Subsections of Version information

Version 1.3.0

Important change

Common

  • working directory name
    work000000 –> work0
  • We used to pickle data by grouping several data into tuples, but we changed it to pickle each item individually.
    For example, rs_id_data.pkl –> id_queueing.pkl and id_running.pkl

BO

Fixed

soiap

  • support for recent pymatgen

Added

  • Random structure generation and structure generation by EA are now available as libraries. see Features > As library

for developer

  • We stopped using global variables (rin), now uses dataclass for input data.
  • Many of the input variables were lists, but we changed them to tuples.

Version 1.2.5

Bug fix

  • simple bug fix

Version 1.2.4

Bug fix

EA

  • default value of cls_lat: equal –> random

EA-vc

  • test version of variable composition EA (EA-vc). only binary system for now.

Version 1.2.2

Enthalpy

You can use enthalpy instead of energy for VASP and QE.

See also

Version 1.2.1

ASE interface

Bug fixed for multiple stages.

Version 1.1.1

Bug fix for spg_error

In random structure generation, when a structure cannot be generated for a certain space group, the space group number is recorded in the variable sgp_error, and the number is skipped thereafter, but a bug was found in which the number was registered incorrectly in rare cases. Therefore, this spg_error function has been removed.

Version 1.1.0

Parallelization with MPI

Random structure generation using MPI has been available.

See also

LAQA

Updated score formula to take into account the stress term (T. Yamashita and H. Sekine, Sci. Technol. Adv. Mater. Meth. 2, 84 (2022).).

See also

Backup

Files are copied to the directory named by the date and time in “backup” directory.
See features/backup in detail.

Version 1.0.0

Install and run

CrySPY is now available in PyPI. You can install by

pip install csp-cryspy

The executable script, cryspy is automatically installed in your PATH. To run CrySPY, just type cryspy:

cryspy &

CrySPY stops once before going to next selection (BO, LAQA) or next generation (EA). For example, EA case:

[old version]

  • cryspy run
    • check jobs (finish current generation?)
    • structure generation by EA automatically starts

[CrySPY 1.0.0]

  • cryspy run
    • check jobs (finish current generation?)
    • stop
  • cryspy run
    • auto backup
    • structure generation by EA automatically starts

Auto and manual backup

Automatically backup:

  • before going to next selection or next generation
  • structure generation

To manually back up:

cryspy -b

See features/backup in detail.

Clean

cryspy -c

See features/clean in detail.

Directory tree

Changed the directory tree.

  • genstruc/RS –> RS/
  • genstruc/EA –> EA/
  • genstruc/struc_util.py –> util/
  • utility.py –> util/

IO

  • Fixed standard output file and standard error file: log_cryspy and err_cryspy
  • cryspy.out is obsoleted

Moved to CrySPY Utility

With the change in installation method, examples and cal_fingerprint have been moved to the CrySPY Utility.

COMBO

The python library COMBO is now optional in CrySPY. If you do not use Bayesian optimizaion, you do not need to install it.

New calc_code

cryspy.in

fppath

New input variable for cal_fingerprint. See Instllation/cryspy/cryspy_1.0

fwpath

New input variable for find_wy. See Instllation/requirements/find_wy

mindist

  • mindist can be omitted in cryspy.in
  • mindist_ea is obsoleted
  • added mindist_mol_bs and mindist_mol_bs_factor in cryspy.in

Version 0.10.3 or earlier

  • [2022 May 17] version 0.10.3 released
    • Bug fixed: LAMMPS IO.
  • [2022 January 24] version 0.10.2 released
    • Added nrot: maximum number of times to rotate molecules in mol_bs
  • [2021 September 30] version 0.10.1 released
    • Fixed the problem of numpy.random.seed in multiprocessing
  • [2021 July 25] version 0.10.0 released
    • Support PyXtal 0.2.9 or later
    • LAQA can be used with QE
    • Upper and lower limits of energy for EA and BO
  • [2021 July 13] paper published
    • Our paper on CrySPY software has been published in STAM:Methods
  • [2021 March 18] version 0.9.2 released
    • Support pymatgen v2022.
  • [2021 February 7] version 0.9.0 released
    • 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 name: [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
  • [2020 March 19] paper published
  • [2020 February 16] version 0.8.0 released
    • Migrate to Python 3
    • CrySPY logo created
    • Change several variable names and data formats
    • Change style of output for energy: eV/cell –> eV/atom
    • IDs of working directories corresponds to structure IDs
    • New features
      • recalculation
      • manual select in BO
  • [2018 December 5] version 0.7.0 released
    • New features
      • Evolutionary algorithm
  • [2018 August 20] version 0.6.4 released
  • [2018 July 2] version 0.6.3 released
  • [2018 June 26] Version 0.6.2 released
  • [2018 March 1] Version 0.6.1 released
  • [2018 January 9] paper published