cryspy-print

Last updated: October 16, 2026

cryspy-print Command

From v1.5.0, cryspy-print lets you inspect pickle files under data/pkl_data/. It replaces CrySPY Utility’s print_pkl.py, displaying contents or a summary according to the file type. For rslt_data.pkl, it also supports sorting by energy, selecting rows, filtering by composition, and regenerating result files.

Usage and Options

cryspy-print infile [options]

The input file can be specified with a relative or absolute path. Gzip-compressed files are also supported. The file type is determined by its filename, so keep names such as rslt_data.pkl unchanged.

Argument or option	Description
`infile`	Pickle file to display. Gzip-compressed files, such as `rslt_data.pkl.gz`, are also accepted.
`--no-sort`	Display `rslt_data.pkl` in its stored row order without sorting.
`--head N`	Display the first `N` rows after filtering and sorting. `N` must be a positive integer.
`--tail N`	Display the last `N` rows after filtering and sorting. `N` must be a positive integer.
`--all`	Display all rows after filtering and sorting.
`-c N [N ...]`, `--composition N [N ...]`	Filter EA-vc results in `rslt_data.pkl` by composition ratio, specified in `atype` order.
`--write`	Regenerate `./data/cryspy_rslt` and `./data/cryspy_rslt_energy_asc` from `rslt_data.pkl`.
`-h`, `--help`	Show help.

--no-sort, --head, --tail, --all, --composition, and --write are options for rslt_data.pkl. --head, --tail, and --all cannot be combined. --write cannot be combined with display options.

Supported Files and Output

File	Output
`input_data.pkl`	Input settings grouped by section. Fields whose value is `None` are omitted.
`init_struc_data.pkl`, `opt_struc_data.pkl`, `struc_step_data.pkl`, `elite_struc.pkl`, `init_dscrpt_data.pkl`, `opt_dscrpt_data.pkl`	Number of stored entries (`Number of structures`). Structure IDs are not listed.
`rslt_data.pkl`	Results table, sorted by energy in ascending order by default.
`hdist_data.pkl`	Latest generation and its number of structures. Prints `No hull distance data` if empty.
`pd_data.pkl`	Latest generation and its numbers of stable entries and all entries. Prints `No phase diagram data` if empty.
`cn_comb_data.pkl`	Charge-neutrality settings and the number of charge-neutral combinations. Reports when `cn_comb` is `None`.

The contents of the following files are pretty-printed.

Common: id_queueing.pkl, id_running.pkl, energy_step_data.pkl, force_step_data.pkl, stress_step_data.pkl, kpt_data.pkl, rng_state_data.pkl
EA: gen.pkl, ea_info.pkl, ea_origin.pkl, elite_fitness.pkl
EA-vc: nat_data.pkl
BO: n_selection.pkl, id_select_hist.pkl, bo_mean.pkl, bo_var.pkl, bo_score.pkl
LAQA: tot_step_select.pkl, laqa_energy.pkl, laqa_bias.pkl, laqa_score.pkl, laqa_step.pkl, laqa_struc.pkl

An unsupported filename causes an error.

Examples

Checking Structure Counts, Input Settings, and Fitness

cryspy-print ./data/pkl_data/init_struc_data.pkl

Output for a file containing ten entries:

Number of structures: 10

opt_struc_data.pkl and elite_struc.pkl also display the structure count. To inspect individual structures, use the -p option of cryspy-extract-struc.

cryspy-print ./data/pkl_data/input_data.pkl
cryspy-print ./data/pkl_data/elite_fitness.pkl

input_data.pkl displays settings grouped into sections such as [basic] and [structure]. elite_fitness.pkl displays a dictionary of structure IDs and fitness values.

Displaying Results

cryspy-print ./data/pkl_data/rslt_data.pkl

Results are sorted in ascending order of Ef_eV_atom if that column exists, or E_eV_atom otherwise. All rows are displayed if there are at most 100 rows. For larger tables, the command displays the count and sort order, followed by the first 100 rows.

cryspy-print ./data/pkl_data/rslt_data.pkl --head 10
cryspy-print ./data/pkl_data/rslt_data.pkl --tail 5
cryspy-print ./data/pkl_data/rslt_data.pkl --all

These display the first ten rows, last five rows, or all rows of the table sorted by energy in ascending order. Use --no-sort to keep the stored row order. It can be combined with row selection.

cryspy-print ./data/pkl_data/rslt_data.pkl --no-sort --head 10

Filtering EA-vc Results by Composition

cryspy-print ./data/pkl_data/rslt_data.pkl -c 1 2 --head 10

This selects structures with a composition ratio of 1:2 in atype order and displays the first ten rows in ascending energy order. Atom counts such as (1, 2) and (2, 4) match the same ratio. Specify one non-negative integer per element, with at least one positive value. This option requires EA-vc results with a Num_atom column. A message is displayed if no structures match.

For an example with output, see Tutorial > EA-vc > Check Results > Checking Results for a Specific Composition.

Inspecting Gzip-Compressed Files

cryspy-print ./data/pkl_data/rslt_data.pkl.gz --head 10

The file is read without decompression beforehand. Other supported files can also be supplied in gzip-compressed form.

Regenerating Result Files

Run the following in the calculation directory containing cryspy.in.

cryspy-print ./data/pkl_data/rslt_data.pkl --write

This regenerates the following files, overwriting existing files.

./data/cryspy_rslt: Results in their stored row order.
./data/cryspy_rslt_energy_asc: Results sorted by Ef_eV_atom in ascending order, or E_eV_atom if the former column is absent.

Files are written to data/ under the directory where the command is run. This directory must exist. The operation is also recorded in log_cryspy.