Load external data

Make sure you have the following in your working directory.

  • (cryspy)
  • cryspy.in

If you need a script to run (cryspy), see Script to run .

$ ls
cryspy  cryspy.in

Then, run CyrSPY!

$ bash ./cryspy &

or, if you move the cryspy script in your $PATH, just type

$ cryspy &

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

If it worked properly, log would look like this.

2022/07/14 19:41:41
CrySPY 0.11.0
Start cryspy.py

Read input file, cryspy.in
Write input data in cryspy.out
Save input data in cryspy.stat

# --------- Generate initial structures
# ------ mindist
Si - Si 1.11
Structure ID      0 was generated. Space group:  88 --> 141 I4_1/amd
Structure ID      1 was generated. Space group: 101 --> 101 P4_2cm
Structure ID      2 was generated. Space group: 204 --> 229 Im-3m
Structure ID      3 was generated. Space group: 199 --> 199 I2_13
Structure ID      4 was generated. Space group:  12 -->  12 C2/m

Unlike normal use, a directory named ext was created. Only the stat_job file exists in ext/.

$ cat ext/stat_job
out

If you run cryspy when “out” is written in the stat_job file, queueing structure files (cif format) are exported in ext/queue.

$ cryspy &
$ ls ext/queue
0.cif  1.cif  2.cif  3.cif  4.cif

The number in the file name is structure ID. The fist line of stat_job was automatically changed.

$ cat ext/stat_job
submitted

Perform structure optimization and energy evaluation in an external program using the output cif files. Once that calculation is done, prepare the optimized structure and energy data in the pickle data format, ext_opt_struc_data.pkl and ext_energy_data.pkl.

The data format of ext_opt_struc_data.pkl is the same as init_struc_data.pkl and opt_struc_data.pkl, see Data format/Initial and optimized structure data .

The data format of ext_energy_data.pkl is similar to ext_opt_struc_data.pkl. Just change the value from the structure data into the energy. An example of the energy data (dict type) is shown below.

  • key: structure ID
  • value: energy
{0: -0.7139331910805997,
 1: -0.5643404689832622,
 2: -0.5832404287259171,
 3: -0.535037327286169,
 4: -0.6316663459586607}

The ext/calc_data directory should be automatically generated, so put the two pickle files here.

$ ls ext/calc_data
ext_energy_data.pkl  ext_opt_struc_data.pkl

When ready, replace the first line of the stat_job file with “done” and run CrySPY.

$ emacs /ext/stat_job
$ cat /ext/stat_job
done
$ cryspy &

CrySPY collects the result data.