jitr 0.3__tar.gz

jitr-0.3/.github/workflows/pypi-publish.yml

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+# This workflow will publish releases to https://pypi.org/project/jitr
+
+name: PyPI publish
+
+on:
+  release:
+    types: [published]
+  
+jobs:
+  pypi-publish:
+    name: Build and upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/jitr/    
+    permissions:
+      id-token: write  
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: >-
+        python3 -m
+        build
+        --sdist
+        --wheel
+        --outdir dist/
+        .
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.PYPI_ACCESS_TOKEN }}

jitr-0.3/.github/workflows/python-package.yml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+    
+    permissions:
+      # Give the default GITHUB_TOKEN write permission to commit and push the changed files back to the repository.
+      contents: write
+
+    runs-on: ubuntu-latest
+    
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9"]
+    
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        token: ${{ secrets.PAT }}
+        ref: ${{ github.head_ref }}
+ 
+    - name: black
+      uses: lgeiger/black-action@v1.0.1
+      with:
+        args: .
+ 
+    - name: Check for modified files
+      id: git-check
+      run: echo "modified=$(if git diff-index --quiet HEAD --; then echo "false"; else echo "true"; fi)" >> $GITHUB_OUTPUT
+ 
+    - name: Push changes
+      if: steps.git-check.outputs.modified == 'true'
+      uses: stefanzweifel/git-auto-commit-action@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    
+    - name: Install package and dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        pip install .
+    
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    
+    - name: Test with pytest
+      run: |
+        pytest

jitr-0.3/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+
+## scm versioning
+__version__.py

jitr-0.3/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2023, Kyle Beyer
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

jitr-0.3/PKG-INFO

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+Metadata-Version: 2.1
+Name: jitr
+Version: 0.3
+Summary: Calculable R-matrix solver for quantum scattering using just-in-time compilation for performance.
+Author-email: Kyle Beyer <beykyle@umich.edu>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2023, Kyle Beyer
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: mpmath
+Requires-Dist: matplotlib
+
+[![Python package](https://github.com/beykyle/jitr/actions/workflows/python-package.yml/badge.svg)](https://github.com/beykyle/jitr/actions/workflows/python-package.yml)
+# Just-In-Time R-matrix (JITR)
+## Quick start
+```
+ pip install jitr
+```
+
+## Description
+Solves the radial Bloch-Shrödinger equation in the continuum using the calculable R-Matrix method on a Lagrange-Legendre mesh, using just-in-time (JIT) compilation from [`numba`](https://numba.pydata.org/). The theory generally follows:
+- Descouvemont, P. (2016). An R-matrix package for coupled-channel problems in nuclear physics. Computer physics communications, 200, 199-219,
+- Baye, D. (2015). The Lagrange-mesh method. Physics reports, 565, 1-107,
+
+with the primary difference being that this code uses the energy-scaled version of the Bloch-Shrödinger equation, with dimensionless domain, $s = kr$, where $r$ is the radial coordinate and $k$ is the channel wavenumber.
+
+Capable of:
+- non-local interactions
+- coupled-channels
+
+
+## Simple example
+
+

jitr-0.3/README.md

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+[![Python package](https://github.com/beykyle/jitr/actions/workflows/python-package.yml/badge.svg)](https://github.com/beykyle/jitr/actions/workflows/python-package.yml)
+# Just-In-Time R-matrix (JITR)
+## Quick start
+```
+ pip install jitr
+```
+
+## Description
+Solves the radial Bloch-Shrödinger equation in the continuum using the calculable R-Matrix method on a Lagrange-Legendre mesh, using just-in-time (JIT) compilation from [`numba`](https://numba.pydata.org/). The theory generally follows:
+- Descouvemont, P. (2016). An R-matrix package for coupled-channel problems in nuclear physics. Computer physics communications, 200, 199-219,
+- Baye, D. (2015). The Lagrange-mesh method. Physics reports, 565, 1-107,
+
+with the primary difference being that this code uses the energy-scaled version of the Bloch-Shrödinger equation, with dimensionless domain, $s = kr$, where $r$ is the radial coordinate and $k$ is the channel wavenumber.
+
+Capable of:
+- non-local interactions
+- coupled-channels
+
+
+## Simple example
+
+

jitr-0.3/examples/coupled.py

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+import numpy as np
+from matplotlib import pyplot as plt
+
+from jitr import (
+    ProjectileTargetSystem,
+    RadialSEChannel,
+    LagrangeRMatrix,
+    woods_saxon_potential,
+    coulomb_potential,
+    surface_peaked_gaussian_potential,
+    complex_det,
+    delta,
+    smatrix,
+    schrodinger_eqn_ivp_order1,
+)
+
+
+def coupled_channels_example(visualize=False):
+    """
+    3 level system example with local diagonal and transition potentials and neutral
+    particles. Potentials are real, so S-matrix is unitary and symmetric
+    """
+    mass = 939  # reduced mass of scattering system MeV / c^2
+
+    # Potential parameters
+    V = 60  # real potential strength
+    W = 0  # imag potential strength
+    R = 4  # Woods-Saxon potential radius
+    a = 0.5  # Woods-Saxon potential diffuseness
+    params = (V, W, R, a)
+
+    nodes_within_radius = 10
+
+    system = ProjectileTargetSystem(
+        incident_energy=50,
+        reduced_mass=939,
+        channel_radius=5 * (2 * np.pi),
+        num_channels=3,
+        level_energies=[0, 12, 20],
+    )
+
+    l = 0
+
+    matrix = np.empty((3, 3), dtype=object)
+
+    # diagonal potentials are just Woods-Saxons
+    for i in range(system.num_channels):
+        matrix[i, i] = RadialSEChannel(
+            l=l,
+            system=system,
+            interaction=lambda r: woods_saxon_potential(r, params),
+            threshold_energy=system.level_energies[i],
+        )
+
+    # transition potentials have depths damped by a factor compared to diagonal terms
+    # and use surface peaked Gaussian form factors rather than Woods-Saxons
+    transition_dampening_factor = 1
+    Vt = V / transition_dampening_factor
+    Wt = W / transition_dampening_factor
+
+    # off diagonal potential terms
+    for i in range(system.num_channels):
+        for j in range(system.num_channels):
+            if i != j:
+                matrix[i, j] = RadialSEChannel(
+                    l=l,
+                    system=system,
+                    interaction=lambda r: surface_peaked_gaussian_potential(
+                        r, (Vt, Wt, R, a)
+                    ),
+                    threshold_energy=system.level_energies[i],
+                )
+
+    solver_lm = LagrangeRMatrix(40, system, matrix)
+
+    H = solver_lm.bloch_se_matrix()
+
+    if visualize:
+        for i in range(3):
+            for j in range(3):
+                plt.imshow(np.real(solver_lm.single_channel_bloch_se_matrix(i, j)))
+                plt.xlabel("n")
+                plt.ylabel("m")
+                plt.colorbar()
+                plt.title(f"({i}, {j})")
+                plt.show()
+
+    # get R and S-matrix, and both internal and external soln
+    R, S, uint = solver_lm.solve_wavefunction()
+
+    # S must be unitary
+    assert np.isclose(complex_det(S), 1.0)
+    # S is symmetric iff the correct factors of momentum are applied
+    # assert np.allclose(S, S.T)
+
+    r_values = np.linspace(0.05, 40, 500)
+    s_values = np.linspace(0.05, system.channel_radius, 500)
+
+    lines = []
+    for i in range(system.num_channels):
+        u_values = uint[i].uint()(s_values)
+        (p1,) = plt.plot(s_values, np.real(u_values), label=r"$n=%d$" % i)
+        (p2,) = plt.plot(s_values, np.imag(u_values), ":", color=p1.get_color())
+        lines.append([p1, p2])
+
+    legend1 = plt.legend(
+        lines[0], [r"$\mathfrak{Re}\, u_n(s) $", r"$\mathfrak{Im}\, u_n(s)$"], loc=3
+    )
+    plt.legend([l[0] for l in lines], [l[0].get_label() for l in lines], loc=1)
+    plt.gca().add_artist(legend1)
+
+    plt.xlabel(r"$s_n = k_n r$")
+    plt.ylabel(r"$u (s) $ [a.u.]")
+    plt.tight_layout()
+    plt.show()
+
+
+if __name__ == "__main__":
+    coupled_channels_example()