pyretis.bin

Here, the PyRETIS executables can be found. These are:

pyretis.bin.pyretisrun module

pyretisrun - An application for running PyRETIS simulations.

This script is a part of the PyRETIS library and can be used for running simulations from an input script.

usage: pyretisrun.py [-h] -i INPUT [-V] [-f LOG_FILE] [-l LOG_LEVEL] [-p]

PyRETIS

optional arguments:

-h, --help	show this help message and exit
-i INPUT, --input INPUT
	Location of PyRETIS input file
-V, --version	show program’s version number and exit
-f LOG_FILE, --log_file LOG_FILE
	Specify log file to write
-l LOG_LEVEL, --log_level LOG_LEVEL
	Specify log level for log file
-p, --progress	Display a progress meter instead of text output for the simulation

More information about running PyRETIS can be found at: www.pyretis.org

pyretis.bin.pyretisrun.bye_bye_world()

Print out the goodbye message for PyRETIS.

pyretis.bin.pyretisrun.entry_point()

entry_point - The entry point for the pip install of pyretisrun.

pyretis.bin.pyretisrun.explore_simulation(sim, sim_settings, progress=False)

Run a RETIS simulation with PyRETIS.

Parameters:

• sim (object like Simulation) – This is the simulation to run.
• sim_settings (dict) – The simulation settings.
• progress (boolean, optional) – If True, we will display a progress bar, otherwise, we print results to the screen.

pyretis.bin.pyretisrun.hello_world(infile, rundir, logfile)

Print out a politically correct greeting for PyRETIS.

Parameters:

• infile (string) – String showing the location of the input file.
• rundir (string) – String showing the location we are running in.
• logfile (string) – The output log file

pyretis.bin.pyretisrun.main(infile, indir, exe_dir, progress, log_level)

Execute PyRETIS.

Parameters:

• infile (string) – The input file to open with settings for PyRETIS.
• indir (string) – The folder containing the settings file.
• exe_dir (string) – The directory we are working from.
• progress (boolean) – Determines if we should use a progress bar or not.
• log_level (integer) – Determines if we should display the error traceback or not.

pyretis.bin.pyretisrun.make_tis_files(_, settings, progress=False)

Create TIS simulations input files PyRETIS.

It just writes out input files for single TIS simulations and

exit without running a simulation.

Parameters:settings (list of dicts or Simulation objects) – The settings for the simulations.

pyretis.bin.pyretisrun.run_generic_simulation(sim, sim_settings, progress=False)

Run a generic PyRETIS simulation.

These are simulations that are just going to complete a given number of steps. Other simulation may consist of several simulations tied together and these are NOT handled here.

Parameters:

• sim (object like Simulation) – This is the simulation to run.
• sim_settings (dict) – The simulation settings.
• progress (boolean, optional) – If True, we will display a progress bar, otherwise, we print results to the screen.

pyretis.bin.pyretisrun.run_md_flux_simulation(sim, sim_settings, progress=False)

Run a MD-FLUX simulation.

Parameters:

• sim (object like Simulation) – This is the simulation to run.
• sim_settings (dict) – The simulation settings.
• progress (boolean, optional) – If True, we will display a progress bar, otherwise, we print results to the screen.

pyretis.bin.pyretisrun.run_md_simulation(sim, sim_settings, progress=False)

Run a MD simulation.

Parameters:

• sim (object like Simulation) – This is the simulation to run.
• sim_settings (dict) – The simulation settings.
• progress (boolean, optional) – If True, we will display a progress bar, otherwise, we print results to the screen.

pyretis.bin.pyretisrun.run_path_simulation(sim, sim_settings, progress=False)

Run a RETIS simulation with PyRETIS.

Parameters:

• sim (object like Simulation) – This is the simulation to run.
• sim_settings (dict) – The simulation settings.
• progress (boolean, optional) – If True, we will display a progress bar, otherwise, we print results to the screen.

pyretis.bin.pyretisrun.set_up_simulation(inputfile, runpath)

Run all the needed generic set-up.

Parameters:

• inputfile (string) – The input file which defines the simulation.
• runpath (string) – The base path we are running the simulation from.

Returns:

• runner (method) – A method which can be used to execute the simulation.
• sim (object like Simulation) – The simulation defined by the input file.
• syst (object like System) – The system created.
• sim_settings (dict) – The input settings read from the input file.

pyretis.bin.pyretisrun.soft_exit_ignore(turn_keyboard_interruption_off=True, exe_dir=None)

Manage the KeyboardInterrupt exception.

Parameters:

• turn_keyboard_interruption_off (boolean) – If True, instead of regular exiting from the program, the file ‘EXIT’ is created to stop the PyRETIS.
• exe_dir (string, optional) – The path where EXIT file is expected.

pyretis.bin.pyretisrun.store_simulation_settings(settings, indir, backup)

Store the parsed input settings.

Parameters:

• settings (dict) – The simulation settings.
• indir (string) – The directory which contains the input script.
• backup (boolean) – If True, an existing settings file will be backed up.

pyretis.bin.pyretisrun.use_tqdm(progress)

Return a progress bar if we want one.

Parameters:progress (boolean) – If True, we should use a progress bar, otherwise not. Returns:out (object like tqdm.tqdm) – The progress bar, if requested. Otherwise, just a dummy iterator.

pyretis.bin.pyretisanalyse module

pyretisanalyse - An application for analysing PyRETIS simulations.

This script is a part of the PyRETIS library and can be used for analysing the result from simulations.

usage: pyretisanalyse.py [-h] -i INPUT [-V]

optional arguments:

-h, --help	show this help message and exit
-i INPUT, --input INPUT
	Location of PyRETIS input file
-V, --version	show program’s version number and exit

pyretis.bin.pyretisanalyse.bye_bye_world()

Print out the goodbye message for PyRETIS.

pyretis.bin.pyretisanalyse.create_reports(settings, analysis_results, report_path)

Create some reports to display the output.

Parameters:

• settings (dict) – Settings for analysis (and the simulation).
• analysis_results (dict) – Results from the analysis.
• report_path (string) – The path to the directory where the reports should be saved.

Yields:

out (string) – The report files created.

pyretis.bin.pyretisanalyse.entry_point()

entry_point - The entry point for the pip install of pyretisanalyse.

pyretis.bin.pyretisanalyse.get_report_name(report_type, ext, prefix=None, path=None)

Generate file name for a report.

Parameters:

• report_type (string) – Identifier for the report we are writing.
• ext (string) – Extension for the file to write.
• prefix (string, optional) – A prefix to add to the file name. Usually just used to mark reports with ensemble number for report_type equal to ‘tis-single’
• path (string) – A directory to use for saving the report to.

Returns:

out (string) – The name of the file written.

pyretis.bin.pyretisanalyse.hello_world(infile, run_dir, report_dir)

Output a standard greeting for PyRETIS analysis.

Parameters:

• infile (string) – String showing the location of the input file.
• run_dir (string) – The location where we are executing the analysis.
• report_dir (string) – String showing the location of where we write the output.

pyretis.bin.pyretisanalyse.main(input_file, run_path, report_dir)

Run the analysis.

Parameters:

• input_file (string) – The input file with settings for the analysis.
• run_path (string) – The location from which we are running the analysis.
• report_dir (string) – The location where we will write the report.

pyretis.bin.pyretisanalyse.write_file(outname, report_txt)

Write a generated report to a given file.

Parameters:

• outname (string) – The name of the file to write/create.
• report_txt (string) – This is the generated report as a string.

Returns:

out (string) – The name of the file written.

pyretis.bin.pyretisanalyse.write_traceback(filename)

Write the error traceback to the given file.

pyretis.bin.pyvisa module

pyvisa - An application for analysing PyRETIS simulations.

This script is a part of the PyRETIS library and can be used for analysing the result from simulations.

usage: pyvisa.py [-h]

optional arguments:

-cmp –pyvisa_compressor use only the compressor tool without GUI. -data –pyvisa-data select the data source. -h, –help show this help message and exit. -i INPUT, –input INPUT location of PyRETIS input files

or PyVisA compressed file.

-oo –only-order read only the order.txt files. -V, –version show program’s version number and exit.

pyretis.bin.pyvisa.bye_pyvisa()

Print out the goodbye message for PyVisA.

pyretis.bin.pyvisa.entry_point()

entry_point - The entry point for the pip install of pyretisanalyse.

pyretis.bin.pyvisa.hello_pyvisa(run_dir, infile)

Output a standard greeting for PyVISA.

Parameters:

• run_dir (string) – The location where we are executing the analysis.
• infile (string) – String showing the location of the input file.

pyretis.bin.pyvisa.main(basepath, input_file, pyvisa_dict=None)

Run the analysis.

Parameters:

• basepath (string) – The execution folder where the input files are.

• input_file (string) – The input file with settings for the analysis.

• pyvisa_dict (dictionary, optional) –

  It determines the section of pyvisa to use, it contains:

  • pyvisa_cmp, boolean If true, only the compressor tool will be executed. A compressed file will be produced.
  • pyvisa_visual, boolean If true, only the visualization tool will be executed.
  • pyvisa_data, str If given, the file or folder containing the files that will be used to feed to PyVisA.
  • pyvisa_recalculate, boolean If true, use the recalculation tool to compute new op and cv values.

pyretis.bin.pyvisa.pyvisa_visual(basepath, input_file, pyvisa_dict)

Load data to PyVisA.

Parameters:

• basepath (string) – The execution folder where the input files are.
• input_file (string) – The input file with settings for the analysis.
• pyvisa_dict (dictionary, optional) – It determines the section of pyvisa to use, it contains: