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Convert and manipulate atomic simulation data formats using dpdata CLI.
LGPL-3.0Auto-check passed
Install Dpdata CLI
$ npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills dpdata-cli --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/tools/dpdata-cli .claude/skills/dpdata-cli && 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 "dpdata-cli" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/tools/dpdata-cli into .claude/skills/dpdata-cli/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "dpdata-cli", 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/tools/dpdata-cliType 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 dpdata-cli -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills dpdata-cli --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/tools/dpdata-cli .agents/skills/dpdata-cli && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "dpdata-cli" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/tools/dpdata-cli into .agents/skills/dpdata-cli/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "dpdata-cli", 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 dpdata-cli -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills dpdata-cli --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/tools/dpdata-cli .cursor/skills/dpdata-cli && 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 "dpdata-cli" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/tools/dpdata-cli into .cursor/skills/dpdata-cli/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "dpdata-cli", 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 tools/dpdata-cli--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 dpdata-cli -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install jinzhezenggroup/computational-chemistry-agent-skills dpdata-cli --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/tools/dpdata-cli .gemini/skills/dpdata-cli && 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 "dpdata-cli" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/tools/dpdata-cli into .gemini/skills/dpdata-cli/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "dpdata-cli", 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 dpdata-cliInstalls 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 dpdata-cli -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/tools/dpdata-cli .github/skills/dpdata-cli && 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 "dpdata-cli" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/tools/dpdata-cli into .github/skills/dpdata-cli/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "dpdata-cli", 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 dpdata-cli -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 dpdata-cli --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/tools/dpdata-cli .opencode/skills/dpdata-cli && 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 "dpdata-cli" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/tools/dpdata-cli into .opencode/skills/dpdata-cli/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "dpdata-cli", 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
dpdata-cli- GitHub stars
- 148
- Token cost
- ~2.6k tokens
- SKILL.md length
- 604 words
- Files
- 2
- Skills in repo
- 62
- Repo updated
- First seen
- Licence
- LGPL-3.0
At a glance
Convert and manipulate atomic simulation data formats using dpdata CLI.
- Works in 3 steps: Use -i extxyz explicitly when working… → Use --multi for any multi-frame extxyz… → All alias names behave identically — -i…
- Converting between DFT/MD output formats
- 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. Convert and manipulate atomic simulation data formats using dpdata CLI. Use when converting between DFT/MD output formats or preparing DeePMD-kit training data. Supports 50+ formats including deepmd, xyz or extxyz, ABACUS, VASP, LAMMPS, CP2K, etc.
Its SKILL.md is about 2.6k 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
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
- Converting between DFT/MD output formats
- Preparing DeePMD-kit training data
Example prompts
- “/dpdata-cli”
Requirements
- Compatibility (from SKILL.md): Requires uvx (uv) for running dpdata
Workflow steps
3 steps, taken from the first numbered list in SKILL.md.
- Use -i extxyz explicitly when working with .xyz files that contain extended XYZ data. Using -i xyz retains only atom species and…
- Use --multi for any multi-frame extxyz file. Without --multi, the CLI constructs a LabeledSystem that keeps only the first frame. This…
- All alias names behave identically — -i mace/xyz, -i nequip/xyz, -i gpumd/xyz, -i quip/gap/xyz, -i quip/gap/xyz_file, and -i extxyz…
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.comgithub.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 2.6k tokens when it runs. Until then it costs about 65 tokens; SKILL.md has 604 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 licence (© jinzhezenggroup). 604 words, ~2,555 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
- Convert and manipulate atomic simulation data formats using dpdata CLI. Use when converting between DFT/MD output formats or preparing DeePMD-kit training data. Supports 50+ formats including deepmd, xyz or extxyz, ABACUS, VASP, LAMMPS, CP2K, etc.
- 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:
uvx dpdata <from_file> [options]Command Line Usage
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_fileArguments
| Argument | Description |
|---|---|
from_file | Read data from a file (positional) |
--to_file, -O | Dump data to a file |
--from_format, -i | Format of from_file (default: "auto") |
--to_format, -o | Format of to_file |
--no-labeled, -n | Labels aren't provided (default: False) |
--multi, -m | System contains multiple directories (default: False) |
--type-map, -t | Type map for atom types |
--version | Show dpdata version and exit |
Common Examples
Convert VASP OUTCAR to deepmd format
uvx dpdata OUTCAR -i vasp/outcar -O deepmd_data -o deepmd/rawConvert LAMMPS dump to VASP POSCAR
uvx dpdata dump.lammps -i lammps/dump -O POSCAR -o vasp/poscarConvert with type map
uvx dpdata OUTCAR -i vasp/outcar -O deepmd_data -o deepmd/raw -t C H O NConvert multiple systems
uvx dpdata data_dir -i vasp/outcar -O output_dir -o deepmd/comp --multiConvert to deepmd/npy (compressed format)
uvx dpdata OUTCAR -i vasp/outcar -O deepmd_npy -o deepmd/npyConvert to deepmd/hdf5
uvx dpdata OUTCAR -i vasp/outcar -O data.h5 -o deepmd/hdf5Supported Formats
Formats may be updated. For the complete and latest list, see:
DeePMD-kit Formats
| Format Name | Description |
|---|---|
deepmd/raw | DeePMD-kit raw text format |
deepmd/comp / deepmd/npy | DeePMD-kit compressed numpy format |
deepmd/npy/mixed | DeePMD-kit mixed type format |
deepmd/hdf5 | DeePMD-kit HDF5 format |
VASP Formats
| Format Name | Description |
|---|---|
vasp/poscar / vasp/contcar / poscar / contcar | VASP structure files |
vasp/outcar / outcar | VASP OUTCAR output |
vasp/xml / xml | VASP XML output |
vasp/string | VASP string format |
LAMMPS Formats
| Format Name | Description |
|---|---|
lammps/lmp / lmp | LAMMPS data file |
lammps/dump / dump | LAMMPS dump file |
ABACUS Formats
| Format Name | Description |
|---|---|
stru / abacus/stru | ABACUS structure file |
abacus/lcao/scf / abacus/pw/scf / abacus/scf | ABACUS SCF output |
abacus/lcao/md / abacus/pw/md / abacus/md | ABACUS MD output |
abacus/lcao/relax / abacus/pw/relax / abacus/relax | ABACUS relax output |
Quantum ESPRESSO Formats
| Format Name | Description |
|---|---|
qe/cp/traj | QE CP trajectory |
qe/pw/scf | QE PWscf output |
CP2K Formats
| Format Name | Description |
|---|---|
cp2k/output | CP2K output |
cp2k/aimd_output | CP2K AIMD output |
Gaussian Formats
| Format Name | Description |
|---|---|
gaussian/log | Gaussian log file |
gaussian/fchk | Gaussian formatted checkpoint |
gaussian/md | Gaussian MD output |
gaussian/gjf | Gaussian input file |
Other Formats
| Format Name | Description |
|---|---|
xyz | XYZ format |
mace/xyz / nequip/xyz / gpumd/xyz / extxyz / quip/gap/xyz | Extended XYZ variants |
ase/structure | ASE structure format |
ase/traj | ASE trajectory |
pymatgen/structure | pymatgen structure |
pymatgen/molecule | pymatgen molecule |
gromacs/gro / gro | GROMACS gro file |
siesta/output | SIESTA output |
siesta/aimd_output | SIESTA AIMD output |
pwmat/output / pwmat/mlmd / pwmat/movement | PWmat output |
pwmat/final.config / pwmat/atom.config | PWmat config |
orca/spout | ORCA output |
psi4/out | PSI4 output |
dftbplus | DFTB+ output |
fhi_aims/output / fhi_aims/md | FHI-aims output |
amber/md | AMBER MD |
n2p2 | n2p2 format |
mol_file / mol | MOL file |
sdf_file / sdf | SDF file |
openmx/md | OpenMX MD |
sqm/out | SQM output |
sqm/in | SQM input |
list | List format |
3dmol | 3Dmol visualization |
Show full SKILL.md (234 more words)Show less
Extended XYZ (extxyz) Format Details
The following format names are all equivalent and invoke the same reader/writer:
extxyz— general-purpose extended XYZquip/gap/xyz/quip/gap/xyz_file— QUIP/GAP framework datasetsmace/xyz— MACE model training datanequip/xyz— NequIP model training datagpumd/xyz— GPUMD simulation data
Important: Plain
xyzis a different, simpler format that stores atom species and coordinates but does not provide per-frame properties such as energies, forces, cell information, or periodic boundary conditions. Do not confusexyzwithextxyz.
CLI Examples for extxyz
# Multi-frame extxyz trajectory → deepmd/npy (--multi preserves all frames)
uvx dpdata data.xyz -i extxyz -O deepmd_data -o deepmd/npy --multi
# Heterogeneous extxyz (mixed compositions) → deepmd/npy/mixed
uvx dpdata data.xyz -i extxyz -O deepmd_data -o deepmd/npy/mixed --multi
# Convert extxyz to VASP POSCAR (single-frame input only)
uvx dpdata data.xyz -i extxyz -O POSCAR -o vasp/poscar
# Convert a single-frame extxyz with explicit type map
uvx dpdata data.xyz -i extxyz -O deepmd_data -o deepmd/npy -t H C N OTips for extxyz
- Use
-i extxyzexplicitly when working with.xyzfiles that contain extended XYZ data. Using-i xyzretains only atom species and coordinates, omitting per-frame properties such as energies, forces, and cell information. - Use
--multifor any multi-frame extxyz file. Without--multi, the CLI constructs aLabeledSystemthat keeps only the first frame. This applies to all multi-frame trajectories, not just heterogeneous (mixed-composition) files. dpdata groups frames by chemical formula internally. - All alias names behave identically —
-i mace/xyz,-i nequip/xyz,-i gpumd/xyz,-i quip/gap/xyz,-i quip/gap/xyz_file, and-i extxyzproduce the same result.
Tips
- Auto-detection: Use
-i auto(default) to let dpdata detect format automatically - Type mapping: Use
-tto specify atom type order for deepmd formats - Multi-system: Use
--multifor directories containing multiple systems - Compressed output: Use
deepmd/npyordeepmd/hdf5for 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 tools/dpdata-cli of jinzhezenggroup/computational-chemistry-agent-skills.
- SKILL.md
- README.md
Open the folder on GitHubat commit 5c19e75
Compare with similar skills
Dpdata CLI 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 |
|---|---|---|---|---|---|---|
| Dpdata CLI this skilljinzhezenggroup/computational-chemistry-agent-skills | 148 | — | ~2.6k | Automated safety check: Pass | LGPL-3.0 | |
| Convertremotion-dev/remotion | 63k | — | ~247 | Automated safety check: Pass | Custom licence | |
| File Format Converterjeremylongshore/tons-of-skills-marketplace | 2.8k | — | ~569 | Automated safety check: Pass | MIT | |
| Tao Convert Dataset FormatNVIDIA/skills | 3.5k | — | ~1.3k | Automated safety check: Notes | Apache-2.0 | |
| Latex Manuscript Format Converteraipoch/medical-research-skills | 2k | — | ~2.9k | Automated safety check: Pass | MIT | |
| Format ConverterAFK-surf/OpenBridge | 430 | — | ~549 | Automated safety check: Pass | MIT |
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Questions about Dpdata CLI
What does Dpdata CLI do?
Convert and manipulate atomic simulation data formats using dpdata CLI. Dpdata CLI is an agent skill from jinzhezenggroup/computational-chemistry-agent-skills. Convert and manipulate atomic simulation data formats using dpdata CLI.
When should I use Dpdata CLI?
Dpdata CLI fits situations like: converting between DFT/MD output formats; preparing DeePMD-kit training data.
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 (tools/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 (tools/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 2.6k tokens (SKILL.md is roughly 10k 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: Convert (remotion-dev/remotion, 63k stars), File Format Converter (jeremylongshore/tons-of-skills-marketplace, 2.8k stars), Tao Convert Dataset Format (NVIDIA/skills, 3.5k stars) and Latex Manuscript Format Converter (aipoch/medical-research-skills, 2k 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.