01 - 解析并检查一个计算¶

本 Notebook 使用与快速上手相同的 water_mp2.out 样例，介绍 batch -> file -> frame 访问关系，并检查源文件实际提供的结果。运行前从文档下载样例并保存为 water_mp2.out。

In [1]:

from pathlib import Path

from molop import AutoParser, molopconfig

molopconfig.quiet()
sample_candidates = (
    Path("docs/assets/examples/water_mp2.out"),
    Path("../../assets/examples/water_mp2.out"),
    Path("water_mp2.out"),
)
sample_path = next((path for path in sample_candidates if path.is_file()), None)
if sample_path is None:
    raise FileNotFoundError("请将 water_mp2.out 放在 Notebook 同目录，或使用文档中的样例文件。")

batch = AutoParser(sample_path, n_jobs=1)
parsed_file = batch[0]
frame = parsed_file[-1]

print("文件数：", len(batch))
print("frame 数：", len(parsed_file))
print("格式：", parsed_file.detected_format_id)
print("原子数与坐标：", len(frame.atoms), frame.coords.shape)
print("能量（hartree）：", frame.energies.total_energy.m_as("hartree"))

from pathlib import Path from molop import AutoParser, molopconfig molopconfig.quiet() sample_candidates = ( Path("docs/assets/examples/water_mp2.out"), Path("../../assets/examples/water_mp2.out"), Path("water_mp2.out"), ) sample_path = next((path for path in sample_candidates if path.is_file()), None) if sample_path is None: raise FileNotFoundError("请将 water_mp2.out 放在 Notebook 同目录，或使用文档中的样例文件。") batch = AutoParser(sample_path, n_jobs=1) parsed_file = batch[0] frame = parsed_file[-1] print("文件数：", len(batch)) print("frame 数：", len(parsed_file)) print("格式：", parsed_file.detected_format_id) print("原子数与坐标：", len(frame.atoms), frame.coords.shape) print("能量（hartree）：", frame.energies.total_energy.m_as("hartree"))

文件数： 1
frame 数： 1
格式： orcaout
原子数与坐标： 3 (3, 3)
能量（hartree）： -74.999374598107

解析器将样例识别为 ORCA 输出；该样例包含一个最终 frame。

In [2]:

import pandas as pd
from IPython.display import display

summary = batch.to_summary_df(
    frame=-1,
    brief=False,
    flatten_columns=True,
)
with pd.option_context("display.max_columns", None, "display.max_rows", None, "display.width", 240):
    display(summary)

import pandas as pd from IPython.display import display summary = batch.to_summary_df( frame=-1, brief=False, flatten_columns=True, ) with pd.option_context("display.max_columns", None, "display.max_rows", None, "display.width", 240): display(summary)

	DiskStorage.FilePath	DiskStorage.FileFormat	General.Charge	General.Multiplicity	General.CanonicalSMILES	General.NumAtoms	General.FrameID	Calc Parameter.Software	Calc Parameter.Version	Calc Parameter.Method	Calc Parameter.BasisSet	Calc Parameter.Functional	Calc Parameter.Keywords	Environment.SolventModel	Environment.Solvent	Status.IsError	Status.IsNormal	Status.IsTS	Status.IsOptimized	Energy.electronic_energy.hartree	Energy.reference_energy.hartree	Energy.mp2_energy.hartree	Energy.total_energy.hartree
0	/home/runner/work/MolOP/MolOP/docs/assets/exam...	.out	0	1	O	3	0	ORCA	6.0.1	MP2	sto-3g		MP2 sto-3g	None	None	False	True	False	False	-74.999375	-74.963574	-74.999375	-74.999375

科学结果容器是可选的，读取字段前先检查容器是否存在。

In [3]:

if frame.energies and frame.energies.total_energy is not None:
    print(frame.energies.total_energy.m_as("eV"))

print("是否有振动结果：", frame.vibrations is not None)

if frame.energies and frame.energies.total_energy is not None: print(frame.energies.total_energy.m_as("eV")) print("是否有振动结果：", frame.vibrations is not None)

-2040.8369503966658
是否有振动结果： False

访问 rdmol 会提供分子图，并记录拓扑恢复状态。

In [4]:

mol = frame.rdmol
print("键数：", mol.GetNumBonds())
print("拓扑状态：", frame.topology_reconstruction_status)

mol = frame.rdmol print("键数：", mol.GetNumBonds()) print("拓扑状态：", frame.topology_reconstruction_status)

键数： 2
拓扑状态： succeeded