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.

InputOutput.create_file_paths()

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.

InputOutput.file_header()

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.

InputOutput.make_directories()

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.

InputOutput.preprocess_sizing(sizes)

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.

InputOutput.screen_figlet()

Print a colored figlet of Sarkas to screen.

InputOutput.setup()

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.