Agent skill

Lammps Deepmd

Run LAMMPS molecular dynamics with DeePMD-kit machine learning potentials.

AGPL-3.0Auto-check passedData & Analytics

Install Lammps Deepmd

skills CLI

$ npx skills add Hello-QM/catgo-LRG --skill lammps-deepmd -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG lammps-deepmd --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/Hello-QM/catgo-LRG.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.claude/skills/lammps-deepmd .claude/skills/lammps-deepmd && rm -rf skills-src

Use ~/.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/

Paste into Claude Code

Install the "lammps-deepmd" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/lammps-deepmd into .claude/skills/lammps-deepmd/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "lammps-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

$skill-installer install https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/lammps-deepmd

Type 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.

skills CLI

$ npx skills add Hello-QM/catgo-LRG --skill lammps-deepmd -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG lammps-deepmd --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/Hello-QM/catgo-LRG.git skills-src && mkdir -p .agents/skills && cp -r skills-src/.claude/skills/lammps-deepmd .agents/skills/lammps-deepmd && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "lammps-deepmd" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/lammps-deepmd into .agents/skills/lammps-deepmd/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "lammps-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.

skills CLI

$ npx skills add Hello-QM/catgo-LRG --skill lammps-deepmd -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG lammps-deepmd --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/Hello-QM/catgo-LRG.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/.claude/skills/lammps-deepmd .cursor/skills/lammps-deepmd && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "lammps-deepmd" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/lammps-deepmd into .cursor/skills/lammps-deepmd/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "lammps-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

$ gemini skills install https://github.com/Hello-QM/catgo-LRG.git --path .claude/skills/lammps-deepmd

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add Hello-QM/catgo-LRG --skill lammps-deepmd -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG lammps-deepmd --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/Hello-QM/catgo-LRG.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/.claude/skills/lammps-deepmd .gemini/skills/lammps-deepmd && rm -rf skills-src

Use ~/.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/

Paste into Gemini CLI

Install the "lammps-deepmd" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/lammps-deepmd into .gemini/skills/lammps-deepmd/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "lammps-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.

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG lammps-deepmd

Installs 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).

skills CLI

$ npx skills add Hello-QM/catgo-LRG --skill lammps-deepmd -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/Hello-QM/catgo-LRG.git skills-src && mkdir -p .github/skills && cp -r skills-src/.claude/skills/lammps-deepmd .github/skills/lammps-deepmd && rm -rf skills-src

Use ~/.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/

Paste into GitHub Copilot

Install the "lammps-deepmd" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/lammps-deepmd into .github/skills/lammps-deepmd/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "lammps-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.

skills CLI

$ npx skills add Hello-QM/catgo-LRG --skill lammps-deepmd -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG lammps-deepmd --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/Hello-QM/catgo-LRG.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/.claude/skills/lammps-deepmd .opencode/skills/lammps-deepmd && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "lammps-deepmd" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/lammps-deepmd into .opencode/skills/lammps-deepmd/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "lammps-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: lammps-deepmd
GitHub stars: 205
Used in: 1 other repo
Token cost: ~1k tokens
SKILL.md length: 323 words
Files: 1
Skills in repo: 75
Repo updated: Sep 22, 2026
First seen: Oct 7, 2026
Licence: AGPL-3.0

At a glance

Run LAMMPS molecular dynamics with DeePMD-kit machine learning potentials.

Works in 3 steps: Verify structure → Create workflow → Add LAMMPS task
The user wants MD simulations driven by a trained DP model
SKILL.md covers When to Use, Prerequisites, Workflow Steps and LAMMPS Input Template — NVT, plus 5 more sections
Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Lammps Deepmd is an agent skill from Hello-QM/catgo-LRG. Run LAMMPS molecular dynamics with DeePMD-kit machine learning potentials. Use when the user wants MD simulations driven by a trained DP model.

Its SKILL.md is about 1k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts. Compatibility notes: Requires LAMMPS compiled with the DEEPMD package. A frozen DeePMD model (.pb) is required.

It sits in Data & Analytics, covering Physical and earth sciences and Machine learning. The repository describes itself as: AI-driven workbench for computational materials science — interactive 3D structure viewer, natural-language CatBot assistant, visual DAG workflow engine, HPC job submission… The licence is AGPL-3.0.

When your agent uses it

The user wants MD simulations driven by a trained DP model
Tasks that involve Physical and earth sciences
Tasks that involve Machine learning

Example prompts

“/lammps-deepmd”

Requirements

Python 3
Compatibility (from SKILL.md): Requires LAMMPS compiled with the DEEPMD package. A frozen DeePMD model (.pb) is required.

Workflow steps

3 steps, taken from the step headings in SKILL.md.

Verify structure
Create workflow
Add LAMMPS task

What it can do on your machine

Read from SKILL.md and the folder at commit fd6291b. 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 (its code samples are python).
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 LAMMPS compiled with the DEEPMD package. A frozen DeePMD model (.pb) is required.
From compatibility in the SKILL.md frontmatter.

Context cost

Lammps Deepmd loads about 1k tokens when it runs. Until then it costs about 39 tokens; SKILL.md has 323 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~39
When it runs · the whole SKILL.md, loaded when a task matches: ~1k

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 Hello-QM/catgo-LRG at commit fd6291b, republished under its AGPL-3.0 licence (© Hello-QM). 323 words, ~1,020 tokens.

Download SKILL.mdSave it as .claude/skills/lammps-deepmd/SKILL.md (or your agent's skills folder).

name: lammps-deepmd
description: Run LAMMPS molecular dynamics with DeePMD-kit machine learning potentials. Use when the user wants MD simulations driven by a trained DP model.
compatibility: Requires LAMMPS compiled with the DEEPMD package. A frozen DeePMD model (.pb) is required.
catalog-hidden: true

LAMMPS + DeePMD Potential

When to Use

User wants to run MD with a trained DeePMD model
User needs large-scale MD (10K-1M atoms) at near-DFT accuracy
User wants to study diffusion, phase transitions, or surface reactions with ML potential
User has a frozen .pb model file

Prerequisites

LAMMPS compiled with DEEPMD package (lmp -h | grep DEEPMD)
Frozen DeePMD model file (.pb)
Initial structure (LAMMPS data file or from CatGo viewer)
Know the type_map used during model training

Workflow Steps

1. Verify structure

catgo_view(action="get_state")

2. Create workflow

catgo_workflow_engine(action="create", params={"name": "LAMMPS DeePMD NVT 300K"})

3. Add LAMMPS task

catgo_workflow_engine(action="add_task", params={
  "workflow_id": "wf_xxx",
  "task_type": "shell",
  "name": "lmp_dpmd",
  "command": "lmp -in lammps.in > lammps.log 2>&1",
  "input_files": {
    "lammps.in": "<input script>",
    "frozen_model.pb": "{{model_path}}"
  },
  "system_name": "TiO2_md"
})

LAMMPS Input Template — NVT

units           metal
boundary        p p p
atom_style      atomic

read_data       structure.lmp

pair_style      deepmd frozen_model.pb
pair_coeff      * *

neighbor        2.0 bin
neigh_modify    every 1 delay 0 check yes

# Velocities
velocity        all create 300.0 12345 dist gaussian

# NVT thermostat
fix             1 all nvt temp 300.0 300.0 0.1

# Timestep (ps in metal units)
timestep        0.001

# Output
thermo          100
thermo_style    custom step temp pe ke etotal press vol

dump            1 all custom 100 traj.lammpstrj id type x y z fx fy fz
dump_modify     1 sort id

# Restart
restart         10000 restart.*.data

run             100000

LAMMPS Input Template — NPT

Replace the fix line:

fix             1 all npt temp 300.0 300.0 0.1 iso 0.0 0.0 1.0

Model Deviation (Multi-Model)

For active learning or reliability checking, use multiple models:

pair_style      deepmd model_0.pb model_1.pb model_2.pb model_3.pb out_freq 100 out_file model_devi.out
pair_coeff      * *

This writes model_devi.out with per-frame max/min/avg force deviation. Use thresholds:

max_devi_f < 0.05 eV/Ang: model is reliable
0.05 < max_devi_f < 0.15: candidate for active learning
max_devi_f > 0.15: model is unreliable, do not trust results

Preparing LAMMPS Data File

Convert from CatGo structure to LAMMPS data format:

python

from ase.io import read, write
# Read pymatgen dict, write LAMMPS data
atoms = read('structure.json')
write('structure.lmp', atoms, format='lammps-data')

Or use dpdata (see data/dpdata/SKILL.md).

Parameter Guidance

Parameter	Typical value	Notes
timestep	0.001 ps (1 fs)	Metal units; can use 2 fs for stiff systems
NVT temp damp	0.1 ps	Nose-Hoover damping; 100x timestep
NPT press damp	1.0 ps	Pressure damping; 1000x timestep
dump frequency	100-1000	Every 100 steps = 0.1 ps
neighbor skin	2.0 Ang	Rebuild neighbor list threshold
run	100K-10M	Depends on property of interest

Common Pitfalls

Wrong units — DeePMD pair_style requires units metal (eV, Ang, ps). Never use units real.
type_map mismatch — atom types in LAMMPS data file must match the order in the DP model's type_map.
Unfrozen model — pair_style deepmd needs a frozen .pb file. Run dp freeze first.
Too large timestep — 1 fs is safe; 2 fs may cause energy drift for light elements (H).
No equilibration — always equilibrate for 10-50 ps before production run. Discard equilibration data.
Memory for large models — GPU memory limits apply. For 1M+ atoms, use CPU or multi-GPU.

Files

Just SKILL.md in .claude/skills/lammps-deepmd of Hello-QM/catgo-LRG.

Open the folder on GitHubat commit fd6291b

Used in 1 other repository

We found 3 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in Hello-QM/catgo-LRG, which our catalogue first saw on October 7, 2026.

majiayu000/claude-skill-registryskills/ai-ml/lammps-deepmd skills/ai-ml/deepmd-hello-qm-catgo-lrg

Compare with similar skills

Lammps 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.

Lammps Deepmd compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Lammps Deepmd this skillHello-QM/catgo-LRG	205	1 repos	~1k	Automated safety check: Pass	AGPL-3.0	16 days ago
LammpsJCLiuGroup/AI-Computational-Chemist	145	1 repos	~539	Automated safety check: Pass	Custom licence	11 days ago
Optimize For GPUmajiayu000/claude-skill-registry	666	1 repos	~8.5k	Automated safety check: Pass	MIT	today
DP-GEN Simplify Workflowjinzhezenggroup/computational-chemistry-agent-skills	148	—	~2.7k	Automated safety check: Pass	LGPL-3.0-or-later	3 days ago
Journal Of Climatebrycewang-stanford/Awesome-Journal-Skills	1.2k	—	~1.8k	Automated safety check: Pass	MIT	11 days ago
scikit-survival Time-to-Event Modelingdavila7/claude-code-templates	32k	12 repos	~3.7k	Automated safety check: Pass	MIT	today

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Questions about Lammps Deepmd

What does Lammps Deepmd do?

Run LAMMPS molecular dynamics with DeePMD-kit machine learning potentials. Lammps Deepmd is an agent skill from Hello-QM/catgo-LRG. Run LAMMPS molecular dynamics with DeePMD-kit machine learning potentials.

When should I use Lammps Deepmd?

Lammps Deepmd fits situations like: the user wants MD simulations driven by a trained DP model; tasks that involve Physical and earth sciences; tasks that involve Machine learning.

How do I install Lammps Deepmd in Claude Code?

Run `npx skills add Hello-QM/catgo-LRG --skill lammps-deepmd -a claude-code`. Or copy the skill folder (.claude/skills/lammps-deepmd in Hello-QM/catgo-LRG) into .claude/skills/lammps-deepmd in your project. Claude Code loads it when a task matches its description.

How do I install Lammps Deepmd in Codex?

Run `npx skills add Hello-QM/catgo-LRG --skill lammps-deepmd -a codex`. Or copy the skill folder (.claude/skills/lammps-deepmd in Hello-QM/catgo-LRG) into .agents/skills/lammps-deepmd in your project. Codex loads it when a task matches its description.

Can I use Lammps 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 Hello-QM/catgo-LRG --skill lammps-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/lammps-deepmd, .gemini/skills/lammps-deepmd, .github/skills/lammps-deepmd and .opencode/skills/lammps-deepmd in your project.

What does Lammps Deepmd need to run?

SKILL.md names no scripts, command-line tools or credentials: Lammps Deepmd is instructions for the agent only. Our summary lists: Python 3. Compatibility (from SKILL.md): Requires LAMMPS compiled with the DEEPMD package. A frozen DeePMD model (.pb) is required. .

Does Lammps 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 Lammps 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. Review the folder before installing.

What licence does Lammps Deepmd use?

Lammps Deepmd is published under the AGPL-3.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Lammps Deepmd use?

About 1k tokens (SKILL.md is roughly 4.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Lammps Deepmd?

Skills that share tags, products or a category with Lammps Deepmd: Lammps (JCLiuGroup/AI-Computational-Chemist, 145 stars), Optimize For GPU (majiayu000/claude-skill-registry, 666 stars), DP-GEN Simplify Workflow (jinzhezenggroup/computational-chemistry-agent-skills, 148 stars) and Journal Of Climate (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 Lammps Deepmd?

Hello-QM (a GitHub user) maintains it in Hello-QM/catgo-LRG, which has 205 GitHub stars. The repository holds 75 skills in this directory. The repository was last updated on September 22, 2026.

Source: Hello-QM/catgo-LRG on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Lammps Deepmd

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Compatibility

Context cost

Safety

SKILL.md

LAMMPS + DeePMD Potential

When to Use

Prerequisites

Workflow Steps

1. Verify structure

2. Create workflow

3. Add LAMMPS task

LAMMPS Input Template — NVT

LAMMPS Input Template — NPT

Model Deviation (Multi-Model)

Preparing LAMMPS Data File

Parameter Guidance

Common Pitfalls

Files

Used in 1 other repository

Compare with similar skills

Similar skills

More from Hello-QM/catgo-LRG

Related

Questions about Lammps Deepmd