TB2J 0.9.9rc9__tar.gz → 0.9.9rc10__tar.gz

tb2j-0.9.9rc10/.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-0.9.9rc10/.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-0.9.9rc10/.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-0.9.9rc10/.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-0.9.9rc10/.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-0.9.9rc10/.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-0.9.9rc10/.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-0.9.9rc10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc9
+Version: 0.9.9rc10
 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-0.9.9rc10/TB2J/.gitignore

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

{tb2j-0.9.9rc9 → tb2j-0.9.9rc10}/TB2J/exchange.py

@@ -96,93 +96,78 @@ 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
-        - self.ind_mag_atoms: List of indices of magnetic atoms
-        - self._spin_dict: Maps atom indices to spin indices
-        - self._atom_dict: Maps spin indices back to atom indices
-        """
-        self._create_orbital_mappings()
-        self._identify_magnetic_atoms()
-        self._validate_orbital_assignments()
-        self._create_spin_mappings()
-        self._prepare_orb_mmat()
+        generate self.ind_mag_atoms and self.orb_dict
+        """
+        # adict: dictionary of {'Fe': ['dxy', 'dyz', ...], ...}
+        adict = OrderedDict()
+        # orb_dict: {ind_atom:[ind_orb,1,2], ...}
+        self.orb_dict = {}
+        # labels: {0:{dxy, ...}}
+        self.labels = {}
+        # magnetic atoms index
+        self.ind_mag_atoms = []
+
+        sdict = symbol_number(self.atoms)
+
+        for i, base in enumerate(self.basis):
+            if i not in self.exclude_orbs:
+                # e.g. Fe2, dxy, _, _
+                if isinstance(base, str):
+                    atom_sym, orb_sym = base.split("|")[:2]
+                    iatom = sdict[atom_sym]
+                else:
+                    try:
+                        atom_sym, orb_sym = base[:2]
+                        iatom = sdict[atom_sym]
+                    except Exception:
+                        iatom = base.iatom
+                        atom_sym = base.iatom
+                        orb_sym = base.sym
+
+                if atom_sym in adict:
+                    adict[atom_sym].append(orb_sym)
+                else:
+                    adict[atom_sym] = [orb_sym]
+                if iatom not in self.orb_dict:
+                    self.orb_dict[iatom] = [i]
+                    self.labels[iatom] = [orb_sym]
+                else:
+                    self.orb_dict[iatom] += [i]
+                    self.labels[iatom] += [orb_sym]
 
-    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]}
-        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]
-                atom_idx = atom_symbols[atom_sym]
-            else:
-                try:
-                    atom_sym, orb_sym = base[:2]
-                    atom_idx = atom_symbols[atom_sym]
-                except Exception:
-                    atom_idx = base.iatom
-                    atom_sym = base.iatom
-                    orb_sym = base.sym
-
-            # Update orbital mappings
-            if atom_idx not in self.orb_dict:
-                self.orb_dict[atom_idx] = [orb_idx]
-                self.labels[atom_idx] = [orb_sym]
-            else:
-                self.orb_dict[atom_idx].append(orb_idx)
-                self.labels[atom_idx].append(orb_sym)
+        # index of magnetic atoms
+        symbols = self.atoms.get_chemical_symbols()
+        tags = self.atoms.get_tags()
+        for i, (sym, tag) in enumerate(zip(symbols, tags)):
+            if sym in self.magnetic_elements or f"{sym}{tag}" in self.magnetic_elements:
+                self.ind_mag_atoms.append(i)
 
-    def _identify_magnetic_atoms(self):
-        """Identify which atoms are magnetic based on elements/tags."""
-        if self.index_magnetic_atoms is not None:
-            self.ind_mag_atoms = self.index_magnetic_atoms
-        else:
-            self.ind_mag_atoms = []
-            symbols = self.atoms.get_chemical_symbols()
-            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:
-                    self.ind_mag_atoms.append(atom_idx)
-        print(f"Magnetic atoms: {self.ind_mag_atoms}")
-
-    def _validate_orbital_assignments(self):
-        """Validate that magnetic atoms have proper orbital assignments."""
-        # Check all magnetic atoms have orbitals
-        for atom_idx in self.ind_mag_atoms:
-            if atom_idx not in self.orb_dict:
+        # sanity check to see if some magnetic atom has no orbital.
+        for iatom in self.ind_mag_atoms:
+            if iatom not in self.orb_dict:
                 raise ValueError(
-                    f"Atom {atom_idx} is magnetic but has no orbitals assigned. "
-                    "Check Wannier function definitions."
+                    f"""Cannot find any orbital for atom {iatom}, which is supposed to be magnetic. Please check the Wannier functions."""
                 )
-
-        # For non-collinear case, check spin-orbital pairing
         if not self._is_collinear:
-            for atom_idx, orbitals in self.orb_dict.items():
-                if len(orbitals) % 2 != 0:
+            for iatom, orb in self.orb_dict.items():
+                # print(f"iatom: {iatom}, orb: {orb}")
+                nsorb = len(self.orb_dict[iatom])
+                if nsorb % 2 != 0 and False:
                     raise ValueError(
-                        f"Atom {atom_idx} has {len(orbitals)} spin-orbitals "
-                        "(should be even). Check Wannier function localization."
+                        f"""The number of spin-orbitals for atom {iatom} is not even,
+{nsorb} spin-orbitals are found near this atom.
+which means the spin up/down does not have same number of orbitals.
+This is often because the Wannier functions are wrongly defined,
+or badly localized. Please check the Wannier centers in the Wannier90 output file.
+"""
                     )
+        self._spin_dict = {}
+        self._atom_dict = {}
+        for ispin, iatom in enumerate(self.ind_mag_atoms):
+            self._spin_dict[iatom] = ispin
+            self._atom_dict[ispin] = iatom
 
-    def _create_spin_mappings(self):
-        """Create mappings between atom indices and spin indices."""
-        self._spin_dict = {}  # {atom_index: spin_index}
-        self._atom_dict = {}  # {spin_index: atom_index}
-
-        for spin_idx, atom_idx in enumerate(self.ind_mag_atoms):
-            self._spin_dict[atom_idx] = spin_idx
-            self._atom_dict[spin_idx] = atom_idx
+        self._prepare_orb_mmat()
 
     def _prepare_orb_mmat(self):
         self.mmats = {}

{tb2j-0.9.9rc9 → tb2j-0.9.9rc10}/TB2J/exchange_params.py

@@ -15,7 +15,6 @@ class ExchangeParams:
     efermi: float
     basis = []
     magnetic_elements = []
-    index_magnetic_atoms = None 
     include_orbs = {}
     _kmesh = [4, 4, 4]
     emin: float = -15
@@ -56,7 +55,6 @@ class ExchangeParams:
         mae_angles=None,
         orth=False,
         ibz=False,
-        index_magnetic_atoms=None,
     ):
         self.efermi = efermi
         self.basis = basis
@@ -81,7 +79,6 @@ class ExchangeParams:
         self.mae_angles = mae_angles
         self.orth = orth
         self.ibz = ibz
-        self.index_magnetic_atoms = index_magnetic_atoms
 
     def set_params(self, **kwargs):
         for key, val in kwargs.items():
@@ -232,21 +229,6 @@ def add_exchange_args_to_parser(parser: argparse.ArgumentParser):
         default=False,
     )
 
-    parser.add_argument(
-        "--mae_angles",
-        help="angles for computing MAE, default is 0 0 0",
-        type=float,
-        nargs="*",
-        default=[0.0, 0.0, 0.0],
-    )
-    parser.add_argument(
-        "--index_magnetic_atoms",
-        help="index of magnetic atoms in the unit cell, default is None. If specified, this will be used to determine the atoms to be considered as magnetic atoms, instead of determined from magnetic elements. Note that the index starts from 1 ",
-        type=int,
-        nargs="*",
-        default=None,
-    )
-
     return parser
 
 
@@ -268,5 +250,4 @@ def parser_argument_to_dict(args) -> dict:
         "orb_decomposition": args.orb_decomposition,
         "output_path": args.output_path,
         "orth": args.orth,
-        "index_magnetic_atoms": args.index_magnetic_atoms,
     }

tb2j-0.9.9rc10/TB2J/interfaces/abacus/.gitignore

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

{tb2j-0.9.9rc9 → tb2j-0.9.9rc10}/TB2J/rotate_siestaDM.py

@@ -1,7 +1,7 @@
 import sisl
 
 def rotate_siesta_DM(DM, noncollinear=False):
-    
+
     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]]
@@ -10,7 +10,6 @@ def rotate_siesta_DM(DM, noncollinear=False):
         yield DM.spin_rotate(angles)
 
 def read_label(fdf_fname):
-
     label = 'siesta'
     with open(fdf_fname, 'r') as File:
         for line in File:

{tb2j-0.9.9rc9 → tb2j-0.9.9rc10}/TB2J.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc9
+Version: 0.9.9rc10
 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