zhenming-xu/CrySPY

CrySPY is a crystal structure prediction tool written in Python.

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 0.10.3 (2022 May 17)

Important changes

• version 0.10.3 (2022 May 17)
  • Bug fixed for LAMMPS IO
• version 0.10.2 (2022 January 24)
  • Added nrot: maximum number of times to rotate molecules in mol_bs mode
• version 0.10.1 (2021 September 30)
  • Bug fixed for numpy.random.seed in multiprocessing
• version 0.10.0 (2021 July 25)
  • Support PyXtal 0.2.9 or later
  • Step data and LAQA for QE
  • Upper and lower limits of energy for EA and BO
• 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
• PyXtal >= 0.2.2
• (PyXtal requires pymatgen) pymatgen >= 2022.0.4

See CrySPY document in detail.

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 group of CrySPY

Reference

CrySPY (software)

• T. Yamashita, S. Kanehira, N. Sato, H. Kino, H. Sawahata, T. Sato, F. Utsuno, K. Tsuda, T. Miyake, and T. Oguchi, Sci. Technol. Adv. Mater. Meth. 1, 87 (2021).
  • https://www.tandfonline.com/doi/full/10.1080/27660400.2021.1943171

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

Baysian optimization and evolutionary algorithm

• T. Yamashita, H. Kino, K. Tsuda, T. Miyake, and T. Oguchi, Sci. Technol. Adv. Mater. Meth. 2, 67 (2022).
  • https://www.tandfonline.com/doi/full/10.1080/27660400.2022.2055987

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

• T. Yamashita and H. Sekine, Sci. Technol. Adv. Mater. Meth. 2, 84 (2022).

  • https://www.tandfonline.com/doi/full/10.1080/27660400.2022.2059335

License

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