extract_struc.py
2023 April 16 update
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
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
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