energy_file_reader

A module containing the EnergyFileReader class.

Summary

Classes:

EnergyFileReader

A class to read energy files from molecular dynamics simulations.

Reference

class EnergyFileReader( filename: str, info_filename: str | None = None, use_info_file: bool = True, engine_format: MDEngineFormat | str = MDEngineFormat.PQ, )[source]

Bases: BaseReader

A class to read energy files from molecular dynamics simulations.

For the initialization of the EnergyFileReader, the filename of the energy file has to be given. The info_filename can be given as well. If no info_filename is given, the energy filename is used to find the info file with the proper extension and the base name of the energy file. If a info_filename is given, this filename is used to find the info file. If the info_filename was explicitly set to a non-existing file, a FileNotFoundError is raised. If use_info_file is set to False, no info file is searched for.

Providing info files is optional, but where possible, it is recommended to provide an info file. The info file contains information about the physical quantities stored in the energy file. If an info file is provided, the physical quantities are assumed to be in the order of the info file. The info file can also contain units for the physical quantities. If units are provided, the units are stored in the Energy object, which is returned by the read method.

For more information about the energy object, see Energy.

Parameters:

filename (str) – The name of the file to read from.
info_filename (str, optional) – The name of the info file to read from, by default None
use_info_file (bool, optional) – If True, the info file is searched for, by default True
engine_format (MDEngineFormat | str, optional) – The format of the file, by default MDEngineFormat.PQ

__info_file_found__() → bool[source]

Checks if a info file exists for the given file.

If no info_filename is given, the energy filename is used to find the info file. If a info_filename is given, this filename is used to find the info file. If the info_filename was explicitly set to a non-existing file, a FileNotFoundError is raised.

Returns:: True if a info file was found, False otherwise.
Return type:: bool
Raises:: FileNotFoundError – If an explicitly given info file does not exist.

read() → Energy[source]

Reads the energy file.

The data of the energy file is returned as a np.array within a Energy object. The data array is stored in a way that each column corresponds to a physical quantity. The order of the columns is the same as in the info file.

Returns:: The data of the energy file as a np.array within a Energy object. In addition, the info and units of the info file are stored in the Energy object, if an info file was found.
Return type:: Energy

logger = <CustomLogger PQAnalysis.EnergyFileReader (INFO)>