pymatgen-structure SKILL.md skillA
pymatgen-structure from jinzhezenggroup/computational-chemistry-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jinzhezenggroup/computational-chemistry-agent-skills/pymatgen-structure@v0.1.0Pins v0.1.0 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jinzhezenggroup/computational-chemistry-agent-skills
- Path
data-processing/pymatgen-structure/SKILL.md- Versions recorded
- 2
- Latest version
- v0.1.0, committed Mar 23, 2026
- First version recorded
- Mar 23, 2026
- Size
- 4,756 bytes
- Repository stars
- 156
- License
- LGPL-3.0
Structure manipulation and crystal analysis workflows based on pymatgen. USE WHEN you need to read/write common atomistic formats (CIF, POSCAR, XYZ), build supercells, perform site substitution/doping, inspect symmetry (space group), or compute local structure descriptors for materials tasks.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# 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` …
Read the whole file at its exact version.
How to install
mdr add jinzhezenggroup/computational-chemistry-agent-skills/pymatgen-structure@sha256:2c0700a85cb8a038The line at the top of this page pins the label v0.1.0, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_ozzs7pfjpxbojx7s)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 2 versions of this file, all committed on Mar 23, 2026.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v0.1.0 latest | 2026-03-23 | 622da72 | 4,756 B | A | view · diff |
| v0.1.0 | 2026-03-23 | 377b980 | 4,742 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (4756 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jinzhezenggroup/computational-chemistry-agent-skills · 156 stars · license LGPL-3.0 · pushed 2026-11-02 · branch master
API
GET https://markdownregistry.com/api/v1/artifacts/art_ozzs7pfjpxbojx7s GET https://markdownregistry.com/api/v1/resolve?ref=jinzhezenggroup/computational-chemistry-agent-skills/pymatgen-structure GET https://markdownregistry.com/api/v1/blob/2c0700a85cb8a0383145a1c6f39e71df830edad43fafd1fdd0e2cc41d9fef2a7
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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