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Project description
vyas_group_scripts
vyas_group_scripts is a python package meant to hold tools built in aiding the Shubham Vyas Research lab in completing repetitive tasks. Most use cases will involve installing the package as a tool through uv of pipx and using the command line tools.
Installation and Updating
To install the command line tools using uv use the command below:
uv tool install vyas_group_scripts
to update the package using uv use the command below:
uv tool install vyas_group_scripts --upgrade
alternatively you can use pipx. To install using pipx run the command below:
pipx install vyas_group_scripts
To update the package using pipx use the following command:
pipx upgrade vyas_group_scripts
Further Setup
In order for pygab and pyrab to correctly format batch files they need to know your account number. They read this account number from an environment variable ACTNUM. Ensure that you have set this environment variable.
There are other optional environment variables you can set below are their names, defaults, and what they change
DEFAULT_DFT_TIME, 00:59:00,The default dft job time in a batch file.DEFAULT_DFT_PROCESSORS, 36, The default number of processors a DFT job will use
Available Commands
All commands with a * next to their name have a help flag that can be accessed by passing the -h flag. This is not placed here to keep documentation succinct.
pygab *
python generate all batch. This generates a batch file for all gjf and inp files that match a pattern (match all by default). Soon it will also process xyz files
pyrab *
python run all batch. This runs all batch files in a directory that match a pattern (match all by default) and have a matching input file.
pysqm
prints the queue for the just the user's jobs
pysff *
python sort from folders. Copies input, output, and batch files from dft jobs in to organized directories.
pyaif
apply in folders. applies a list of commands in all subfolders. If a command includes space it must be in quotes.
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