DChristensen12/na-electrolyte-solvation-boxes

SolvationNet

This Repository is being used for machine learning simulations to study the molecular structure and dynamics of sodium ion battery electrolytes and research into lanthanide and actinide chemistry. It is part of my ongoing research at the Lawrence Berkeley National Lab under Nitesh Kumar and Samuel Blau.

This contains scripts and notebooks used during the research, the datasets produced by them, and other research outputs such as the poster below that was presented at the UC Berkeley College of Chemistry's 18th Annual Saegebarth Undergraduate Research Fair.

Research Poster

Dataset: Na-Ion Electrolyte Solvation Boxes

Published on Hugging Face as a single repository with multiple subsets. Covers 9 sodium salts, 21 solvents/cosolvents, and concentrations from 0.1 M through 21 M across carbonate, ether, glyme, ionic liquid, phosphate, and aqueous systems. Both MLIPs were trained on the OMol25 dataset.

Subset	Boxes	What it is
NPT_FAIRChem-UMA/	83	NPT equilibrated (300 K, 1 atm) with UMA-s-1.2 (FAIRChem/Meta). Density-validated.
NVT_OrbMolV2/	79	NVT thermalized (50 ps, 300 K) with OrbMol-v2 (Orbital Materials). Fixed volume, no density adjustment.
NVT_OrbMolV2/npt_extended/	4	Subset of NVT boxes further equilibrated with NPT using OrbMol-v2.
molecules/	32	Individual molecule PDB files used as Packmol inputs.

See the dataset README for the full file list, naming convention, and abbreviation tables.

Deep-Shell

Will contain the scripts for lanthanide and actinide chemistry. I am using perlmutter (a supercomputer) for many of these calculations, however you can still run it via google colab or via any GPU you have access to (CPU works too, but would take much longer to run).

Electrolyte Molecular Dynamics Toolkit

The electrolyte_toolkit/ folder contains modular Python scripts for battery electrolyte molecular dynamics simulations. This is the work directly relating to the research poster and Na-Ion Electrolyte Solvation Boxes shown above.

Pipeline

Input geometries (.pdb)
    │
    ▼
pack_cell.py          Pack molecules into a periodic box (Packmol)
    │
    ▼
equilibrate.py        NVT and/or NPT equilibration with checkpointing
    │
    ▼
analyze_trajectory.py   Diagnostic plots (T, PE, density vs time)
    │
    ▼
export_vmd.py         Export trajectory for VMD visualization

Setup

Prerequisites

• Python 3.10+
• A CUDA GPU is strongly recommended (CPU works but is very slow for MD)
• Packmol for cell packing

Quick Start

cd electrolyte_toolkit
./setup.sh

setup.sh creates a virtual environment, installs all Python dependencies, and checks that Packmol and a GPU are available.

Manual Setup

python -m venv venv
source venv/bin/activate       # Linux/Mac
# venv\Scripts\activate        # Windows

pip install -r requirements.txt

Install Packmol separately (it's a compiled binary, not a Python package):

conda install -c conda-forge packmol
# or: sudo apt install packmol

Verify

source venv/bin/activate
python -c "import ase; import torch; print('OK')"
packmol < /dev/null   # should print Packmol banner, not "command not found"

equilibrate.py

The main equilibration script. Supports multiple workflows and potentials with persistent checkpointing. If it gets interrupted, rerun the same command and it picks up where it left off. Only the latest checkpoint per box is kept.

# NPT-only with FAIRChem UMA (default)
python equilibrate.py my_box.xyz --model uma --workflow npt

# NVT+NPT with OrbMol-v2
python equilibrate.py my_box.xyz --model orbmol_v2 --workflow nvt+npt

# NVT only
python equilibrate.py my_box.xyz --model orbmol_v2 --workflow nvt

# Custom step counts
python equilibrate.py my_box.xyz --model uma --workflow npt --npt-steps 50000

# Resume an interrupted run
python equilibrate.py --resume my_box_name --model uma

# Check status of all boxes
python equilibrate.py --status

Flag	Values	Default	Description
--model	uma, orbmol_v2	uma	ML potential
--workflow	npt, nvt, nvt+npt	npt	Equilibration protocol
--nvt-steps	integer	50000	NVT steps (50 ps at 1 fs)
--npt-steps	integer	100000	NPT steps (100 ps at 1 fs)
--device	cuda, cpu	cuda	Compute device
--checkpoint-dir	path	~/electrolyte_equilibration	Checkpoint storage
--resume	box name	none	Resume from last checkpoint
--status	flag	off	Print status of all boxes

NPT parameters are set automatically per model. UMA gets externalstress=1 bar, pfactor=0.1, ttime=100 fs and an isotropic mask. OrbMol-v2 gets externalstress in eV/ų, pfactor=(75 fs)²·bulk_mod, ttime=25 fs.

Live output includes a density convergence check (drift < 1% = converged).

pack_cell.py

Packs molecules into a cubic periodic box using Packmol.

python pack_cell.py --project ./my-project \
  -m Na:inputs/Na.pdb:0.5M \
  -m PF6:inputs/PF6.pdb:0.5M \
  -m DME:inputs/DME.pdb:200 \
  --box-size 30

Amounts can be molar concentrations (0.5M) or explicit counts (200). Use --dry-run to preview without running, --seed 42 for reproducible packing.

run_md.py

Single-phase MD without checkpointing. Good for quick tests. Supports NVT, NPT, and annealing.

python run_md.py --project ./my-project -p npt -T 300 -P 1.0 -n 100000
python run_md.py --project ./my-project -p anneal --t-low 300 --t-high 500 --total-steps 200000 --num-cycles 5

analyze_trajectory.py

Plots temperature, density, and energy vs time from a completed run.

python analyze_trajectory.py --project ./my-project --protocol npt

export_vmd.py

Converts ASE trajectories to extended XYZ or multi-model PDB for VMD.

python export_vmd.py --project ./my-project --protocol npt --stride 10

ML Potentials

The toolkit supports three ML potential families via utils.get_calculator():

Model	Install	Description
uma	pip install fairchem-core	UMA-s-1.2 (FAIRChem/Meta), trained on OMol25. HuggingFace login required.
orbmol_v2	pip install orb-models	OrbMol-v2 (Orbital Materials), trained on OMol25. Includes learnable electrostatics.
mace_*	pip install mace-torch	MACE-MP-0 (Materials Project). General-purpose, full periodic table.

To use a specific model, pass --model to equilibrate.py or run_md.py. To add a new calculator, edit get_calculator() in utils.py.

File Reference

File	Purpose
utils.py	Shared constants, calculator factory (UMA, OrbMol, MACE), project layout
pack_cell.py	Pack molecules into a periodic box (Packmol wrapper)
equilibrate.py	NVT/NPT equilibration with checkpointing and resume
run_md.py	Single-phase MD (NVT, NPT, annealing) without checkpointing
analyze_trajectory.py	Equilibration diagnostic plots
export_vmd.py	Trajectory export for VMD
requirements.txt	Python dependencies
setup.sh	One-command environment setup

Colab Notebooks

Google Colab notebooks for running equilibration on cloud GPUs with persistent checkpointing to Google Drive:

Notebook	Workflow
NVT_OrbMolV2_Equilibration.ipynb	NVT + NPT with OrbMol-v2
NPT_FAIRChem-UMA_Equilibration.ipynb	NPT-only with FAIRChem UMA

Located in notebooks/. Upload input boxes, run cells, checkpoints save to Drive automatically. If runtime disconnects, reconnect and resume from the last checkpoint.

Project Directory Layout

When using --project, scripts auto-derive paths from this structure:

my-project/
  inputs/       Avogadro PDB files (one per molecule)
  packed/       Packed cell output (system.pdb)
  nvt/          NVT equilibration (trajectory.traj, md.log, final.xyz)
  npt/          NPT equilibration
  anneal/       Annealing equilibration
  analysis/     Diagnostic plots (temperature, density, energy vs time)
  vmd/          VMD-ready trajectory exports (.xyz or .pdb)

You don't have to use --project. Every script also accepts explicit paths (--input, --output, etc.).