TB2J 0.9.9rc9__tar.gz → 0.9.9rc11__tar.gz

tb2j-0.9.9rc11/.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-0.9.9rc11/.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-0.9.9rc11/.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-0.9.9rc11/.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-0.9.9rc11/.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-0.9.9rc11/.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-0.9.9rc11/.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-0.9.9rc9 → tb2j-0.9.9rc11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc9
+Version: 0.9.9rc11
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -21,7 +21,7 @@ Requires-Dist: ase>=3.19
 Requires-Dist: tqdm
 Requires-Dist: pathos
 Requires-Dist: packaging>=20.0
-Requires-Dist: HamiltonIO>=0.1.9
+Requires-Dist: HamiltonIO>=0.1.10
 Requires-Dist: pre-commit
 Requires-Dist: sympair>0.1.0
 Requires-Dist: sisl>=0.9.0

tb2j-0.9.9rc11/TB2J/.gitignore

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

{tb2j-0.9.9rc9 → tb2j-0.9.9rc11}/TB2J/exchange.py

@@ -1,6 +1,6 @@
 import os
 import pickle
-from collections import OrderedDict, defaultdict
+from collections import defaultdict
 
 import numpy as np
 from tqdm import tqdm
@@ -97,7 +97,7 @@ class Exchange(ExchangeParams):
     def _prepare_orb_dict(self):
         """
         Generate orbital and magnetic atom mappings needed for exchange calculations.
-        
+
         Creates:
         - self.orb_dict: Maps atom indices to their orbital indices
         - self.labels: Maps atom indices to their orbital labels
@@ -114,13 +114,13 @@ class Exchange(ExchangeParams):
     def _create_orbital_mappings(self):
         """Create mappings between atoms and their orbitals."""
         self.orb_dict = {}  # {atom_index: [orbital_indices]}
-        self.labels = {}     # {atom_index: [orbital_labels]}
+        self.labels = {}  # {atom_index: [orbital_labels]}
         atom_symbols = symbol_number(self.atoms)
 
         for orb_idx, base in enumerate(self.basis):
             if orb_idx in self.exclude_orbs:
                 continue
-                
+
             # Extract atom and orbital info
             if isinstance(base, str):
                 atom_sym, orb_sym = base.split("|")[:2]
@@ -152,7 +152,10 @@ class Exchange(ExchangeParams):
             tags = self.atoms.get_tags()
 
             for atom_idx, (sym, tag) in enumerate(zip(symbols, tags)):
-                if sym in self.magnetic_elements or f"{sym}{tag}" in self.magnetic_elements:
+                if (
+                    sym in self.magnetic_elements
+                    or f"{sym}{tag}" in self.magnetic_elements
+                ):
                     self.ind_mag_atoms.append(atom_idx)
         print(f"Magnetic atoms: {self.ind_mag_atoms}")
 

{tb2j-0.9.9rc9 → tb2j-0.9.9rc11}/TB2J/exchange_params.py

@@ -15,7 +15,7 @@ class ExchangeParams:
     efermi: float
     basis = []
     magnetic_elements = []
-    index_magnetic_atoms = None 
+    index_magnetic_atoms = None
     include_orbs = {}
     _kmesh = [4, 4, 4]
     emin: float = -15

tb2j-0.9.9rc11/TB2J/interfaces/abacus/.gitignore

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

{tb2j-0.9.9rc9 → tb2j-0.9.9rc11}/TB2J/rotate_siestaDM.py

@@ -1,28 +1,28 @@
 import sisl
 
+
 def rotate_siesta_DM(DM, noncollinear=False):
-    
-    angles_list = [ [0.0, 90.0, 0.0], [0.0, 90.0, 90.0] ]
+    angles_list = [[0.0, 90.0, 0.0], [0.0, 90.0, 90.0]]
     if noncollinear:
         angles_list += [[0.0, 45.0, 0.0], [0.0, 90.0, 45.0], [0.0, 45.0, 90.0]]
 
     for angles in angles_list:
         yield DM.spin_rotate(angles)
 
-def read_label(fdf_fname):
 
-    label = 'siesta'
-    with open(fdf_fname, 'r') as File:
+def read_label(fdf_fname):
+    label = "siesta"
+    with open(fdf_fname, "r") as File:
         for line in File:
-            corrected_line = line.lower().replace('.', '').replace('-', '')
-            if 'systemlabel' in corrected_line:
+            corrected_line = line.lower().replace(".", "").replace("-", "")
+            if "systemlabel" in corrected_line:
                 label = line.split()[1]
                 break
 
     return label
 
-def rotate_DM(fdf_fname, noncollinear=False):
 
+def rotate_DM(fdf_fname, noncollinear=False):
     fdf = sisl.get_sile(fdf_fname)
     DM = fdf.read_density_matrix()
     label = read_label(fdf_fname)
@@ -33,4 +33,6 @@ def rotate_DM(fdf_fname, noncollinear=False):
         rotated_DM.write(f"{label}_{i+1}.DM")
     DM.write(f"{label}_0.DM")
 
-    print(f"The output has been written to the {label}_i.DM files. {label}_0.DM contains the reference density matrix.")
+    print(
+        f"The output has been written to the {label}_i.DM files. {label}_0.DM contains the reference density matrix."
+    )

{tb2j-0.9.9rc9 → tb2j-0.9.9rc11}/TB2J.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc9
+Version: 0.9.9rc11
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -21,7 +21,7 @@ Requires-Dist: ase>=3.19
 Requires-Dist: tqdm
 Requires-Dist: pathos
 Requires-Dist: packaging>=20.0
-Requires-Dist: HamiltonIO>=0.1.9
+Requires-Dist: HamiltonIO>=0.1.10
 Requires-Dist: pre-commit
 Requires-Dist: sympair>0.1.0
 Requires-Dist: sisl>=0.9.0