feectools 0.1.0__tar.gz

feectools-0.1.0/AUTHORS

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+Maintainers
+-----------
+* Yaman Güçlü <yaman.guclu@gmail.com> (original author, project lead)
+* Martin Campos Pinto <martin.campos-pinto@ipp.mpg.de>
+* Ahmed Ratnani <ratnaniahmed@gmail.com> (original author)
+
+Contributors
+------------
+* Said Hadjout (original author)
+* Julian Owezarek
+* Antoine Lavandier
+* Tom Caruso
+* Elena Moral Sánchez
+* Paul Rigor
+* Frederik Schnack
+* David Schneller
+* Valentin Carlier
+* Stefan Possanner
+* Jalal Lakhlili (original author)
+* William Barham
+* Max Lindqvist
+* Emily Bourne

feectools-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2018-2023, Psydac Developers.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

feectools-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: feectools
+Version: 0.1.0
+Summary: Slimmed-down fork of Psydac (https://github.com/pyccel/psydac) with less functionality and fewer dependencies.
+Author-email: Psydac development team <psydac@googlegroups.com>
+Maintainer-email: Stefan Possanner <stefan.possanner@ipp.mpg.de>, Max Lindqvist <max.lindqvist@ipp.mpg.de>, Yaman Güçlü <yaman.guclu@gmail.com>, Martin Campos Pinto <martin.campos-pinto@ipp.mpg.de>, Ahmed Ratnani <ratnaniahmed@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2018-2023, Psydac Developers.
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/struphy-hub/psydac-for-struphy
+Project-URL: Documentation, https://github.com/struphy-hub/psydac-for-struphy
+Project-URL: Repository, https://github.com/struphy-hub/psydac-for-struphy
+Keywords: FEM,IGA,B-spline,NURBS
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: AUTHORS
+Requires-Dist: numpy>=1.16
+Requires-Dist: scipy>=1.12
+Requires-Dist: sympy>=1.5
+Requires-Dist: matplotlib
+Requires-Dist: pyyaml>=5.1
+Requires-Dist: packaging
+Requires-Dist: pyevtk
+Requires-Dist: pyccel>=2.0.1
+Requires-Dist: h5py
+Requires-Dist: tblib
+Provides-Extra: test
+Requires-Dist: pytest-cov>=5.0.0; extra == "test"
+Requires-Dist: pytest>=4.5; extra == "test"
+Requires-Dist: pytest-xdist>=1.16; extra == "test"
+Requires-Dist: pytest-testmon; extra == "test"
+Requires-Dist: Pillow; extra == "test"
+Provides-Extra: mpi
+Requires-Dist: mpi4py>=4; extra == "mpi"
+Dynamic: license-file
+
+# Welcome!
+
+This is a fork of [Psydac](https://github.com/pyccel/psydac) that provides Finite Element Exterior Calculus (FEEC) for [Struphy](https://github.com/struphy-hub/struphy). It is a stripped-down version of the original repo with less functionality and fewer dependencies.
+
+The latest version can be installed with
+```
+pip install -U feectools
+```
+See the [Struphy documentation](https://struphy-hub.github.io/struphy/index.html) for details on how to use.

feectools-0.1.0/README.md

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+# Welcome!
+
+This is a fork of [Psydac](https://github.com/pyccel/psydac) that provides Finite Element Exterior Calculus (FEEC) for [Struphy](https://github.com/struphy-hub/struphy). It is a stripped-down version of the original repo with less functionality and fewer dependencies.
+
+The latest version can be installed with
+```
+pip install -U feectools
+```
+See the [Struphy documentation](https://struphy-hub.github.io/struphy/index.html) for details on how to use.

feectools-0.1.0/feectools/accelerate/accelerate.py

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+# Based on https://gitlab.mpcdf.mpg.de/struphy/struphy/-/blob/devel/src/struphy/console/compile.py
+import argparse
+import os
+import sys
+from shutil import which, rmtree
+from subprocess import run as sub_run, PIPE, STDOUT  # nosec B404
+import subprocess
+import sysconfig
+
+import feectools
+
+# Get the absolute path to the psydac directory
+psydac_path = os.path.abspath(feectools.__path__[0])
+libdir = sysconfig.get_config_var("LIBDIR")
+psydac_makefile_dir = os.path.join(psydac_path, "accelerate")
+
+def subp_run(cmd, cwd=None, check=True):
+    """Call subprocess.run and print run command."""
+
+    if cwd is None:
+        cwd = psydac_path
+
+    print(f"\nRunning the following command as a subprocess:\n{' '.join(cmd)}")
+    print(f"Running in directory: {cwd}")
+    subprocess.run(cmd, cwd=cwd, check=check)
+
+
+def psydac_compile(language, compiler_family, compiler_config, omp, delete, status, verbose, dependencies, yes):
+    """
+    Compile Psydac kernels. All files that contain "kernels" are detected automatically and saved to state.yml.
+
+    Parameters
+    ----------
+    language : str
+        Either "c" (default) or "fortran".
+
+    compiler_family : str
+        Either "GNU" (default), "intel", "PGI", "nvidia", "LLVM"
+
+    compiler_config: str
+        Path to a JSON compiler file.
+
+    omp_pic : bool
+        Whether to compile PIC kernels with OpenMP (default=False).
+
+    omp_feec : bool
+        WHether to compile FEEC kernels with OpenMP (default=False).
+
+    delete : bool
+        If True, deletes generated Fortran/C files and .so files (default=False).
+
+    status : bool
+        If true, prints the current Psydac compilation status on screen.
+
+    verbose : bool
+        Call pyccel in verbose mode (default=False).
+
+    dependencies : bool
+        Whether to print Psydac kernels (to be compiled) and their dependencies on screen.
+
+    yes : bool
+        Whether to say yes to prompt when changing the language.
+    """
+    if delete:
+        cleanup_files(psydac_path)
+        return
+
+    pyccel_path = which("pyccel")
+    if pyccel_path is None:
+        print(
+            "`pyccel` not found in PATH. Please ensure it is installed and accessible."
+        )
+        return
+
+    sources = []
+    # Cleanup if any files of the opposite language exist
+    cleanup = False
+    for root, _, files in os.walk(psydac_path):
+        for name in files:
+            if name.endswith("_kernels.py"):
+                file_path = os.path.join(root, name)
+                sources.append(file_path)
+                # Check if the corresponding pyccelized file already exists
+                subdir = "__pyccel__"
+                generated_file_fortran = os.path.join(root, subdir, name[:-3] + ".f90")
+                generated_file_c = os.path.join(root, subdir, name[:-3] + ".c")
+                if language == "fortran" and os.path.isfile(generated_file_c):
+                    cleanup = True
+                elif language == "c" and os.path.isfile(generated_file_fortran):
+                    cleanup = True
+    if cleanup:
+        if yes:
+            yesno = "Y"
+        else:
+            if language == "fortran":
+                compiled_in = "C"
+            else:
+                compiled_in = "fortran"
+            yesno = input(
+                f"Kernels compiled in language {compiled_in} exist, will be deleted, continue (Y/n)?"
+            )
+        if yesno in ("", "Y", "y", "yes"):
+            cleanup_files(psydac_path)
+        else:
+            return
+
+    # pyccel flags
+    # TODO: Compile psydac with OpenMP
+    flag_omp = ""
+    if omp:
+        flag_omp = "--openmp"
+    sources = " ".join(sources)
+    flags = "--language=" + language
+
+    if compiler_config:
+        flags += " --compiler-config=" + compiler_config
+    else:
+        flags += " --compiler-family=" + compiler_family
+
+    cmd = [
+        "make",
+        "-f",
+        "compile_psydac.mk",
+        "sources=" + sources,
+        "flags=" + flags,
+        "flags_openmp=" + flag_omp,
+    ]
+    print(os.path.join(libdir, "accelerate"))
+    subp_run(cmd, cwd=psydac_makefile_dir),
+
+
+def cleanup_files(root_path: str):
+    """
+    Remove unnecessary build artifacts, such as `__pyccel__` directories and `.lock_acquisition.lock` files.
+    """
+    sources = []
+    for root, _, files in os.walk(root_path):
+        for filename in files:
+            if filename.endswith("_kernels.py"):
+                file_path = os.path.join(root, filename)
+                sources.append(file_path)
+    sources = " ".join(sources)
+    # Delete using the makefile
+    cmd = [
+        "make",
+        "clean",
+        "-f",
+        "compile_psydac.mk",
+        "sources=" + sources,
+    ]
+    subp_run(cmd, cwd=psydac_makefile_dir)
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Pyccelize Psydac kernel files and optionally clean up build artifacts.",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    parser.add_argument(
+        "--language",
+        type=str,
+        default="c",
+        choices=["fortran", "c"],
+        help="Language used to pyccelize kernel files.",
+    )
+    parser.add_argument(
+        "--openmp",
+        action="store_true",
+        help="Use OpenMP multithreading in generated code.",
+    )
+    parser.add_argument(
+        "--cleanup",
+        action="store_true",
+        help="If True, deletes generated Fortran/C files and .so files (default=False).",
+    )
+    parser.add_argument(
+        "--compiler-family",
+        type=str,
+        default="GNU",
+        help='either "GNU" (default), "intel", "PGI", "nvidia" or the path to a JSON compiler file.',
+    )
+
+    parser.add_argument(
+        "--compiler-config",
+        type=str,
+        default=None,
+        help='Path to a JSON compiler file.',
+    )
+
+    parser.add_argument(
+        "--status", action="store_true", help="Show the status of pyccelization."
+    )
+    parser.add_argument("--verbose", action="store_true", help="Enable verbose output.")
+    parser.add_argument(
+        "--dependencies",
+        action="store_true",
+        help="Print Psydac kernels to be compiled (.py) and their dependencies (.so) on screen.",
+    )
+    parser.add_argument(
+        "--yes", action="store_true", help="Automatically answer 'yes' to prompts."
+    )
+
+    args = parser.parse_args()
+
+    # Assuming psydac_compile is a function defined elsewhere
+    psydac_compile(
+        language=args.language,
+        compiler_family=args.compiler_family,
+        compiler_config=args.compiler_config,
+        omp=args.openmp,
+        delete=args.cleanup,
+        status=args.status,
+        verbose=args.verbose,
+        dependencies=args.dependencies,
+        yes=args.yes,
+    )
+
+
+if __name__ == "__main__":
+    main()

feectools-0.1.0/feectools/accelerate/compile_psydac.mk

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+# Based on https://gitlab.mpcdf.mpg.de/struphy/struphy/-/blob/devel/src/struphy/compile_struphy.mk
+#--------------------------------------
+# CONFIGURATION
+#--------------------------------------
+
+PYTHON  := python3
+SO_EXT  := $(shell $(PYTHON) -c "import sysconfig; print(sysconfig.get_config_var('EXT_SUFFIX'))")
+LIBDIR  := $(shell $(PYTHON) -c "import sysconfig; print(sysconfig.get_config_var('LIBDIR'))")
+psydac_path := $(shell $(PYTHON) -c "import feectools as _; print(_.__path__[0])")
+
+# Arguments to this script are: 
+PSYDAC_SOURCES := $(sources)
+FLAGS := --libdir $(LIBDIR) $(flags) 
+FLAGS_openmp := $(flags_openmp)
+
+#--------------------------------------
+# SOURCE FILES 
+#--------------------------------------
+
+SOURCES := $(PSYDAC_SOURCES)
+
+OUTPUTS := $(SOURCES:.py=$(SO_EXT))
+
+#--------------------------------------
+# PYCCELIZE
+#--------------------------------------
+
+.PHONY: all
+all: $(OUTPUTS)
+
+# %$(SO_EXT) : %.py $$(shell $$(PYTHON)) $$(psydac_path)/dependencies.py $$@)
+.SECONDEXPANSION:
+%$(SO_EXT): %.py
+
+	@echo "Building $@"
+	@echo "from dependencies:"
+	@for dep in $^ ; do \
+		echo $$dep ; \
+    done
+	pyccel $(FLAGS)$(FLAGS_openmp) $<
+	@echo ""
+
+#--------------------------------------
+# CLEAN UP
+#--------------------------------------
+
+.PHONY: clean
+clean:
+	rm -rf $(OUTPUTS)
+	find $(psydac_path)/ -type d -name '__pyccel__' -prune -exec rm -rf {} \;
+	find $(psydac_path)/ -type d -name '__pycache__' -prune -exec rm -rf {} \;
+	find $(psydac_path)/ -type f -name '*.lock' -delete

feectools-0.1.0/feectools/api/essential_bc.py

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+# coding: utf-8
+from feectools.linalg.basic   import ComposedLinearOperator
+from feectools.linalg.stencil import StencilVector, StencilMatrix
+from feectools.linalg.stencil import StencilInterfaceMatrix
+from feectools.linalg.kron    import KroneckerDenseMatrix
+from feectools.linalg.block   import BlockVector, BlockLinearOperator
+
+
+#==============================================================================
+def apply_essential_bc_kronecker_dense_matrix(a, *, axis, ext, order, identity=False):
+    """ This function applies the homogeneous boundary condition to the Kronecker product matrix objects,
+        If the identity keyword argument is set to True, the boundary diagonal terms are set to 1.
+
+    Parameters
+    ----------
+    a : KroneckerDenseMatrix
+        The matrix to be modified.
+
+    axis : int
+        Axis of the boundary, i.e. the index of the coordinate which remains constant.
+
+    ext : int
+        Extremity of the boundary, it takes the value of -1 or 1.
+
+    order : int
+        All function derivatives up to `order` are set to zero
+        on the specified boundary. `order >= 0` is required.
+
+    identity : bool
+        If true, the diagonal terms corresponding to boundary coefficients are set to 1.
+    """
+
+    mats = a.mats
+    p = a.codomain.pads[axis]
+
+    if ext == 1:
+        mats[axis][-p-1] = 0.
+    elif ext == -1:
+        mats[axis][p] = 0.
+
+    if identity and ext == 1:
+        mats[axis][-p-1,mats[axis].shape[0]-2*p-1] = 1
+    elif identity and ext == -1:
+        mats[axis][p][0] = 1
+
+#==============================================================================
+def apply_essential_bc_stencil(a, *, axis, ext, order, identity=False):
+    """ This function applies the homogeneous boundary condition to the Stencil objects,
+        by setting the boundary degrees of freedom to zero in the StencilVector,
+        and the corresponding rows in the StencilMatrix/StencilInterfaceMatrix to zeros.
+        If the identity keyword argument is set to True, the boundary diagonal terms are set to 1.
+
+    Parameters
+    ----------
+    a : StencilVector, StencilMatrix or StencilInterfaceMatrix
+        The matrix or the Vector to be modified.
+
+    axis : int
+        Axis of the boundary, i.e. the index of the coordinate which remains constant.
+
+    ext : int
+        Extremity of the boundary, it takes the value of -1 or 1.
+
+    order : int
+        All function derivatives up to `order` are set to zero
+        on the specified boundary. `order >= 0` is required.
+
+    identity : bool
+        If True, the diagonal terms corresponding to boundary coefficients are set to 1.
+    """
+
+    if isinstance(a, StencilVector):
+        V = a.space
+        n = V.ndim
+    elif isinstance(a, StencilMatrix):
+        V = a.codomain
+        n = V.ndim * 2
+    elif isinstance(a, StencilInterfaceMatrix):
+        V = a.codomain
+        n = V.ndim * 2
+
+        if axis == a.codomain_axis:
+            return
+    else:
+        raise TypeError('Cannot apply essential BC to object {} of type {}'\
+                .format(a, type(a)))
+
+    if V.parallel and V.cart.is_comm_null:
+        return
+
+    if axis not in range(V.ndim):
+        raise ValueError('Cannot apply essential BC along axis x{} in {}D'\
+                .format(axis + 1, V.ndim))
+
+    if ext not in (-1, 1):
+        raise ValueError("Argument 'ext' can only be -1 or 1, got {} instead"\
+                .format(ext))
+
+    if not isinstance(order, int) or order < 0:
+        raise ValueError("Argument 'order' must be a non-negative integer, got "
+                "{} instead".format(order))
+
+    if V.periods[axis]:
+        raise ValueError('Cannot apply essential BC along periodic direction '\
+                'x{}'.format(axis + 1))
+
+    if ext == -1 and V.starts[axis] == 0:
+        s = V.starts[axis]
+        index = [(s + order if j == axis else slice(None)) for j in range(n)]
+        a[tuple(index)] = 0.0
+        if isinstance(a, StencilMatrix) and identity:
+            a[tuple(index[:n//2])+(0,)*(n//2)] = 1.
+
+    elif ext == 1 and V.ends[axis] == V.npts[axis] - 1:
+        e = V.ends[axis]
+        index = [(e - order if j == axis else slice(None)) for j in range(n)]
+        a[tuple(index)] = 0.0
+        if isinstance(a, StencilMatrix) and identity:
+            a[tuple(index[:n//2])+(0,)*(n//2)] = 1.
+    else:
+        pass
+