Append structures

Of course only 5 structures are not enough to find stable structures. You can append structures whenever you want. Here let’s append more 5 structures.

For Si-Si mindist, the default value of 1.11 Å is used in the first structure generation (see log_cryspy), which is a little too close. Let us try to set the mindist to 2.0 Å.

Info

For mindist, see also Features > Restriction on interatomic distances.

Edit cryspy.in and change the value of tot_struc into 10, and add mindist_1 = 2.0

emacs cryspy.in
cat cryspy.in

[basic]
algo = RS
calc_code = soiap
tot_struc = 10
nstage = 1
njob = 2
jobcmd = zsh
jobfile = job_cryspy

[structure]
atype = Si
nat = 8
mindist_1 = 2.0

[soiap]
soiap_infile = soiap.in
soiap_outfile = soiap.out
soiap_cif = initial.cif

[option]

Then run cryspy, and check log_cryspy file.

cryspy &
cat log_cryspy

...
(omit)
...

2023/03/19 00:01:47
CrySPY 1.0.0
Restart cryspy.py


Changed tot_struc from 5 to 10
Changed mindist from None to [[2.0]]

Backup data

# ---------- Append structures
# ------ mindist
Si - Si 2.0
Structure ID      5 was generated. Space group: 218 --> 221 Pm-3m
Structure ID      6 was generated. Space group:  86 --> 129 P4/nmm
Structure ID      7 was generated. Space group: 129 --> 129 P4/nmm
Structure ID      8 was generated. Space group: 191 --> 191 P6/mmm
Structure ID      9 was generated. Space group:  31 -->  31 Pmn2_1

Remember that CrySPY goes into structure generation mode whenever you change the value of tot_struc. In this mode, CrySPY does not do any other action such as collecting data, submitting jobs, and so on.

Note

Structure generation mode whenever you change the value of tot_struc.
From version 1.0.0, CrySPY automatically backs up when adding structures. See features/backup.

Repeat cryspy & several times until all appended structures are done. The auto script (repeat_cryspy) may help you.