GraphAtoms 2.0.0__tar.gz → 2.1.1__tar.gz

{graphatoms-2.0.0 → graphatoms-2.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: graphatoms
-Version: 2.0.0
+Version: 2.1.1
 Summary: The Chemical Core Class for Graph Theory Analysis.
 Keywords: chemistry,graph theory,reaction,event,KMC
 Author: LiuGaoyong
@@ -29,12 +29,8 @@ 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: plotext
-Requires-Dist: plotext-plus
-Requires-Dist: matplotlib
 Requires-Dist: executorlib
 Requires-Dist: hydra-core
-Requires-Dist: pipefunc
 Requires-Dist: typer
 Requires-Dist: loguru
 Requires-Python: >=3.12
@@ -62,6 +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
 
@@ -69,18 +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
 ```
 
@@ -103,6 +122,10 @@ src/graphatoms/
 - pydantic >= 2.10
 - python-snappy >= 0.7.3
 - loguru
+- pandas >= 2
+- scipy >= 1.10
+- typer
+- executorlib
 
 ## Installation
 

{graphatoms-2.0.0 → graphatoms-2.1.1}/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-2.0.0 → graphatoms-2.1.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "graphatoms"
-version = "2.0.0"
+version = "2.1.1"
 readme = "README.md"
 description = "The Chemical Core Class for Graph Theory Analysis."
 license-files = ["src/LICENSE"]
@@ -42,12 +42,8 @@ dependencies = [
     "tomli; python_version < '3.11'",
     "tomli-w",
     "typing-extensions",
-    "plotext",
-    "plotext-plus",
-    "matplotlib",
     "executorlib",
     "hydra-core",
-    "pipefunc",
     "typer",
     "loguru",
 ]

{graphatoms-2.0.0 → graphatoms-2.1.1}/pyproject.toml.orig

@@ -12,7 +12,7 @@ graphatoms-network = "graphatoms.enterpoint.view:main"
 graphatoms-run = "graphatoms.enterpoint.runner:run"
 [project]
 name = "graphatoms"
-version = "2.0.0"
+version = "2.1.1"
 readme = "README.md"
 description = "The Chemical Core Class for Graph Theory Analysis."
 authors = [{ name = "LiuGaoyong", email = "liugaoyong_88@163.com" }]
@@ -60,12 +60,8 @@ dependencies = [
     "typing-extensions",
 
     # Other
-    "plotext",
-    "plotext-plus",
-    "matplotlib",
     "executorlib",
     "hydra-core",
-    "pipefunc",
     "typer",
     "loguru",
 ]

{graphatoms-2.0.0 → graphatoms-2.1.1}/src/graphatoms/enterpoint/config/__init__.py

@@ -66,7 +66,7 @@ class Config:
 
     calculator: CalcConfig = MISSING
 
-    outputs: str = "./zzz"
+    outputs: str = "."
     max_steps: int = 100000
     max_times: float = 1000.0  # seconds
     run_type: str = "otfkmc"  # otfkmc, rxngen
@@ -98,8 +98,6 @@ cs.store(group="calculator", name="calc_nequip", node=NequipConfig)
     version_base=None,
 )
 def print_config(cfg: Config) -> None:
-    from shutil import rmtree
-
     print(OmegaConf.to_yaml(cfg))
     print("""
 hydra:
@@ -107,4 +105,3 @@ hydra:
     dir: ${outputs}
   verbose: ${debug}
 """)
-    rmtree(Path(cfg.outputs))

{graphatoms-2.0.0 → graphatoms-2.1.1}/src/graphatoms/enterpoint/network/__init__.py

@@ -4,8 +4,14 @@ from pathlib import Path
 from typing import Literal
 
 from graphatoms.enterpoint.config import EventConfig
-from graphatoms.reaction import EventBase, EventInfo, Reaction
-from graphatoms.system import Cluster, SysGraph
+from graphatoms.reaction import (
+    Adsorption,
+    Desorption,
+    EventBase,
+    EventInfo,
+    Reaction,
+)
+from graphatoms.system import Gas, SysGraph
 from graphatoms.system.database import DatabaseABC, get_db
 
 from ._metadata import MetaData
@@ -14,14 +20,14 @@ from ._recorder import Recorder
 from ._scheduler import Scheduler
 
 __all__ = [
-    "RxNet",
     "MetaData",
     "Recorder",
     "Scheduler",
+    "ReactionNetwork",
 ]
 
 
-class RxNet:
+class ReactionNetwork:
     def __init__(
         self,
         path: Path | str,
@@ -81,16 +87,26 @@ class RxNet:
                 self.metadata: MetaData = MetaData()
 
         # initialize the databases
-        lst: list[DatabaseABC] = [
+        (
+            self.db_ts,
+            self.db_gas,
+            self.db_minima,
+            self.db_cluster,
+            self.db_system,
+        ) = [
             get_db(
                 path=path,
                 format=format,
                 prefix=prefix,
                 append=restart,
             )
-            for prefix in ["ts", "gas", "minima"]
+            for prefix in ["ts", "gas", "minima", "cluster", "system"]
         ]
-        self.db_ts, self.db_gas, self.db_minima = lst
+        assert isinstance(self.db_ts, DatabaseABC)
+        assert isinstance(self.db_gas, DatabaseABC)
+        assert isinstance(self.db_minima, DatabaseABC)
+        assert isinstance(self.db_cluster, DatabaseABC)
+        assert isinstance(self.db_system, DatabaseABC)
 
     def summary(self) -> str:
         """Return the summary of the network."""
@@ -102,16 +118,24 @@ class RxNet:
         self.scheduler.write_npz(self.__path / "scheduler.npz")
         self.metadata.persistence(self.__path)
 
-    def read(self, key: str) -> tuple[EventInfo, EventBase]:
+    def read_event(self, key: str) -> tuple[EventInfo, EventBase]:
+        """Read the event from the database."""
         if self.metadata.has(key):
             info = self.metadata.read(key)
             if info.key_g is not None:
-                raise NotImplementedError("Ads/Des is not supported.")
+                assert info.key_t is None
+                g = Gas.from_ase(self.db_gas[info.key_g])
+                r = SysGraph.from_ase(self.db_minima[info.key_r])
+                p = SysGraph.from_ase(self.db_minima[info.key_p])
+                if r.natoms < p.natoms:
+                    return info, Adsorption(G=g, R=r, P=p)
+                else:
+                    return info, Desorption(G=g, R=r, P=p)
             else:
                 assert info.key_t is not None
-                ts = Cluster.from_ase(self.db_ts[info.key_t])
-                r = Cluster.from_ase(self.db_minima[info.key_r])
-                p = Cluster.from_ase(self.db_minima[info.key_p])
+                ts = SysGraph.from_ase(self.db_ts[info.key_t])
+                r = SysGraph.from_ase(self.db_minima[info.key_r])
+                p = SysGraph.from_ase(self.db_minima[info.key_p])
                 return info, Reaction(T=ts, R=r, P=p)
         else:
             raise ValueError(f"Event {key} is not in the database.")
@@ -143,7 +167,7 @@ class RxNet:
                     fname.write_bytes(pickle.dumps(event))
                     fname.with_suffix(".err").write_text(msg)
                     raise ValueError(msg)
-            is_new = self._write(
+            is_new = self.write_event(
                 event,
                 for_cluster,
                 for_system,
@@ -154,7 +178,7 @@ class RxNet:
         else:
             raise ValueError(f"Unknown event type: {type(event)}")
 
-    def _write(
+    def write_event(
         self,
         event: EventBase,
         for_cluster: str,
@@ -170,12 +194,12 @@ class RxNet:
         else:
             self.metadata.write(event, for_cluster, for_system)
             try:
-                self.__write(event.R, "minima")
-                self.__write(event.P, "minima")
+                self.write_sysgraph(event.R, "minima")
+                self.write_sysgraph(event.P, "minima")
                 if event.G is not None:
-                    self.__write(event.G, "gas")
+                    self.write_sysgraph(event.G, "gas")
                 if event.T is not None:
-                    self.__write(event.T, "ts")
+                    self.write_sysgraph(event.T, "ts")
                 if persist:
                     self.persistence()
                 return True
@@ -201,17 +225,21 @@ class RxNet:
                 self.persistence()
                 raise e
 
-    def __write(
+    def write_sysgraph(
         self,
         sysgraph: SysGraph,
-        type: Literal["minima", "ts", "gas"] | str,
+        type: Literal["minima", "ts", "gas", "cluster", "system"] | str,
     ) -> bool:
         """Return True if the value is new, False otherwise."""
-        if type == "minima":
+        if type.lower() == "minima":
             return self.db_minima.add(sysgraph, check_positions=True)
-        elif type == "ts":
+        elif type.lower() == "ts":
             return self.db_ts.add(sysgraph, check_positions=True)
-        elif type == "gas":
+        elif type.lower() == "gas":
             return self.db_gas.add(sysgraph, check_positions=False)
+        elif type.lower() == "system":
+            return self.db_system.add(sysgraph, check_positions=True)
+        elif type.lower() == "cluster":
+            return self.db_cluster.add(sysgraph, check_positions=True)
         else:
             raise ValueError(f"Unknown type: {type}")

{graphatoms-2.0.0 → graphatoms-2.1.1}/src/graphatoms/enterpoint/network/_metadata.py

@@ -14,6 +14,7 @@ from pydantic import (
 from graphatoms.dataclasses import OurBaseModel
 from graphatoms.enterpoint.config import EventConfig
 from graphatoms.reaction import EventBase, EventInfo
+from graphatoms.system.bonds import matchmode2nmatch
 
 __all__ = ["MetaData"]
 
@@ -110,6 +111,7 @@ class _MetaDataTable(BaseModel):
         *,
         cluster_key: str | None = None,
         system_key: str | None = None,
+        exclude_gas: bool = False,
         **kwargs,
     ) -> int:
         if cluster_key is not None:
@@ -117,7 +119,10 @@ class _MetaDataTable(BaseModel):
                 [
                     self.count[i]
                     for i, ck in enumerate(self.for_cluster)
-                    if ck == cluster_key
+                    if (
+                        ck == cluster_key
+                        and ((not exclude_gas) or self.key_g[i] is None)
+                    )
                 ]
                 + [0]
             )
@@ -126,7 +131,10 @@ class _MetaDataTable(BaseModel):
                 [
                     self.count[i]
                     for i, sk in enumerate(self.for_system)
-                    if sk == system_key
+                    if (
+                        sk == system_key
+                        and ((not exclude_gas) or self.key_g[i] is None)
+                    )
                 ]
                 + [0]
             )
@@ -174,7 +182,8 @@ class MetaData(BaseModel):
         names = ["rxn_key", "is_forward", "nmatched", "rate"]
         for (rxn_key, is_forward), single_match_res in matching_dct.items():
             i: int = self.table.key_rxn.index(rxn_key)
-            nmatched = int(single_match_res.shape[0])
+            # Eliminate the overestimation caused by permutation symmetry.
+            nmatched = matchmode2nmatch(single_match_res)
             if is_forward:
                 rate = self.table.rate_forword[i]
             else:

{graphatoms-2.0.0 → graphatoms-2.1.1}/src/graphatoms/enterpoint/network/_recorder.py

@@ -23,14 +23,15 @@ Ref:
 """
 
 from collections import defaultdict
-from typing import override
+from datetime import datetime
+from typing import Annotated, override
 
 import pydantic
 
 from graphatoms.dataclasses import OurBaseModel  # type: ignore
 
 
-class _OldNewRecorder(OurBaseModel):
+class _RecorderBase(pydantic.BaseModel):
     old: pydantic.NonNegativeInt = 0
     new: pydantic.NonNegativeInt = 0
     fail: pydantic.NonNegativeInt = 0
@@ -47,6 +48,70 @@ class _OldNewRecorder(OurBaseModel):
         """
         return sum([self.old, self.new, self.fail])
 
+class RecorderInfo(_RecorderBase):
+    create_at: datetime = pydantic.Field(default_factory=lambda: datetime.now())
+    confidence: Annotated[float, pydantic.Field(ge=0.5, lt=1.0)]
+    for_cluster: str = pydantic.Field(default="")
+    for_system: str = pydantic.Field(default="")
+    for_gas: str = pydantic.Field(default="")
+
+    @classmethod
+    def get_csv_title(cls) -> str:
+        return ",".join(
+            [
+                "old",
+                "new",
+                "fail",
+                "total",
+                "skip",
+                "continuous_old",
+                "continuous_nonnew",
+                "confidence",
+                "create_at",
+                "for_cluster",
+                "for_system",
+                "for_gas",
+            ]
+        )
+
+    def to_csv_line(self) -> str:
+        return ",".join(
+            [
+                f"{self.old}",
+                f"{self.new}",
+                f"{self.fail}",
+                f"{self.total}",
+                f"{self.skip}",
+                f"{self.continuous_old}",
+                f"{self.continuous_nonnew}",
+                f"{self.confidence}",
+                f"{self.create_at.strftime('%Y-%m-%d %H:%M:%S.%f')}",
+                f"{self.for_cluster}",
+                f"{self.for_system}",
+                f"{self.for_gas}",
+            ]
+        )
+
+
+class _OldNewRecorder(OurBaseModel, _RecorderBase):
+    @pydantic.validate_call
+    def get_williams_confidence(
+        self, min_found: pydantic.NonNegativeInt
+    ) -> Annotated[float, pydantic.Field(ge=0.5, lt=1.0)]:
+        """The Williams confidence formula.
+
+        Args:
+            min_found: The minimum time found for all events.
+
+        Returns:
+            The confidence value.
+        """
+        m = self.continuous_nonnew
+        factor = min_found / self.total
+        factor2 = 1 / (1 + factor)
+        value = 1 / (1 + factor2**m)
+        return value
+
     @pydantic.validate_call
     def exploration_can_be_finished(
         self,
@@ -61,10 +126,7 @@ class _OldNewRecorder(OurBaseModel):
                 "min_found must be provided for Williams"
                 + " formula (i.e. confidence < 1)."
             )
-            m = self.continuous_nonnew
-            factor = min_found / self.total
-            factor2 = 1 / (1 + factor)
-            value = 1 / (1 + factor2**m)
+            value = self.get_williams_confidence(min_found)
         else:
             # Use Xu-Henkelman formula
             value = self.continuous_old
@@ -106,7 +168,7 @@ class _OldNewRecorder(OurBaseModel):
 class Recorder(OurBaseModel):
     system: set[str] = set()
     cluster: dict[str, _OldNewRecorder] = defaultdict(_OldNewRecorder)
-    adsorption: set[str] = set()
+    adsorption: dict[str, _OldNewRecorder] = defaultdict(_OldNewRecorder)
     bulk: set[str] = set()
 
     @override
@@ -119,8 +181,10 @@ class Recorder(OurBaseModel):
 
 
 if __name__ == "__main__":
+    from io import StringIO
     from pathlib import Path
 
+    import pandas as pd
     obj = Recorder()
     obj.system.add("fdsafs")
     obj.cluster["fdsafs"].new += 1
@@ -128,3 +192,17 @@ if __name__ == "__main__":
     print(obj)
     print(repr(obj))
     obj.write_json(Path("a.json"))
+
+    io = StringIO()
+    io.write(RecorderInfo.get_csv_title() + "\n")
+    a = RecorderInfo(confidence=0.6)
+    io.write(RecorderInfo(confidence=0.5).to_csv_line() + "\n")
+    io.write(RecorderInfo(confidence=0.5).to_csv_line() + "\n")
+    io.write(a.to_csv_line() + "\n")
+
+    s = io.getvalue()
+    print(s)
+    df = pd.read_csv(StringIO(s))
+    print("df:")
+    print(df)
+    print(df.sort_values(by="create_at", ascending=True))

graphatoms-2.1.1/src/graphatoms/enterpoint/runner/__init__.py

@@ -0,0 +1,32 @@
+import os
+
+os.environ["HYDRA_FULL_ERROR"] = "1"
+
+import hydra
+
+from graphatoms.enterpoint.config import CONFIG_DIR, Config
+
+from .general.otfkmc import OTFKMC as OnTheFlyKMC
+from .general.rxngen import ReactionNetworkGenerator
+from .ray.otfkmc import RayOTFKMC as RayOnTheFlyKMC
+from .ray.rxngen import RayReactionNetworkGenerator
+
+
+@hydra.main(
+    config_path=CONFIG_DIR.as_posix(),
+    config_name="run",
+    version_base=None,
+)
+def run(cfg: Config) -> None:
+    if str(cfg.run_type).lower() == "otfkmc":
+        if str(cfg.parallel).lower() == "ray":
+            RayOnTheFlyKMC(config=cfg).run()
+        else:
+            OnTheFlyKMC(config=cfg).run()
+    elif str(cfg.run_type).lower() == "rxngen":
+        if str(cfg.parallel).lower() == "ray":
+            RayReactionNetworkGenerator(config=cfg).run()
+        else:
+            ReactionNetworkGenerator(config=cfg).run()
+    else:
+        raise ValueError(f" run_type `{cfg.run_type}` is not supported.")

graphatoms-2.1.1/src/graphatoms/enterpoint/runner/common/__init__.py

@@ -0,0 +1,21 @@
+from ._base import RunnerABC
+from ._errors import CheckVibrationFailed, HelperException, OptimizationFailed
+from ._helper import (
+    helper_adsorption,
+    helper_apply,
+    helper_dimer,
+    helper_match,
+    helper_optimization,
+)
+
+__all__ = [
+    "RunnerABC",
+    "CheckVibrationFailed",
+    "HelperException",
+    "OptimizationFailed",
+    "helper_adsorption",
+    "helper_apply",
+    "helper_dimer",
+    "helper_match",
+    "helper_optimization",
+]