structure-conversion

name	structure-conversion
description	Convert crystal structure files between extxyz and CIF, including splitting multi-frame extxyz into per-frame CIF files.
metadata	{"tools":["run_python_file"],"tags":["structure","conversion","extxyz","cif","ASE"]}

Overview

Use the CLI script structure_conversion_tools.py (located alongside this file) to convert structure files between extxyz and cif. It mirrors the behavior of the former ase_structure_convert_tool and is especially useful for turning MatterGen multi-frame extxyz outputs into per-frame cif files.

Every command writes a JSON object to stdout and exits 0 on success or 1 on error. Always parse the JSON output and confirm "status": "success".

python skills/structure_conversion/structure_conversion_tools.py convert <input_file> <output_path> [options]

Supported Conversions

• cif -> extxyz
• single-frame extxyz or xyz -> single cif
• multi-frame extxyz or xyz -> directory of per-frame cif files
• extxyz or xyz -> extxyz

For multi-frame extxyz input, never collapse all frames into one cif. Write one cif file per frame using stable names such as frame_000001.cif.

Command

convert

Convert a structure file and return output metadata.

Positional arguments

Argument	Description
input_file	Source structure path. Supported: .extxyz, .xyz, .cif
output_path	Output file path or output directory

Optional arguments

Flag	Type	Description
--output-format	str	Explicit target format: cif or extxyz. If omitted, infer from output_path

JSON response fields

status, message, output_mode, output_format, frame_count, output_path, output_paths

Recommended Behavior

• Prefer directory outputs when converting multi-frame extxyz to cif
• Always return absolute paths
• Report the output mode, frame count, output directory or file, and all generated paths
• Surface exact parsing or conversion errors from ASE

Examples

# Multi-frame extxyz to per-frame CIF directory
python skills/structure_conversion/structure_conversion_tools.py convert \
    generated.extxyz converted_cifs --output-format cif

# Single CIF to extxyz
python skills/structure_conversion/structure_conversion_tools.py convert \
    structure.cif structure.extxyz

Notes

• This skill is commonly used after mattergen generation and before downstream property prediction
• If output_format is omitted, the script infers it from output_path
• If the input contains multiple frames and the target is cif, the result is a directory, not a single file