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.datetime_stamp`()	Add a Date and Time stamp to the log file.
`InputOutput.directory_size_report`(sizes, process)	Print the estimated file sizes.
`InputOutput.dump`(phase, ptcls, it)	Save particles' position, velocity, and acceleration data to binary file for future restart.
`InputOutput.dump_observables`(phase, ptcls, it)	Save particles' data to binary file (uncompressed npz) for future restart.
`InputOutput.dump_potfit_config`([phase, ...])	Write configuration files for PotFit by reading the npz dumps.
`InputOutput.dump_thermodynamics`(phase, ptcls, it)	Save particles' data to binary file for future restart.
`InputOutput.dump_xyz`([phase, dump_start, ...])	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`()	Make directories in `directory_tree` where to store the MD results.
`InputOutput.make_directory_tree`()	Construct the tree of directory paths of the MD simulation and save it into `directory_tree`.
`InputOutput.make_files_tree`()	Make the dictionary of files' names and paths, `filenames_tree`.
`InputOutput.postprocess_info`(simulation[, ...])
`InputOutput.potential_info`(simulation)	Print potential information.
`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_particles_npz`(fldr, filename)	Load particles' data from dumps.
`InputOutput.read_pickle`(process[, dir_path])	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.
`InputOutput.write_to_logger`(message)	Append the message to log file.