Subsections of Version Information

Version 1.5.0

Important change

Composition constraints in EA-vc

  • Added min_comp and max_comp to specify lower and upper bounds on each atom type’s composition fraction. These constraints can be combined with charge neutrality.
  • Features > Composition Constraints

Input file

  • Moved plotting parameters from the [EA] section to the new [visual] section.
  • Deprecated cgen. Use plot_min_gen and plot_max_gen to select generations to display, and ref_gen to specify the reference generation.
  • Renamed the reference energies for formation energy calculations from end_point to ref_energies. end_point is still accepted for backward compatibility.
  • Removed target and timeout_mol.
  • Input File > [EA] Section, Input File > [visual] Section, Input File > [structure] Section

Common

  • Updated the minimum requirements to Python 3.10 and PyXtal 1.0.7.
  • Removed support for using random and evolutionary structure generation as a standalone library.

Added

Subcommand

  • cryspy-print: Display the contents or a summary of a pickle file. For rslt_data.pkl, row selection, composition filtering, and regeneration of text result files are also supported.
  • cryspy-extract-struc: Extract structures from structure data and save them as CIF files or display their information.
  • Integrated these commands into CrySPY as replacements for CrySPY Utility’s print_pkl.py and extract_struc.py.

Plotting and replotting

  • Added support for RS and EA energy plots in cryspy-Eplot.
  • Added separate controls for the displayed generation range and the reference generation in EA and EA-vc.
  • Added axis_order to change element positions and support for displaying the allowed composition range in EA-vc.
  • Added cryspy-Eplot -c to check the allowed composition range specified in the input before starting a search.
  • Added terminals to plot convex hulls with compound terminals.
  • Commands > cryspy-Eplot, Input File > [visual] Section

Input parameters

Niggli reduction

Result and figure output

  • Added rslt_out to control when cryspy_rslt and cryspy_rslt_energy_asc are written. The default is always.
  • Added energy_output_interval to control the output interval for EA energy plots and EA-vc convex hull plots and hull-distance files. The default is 1 (every generation); 0 disables automatic output.
  • EA-vc convex hulls and hull distances are still calculated every generation, regardless of the output interval.
  • Input File > [option] Section

Charge neutrality condition

  • Improved the calculation of atom-count combinations that satisfy charge neutrality.
  • Added support for multivalent species, for example, charge = (2 3) -2.
  • Added cn_mode to select enumeration or sampling of atom-count combinations. In auto mode, the method is selected based on max_cn_grid_points.
  • Features > Charge Neutrality Condition

Backup

  • Added backup_interval to specify the automatic backup interval.
  • Backup directory names now include the progress number and unit. Manual backups also include manual.
  • Features > Backup

Changed

Default values in EA-vc

Loading initial structures

  • Added stricter validation of data loaded with load_struc_flag = True. Structure IDs, structure counts, atom types, and atom counts are checked. EA-vc also checks composition constraints and charge neutrality.
  • If fewer structures than required are loaded, the remaining structures are generated randomly.
  • Features > Loading Initial Structures

Fixed

  • Fixed an infinite loop in EA parent selection when the same parent was repeatedly selected while attempting to choose two distinct parents.
  • Fixed roulette selection probabilities when all candidates have the same fitness.
  • Fixed EA-vc elite reselection after changes to atom-count bounds, composition constraints, or n_elite. Elites are now reselected from past results.
  • Fixed errors when structures excluded from convex hull calculations were considered as elites or parent candidates in EA-vc.
  • Fixed a missing random number generator argument in the atom-addition step of crossover that affected reproducibility.
  • Fixed cases where lock_cryspy was left behind after input errors in interactive mode.

Version 1.4.3

Fixed

  • Elimintion in EA-vc: fixed a bug that let the atom count go below the minimum.
  • Substitution in EA-vc: fixed a bug where the atom count went negative mid-run.

Version 1.4.2

Important change

Added

Changed

Job file auto-rewriting

Priority order of structure optimization input file names

x is the stage number.

  1. x_ase_in.py
  2. ase_in.py_x
  3. ase_in.py

In previous versions, the second style ase_in.py_x was used.

Fixed

  • Fixed a bug in mindist check after structure optimization (when structure data could not be obtained correctly)

Version 1.4.1

Important change

EA-vc

Added

Charge neutral condition

Subcommand

Version 1.4.0

Important change

New algorithm: EA-vc

Interactive mode

EA

  • tot_struc is no longer used in EA. The number of structures in the first generation is now determined by n_pop.

Interatomic distance check after structrue optimization

  • Added check_mindist_opt to the [option] section in cryspy.in.
  • Default: check_mindist_opt = True.
  • After structure relaxation, a check is performed to ensure that the minimum interatomic distance constraint is satisfied.

Common

  • The natot parameter in cryspy.in has been removed.
  • Ctrl_ext has been removed.

Fixed

  • Fixed a bug related to using TS as the score in BO.
  • Several other minor fixes.

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. (removed in version 1.5.0)

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

  • ext: Deprecated in version 1.4.0.

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