CrySPY

CrySPY is a crystal structure prediction tool written in Python.
Document site is moved to https://tomoki-yamashita.github.io/CrySPY_doc/

Latest version

version 0.9.2 (2021 March 18)

This version supports pymatgen v2022. If you use pymatgen v2021 or older, use CrySPY 0.9.1.

Important changes

• version 0.9.2 (2021 Mar 18)
  • support pymatgen major change (v2022)
• version 0.9.0 (2021 Feb 7)
  • Interfaced with OpenMX
  • Employ PyXtal library to generate initial structures
  • If you use PyXtal (default), find_wy program is not required
  • LAQA can be used with soiap
  • Change the section name in the input file: [lattice] section –> [structure] section
  • Several input variables move to [structure] section
    • natot: [basic] –> [structure]
    • atype: [basic] –> [structure]
    • nat: [basic] –> [structure]
    • maxcnt: [option] –> [structure]
    • symprec: [option] –> [structure]
    • spgnum: [option] –> [structure]
  • New features
    • Molecular crystal structure generation
    • Scale volume
• version 0.8.0
  • Migrated to Python 3
  • Several variable names
  • Several data formats
  • Unit of energy in output: eV/cell --> eV/atom
  • No. of working directories corresponds to structure ID
• version 0.7.0
  • Evolutionary algorithm is now available
• version 0.6.2
  • LAMMPS can be used in CrySPY
• version 0.6.0
  • LAQA is now available
  • Changed the data format of init_struc_data and opt_struc_data from list to dict

System requirements

Python

• Python 3.8.x, 3.9.x (3.7.x may work)
• COMBO
• pymatgen >= 2022.0.4
• PyXtal >= 0.2.2

There is a breaking change in pymatgen v2022.
PyXtal v0.2.2 and CrySPY 0.9.2 support this change in pymatgen.
If you use pymatgen v2021 or older, choose PyXtal v0.2.1 or older and CrySPY 0.9.1.

PyXtal requires SciPy, but SciPy v1.6.0 includes a bug for deepcopy. (2021 Feb 7)
This bug has already been fixed in SciPy v1.6.1 (2021 March 7).

Structure optimizer

At least one optimizer is required.

• VASP (tested with version 5.4.4)
• QUANTUM ESPRESSO (tested with version 6.x, version 5.x does not work)
• OpenMX
• soiap (tested with version 0.2.2)
• LAMMPS

Others

• find_wy: find_wy can randomly select a combination of Wyckoff positions for a given chemical composition and space group. (optional)

Document (English/Japanese)

CrySPY document

Google group

Google gruop of CrySPY

Reference

Bayesian optimization

• T. Yamashita, N. Sato, H. Kino, T. Miyake, K. Tsuda, and T. Oguchi, Phys. Rev. Mater. 2, 013803 (2018).

  • https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.2.013803

• N. Sato, T. Yamashita, T. Oguchi, K. Hukushima, and T. Miyake, Phys. Rev. Mater. 4, 033801 (2020).

  • https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.4.033801

LAQA

• K.Terayama, T. Yamashita, T. Oguchi, and K. Tsuda, npj Comput. Mater. 4, 32 (2018).
  • https://www.nature.com/articles/s41524-018-0090-y

License

CrySPY is distributed under the MIT License.
Copyright (c) 2018 CrySPY Development Team