Mat Lammps Md
learningmatter-mit/AtomisticSkills
Build and run LAMMPS molecular dynamics with isolated MLIP-specific binaries (MACE, MatGL/CHGNet, FairChem) to avoid Python and Torch stack conflicts.
DeePMD-kit and Deep Potential Molecular Dynamics workflows. An agent skill from JCLiuGroup/AI-Computational-Chemist.
Install Deepmd
$ npx skills add JCLiuGroup/AI-Computational-Chemist --skill deepmd -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist deepmd --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/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .claude/skills && cp -r skills-src/tools/deepmd .claude/skills/deepmd && 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 "deepmd" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/deepmd into .claude/skills/deepmd/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deepmd", 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/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/deepmdType 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 JCLiuGroup/AI-Computational-Chemist --skill deepmd -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist deepmd --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .agents/skills && cp -r skills-src/tools/deepmd .agents/skills/deepmd && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "deepmd" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/deepmd into .agents/skills/deepmd/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deepmd", 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 JCLiuGroup/AI-Computational-Chemist --skill deepmd -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist deepmd --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/tools/deepmd .cursor/skills/deepmd && 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 "deepmd" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/deepmd into .cursor/skills/deepmd/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deepmd", 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/JCLiuGroup/AI-Computational-Chemist.git --path tools/deepmd--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 JCLiuGroup/AI-Computational-Chemist --skill deepmd -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist deepmd --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/tools/deepmd .gemini/skills/deepmd && 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 "deepmd" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/deepmd into .gemini/skills/deepmd/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deepmd", 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 JCLiuGroup/AI-Computational-Chemist deepmdInstalls 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 JCLiuGroup/AI-Computational-Chemist --skill deepmd -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .github/skills && cp -r skills-src/tools/deepmd .github/skills/deepmd && 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 "deepmd" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/deepmd into .github/skills/deepmd/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deepmd", 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 JCLiuGroup/AI-Computational-Chemist --skill deepmd -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install JCLiuGroup/AI-Computational-Chemist deepmd --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/JCLiuGroup/AI-Computational-Chemist.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/tools/deepmd .opencode/skills/deepmd && 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 "deepmd" agent skill from https://github.com/JCLiuGroup/AI-Computational-Chemist/tree/main/tools/deepmd into .opencode/skills/deepmd/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deepmd", 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
deepmd- GitHub stars
- 143
- Used in
- 1 other repo
- Token cost
- ~780 tokens
- SKILL.md length
- 297 words
- Files
- 11 (incl. scripts, references)
- Skills in repo
- 21
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
DeePMD-kit and Deep Potential Molecular Dynamics workflows. An agent skill from JCLiuGroup/AI-Computational-Chemist.
- Works in 4 steps: Define the production domain,… → Convert and split data, configure… → Apply references/validation.md and… → …
- Dpdata dataset conversion from VASP/CP2K
- SKILL.md covers Required inputs, Route map, Workflow and Hard guardrails
- Runs Python scripts from its folder
What it does
Deepmd is an agent skill from JCLiuGroup/AI-Computational-Chemist. DeePMD-kit and Deep Potential Molecular Dynamics workflows. Use for dpdata dataset conversion from VASP/CP2K, DeepMD input.json setup, dp train/freeze/compress/test, DP descriptor PCA/t-SNE dataset-distribution visualization, DP model deviation, DPLibrary reuse checks, and LAMMPS DPMD deployment.
Its SKILL.md is about 780 tokens, which your agent loads only when the skill is triggered. The skill folder holds 13 other files, including scripts and reference files (for example `examples/README.md`, `references/dataset-embedding.md` and `references/errors.md`).
It sits in Research & Science, covering Physical and earth sciences and Deployment.
When your agent uses it
- Dpdata dataset conversion from VASP/CP2K
- DeepMD input.json setup
- Dp train/freeze/compress/test
- DP descriptor PCA/t-SNE dataset-distribution visualization
Example prompts
- “/deepmd”
Requirements
- Python 3
Workflow steps
4 steps, taken from the first numbered list in SKILL.md.
- Define the production domain, assemble/filter labels according to
- Convert and split data, configure input.json, then use
- Apply references/validation.md and scripts/check_deepmd_qa.py; expand data or
- Hand a passing or explicitly waived model to LAMMPS DPMD through hpc-submit, then
What it can do on your machine
Read from SKILL.md and the folder at commit e27b555. 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
Ships 4 files in scripts/ (Python), which the agent can run.
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.
Context cost
Deepmd loads about 780 tokens when it runs, and up to ~11k if it reads all its reference files. Until then it costs about 76 tokens; SKILL.md has 297 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); the scripts in this folder are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 297 words (~780 tokens).
- name
- deepmd
Files
SKILL.md and 10 other files (scripts, references) in tools/deepmd of JCLiuGroup/AI-Computational-Chemist.
- SKILL.md
- examples/README.md
- references/dataset-embedding.md
- references/errors.md
- references/resources.md
- references/running.md
- references/validation.md
- scripts/check_deepmd_qa.py
- scripts/deepmd_descriptor_pca.py
- scripts/plot_deepmd_postprocess.py
- scripts/run_deepmd_chain.py
Open the folder on GitHubat commit e27b555
Used in 1 other repository
We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in JCLiuGroup/AI-Computational-Chemist, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Deepmd 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 |
|---|---|---|---|---|---|---|
| Deepmd this skillJCLiuGroup/AI-Computational-Chemist | 143 | 1 repos | ~780 | Automated safety check: Pass | Custom licence | |
| Mat Lammps Mdlearningmatter-mit/AtomisticSkills | 175 | — | ~1.2k | Automated safety check: Pass | MIT | |
| Embodied AI NewsLeoYeAI/openclaw-master-skills | 2.2k | — | ~4.8k | Automated safety check: Pass | MIT | |
| Sensys Reproducibilitybrycewang-stanford/Awesome-Journal-Skills | 1.2k | — | ~1.2k | Automated safety check: Pass | MIT | |
| Sigcomm Experimentsbrycewang-stanford/Awesome-Journal-Skills | 1.2k | — | ~988 | Automated safety check: Pass | MIT | |
| AstropyzLanqing/codex-claude-academic-skills | 4.6k | 14 repos | ~2.9k | Automated safety check: Pass | BSD-3-Clause |
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Aggregates publicly available Embodied AI and Robotics news from curated sources (robotics media, arXiv, company blogs).
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Astropy
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Entry point and controller for computational chemistry and materials workflows.
Cp2k
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Prepare, validate, run, and troubleshoot CP2K calculations for periodic and large molecular systems.
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Prepare, validate, run, resume, troubleshoot, and analyze GROMACS molecular dynamics.
Hpc Submit
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Related
Questions about Deepmd
What does Deepmd do?
DeePMD-kit and Deep Potential Molecular Dynamics workflows. An agent skill from JCLiuGroup/AI-Computational-Chemist. Deepmd is an agent skill from JCLiuGroup/AI-Computational-Chemist. DeePMD-kit and Deep Potential Molecular Dynamics workflows.
When should I use Deepmd?
Deepmd fits situations like: dpdata dataset conversion from VASP/CP2K; deepMD input.json setup; dp train/freeze/compress/test; DP descriptor PCA/t-SNE dataset-distribution visualization.
How do I install Deepmd in Claude Code?
Run `npx skills add JCLiuGroup/AI-Computational-Chemist --skill deepmd -a claude-code`. Or copy the skill folder (tools/deepmd in JCLiuGroup/AI-Computational-Chemist) into .claude/skills/deepmd in your project. Claude Code loads it when a task matches its description.
How do I install Deepmd in Codex?
Run `npx skills add JCLiuGroup/AI-Computational-Chemist --skill deepmd -a codex`. Or copy the skill folder (tools/deepmd in JCLiuGroup/AI-Computational-Chemist) into .agents/skills/deepmd in your project. Codex loads it when a task matches its description.
Can I use Deepmd 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 JCLiuGroup/AI-Computational-Chemist --skill deepmd -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/deepmd, .gemini/skills/deepmd, .github/skills/deepmd and .opencode/skills/deepmd in your project.
What does Deepmd need to run?
Going by SKILL.md and its folder, Deepmd needs Python for the scripts in its folder. Our summary lists: Python 3.
Does Deepmd 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 Deepmd 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Deepmd use?
Deepmd has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Deepmd use?
About 780 tokens (SKILL.md is roughly 3.1k 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 10k tokens, read only when the agent opens those files.
What are the alternatives to Deepmd?
Skills that share tags, products or a category with Deepmd: Mat Lammps Md (learningmatter-mit/AtomisticSkills, 175 stars), Embodied AI News (LeoYeAI/openclaw-master-skills, 2.2k stars), Sensys Reproducibility (brycewang-stanford/Awesome-Journal-Skills, 1.2k stars) and Sigcomm Experiments (brycewang-stanford/Awesome-Journal-Skills, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Deepmd?
JCLiuGroup (a GitHub organization) maintains it in JCLiuGroup/AI-Computational-Chemist, which has 143 GitHub stars. The repository holds 21 skills in this directory. The repository was last updated on September 27, 2026.
Source: JCLiuGroup/AI-Computational-Chemist on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.