Firsrt run

2023 July 10, update

Make sure you have the following in your working directory.

  • calc_in/
  • (cryspy)
  • cryspy.in
$ ls
calc_in/  cryspy.in

Then, run CyrSPY!

cryspy

If you use old version (0.10.3 or earlier):

bash ./cryspy

At the first run, CrySPY goes into structure generation mode. CrySPY stops after 5 structure generation.

If it worked properly, the following output appears on the screen:

[2023-07-10 18:40:54,389][cryspy_init][INFO] 


Start CrySPY 1.2.0


[2023-07-10 18:40:54,389][cryspy_init][INFO] # ---------- Read input file, cryspy.in
[2023-07-10 18:40:54,390][read_input][INFO] Save input data in cryspy.stat
[2023-07-10 18:40:54,391][cryspy_init][INFO] # ---------- Initial structure generation
[2023-07-10 18:40:54,391][cryspy_init][INFO] Number of MPI processes: 1
[2023-07-10 18:40:54,391][gen_init_struc][INFO] # ------ mindist
[2023-07-10 18:40:54,395][struc_util][INFO] Cu - Cu: 1.32
[2023-07-10 18:40:54,395][gen_init_struc][INFO] # ------ generate structures
[2023-07-10 18:40:54,481][gen_pyxtal][INFO] Structure ID      0 was generated. Space group:   1 -->   1 P1
[2023-07-10 18:40:54,493][gen_pyxtal][INFO] Structure ID      1 was generated. Space group:  28 -->  28 Pma2
[2023-07-10 18:40:54,498][gen_pyxtal][INFO] Structure ID      2 was generated. Space group:  29 -->  29 Pca2_1
[2023-07-10 18:40:54,704][gen_pyxtal][INFO] Structure ID      3 was generated. Space group: 137 --> 137 P4_2/nmc
[2023-07-10 18:40:54,725][gen_pyxtal][INFO] Structure ID      4 was generated. Space group: 212 --> 214 I4_132
[2023-07-10 18:40:54,800][cryspy_init][INFO] Elapsed time for structure generation: 0:00:00.408367
cryspy  4.35s user 1.04s system 145% cpu 3.697 total

Several output files are also generated.

  • (cryspy.out): Short log. only version 0.10.3 or earlier.
  • cryspy.stat: Status file.
  • data/init_POSCARS: Initial struture file in POSCAR format. You can open this file using VESTA
  • data/pkl_data: Directory to save pickled data.
  • log_cryspy: log.
  • err_cryspy: error and warning.

Let’s take a look at cryspy.stat file.

...
(omit)
...
[status]
id_queueing = 0 1 2 3 4

Structure ID 0 – 4 are queueing because we just generated structures, and have not submitted yet.

ヒント

Check the initial structures, if the distance between atoms is too close, you should set the mindist in cryspy.in.