Astropy
zLanqing/codex-claude-academic-skills
Comprehensive Python library for astronomy and astrophysics.
Agent skill
Pymatgen Structure
by jinzhezenggroup in jinzhezenggroup/computational-chemistry-agent-skills
Structure manipulation and crystal analysis workflows based on pymatgen.
Install Pymatgen Structure
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill pymatgen-structure -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills pymatgen-structure --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/data-processing/pymatgen-structure .claude/skills/pymatgen-structure && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "pymatgen-structure" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/pymatgen-structure into .claude/skills/pymatgen-structure/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pymatgen-structure", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/pymatgen-structureType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill pymatgen-structure -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills pymatgen-structure --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/data-processing/pymatgen-structure .agents/skills/pymatgen-structure && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "pymatgen-structure" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/pymatgen-structure into .agents/skills/pymatgen-structure/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pymatgen-structure", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill pymatgen-structure -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills pymatgen-structure --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/data-processing/pymatgen-structure .cursor/skills/pymatgen-structure && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "pymatgen-structure" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/pymatgen-structure into .cursor/skills/pymatgen-structure/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pymatgen-structure", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git --path data-processing/pymatgen-structure--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill pymatgen-structure -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills pymatgen-structure --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/data-processing/pymatgen-structure .gemini/skills/pymatgen-structure && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "pymatgen-structure" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/pymatgen-structure into .gemini/skills/pymatgen-structure/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pymatgen-structure", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills pymatgen-structureInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill pymatgen-structure -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/data-processing/pymatgen-structure .github/skills/pymatgen-structure && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "pymatgen-structure" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/pymatgen-structure into .github/skills/pymatgen-structure/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pymatgen-structure", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill pymatgen-structure -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills pymatgen-structure --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/data-processing/pymatgen-structure .opencode/skills/pymatgen-structure && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "pymatgen-structure" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/pymatgen-structure into .opencode/skills/pymatgen-structure/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pymatgen-structure", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
pymatgen-structure- GitHub stars
- 148
- Token cost
- ~1.2k tokens
- SKILL.md length
- 521 words
- Files
- 2 (incl. references)
- Skills in repo
- 62
- Repo updated
- First seen
- Licence
- LGPL-3.0-or-later
At a glance
Structure manipulation and crystal analysis workflows based on pymatgen.
- Works in 7 steps: Read user-provided structure. → Validate periodicity and cell information. → Confirm requested operation (convert,… → …
- You need to read/write common atomistic formats (CIF
- SKILL.md covers Scope, Hard requirement, Supported input/output formats and Expected workflow, plus 6 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Pymatgen Structure is an agent skill from jinzhezenggroup/computational-chemistry-agent-skills. 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.
Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files, including reference files (for example `references/commands-and-workflow.md`). Compatibility notes: Requires Python 3.10+ and pymatgen (recommended via uv).
It sits in Research & Science, covering Physical and earth sciences. The repository describes itself as: Agent skills to run computational-chemistry tasks, used in OpenClaw. The licence is LGPL-3.0-or-later.
When your agent uses it
- You need to read/write common atomistic formats (CIF
- Build supercells
- Perform site substitution/doping
- Inspect symmetry (space group)
Example prompts
- “/pymatgen-structure”
Requirements
- Python 3
- Compatibility (from SKILL.md): Requires Python 3.10+ and pymatgen (recommended via uv).
Workflow steps
7 steps, taken from the first numbered list in SKILL.md.
- 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.
What it can do on your machine
Read from SKILL.md and the folder at commit 5c19e75. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md.
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Compatibility
Requires Python 3.10+ and pymatgen (recommended via uv).
From compatibility in the SKILL.md frontmatter.
Context cost
Pymatgen Structure loads about 1.2k tokens when it runs, and up to ~1.9k if it reads all its reference files. Until then it costs about 78 tokens; SKILL.md has 521 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from jinzhezenggroup/computational-chemistry-agent-skills at commit 5c19e75, republished under its LGPL-3.0-or-later licence (© jinzhezenggroup). 521 words, ~1,189 tokens.
Download SKILL.mdSave it as
.claude/skills/pymatgen-structure/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.- name
- pymatgen-structure
- description
- 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.
- compatibility
- Requires Python 3.10+ and pymatgen (recommended via uv).
- license
- LGPL-3.0-or-later
- metadata.author
- qqgu
- metadata.version
- 0.1.0
- metadata.repository
- https://github.com/materialsproject/pymatgen
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:
cifPOSCAR/CONTCARxyz(for non-periodic or when cell is provided separately)- other formats supported by
pymatgenIO backends
Typical output formats:
cifPOSCARxyz- 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
Show full SKILL.md (214 more words)Show less
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
pymatgenwhen 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
© jinzhezenggroup, LGPL-3.0-or-later. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 1 other file (references) in data-processing/pymatgen-structure of jinzhezenggroup/computational-chemistry-agent-skills.
- SKILL.md
- references/commands-and-workflow.md
Open the folder on GitHubat commit 5c19e75
Compare with similar skills
Pymatgen Structure next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Pymatgen Structure this skilljinzhezenggroup/computational-chemistry-agent-skills | 148 | — | ~1.2k | Automated safety check: Pass | LGPL-3.0-or-later | |
| AstropyzLanqing/codex-claude-academic-skills | 4.7k | 13 repos | ~2.9k | Automated safety check: Pass | BSD-3-Clause | |
| PymatgenzLanqing/codex-claude-academic-skills | 4.7k | 11 repos | ~5k | Automated safety check: Pass | MIT | |
| Cantera Ignition DelayK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~2.2k | Automated safety check: Pass | MIT | |
| Weathertrpc-group/trpc-agent-go | 1.9k | 8 repos | ~591 | Automated safety check: Pass | Apache-2.0 | |
| Pymol VisualizationChatMol/ChatMol | 373 | — | ~1.2k | Automated safety check: Pass | MIT |
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Related
Categories
Questions about Pymatgen Structure
What does Pymatgen Structure do?
Structure manipulation and crystal analysis workflows based on pymatgen. Pymatgen Structure is an agent skill from jinzhezenggroup/computational-chemistry-agent-skills. Structure manipulation and crystal analysis workflows based on pymatgen.
When should I use Pymatgen Structure?
Pymatgen Structure fits situations like: you need to read/write common atomistic formats (CIF; build supercells; perform site substitution/doping; inspect symmetry (space group).
How do I install Pymatgen Structure in Claude Code?
Run `npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill pymatgen-structure -a claude-code`. Or copy the skill folder (data-processing/pymatgen-structure in jinzhezenggroup/computational-chemistry-agent-skills) into .claude/skills/pymatgen-structure in your project. Claude Code loads it when a task matches its description.
How do I install Pymatgen Structure in Codex?
Run `npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill pymatgen-structure -a codex`. Or copy the skill folder (data-processing/pymatgen-structure in jinzhezenggroup/computational-chemistry-agent-skills) into .agents/skills/pymatgen-structure in your project. Codex loads it when a task matches its description.
Can I use Pymatgen Structure in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill pymatgen-structure -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/pymatgen-structure, .gemini/skills/pymatgen-structure, .github/skills/pymatgen-structure and .opencode/skills/pymatgen-structure in your project.
What does Pymatgen Structure need to run?
SKILL.md names no scripts, command-line tools or credentials: Pymatgen Structure is instructions for the agent only. Our summary lists: Python 3. Compatibility (from SKILL.md): Requires Python 3.10+ and pymatgen (recommended via uv)..
Does Pymatgen Structure access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Pymatgen Structure safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Pymatgen Structure use?
Pymatgen Structure is published under the LGPL-3.0-or-later licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Pymatgen Structure use?
About 1.2k tokens (SKILL.md is roughly 4.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 713 tokens, read only when the agent opens those files.
What are the alternatives to Pymatgen Structure?
Skills that share tags, products or a category with Pymatgen Structure: Astropy (zLanqing/codex-claude-academic-skills, 4.7k stars), Pymatgen (zLanqing/codex-claude-academic-skills, 4.7k stars), Cantera Ignition Delay (K-Dense-AI/scientific-agent-skills, 48k stars) and Weather (trpc-group/trpc-agent-go, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Pymatgen Structure?
jinzhezenggroup (a GitHub organization) maintains it in jinzhezenggroup/computational-chemistry-agent-skills, which has 148 GitHub stars. The repository holds 62 skills in this directory. The repository was last updated on October 9, 2026.
Source: jinzhezenggroup/computational-chemistry-agent-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.