extract_struc.py (legacy)

Last updated: October 16, 2026

Info

In CrySPY v1.5.0 and later, these features are available through Commands > cryspy-extract-struc. This page describes the standalone utility script.

Link: CrySPY_utility/script/extract_struc.py

Script to extract structures from init_struc_data.pkl or opt_struc_data.pkl. This script can print stucture information and output cif files.

One can specify structure ID(s) using -i option. Top k structures (the k most stable structures) can be extracted using -t option. -a option is for outputting all the structures. (note that many cif files will be output.) Symmetrized cif files can be generated with -s option. When outputting a symmetrized CIF file, you can also specify a tolerance with --tolerance. Structure information is printed with -p. If you use -p option, cif files are not output. You can also read a gzipped file (e.g., opt_struc_data.pkl.gz).

Update History

  • 2024 April 16: –tolerance option, gzip
  • 2023 July 21: –print option

Usage

python3 extract_struc.py -h

or if you put the script in your PATH, you can omit python3

extract_struc.py -h
usage: extract_struc.py [-h] [-p] [-a] [-i [INDEX ...]] [-t TOP] [-r] [-s] [--tolerance TOLERANCE] infile

positional arguments:
  infile                input file

options:
  -h, --help            show this help message and exit
  -p, --print           just print, e.g., extract_struc.py opt_struc_data.pkl -i 7 10 12 -ps
  -a, --all_id          all structures, e.g., extract_struc.py opt_struc_data.pkl -as
  -i [INDEX ...], --index [INDEX ...]
                        structure ID, e.g., extract_struc.py opt_struc_data.pkl -i 7 10 12 -s
  -t TOP, --top TOP     top k structures, e.g. (k = 3), extract_struc.py opt_struc_data.pkl -t 3 -s
  -r, --rank            add rank in file names, e.g., extract_struc.py opt_struc_data.pkl -t 3 -rs
  -s, --symmetrized     symmetrized structure, e.g., extract_struc.py opt_struc_data.pkl -i 7 10 12 -s
  --tolerance TOLERANCE
                        tolerance for symmetrization (default 0.01), e.g., extract_struc.py opt_struc_data.pkl -i 0 1 -s --tolerance 0.01

Examples

Print

The -p option can be used in combination with any option except for -s option.

extract_struc.py -p opt_struc_data.pkl -i 0 1
ID 0
Full Formula (Na8 Cl8)
Reduced Formula: NaCl
abc   :   6.823618   6.823618   7.566454
angles:  90.000000  90.000000  96.650518
pbc   :       True       True       True
Sites (16)
  #  SP           a         b         c
---  ----  --------  --------  --------
  0  Na    0         0         1
  1  Na    0         0         0.5
  2  Na    0.704707  0.295293  0.75
  3  Na    0.295293  0.704707  0.25
  4  Na    0.5       0         1
  5  Na    0.5       0         0.5
  6  Na    0         0.5       0.5
  7  Na    0         0.5       0
  8  Cl    0.5       0.5       0
  9  Cl    0.5       0.5       0.5
 10  Cl    0.484753  0.515247  0.75
 11  Cl    0.515247  0.484753  0.25
 12  Cl    0.828247  0.171753  0.851096
 13  Cl    0.171753  0.828247  0.351096
 14  Cl    0.828247  0.171753  0.648904
 15  Cl    0.171753  0.828247  0.148904

ID 1
Full Formula (Na8 Cl8)
Reduced Formula: NaCl
abc   :   8.145021   8.145021   4.324235
angles:  90.000000  90.000000 120.000000
pbc   :       True       True       True
Sites (16)
  #  SP            a          b         c
---  ----  ---------  ---------  --------
  0  Na     0.666667   0.333333  0.736206
  1  Na     0.666667   0.333333  0.263794
  2  Na     0.913147   0.086853  0.5
  3  Na     0.913147   0.826295  0.5
  4  Na     0.173705   0.086853  0.5
  5  Na     0.77711    0.22289   0
  6  Na     0.77711    0.55422   0
  7  Na     0.44578    0.22289   0
  8  Cl     0.027675   0.423376  0.5
  9  Cl    -0.423376  -0.395701  0.5
 10  Cl     0.395701  -0.027675  0.5
 11  Cl    -0.423376  -0.027675  0.5
 12  Cl     0.395701   0.423376  0.5
 13  Cl     0.027675  -0.395701  0.5
 14  Cl     0.333333   0.666667  0.5
 15  Cl     0          0         0

Structure ID

extract_struc.py opt_struc_data.pkl -i 7 10 12

7.cif, 10.cif, and 12.cif are output.

For symmetrized cif,

extract_struc.py opt_struc_data.pkl -i 7 10 12 -s

2024 April 16
With the tolerance parameter (default 0.01)

extract_struc.py opt_struc_data.pkl -i 7 10 12 -s --tolerance 0.01

Top k Structures

Info

rslt_data.pkl is required in the same directory as the input.

Let us suppose

  • ./data/pkl_data/opt_struc_data.pkl
  • ./data/pkl_data/rslt_data.pkl

and cryspy_rslt_energy_asc file is as follows:

    Spg_num     Spg_sym  Spg_num_opt Spg_sym_opt    E_eV_atom  Magmom      Opt
9       110      I4_1cd          110      I4_1cd -1284.708037     NaN  not_yet
16        4        P2_1            4        P2_1 -1284.693651     NaN     done
97       92    P4_12_12           91      P4_122 -1284.692494     NaN     done
8        57        Pbcm           57        Pbcm -1284.668504     NaN     done
81       19  P2_12_12_1           19  P2_12_12_1 -1284.635684     NaN     done
...

Top k(=3) structures can be extracted with:

extract_struc.py ./data/pkl_data/opt_struc_data.pkl -t 3

In this example, rlst_data.pkl must be in ./data/pkl_data/. 9.cif, 16.cif, and 97.cif are output.

The rank can be included in cif file names with -r option:

extract_struc.py ./data/pkl_data/opt_struc_data.pkl -t 3 -r

1_9.cif, 2_16.cif, and 3_97.cif are output.

For symmetrized cif:

extract_struc.py ./data/pkl_data/opt_struc_data.pkl -t 3 -rs

All the Structures

You should make a directory.

mkdir init_cifs
cd init_cifs
extract_struc.py /path/to/opt_struc_data.pkl -a

For symmetrized cif,

extract_struc.py /path/to/init_struc_data.pkl -as

Gzipped Files

2024 April 16
Gzipped files (end with .gz) can be read:

extract_struc.py opt_struc_data.pkl.gz -i 0 1 -s