TB2J 0.9.11.3__tar.gz → 0.9.12.3__tar.gz

tb2j-0.9.12.3/.github/workflows/pylint.yml.bak

@@ -0,0 +1,23 @@
+name: Pylint
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pylint
+    - name: Analysing the code with pylint
+      run: |
+        pylint $(git ls-files '*.py')

tb2j-0.9.12.3/.github/workflows/python-app.yml

@@ -0,0 +1,44 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python application
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - 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
+        #  - pwd
+        python -m pip install . 
+        cd examples/abinit-w90/SrMnO3
+        ls -lah
+        sh get_J.sh
+        cd TB2J_results/Multibinit
+        TB2J_magnon.py --figfname magnon.png

tb2j-0.9.12.3/.gitignore

@@ -0,0 +1,131 @@
+doc/refs/*.pdf
+
+
+*.swp
+
+# Latex 
+*.aux
+
+# xyz files
+
+.DS_Store
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# numpy results
+*.npy
+
+# png files
+
+# C extensions
+*.so
+*.a
+
+# Fortran extensions
+*.fpp
+*.mod
+*.o
+
+# F90wrap files
+*.plist
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+*.egg-info/*
+.installed.cfg
+*.egg
+
+# temporary files
+temp/
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/

tb2j-0.9.12.3/.pre-commit-config.yaml

@@ -0,0 +1,11 @@
+repos:
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.3.5
+    hooks:
+      # Run the linter.
+      - id: ruff
+        # --select I sorts imports
+        args: [ --fix, --extend-select, I  ]
+      # Run the formatter.
+      - id: ruff-format

tb2j-0.9.12.3/.readthedocs.yml

@@ -0,0 +1,28 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  install:
+    - requirements: requirements.txt
+    - requirements: docs/requirements.txt

tb2j-0.9.12.3/.ruff.toml

@@ -0,0 +1,78 @@
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".ipynb_checkpoints",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pyenv",
+    ".pytest_cache",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    ".vscode",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "site-packages",
+    "venv",
+]
+
+# Same as Black.
+line-length = 88
+indent-width = 4
+
+# Assume Python 3.8
+target-version = "py38"
+
+[lint]
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
+# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
+# McCabe complexity (`C901`) by default.
+select = ["E4", "E7", "E9", "F"]
+ignore = ["E741"]
+
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
+# Enable auto-formatting of code examples in docstrings. Markdown,
+# reStructuredText code/literal blocks and doctests are all supported.
+#
+# This is currently disabled by default, but it is planned for this
+# to be opt-out in the future.
+docstring-code-format = false
+
+# Set the line length limit used when formatting code snippets in
+# docstrings.
+#
+# This only has an effect when the `docstring-code-format` setting is
+# enabled.
+docstring-code-line-length = "dynamic"
+

tb2j-0.9.12.3/.travis.yml

@@ -0,0 +1,33 @@
+language: python
+python:
+  - "3.7"
+  - "3.8"
+  - "3.9"
+  - "3.10"
+  - "3.11"
+cache: pip
+
+addons:
+  apt:
+    packages: &common_packages
+      - gfortran
+      - libatlas-base-dev
+      - liblapack-dev
+      - libnetcdf-dev
+      - libnetcdff-dev
+      - eatmydata
+      - ccache
+before_install:
+ - if [[ $TRAVIS_PYTHON_VERSION == 3.7 ]]; then pip install -U importlib_metadata; fi
+
+install:
+  - pip install -r requirements.txt
+  - pip install sisl
+  - pip install -e .
+script:
+  - pwd
+  - cd examples/abinit-w90/SrMnO3
+  - ls -lah
+  - sh get_J.sh
+  - cd TB2J_results/Multibinit
+  - TB2J_magnon.py --figfname magnon.png

{tb2j-0.9.11.3 → tb2j-0.9.12.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.11.3
+Version: 0.9.12.3
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author-email: Xu He <mailhexu@gmail.com>
 Maintainer-email: Xu He <mailhexu@gmail.com>

tb2j-0.9.12.3/TB2J/.gitignore

@@ -0,0 +1,5 @@
+*.o
+*.x
+*.mod
+exchanges.sublime-project
+exchanges.sublime-workspace

tb2j-0.9.12.3/TB2J/interfaces/abacus/.gitignore

@@ -0,0 +1,2 @@
+TB2J_results/
+*.png

{tb2j-0.9.11.3 → tb2j-0.9.12.3}/TB2J/magnon/magnon3.py

@@ -733,10 +733,25 @@ def plot_magnon_bands_from_TB2J(
     return magnon
 
 
-def main():
-    """Command line interface for plotting magnon bands from TB2J results."""
+def plot_magnon_bands_cli():
     import argparse
-
+    import warnings
+
+    warnings.warn(
+        """ 
+        # !!!!!!!!!!!!!!!!!! WARNING: =============================
+        # 
+        # This functionality is under development and should not be used in production.
+        # It is provided for testing and development purposes only.
+        # Please use with caution and report any issues to the developers.
+        #
+        # This warning will be removed in future releases.
+        # =====================================
+
+        """,
+        UserWarning,
+        stacklevel=2,
+    )
     parser = argparse.ArgumentParser(
         description="Plot magnon band structure from TB2J results"
     )
@@ -877,10 +892,6 @@ def main():
     plot_magnon_bands_from_TB2J(params)
 
 
-if __name__ == "__main__":
-    main()
-
-
 class MagnonASEWrapper:
     def __init__(self, magnon: Magnon):
         self.magnon = magnon

{tb2j-0.9.11.3 → tb2j-0.9.12.3}/TB2J/scripts/TB2J_plot_magnon_bands.py

@@ -1,15 +1,10 @@
 #!/usr/bin/env python3
+import warnings
 
+from TB2J.magnon.magnon3 import main
 
-if __name__ == "__main__":
-    # add a warning messege that this functionality is under development and should not be used in production.
-    # make it visually distinct, e.g. with a different color or formatting.
-    import warnings
-
-    from TB2J.magnon.magnon3 import main
-
-    warnings.warn(
-        """ 
+warnings.warn(
+    """ 
         # !!!!!!!!!!!!!!!!!! WARNING: =============================
         # 
         # This functionality is under development and should not be used in production.
@@ -20,8 +15,8 @@ if __name__ == "__main__":
         # =====================================
 
         """,
-        UserWarning,
-        stacklevel=2,
-    )
-    # Call the main function from the magnons module
-    main()
+    UserWarning,
+    stacklevel=2,
+)
+# Call the main function from the magnons module
+main()

{tb2j-0.9.11.3 → tb2j-0.9.12.3}/TB2J.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.11.3
+Version: 0.9.12.3
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author-email: Xu He <mailhexu@gmail.com>
 Maintainer-email: Xu He <mailhexu@gmail.com>

tb2j-0.9.12.3/TB2J.egg-info/SOURCES.txt

@@ -0,0 +1,232 @@
+.gitignore
+.pre-commit-config.yaml
+.readthedocs.yml
+.ruff.toml
+.travis.yml
+LICENSE
+README.md
+buildimage.sh
+pyproject.toml
+requirements.txt
+upload_to_pip.sh
+.github/workflows/pylint.yml.bak
+.github/workflows/python-app.yml
+TB2J/.gitignore
+TB2J/Jdownfolder.py
+TB2J/Jtensor.py
+TB2J/MAE.py
+TB2J/MAEGreen.py
+TB2J/Oiju.py
+TB2J/Oiju_epc.py
+TB2J/__init__.py
+TB2J/anisotropy.py
+TB2J/basis.py
+TB2J/citation.py
+TB2J/contour.py
+TB2J/density_matrix.py
+TB2J/epc.py
+TB2J/exchange.py
+TB2J/exchangeCL2.py
+TB2J/exchange_params.py
+TB2J/exchange_pert.py
+TB2J/exchange_qspace.py
+TB2J/gpaw_wrapper.py
+TB2J/green.py
+TB2J/greentest.py
+TB2J/io_merge.py
+TB2J/kpoints.py
+TB2J/myTB.py
+TB2J/mycfr.py
+TB2J/orbital_magmom.py
+TB2J/orbmap.py
+TB2J/pauli.py
+TB2J/pert.py
+TB2J/plot.py
+TB2J/rotate_atoms.py
+TB2J/rotate_siestaDM.py
+TB2J/sisl_wrapper.py
+TB2J/symmetrize_J.py
+TB2J/tensor_rotate.py
+TB2J/thetaphi.py
+TB2J/utest.py
+TB2J/utils.py
+TB2J/versioninfo.py
+TB2J.egg-info/PKG-INFO
+TB2J.egg-info/SOURCES.txt
+TB2J.egg-info/dependency_links.txt
+TB2J.egg-info/entry_points.txt
+TB2J.egg-info/requires.txt
+TB2J.egg-info/top_level.txt
+TB2J/downfold/Hdownfolder.py
+TB2J/external/__init__.py
+TB2J/external/p_tqdm.py
+TB2J/interfaces/__init__.py
+TB2J/interfaces/gpaw_interface.py
+TB2J/interfaces/lawaf_interface.py
+TB2J/interfaces/manager.py
+TB2J/interfaces/siesta_interface.py
+TB2J/interfaces/wannier90_interface.py
+TB2J/interfaces/abacus/.gitignore
+TB2J/interfaces/abacus/__init__.py
+TB2J/interfaces/abacus/abacus_api.py
+TB2J/interfaces/abacus/abacus_wrapper.py
+TB2J/interfaces/abacus/gen_exchange_abacus.py
+TB2J/interfaces/abacus/orbital_api.py
+TB2J/interfaces/abacus/stru_api.py
+TB2J/interfaces/abacus/test_density_matrix.py
+TB2J/interfaces/abacus/test_read_HRSR.py
+TB2J/interfaces/abacus/test_read_stru.py
+TB2J/io_exchange/__init__.py
+TB2J/io_exchange/io_exchange.py
+TB2J/io_exchange/io_multibinit.py
+TB2J/io_exchange/io_tomsasd.py
+TB2J/io_exchange/io_txt.py
+TB2J/io_exchange/io_uppasd.py
+TB2J/io_exchange/io_vampire.py
+TB2J/magnon/__init__.py
+TB2J/magnon/io_exchange2.py
+TB2J/magnon/magnon3.py
+TB2J/magnon/magnon_band.py
+TB2J/magnon/magnon_dos.py
+TB2J/magnon/magnon_io.py
+TB2J/magnon/magnon_math.py
+TB2J/magnon/plot.py
+TB2J/magnon/plot_magnon_dos_cli.py
+TB2J/magnon/structure.py
+TB2J/mathutils/__init__.py
+TB2J/mathutils/auto_kpath.py
+TB2J/mathutils/fermi.py
+TB2J/mathutils/fibonacci_sphere.py
+TB2J/mathutils/kR_convert.py
+TB2J/mathutils/lowdin.py
+TB2J/mathutils/rotate_spin.py
+TB2J/scripts/TB2J_downfold.py
+TB2J/scripts/TB2J_eigen.py
+TB2J/scripts/TB2J_magnon.py
+TB2J/scripts/TB2J_magnon2.py
+TB2J/scripts/TB2J_magnon_dos.py
+TB2J/scripts/TB2J_merge.py
+TB2J/scripts/TB2J_plot_magnon_bands.py
+TB2J/scripts/TB2J_rotate.py
+TB2J/scripts/TB2J_rotateDM.py
+TB2J/scripts/__init__.py
+TB2J/scripts/abacus2J.py
+TB2J/scripts/siesta2J.py
+TB2J/scripts/wann2J.py
+TB2J/spinham/__init__.py
+TB2J/spinham/base_parser.py
+TB2J/spinham/constants.py
+TB2J/spinham/hamiltonian.py
+TB2J/spinham/hamiltonian_terms.py
+TB2J/spinham/plot.py
+TB2J/spinham/qsolver.py
+TB2J/spinham/spin_api.py
+TB2J/spinham/spin_xml.py
+TB2J/spinham/supercell.py
+TB2J/wannier/__init__.py
+TB2J/wannier/w90_parser.py
+TB2J/wannier/w90_tb_parser.py
+docs/Makefile
+docs/conf.py
+docs/index.rst
+docs/make.bat
+docs/requirements.txt
+docs/_static/Logo-ULG.png
+docs/_static/logo_TB2J_horizon.png
+docs/src/BFOvarT.png
+docs/src/Contributors.rst
+docs/src/ReleaseNotes.md
+docs/src/SrMnO3_DOS.png
+docs/src/abacus.md
+docs/src/applications.rst
+docs/src/convention.rst
+docs/src/development.md
+docs/src/downfold.md
+docs/src/ecosystem.md
+docs/src/eigen.rst
+docs/src/extend.rst
+docs/src/faq.rst
+docs/src/install.rst
+docs/src/mae.md
+docs/src/magnon_band.rst
+docs/src/magnon_bands.md
+docs/src/multibinit.rst
+docs/src/openmx.rst
+docs/src/orbital_contribution.md
+docs/src/output.rst
+docs/src/parameters.rst
+docs/src/references.rst
+docs/src/roadmap.md
+docs/src/rotate_and_merge.rst
+docs/src/siesta.rst
+docs/src/symmetry.md
+docs/src/tutorial.rst
+docs/src/wannier.rst
+docs/src/magnon_band.assets/exchange_magnon-1593690872101.png
+docs/src/magnon_band.assets/exchange_magnon.png
+docs/src/magnon_band.assets/magnon_dos.png
+docs/src/spin_model_assets/canting_DMI.png
+docs/src/spin_model_assets/tmulti5_2.png
+examples/Siesta/BccFe/Fe.1.psml
+examples/Siesta/BccFe/getJ.sh
+examples/Siesta/BccFe/run.sh
+examples/Siesta/BccFe/siesta.fdf
+examples/Siesta/BccFe/TB2J_results/EigenJq.txt
+examples/Siesta/BccFe/TB2J_results/TB2J.pickle
+examples/Siesta/BccFe/TB2J_results/exchange.out
+examples/Siesta/BccFe/TB2J_results/Multibinit/exchange.xml
+examples/Siesta/BccFe/TB2J_results/Multibinit/exchange_kpth.txt
+examples/Siesta/BccFe/TB2J_results/Multibinit/exchange_magnon.png
+examples/Siesta/BccFe/TB2J_results/Multibinit/magnon.py
+examples/Siesta/BccFe/TB2J_results/Multibinit/magnon_band.json
+examples/Siesta/BccFe/TB2J_results/Multibinit/magnon_band.pdf
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+examples/Siesta/BccFe/TB2J_results/Multibinit/plot_magnon_dos.sh
+examples/Siesta/BccFe/TB2J_results/Multibinit/plot_magnon_from_json_file.py
+examples/Siesta/BccFe/TB2J_results/TomASD/exchange.exch
+examples/Siesta/BccFe/TB2J_results/TomASD/exchange.ucf
+examples/Siesta/HcpCo/Co.1.psml
+examples/Siesta/HcpCo/getJ.sh
+examples/Siesta/HcpCo/run.sh
+examples/Siesta/HcpCo/siesta.fdf
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+examples/Siesta/HcpCo/TB2J_results/Vampire/input
+examples/Siesta/HcpCo/TB2J_results/Vampire/vampire.UCF
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+examples/abinit-w90/SrMnO3/abinito_w90_up_hr.dat
+examples/abinit-w90/SrMnO3/get_J.sh
+examples/abinit-w90/SrMnO3/run.sh
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+examples/abinit-w90/SrMnO3/TB2J_results/Multibinit/mb.in
+examples/abinit-w90/SrMnO3/TB2J_results/TomASD/exchange.exch
+examples/abinit-w90/SrMnO3/TB2J_results/TomASD/exchange.ucf
+examples/abinit-w90/SrMnO3/TB2J_results/Vampire/input
+examples/abinit-w90/SrMnO3/TB2J_results/Vampire/vampire.UCF
+examples/abinit-w90/SrMnO3/TB2J_results/Vampire/vampire.mat
+examples/abinit-w90/SrMnO3/psp/Mn.GGA-PBESOL-JTH.xml
+examples/abinit-w90/SrMnO3/psp/O.GGA-PBESOL-JTH.xml
+examples/abinit-w90/SrMnO3/psp/Sr.GGA-PBESOL-JTH.xml

{tb2j-0.9.11.3 → tb2j-0.9.12.3}/TB2J.egg-info/entry_points.txt

@@ -5,7 +5,7 @@ TB2J_magnon.py = TB2J.scripts.TB2J_magnon:main
 TB2J_magnon2.py = TB2J.scripts.TB2J_magnon2:main
 TB2J_magnon_dos.py = TB2J.scripts.TB2J_magnon_dos:main
 TB2J_merge.py = TB2J.scripts.TB2J_merge:main
-TB2J_plot_magnon_bands.py = TB2J.scripts.TB2J_plot_magnon_bands:main
+TB2J_plot_magnon_bands.py = TB2J.magnon.magnon3:plot_magnon_bands_cli
 TB2J_plot_magnon_dos.py = TB2J.magnon.plot_magnon_dos_cli:main
 TB2J_rotate.py = TB2J.scripts.TB2J_rotate:main
 TB2J_rotateDM.py = TB2J.scripts.TB2J_rotateDM:main