Genarris

Genarris

A random structure generation package for molecular crystals

Genarris performs configuration space screening for crystals of (semi-)rigid molecules with no internal rotational degrees of freedom by random sampling with physical constraints. Genarris uses the Harris approximation to perform fast energy evaluations. The Harris density of a molecular crystal is constructed by replicating a single molecule density, which is calculated only once. The DFT energy is then evaluated for the Harris density without performing a self-consistency cycle. Genarris is written in Python and distributed under a BSD-3 license. Genarris interfaces with the FHI-aims electronic structure package for energy evaluations and geometry relaxations with dispersion-inclusive DFT.

Features:

  • A variety of breeding operators (crossover and mutation) tailored for molecular crystals provide a balance between exploration and exploitation.
  • Evolutionary niching, performed by using machine learning for clustering on the fly and then using a cluster-based fitness function, helps overcome initial pool biases and selection biases by steering the GA to under-explored regions of the configuration space.
  • A massive parallelization scheme, tested on up to 105 CPU cores, enables effective utilization of high performance computing resources.