amep.reader.LammpsReader#

class amep.reader.LammpsReader(directory: str, savedir: str, start: float = 0.0, stop: float = 1.0, nth: int = 1, dumps: str = 'dump*.txt', trajfile: str = 'traj.h5amep', deleteold: bool = False, verbose: bool = False)#

Bases: BaseReader

Reads LAMMPS simulation data and writes it to an hdf5 file.

__init__(directory: str, savedir: str, start: float = 0.0, stop: float = 1.0, nth: int = 1, dumps: str = 'dump*.txt', trajfile: str = 'traj.h5amep', deleteold: bool = False, verbose: bool = False) → None#

Reader for LAMMPS simulation data in dump-file format. Requires the log.lammps file to read certain information about the simulation parameters.

Parameters:

directory (str) – Simulation directory.
savedir (str) – Directory in which the trajectory file will be stored.
start (float, optional) – Start reading data from this fraction of the whole trajectory. The default is None.
stop (float, optional) – Stop reading data from this fraction of the whole trajectory. The default is None.
nth (int, optional) – Read each nth dump file. The default is None.
dumps (str, optional) – File name of the dump files. The default is ‘dump*.txt’.
trajfile (str, optional) – Name of the hdf5 trajectory file that is created when an object of this class is initialized. The default is TRAJFILENAME.
deleteold (bool, optional) – If True, an existing old h5amep trajectory file #<trajfile> will be removed. The default is False.
verbose (bool, optional) – If True, runtime information is printed. The default is False.

Return type:

None.

Methods

__init__(directory, savedir[, start, stop, ...])

Reader for LAMMPS simulation data in dump-file format.

Attributes

`d`
`dt`
`filename`	The path to the HDF5-file that contains the writers data.
`nth`
`savedir`
`start`
`steps`	The array of simulation steps for each saved frame.
`stop`
`times`	The array of physical times for each saved frame.

property filename: Path#: The path to the HDF5-file that contains the writers data.

property steps: ndarray#

The array of simulation steps for each saved frame.

The simulation steps are also used to index the frame data in the HDF5-File.

property times#: The array of physical times for each saved frame.