BeamMe 0.0.0__tar.gz

beamme-0.0.0/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2018-2025 MeshPy Authors
+
+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.

beamme-0.0.0/MANIFEST.in

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+include src/meshpy/geometric_search/cython_lib.pyx

beamme-0.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: BeamMe
+Version: 0.0.0
+Summary: BeamMe: A general purpose 3D beam finite element input generator
+Author: MeshPy Authors
+Maintainer-email: Ivo Steinbrecher <ivo.steinbrecher@unibw.de>, David Rudlstorfer <david.rudlstorfer@tum.de>
+License: The MIT License (MIT)
+        
+        Copyright (c) 2018-2025 MeshPy Authors
+        
+        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://imcs-compsim.github.io/meshpy/
+Project-URL: Documentation, https://imcs-compsim.github.io/meshpy/api-documentation/
+Project-URL: Repository, https://github.com/imcs-compsim/meshpy/
+Project-URL: Issues, https://github.com/imcs-compsim/meshpy/issues/
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: autograd
+Requires-Dist: geomdl
+Requires-Dist: ipykernel
+Requires-Dist: notebook
+Requires-Dist: numpy
+Requires-Dist: numpy-quaternion
+Requires-Dist: pyvista
+Requires-Dist: scipy
+Requires-Dist: splinepy
+Requires-Dist: vedo==2024.5.2
+Requires-Dist: vtk
+Provides-Extra: dev
+Requires-Dist: coverage-badge; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: pdoc; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: testbook; extra == "dev"
+Dynamic: license-file
+
+<div align="center">
+
+# MeshPy <!-- omit from toc -->
+</div>
+
+<div align="center">
+
+[![website](https://raw.githubusercontent.com/imcs-compsim/meshpy/refs/heads/main/doc/badges/website.svg)](https://imcs-compsim.github.io/meshpy/)
+[![documentation](https://raw.githubusercontent.com/imcs-compsim/meshpy/refs/heads/main/doc/badges/documentation.svg)](https://imcs-compsim.github.io/meshpy/api-documentation)
+
+</div>
+
+<div align="center">
+
+[![Code quality](https://github.com/imcs-compsim/meshpy/actions/workflows/check_code.yml/badge.svg)](https://github.com/imcs-compsim/meshpy/actions/workflows/check_code.yml?query=event%3Aschedule)
+[![Test suite](https://github.com/imcs-compsim/meshpy/actions/workflows/testing.yml/badge.svg)](https://github.com/imcs-compsim/meshpy/actions/workflows/testing.yml?query=event%3Aschedule)
+[![Coverage](https://imcs-compsim.github.io/meshpy/coverage-badge/coverage_badge.svg)](https://imcs-compsim.github.io/meshpy/coverage-report/)
+
+</div>
+
+<div align="center">
+
+[![Testing Linux/Ubuntu](https://raw.githubusercontent.com/imcs-compsim/meshpy/refs/heads/main/doc/badges/testing_linux_ubuntu.svg)](https://github.com/imcs-compsim/meshpy/actions/workflows/testing.yml?query=event%3Aschedule)
+[![Testing macOS](https://raw.githubusercontent.com/imcs-compsim/meshpy/refs/heads/main/doc/badges/testing_macos.svg)](https://github.com/imcs-compsim/meshpy/actions/workflows/testing.yml?query=event%3Aschedule)
+[![Testing Windows](https://raw.githubusercontent.com/imcs-compsim/meshpy/refs/heads/main/doc/badges/testing_windows.svg)](https://github.com/imcs-compsim/meshpy/actions/workflows/testing.yml?query=event%3Aschedule)
+
+</div>
+
+<div align="center">
+
+[![pre-commit](https://raw.githubusercontent.com/imcs-compsim/meshpy/refs/heads/main/doc/badges/pre-commit.svg)](https://pre-commit.com/)
+[![ruff-formatter](https://raw.githubusercontent.com/imcs-compsim/meshpy/refs/heads/main/doc/badges/ruff-formatter.svg)](https://docs.astral.sh/ruff/formatter)
+[![ruff-linter](https://raw.githubusercontent.com/imcs-compsim/meshpy/refs/heads/main/doc/badges/ruff-linter.svg)](https://docs.astral.sh/ruff/linter)
+
+</div>
+
+MeshPy is a general purpose 3D beam finite element input generator written in Python.
+It contains advanced geometry creation and manipulation functions to create complex beam geometries, including a consistent handling of finite rotations.
+It can be used to create input files for the following finite element solvers (adaption to other solvers is easily possibly):
+- [4C](https://www.4c-multiphysics.org/) (academic finite element solver)
+- [Abaqus](https://en.wikipedia.org/wiki/Abaqus) (commercial software package)
+- [AceFEM](http://symech.fgg.uni-lj.si) (Finite element package for automation of the finite element method in [Mathematica](https://www.wolfram.com/mathematica/))
+
+MeshPy is developed at the [Institute for Mathematics and Computer-Based Simulation (IMCS)](https://www.unibw.de/imcs-en) at the Universität der Bundeswehr München.
+
+## Overview <!-- omit from toc -->
+- [Examples](#examples)
+- [How to use MeshPy?](#how-to-use-meshpy)
+- [How to cite MeshPy?](#how-to-cite-meshpy)
+- [Work that uses MeshPy](#work-that-uses-meshpy)
+- [Installation](#installation)
+  - [Python environment](#python-environment)
+  - [Install MeshPy from source](#install-meshpy-from-source)
+- [Optional dependencies](#optional-dependencies)
+  - [4C](#4c)
+  - [CubitPy](#cubitpy)
+  - [ArborX geometric search](#arborx-geometric-search)
+- [Developing MeshPy](#developing-meshpy)
+  - [Coding guidelines](#coding-guidelines)
+  - [Testing](#testing)
+  - [Cython geometric search](#cython-geometric-search)
+- [Contributing](#contributing)
+- [Authors](#authors)
+
+## Examples
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/imcs-compsim/meshpy/refs/heads/main/doc/assets/honeycomb.png" width="350" title="Honeycomb structure under tension (simulated with 4C)">
+</p>
+<p align="center" style="font-style: italic; color: gray;">Honeycomb structure under tension (simulated with 4C)</p>
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/imcs-compsim/meshpy/refs/heads/main/doc/assets/composite_plate.png" width="400" title="Fiber reinforced composite plate (simulated with 4C)">
+</p>
+<p align="center" style="font-style: italic; color: gray;">Fiber reinforced composite plate (simulated with 4C)</p>
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/imcs-compsim/meshpy/refs/heads/main/doc/assets/pressure_pipe.png" width="350" title="Fiber reinforced pipe under pressure (simulated with 4C)">
+</p>
+<p align="center" style="font-style: italic; color: gray;">Fiber reinforced pipe under pressure (simulated with 4C)</p>
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/imcs-compsim/meshpy/refs/heads/main/doc/assets/twisted_plate.png" width="350" title="Fiber reinforcements of a twisted plate (simulated with 4C)">
+</p>
+<p align="center" style="font-style: italic; color: gray;">Fiber reinforcements of a twisted plate (simulated with 4C)</p>
+
+## How to use MeshPy?
+
+MeshPy provides example notebooks to showcase its core features and functionality.
+The examples can be found in the `examples/` directory.
+They can be run locally or directly tested from your browser via the following links:
+
+- Example 1: **Finite rotation framework** [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/imcs-compsim/meshpy/main?labpath=examples%2Fexample_1_finite_rotations.ipynb)
+- Example 2: **Core mesh generation functions** [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/imcs-compsim/meshpy/main?labpath=examples%2Fexample_2_core_mesh_generation_functions.ipynb)
+
+You can also interactively test the entire MeshPy framework directly from your browser here [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/imcs-compsim/meshpy/main)
+
+
+## How to cite MeshPy?
+
+Whenever you use or mention MeshPy in some sort of scientific document/publication/presentation, please cite MeshPy as
+> Steinbrecher, I., Popp, A.: MeshPy - A general purpose 3D beam finite element input generator, https://imcs-compsim.github.io/meshpy
+
+This can be done with the following BiBTeX entry:
+```TeX
+@Misc{MeshPyWebsite,
+  author       = {Steinbrecher, I. and Popp, A.},
+  howpublished = {\url{https://imcs-compsim.github.io/meshpy}},
+  title        = {{M}esh{P}y -- {A} general purpose {3D} beam finite element input generator},
+  year         = {2021},
+  key          = {MeshPyWebsite},
+  url          = {https://imcs-compsim.github.io/meshpy},
+}
+```
+
+Feel free to leave a ⭐️ on [GitHub](https://github.com/imcs-compsim/meshpy).
+
+
+## Work that uses MeshPy
+
+### Peer-reviewed articles <!-- omit from toc -->
+
+1. </span><span class="csl-right-inline">Datz, J.C., Steinbrecher, I.,
+Meier, C., Engel, L.C., Popp, A., Pfaller, M.R., Schunkert, H., Wall, W.A.:
+Patient-specific coronary angioplasty simulations — A mixed-dimensional
+finite element modeling approach. Computers in Biology and Medicine. 189,
+109914 (2025).
+<https://doi.org/10.1016/j.compbiomed.2025.109914></span>
+1. </span><span class="csl-right-inline">Firmbach, M., Steinbrecher, I.,
+Popp, A., Mayr, M.: An approximate block factorization preconditioner
+for mixed-dimensional beam-solid interaction. Computer Methods in
+Applied Mechanics and Engineering. 431, 117256 (2024).
+<https://doi.org/10.1016/j.cma.2024.117256></span>
+1. </span><span class="csl-right-inline">Hagmeyer, N., Mayr, M., Popp, A.:
+A fully coupled regularized mortar-type finite element approach for
+embedding one-dimensional fibers into three-dimensional fluid flow.
+International Journal for Numerical Methods in Engineering. 125, e7435
+(2024). <https://doi.org/10.1002/nme.7435></span>
+1. </span><span class="csl-right-inline">Steinbrecher, I., Popp, A., Meier,
+C.: Consistent coupling of positions and rotations for embedding 1D
+Cosserat beams into 3D solid volumes. Computational Mechanics. 69,
+701–732 (2022). <https://doi.org/10.1007/s00466-021-02111-4></span>
+1. </span><span class="csl-right-inline">Hagmeyer, N., Mayr, M.,
+Steinbrecher, I., Popp, A.: One-way coupled fluid-beam interaction:
+Capturing the effect of embedded slender bodies on global fluid flow and
+vice versa. Advanced Modeling and Simulation in Engineering Sciences. 9,
+9 (2022). <https://doi.org/10.1186/s40323-022-00222-y></span>
+1. </span><span class="csl-right-inline">Steinbrecher, I., Mayr, M., Grill,
+M.J., Kremheller, J., Meier, C., Popp, A.: A mortar-type finite element
+approach for embedding 1D beams into 3D solid volumes. Computational
+Mechanics. 66, 1377–1398 (2020).
+<https://doi.org/10.1007/s00466-020-01907-0></span>
+
+### PhD thesis <!-- omit from toc -->
+
+1. </span><span class="csl-right-inline">Hagmeyer, N.: A computational
+framework for balloon angioplasty and stented arteries based on
+mixed-dimensional modeling,
+<https://athene-forschung.rz.unibw-muenchen.de/146359>, (2023)</span>
+1. </span><span class="csl-right-inline">Steinbrecher, I.:
+Mixed-dimensional finite element formulations for beam-to-solid
+interaction, <https://athene-forschung.unibw.de/143755>, (2022)</span>
+
+
+## Installation
+
+### Python environment
+
+MeshPy is tested with, and supports Python versions 3.9-3.12. It is recommended to use a virtual Python environment such as [Conda](https://anaconda.org/anaconda/conda)/[Miniforge](https://conda-forge.org/download/) or [venv](https://docs.python.org/3/library/venv.html).
+- A [Conda](https://anaconda.org/anaconda/conda)/[Miniforge](https://conda-forge.org/download/) environment can be created and loaded with
+  ```bash
+  # Create the environment (this only has to be done once)
+  conda create -n meshpy python=3.12
+  # Activate the environment
+  conda activate meshpy
+  ```
+- A [venv](https://docs.python.org/3/library/venv.html) virtual environment can be created and loaded with (on Debian systems the following packages might have to be installed:
+    `sudo apt-get install python3-venv python3-dev`)
+  ```bash
+  # Create the environment (this only has to be done once)
+  python -m venv <path-to-env-folder>/meshpy-env
+  # Activate the environment
+  source <path-to-env-folder>/meshpy-env/bin/activate
+  ```
+
+### Install MeshPy from source
+
+You can either install MeshPy directly from the source in a non-editable and editable fashion like:
+- Non-editable:
+  This allows you to use MeshPy, but changing the source code will not have any effect on the installed package
+  ```bash
+  git clone git@github.com:imcs-compsim/meshpy.git
+  cd meshpy
+  pip install .
+  ```
+- Editable:
+  This allows you to change the source code without reinstalling the module
+  ```bash
+  git clone git@github.com:imcs-compsim/meshpy.git
+  cd meshpy
+  pip install -e .
+  ```
+Now you are able to use MeshPy. A good way to get started is by going through the examples
+```bash
+jupyter notebook examples/
+```
+If you also want to execute the associated test suite check out our [development](#developing-meshpy) section.
+
+
+## Optional dependencies
+
+### [4C](https://www.4c-multiphysics.org)
+
+MeshPy can run 4C simulations directly from within a Python script, allowing for full control over arbitrarily complex simulation workflows. Fore more information, please have a look at the `meshpy.four_c.run_four_c` module.
+
+### [CubitPy](https://github.com/imcs-compsim/cubitpy)
+
+CubitPy is a Python library that contains utility functions extending the Cubit/Coreform Python interface. Furthermore, it allows for the easy creation of 4C-compatible input files directly from within Python. MeshPy can import meshes created with CubitPy and allows for further modification and manipulation of them.
+
+CubitPy can be installed as an optional dependency with:
+```bash
+pip install -e .[cubitpy]
+```
+
+### [ArborX](https://github.com/arborx/ArborX) geometric search
+
+MeshPy can optionally execute its geometric search functions using the C++ library [ArborX](https://github.com/arborx/ArborX).
+First make sure the [pybind11](https://pybind11.readthedocs.io/en/stable/) submodule is loaded
+```bash
+cd <path_to_meshpy>
+git submodule update --init
+```
+To setup MeshPy with ArborX, [CMake](https://cmake.org) and [Kokkos](https://kokkos.org) have to be available on your system (the preferred variant is via [Spack](https://spack.io/)).
+Create a build directory
+```bash
+mkdir -p <path_to_meshpy>/src/build/geometric_search
+```
+Configure cmake and build the extension
+```bash
+cd <path_to_meshpy>/build/geometric_search
+cmake ../../meshpy/geometric_search/src/
+make -j4
+```
+> Note: Currently ArborX only works if MeshPy is installed in _editable_ mode.
+
+## Developing MeshPy
+
+If you want to actively develop MeshPy or run the test suite, you must install MeshPy in _editable_ (`-e`) mode and with our optional developer dependencies (`[dev]`) like
+```bash
+pip install -e ".[dev]" # Quotation marks are required for some shells
+```
+You can now run the MeshPy test suite to check that everything worked as expected
+```bash
+pytest
+```
+
+### Coding guidelines
+
+- When working on MeshPy, use a leading underscore (`_`) to indicate functions, classes, and variables that are intended for internal use only. This is a coding convention rather than an enforced rule, so apply it where it improves code clarity, especially for functions that check consistency or modify internal states.
+- To avoid ambiguous or incorrect imports when using MeshPy as a library, internal imports must follow a strict aliasing convention as illustrated below:
+  <details>
+
+  <summary>Import guidelines</summary>
+
+  ```python
+  # Not OK
+  import numpy  # No alias
+  import numpy as np  # Missing leading underscore
+
+  from numpy import *  # Wildcard imports
+  from numpy import _core  # We don't allow the import of private functionality
+  from numpy.linalg import norm  # No alias
+  from numpy import sin as sin2  # Missing leading underscore
+  from meshpy.core.mesh import Mesh as _BeamMesh  # MeshPy imports have to be aliased with the same name, i.e., should be `_Mesh` (imports from third party libraries can be renamed)
+
+  # OK
+  import numpy as _np
+  import sys as _sys
+
+  from pathlib import Path as _Path
+
+  from math import sin as _math_sin
+  from numpy import sin as _np_sin
+
+  import meshpy.core.conf as _conf
+  from meshpy.core.mesh import Mesh as _Mesh
+  from meshpy.core.node import Node as _Node
+  from meshpy.core.node import NodeCosserat as _NodeCosserat
+  ```
+  </details>
+
+### Testing
+
+MeshPy provides a flexible testing system where additional tests can be enabled using specific flags. The following flags can be used with [pytest](https://pytest-cov.readthedocs.io/en/latest/config.html) to enable specific test sets:
+ - `--exclude-standard-tests`: Disables the default test suite
+ - `--4C`: Runs tests related to 4C integration
+ - `--ArborX`: Enables tests for ArborX-related functionality
+ - `--CubitPy`: Runs tests for CubitPy integration
+ - `--performance-tests`: Includes performance tests
+
+These flags can be combined arbitrarily; for example, to run the 4C, CubitPy, and ArborX tests but exclude the default test suite, use:
+```bash
+# 4C Tests require a path to a 4C executable
+export MESHPY_FOUR_C_EXE=<path_to_4C>
+# CubitPy Tests require a path to a Cubit/Coreform installation
+export CUBIT_ROOT=<path_to_Cubit_or_Coreform>
+
+pytest --4C --ArborX --CubitPy --exclude-standard-tests
+```
+
+### Cython geometric search
+
+Some performance critical geometric search algorithms in MeshPy are written in [Cython](https://cython.readthedocs.io/en/stable/index.html). If Cython code is changed, it has to be recompiled. This can be done by running
+```bash
+python setup.py build_ext --inplace
+```
+
+## Contributing
+
+If you are interested in contributing to MeshPy, we welcome your collaboration.
+For general questions, feature request and bug reports please open an [issue](https://github.com/imcs-compsim/meshpy/issues).
+
+If you contribute actual code, fork the repository and make the changes in a feature branch.
+Depending on the topic and amount of changes you also might want to open an [issue](https://github.com/imcs-compsim/meshpy/issues).
+To merge your changes into the MeshPy repository, create a pull request to the `main` branch.
+A few things to keep in mind:
+- Read our [coding guidelines](#coding-guidelines).
+- It is highly encouraged to add tests covering the functionality of your changes, see the test suite in `tests/`.
+- To maintain high code quality, MeshPy uses a number of different pre-commit hooks to check committed code. Make sure to set up the pre-commit hooks before committing your changes
+  ```bash
+  pre-commit install
+  ```
+- Check that you did not break anything by running the MeshPy tests.
+  For most changes it should be sufficient to run the standard test suite:
+  ```bash
+  pytest
+  ```
+- Feel free to add yourself to the authors section in the [README.md](https://github.com/imcs-compsim/meshpy/blob/main/README.md) file.
+
+
+## Authors
+
+### Maintainers <!-- omit from toc -->
+- Ivo Steinbrecher (@isteinbrecher)
+- David Rudlstorfer (@davidrudlstorfer)
+
+### Contributors (in alphabetical order) <!-- omit from toc -->
+- Dao Viet Anh
+- Max Firmbach (@maxfirmbach)
+- Martin Frank (@knarfnitram)
+- Nora Hagmeyer (@NoraHagmeyer)
+- Matthias Mayr (@mayrmt)
+- Gabriela Loera (@eulovi)