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Read and validate atomic structures — summarize a file, dump raw text, measure inter-atomic distances, detect overlapping atoms.
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基于 SOC 职业分类
Build common bulk crystal structures (FCC/BCC/HCP/diamond/zincblende/...) using ASE.
Build a coherent lattice-matched interface between two bulk structures using the pymatgen ZSL algorithm.
Workflow, lattice-matching strategies, and pitfalls for building interfaces between two crystals/surfaces.
Strategies for searching, filtering, and downloading structures from the Materials Project (MP) database.
Workflow for building Metal-Organic Framework (MOF) structures (MOF-5, Cu-BTC, IRMOF series, custom).
Methods for building isolated molecules (ASE database, SMILES via RDKit, organometallics, endohedral cages, NEB pathways).
| name | structure-inspect |
| description | Read and validate atomic structures — summarize a file, dump raw text, measure inter-atomic distances, detect overlapping atoms. |
| when_to_use | Use to confirm what is in a structure file before / after another step (atom count, formula, cell, PBC), to measure a specific bond distance, or to flag unrealistic close contacts. |
| entry | scripts/structure_inspect.py |
Four CLI sub-commands for reading and checking structure files (no writes):
read_structure — formula, num atoms, cell, PBC, full atom list if ≤ 10 atoms.read_structures_in_text— raw file contents (text formats only).calculate_distance — distance between two atom indices.check_close_atoms — pairs whose distance is below covalent_radii_sum + tolerance.python3 scripts/structure_inspect.py read_structure --folder . --file-name Fe_bcc.extxyz
python3 scripts/structure_inspect.py calculate_distance --folder . --file-name slab.extxyz --index1 0 --index2 5
python3 scripts/structure_inspect.py check_close_atoms --folder . --file-name slab.extxyz --tolerance -0.3
folder may be "." to use the sandbox root. Large CIF files (> 1 MB) are
parsed via pymatgen.io.cif.CifParser to avoid ASE's slow path.