GraphAtoms 1.2.2__tar.gz → 2.1.0__tar.gz

{graphatoms-1.2.2 → graphatoms-2.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: graphatoms
-Version: 1.2.2
+Version: 2.1.0
 Summary: The Chemical Core Class for Graph Theory Analysis.
 Keywords: chemistry,graph theory,reaction,event,KMC
 Author: LiuGaoyong
@@ -13,14 +13,15 @@ Classifier: Intended Audience :: Science/Research
 Requires-Dist: ase
 Requires-Dist: pymatgen>2023.6
 Requires-Dist: rdkit>=2025
+Requires-Dist: numpy>=2,<3
+Requires-Dist: pandas>=2,<4
+Requires-Dist: scipy>=1.10,<2
 Requires-Dist: scikit-learn>=1.5
 Requires-Dist: array-api-compat>=1.10
 Requires-Dist: array-api-extra>=0.10
 Requires-Dist: pyarrow
 Requires-Dist: igraph>=0.11
 Requires-Dist: h5py>=3.16
-Requires-Dist: hydra-core
-Requires-Dist: numpy>=2.0.0,<3
 Requires-Dist: numpydantic
 Requires-Dist: ovld
 Requires-Dist: pydantic>=2.10
@@ -28,6 +29,9 @@ 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: executorlib
+Requires-Dist: hydra-core
+Requires-Dist: typer
 Requires-Dist: loguru
 Requires-Python: >=3.12
 Project-URL: Homepage, https://github.com/LiuGaoyong/GraphAtoms
@@ -54,6 +58,14 @@ The `graphatoms` is a Python library designed for chemical graph theory analysis
 - **Dataclasses**: Pydantic-based data models for type-safe data handling
 - **Array API Compatibility**: Full support for array API standard for cross-framework compatibility (NumPy, PyTorch, JAX, CuPy, etc.)
 - **Subgraph Operations**: Backend-agnostic subgraph extraction with relabeling support using array-api-compat and array-api-extra
+- **CLI Entry Points**: Three console scripts for configuration, execution, and inspection:
+  - `graphatoms-config`: Resolve and print the Hydra/OmegaConf run configuration
+  - `graphatoms-run`: Launch a run
+    - `run_type=otfkmc` for on-the-fly kinetic Monte Carlo simulation
+    - `run_type=rxngen` for reaction network generation
+  - `graphatoms-network`: Inspect and visualize a stored reaction network
+- **Hydra-driven Configuration**: Composable, override-friendly config via Hydra/OmegaConf with grouped groups (`atoms`, `bonds`, `calculator`)
+- **Pluggable Parallel Backends**: Switch executors at the config level — `serial`, `multiprocessing`, `ray`, `dask`, `executorlib` — for distributed/on-the-fly KMC workflows
 
 ## Module Structure
 
@@ -61,18 +73,33 @@ The `graphatoms` is a Python library designed for chemical graph theory analysis
 src/graphatoms/
 ├── arrayapi/        # Array API compatibility layer
 ├── dataclasses/     # Pydantic-based data models
+├── enterpoint/      # Entry points: CLI, config, runners, network, parallel
+│   ├── config/      # Hydra/OmegaConf configuration (atoms, bonds, calculator)
+│   ├── network/     # Reaction network: scheduler, recorder, metadata
+│   ├── parallel/    # Pluggable executors (serial, multiprocessing, ray, dask, executorlib)
+│   ├── runner/      # Runners (otfkmc, rxngen) and helpers
+│   ├── steps/       # Step primitives for runners
+│   └── view.py      # CLI viewer for reactions
 ├── geometry/        # Geometric operations
 ├── reaction/        # Reaction classes and KMC events
-│   ├── base/        # Abstract base classes
-│   ├── event/       # KMC events (adsorption, desorption, reaction)
-│   ├── mcmove/      # Monte Carlo moves
-│   ├── mdwarpper/   # MD wrapper
-│   └── network/     # Reaction network
+│   ├── _event.py    # Event base and event info
+│   ├── reaction.py  # Reaction class
+│   └── xxsorption.py # Adsorption/Desorption events
 ├── system/          # Core system classes
-│   ├── atoms/       # Atomic structure handling
-│   ├── database/    # Database storage backends
-│   └── graph/       # Graph-based system representation
+│   ├── atoms.py     # Atomic structure handling
+│   ├── bonds.py     # Bond list operations
+│   ├── graph.py     # Graph-based system representation
+│   ├── system.py    # System abstract base
+│   ├── sysCluster.py # Cluster system
+│   ├── sysGas.py    # Gas molecule system
+│   └── database/    # Database storage backends (HDF5, SQLite, folder)
 └── utils/           # Utility functions
+    ├── adsorption.py # Adsorption site helper
+    ├── asetools.py  # ASE-related tools
+    ├── bytestool.py # Byte-level helpers
+    ├── logger.py    # Logging setup
+    ├── parser.py    # Hydra argument parsing
+    ├── rdutils.py   # RDKit utilities
     └── subgraph.py  # Array API compatible subgraph operations
 ```
 
@@ -95,6 +122,10 @@ src/graphatoms/
 - pydantic >= 2.10
 - python-snappy >= 0.7.3
 - loguru
+- pandas >= 2
+- scipy >= 1.10
+- typer
+- executorlib
 
 ## Installation
 

{graphatoms-1.2.2 → graphatoms-2.1.0}/README.md

@@ -17,6 +17,14 @@ The `graphatoms` is a Python library designed for chemical graph theory analysis
 - **Dataclasses**: Pydantic-based data models for type-safe data handling
 - **Array API Compatibility**: Full support for array API standard for cross-framework compatibility (NumPy, PyTorch, JAX, CuPy, etc.)
 - **Subgraph Operations**: Backend-agnostic subgraph extraction with relabeling support using array-api-compat and array-api-extra
+- **CLI Entry Points**: Three console scripts for configuration, execution, and inspection:
+  - `graphatoms-config`: Resolve and print the Hydra/OmegaConf run configuration
+  - `graphatoms-run`: Launch a run
+    - `run_type=otfkmc` for on-the-fly kinetic Monte Carlo simulation
+    - `run_type=rxngen` for reaction network generation
+  - `graphatoms-network`: Inspect and visualize a stored reaction network
+- **Hydra-driven Configuration**: Composable, override-friendly config via Hydra/OmegaConf with grouped groups (`atoms`, `bonds`, `calculator`)
+- **Pluggable Parallel Backends**: Switch executors at the config level — `serial`, `multiprocessing`, `ray`, `dask`, `executorlib` — for distributed/on-the-fly KMC workflows
 
 ## Module Structure
 
@@ -24,18 +32,33 @@ The `graphatoms` is a Python library designed for chemical graph theory analysis
 src/graphatoms/
 ├── arrayapi/        # Array API compatibility layer
 ├── dataclasses/     # Pydantic-based data models
+├── enterpoint/      # Entry points: CLI, config, runners, network, parallel
+│   ├── config/      # Hydra/OmegaConf configuration (atoms, bonds, calculator)
+│   ├── network/     # Reaction network: scheduler, recorder, metadata
+│   ├── parallel/    # Pluggable executors (serial, multiprocessing, ray, dask, executorlib)
+│   ├── runner/      # Runners (otfkmc, rxngen) and helpers
+│   ├── steps/       # Step primitives for runners
+│   └── view.py      # CLI viewer for reactions
 ├── geometry/        # Geometric operations
 ├── reaction/        # Reaction classes and KMC events
-│   ├── base/        # Abstract base classes
-│   ├── event/       # KMC events (adsorption, desorption, reaction)
-│   ├── mcmove/      # Monte Carlo moves
-│   ├── mdwarpper/   # MD wrapper
-│   └── network/     # Reaction network
+│   ├── _event.py    # Event base and event info
+│   ├── reaction.py  # Reaction class
+│   └── xxsorption.py # Adsorption/Desorption events
 ├── system/          # Core system classes
-│   ├── atoms/       # Atomic structure handling
-│   ├── database/    # Database storage backends
-│   └── graph/       # Graph-based system representation
+│   ├── atoms.py     # Atomic structure handling
+│   ├── bonds.py     # Bond list operations
+│   ├── graph.py     # Graph-based system representation
+│   ├── system.py    # System abstract base
+│   ├── sysCluster.py # Cluster system
+│   ├── sysGas.py    # Gas molecule system
+│   └── database/    # Database storage backends (HDF5, SQLite, folder)
 └── utils/           # Utility functions
+    ├── adsorption.py # Adsorption site helper
+    ├── asetools.py  # ASE-related tools
+    ├── bytestool.py # Byte-level helpers
+    ├── logger.py    # Logging setup
+    ├── parser.py    # Hydra argument parsing
+    ├── rdutils.py   # RDKit utilities
     └── subgraph.py  # Array API compatible subgraph operations
 ```
 
@@ -58,6 +81,10 @@ src/graphatoms/
 - pydantic >= 2.10
 - python-snappy >= 0.7.3
 - loguru
+- pandas >= 2
+- scipy >= 1.10
+- typer
+- executorlib
 
 ## Installation
 

{graphatoms-1.2.2 → graphatoms-2.1.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "graphatoms"
-version = "1.2.2"
+version = "2.1.0"
 readme = "README.md"
 description = "The Chemical Core Class for Graph Theory Analysis."
 license-files = ["src/LICENSE"]
@@ -26,14 +26,15 @@ dependencies = [
     "ase",
     "pymatgen>2023.6",
     "rdkit>=2025",
+    "numpy>=2,<3",
+    "pandas>=2,<4",
+    "scipy>=1.10,<2",
     "scikit-learn>=1.5",
     "array-api-compat>=1.10",
     "array_api-extra>=0.10",
     "pyarrow",
     "igraph>=0.11",
     "h5py>=3.16",
-    "hydra-core",
-    "numpy>=2.0.0,<3",
     "numpydantic",
     "ovld",
     "pydantic>=2.10",
@@ -41,6 +42,9 @@ dependencies = [
     "tomli; python_version < '3.11'",
     "tomli-w",
     "typing-extensions",
+    "executorlib",
+    "hydra-core",
+    "typer",
     "loguru",
 ]
 
@@ -49,6 +53,11 @@ Homepage = "https://github.com/LiuGaoyong/GraphAtoms"
 Repository = "https://github.com/LiuGaoyong/GraphAtoms"
 Issues = "https://github.com/LiuGaoyong/GraphAtoms/issues/"
 
+[project.scripts]
+graphatoms-config = "graphatoms.enterpoint.config:print_config"
+graphatoms-network = "graphatoms.enterpoint.view:main"
+graphatoms-run = "graphatoms.enterpoint.runner:run"
+
 [[project.authors]]
 name = "LiuGaoyong"
 email = "liugaoyong_88@163.com"
@@ -56,19 +65,21 @@ email = "liugaoyong_88@163.com"
 [dependency-groups]
 dev = [
     "ruff>=0.11",
+    "openbabel-wheel",
     "array-api-strict",
     "pytest>=8.3",
     "pytest-xdist",
-    "jupyter",
-    "sqlmodel",
-    "openbabel-wheel",
+    "jupyterlab",
+    "chemiscope",
+    "nglview",
+    "ray",
 ]
 
 [tool.uv]
 package = true
 
 [[tool.uv.index]]
-url = "https://mirrors.cernet.edu.cn/pypi/web/simple"
+url = "https://mirrors.nju.edu.cn/pypi/web/simple"
 default = true
 
 [tool.pytest.ini_options]
@@ -76,6 +87,8 @@ filterwarnings = [
     "error",
     "ignore::RuntimeWarning",
     "ignore::DeprecationWarning",
+    "ignore::pytest.PytestAssertRewriteWarning",
+    "ignore:unclosed file.*:ResourceWarning",
 ]
 addopts = "--maxfail=1 -rf"
 testpaths = ["src/tests"]
@@ -111,6 +124,7 @@ channels = ["conda-forge"]
 platforms = [
     "linux-64",
     "osx-arm64",
+    "win-64",
 ]
 
 [tool.pixi.pypi-dependencies.graphatoms]
@@ -149,8 +163,8 @@ h5py = ">=3.16.0,<4"
 hydra-core = ">=1.3.2,<2"
 tomli-w = ">=1.2.0,<2"
 loguru = ">=0.7.3,<0.8"
-pytorch = ">=2.10.0,<3"
-jax = ">=0.9.0,<0.10"
 jupyterlab = ">=4.5.8,<5"
 ovld = ">=0.5.15,<0.6"
 pytest-xdist = ">=3.8.0,<4"
+executorlib = ">=1.8,<2"
+typer = ">=0.20,<1"

{graphatoms-1.2.2 → graphatoms-2.1.0}/pyproject.toml.orig

@@ -6,10 +6,13 @@ build-backend = "uv_build"
 Homepage = "https://github.com/LiuGaoyong/GraphAtoms"
 Repository = "https://github.com/LiuGaoyong/GraphAtoms"
 Issues = "https://github.com/LiuGaoyong/GraphAtoms/issues/"
-
+[project.scripts]
+graphatoms-config = "graphatoms.enterpoint.config:print_config"
+graphatoms-network = "graphatoms.enterpoint.view:main"
+graphatoms-run = "graphatoms.enterpoint.runner:run"
 [project]
 name = "graphatoms"
-version = "1.2.2"
+version = "2.1.0"
 readme = "README.md"
 description = "The Chemical Core Class for Graph Theory Analysis."
 authors = [{ name = "LiuGaoyong", email = "liugaoyong_88@163.com" }]
@@ -24,9 +27,9 @@ keywords = [
     "KMC",
 ]
 classifiers = [
-    'Development Status :: 5 - Production/Stable',
-    'Topic :: Scientific/Engineering :: Chemistry',
-    'Intended Audience :: Science/Research',
+    "Development Status :: 5 - Production/Stable",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Intended Audience :: Science/Research",
 ]
 dependencies = [
     # Chemoinformatics
@@ -35,7 +38,9 @@ dependencies = [
     "rdkit>=2025",
 
     # Scientific Computing
-    # numpy pandas, scipy
+    "numpy>=2,<3",
+    "pandas>=2,<4",
+    "scipy>=1.10,<2",
     "scikit-learn>=1.5",
     "array-api-compat>=1.10",
     "array_api-extra>=0.10",
@@ -46,33 +51,40 @@ dependencies = [
 
     # Data Model
     "h5py>=3.16",
-    "hydra-core",
-    "numpy>=2.0.0,<3",
     "numpydantic",
-    "ovld",                           # singledispatch which works for multiple arguments.
+    "ovld",                           # singledispatch
     "pydantic>=2.10",
     "python-snappy>=0.7.3",           # More Fase Data Compression
     "tomli; python_version < '3.11'", # use tomllib in python>=3.11
     "tomli-w",                        # TOML writer
     "typing-extensions",
+
+    # Other
+    "executorlib",
+    "hydra-core",
+    "typer",
     "loguru",
 ]
 [dependency-groups]
 dev = [
     "ruff>=0.11",
+    "openbabel-wheel",
     "array-api-strict",
     "pytest>=8.3",
     "pytest-xdist",
-    "jupyter",
-    "sqlmodel",         # SQL + pydantic
-    'openbabel-wheel',
+    "jupyterlab",
+    "chemiscope",
+    # "playwright>=1.52", # chemiscope [headless]
+    "nglview",
+    "ray",
 ]
 
 # uv config
 [tool.uv]
 package = true
 [[tool.uv.index]]
-url = "https://mirrors.cernet.edu.cn/pypi/web/simple" # CERNET
+# url = "https://mirrors.cernet.edu.cn/pypi/web/simple" # CERNET
+url = "https://mirrors.nju.edu.cn/pypi/web/simple" # NJU
 default = true
 # [[tool.uv.index]]
 # name = "pytorch-cpu"
@@ -87,13 +99,15 @@ default = true
 filterwarnings = [
     "error", # All other warnings are transformed into errors.
     # ignore the following warnings that matching a regex
-    # example: 'ignore:function ham\(\) is deprecated:DeprecationWarning',
+    # example: "ignore:function ham\(\) is deprecated:DeprecationWarning",
     "ignore::RuntimeWarning",
     "ignore::DeprecationWarning",
+    "ignore::pytest.PytestAssertRewriteWarning",
+    "ignore:unclosed file.*:ResourceWarning",
 
 ]
-addopts = '--maxfail=1 -rf' # exit after 1 failures, report fail info
-testpaths = ['src/tests']
+addopts = "--maxfail=1 -rf" # exit after 1 failures, report fail info
+testpaths = ["src/tests"]
 
 # ruff config
 [tool.ruff]
@@ -114,7 +128,7 @@ backend = { name = "pixi-build-python", version = "*" }
 [tool.pixi.workspace]
 preview = ["pixi-build"]
 channels = ["conda-forge"]
-platforms = ["linux-64", "osx-arm64"]
+platforms = ["linux-64", "osx-arm64", "win-64"]
 
 [tool.pixi.pypi-dependencies]
 graphatoms = { path = ".", editable = true }
@@ -125,7 +139,7 @@ dev = { features = ["dev"], solve-group = "default" }
 
 [tool.pixi.tasks]
 test = "pytest -s -vv"
-benchmark = 'pytest -s src/tests-benchmark/*.py'
+benchmark = "pytest -s src/tests-benchmark/*.py"
 
 [tool.pixi.dependencies]
 python = ">=3.12"
@@ -148,8 +162,8 @@ h5py = ">=3.16.0,<4"
 hydra-core = ">=1.3.2,<2"
 tomli-w = ">=1.2.0,<2"
 loguru = ">=0.7.3,<0.8"
-pytorch = ">=2.10.0,<3"
-jax = ">=0.9.0,<0.10"
 jupyterlab = ">=4.5.8,<5"
 ovld = ">=0.5.15,<0.6"
 pytest-xdist = ">=3.8.0,<4"
+executorlib = ">=1.8,<2"
+typer = ">=0.20,<1"

{graphatoms-1.2.2 → graphatoms-2.1.0}/src/graphatoms/dataclasses/_numpydantic.py

@@ -14,11 +14,20 @@ from pydantic import (
 __all__ = ["NDArray", "numpy_validator"]
 _ENCODING = "latin1"
 
+
+@validate_call
+def __convert2str(x: Any) -> str:
+    if isinstance(x, np.ndarray):
+        return x.tobytes().decode(_ENCODING)
+    else:
+        return str(x)
+
+
 NDArray = Annotated[
     _NDArray,
-    PlainSerializer(lambda x: x.tobytes().decode(_ENCODING), return_type=str),
-    # for pyarrow compatibility, we need to convert bytes to str
-    #                   for numpy.ndarray before serialization.
+    PlainSerializer(__convert2str, return_type=str, when_used="json"),
+    # # for pyarrow compatibility, we need to convert bytes to str
+    # #                   for numpy.ndarray before serialization.
     WithJsonSchema({"type": str}, mode="serialization"),
 ]
 if TYPE_CHECKING:

{graphatoms-1.2.2 → graphatoms-2.1.0}/src/graphatoms/dataclasses/_pydanticMixin.py

@@ -1,4 +1,5 @@
 # ruff: noqa: D100 D102 E501
+import json
 from collections.abc import Mapping, Sequence
 from sys import version_info
 from typing import Any, Self
@@ -34,6 +35,7 @@ class PydanticConvertFactoryMixin(pydantic.BaseModel):
         exclude_computed_fields: bool = True,
         numpy_ndarray_compatible: bool = True,
         numpy_convert_to_list: bool = False,
+        pyarrow_compatible: bool = False,
         **kwargs,
     ) -> dict[str, Any]:
         """Convert model to dictionary."""
@@ -46,27 +48,43 @@ class PydanticConvertFactoryMixin(pydantic.BaseModel):
                 exclude_computed_fields=exclude_computed_fields,
             )
         )
-        result = self.model_dump(**kwargs)
-        if numpy_ndarray_compatible:
-            for k, v0 in result.items():
-                v1 = getattr(self, k, None)
-                if type(v0) is not type(v1) and isinstance(v1, np.ndarray):
-                    result[k] = v1
-                if np.isscalar(v1):
+        if not pyarrow_compatible:
+            result = self.model_dump(**kwargs)
+            if numpy_ndarray_compatible:
+                for k, v0 in result.items():
+                    v1 = getattr(self, k, None)
+                    if type(v0) is not type(v1) and isinstance(v1, np.ndarray):
+                        result[k] = v1
+                    if np.isscalar(v1):
+                        pass
+                    elif isinstance(v1, list | tuple):
+                        assert isinstance(
+                            np.asarray(list(v1)).flat[0], np.str_
+                        ), "Only list[str] is supported."
+                    else:
+                        assert isinstance(v1, np.ndarray) or (
+                            "Only numpy array or scalar is supported. "
+                            f"But got `{type(v0)}` for {k}."
+                        )
+            if numpy_convert_to_list:
+                for k, v in result.items():
+                    if isinstance(v, np.ndarray):
+                        result[k] = v.tolist()
+        else:
+            jsonstr: str = self.to_str(**kwargs)
+            result: dict[str, Any] = json.loads(jsonstr)
+            assert isinstance(result, dict), "Only dict is supported."
+            for k, v in result.items():
+                if isinstance(v, str | float | int | bool):
                     pass
-                elif isinstance(v1, list | tuple):
-                    assert isinstance(np.asarray(list(v1)).flat[0], np.str_), (
-                        "Only list[str] is supported."
-                    )
+                elif isinstance(v, list | tuple):
+                    assert k == "hashes", "Only hashes is supported."
+                    result[k] = str(v)
                 else:
-                    assert isinstance(v1, np.ndarray) or (
-                        "Only numpy array or scalar is supported. "
-                        f"But got `{type(v0)}` for {k}."
+                    raise ValueError(
+                        f"But got unsupported type: `{type(v)}` for {k}."
                     )
-        if numpy_convert_to_list:
-            for k, v in result.items():
-                if isinstance(v, np.ndarray):
-                    result[k] = v.tolist()
+
         return result
 
     @pydantic.validate_call
@@ -94,6 +112,7 @@ class PydanticConvertFactoryMixin(pydantic.BaseModel):
                 indent=indent,
             )
         )
+        kwargs.pop("mode", None)
         return self.model_dump_json(**kwargs)
 
     @pydantic.validate_call
@@ -184,7 +203,8 @@ class PydanticConvertFactoryMixin(pydantic.BaseModel):
     @classmethod
     @pydantic.validate_call
     def from_dict(cls, data: Mapping[str, Any], **kw) -> Self:
-        return cls.model_validate({**data, **kw})
+        kw.update(data)  # Update kwargs with data.
+        return cls.model_validate(kw)
 
 
 class __Json(PydanticConvertFactoryMixin):

{graphatoms-1.2.2 → graphatoms-2.1.0}/src/graphatoms/dataclasses/_pydanticModel.py

@@ -6,9 +6,9 @@ from numbers import Real
 from typing import override
 
 import numpy as np
+import pyarrow as pa
 import pydantic
 from numpy.typing import ArrayLike
-from pyarrow import Schema
 
 from graphatoms.dataclasses._pydantic2pyarrow import get_pyarrow_schema
 from graphatoms.dataclasses._pydanticMixin import (
@@ -79,9 +79,15 @@ class OurBaseModel(PydanticFactoryMixin, _IndexMaskMixin):
     """
 
     @classmethod
-    def get_pyarrow_schema(cls) -> Schema:
+    def get_pyarrow_schema(cls) -> pa.Schema:
         """Get the pyarrow schema of this class."""
-        return get_pyarrow_schema(cls)
+        schema: pa.Schema = get_pyarrow_schema(cls)
+        if "hashes" not in cls.__pydantic_fields__:
+            return schema
+        else:
+            target_index: int = schema.get_field_index("hashes")
+            new_field = schema.field("hashes").with_type(pa.string())
+            return schema.set(target_index, new_field)
 
     def __repr__(self) -> str:
         return super().__repr__()
@@ -157,6 +163,6 @@ class OurFrozenModel(OurBaseModel):
         return hash(self.hash)
 
     @cached_property
-    @abstractmethod
     def hash(self) -> str:
         """Get the HASH string of this object."""
+        raise NotImplementedError("hash is not implemented for this class.")

graphatoms-2.1.0/src/graphatoms/enterpoint/config/__init__.py

@@ -0,0 +1,110 @@
+import os
+from dataclasses import dataclass, field
+from pathlib import Path
+from typing import Any
+
+os.environ["HYDRA_FULL_ERROR"] = "1"
+import hydra
+from hydra.core.config_store import ConfigStore
+from omegaconf import MISSING, OmegaConf
+
+from .atoms import AseReadAtomsConfig, AtomsConfig
+from .atoms import OctahedronAtomsConfig as OctAtomsConfig
+from .bonds import BondsConfig, RawBondsConfig
+from .calculator import CalcConfig, EMTCalcConfig
+from .calculator import NequipCalcConfig as NequipConfig
+
+CONFIG_DIR = Path(__file__).parent
+
+
+@dataclass
+class SiteConfig:
+    method: str = "distance"  # or hop
+    env_threshold: float = 15  # the environment threshold
+    max_moved_threshold: float = 8  # the maximum moved threshold
+
+
+@dataclass
+class ExplConfig:
+    maxtry: int = 1000
+    maxconfidence: float = 10
+    max_ncore_for_surface: int = 3  # 4, 5, 6
+    surface_only_explore_single_core: bool = True
+    allow_multiple_adsorption: bool = False
+    allow_explore_bulk: bool = False
+    thetacutoff: float = -1  # 0-180, -1 means no cutoff
+    nfibonacci: int = 200
+
+
+@dataclass
+class EventConfig:
+    db_format: str = "folder"
+    check_frequency: bool = True  # whether to check the frequency
+    max_force: float = 0.05  # eV / Angstrom
+    min_frequency: float = 10.0  # cm^-1
+    min_frequency_for_ts: float = 20.0  # cm^-1
+    simplified_threshold: float = 7.0  # the simplified threshold for event
+    gas_sticking: dict[str, float] = field(default_factory=dict)
+    gas_pressure: dict[str, float] = field(default_factory=dict)
+    default_pressure: float = 101325
+    default_sticking: float = 1.0
+    temperature: float = 300
+
+
+@dataclass
+class OptConfig:
+    method: str = "lbfgs"
+    fmax: float = 0.05
+    steps: int = 200
+
+
+@dataclass
+class Config:
+    atoms: AtomsConfig = MISSING
+    bonds: BondsConfig = MISSING
+    system: Any = MISSING
+
+    calculator: CalcConfig = MISSING
+
+    outputs: str = "./zzz"
+    max_steps: int = 100000
+    max_times: float = 1000.0  # seconds
+    run_type: str = "otfkmc"  # otfkmc, rxngen
+    parallel_workers: int = 0  # 0 means use all cores
+    parallel: str = "serial"  # serial, multiprocessing, ray, dask, executorlib
+    loglevel: str = "info"  # Literal["debug", "info", "warning", "error"]
+    logfile: str = "log.txt"
+    restart: bool = True
+    debug: bool = False
+
+    site: SiteConfig = field(default_factory=SiteConfig)
+    exploration: ExplConfig = field(default_factory=ExplConfig)
+    event: EventConfig = field(default_factory=EventConfig)
+    optimizer: OptConfig = field(default_factory=OptConfig)
+
+
+cs = ConfigStore.instance()
+cs.store(name="base_config", node=Config)
+cs.store(group="atoms", name="atoms_aseread", node=AseReadAtomsConfig)
+cs.store(group="atoms", name="atoms_octahedron", node=OctAtomsConfig)
+cs.store(group="bonds", name="bonds_raw", node=RawBondsConfig)
+cs.store(group="calculator", name="calc_emt", node=EMTCalcConfig)
+cs.store(group="calculator", name="calc_nequip", node=NequipConfig)
+
+
+@hydra.main(
+    config_path=CONFIG_DIR.as_posix(),
+    config_name="run",
+    version_base=None,
+)
+def print_config(cfg: Config) -> None:
+    from shutil import rmtree
+
+    print(OmegaConf.to_yaml(cfg))
+    print("""
+hydra:
+  run:
+    dir: ${outputs}
+  verbose: ${debug}
+""")
+    rmtree(Path(cfg.outputs))