md.simulation_hooks.FileLogger

class md.simulation_hooks.FileLogger(*args: Any, **kwargs: Any)[source]

Class for monitoring the simulation and storing the resulting data to a hfd5 dataset. The properties to monitor are given via instances of the DataStream class. Uses buffers of a given size, which are accumulated and fushed to the main file in regular intervals in order to reduce I/O overhead. All arrays are initialized for the full number of requested simulation steps, the current positions in each data group is handled via the ‘entries’ attribute.

Parameters:

  • filename (str) – Path to the hdf5 database file.

  • buffer_size (int) – Size of the buffer, once full, data is stored to the hdf5 dataset.

  • list (data_streams) – List of DataStreams used to collect and log information to the main hdf5 dataset, default are properties and molecules.

  • every_n_steps (int) – Frequency with which the buffer is updated.

  • precision (int) – Precision used for storing float data (16, 32, 64 bit, default 32).