Software

Code I have written for my own research and made public. Everything is on GitHub.

Structure building and visualisation

• AtomForgeC++ · Windows, Linux

  A desktop application for building and inspecting atomic structures. It covers bulk crystals from space groups, substitutional solid solutions, CSL grain-boundary bicrystals, nanoparticles from shapes or Wulff constructions, Voronoi polycrystals and structures filling an OBJ/STL mesh, along with electronic post-processing. It comes with an illustrated manual. Download · manual · Python package

• atoms_visualizerPython · Blender add-on

  Imports .xyz files into Blender as shaded atoms with automatic bonds, for rendering figures.

DFT and atomistic workflows

• SOTCPython

  Special optimal thermal cells. The idea borrows from SQS: instead of averaging over hundreds of stochastic snapshots, one 32–64 atom cell is optimised to reproduce the thermal displacement correlations of the crystal. Phonon dispersions, DOS and thermodynamic properties at high temperature then need only a few DFT calls.

• QEPPC++17

  A command-line pre- and post-processor for Quantum ESPRESSO. It generates inputs from CIF files and handles band structures, DOS and d-band centres, elastic constants, DFPT phonons, quasi-harmonic thermal expansion and C_ij(T), Bader charges, STM images and convergence tests.

• fcc_gsfePython

  Introduces stacking faults into an FCC POSCAR to set up generalized stacking-fault energy calculations.

• convert_SQSPython

  Converts ATAT special quasirandom structures to Quantum ESPRESSO or VASP format.

Machine learning

• LatentMatFusionPython

  Compresses VASP CHGCAR charge densities with a 3D convolutional autoencoder and combines the latent vector with Magpie descriptors in gradient-boosted models. It predicts bulk, Young's and shear moduli, formation energy and Debye temperature. This is the code behind our JCIM paper.

Web tools

These run entirely in your browser; files are not uploaded anywhere.

• AtomForge Webbrowser port of AtomForge · three.js

  Build crystals from any of the 230 space groups, then cut surface slabs, CSL tilt grain boundaries, nanoparticles (shapes or Wulff constructions), Voronoi polycrystals, amorphous structures, FCC stacking faults and random solid solutions, each with a live preview. Edit atoms and cells with undo, measure distances and angles, compute g(r), and export POSCAR, extended XYZ, CIF or LAMMPS data. Opens XYZ, POSCAR, CIF, PDB and LAMMPS files.

• SQS to POSCAR

  Converts an ATAT bestsqs.out file to a VASP POSCAR.

• Phase-Field Lab3D · WebGPU

  Ten 3D phase-field models running on the GPU in the browser: spinodal decomposition, grain growth, precipitation and coarsening, a multi-phase-field model, magnetic domains (LLG with DMI), dendritic solidification, block-copolymer self-assembly, nucleation and growth, antiphase domains and Swift–Hohenberg patterns. Rendered as surfaces, volumes or isosurfaces, with a 2D slice along any plane and export to ParaView (VTK).