PAFI: Anharmonic free energy barriers in LAMMPS
A linear scaling algorithm to evaluate transition rates or free energy differences beyond harmonic transition state theory
GitHub  /  Physical Review Letters 2018

Applications
Y Sato et al., D Rodney MRL (2021)
R Namakian et al. Computational Material Science (2022, 2023, and 2024, in prep),
Matthew et al. Computational Material Science 2024
Allera et al. under review

---

TAMMBER: Temperature Accelerated Markov Models with Bayesian Estimation of Rates
Massively parallel, autonomous exploration of atomic systems guided by Bayesian UQ on model incompleteness
GitHub  /  Physical Review Materials 2018  /  Presentation (CIRM, 2018)

Applications
NPJ Computational Materials (2020)
K Ferasat et al. Materialia (2021)
Goryaeva et al. Nat Comm (2023)
ANR HEBERTUNE project, in prep
More coming soon…..

---

LML Retrain- QM/ML embedding
Retrained ML potentials to embed DFT in large-scale, fully three-dimensional MD.
GitHub  /  Acta Mat 2023

Applications
Malyiov et al. 2024 In Prep..
Grigorev et al. 2024 In Prep..

---

PyGT- Graph Transformation in Python
Stable analysis of ill-conditioned Markov chains, generalizing Prof DJ Wales’ graph transformation method
GitHub  /  J Chem. Th. Comp. 2020  /  ReadTheDocs

Applications
TDS et al. JCP (2020)
D Kannan et al. JCP (2020)
E Woods et al. Proc. Roy. Soc. 2022

---

BLaSa- Bond Lattice Sampling
Analytic mean-field approach for anharmonic vibrational phase free energies in CPU milliseconds
GitHub  /  PRB Rapid Communications (2020)

Applications
Dsouza et al. PRB 2024
Dsouza et al. in Prep…