baderkit 0.1.1__tar.gz

baderkit-0.1.1/LICENSE.txt

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2021, Jack D. Sundberg
+All rights reserved.
+
+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.

baderkit-0.1.1/PKG-INFO

@@ -0,0 +1,36 @@
+Metadata-Version: 2.4
+Name: baderkit
+Version: 0.1.1
+Author-email: "Sam M. Weaver" <sammweaver@gmail.com>
+License: BSD 3-Clause License
+Project-URL: repository, https://github.com/SWeav02/baderkit
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+License-File: LICENSE.txt
+Requires-Dist: numpy>=1.26.0
+Requires-Dist: pandas>=2.1.0
+Requires-Dist: typer>=0.6.1
+Requires-Dist: pymatgen>=2022.1.9
+Requires-Dist: scipy>=1.7.2
+Requires-Dist: numba>=0.59.0
+Requires-Dist: pyvista>=0.44.0
+Requires-Dist: streamlit>=1.40.0
+Requires-Dist: rich>=11.0
+Requires-Dist: trame
+Requires-Dist: trame-vtk
+Requires-Dist: trame-vuetify
+Requires-Dist: nest_asyncio
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: isort; extra == "dev"
+Requires-Dist: mkdocs; extra == "dev"
+Requires-Dist: mkdocs-material; extra == "dev"
+Requires-Dist: mkdocstrings-python; extra == "dev"
+Provides-Extra: extras
+Requires-Dist: spyder; extra == "extras"
+Dynamic: license-file

baderkit-0.1.1/README.md

@@ -0,0 +1,12 @@
+# BaderKit
+
+## About
+
+BaderKit is a python implementation of Bader's Atomic Theory of Atoms in Molecules. It is largely based on the algorithms of [Henkelman et. al.](https://theory.cm.utexas.edu/henkelman/code/bader/) at UT Austin. The app is partially part of my PhD at UNC Chapel Hill in the [Warren Lab](https://materials-lab.io/) with funding from the [NSF's GRFP](https://nsfgrfp.org/), but is largely my own passion project aimed at making my life easier when developing other packages.
+
+For information on installation and use, see the [docs](https://sweav02.github.io/baderkit/)
+
+
+## Contributing
+
+If you are interested in this project and have suggestions, please use this repositories Issues or Discussions tab. Any suggestions or discussion would be deeply appreciated!

baderkit-0.1.1/pyproject.toml

@@ -0,0 +1,136 @@
+
+# This file establishes the info needed to install baderkit via pip, how to
+# upload it to PyPI, and how to run python packages like pytest and coverage.
+
+# For more information on this file and how to make similar ones, see:
+#    https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html
+#    https://github.com/pypa/sampleproject
+
+# -----------------------------------------------------------------------------
+
+[build-system]
+# These are the assumed default build requirements from pip:
+# https://pip.pypa.io/en/stable/reference/pip/#pep-517-and-518-support
+requires = ["setuptools>=64.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+# -----------------------------------------------------------------------------
+
+[project]
+
+# published name for pip install to use
+name="baderkit"
+
+# Versions should comply with PEP 440:
+# https://www.python.org/dev/peps/pep-0440/
+# https://semver.org/
+version="0.1.1"
+
+# Maintainer info
+authors = [{name = "Sam M. Weaver", email = "sammweaver@gmail.com"}]
+
+# General name for our LICENSE file
+license = {text = "BSD 3-Clause License"}
+
+# Classifiers help users find your project by categorizing it.
+# For a list of valid classifiers, see https://pypi.org/classifiers/
+classifiers=[
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python :: 3.11",
+    "Operating System :: OS Independent",
+]
+
+# Specify which Python versions are supported.
+requires-python=">=3.10"
+
+# This field lists other packages that your project depends on to run.
+dependencies=[
+    # Core dependencies
+    "numpy>=1.26.0",
+    "pandas>=2.1.0",
+    "typer>=0.6.1",
+    "pymatgen>=2022.1.9",
+    "scipy>=1.7.2",
+    "numba>=0.59.0",
+    "pyvista>=0.44.0", # for plotting grid
+    "streamlit>=1.40.0", # for web GUI
+    # Extra (smaller) dependencies & utilities
+    "rich>=11.0", # for coloring CLI outputs and progress bars
+    # For webapp plotter html export. Not used directly in the app.
+    "trame",
+    "trame-vtk",
+    "trame-vuetify",
+    "nest_asyncio",
+]
+
+# optional dependencies that are not installed by default
+[project.optional-dependencies]
+# For development and testing. Taken straight from simmate
+DEV = [
+    "pytest",
+    "black",
+    "isort",
+    "mkdocs",
+    "mkdocs-material",
+    "mkdocstrings-python",
+#    "mkdocs_autorefs",
+]
+
+EXTRAS = [
+    "spyder",  # IDE for writing/editting
+]
+
+# Link to our homepage. Use github for now.
+[project.urls]
+repository = "https://github.com/SWeav02/baderkit"
+
+# Register command line interface
+[project.scripts]
+baderkit = "baderkit.command_line.base:baderkit_app"
+
+# -----------------------------------------------------------------------------
+
+# Indicate which directory the source coude is in
+[tool.setuptools.packages.find]
+where = ["src"]
+
+# All files that aren't *.py need to be defined explicitly. Don't "automate"
+# this to grab all files because this could break installation. This can
+# be effectively the opposite of .gitignore.
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.package-data]
+baderkit = [
+    "**/*.md",
+    "**/*.rst",
+    "**/*.json",
+    "**/*.csv",
+    "**/*.yaml",
+    "**/*.html",
+    "**/*.svg",
+    "**/*.toml",
+    "**/*.css",
+    "**/*.js",
+]
+# Note, the default is to include everything, but I don't want to ship test
+# files. I could switch this to use exclude-package-data in the future.
+# https://setuptools.pypa.io/en/latest/userguide/datafiles.html#exclude-package-data
+
+# -----------------------------------------------------------------------------
+# Section for pytests
+# -----------------------------------------------------------------------------
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+
+# -----------------------------------------------------------------------------
+
+# isort is a tool for organizing imports at the top of python files. By default,
+# it conflicts with the black formatter we use, so we need to configure it here.
+
+[tool.isort]
+profile = "black"
+
+# -----------------------------------------------------------------------------

baderkit-0.1.1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

baderkit-0.1.1/src/baderkit/__init__.py

@@ -0,0 +1,25 @@
+# -*- coding: utf-8 -*-
+# high level imports
+import importlib.metadata
+import logging
+
+from rich.logging import RichHandler
+
+from .core import Bader
+
+__version__ = importlib.metadata.version("baderkit")
+
+# Configure our logger to output timestamps with logs
+# Also changes the logging level to info
+logging.basicConfig(
+    format="%(message)s",
+    level=logging.INFO,
+    datefmt="%Y-%m-%d %H:%M:%S",
+    handlers=[
+        RichHandler(
+            show_path=False,
+            markup=True,
+            rich_tracebacks=True,
+        )
+    ],
+)

baderkit-0.1.1/src/baderkit/command_line/__init__.py

@@ -0,0 +1 @@
+# -*- coding: utf-8 -*-

baderkit-0.1.1/src/baderkit/command_line/base.py

@@ -0,0 +1,136 @@
+# -*- coding: utf-8 -*-
+
+"""
+Defines the base 'baderkit' command that all other commands stem from.
+"""
+
+from enum import Enum
+from pathlib import Path
+
+import typer
+from typing_extensions import Annotated
+
+from baderkit.command_line.tools import tools_app
+
+baderkit_app = typer.Typer(rich_markup_mode="markdown")
+
+
+@baderkit_app.callback(no_args_is_help=True)
+def base_command():
+    """
+    This is the base command that all baderkit commands stem from
+    """
+    pass
+
+
+@baderkit_app.command()
+def version():
+    """
+    Prints the version of baderkit that is installed
+    """
+    import baderkit
+
+    print(f"Installed version: v{baderkit.__version__}")
+
+
+class Method(str, Enum):
+    weight = "weight"
+    hybrid_weight = "hybrid-weight"
+    ongrid = "ongrid"
+    neargrid = "neargrid"
+
+
+class Format(str, Enum):
+    vasp = "vasp"
+    cube = "cube"
+
+
+class PrintOptions(str, Enum):
+    all_atoms = "all_atoms"
+    sel_atoms = "sel_atoms"
+    sum_atoms = "sum_atoms"
+    all_basins = "all_basins"
+    sel_basins = "sel_basins"
+    sum_basins = "sum_basins"
+
+
+@baderkit_app.command()
+def run(
+    charge_file: Path = typer.Argument(
+        default=...,
+        help="The path to the charge density file",
+    ),
+    reference_file: Path = typer.Option(
+        None,
+        "--reference_file",
+        "-ref",
+        help="The path to the reference file",
+    ),
+    method: Method = typer.Option(
+        Method.weight,
+        "--method",
+        "-m",
+        help="The method to use for separating bader basins",
+        case_sensitive=False,
+    ),
+    format: Format = typer.Option(
+        None,
+        "--format",
+        "-f",
+        help="The format of the files",
+        case_sensitive=False,
+    ),
+    print: PrintOptions = typer.Option(
+        None,
+        "--print",
+        "-p",
+        help="Optional printing of atom or bader basins",
+        case_sensitive=False,
+    ),
+    indices=typer.Argument(
+        default=[],
+        help="The indices used for print method. Can be added at the end of the call. For example: `baderkit run CHGCAR -p sel_basins 0 1 2`",
+    ),
+    # indices: Annotated[
+    #     list[int],
+    #     typer.Argument(
+    #         help="The indices used for print method. Can be added at the end of the call. For example: `baderkit run CHGCAR -p sel_basins 0 1 2`"
+    #     ),
+    # ] = None,
+):
+    """
+    Runs a bader analysis on the provided files. File formats are automatically
+    parsed based on the name. Current accepted files include VASP's CHGCAR/ELFCAR
+    or .cube files.
+    """
+    from baderkit.core import Bader
+
+    # instance bader
+    bader = Bader.from_dynamic(
+        charge_filename=charge_file,
+        reference_filename=reference_file,
+        method=method,
+        format=format,
+    )
+    # write summary
+    bader.write_results_summary()
+
+    # write basins
+    if indices is None:
+        indices = []
+    if print == "all_atoms":
+        bader.write_all_atom_volumes()
+    elif print == "all_basins":
+        bader.write_all_basin_volumes()
+    elif print == "sel_atoms":
+        bader.write_atom_volumes(atom_indices=indices)
+    elif print == "sel_basins":
+        bader.write_basin_volumes(basin_indices=indices)
+    elif print == "sum_atoms":
+        bader.write_atom_volumes_sum(atom_indices=indices)
+    elif print == "sum_basins":
+        bader.write_basin_volumes_sum(basin_indices=indices)
+
+
+# Register other commands
+baderkit_app.add_typer(tools_app, name="tools")

baderkit-0.1.1/src/baderkit/command_line/tools.py

@@ -0,0 +1,125 @@
+# -*- coding: utf-8 -*-
+
+import logging
+import os
+import subprocess
+from enum import Enum
+from pathlib import Path
+
+import typer
+
+tools_app = typer.Typer(rich_markup_mode="markdown")
+
+
+@tools_app.callback(no_args_is_help=True)
+def base_command():
+    """
+    A collection of tools for assisting in bader analysis
+    """
+    pass
+
+
+@tools_app.command()
+def sum(
+    file1: Path = typer.Argument(
+        ...,
+        help="The path to the first file to sum",
+    ),
+    file2: Path = typer.Argument(
+        ...,
+        help="The path to the second file to sum",
+    ),
+):
+    """
+    A helper function for summing two grids. Note that the output is currently
+    always a VASP file.
+    """
+    from baderkit.core import Grid
+
+    # make sure files are paths
+    file1 = Path(file1)
+    file2 = Path(file2)
+    logging.info(f"Summing files {file1.name} and {file2.name}")
+
+    grid1 = Grid.from_dynamic(file1)
+    grid2 = Grid.from_dynamic(file2)
+    # sum grids
+    summed_grid = Grid.sum_grids(grid1, grid2)
+    # get name to use
+    if "elf" in file1.name.lower():
+        file_pre = "ELFCAR"
+    else:
+        file_pre = "CHGCAR"
+    summed_grid.write_file(f"{file_pre}_sum")
+
+
+class Method(str, Enum):
+    weight = "weight"
+    hybrid_weight = "hybrid-weight"
+    ongrid = "ongrid"
+    neargrid = "neargrid"
+
+
+@tools_app.command()
+def webapp(
+    charge_file: Path = typer.Argument(
+        ...,
+        help="The path to the charge density file",
+    ),
+    reference_file: Path = typer.Option(
+        None,
+        "--reference_file",
+        "-ref",
+        help="The path to the reference file",
+    ),
+    method: Method = typer.Option(
+        "weight",
+        "--method",
+        "-m",
+        help="The method to use for separating bader basins",
+        case_sensitive=False,
+    ),
+    # dev: bool = typer.Option(
+    #     False,
+    #     "--dev",
+    #     "-d",
+    #     help="Launches panel in development version",
+    #     )
+):
+    """
+    Starts the web interface
+    """
+    # get this files path
+    current_file = Path(__file__).resolve()
+    # get relative path to streamlit app
+    webapp_path = (
+        current_file.parent.parent / "plotting" / "web_gui" / "streamlit" / "webapp.py"
+    )
+    # set environmental variables
+    os.environ["CHARGE_FILE"] = str(charge_file)
+    os.environ["BADER_METHOD"] = method
+
+    if reference_file is not None:
+        os.environ["REFERENCE_FILE"] = str(reference_file)
+
+    args = [
+        "streamlit",
+        "run",
+        str(webapp_path),
+    ]
+
+    process = subprocess.Popen(
+        args=args,
+        stdin=subprocess.PIPE,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.STDOUT,
+        text=True,
+        bufsize=1,
+    )
+    # Look for prompt and send blank input if needed
+    for line in process.stdout:
+        print(line, end="")  # Optional: show Streamlit output
+        if "email" in line:
+            process.stdin.write("\n")
+            process.stdin.flush()
+            break  # After this, Streamlit should proceed normally

baderkit-0.1.1/src/baderkit/core/__init__.py

@@ -0,0 +1,19 @@
+# -*- coding: utf-8 -*-
+
+from .bader import Bader
+from .grid import Grid
+from .numba_functions import (  # get_hybrid_basin_weights,
+    get_basin_charge_volume_from_label,
+    get_edges,
+    get_maxima,
+    get_multi_weight_voxels,
+    get_near_grid_assignments,
+    get_neighbor_diffs,
+    get_neighbor_flux,
+    get_single_weight_voxels,
+    get_steepest_pointers,
+    propagate_edges,
+    refine_near_grid_edges,
+    unmark_isolated_voxels,
+)
+from .structure import Structure