ilustrado is a Python package that implements a highly-customisable massively-parallel genetic algorithm for ab initio crystal structure prediction (CSP), with a focus on mapping out compositional phase diagrams. The aim of ilustrado was to provide a method of extending CSP results generated with random structure searching (AIRSS) or extrapolating from known chemically-relevant systems (species-swapping/prototyping).
The API is fully-documented and the source code can be found on GitHub. ilustrado makes extensive use of the matador API and interfaces with CASTEP for DFT-level relaxations. Written by Matthew Evans ([email protected]).
By default, fitnesses are evaluated as the distance from a binary or ternary convex hull that is passed as input. Duplicate structures are filtered out post-relaxation based on pair distribution function overlap. The standard mutation operators are implemented: cell and position noise, vacancies, and atom permutation and transmutation. Additionally a Voronoi-based mutation has been implemented:
- Each of the N atoms of randomly chosen species A are removed from the cell.
- The Voronoi decomposition of the remaining atoms is calculated.
- K-means clustering is applied to the Voronoi points to split them into N \pm D clusters, where D is a random integer less than \sqrt{(N)}.
- N \pm D atoms of species A are added to the cell at the centres of these clusters. The species A can be specified by the user or chosen randomly. This mutation is effective when studying materials that have one light, mobile element, for example Li.
Crossover is performed with the standard cut-and-splice method [1] to ensure transferrability over many types of material systems. This method cuts a random fraction from each parent cell and splices them back together; in ilustrado efforts are made to align the cells such that the cutting axes are approximately commensurate before crossover.
Several physical constraints (minimum atomic separations, densities, cell shapes) are applied to the trial structures before relaxation to improve efficiency. In order to maintain population diversity as the simulation progresses, the user can optionally disfavour frequently-visited regions of composition space.
The entrypoint is a Python script that creates an ArtificialSelector object with the desired parameters. Many examples can be found in examples/. There are two modes in which to run ilustrado:
compute_mode='direct'involves one ilustrado processes spawningmpirunjobs either on local or remote partitions (i.e. either a node list is passed for running on a local cluster, or ilustrado itself is submitted as a HPC job). In this case, the user must manually restart the GA when the job finishes.compute_mode='slurm'performs the GA in interruptible steps; submitting ilustrado as a job will lead to the submission of many slurm array jobs for the relaxation, and a dependency job that re-runs the ilustrado process to check on the relaxations. In this case, the user only needs to submit one job (tested on 6400 cores/200 nodes without issue).
[1] Deaven, D. M.; Ho, K. M. Molecular Geometry Optimization with a Genetic Algorithm. Phys. Rev. Lett. 1995, 75, 288, 10.1103/PhysRevLett.75.288.
- There are no stopping criteria implemented in ilustrado. Due to the multi-composition nature of the method, it is not easy to define either success or stagnation. Instead, users can perform their own analysis on the output of each generation.
- Due to the way it initialised in our group, generation of random structures is not performed as part of ilustrado. Instead, we typically start from a phase diagram that has already been well-sampled with a random search.
- None of the mutation or crossover operators make use of symmetry.