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
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pyretis.bin.pyretisrun.
entry_point
()[source]¶ entry_point - The entry point for the pip install of pyretisrun.
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pyretis.bin.pyretisrun.
explore_simulation
(sim, sim_settings, progress=False)[source]¶ 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.
- sim (object like
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pyretis.bin.pyretisrun.
hello_world
(infile, rundir, logfile)[source]¶ 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
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pyretis.bin.pyretisrun.
main
(infile, indir, exe_dir, progress, log_level)[source]¶ 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.
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pyretis.bin.pyretisrun.
make_tis_files
(_, settings, progress=False)[source]¶ 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.
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pyretis.bin.pyretisrun.
run_generic_simulation
(sim, sim_settings, progress=False)[source]¶ 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.
- sim (object like
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pyretis.bin.pyretisrun.
run_md_flux_simulation
(sim, sim_settings, progress=False)[source]¶ 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.
- sim (object like
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pyretis.bin.pyretisrun.
run_md_simulation
(sim, sim_settings, progress=False)[source]¶ 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.
- sim (object like
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pyretis.bin.pyretisrun.
run_path_simulation
(sim, sim_settings, progress=False)[source]¶ 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.
- sim (object like
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pyretis.bin.pyretisrun.
set_up_simulation
(inputfile, runpath)[source]¶ 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.
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pyretis.bin.pyretisrun.
soft_exit_ignore
(turn_keyboard_interruption_off=True, exe_dir=None)[source]¶ 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.
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pyretis.bin.pyretisrun.
store_simulation_settings
(settings, indir, backup)[source]¶ 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.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
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pyretis.bin.pyretisanalyse.
create_reports
(settings, analysis_results, report_path)[source]¶ 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.
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pyretis.bin.pyretisanalyse.
entry_point
()[source]¶ entry_point - The entry point for the pip install of pyretisanalyse.
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pyretis.bin.pyretisanalyse.
get_report_name
(report_type, ext, prefix=None, path=None)[source]¶ 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.
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pyretis.bin.pyretisanalyse.
hello_world
(infile, run_dir, report_dir)[source]¶ 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.
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pyretis.bin.pyretisanalyse.
main
(input_file, run_path, report_dir)[source]¶ 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.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.
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pyretis.bin.pyvisa.
entry_point
()[source]¶ entry_point - The entry point for the pip install of pyretisanalyse.
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pyretis.bin.pyvisa.
hello_pyvisa
(run_dir, infile)[source]¶ 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.
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pyretis.bin.pyvisa.
main
(basepath, input_file, pyvisa_dict=None)[source]¶ 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.
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pyretis.bin.pyvisa.
pyvisa_visual
(basepath, input_file, pyvisa_dict)[source]¶ 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: