命令行批量获取 bader

这是一个获取bader 电荷的示例。

使用 CMD

1. 确保相关软件及相关输入无误 (仅第一次运行)。

1.1 设置 vasp INCAR 参数:

LCHARG = T
LWAVE = T
LAECHG= T
LORBIT= 11

1.2 确保每个案例下以下文件存在 [“AECCAR0”, “AECCAR2”, “CHGCAR”, “POTCAR”, “CONTCAR”] 。

1.3 安装软件 [“chgsum.pl”, “bader”], 并确保具有权限。

下载软件参考: 性质提取器。

2. 使用 findpath 命令获取所有子路径并输出到文件:

   findpath -if AECCAR2
   

3. 调用fbx（featurebox）运行。

   fbx bader -j 0
   

4. 后续处理。

   >>> # Ture to python code.
   >>> # More part: The following is not in command model.
   >>> # final treatment to extractor need message and formatting.
   >>> from featurebox.cli.vasp_bader import BaderStartInter, BaderStartSingleResult
   >>> # use  BaderStartInter or BaderStartSingleResult rather than BaderStartZero to escape repetition calculation.
   >>> bsi = BaderStartInter()
   >>> res = pd.read_csv("bader_all.csv")
   >>> features = bsi.extract(res, atoms=[0,1,2,3], format_path=None)
   >>> print(type(result))  # return one formed pd.Dataframe with necessary message.
   

传统的python方式

1. 确保相关软件及相关输入无误 (仅第一次运行)。

2. 获取所有子路径。

   >>> from mgetool.imports.batchfilematch import BatchFileMatch
   >>> bfm = BatchFileMatch(".")
   >>> bfm.filter_file_name(include="AECCAR2")
   >>> paths_list = bfm.merge()
   >>> paths_list = bfm.get_leaf_dir(paths_list)
   >>> print(paths_list)
   

3. 调用featurebox运行。

   >>> from featurebox.cli.vasp_bader import BaderStartZero
   >>> bsz = BaderStartZero(n_jobs=4, tq= True, store_single=True)
   >>> result = bsz.transform(paths_list)
   >>> print(type(result))  # return pd.Dataframe
   

4. 后续处理。

   >>> # More part: The following is not in command model.
   >>> # final treatment to extractor need message and formatting.
   >>> features = bsz.extract(res, atoms=[0,1,2,3],format_path=None)
   >>> print(type(features))  # return one formed pd.Dataframe with necessary message.