Pymatgen Structure

pymatgen Structure Operations

Use this skill to perform structure preprocessing and analysis with pymatgen.

Scope

This skill should:

• require at least one user-provided structure file
• parse and normalize common structure formats
• perform requested geometry edits (for example supercell, substitution)
• run basic crystal analysis (for example symmetry, composition)
• write explicit output files and summarize key changes

This skill should not:

• submit HPC jobs
• run expensive DFT/MD production calculations
• invent missing scientific intent (for example random doping strategy) without confirmation

If the user asks for DFT submission, hand off to a submission skill such as dpdisp-submit after preprocessing is done.

Hard requirement

The user must provide an input structure source (file path or explicit coordinates + lattice).

If structure input is missing, stop and ask for it.

Supported input/output formats

Typical input formats:

• cif
• POSCAR / CONTCAR
• xyz (for non-periodic or when cell is provided separately)
• other formats supported by pymatgen IO backends

Typical output formats:

• cif
• POSCAR
• xyz
• optional JSON summaries

Expected workflow

• Read user-provided structure.
• Validate periodicity and cell information.
• Confirm requested operation (convert, supercell, substitution, analysis).
• Collect only missing critical parameters.
• Execute operation via pymatgen.
• Write output structure(s) and a short result summary.
• If requested, prepare handoff-ready files for downstream skills.

For concrete command patterns, see references/commands-and-workflow.md.

Operations this skill should handle

A) Format conversion

• convert between cif / POSCAR / xyz
• preserve lattice and species ordering when possible

B) Supercell construction

• apply scaling matrix, for example [[2,0,0],[0,2,0],[0,0,1]]
• report final atom count and new lattice vectors

C) Substitution / doping-like edits

• deterministic site substitution by species or by explicit site index
• report stoichiometry before/after
• ask user before applying random substitutions

D) Symmetry and composition analysis

• reduced formula
• lattice parameters
• space group symbol/number
• optional primitive/conventional standardization when explicitly requested

E) Local environment quick checks

• nearest-neighbor distances or coordination-style summaries
• report method/threshold assumptions

Parameters to collect

Must provide

• input structure path
• target operation type
• output path (or output naming rule)

Operation-specific

For format conversion:

• output format

For supercell:

• scaling matrix or (na, nb, nc)

For substitution:

• source species/site selection
• target species
• substitution fraction or exact indices

For symmetry analysis:

• symmetry tolerance (if non-default behavior is desired)

Required behavior

• Check file existence/readability before processing.
• Detect and report missing lattice info for periodic workflows.
• Do not silently drop atoms or reorder species without notice.
• Explicitly show assumptions (for example tolerance values).
• Return exact output file paths.

Defaulting policy

Allowed only for low-risk defaults, clearly labeled.

Reasonable defaults:

• symmetry tolerance defaults from pymatgen when user does not specify
• output basename derived from input name + operation suffix

Do not silently invent:

• lattice for periodic systems
• substitution ratio for doping tasks
• magnetic/electronic settings (outside this skill's scope)

Expected output

Provide:

• output file path(s)
• concise summary of changes (atom count, composition, lattice deltas)
• analysis result highlights (for example space group)
• explicit assumptions and unresolved choices
• next-step suggestion when user wants downstream DFT/MD submission

Common failure points

• unreadable input file or ambiguous format
• xyz input lacking periodic cell when periodic workflow is requested
• invalid scaling matrix or impossible substitution request
• too aggressive tolerances causing unstable symmetry classification