TB2J 0.9.11.2__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-0.9.11.2 → tb2j-0.9.12.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.11.2
+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-0.9.11.2 → tb2j-0.9.12.3}/TB2J/magnon/magnon3.py

@@ -31,6 +31,7 @@ class MagnonParameters:
     Q: Optional[List[float]] = None
     uz_file: Optional[str] = None
     n: Optional[List[float]] = None
+    spin_conf_file: Optional[str] = None
     show: bool = False
 
     @classmethod
@@ -57,6 +58,8 @@ class MagnonParameters:
         # Convert path to absolute path if uz_file is relative to it
         if self.uz_file and not Path(self.uz_file).is_absolute():
             self.uz_file = str(Path(self.path) / self.uz_file)
+        if self.spin_conf_file and not Path(self.spin_conf_file).is_absolute():
+            self.spin_conf_file = str(Path(self.path) / self.spin_conf_file)
 
 
 @dataclass
@@ -76,7 +79,7 @@ class Magnon:
     _n: np.ndarray
     pbc: tuple = (True, True, True)
 
-    def set_reference(self, Q, uz, n):
+    def set_reference(self, Q, uz, n, magmoms=None):
         """
         Set reference propagation vector and quantization axis
 
@@ -92,6 +95,8 @@ class Magnon:
         self.set_propagation_vector(Q)
         self._uz = np.array(uz, dtype=float)
         self._n = np.array(n, dtype=float)
+        if magmoms is not None:
+            self.magmom = np.array(magmoms, dtype=float)
 
     def set_propagation_vector(self, Q):
         """Set propagation vector"""
@@ -653,26 +658,40 @@ def plot_magnon_bands_from_TB2J(
     )
 
     # Set reference vectors if provided
-    if any(x is not None for x in [params.Q, params.uz_file, params.n]):
-        Q = [0, 0, 0] if params.Q is None else params.Q
-        n = [0, 0, 1] if params.n is None else params.n
-
-        # Handle quantization axes
-        if params.uz_file is not None:
-            uz = np.loadtxt(params.uz_file)
-            if uz.shape[1] != 3:
-                raise ValueError(
-                    f"Quantization axes file should contain a natom×3 array. Got shape {uz.shape}"
-                )
-            if uz.shape[0] != magnon.nspin:
-                raise ValueError(
-                    f"Number of spins in uz file ({uz.shape[0]}) does not match the system ({magnon.nspin})"
-                )
-        else:
-            # Default: [0, 0, 1] for all spins
-            uz = np.array([[0.0, 0.0, 1.0] for _ in range(magnon.nspin)])
+    Q = [0, 0, 0] if params.Q is None else params.Q
+    n = [0, 0, 1] if params.n is None else params.n
+
+    # Handle quantization axes
+    if params.uz_file is not None:
+        uz = np.loadtxt(params.uz_file)
+        if uz.shape[1] != 3:
+            raise ValueError(
+                f"Quantization axes file should contain a natom×3 array. Got shape {uz.shape}"
+            )
+        if uz.shape[0] != magnon.nspin:
+            raise ValueError(
+                f"Number of spins in uz file ({uz.shape[0]}) does not match the system ({magnon.nspin})"
+            )
+    else:
+        # Default: [0, 0, 1] for all spins
+        # uz = np.array([[0.0, 0.0, 1.0] for _ in range(magnon.nspin)])
+        uz = np.array([[0, 0, 1]], dtype=float)
+
+    print(params)
+    if params.spin_conf_file is not None:
+        magmoms = np.loadtxt(params.spin_conf_file)
+        if magmoms.shape[1] != 3:
+            raise ValueError(
+                f"Spin configuration file should contain a nspin×3 array. Got shape {magmoms.shape}"
+            )
+        if magmoms.shape[0] != magnon.nspin:
+            raise ValueError(
+                f"Number of spins in spin configuration file ({magmoms.shape[0]}) does not match the system ({magnon.nspin})"
+            )
+    else:
+        magmoms = None
 
-        magnon.set_reference(Q, uz, n)
+    magnon.set_reference(Q, uz, n, magmoms)
 
     # Get band structure data
     print(f"\nCalculating bands along path {params.kpath}...")
@@ -714,10 +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"
     )
@@ -737,27 +771,32 @@ def main():
 
     # Command line arguments (used if no config file is provided)
     parser.add_argument(
+        "-p",
         "--path",
         default="TB2J_results",
         help="Path to TB2J results directory (default: TB2J_results)",
     )
     parser.add_argument(
+        "-k",
         "--kpath",
         default=None,
         help="k-path specification (default: auto-detected from type of cell)",
     )
     parser.add_argument(
+        "-n",
         "--npoints",
         type=int,
         default=300,
         help="Number of k-points along the path (default: 300)",
     )
     parser.add_argument(
+        "-o",
         "--output",
         default="magnon_bands.png",
         help="Output file name (default: magnon_bands.png)",
     )
     parser.add_argument(
+        "-j",
         "--Jiso",
         action="store_true",
         default=True,
@@ -770,18 +809,21 @@ def main():
         help="Exclude isotropic exchange interactions",
     )
     parser.add_argument(
+        "-a",
         "--Jani",
         action="store_true",
         default=False,
         help="Include anisotropic exchange interactions (default: False)",
     )
     parser.add_argument(
+        "-d",
         "--DMI",
         action="store_true",
         default=False,
         help="Include Dzyaloshinskii-Moriya interactions (default: False)",
     )
     parser.add_argument(
+        "-q",
         "--Q",
         nargs=3,
         type=float,
@@ -789,11 +831,19 @@ def main():
         help="Propagation vector [Qx, Qy, Qz] (default: [0, 0, 0])",
     )
     parser.add_argument(
+        "-u",
         "--uz-file",
         type=str,
-        help="Path to file containing quantization axes for each spin (natom×3 array)",
+        help="Path to file containing quantization axes for each spin (nspin×3 array)",
+    )
+    parser.add_argument(
+        "-c",
+        "--spin-conf-file",
+        type=str,
+        help="Path to file containing magnetic moments for each spin (nspin×3 array)",
     )
     parser.add_argument(
+        "-v",
         "--n",
         nargs=3,
         type=float,
@@ -802,6 +852,7 @@ def main():
     )
 
     parser.add_argument(
+        "-s",
         "--show",
         action="store_true",
         default=False,
@@ -833,6 +884,7 @@ def main():
             DMI=args.DMI,
             Q=args.Q if args.Q is not None else None,
             uz_file=args.uz_file,
+            spin_conf_file=args.spin_conf_file,
             n=args.n if args.n is not None else None,
             show=args.show,
         )
@@ -840,10 +892,6 @@ def main():
     plot_magnon_bands_from_TB2J(params)
 
 
-if __name__ == "__main__":
-    main()
-
-
 class MagnonASEWrapper:
     def __init__(self, magnon: Magnon):
         self.magnon = magnon