Software & code

Open-source tools, pipelines & datasets

All code and datasets associated with publications are made publicly available on GitHub and Zenodo/FairData/FigShare upon publication. Below are the main repositories.

RuP project
This is the supporting code for the manuscript “Local Symmetry Breaking and Two-Stage Phase Transitions in RuP Uncovered by a Fine-Tuned Atomistic Foundation Model“.
Associated with: ChemRxiv 2026, 0330  ·  Paper  ·  GitHub: data-RuP
Shell VASP Python ASE MACE LAMMPS Spglib Phonopy dynosor VESTA OVITO
C60 fullerene project
This is the supporting code for the manuscript “Machine Learning-Accelerated Path Integral Molecular Dynamics and 13C NMR Simulations Unlock New Insights Into Quantum Effects in C60 Fullerene“.
Associated with: J. Phys. Chem. A 2026, 130, 2169–2181  ·  Paper  ·  GitHub: data-C60_ML
Shell DFTB+ TURBOMOLE Python ASE NEP SchNet GPUMD VMD
Porous liquids project
This is the supporting code for the manuscript “Equivariant Neural Networks Reveal How Host–Guest Interactions Shape 129Xe NMR in Porous Liquids”.
Associated with: J. Phys. Chem. Lett. 2025, 16, 12095–12103  ·  Paper  ·  GitHub: data-Xe_at_CC3_at_TBA
Shell DFTB+ TURBOMOLE VASP Python ASE Allegro MatTen scikit-learn LAMMPS VMD OVITO
Local atomic environmnent analyzer
A Python tool for analyzing the local environment around Xenon atoms in molecular clusters and identifying anomalous structures based on coordination number thresholds.
Python ASE
MD simulations trajectory slicer
A versatile Python tool for converting LAMMPS dump files to XYZ format and sampling molecular dynamics trajectories with precise frame control.
Python
NMR parameters extraction from VASP (versions < 6.6)
The VASP NMR Parameter Calculator extracts and processes NMR data from VASP output files (OUTCAR) that the standard VASP processing doesn't provide directly. This tool is particularly useful for researchers working with NMR computations in material science.
Python VASP
PIMD GUI for teaching
This is Exercise N°4 from the Computational Physics and Chemistry 2025 course.
I-PI LAMMPS Python Shell Jpyter Notebook Tkinter Ipykernel
Pyrochlore oxyfluorides project
This is the Supporting Dataset for the manuscript “Revealed Preferential Short-Range Anion Ordering in Disordered RbM2O5F (M = Nb, Ta) Pyrochlore-Type Oxyfluorides”.
Associated with: Inorg. Chem. 2025, 64, 5764–5777  ·  Paper  ·  GitHub: data-RbM2O5F
Shell VASP Python ASE mrsimulator Supercell DMFit VESTA
Ordered oxyfluorides project
This is the Supporting Dataset for the manuscript “Different Magnitudes of Second-Order Jahn-Teller Effect in Isostructural NaMO2F2 (M = Nb, Ta) Oxyfluorides”.
Associated with: J. Alloys Compd. 2025, 1010, 177457  ·  Paper  ·  GitHub: data-NaMO2F2
Shell VASP Python DMFit VESTA
© 2026 Ouail Zakary  ·  ozakary.github.io