crystallograpy 0.1.0__tar.gz

crystallograpy-0.1.0/.gitignore

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crystallograpy-0.1.0/LICENSE

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+[SOFTWARE NAME] Copyright (YEAR) (COPYRIGHT HOLDER(S)/AUTHOR(S))(“Licensor”)
+Hippocratic License Version Number: 2.1.
+Purpose. The purpose of this License is for the Licensor named above to permit the Licensee (as defined below) broad permission, if consistent with Human Rights Laws and Human Rights Principles (as each is defined below), to use and work with the Software (as defined below) within the full scope of Licensor’s copyright and patent rights, if any, in the Software, while ensuring attribution and protecting the Licensor from liability.
+Permission and Conditions. The Licensor grants permission by this license (“License”), free of charge, to the extent of Licensor’s rights under applicable copyright and patent law, to any person or entity (the “Licensee”) obtaining a copy of this software and associated documentation files (the “Software”), to do everything with the Software that would otherwise infringe (i) the Licensor’s copyright in the Software or (ii) any patent claims to the Software that the Licensor can license or becomes able to license, subject to all of the following terms and conditions:
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crystallograpy-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: crystallograpy
+Version: 0.1.0
+Summary: Lightweight Python utilities about crystallography properties
+Project-URL: Homepage, https://github.com/milaforscience/crystallograpy
+Project-URL: Issues, https://github.com/milaforscience/crystallograpy/issues
+Author-email: alexhernandezgarcia <alex.hernandez-garcia@mila.quebec>
+License-Expression: Hippocratic-2.1
+License-File: LICENSE
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.10
+Requires-Dist: pyyaml>=6.0.1
+Provides-Extra: dev
+Requires-Dist: black>=23.9.1; extra == 'dev'
+Requires-Dist: flake8>=6.1.0; extra == 'dev'
+Requires-Dist: ipdb>=0.13.13; extra == 'dev'
+Requires-Dist: isort>=5.12.0; extra == 'dev'
+Requires-Dist: jupyter>=1.0.0; extra == 'dev'
+Requires-Dist: pylint>=2.17.6; extra == 'dev'
+Requires-Dist: pytest-repeat>=0.9.1; extra == 'dev'
+Requires-Dist: pytest>=7.4.2; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# crystallograpy (cryspy)
+
+A simple package with data structures containing crystallographic properties and their relationships, such as space groups, Wyckoff positions, etc. as well utilities for accessing them.

crystallograpy-0.1.0/README.md

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+# crystallograpy (cryspy)
+
+A simple package with data structures containing crystallographic properties and their relationships, such as space groups, Wyckoff positions, etc. as well utilities for accessing them.

crystallograpy-0.1.0/pyproject.toml

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+[project]
+name = "crystallograpy"
+version = "0.1.0"
+description = "Lightweight Python utilities about crystallography properties"
+authors = [
+    {name = "alexhernandezgarcia", email = "alex.hernandez-garcia@mila.quebec"},
+]
+readme = "README.md"
+requires-python = ">=3.10"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "PyYAML >=6.0.1",
+]
+license = "Hippocratic-2.1"
+license-files = ["LICEN[CS]E*"]
+
+[project.urls]
+Homepage = "https://github.com/milaforscience/crystallograpy"
+Issues = "https://github.com/milaforscience/crystallograpy/issues"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[build-system]
+requires = ["hatchling >= 1.26"]
+build-backend = "hatchling.build"
+
+[project.optional-dependencies]
+dev = [
+    "black >=23.9.1",
+    "flake8 >=6.1.0",
+    "isort >=5.12.0",
+    "ipdb >=0.13.13",
+    "jupyter >=1.0.0",
+    "pylint >=2.17.6",
+    "pytest >=7.4.2",
+    "pytest-repeat >=0.9.1",
+]

crystallograpy-0.1.0/scripts/build_lattice_dicts.py

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+"""
+Creates dictionaries of crystal systems, crystal lattices, point symmetries and space
+groups containing their releationships.
+
+It uses pre-stored simple variables as well as databases and methods from pymatgen.
+
+Example:
+    python scripts/build_lattice_dicts.py \
+            --print \
+            --output_sg_yaml yaml/space_groups.yaml \
+            --output_cls_yaml yaml/crystal_lattice_systems.yaml \
+            --output_ps_yaml yaml/point_symmetries.yaml
+"""
+
+import sys
+from argparse import ArgumentParser
+
+from lattice_constants import (
+    CRYSTAL_CLASSES_WIKIPEDIA,
+    CRYSTAL_LATTICE_SYSTEMS,
+    POINT_SYMMETRIES,
+    RHOMBOHEDRAL_SPACE_GROUPS_WIKIPEDIA,
+)
+from pymatgen.symmetry.groups import SpaceGroup, sg_symbol_from_int_number
+
+import yaml
+
+N_SPACE_GROUPS = 230
+
+
+def parsed_args():
+    """
+    Parse and returns command-line args
+
+    Returns:
+        argparse.Namespace: the parsed arguments
+    """
+    parser = ArgumentParser()
+    parser.add_argument(
+        "--output_sg_yaml",
+        default=None,
+        type=str,
+        help="Output space groups YAML dict",
+    )
+    parser.add_argument(
+        "--output_cls_yaml",
+        default=None,
+        type=str,
+        help="Output crystal-lattice system YAML dict",
+    )
+    parser.add_argument(
+        "--output_ps_yaml",
+        default=None,
+        type=str,
+        help="Output point symmetry YAML dict",
+    )
+    parser.add_argument(
+        "--print",
+        default=False,
+        action="store_true",
+        help="If True, print progress",
+    )
+    return parser.parse_args()
+
+
+def _crystal_lattice_system_index(crystal_lattice_system):
+    for idx, crystal_lattice_system_iter in CRYSTAL_LATTICE_SYSTEMS.items():
+        if crystal_lattice_system == crystal_lattice_system_iter:
+            return idx
+    raise ValueError(
+        f"Crystal-lattice system {crystal_lattice_system} not found in "
+        "crystal-lattice systems dictionary"
+    )
+
+
+def _point_symmetry_index(point_symmetry):
+    for idx, point_symmetry_iter in POINT_SYMMETRIES.items():
+        if point_symmetry == point_symmetry_iter:
+            return idx
+    raise ValueError(
+        f"Point symmetry {point_symmetry} not found in point symmetries dictionary"
+    )
+
+
+def _point_group_to_crystal_class_and_point_symmetry(point_group):
+    for crystal_class_idx, pg_list in CRYSTAL_CLASSES_WIKIPEDIA.items():
+        if point_group in pg_list[2]:
+            crystal_class = pg_list[0]
+            point_symmetry = pg_list[3]
+            point_symmetry_idx = _point_symmetry_index(point_symmetry)
+            return (
+                crystal_class_idx,
+                crystal_class,
+                point_symmetry_idx,
+                point_symmetry,
+            )
+    raise ValueError(f"Point group {point_group} not found in point group dictionary")
+
+
+def _crystal_system_and_space_group_to_lattice_system(crystal_system, sg_symbol):
+    if crystal_system == "trigonal":
+        if sg_symbol in RHOMBOHEDRAL_SPACE_GROUPS_WIKIPEDIA:
+            return "rhombohedral"
+        else:
+            return "hexagonal"
+    else:
+        return crystal_system
+
+
+def _crystal_system_and_space_groups_to_lattice_system(
+    crystal_system, sg_symbol, sg_symbol_rhombohedral
+):
+    if crystal_system == "trigonal":
+        if sg_symbol_rhombohedral != sg_symbol:
+            return "rhombohedral"
+        else:
+            return "hexagonal"
+    else:
+        return crystal_system
+
+
+if __name__ == "__main__":
+    # Arguments
+    args = parsed_args()
+
+    # Make space group dictionary
+    space_groups_dict = {}
+    for idx in range(1, N_SPACE_GROUPS + 1):
+        sg_symbol = sg_symbol_from_int_number(idx, hexagonal=True)
+        sg_symbol_rhombohedral = sg_symbol_from_int_number(idx, hexagonal=False)
+        sg = SpaceGroup(sg_symbol)
+        sg_hmsymbol = sg.symbol
+        point_group = sg.point_group
+        crystal_system = sg.crystal_system
+        (
+            crystal_class_idx,
+            crystal_class,
+            point_symmetry_idx,
+            point_symmetry,
+        ) = _point_group_to_crystal_class_and_point_symmetry(point_group)
+        lattice_system = _crystal_system_and_space_group_to_lattice_system(
+            crystal_system, sg_symbol_rhombohedral
+        )
+        lattice_system_pymatgen = _crystal_system_and_space_groups_to_lattice_system(
+            crystal_system, sg_symbol, sg_symbol_rhombohedral
+        )
+        assert lattice_system == lattice_system_pymatgen
+        if crystal_system != lattice_system:
+            crystal_lattice_system = f"{crystal_system}-{lattice_system}"
+        else:
+            crystal_lattice_system = crystal_system
+        crystal_lattice_system_idx = _crystal_lattice_system_index(
+            crystal_lattice_system
+        )
+        # Update dictionary
+        space_groups_dict.update(
+            {
+                idx: {
+                    "full_symbol": sg_hmsymbol,
+                    "symbol": sg_symbol_rhombohedral,
+                    "crystal_system": crystal_system,
+                    "lattice_system": lattice_system,
+                    "crystal_lattice_system_idx": crystal_lattice_system_idx,
+                    "point_symmetry_idx": point_symmetry_idx,
+                    "point_symmetry": point_symmetry,
+                    "point_group": point_group,
+                    "crystal_class": crystal_class,
+                }
+            }
+        )
+        # Print
+        if args.print:
+            print(f"International number: {idx}")
+            for k, v in space_groups_dict[idx].items():
+                print(f"{k}: {v}")
+            print("---")
+    # Save YAML
+    if args.output_sg_yaml:
+        with open(args.output_sg_yaml, "w") as f:
+            yaml.dump(space_groups_dict, f)
+
+    # Make crystal-lattice system dictionary
+    crystal_lattice_system_dict = {}
+    for idx, crystal_lattice_system in CRYSTAL_LATTICE_SYSTEMS.items():
+        crystal_system = crystal_lattice_system.split("-")[0]
+        lattice_system = crystal_lattice_system.split("-")[-1]
+        space_groups = []
+        point_symmetries = []
+        for sg, sg_dict in space_groups_dict.items():
+            if (
+                sg_dict["crystal_system"] == crystal_system
+                and sg_dict["lattice_system"] == lattice_system
+            ):
+                space_groups.append(sg)
+                point_symmetry_index = _point_symmetry_index(sg_dict["point_symmetry"])
+                if point_symmetry_index not in point_symmetries:
+                    point_symmetries.append(point_symmetry_index)
+        # Update dictionary
+        crystal_lattice_system_dict.update(
+            {
+                idx: {
+                    "crystal_system": crystal_system,
+                    "lattice_system": lattice_system,
+                    "point_symmetries": point_symmetries,
+                    "space_groups": space_groups,
+                }
+            }
+        )
+        # Print
+        if args.print:
+            print(f"Crystal-lattice system index: {idx}")
+            for k, v in crystal_lattice_system_dict[idx].items():
+                print(f"{k}: {v}")
+            print("---")
+    # Save YAML
+    if args.output_cls_yaml:
+        with open(args.output_cls_yaml, "w") as f:
+            yaml.dump(crystal_lattice_system_dict, f)
+
+    # Make point symmetry dictionary
+    point_symmetry_dict = {}
+    for idx, point_symmetry in POINT_SYMMETRIES.items():
+        space_groups = []
+        crystal_lattice_systems = []
+        for sg, sg_dict in space_groups_dict.items():
+            if sg_dict["point_symmetry"] == point_symmetry:
+                space_groups.append(sg)
+                crystal_system = sg_dict["crystal_system"]
+                lattice_system = sg_dict["lattice_system"]
+                if crystal_system != lattice_system:
+                    crystal_lattice_system = f"{crystal_system}-{lattice_system}"
+                else:
+                    crystal_lattice_system = crystal_system
+                crystal_lattice_system_idx = _crystal_lattice_system_index(
+                    crystal_lattice_system
+                )
+                if crystal_lattice_system_idx not in crystal_lattice_systems:
+                    crystal_lattice_systems.append(crystal_lattice_system_idx)
+        # Update dictionary
+        point_symmetry_dict.update(
+            {
+                idx: {
+                    "point_symmetry": point_symmetry,
+                    "crystal_lattice_systems": crystal_lattice_systems,
+                    "space_groups": space_groups,
+                }
+            }
+        )
+        # Print
+        if args.print:
+            print(f"Point symmetry index: {idx}")
+            for k, v in point_symmetry_dict[idx].items():
+                print(f"{k}: {v}")
+            print("---")
+    # Save YAML
+    if args.output_cls_yaml:
+        with open(args.output_ps_yaml, "w") as f:
+            yaml.dump(point_symmetry_dict, f)
+
+    # Exit
+    sys.exit()

crystallograpy-0.1.0/src/crystallograpy/__init__.py

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+from .utils import get_wyckoff_index, load_database
+
+# Load space group and Wyckoff data when the package is imported
+spacegroups = load_database("spacegroups.yaml")
+wyckoff = load_database("wyckoff.yaml")
+
+# Make configurations available at package level
+__all__ = ["spacegroups", "wyckoff", "get_wyckoff_index"]

crystallograpy-0.1.0/src/crystallograpy/spacegroup.py

@@ -0,0 +1,36 @@
+from cyrstallograpy import spacegroups
+
+
+class SpaceGroup:
+    """Class to represent space groups.
+
+    An instance of this SpaceGroup class is meant to represent one of the 230 space
+    groups as stored in ``yaml/spacegroups.yaml``.
+
+    A space group is identified by an integer corresponding to the international
+    number, as per the International Tables for Crystallography.
+    """
+
+    def __init__(self, number: int):
+        """Initialize a SpaceGroup instance.
+
+        Parameters
+        ----------
+        number : int
+            An integer between 1 and 230 corresponding to an international number, as
+            per the data stored in ``yaml/spacegroup.yaml`` and the International
+            Tables for Crystallography.
+        """
+        # Read space group by its number
+        assert number >= 1 and number <= 230
+        data = spacegroups[index]
+
+        self.symbol = data.symbol
+        self.full_symbol = data.full_symbol
+        self.crystal_system = data.crystal_system
+        self.crystal_lattice = data.crystal_lattice
+        self.crystal_lattice_system_index = data.crystal_lattice_system_index
+        self.point_symmetry = data.point_symmetry
+        self.point_symmetry_idx = data.point_symmetry_idx
+        self.point_group = data.point_group
+        self.crystal_class = data.crystal_class