Hypothesis Generation
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
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.).
$ 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/data-processing/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/data-processing/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/data-processing/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/data-processing/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/data-processing/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/data-processing/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/data-processing/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 data-processing/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/data-processing/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/data-processing/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/data-processing/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/data-processing/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/data-processing/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/data-processing/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.
dpdata-cliA 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. 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.
4 steps, taken from the first numbered list in SKILL.md.
Read from SKILL.md and the folder at commit 5c19e75. It shows what the files ask for, not the result of running them.
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.
Shell commands in SKILL.md call:
uvxFrom the folder's file list and the shell code blocks in SKILL.md.
Links to these hosts (documentation or services it may open):
docs.deepmodeling.comgithub.comFrom URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Requires uvx (uv) for running dpdata
From compatibility in the SKILL.md frontmatter.
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.
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.
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.
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.
.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.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.
Run dpdata via uvx:
uvx dpdata <from_file> [options]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| 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 |
uvx dpdata OUTCAR -i vasp/outcar -O deepmd_data -o deepmd/rawuvx dpdata dump.lammps -i lammps/dump -O POSCAR -o vasp/poscaruvx dpdata OUTCAR -i vasp/outcar -O deepmd_data -o deepmd/raw -t C H O Nuvx dpdata data_dir -i vasp/outcar -O output_dir -o deepmd/comp --multiuvx dpdata OUTCAR -i vasp/outcar -O deepmd_npy -o deepmd/npyuvx dpdata OUTCAR -i vasp/outcar -O data.h5 -o deepmd/hdf5Formats may be updated. For the complete and latest list, see:
| 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 |
| 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 |
| Format Name | Description |
|---|---|
lammps/lmp / lmp | LAMMPS data file |
lammps/dump / dump | LAMMPS dump file |
| 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 |
| Format Name | Description |
|---|---|
qe/cp/traj | QE CP trajectory |
qe/pw/scf | QE PWscf output |
| Format Name | Description |
|---|---|
cp2k/output | CP2K output |
cp2k/aimd_output | CP2K AIMD output |
| Format Name | Description |
|---|---|
gaussian/log | Gaussian log file |
gaussian/fchk | Gaussian formatted checkpoint |
gaussian/md | Gaussian MD output |
gaussian/gjf | Gaussian input file |
| 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 |
-i auto (default) to let dpdata detect format automatically-t to specify atom type order for deepmd formats--multi for directories containing multiple systemsdeepmd/npy or deepmd/hdf5 for smaller file sizes© 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
SKILL.md and 1 other file in data-processing/dpdata-cli of jinzhezenggroup/computational-chemistry-agent-skills.
Open the folder on GitHubat commit 5c19e75
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 | — | ~2.1k | Automated safety check: Pass | LGPL-3.0 | |
| Hypothesis Generationspacering-net/codeg | 3.9k | 14 repos | ~3.6k | Automated safety check: Notes | MIT | |
| GitHub Deep Researchbytedance/deer-flow | 84k | 4 repos | ~1.3k | Automated safety check: Pass | MIT | |
| Nature Paper CardYuan1z0825/nature-skills | 47k | 2 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | |
| Content Research Writerweapp-tailwindcss/weapp-tailwindcss | 1.9k | 25 repos | ~3.5k | Automated safety check: Pass | MIT | |
| Peer Reviewspacering-net/codeg | 3.9k | 17 repos | ~5.9k | Automated safety check: Notes | MIT |
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
bytedance/deer-flow
Researches a GitHub repository over four rounds using the GitHub API and web search, then writes a structured markdown report with timeline, metrics and Mermaid diagrams.
Yuan1z0825/nature-skills
Builds a structured deep-reading card for one scientific paper, covering methods, how experiments support claims, limitations and research ideas, with a script to prepare the source.
weapp-tailwindcss/weapp-tailwindcss
Assists in writing high-quality content by conducting research, adding citations, improving hooks, iterating on outlines, and providing real-time feedback on each section.
spacering-net/codeg
Structured manuscript/grant review with checklist-based evaluation.
mvanhorn/last30days-skill
Research what people actually say about any topic in the last 30 days.
jinzhezenggroup/computational-chemistry-agent-skills
Turns a user-supplied atomic structure and DFT settings into a runnable Quantum ESPRESSO input file, stopping short of submitting the job.
jinzhezenggroup/computational-chemistry-agent-skills
Prepares, validates and runs DP-GEN simplify jobs that thin out repeated or redundant DeepMD datasets, generating param.json and machine.json for local or scheduler runs.
jinzhezenggroup/computational-chemistry-agent-skills
Prepares and runs molecular dynamics simulations in LAMMPS with a DeePMD machine-learning potential, writing the input script and choosing NVE, NVT or NPT.
jinzhezenggroup/computational-chemistry-agent-skills
Prepares and explains LAMMPS input scripts for reactive molecular dynamics with the ReaxFF potential, including charge equilibration and ensemble choice.
jinzhezenggroup/computational-chemistry-agent-skills
Generates 3D molecular conformers from SMILES strings or files with RDKit, keeps the lowest-energy one per molecule, and falls back to 2D coordinates when embedding fails.
jinzhezenggroup/computational-chemistry-agent-skills
Computes RDKit physicochemical descriptors and molecular fingerprints from SMILES through a uv-run CLI script that skips and logs invalid molecules.
Categories
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.).
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.