilVector`, `BlockVector`, and `DenseVector`, because the default methods of the base class already provide a sufficient implementation. This fixes pyccel#330. Necessary additional changes ------------------------------ * Update all linear solvers in `linalg.solvers` with the new method calls; * Update all unit tests with the new method calls, in files: - `api/tests/test_assembly.py` - `feec/tests/test_commuting_projections.py` - `feec/tests/test_global_projectors.py` - `linalg/tests/test_block.py` - `linalg/tests/test_linalg.py` - `linalg/tests/test_stencil_interface_matrix.py` - `linalg/tests/test_stencil_vector.py` Unrelated additional changes ----------------------------- * Rename the class `VectorDot` as `VectorInner` in module `api.ast.linalg`, although never used in Psydac. * Speed up 3D unit tests in: - `feec/tests/test_commuting_projectors.py` - `feec/tests/test_global_projectors.py`
--------- Co-authored-by: Yaman Güçlü <yaman.guclu@gmail.com>
…yccel#493) Implement `M.dot(u).inner(v)`, or `(M @ u).inner(v)`, without creating a temporary vector. The result of the dot product is written to a local work vector stored in the `LinearOperator` object. This work vector is then used to compute the inner product with the vector `v`. The subclasses do not need to override this method, unless a more efficient implementation which avoids writing to the work vector altogether (reducing memory pressure) is needed. A unit test is added: function `test_dot_inner` in file psydac/linalg/tests/test_linalg.py. Additionally, the helper function `get_StencilVectorSpace` defined in psydac/linalg/tests/test_linalg.py (only used in the same file and in test_matrix_free.py) has a new signature and now works in any number of dimensions. Fixes pyccel#491.
This PR changes the code generation involved in the `discretize` function to avoid calculating unnecessary derivatives. This allows for using constant spline (degree 0) discretizations, for which we have to make a special case in the calculation of ghost regions in `psydac/linalg/stencil.py`. Additionally, we add basic unit tests checking discretizations using zero-degree splines. This fixes pyccel#489 and fixes pyccel#307. On this occasion, we also do small changes in the `.github/workflows/testing.yml` script as some tests had complications without them. --------- Co-authored-by: Yaman Güçlü <yaman.guclu@gmail.com>
Always use the maximum padding between test and trial spaces in `allocate_matrices` in `DiscreteBilinearForm`. (Earlier this was not done in the case of scalar spaces.) Fixes pyccel#504.
Pyccel 2.0 was just released, which means some of the kernels in Psydac need to be updated: - Remove the `template` decorator (see pyccel/pyccel#2331) * Add `T` as `TypeVar` * Specify `T`, `T[:]`, `T[:,:]`, ... in function arguments. - Replace `@types` decorators (see pyccel/pyccel#2329) - Replace `const` with `Final` (see pyccel/pyccel#2340) Further changes: - Update import path for `epyccel` (fixes pyccel#426) - Update arguments to `epyccel` (see pyccel/pyccel#2348): * Rename `fflags` to `flags` * Replace `accelerators` list with `openmp` bool - Require Pyccel >= 2.0.1 (fixes pyccel#471) --------- Co-authored-by: Yaman Güçlü <yaman.guclu@gmail.com> Co-authored-by: Elena Moral Sánchez <Elena.Moral.Sanchez@ipp.mpg.de> Co-authored-by: Emily Bourne <louise.bourne@gmail.com>
Recently the installation of `h5py` in parallel mode (i.e. with MPI support through `mpi4py`) seems to have been simplified. This may be due to the recent move of `mpi4py` to wheels, or other factors. Therefore we can now simplify our installation procedure as follows: ```sh pip install h5py --no-cache-dir --no-binary h5py pip install .[test] ``` We update here the CI workflows and completely rewrite our README file. **Commit summary** - Completely rewrite `README.md`: * Expand initial description * Add Citing and Contributing sections * Shorten Installation section * Reorganize documentation sections * Move detailed installation instructions to separate file `docs/installation.md` * Move mesh generation to separate file `docs/psydac-mesh.md` - Add BibTeX file `CITING.bib` with citation of 2022 ECCOMAS proceedings - Remove obsolete files `requirements.txt` and `requirements_extra.txt` - Rename (and move) `docs_requirements.txt` as `docs/requirements.txt` - Update installation procedure in `testing` CI workflow - Change name in `testing` workflow from "Run tests" to "Unit tests" - Modify `testing` and `documentation` workflows so that they only run when needed - Allow running workflows manually - Fix broken CI badge in `README.md`
This PR implements the sum factorization algorithm as shown in **Sum factorization techniques in Isogeometric Analysis** by Andrea Bressan & Stefan Takacs for **bilinear forms on 3D volumes**. The old element-by-element assembly can still be employed by passing a corresponding flag ```python # a some BilinearForm a_h = discretize(a, domain_h, (Vh, Vh), backend=backend, sum_factorization=False) ``` Currently, the new generated code does not make use of OpenMP. Main changes -------------- - Write new module `psydac.api.fem_common` which: * Contains the old functions previously in module `psydac.api.fem`. * Has functions `construct_test_space_arguments` and `construct_trial_space_arguments` returning also the multiplicity. * Has new functions `compute_max_nderiv`, `compute_imports`, `compute_free_arguments`. - Move `DiscreteSumForm` to a new module `psydac.api.fem_sum_form`. - Create a new module `psydac.api.fem_bilinear_form` which only contains one new class `DiscreteBilinearForm`. The new module shows all imports clearly. The new class: * Generates the code to assemble the given discrete bilinear form into a matrix (a `BlockLinearOperator` object of `StencilMatrix` objects, or just a single `StencilMatrix` object), using sum factorization. * Does not inherit from `BasicDiscrete` (and hence `BasicCodeGen`). Accordingly, no PSYDAC abstract syntax tree (an object representing a function, of class `DefNode`) is created by the constructor of `AST`, which stores it in its `expr` attribute. (Both classes `DefNode` and `AST` are defined in module `psydac.api.ast.fem`.) * Does not create a `Parser` object from `psydac.api.ast.parser`, which used to convert a PSYDAC `DefNode` to an old-Pyccel `FunctionDef` from `psydac.pyccel.ast.core`. * Does not generate the old assembly Python code (in the form of a string) using the function `pycode` from `psydac.pyccel.codegen.printing.pycode`. - Add a new unit test file `api/tests/test_sum_factorization_assembly_3d`. - Modify function `discretize` in module `psydac.api.discretization` so that, given a bilinear form in 3D and not asking for OpenMP support, it creates an object of type `DiscreteBilinearForm` from module `psydac.api.fem_bilinear_form`. In all other cases, or if `sum_factorization=False`, it creates an object of namesake type from the old module `psydac.api.fem`. Other changes -------------- - Expand docstring of class `AST` in module `psydac.api.ast.fem`. - Expand docstrings of function `parse` and class `Parser` in module `psydac.api.ast.parser`. Clean up `Parser.__init__`. - Minor cleanup in class `BasicCodeGen` in module `psydac.api.basic`. - Generate random filenames using `random.choice()` instead of `random.SystemRandom().choice()`. Unrelated to matrix assembly: - Add method `set_scalar` to `ScaledLinearOperator`. - Reimplement method `idot` of `LinearOperator` using local storage. This avoids creating unnecessary temporary vectors (especially beneficial for the method `dot` of `SumLinearOperator`). --------- Co-authored-by: Yaman Güçlü <yaman.guclu@gmail.com> Co-authored-by: elmosa <Elena.Moral.Sanchez@ipp.mpg.de>
### Commit summary - Fix pyccel#461 : Move contents of `psydac/feec/multipatch/api.py` to `psydac/api/feec.py` and `psydac/api/discretization.py`. - Remove old code from `psydac/feec/multipatch/operators.py` and replace it by the contents in `psydac/feec/multipatch/non_matching_operators.py` to make the structure more clear. - Fix pyccel#463 - Fix pyccel#272 : keep the `FEMLinearOperator` as a more light-weight class that encapsulates a `LinearOperator` and has a `apply` and `__call__` function to make it act on a `FEMField`. Remove duplicated code with `LinearOperator`. Make operators in `psydac/feec` subclasses of `LinearOperator`. - Fix pyccel#462: Add conforming projections and Hodge operators to single-patch `DiscreteDeRham` - Add single-patch test for the conforming projectors - Adapt all the tests/files to the new notations. For the single patch cases mostly renaming `derham_h.derivatives` to `derham_h.derivatives()` and `derham_h.derivatives_as_matrices` to `derham_h.derivatives(kind='linop')` - Merge single-patch and multi-patch operators to the same file if it makes things clearer. Take Hodge and conforming projection operators out of the multipatch subdirectory. - Fix pyccel#409 : the global projector interface in DiscreteDeRhamMultipatch - Fix pyccel#331. - Add a `SparseMatrixLinearOperator` in `psydac/linalg/sparse.py` to use a sparse matrix as a `LinearOperator`. This is needed for the conforming projections. - Rename `GlobalProjectors` to `GlobalGeometricProjectors` ### Notes With the current changes, we get all FEEC operators directly from the discrete de Rham object. Further, the same code also runs if the domain is a single patch. --------- Co-authored-by: Yaman Güçlü <yaman.guclu@gmail.com>
Add the optional parameter `mpi_dims_mask` to the constructor of class `Geometry`, as well as its class methods `from_discrete_mapping` and `from_topological_domain`. Add unit tests to verify that the domain is correctly decomposed. --------- Co-authored-by: Alisa Kirkinskaia <alisa.kirkinskaia@tum.de> Co-authored-by: Alisa Kirkinskaia <alisa.kirkinsk@gmail.com>
Fix `examples/poisson_2d_mapping.py`: - Use renamed method `get_assembly_grids` (formerly `get_quadrature_grids`) of class `TensorFemSpace` - Add missing definition of `Vnew` variable in the case of distributed visualization - Avoid string warnings
Fix bug in method `plot_2d_decomposition` of `TensorFemSpace`, which was failing when run in parallel with a distributed spline mapping. - Create a new test file `psydac/fem/tests/test_tensor.py` with a unit test which fails on the `devel` branch. This compares the generated PNG images with "reference" ones which are known to be correct, within a 2 % relative tolerance on each of the RGB channels. - Only evaluate mapping in local subdomain owned by process - Gather global mapping information on root process - Add optional parameters `fig`, `ax`, and `mpi_root` - Add docstring - Update `examples/poisson_2d_mapping.py` to pass the correct mapping (i.e. also a distributed spline mapping if that is used in the computations) to `plot_2d_decomposition`.
Add a NOTE block with the meaning of the PSYDAC acronym, as well as its pronounciation.
spossann
marked this pull request as ready for review
November 7, 2025 07:06
spossann
marked this pull request as draft
November 7, 2025 07:06
spossann
marked this pull request as ready for review
November 10, 2025 09:16
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Version number changed to
2.6.0.dev0.There are some important changes to Psydac routines we use, see struphy-hub/struphy#108
For testing Psydac, Struphy is installed from branch 108-psydac-change-renaming-of-globalpojector here, this will be changes back in the next PR.