High Throughput Python Packages

atomate2

atomate2 is a library of computational materials science workflows

quacc

quacc is a flexible platform for computational materials science and quantum chemistry that is built for the big data era.

spindry

Low-cost host-guest conformer generation

mchammer

Implementation of cheap Monte Carlo optimisation of bonds in molecules

masci-tools

Post-processing toolkit for electronic structure calculations

aiida-kkr

AiiDA plugin of the high-performance density functional theory code JuKKR (www.judft.de) for high-throughput electronic structure calculations.

py-sharedmemory

Optimized Python IPC: Uses shared memory to bypass multiprocessing queue I/O bottlenecks, ideal for large data (1MB+) in scientific computing, RL, etc. Reduces system load and improves latency

aiida-fleur

AiiDA plugin of the high-performance density functional theory code FLEUR (www.judft.de) for high-throughput electronic structure calculations.

cifkit

High-throughput .cif analysis made easy. DOI: https://doi.org/10.21105/joss.07205

flowstate-asof-core

High-throughput, Rust-accelerated temporal join engine for quantitative finance ML pipelines. Engineered via PyO3 to eliminate look-ahead bias and accelerate point-in-time feature generation on massive time-series market datasets

rl-warp-drive

Extremely Fast End-to-End Deep Multi-Agent Reinforcement Learning Framework on a GPU (JMLR 2022)

shapeout

Shape-Out has been superseded by Shape-Out 2.

flowstate-asof

High-throughput, Rust-accelerated temporal join engine for quantitative finance ML pipelines. Engineered via PyO3 to eliminate look-ahead bias and accelerate point-in-time feature generation on massive time-series market datasets

flexgen

Running large language models on a single GPU for throughput-oriented scenarios.

bindflow

A snakemake-based workflow for FEP and MM(PB/GB)SA calculations with GROMACS

hts-tools

🏮 Parsing and analysing platereader absorbance and fluorescence data.

quasar-core

QUASAR is an autonomous system for end-to-end scientific discovery, integrating LLMs with simulation tools to automate workflows across quantum chemistry, materials science, and molecular simulation.

pyfgcz

Move and Convert Mass Spectrometry Data using BioBeamer and FCC

poremapper

cavity shape and size mapping by growing a guest inside a host

muse-xtal

A python package for fast building amorphous solids and liquid mixtures from @materialsproject computed structures and machine learning interatomic potentials

mol-ellipsize

Molecular size calculation based on ellipsoid fitting over N conformers

openrt

Open-source red teaming framework for MLLMs with 42+ attack methods

annotate-ez

High-throughput curation and visualization of large-scale single-cell microscopy images, in a lightweight GUI.

shadowkv

[ICML 2025 Spotlight] ShadowKV: KV Cache in Shadows for High-Throughput Long-Context LLM Inference