uf3.data.io¶

This module provides the DataCoordinator class for reading data from atomistic codes and organizing data into DataFrames using Pandas.

Functions

`analyze_hdf_tables`	Read hdf5 file and analyze table names and lengths
`atoms_from_df`	Create ase.Atoms from DataFrame.
`cache_data`	Save dataframe from data_coordinator as ase Database.
`concat_dataframes`	Concatenate list of dataframes with optional removal of duplicate keys.
`dataframe_batch_loader`	Iterator for reading DataFrames from HDF5 using a list of table names, i.e. from io.analyze_hdf_tables.
`df_from_tsv_text`	Convenience function for converting tab-separated values (text) into DataFrame.
`identify_paths`	Generate list of paths to files according to filename_pattern, searching recursively from experiment_path.
`parse_lammps_dump`	Read LAMMPS text dump file.
`parse_lammps_log`	Parse lammps log file into pd.DataFrame.
`parse_lammps_outputs`	Convenience wrapper for parsing both LAMMPS log and dump in a run directory.
`parse_trajectory`	Wrapper for ase.io.read, which is compatible with many file formats (notably VASP's vasprun.xml and extended xyz).
`parse_with_subsampling`	TODO: refactor to break up into smaller, reusable functions
`prepare_dataframe_from_lists`	Convenience function for arranging data into pandas DataFrame with expected column names.
`read_database`	Read ase.db-type database file.
`read_vasp_pressure`	Utility for reading external pressure (kbar) from PSTRESS INCAR tag.
`resolve_name_conflict`	Simple renaming by incrementing an integer preceding file extension.
`update_dataframe_from_geometries`	Intermediate function for object-dataframe consistency
`update_geometries_from_calc`	Query attached calculators for energy and forces.
`update_geometries_from_dataframe`	Intermediate function for object-dataframe consistency

Classes

DataCoordinator

Handler class for reading data from atomistic codes and organizing data into DataFrames using Pandas.