ReactionFlow
Watches molecular dynamics runs for bonds breaking or forming. When a change sticks, it pauses the run, finds the reaction path with NEB, checks the transition state, then picks the trajectory back up exactly where it left off.
hpc/
Clusters, scripts, and code
austin ~/austin-ellis $ cat hpc/README
Things I used to do by hand
For a while I ran two NSF-funded research clusters for CSUN’s College of Science and Mathematics. This is what that involved, back before I could text a chatbot from my phone and have it all done before I got out of bed.
- making accounts and groups, fixing permissions, and setting up Samba shares
- keeping an eye on Slurm queues, node states, and GPU jobs
- figuring out why someone’s job died (usually the environment, sometimes the disk)
- building and repairing Python, Conda, CUDA, and compiler setups for VASP, Quantum ESPRESSO, ASE, pymatgen, and PyTorch
- writing Bash and Python scripts to set up VASP jobs, fill in Slurm templates, parse logs, and collect outputs
- cleaning up shared disks when they filled up
- writing down how everything was set up, so the next person could rerun it
Since starting at ORNL, I’ve set up packages to run on several DOE supercomputers, including Perlmutter and Frontier.
austin ~/austin-ellis $ module list
Linux Slurm SSH Samba Bash Python Conda CUDA PyTorch NumPy pandas Matplotlib VASP Quantum ESPRESSO ASE pymatgen VESTA Git
code/
Some of my code on GitHub
austin ~/austin-ellis $ gh repo list Austin243
ELFNet
Predicts a crystal’s electron localization function from its superposed atomic densities. Inference and training code, with the whole dataset on Zenodo.
ElecTrace
Follows Bader charges, ELF and QTAIM topology, and LOBSTER bonding frame by frame along a VASP NEB path or a pressure series, matching atoms and features from one frame to the next.
layer-toolkit
Builds layered VASP inputs from Materials Project prototypes, sets up the relax and SCF runs, and pulls out ELF hotspots and bonding afterward.
calypso-setup
Writes the boilerplate for a CALYPSO + VASP structure search: POTCARs, INCARs, input.dat, and job scripts, with a lot of options for 2D searches.
ani-1xnr-npt-driver
An experimental PyTorch MD driver for running the ANI-1xnr potential at constant pressure, with restarts, HDF5 trajectories, and a TorchANI patch for stresses.