A command-line utility for converting and manipulating over 50 atomic simulation data formats, including outputs from DFT and MD software (VASP, LAMMPS, Gaussian, QE, CP2K, ABACUS, etc.).

LGPL-3.0Auto-check passedResearch & Science

Install Dpdata CLI

skills CLI
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli -a claude-code

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

GitHub CLI
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills dpdata-cli --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/jinzhezenggroup/computational-chemistry-agent-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/data-processing/dpdata-cli .claude/skills/dpdata-cli && 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/

Facts

Skill name
dpdata-cli
GitHub stars
148
Token cost
~2.1k tokens
SKILL.md length
425 words
Files
2
Skills in repo
62
Repo updated
First seen
Licence
LGPL-3.0

At a glance

A command-line utility for converting and manipulating over 50 atomic simulation data formats, including outputs from DFT and MD software (VASP, LAMMPS, Gaussian, QE, CP2K, ABACUS, etc.).

  • Works in 4 steps: Auto-detection: Use -i auto (default) to… → Type mapping: Use -t to specify atom… → Multi-system: Use --multi for… → …
  • You need to convert structural
  • SKILL.md covers Quick Start, Command Line Usage, Common Examples and Supported Formats, plus 2 more sections
  • Calls uvx

What it does

Dpdata CLI is an agent skill from jinzhezenggroup/computational-chemistry-agent-skills. A command-line utility for converting and manipulating over 50 atomic simulation data formats, including outputs from DFT and MD software (VASP, LAMMPS, Gaussian, QE, CP2K, ABACUS, etc.). USE WHEN you need to convert structural or trajectory files between different computational chemistry formats, or when parsing raw simulation outputs into structured training datasets (e.g., deepmd/raw, deepmd/npy, deepmd/hdf5) for DeePMD-kit.

Its SKILL.md is about 2.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 1 other file (for example `README.md`). Compatibility notes: Requires uvx (uv) for running dpdata

It sits in Research & Science. The repository describes itself as: Agent skills to run computational-chemistry tasks, used in OpenClaw. The licence is LGPL-3.0.

When your agent uses it

  • You need to convert structural
  • Trajectory files between different computational chemistry formats
  • Parsing raw simulation outputs into structured training datasets (e.g.

Example prompts

  • “/dpdata-cli”

Requirements

  • Compatibility (from SKILL.md): Requires uvx (uv) for running dpdata

Workflow steps

4 steps, taken from the first numbered list in SKILL.md.

  1. Auto-detection: Use -i auto (default) to let dpdata detect format automatically
  2. Type mapping: Use -t to specify atom type order for deepmd formats
  3. Multi-system: Use --multi for directories containing multiple systems
  4. Compressed output: Use deepmd/npy or deepmd/hdf5 for smaller file sizes

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

    Shell commands in SKILL.md call:

    • uvx

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • docs.deepmodeling.com
    • github.com

    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 uvx (uv) for running dpdata

    From compatibility in the SKILL.md frontmatter.

Context cost

Dpdata CLI loads about 2.1k tokens when it runs. Until then it costs about 111 tokens; SKILL.md has 425 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~111
When it runs · the whole SKILL.md, loaded when a task matches
~2.1k

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 jinzhezenggroup/computational-chemistry-agent-skills at commit 5c19e75, republished under its LGPL-3.0 licence (© jinzhezenggroup). 425 words, ~2,125 tokens.

Download SKILL.mdSave it as .claude/skills/dpdata-cli/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.
name
dpdata-cli
description
A command-line utility for converting and manipulating over 50 atomic simulation data formats, including outputs from DFT and MD software (VASP, LAMMPS, Gaussian, QE, CP2K, ABACUS, etc.). USE WHEN you need to convert structural or trajectory files between different computational chemistry formats, or when parsing raw simulation outputs into structured training datasets (e.g., deepmd/raw, deepmd/npy, deepmd/hdf5) for DeePMD-kit.
compatibility
Requires uvx (uv) for running dpdata
metadata.author
njzjz-bot
metadata.version
1.0
metadata.repository
https://github.com/deepmodeling/dpdata

dpdata CLI

dpdata is a tool for manipulating multiple atomic simulation data formats. This skill enables format conversion between various DFT/MD software outputs via command line.

Quick Start

Run dpdata via uvx:

bash
uvx dpdata <from_file> [options]

Command Line Usage

text
dpdata: Manipulating multiple atomic simulation data formats
usage: dpdata [-h] [--to_file TO_FILE] [--from_format FROM_FORMAT]
              [--to_format TO_FORMAT] [--no-labeled] [--multi]
              [--type-map TYPE_MAP [TYPE_MAP ...]] [--version]
              from_file
Arguments
ArgumentDescription
from_fileRead data from a file (positional)
--to_file, -ODump data to a file
--from_format, -iFormat of from_file (default: "auto")
--to_format, -oFormat of to_file
--no-labeled, -nLabels aren't provided (default: False)
--multi, -mSystem contains multiple directories (default: False)
--type-map, -tType map for atom types
--versionShow dpdata version and exit

Common Examples

Convert VASP OUTCAR to deepmd format
bash
uvx dpdata OUTCAR -i vasp/outcar -O deepmd_data -o deepmd/raw
Convert LAMMPS dump to VASP POSCAR
bash
uvx dpdata dump.lammps -i lammps/dump -O POSCAR -o vasp/poscar
Convert with type map
bash
uvx dpdata OUTCAR -i vasp/outcar -O deepmd_data -o deepmd/raw -t C H O N
Convert multiple systems
bash
uvx dpdata data_dir -i vasp/outcar -O output_dir -o deepmd/comp --multi
Convert to deepmd/npy (compressed format)
bash
uvx dpdata OUTCAR -i vasp/outcar -O deepmd_npy -o deepmd/npy
Convert to deepmd/hdf5
bash
uvx dpdata OUTCAR -i vasp/outcar -O data.h5 -o deepmd/hdf5

Supported Formats

Formats may be updated. For the complete and latest list, see:

DeePMD-kit Formats
Format NameDescription
deepmd/rawDeePMD-kit raw text format
deepmd/comp / deepmd/npyDeePMD-kit compressed numpy format
deepmd/npy/mixedDeePMD-kit mixed type format
deepmd/hdf5DeePMD-kit HDF5 format
VASP Formats
Format NameDescription
vasp/poscar / vasp/contcar / poscar / contcarVASP structure files
vasp/outcar / outcarVASP OUTCAR output
vasp/xml / xmlVASP XML output
vasp/stringVASP string format
LAMMPS Formats
Format NameDescription
lammps/lmp / lmpLAMMPS data file
lammps/dump / dumpLAMMPS dump file
ABACUS Formats
Format NameDescription
stru / abacus/struABACUS structure file
abacus/lcao/scf / abacus/pw/scf / abacus/scfABACUS SCF output
abacus/lcao/md / abacus/pw/md / abacus/mdABACUS MD output
abacus/lcao/relax / abacus/pw/relax / abacus/relaxABACUS relax output
Quantum ESPRESSO Formats
Format NameDescription
qe/cp/trajQE CP trajectory
qe/pw/scfQE PWscf output
CP2K Formats
Format NameDescription
cp2k/outputCP2K output
cp2k/aimd_outputCP2K AIMD output
Show full SKILL.md (168 more words)Show less
Gaussian Formats
Format NameDescription
gaussian/logGaussian log file
gaussian/fchkGaussian formatted checkpoint
gaussian/mdGaussian MD output
gaussian/gjfGaussian input file
Other Formats
Format NameDescription
xyzXYZ format
mace/xyz / nequip/xyz / gpumd/xyz / extxyz / quip/gap/xyzExtended XYZ variants
ase/structureASE structure format
ase/trajASE trajectory
pymatgen/structurepymatgen structure
pymatgen/moleculepymatgen molecule
gromacs/gro / groGROMACS gro file
siesta/outputSIESTA output
siesta/aimd_outputSIESTA AIMD output
pwmat/output / pwmat/mlmd / pwmat/movementPWmat output
pwmat/final.config / pwmat/atom.configPWmat config
orca/spoutORCA output
psi4/outPSI4 output
dftbplusDFTB+ output
fhi_aims/output / fhi_aims/mdFHI-aims output
amber/mdAMBER MD
n2p2n2p2 format
mol_file / molMOL file
sdf_file / sdfSDF file
openmx/mdOpenMX MD
sqm/outSQM output
sqm/inSQM input
listList format
3dmol3Dmol visualization

Tips

  1. Auto-detection: Use -i auto (default) to let dpdata detect format automatically
  2. Type mapping: Use -t to specify atom type order for deepmd formats
  3. Multi-system: Use --multi for directories containing multiple systems
  4. Compressed output: Use deepmd/npy or deepmd/hdf5 for smaller file sizes

References

© jinzhezenggroup, LGPL-3.0. 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 in data-processing/dpdata-cli of jinzhezenggroup/computational-chemistry-agent-skills.

  • SKILL.md
  • README.md

Open the folder on GitHubat commit 5c19e75

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Questions about Dpdata CLI

What does Dpdata CLI do?

A command-line utility for converting and manipulating over 50 atomic simulation data formats, including outputs from DFT and MD software (VASP, LAMMPS, Gaussian, QE, CP2K, ABACUS, etc.). Dpdata CLI is an agent skill from jinzhezenggroup/computational-chemistry-agent-skills.).

When should I use Dpdata CLI?

Dpdata CLI fits situations like: you need to convert structural; trajectory files between different computational chemistry formats; parsing raw simulation outputs into structured training datasets (e.g.

How do I install Dpdata CLI in Claude Code?

Run `npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli -a claude-code`. Or copy the skill folder (data-processing/dpdata-cli in jinzhezenggroup/computational-chemistry-agent-skills) into .claude/skills/dpdata-cli in your project. Claude Code loads it when a task matches its description.

How do I install Dpdata CLI in Codex?

Run `npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli -a codex`. Or copy the skill folder (data-processing/dpdata-cli in jinzhezenggroup/computational-chemistry-agent-skills) into .agents/skills/dpdata-cli in your project. Codex loads it when a task matches its description.

Can I use Dpdata CLI 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 dpdata-cli -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/dpdata-cli, .gemini/skills/dpdata-cli, .github/skills/dpdata-cli and .opencode/skills/dpdata-cli in your project.

What does Dpdata CLI need to run?

Going by SKILL.md and its folder, Dpdata CLI needs the command-line tools its instructions call (uvx). Compatibility (from SKILL.md): Requires uvx (uv) for running dpdata.

Does Dpdata CLI access the network?

SKILL.md names 2 domains. As links in the text: docs.deepmodeling.com and github.com. This is read from the text; nothing was executed.

Is Dpdata CLI 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 Dpdata CLI use?

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

How many tokens does Dpdata CLI use?

About 2.1k tokens (SKILL.md is roughly 8.5k 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 Dpdata CLI?

Skills that share tags, products or a category with Dpdata CLI: Hypothesis Generation (spacering-net/codeg, 3.9k stars), GitHub Deep Research (bytedance/deer-flow, 84k stars), Nature Paper Card (Yuan1z0825/nature-skills, 47k stars) and Content Research Writer (weapp-tailwindcss/weapp-tailwindcss, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Dpdata CLI?

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.