opennucleome

#!/usr/bin/env bash

## SBGrid OpenNucleome Example

## https://github.com/ZhangGroup-MITChemistry/OpenNucleome
##
## Run three tutorials from tutorials/init_configs dir 
## 3.2 hours on one NVIDIA GeForce RTX 3070 with 8GB memory
##
## James Vincent help@sbgrid.org
## Jan 6, 2025

echo "SBGrid OpenNucleome Example"

## Start SBGrid environment
export SBGRID_ALLOW=true   ## sbgrid dev only
source /programs/sbgrid.shrc
 
## Set OpenNucleome version - from command: $ sbgrid-info -l opennucleome
export OPENNUCLEOME_X=1.3.0

## Verify CUDA GPU for OpenNucleome
python.opennucleome -m testInstallation

## Get repo
rm -rf ./OpenNucleome
git clone https://github.com/ZhangGroup-MITChemistry/OpenNucleome.git

## configs_generation  
cd ./OpenNucleome/tutorials/init_configs/configs_generation/
jupyter.opennucleome nbconvert --to python ConfigsGeneration.ipynb
python.opennucleome ./ConfigsGeneration.py

## configs_relaxation  
cd ../configs_relaxation/
jupyter.opennucleome nbconvert --to python ConfigsRelaxation.ipynb
python.opennucleome ./ConfigsRelaxation.py
 
## configs_selection
cd ../configs_selection
jupyter.opennucleome nbconvert --to python ConfigsSelection.ipynb
python.opennucleome ./ConfigsSelection.py