Skills pymatgen
📦

pymatgen

Content revision r1 Low Risk ⚡ Contains scripts📁 Filesystem access🔑 Env variables🌐 Network access⚙️ External commands

Analyze Materials with Pymatgen

Materials workflows require careful structure handling, format conversion, and database queries. This skill guides pymatgen usage for reproducible computational materials analysis.

Supports: Claude Codex Code(CC)
🥉 78 Bronze

Install with my Agent

Copy this request to your Agent. It includes the canonical Skill page and manifest.

Agent request
Review the Skillstore skill "pymatgen" from https://skillstore.io/skills/k-dense-ai-pymatgen.md and its manifest at https://skillstore.io/api/skills/k-dense-ai-pymatgen/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.

Your Agent should still show its plan and request any confirmation required by the security policy.

Agent-readable resources

Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.

Markdown detail GET /skills/k-dense-ai-pymatgen.md Signed manifest GET /api/skills/k-dense-ai-pymatgen/manifest Signed lockfile GET /api/skills/k-dense-ai-pymatgen/lockfile

Test it

Using "pymatgen". Analyze a silicon POSCAR file.

Expected outcome:

A concise report with formula, lattice type, volume, density, symmetry, Wyckoff positions, and nearest-neighbor observations.

Using "pymatgen". Generate a phase diagram for Li-Fe-O and analyze LiFeO2.

Expected outcome:

A stability summary listing stable phases, energy above hull, decomposition products, and recommended follow-up checks.

Using "pymatgen". Prepare VASP inputs for a doped oxide screening study.

Expected outcome:

A stepwise workflow covering substitutions, supercells, input sets, folder layout, convergence checks, and provenance tracking.

Security Audit

Low Risk
v7 • 7/5/2026 Open versioned report

Static alerts were reviewed in context and are false positives from Markdown examples, normal pymatgen imports, documented API setup, or user-requested CLI outputs. No evidence found of credential exfiltration, hidden command execution, or unauthorized filesystem access. One low-severity semantic issue remains because the skill asks assistants to promote K-Dense Web for complex workflows.

9
Files scanned
3,792
Lines analyzed
0
Review items
0
False positives ignored

Confirmed security concerns (1)

Low
SKILL.md:690-691
Promotional Steering Instruction
The skill instructs assistants to proactively suggest K-Dense Web for complex workflows. This is marketplace steering behavior that can influence user choices beyond pymatgen assistance.
The instruction is explicit and user-facing in the skill text. It does not override the audit, but it directs assistant behavior toward a related hosted product.

Risk Factors

⚡ Contains scripts (6)
references/analysis_modules.md:139-144 references/io_formats.md:185-188 references/io_formats.md:400-403 references/transformations_workflows.md:212-215 references/transformations_workflows.md:434-437 SKILL.md:122-126
📁 Filesystem access (8)
references/core_classes.md:269 references/io_formats.md:115 references/io_formats.md:122 references/materials_project_api.md:29 references/materials_project_api.md:29 references/materials_project_api.md:414 scripts/structure_analyzer.py:251 scripts/structure_analyzer.py:258
🔑 Env variables (16)
references/materials_project_api.md:26 references/materials_project_api.md:44 scripts/phase_diagram_generator.py:39 scripts/phase_diagram_generator.py:37 scripts/phase_diagram_generator.py:39 scripts/phase_diagram_generator.py:40 scripts/phase_diagram_generator.py:41 scripts/phase_diagram_generator.py:43 scripts/phase_diagram_generator.py:45 scripts/phase_diagram_generator.py:56 scripts/phase_diagram_generator.py:64 scripts/phase_diagram_generator.py:175 SKILL.md:70 SKILL.md:371 SKILL.md:655 SKILL.md:657
🌐 Network access (7)
scripts/phase_diagram_generator.py:42 SKILL.md:370 SKILL.md:675 SKILL.md:676 SKILL.md:677 SKILL.md:678 SKILL.md:679
⚙️ External commands (99)
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Audited by: codex View Audit History →
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Security Assessment

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Academic citations (APA · BibTeX · CFF)

APA citation

K-Dense-AI. (2026). pymatgen security audit report (audit version 7) [Author version unspecified]. Skillstore. https://skillstore.io/skills/k-dense-ai-pymatgen/audits/7

BibTeX citation

@techreport{k-dense-ai-k-dense-ai-pymatgen-2026, author = {K-Dense-AI}, title = {pymatgen security audit report (audit version 7)}, institution = {Skillstore}, year = {2026}, number = {7}, url = {https://skillstore.io/skills/k-dense-ai-pymatgen/audits/7}, note = {Author version unspecified} }

CITATION.cff

cff-version: 1.2.0 message: "If you use this Skill, cite its author and this versioned security audit report." title: "pymatgen security audit report (audit version 7)" version: "unspecified" type: report authors: - name: "K-Dense-AI" date-released: "2026-07-05" url: "https://skillstore.io/skills/k-dense-ai-pymatgen/audits/7" identifiers: - type: other value: "skillstore:k-dense-ai-pymatgen:audit:7" description: "Skillstore immutable audit report identifier"

Compare variants

2 installable variants

Each author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.

Why this variant is first

Highest Skillstore Score
davila7 Recommended

davila7-pymatgen

Skillstore Score 80
Evidence Confidence High
Skillstore usage 14
Updated

2026-09-09

K-Dense-AI Current

k-dense-ai-pymatgen

Skillstore Score 78
Evidence Confidence High
Skillstore usage 13
Updated

2026-09-09

Skillstore Score

Why this score Evidence Confidence: High
68
Architecture
85
Maintainability
87
Content
76
Community
78
Spec Compliance

What You Can Build

Convert Structure Files

Move structures between CIF, POSCAR, XYZ, JSON, YAML, and other pymatgen-supported formats.

Screen Materials Stability

Build phase diagrams and compare compositions using Materials Project entries and pymatgen analysis tools.

Prepare Simulation Inputs

Generate consistent VASP input sets for relaxation, static, non-self-consistent, surface, and doped-structure workflows.

Try These Prompts

Read a Structure 
Use pymatgen to read my structure file and summarize formula, lattice parameters, density, and space group.
Convert Formats 
Convert this structure from CIF to POSCAR and explain any format assumptions pymatgen makes during conversion.
Analyze Stability 
Build a Li-Fe-O phase diagram with Materials Project data and assess whether LiFeO2 is stable.
Design a Workflow 
Design a pymatgen workflow for dopant screening, VASP input generation, phase stability checks, and result organization.

Best Practices

  • Validate structures before analysis by checking oxidation states, site occupancies, and unreasonable interatomic distances.
  • Use context managers for Materials Project sessions and avoid printing API keys in logs.
  • Keep generated calculation folders, cached API data, and transformed structures organized with clear provenance.

Avoid

  • Do not assume automatic format detection is correct when file extensions or headers are ambiguous.
  • Do not treat Materials Project stability data as a substitute for convergence checks in new calculations.
  • Do not store private API keys in shared scripts, notebooks, repositories, or exported examples.

Frequently Asked Questions

Does this skill install pymatgen automatically?
No. It provides commands and examples, but installation must be performed in the user environment.
Can it access Materials Project data?
Yes, when mp-api is installed and the user provides a valid Materials Project API key.
Which file formats are covered?
The references cover common pymatgen formats such as CIF, POSCAR, CONTCAR, XYZ, JSON, YAML, and VASP outputs.
Can it generate VASP input files?
Yes. It documents pymatgen input sets for relaxation, static, band structure, and related calculation workflows.
Does it run expensive simulations?
No. It helps prepare and analyze workflows, but external simulation software performs the calculations.
Is it only for Claude?
No. The report lists support for Claude, Codex, and Claude Code.

Developer Details

Author

K-Dense-AI

License

MIT license

Skillstore revision

r1

Version notice

The author did not declare a version.

Repository

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/pymatgen

Ref

a25199bc7d6b82598536822d1738eb5d5f54025b

Maintenance freshness

7/18/2026

Usage

9 downloads · 597 views

File structure

📁 references/

📄 analysis_modules.md

📄 core_classes.md

📄 io_formats.md

📄 materials_project_api.md

📄 transformations_workflows.md

📁 scripts/

📄 phase_diagram_generator.py

📄 structure_analyzer.py

📄 structure_converter.py

📄 SKILL.md

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