graphatoms 2.2.0__tar.gz → 2.3.0__tar.gz

{graphatoms-2.2.0 → graphatoms-2.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: graphatoms
-Version: 2.2.0
+Version: 2.3.0
 Summary: The Chemical Core Class for Graph Theory Analysis.
 Keywords: chemistry,graph theory,reaction,event,KMC
 Author: LiuGaoyong
@@ -29,6 +29,7 @@ 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: joblib
 Requires-Dist: executorlib
 Requires-Dist: hydra-core
 Requires-Dist: typer

{graphatoms-2.2.0 → graphatoms-2.3.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "graphatoms"
-version = "2.2.0"
+version = "2.3.0"
 readme = "README.md"
 description = "The Chemical Core Class for Graph Theory Analysis."
 license-files = ["src/LICENSE"]
@@ -42,6 +42,7 @@ dependencies = [
     "tomli; python_version < '3.11'",
     "tomli-w",
     "typing-extensions",
+    "joblib",
     "executorlib",
     "hydra-core",
     "typer",
@@ -165,7 +166,9 @@ hydra-core = ">=1.3.2,<2"
 tomli-w = ">=1.2.0,<2"
 loguru = ">=0.7.3,<0.8"
 jupyterlab = ">=4.5.8,<5"
+joblib = ">=1.1.0,<2"
 ovld = ">=0.5.15,<0.6"
 pytest-xdist = ">=3.8.0,<4"
 executorlib = ">=1.8,<2"
 typer = ">=0.20,<1"
+grpcio = ">=1.52.0,<2"

{graphatoms-2.2.0 → graphatoms-2.3.0}/pyproject.toml.orig

@@ -12,7 +12,7 @@ graphatoms-network = "graphatoms.enterpoint.view:main"
 graphatoms-run = "graphatoms.enterpoint.runner:run"
 [project]
 name = "graphatoms"
-version = "2.2.0"
+version = "2.3.0"
 readme = "README.md"
 description = "The Chemical Core Class for Graph Theory Analysis."
 authors = [{ name = "LiuGaoyong", email = "liugaoyong_88@163.com" }]
@@ -60,6 +60,7 @@ dependencies = [
     "typing-extensions",
 
     # Other
+    "joblib",
     "executorlib",
     "hydra-core",
     "typer",
@@ -164,7 +165,9 @@ hydra-core = ">=1.3.2,<2"
 tomli-w = ">=1.2.0,<2"
 loguru = ">=0.7.3,<0.8"
 jupyterlab = ">=4.5.8,<5"
+joblib = ">=1.1.0,<2"
 ovld = ">=0.5.15,<0.6"
 pytest-xdist = ">=3.8.0,<4"
 executorlib = ">=1.8,<2"
 typer = ">=0.20,<1"
+grpcio = ">=1.52.0,<2"

{graphatoms-2.2.0 → graphatoms-2.3.0}/src/graphatoms/enterpoint/config/__init__.py

@@ -1,5 +1,4 @@
 import os
-from collections import defaultdict
 from dataclasses import dataclass, field
 from pathlib import Path
 from typing import Any
@@ -35,7 +34,10 @@ class ExplConfig:
     allow_multiple_adsorption: bool = False
     allow_explore_bulk: bool = False
     thetacutoff: float = -1  # 0-180, -1 means no cutoff
-    nfibonacci: int = 200
+    step_distance: float = 0.4  # the step distance for adsorption
+    min_distance: float = 1.0  # the minimum distance for adsorption
+    max_distance: float = 3.0  # the maximum distance for adsorption
+    nfibonacci: int = 10  # the number of fibonacci points for adsorption
 
 
 @dataclass
@@ -46,7 +48,7 @@ class EventConfig:
     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_sticking: dict[str, float] = field(default_factory=dict)  # MISSING
     temperature: float = 300
 
 
@@ -77,6 +79,7 @@ class Config:
     # 1. if the key of `gas_sticking` is not in `initial_gas_pressure`, then the gas sticking is 1.0            # noqa: E501
 
     parallel_workers: int = 0  # 0 means use all cores
+    parallel_ncpus_for_tasks: int = 1  # the number of cpus for tasks, only effect for `parallel=ray` # noqa: E501
     parallel: str = "serial"  # serial, multiprocessing, ray, dask, executorlib
     loglevel: str = "info"  # Literal["debug", "info", "warning", "error"]
     logfile: str = "log.txt"

graphatoms-2.3.0/src/graphatoms/enterpoint/network/__init__.py

@@ -0,0 +1,11 @@
+from ._clsnetwork import ReactionNetwork
+from ._metadata import MetaData
+from ._recorder import Recorder
+from ._scheduler import Scheduler
+
+__all__ = [
+    "MetaData",
+    "Recorder",
+    "Scheduler",
+    "ReactionNetwork",
+]