ai2_kit.lib.plumed module

ai2_kit.lib.plumed.get_cvs_bias_from_df(df, cv_names: List[str] | str, bias_name: str)

get collective variables and bias from pandas dataframe

Parameters:

• df – pandas dataframe

• cv_names – names of collective variable columns

• bias_name – name of bias column

Returns:

cvs, bias in numpy array for gaussian_kde

ai2_kit.lib.plumed.load_colvar(fp, skip='#! FIELDS')

load plumed colvar file as DataFrame

Parameters:

• fp – file pointer

• skip – skip the header line

Returns:

DataFrame

ai2_kit.lib.plumed.load_colvar_from_files(*files)

load plumed colvar from multiple files and concatenate into a single DataFrame