Mmcp.market

pymatgen skill

by K-Dense-AI·K-Dense-AI/scientific-agent-skills·47k stars·MIT

Analyze, validate, convert, and transform materials structures and computed materials data with current pymatgen APIs, including local phase diagrams, symmetry sensitivity, electronic-structure I/O, and explicitly bounded Materials Project queries.

A100/100content scan

Is the pymatgen skill safe?

Clean: nothing in its files matched our rules. We read 15 files in the folder on 2026-09-28.

No findings.

Install the pymatgen skill

A skill is a folder. Copy it into your agent's skills folder and the agent loads it when the task matches its description. 

git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git /tmp/scientific-agent-skills
mkdir -p ~/.claude/skills
cp -r /tmp/scientific-agent-skills/skills/pymatgen ~/.claude/skills/pymatgen
available in every project

In the Claude apps, zip the folder and upload it from the Skills settings. The folder on GitHub

The instructions your agent would load

SKILL.md as published, without the frontmatter. Read it on GitHub

pymatgen

Use pymatgen for explicit, provenance-preserving work with compositions, molecules, periodic structures, computed entries, symmetry, phase diagrams, electronic structures, and electronic-structure-code files. Treat every parse, conversion, symmetry assignment, transformation, and database result as method- and parameter-dependent.

The MIT frontmatter license covers this skill. pymatgen and pymatgen-core are MIT; mp-api declares BSD-3-Clause-LBNL. Materials Project data is generally CC BY 4.0, while contributed data remains owned by its contributors. Check the exact artifact and data terms before redistribution.

Verified snapshot (2026-07-23)

Package metadata requires Python 3.11+ and directly requires pymatgen-core>=2026.4.16.

  • pymatgen==2026.5.4 is the latest stable wrapper release (2026-05-04).

It now contains core objects, symmetry/lattice operations, and the I/O layer, all under the existing pymatgen.* namespace.

  • pymatgen-core==2026.7.16 is the latest stable core release (2026-07-16).

(2026-06-15), requires Python 3.11+, and depends on pymatgen>2024.2.20.

  • mp-api==0.46.4 is the latest stable Materials Project client

distributions prevents pymatgen==2026.5.4 from silently resolving to a different future core.

  • The current API site is built from 2026.7.16 core documentation. Pinning both

infer semantic-version compatibility from the numbers.

  • Pymatgen uses date-based versions. PyPI renders the date with dots; do not

Create a project lock for reproducibility:

uv init --python 3.11
uv add "pymatgen==2026.5.4" "pymatgen-core==2026.7.16" "mp-api==0.46.4"
uv lock
uv sync --frozen

For a disposable reviewed environment:

uv venv --python 3.11 .venv-pymatgen
uv pip install --python .venv-pymatgen/bin/python \
  "pymatgen==2026.5.4" "pymatgen-core==2026.7.16" "mp-api==0.46.4"

Direct pins do not freeze all transitive wheels. Preserve uv.lock, platform, Python version, package versions, and artifact hashes.

Required workflow

Structure; record lattice and periodic boundary conditions.

  1. State whether the object is a non-periodic Molecule or periodic

g/cm³, but each API's documented contract is authoritative.

  1. State units. Pymatgen commonly uses Å, degrees, eV, eV/atom, amu, and

coordsarecartesian=True; Molecule coordinates are Cartesian.

  1. State coordinate mode. Structure coordinates are fractional unless

stoichiometry, and correction warnings; do not silently accept fixes.

  1. Inspect every parser warning. For CIF, preserve occupancy, site-merging,

guess oxidation states implicitly.

  1. Report disorder/partial occupancies and oxidation-state decoration. Never

thermodynamic analysis.

  1. Run validation before symmetry, neighbor, transformation, conversion, or

angle_tolerance in degrees with every assignment.

  1. Sweep symmetry tolerances and report symprec in Å and

software versions, warnings, and parent/child checksums.

  1. Treat transformations as new artifacts. Preserve the input, parameters,

and round-trip-check scientifically relevant properties.

  1. Before conversion, identify representation loss. Write only to a new path

schemes. A computed hull is conditional on the supplied entry set.

  1. Build phase diagrams only from compatible total energies and correction

fields, result limit, cache behavior, output, license, and citation before an explicit execution step.

  1. Keep all database access off by default. Disclose endpoint, filters,

general object graph; use schema-validated JSON and explicit constructors.

  1. Preserve an artifact manifest. Never use pickle or load an untrusted

Core objects

Use the public convenience imports:

from pymatgen.core import Composition, Element, Lattice, Molecule, Structure

composition = Composition("LiFePO4", strict=True)
iron = Element("Fe")

lattice = Lattice.cubic(5.64)  # Å
structure = Structure(
    lattice,
    ["Na", "Cl"],
    [[0, 0, 0], [0.5, 0.5, 0.5]],
    coords_are_cartesian=False,
    validate_proximity=True,
)

molecule = Molecule(
    ["O", "H", "H"],
    [[0.0, 0.0, 0.0], [0.758, 0.0, 0.504], [-0.758, 0.0, 0.504]],
    charge=0,
    spin_multiplicity=1,
)

Structure and Molecule are mutable; use IStructure/IMolecule or an explicit copy when mutation would compromise provenance. See core classes.

Safe local structure intake

Prefer the bundled validator, which captures CIF and Python warnings and reports units, occupancy, disorder, oxidation states, periodicity, coordinate mode, and minimum distances:

python scripts/composition_structure_validator.py composition "Fe2O3"
python scripts/composition_structure_validator.py structure structure.cif
python scripts/structure_analyzer.py structure.cif --symmetry

For direct CIF work, use the current parser method and inspect both warning channels:

import warnings
from pymatgen.io.cif import CifParser

with warnings.catch_warnings(record=True) as caught:
    warnings.simplefilter("always")
    parser = CifParser("input.cif", check_cif=True)
    structures = parser.parse_structures(
        primitive=False,
        check_occu=True,
        on_error="raise",
    )

parser_messages = list(parser.warnings)
python_messages = [str(item.message) for item in caught]

Do not parse untrusted files in a privileged process. A critical malicious-CIF code-execution flaw affected pymatgen through 2024.2.8 and was fixed in 2024.2.20; the pinned release is newer, but parsers still process attacker controlled input. Use isolation and CPU/RAM/disk/time limits.

Symmetry

Space-group assignment depends on tolerances and structure quality:

from pymatgen.symmetry.analyzer import SpacegroupAnalyzer

analyzer = SpacegroupAnalyzer(
    structure,
    symprec=0.01,          # Å
    angle_tolerance=5.0,   # degrees
)
symbol = analyzer.get_space_group_symbol()
number = analyzer.get_space_group_number()

The Materials Project pipeline commonly uses symprec=0.1 Å, while pymatgen's documented default is 0.01 Å; these can produce different assignments. Generate a sensitivity report instead of changing tolerance until a preferred answer appears:

python scripts/symmetry_sensitivity_report.py structure.cif \
  --symprec 0.001,0.01,0.1 --angle-tolerance 1,5

See analysis modules.

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