Firsrt run

2025 March 6, updated

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:

[2025-03-06 18:52:21,495][cryspy_init][INFO] 


Start CrySPY 1.4.0b10


[2025-03-06 18:52:21,495][cryspy_init][INFO] # ---------- Library version info
[2025-03-06 18:52:21,495][cryspy_init][INFO] pandas version: 2.2.2
[2025-03-06 18:52:21,495][cryspy_init][INFO] pymatgen version: 2025.1.24
[2025-03-06 18:52:21,495][cryspy_init][INFO] pyxtal version: 1.0.6
[2025-03-06 18:52:21,495][cryspy_init][INFO] # ---------- Read input file, cryspy.in
[2025-03-06 18:52:21,496][write_input][INFO] [basic]
[2025-03-06 18:52:21,496][write_input][INFO] algo = RS
[2025-03-06 18:52:21,496][write_input][INFO] calc_code = ASE
[2025-03-06 18:52:21,496][write_input][INFO] tot_struc = 5
[2025-03-06 18:52:21,496][write_input][INFO] nstage = 1
[2025-03-06 18:52:21,496][write_input][INFO] njob = 2
[2025-03-06 18:52:21,496][write_input][INFO] jobcmd = zsh
[2025-03-06 18:52:21,496][write_input][INFO] jobfile = job_cryspy
...
(omitted)
...
[2025-03-06 18:52:21,497][rs_gen][INFO] # ---------- Initial structure generation
[2025-03-06 18:52:21,497][rs_gen][INFO] # ------ mindist
[2025-03-06 18:52:21,498][struc_util][INFO] Cu - Cu: 1.32
[2025-03-06 18:52:21,498][rs_gen][INFO] # ------ generate structures
[2025-03-06 18:52:21,519][gen_pyxtal][INFO] Structure ID      0: (8,) Space group:  31 -->  31 Pmn2_1
[2025-03-06 18:52:21,525][gen_pyxtal][INFO] Structure ID      1: (8,) Space group: 198 --> 198 P2_13
[2025-03-06 18:52:21,554][gen_pyxtal][INFO] Structure ID      2: (8,) Space group:   4 -->   4 P2_1
[2025-03-06 18:52:21,580][gen_pyxtal][INFO] Structure ID      3: (8,) Space group: 193 --> 191 P6/mmm
[2025-03-06 18:52:21,581][gen_pyxtal][WARNING] Compoisition [8] not compatible with symmetry 172:     spg = 172 retry.
[2025-03-06 18:52:21,625][gen_pyxtal][INFO] Structure ID      4: (8,) Space group:  64 -->  64 Cmce
[2025-03-06 18:52:22,013][cryspy_init][INFO] Elapsed time for structure generation: 0:00:00.516183

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.

[status]
id_queueing = 0 1 2 3 4

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

Tip

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