# HPC_Submission_Tools
Repo for tools to help with slurm submission and management within ARCHIE-WeST HPC cluster
## Install
From cloning repo
```
git clone https://www.github.com/RossJamesUrquhart/HPC_submission_tools
pip install .
```
From PyPi
```
pip install HPC-submission-tools
```
## JobSubmitter - Usage
```
from HPC_submission_tools import JobSubmission
JobSubmitter = JobSubmitter()
JobSubmitter.submit_jobs([path/to/sbatch/files], additional_ext=None)
```
The ```additional_ext``` keyword will take a list of any extensions not already considered by the script to search for those to mvoe alongside the sbatch files.
## XYZ2ORCA - Usage
```
from HPC_submission_tools import XYZ2ORCA
xyz = ["2,6-XylH+.xyz"] # list of xyz files to process
functional = "wB97X"
job = "Opt Freq"
basis_set= "Def2-SVP"
solvation = "CPCM(Water)"
time = "01:00:00"
cores = 4
charge = 1
kwargs = ["SlowConv", "TightSCF", "DEFGRID2", "Def2/J", "RIJCOSX"]
for x in xyz:
process = XYZ2ORCA(x, job, functional, basis_set, charge, solvation, cores, time, kwargs)
process.xyz2orca()
```
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"description": "# HPC_Submission_Tools\r\n\r\nRepo for tools to help with slurm submission and management within ARCHIE-WeST HPC cluster\r\n\r\n## Install\r\n\r\nFrom cloning repo\r\n\r\n```\r\ngit clone https://www.github.com/RossJamesUrquhart/HPC_submission_tools\r\npip install .\r\n```\r\n\r\nFrom PyPi\r\n\r\n```\r\npip install HPC-submission-tools\r\n```\r\n\r\n## JobSubmitter - Usage\r\n\r\n```\r\nfrom HPC_submission_tools import JobSubmission\r\nJobSubmitter = JobSubmitter()\r\n\r\nJobSubmitter.submit_jobs([path/to/sbatch/files], additional_ext=None)\r\n\r\n```\r\n\r\nThe ```additional_ext``` keyword will take a list of any extensions not already considered by the script to search for those to mvoe alongside the sbatch files.\r\n\r\n## XYZ2ORCA - Usage\r\n\r\n```\r\nfrom HPC_submission_tools import XYZ2ORCA\r\n\r\nxyz = [\"2,6-XylH+.xyz\"] # list of xyz files to process\r\n\r\nfunctional = \"wB97X\"\r\njob = \"Opt Freq\"\r\nbasis_set= \"Def2-SVP\"\r\nsolvation = \"CPCM(Water)\"\r\ntime = \"01:00:00\"\r\ncores = 4\r\ncharge = 1\r\nkwargs = [\"SlowConv\", \"TightSCF\", \"DEFGRID2\", \"Def2/J\", \"RIJCOSX\"]\r\n\r\nfor x in xyz:\r\n process = XYZ2ORCA(x, job, functional, basis_set, charge, solvation, cores, time, kwargs)\r\n process.xyz2orca()\r\n```\r\n",
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