sarkas.utilities.io.InputOutput
sarkas.utilities.io.InputOutput#
- class sarkas.utilities.io.InputOutput(process='preprocess')[source]#
Class handling the input and output functions of the MD run.
- Parameters
process (str) – Name of the process class containing MD run info.
Methods
InputOutput.__init__
([process])InputOutput.algorithm_info
(simulation)Print algorithm information.
InputOutput.copy_params
(params)Copy necessary parameters.
Create all directories', subdirectories', and files' paths.
InputOutput.dump
(phase, ptcls, it)Save particles' data to binary file for future restart.
InputOutput.dump_xyz
([phase])Save the XYZ file by reading Sarkas dumps.
Create the log file and print the figlet if not a restart run.
InputOutput.from_dict
(input_dict)Update attributes from input dictionary.
InputOutput.from_yaml
(filename)Parse inputs from YAML file.
Create directories where to store MD results.
InputOutput.postprocess_info
(simulation[, ...])Print Post-processing info to file and/or screen in a reader-friendly format.
InputOutput.potential_info
(simulation)Print potential information.
Print the estimated file sizes.
InputOutput.preprocess_timing
(str_id, t, loops)Print times estimates of simulation to file first and then to screen if verbose.
InputOutput.read_npz
(fldr, filename)Load particles' data from dumps.
InputOutput.read_pickle
(process)Read pickle files containing all the simulation information.
InputOutput.read_pickle_single
(class_to_read)Read the desired pickle file.
InputOutput.save_pickle
(simulation)Save all simulations parameters in pickle files.
Print a colored figlet of Sarkas to screen.
Create file paths and directories for the simulation.
InputOutput.setup_checkpoint
(params)Assign attributes needed for saving dumps.
InputOutput.simulation_summary
(simulation)Print out to file a summary of simulation's parameters.
InputOutput.time_info
(simulation)Print time simulation's parameters.
InputOutput.time_stamp
(time_stamp, t)Print out to screen elapsed times.
InputOutput.timing_study
(simulation)Info specific for timing study.