Hello! This is a repository of commands for RASPA. RASPA GitHub
| Command | Description |
|---|---|
infoRASPA |
List all running jobs and working folders |
runSim |
A tool to run batches of simulatons |
runDataAnalysis |
A tool to collect data and calculate stats |
Warning
Documentation is still partial and it does not reflect all commands available.
Installation
To download the repository in a folder you need to
git pull https://github.com/asprediatribe/out_of_RASPAthen run the command
PATH={YOUR-FOLDER}/out_of_RASPA:$PATHto make it executable from any folder. Add this string to ~/.bashrc, so it runs every time.
The command infoRASPA is useful to check the RASPA simulation progression. It prints the PID and the directory of each job.
infoRASPA
The command runSim may be used to run a batch of GCMC with an adsorbate and water at different concentrations of urea; the input files and a nested system of folders is created. A folder with the name of the simulated structure contains subfolders named like the adsorbate, each of it contains different folders containing simulation files for each condition. The simulation is run according to protocol that can be selected through the flag -p between
- widom run a set of Widom
- isotherm running a set of simulation at different concentrations
- water-filling
The user is free to specify whether the simulations need to restart from a Restart File and overwriting is allowed.
runSim -p [widom/isotherm/water-filling] -r [yes/no] -o [yes/no]
-p flag REQUIRED (protocol) to pick the right protocol
-r flag OPTIONAL (RestartInitial) default is no, -r [yes/no]
-o flag OPTIONAL (overwrite) overwrite the folder / simulation if it already exists.
Example of runSim to create an isotherm for urea and water
This is the command
runSim -p isotherm The command runDataAnalysis is useful for data analysis. It relies on Python.
runDataAnalysis
Copyright (c) 2024, Thomas Fabiani
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation.