GraphAtoms 1.1.2__tar.gz → 1.1.3__tar.gz

graphatoms-1.1.3/PKG-INFO

@@ -0,0 +1,105 @@
+Metadata-Version: 2.4
+Name: graphatoms
+Version: 1.1.3
+Summary: The Chemical Core Class for Graph Theory Analysis.
+Keywords: chemistry,graph theory,reaction,event,KMC
+Author: LiuGaoyong
+Author-email: LiuGaoyong <liugaoyong_88@163.com>
+License-Expression: GPL-3.0-or-later
+License-File: src/LICENSE
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Intended Audience :: Science/Research
+Requires-Dist: ase
+Requires-Dist: pymatgen>2023.6
+Requires-Dist: rdkit>=2025
+Requires-Dist: scikit-learn>=1.5
+Requires-Dist: pyarrow
+Requires-Dist: igraph>=0.11
+Requires-Dist: h5py>=3.16
+Requires-Dist: hydra-core
+Requires-Dist: numpydantic
+Requires-Dist: pydantic>=2.11
+Requires-Dist: python-snappy>=0.7.3
+Requires-Dist: tomli ; python_full_version < '3.11'
+Requires-Dist: tomli-w
+Requires-Dist: typing-extensions
+Requires-Dist: loguru
+Requires-Python: >=3.12
+Project-URL: Homepage, https://github.com/LiuGaoyong/GraphAtoms
+Project-URL: Repository, https://github.com/LiuGaoyong/GraphAtoms
+Project-URL: Issues, https://github.com/LiuGaoyong/GraphAtoms/issues/
+Description-Content-Type: text/markdown
+
+# graphatoms
+
+[![Conda Version](https://img.shields.io/conda/vn/conda-forge/graphatoms.svg)](https://anaconda.org/conda-forge/graphatoms)  [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/graphatoms.svg)](https://anaconda.org/conda-forge/graphatoms)    [![Pypi version](https://img.shields.io/pypi/v/graphatoms)](https://pypi.org/project/graphatoms/) [![PyPI Downloads](https://static.pepy.tech/badge/graphatoms)](https://pepy.tech/projects/graphatoms)
+
+
+The Chemical Core Class for Graph Theory Analysis & Graph Neural Network.
+
+## Overview
+
+The `graphatoms` is a Python library designed for chemical graph theory analysis and graph neural network applications. It provides core classes for representing chemical systems and reactions with graph-based data structures.
+
+## Features
+
+- **Graph-based Chemical System Representation**: Represent chemical systems, clusters, and gas molecules using graph theory
+- **Reaction Modeling**: Support for reaction classes, KMC (Kinetic Monte Carlo) events, and MC (Monte Carlo) moves
+- **Geometry Operations**: Bond lists, distance calculations, neighbor lists, rotations, and sampling
+- **Data Storage**: Support for HDF5 and SQLite databases for efficient data persistence
+- **Dataclasses**: Pydantic-based data models for type-safe data handling
+
+## Module Structure
+
+```
+src/graphatoms/
+├── dataclasses/     # Pydantic-based data models
+├── geometry/        # Geometric operations
+├── reaction/        # Reaction classes and KMC events
+├── system/          # Core system classes (System, Cluster, Gas)
+└── utils/           # Utility functions
+```
+
+## Requirements
+
+- Python >= 3.10
+- ase
+- pymatgen > 2023.6
+- rdkit >= 2025
+- scikit-learn >= 1.5
+- pyarrow
+- igraph >= 0.11
+- h5py >= 3.16
+- hydra-core
+- numpydantic
+- pydantic >= 2.11
+
+## Installation
+
+```bash
+pip install graphatoms
+```
+
+## Development
+
+For development setup with pixi:
+
+```bash
+pixi install
+pixi run test
+```
+
+## License
+
+GPL-3.0-or-later
+
+## Authors
+
+- LiuGaoyong (liugaoyong_88@163.com)
+
+## Links
+
+- Homepage: https://github.com/LiuGaoyong/GraphAtoms
+- Repository: https://github.com/LiuGaoyong/GraphAtoms
+- Issues: https://github.com/LiuGaoyong/GraphAtoms/issues/

graphatoms-1.1.3/README.md

@@ -0,0 +1,72 @@
+# graphatoms
+
+[![Conda Version](https://img.shields.io/conda/vn/conda-forge/graphatoms.svg)](https://anaconda.org/conda-forge/graphatoms)  [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/graphatoms.svg)](https://anaconda.org/conda-forge/graphatoms)    [![Pypi version](https://img.shields.io/pypi/v/graphatoms)](https://pypi.org/project/graphatoms/) [![PyPI Downloads](https://static.pepy.tech/badge/graphatoms)](https://pepy.tech/projects/graphatoms)
+
+
+The Chemical Core Class for Graph Theory Analysis & Graph Neural Network.
+
+## Overview
+
+The `graphatoms` is a Python library designed for chemical graph theory analysis and graph neural network applications. It provides core classes for representing chemical systems and reactions with graph-based data structures.
+
+## Features
+
+- **Graph-based Chemical System Representation**: Represent chemical systems, clusters, and gas molecules using graph theory
+- **Reaction Modeling**: Support for reaction classes, KMC (Kinetic Monte Carlo) events, and MC (Monte Carlo) moves
+- **Geometry Operations**: Bond lists, distance calculations, neighbor lists, rotations, and sampling
+- **Data Storage**: Support for HDF5 and SQLite databases for efficient data persistence
+- **Dataclasses**: Pydantic-based data models for type-safe data handling
+
+## Module Structure
+
+```
+src/graphatoms/
+├── dataclasses/     # Pydantic-based data models
+├── geometry/        # Geometric operations
+├── reaction/        # Reaction classes and KMC events
+├── system/          # Core system classes (System, Cluster, Gas)
+└── utils/           # Utility functions
+```
+
+## Requirements
+
+- Python >= 3.10
+- ase
+- pymatgen > 2023.6
+- rdkit >= 2025
+- scikit-learn >= 1.5
+- pyarrow
+- igraph >= 0.11
+- h5py >= 3.16
+- hydra-core
+- numpydantic
+- pydantic >= 2.11
+
+## Installation
+
+```bash
+pip install graphatoms
+```
+
+## Development
+
+For development setup with pixi:
+
+```bash
+pixi install
+pixi run test
+```
+
+## License
+
+GPL-3.0-or-later
+
+## Authors
+
+- LiuGaoyong (liugaoyong_88@163.com)
+
+## Links
+
+- Homepage: https://github.com/LiuGaoyong/GraphAtoms
+- Repository: https://github.com/LiuGaoyong/GraphAtoms
+- Issues: https://github.com/LiuGaoyong/GraphAtoms/issues/

{graphatoms-1.1.2 → graphatoms-1.1.3}/pyproject.toml

@@ -9,13 +9,13 @@ Issues = "https://github.com/LiuGaoyong/GraphAtoms/issues/"
 
 [project]
 name = "graphatoms"
-version = "1.1.2"
+version = "1.1.3"
 readme = "README.md"
 description = "The Chemical Core Class for Graph Theory Analysis."
 authors = [{ name = "LiuGaoyong", email = "liugaoyong_88@163.com" }]
 license-files = ["src/LICENSE"]
 license = "GPL-3.0-or-later"
-requires-python = ">=3.10"
+requires-python = ">=3.12"
 keywords = [
     "chemistry",    #
     "graph theory",

{graphatoms-1.1.2 → graphatoms-1.1.3}/src/graphatoms/reaction/_abc/rtgp.py

@@ -138,7 +138,7 @@ class RTGP(OurFrozenModel, MoveABC):
 
     @override
     def __call__(self, atoms: Atoms, *args, **kwargs) -> Atoms:
-        r = self.R.__class__.from_ase(atoms, *args, **kwargs)
+        self.R.__class__.from_ase(atoms, *args, **kwargs)
         raise NotImplementedError()
 
     def __reversed__(self) -> Self:  # type: ignore

{graphatoms-1.1.2 → graphatoms-1.1.3}/src/graphatoms/reaction/_mcmove/__init__.py

@@ -1,3 +1,5 @@
 """The move is a variation between two structures."""
 
 from ._abc import MoveABC
+
+__all__ = ["MoveABC"]

{graphatoms-1.1.2 → graphatoms-1.1.3}/src/graphatoms/reaction/_mcmove/_moveFB.py

@@ -164,7 +164,7 @@ class FBDispC(FBDisp):
             atoms0: Atoms = self.atoms.__getitem__(nbrs)  # type: ignore
             atoms0.calc = self.calc
             atoms0.calc.reset()
-            e0 = atoms0.get_potential_energy()
+            atoms0.get_potential_energy()
             f0: np.ndarray = atoms0.get_forces()
             f = f0[nbrs == i].ravel()
             assert f.shape == (3,)
@@ -176,4 +176,3 @@ class FBDispC(FBDisp):
                 lambda_param=lambda_param,
             )
             displacement[i, :] = disp_i
-            how_to_change = f"Disp({i}),ForceBias"

{graphatoms-1.1.2 → graphatoms-1.1.3}/src/graphatoms/system/_graph/__init__.py

@@ -1,6 +1,11 @@
 """The graph representation of the system."""
+# ruff: noqa: F401
 
-from ._bonds import BondGraph
+from ._bonds import (
+    DEFAULT_WH_HASH_DEPTH,
+    DEFAULT_WH_HASH_SIZE,
+    BondGraph,
+)
 from ._sysGraph import SysGraph
 
 __all__ = ["BondGraph", "SysGraph"]

{graphatoms-1.1.2 → graphatoms-1.1.3}/src/graphatoms/system/_graph/_bonds.py

@@ -136,12 +136,15 @@ class BondGraph(Matter, OurFrozenModel):
 
     def get_chordless_cycles(
         self,
+        batch_nbr_order: int = 3,
         batch: ArrayLike | list[int | bool] | int | None = None,
         max_ncore: Literal[3, 4, 5, 6] = 3,
     ) -> np.ndarray:
         """Got chordless cycles mask array for specific core numbers.
 
         Args:
+            batch_nbr_order (int, optional): the max number of neighbors
+                of a site. Defaults to 3.
             batch (np.ndarray | list[int | bool] | None, optional):
                 the batch atoms of calculation. Default to None.
             max_ncore (Literal[3, 4, 5, 6], optional): The maximum
@@ -150,7 +153,12 @@ class BondGraph(Matter, OurFrozenModel):
         Returns:
             np.ndarray: (n_site, n_atoms) boolean matrix
         """
-        return chordless_cycles(self.__IGRAPH, batch, max_ncore)
+        return chordless_cycles(
+            igraph=self.__IGRAPH,
+            batch_nbr_order=batch_nbr_order,
+            max_ncore=max_ncore,
+            batch=batch,
+        )
 
     def get_match_mode(
         self,
@@ -390,17 +398,20 @@ class BondGraph(Matter, OurFrozenModel):
 
 def chordless_cycles(
     igraph: IGraph,
-    batch: ArrayLike | list[int | bool] | int | None = None,
     max_ncore: Literal[3, 4, 5, 6] = 3,
+    batch: ArrayLike | list[int | bool] | int | None = None,
+    batch_nbr_order: int = 3,
 ) -> np.ndarray:
     """Got chordless cycles mask array for specific core numbers.
 
     Args:
         igraph (igraph.Graph): The graph to calculate.
-        batch (np.ndarray | list[int | bool] | None, optional):
-            the batch atoms of calculation. Default to None.
         max_ncore (Literal[3, 4, 5, 6], optional): The maximum
             number of core atoms in a site. Defaults to 3.
+        batch (np.ndarray | list[int | bool] | None, optional):
+            the batch atoms of calculation. Default to None.
+        batch_nbr_order (int, optional): The order of neighborhood.
+            Defaults to 3.
 
     Returns:
         np.ndarray: (n_site, n_atoms) boolean matrix
@@ -420,7 +431,7 @@ def chordless_cycles(
         f"Invalid max_ncore value: {max_ncore}."
         " Only 3, 4, 5 and 6 are supported here."
     )
-    nbr = igraph.neighborhood(batch, order=3, mindist=0)
+    nbr = igraph.neighborhood(batch, order=batch_nbr_order, mindist=0)
     nbr = np.unique(reduce(np.append, nbr))
     g: IGraph = _subgraph_edges(igraph, nbr)
     if not g.is_simple():

graphatoms-1.1.3/src/graphatoms/system/helper.py

@@ -0,0 +1,104 @@
+from collections.abc import Mapping
+from typing import Any
+
+import numpy as np
+from ase import Atoms
+
+from ..geometry._inner_outer import check_atom_is_inner
+from ..utils.bytestool import hash_string
+from ._graph import SysGraph
+from ._graph._bonds import DEFAULT_WH_HASH_SIZE
+from ._sys import System
+
+
+def get_hash_of_atoms(
+    atoms: Atoms,
+    parse_bonds: Mapping[str, Any] | None = {"method": "raw"},
+    **kwargs,
+) -> str:
+    """A helper function for hash calculation for `ase.Atoms`."""
+    return SysGraph.from_ase(
+        atoms=atoms,
+        parse_bonds=parse_bonds,
+        **kwargs,
+    ).hash
+
+
+def analysis(atoms: Atoms, bonds_cfg: Mapping[str, Any] = {}) -> System:
+    """A helper function for analysis of `ase.Atoms`."""
+    sys = System.from_ase(
+        atoms,
+        parse_bonds=bonds_cfg.get("parser", {"method": "raw"}),
+        parse_bonds_distance=bonds_cfg.get("parse_distance", False),
+        parse_bonds_order=bonds_cfg.get("parse_order", False),
+    )
+    is_inner = [
+        check_atom_is_inner(
+            i,
+            numbers=sys.numbers,
+            geometry=sys.positions,
+            adjacency_array=sys.MATRIX[i : i + 1, :],
+            cell=atoms.cell,
+        )
+        for i in range(len(atoms))
+    ]
+    is_outer = np.logical_not(is_inner)
+    result = sys.from_dict(sys.to_dict(), is_outer=is_outer)
+    result.hash  # call hash calculation to set hash & hashes
+    return result
+
+
+def analysis_site(
+    sys: System,
+    active: np.ndarray | None = None,
+    max_ncore: int = 3,
+) -> np.ndarray:
+    """A helper function for analysis of `graphatoms.system.System`."""
+    sys.hash  # call hash calculation to set hash & hashes
+    assert sys.pair is not None, "Please run analysis first on the System."
+    assert sys.hashes is not None, "Please run analysis first on the System."
+    assert sys.is_outer is not None, "Please run analysis first on the System."
+    if active is None:
+        active = sys.is_outer
+    else:
+        active0 = sys.is_outer
+        assert active.shape == active0.shape
+        active = active & active0
+    arange = np.arange(len(sys))
+
+    result_1 = np.asarray(
+        [
+            np.isin(arange, [i])
+            for i in arange  #
+            if active[i]
+        ]
+        + [
+            np.isin(arange, [i, j])
+            for i, j in sys.pair  #
+            if active[i] and active[j]
+        ]
+    )
+    result_2 = sys.get_chordless_cycles(
+        batch_nbr_order=0,
+        max_ncore=max_ncore,  # type: ignore
+        batch=active,
+    )
+    # result_2 = [
+    #     site
+    #     for site in sys.get_chordless_cycles(
+    #         batch_nbr_order=0,
+    #         max_ncore=max_ncore,  # type: ignore
+    #         batch=active,
+    #     )
+    #     if np.sum(site) == np.sum(active & site)
+    # ]
+    result = np.vstack([result_1, result_2])
+    hashes = [
+        hash_string(
+            "-".join([sys.hashes[i] for i in range(len(sys)) if site[i]]),
+            digest_size=DEFAULT_WH_HASH_SIZE,
+        )
+        for site in result
+    ]
+    _, idx = np.unique(hashes, return_index=True)
+    return result[idx]

graphatoms-1.1.2/PKG-INFO

@@ -1,36 +0,0 @@
-Metadata-Version: 2.4
-Name: graphatoms
-Version: 1.1.2
-Summary: The Chemical Core Class for Graph Theory Analysis.
-Keywords: chemistry,graph theory,reaction,event,KMC
-Author: LiuGaoyong
-Author-email: LiuGaoyong <liugaoyong_88@163.com>
-License-Expression: GPL-3.0-or-later
-License-File: src/LICENSE
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Topic :: Scientific/Engineering :: Chemistry
-Classifier: Intended Audience :: Science/Research
-Requires-Dist: ase
-Requires-Dist: pymatgen>2023.6
-Requires-Dist: rdkit>=2025
-Requires-Dist: scikit-learn>=1.5
-Requires-Dist: pyarrow
-Requires-Dist: igraph>=0.11
-Requires-Dist: h5py>=3.16
-Requires-Dist: hydra-core
-Requires-Dist: numpydantic
-Requires-Dist: pydantic>=2.11
-Requires-Dist: python-snappy>=0.7.3
-Requires-Dist: tomli ; python_full_version < '3.11'
-Requires-Dist: tomli-w
-Requires-Dist: typing-extensions
-Requires-Dist: loguru
-Requires-Python: >=3.10
-Project-URL: Homepage, https://github.com/LiuGaoyong/GraphAtoms
-Project-URL: Repository, https://github.com/LiuGaoyong/GraphAtoms
-Project-URL: Issues, https://github.com/LiuGaoyong/GraphAtoms/issues/
-Description-Content-Type: text/markdown
-
-# graphatoms
-
-The Chemical Core Class for Graph Theory Analysis & Graph Neural Network.

graphatoms-1.1.2/README.md

@@ -1,3 +0,0 @@
-# graphatoms
-
-The Chemical Core Class for Graph Theory Analysis & Graph Neural Network.

graphatoms-1.1.2/src/graphatoms/system/helper.py

@@ -1,19 +0,0 @@
-from collections.abc import Mapping
-from typing import Any
-
-from ase import Atoms
-
-from ._graph import SysGraph
-
-
-def get_hash_of_atoms(
-    atoms: Atoms,
-    parse_bonds: Mapping[str, Any] | None = {"method": "raw"},
-    **kwargs,
-) -> str:
-    """A helper function for hash calculation for `ase.Atoms`."""
-    return SysGraph.from_ase(
-        atoms=atoms,
-        parse_bonds=parse_bonds,
-        **kwargs,
-    ).hash