Prepare the cluster account so the combined gas-phase workflow can run cleanly.
Use the provided setup script:
- File:
defualt_bashrc_setup.sh - Edit your cluster's bash configuration with:
vi ~/.bashrc- And edit and save using common terminal commands (i.e I, wq, ESC)
Make sure the following directories are present in your home directory (cd will that you to your home directory):
nearlineprojectsscratchvaspvirtenv
If missing flders continue below:
- Create a virtual environment if
virtenvis not already present.
python -m venv virtenv- Edit the virtual environment path here:
# Path to your virtual environment
export VENV_PATH="/home/your_path/virtenv"
export ASE_ENV="/home/your_path/virtenv/bin/activate"- Assume placeholder paths are correct in the tutorial examples and replace them only when adapting to your own account.
Created vasp with mkdir and a vasp_PP sub-folder within vasp.
Expected structure:
~/vasp/
~/vasp/vasp_PP/
Then unzip:
potpaw_PBE.64 1.tgz(https://1sfu-my.sharepoint.com/:u:/g/personal/dkm7_sfu_ca/IQBMzeXteduTRIXB7vOF3j_AAa0A3J66l-7L94bLFGVhx60?e=joUI57)
tar -xf potpaw_PBE.64 1.tgz
Rename the extracted folder to:
potpaw_PBE
- The combined workflow uses one SLURM submission per molecule.