Creator · jinzhezenggroup
Last updated · Sep 4, 2026
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
Creator · jinzhezenggroup
Last updated · Sep 4, 2026
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
Creator · jinzhezenggroup
Last updated · Sep 4, 2026
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
Creator · jinzhezenggroup
Last updated · Sep 4, 2026
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
Sandbox only
Install targets
Codex install prompt
Install the "dpdata-cli" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/dpdata-cli. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {"event_id":"install_<unique-id>","skill_slug":"jinzhezenggroup-dpdata-cli","task":"Install dpdata-cli","agent":"codex","outcome":"success","install_used":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.Supply asset profile
Code review, repo analysis, testing, CI, GitHub, DevOps, and developer workflow skills.
Scenario
GitHub automation
I need my agent to triage GitHub issues, review pull requests, and summarize repository changes.
Agent fit
Claude Code + CLI + Codex
Codex, Claude Code, Cursor, CLI, or custom agents.
Install
Ready
npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli
Maintenance
fresh
1d since push
Risk
Needs review
Financial research output is not financial advice; require human review before any live investment decision
GitHub quality
135
68/100 Quality · 78/100 Trust
Coverage tags
Review notes
Financial research output is not financial advice; require human review before any live investment decision · Financial research output is not financial advice; require human review before any live investment decision.
Agent adoption scorecard
These scores combine public repository metadata, OpenAgentSkill review signals, maintenance freshness, and install readiness. They are a shortlist signal, not a replacement for human review.
Quality
PromisingUseful candidate, but compare it with alternatives before adopting.
Trust
Sandbox onlyUseful candidate with missing or mixed trust signals. Keep it in an isolated workspace until the outcome loop proves task fit.
Audit
Needs reviewA machine-readable review of install readiness, security metadata, maintenance, and adoption risk.
OpenAgentSkill Trust Score v5
Run only in a sandbox and compare close alternatives before using it for real work.
Stars
135 GitHub stars
Repo activity
135 stars, 27 forks
Maintenance
1d since push
License
LGPL-3.0
Install
npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli
Install safety
Agent-readable metadata
Use this block or the embedded JSON to decide whether an agent should install this skill, choose an alternative, or ask for human review first.
Suited tasks
Suited agents
Install decision
Trust and risk
Outcome loop
Install command
npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cliDo not use when
Agent safety v2
Sparse or mixed signals. Useful for discovery, but not for autonomous installation.
Test manually in an isolated workspace and compare against safer alternatives.
high
Skill metadata references terminal, CLI, shell, subprocess, or command execution workflows.
medium
Skill likely fetches remote pages, APIs, repositories, or external services.
medium
Skill may read or write project files, documents, generated artifacts, or local workspace state.
Agent resolve plan
The Resolve API returns the selected skill, alternatives, safety policy, audit notes, install target, and copy-paste prompt an agent can follow without scraping this page.
Open JSON
/api/agent/resolve?task=Use%20dpdata-cli%20for%20an%20agent%20workflow&agent=codex&max_risk=medium
Resolve text
/api/agent/resolve?task=Use%20dpdata-cli%20for%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text
Install handoff
/api/skills/jinzhezenggroup-dpdata-cli/install
Agent should check
Copy prompt
Task: Use dpdata-cli in this workspace.
Resolve first: https://www.openagentskill.com/api/agent/resolve?task=Use%20dpdata-cli%20for%20an%20agent%20workflow&agent=codex&max_risk=medium
Review install handoff: https://www.openagentskill.com/api/skills/jinzhezenggroup-dpdata-cli/install
Install command: npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli
Before running it, summarize audit warnings, required permissions, and the fallback skill if install is risky.Agent handoff
Use the public install endpoint to fetch the command, safety checklist, target prompts, and canonical links for this skill.
Install handoff
/api/skills/jinzhezenggroup-dpdata-cli/install
LLM text format
/api/skills/jinzhezenggroup-dpdata-cli/install?format=text
Find alternatives
/api/skills/search?q=dpdata-cli&limit=3
Agent prompt
Use dpdata-cli for this task. Review https://www.openagentskill.com/api/skills/jinzhezenggroup-dpdata-cli/install, then install with: npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cliRegistry metadata
This page exposes the same decision, trust, audit, use-case, and install signals through the Registry API, so agents can rank this skill without scraping the UI.
Manifest
/api/registry/manifest/jinzhezenggroup-dpdata-cli
LLM text
/api/registry/manifest/jinzhezenggroup-dpdata-cli?format=text
Install alias
/api/registry/install/jinzhezenggroup-dpdata-cli
Recommend
/api/registry/recommend?task=Use%20dpdata-cli%20in%20an%20agent%20workflow&limit=3
Agent fit
GitHub automation
Use-case tags
Platforms
Claude Code
Audit report
A machine-readable review of install readiness, security metadata, maintenance, and adoption risk.
Agent decision cockpit
Prototype with this skill first; keep a fallback candidate ready.
Role in stack
Fallback candidate
Primary fit
GitHub automation
Trust label
Prototype first
Install path
Command ready
Use when
Evidence
review first
Implementation path
Trust profile
Useful candidate with missing or mixed trust signals. Keep it in an isolated workspace until the outcome loop proves task fit.
GitHub adoption
INFO135 GitHub stars
Stars/forks activity
CHECK135 stars, 27 forks; issue activity unavailable in current metadata
Recent maintenance
PASS1d since push
License clarity
PASSLGPL-3.0
Good signals
Review before install
Recommended action
Run only in a sandbox and compare close alternatives before using it for real work.
Quality profile
Useful candidate, but compare it with alternatives before adopting.
Workflow fit
Manage repositories
I need my agent to triage GitHub issues, review pull requests, and summarize repository changes.
Operate web apps
I need my agent to control a browser, fill forms, and verify web app workflows.
Build and ship code
I need a coding agent that can understand a repository, edit code, and review pull requests.
Workflow fit
Operate and verify web apps
A workflow for agents that navigate products, fill forms, take screenshots, and verify real user flows across web applications.
Inspect, patch, and verify code
A workflow for software agents that inspect repositories, review pull requests, generate tests, and turn findings into shippable patches.
Scrape, clean, and reuse web data
A practical workflow for agents that crawl public pages, extract clean content, normalize data, and hand it to downstream research or RAG workflows.
Alternative shortlist
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--- 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 version: '1.0' 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
| 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
```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:
- [Formats Reference (stable)](https://docs.deepmodeling.com/projects/dpdata/en/stable/formats.html)
### 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 |
## Tips
1. **Auto-detection**: Use `-i auto` (default) to let dpdata detect format automatically 1. **Type mapping**: Use `-t` to specify atom type order for deepmd formats 1. **Multi-system**: Use `--multi` for directories containing multiple systems 1. **Compressed output**: Use `deepmd/npy` or `deepmd/hdf5` for smaller file sizes
## References
- [dpdata Documentation](https://docs.deepmodeling.com/projects/dpdata/) - [CLI Reference](https://docs.deepmodeling.com/projects/dpdata/en/stable/cli.html) - [Formats Reference](https://docs.deepmodeling.com/projects/dpdata/en/stable/formats.html) - [GitHub Repository](https://github.com/deepmodeling/dpdata)
Source provenance
Decision snapshot
recent repository activity
Audit
Install and adoption review
Agent-proven evidence
Outcome reports after resolve, review, install, and one narrow run.
No agent outcome data yet. The first agent run can report success, setup needs, risk blocks, failure, or not-relevant through /api/agent/outcome.
Install
Free and open source. Review the report before installing into production agents.
Growth loop
Scenario-led draft for dpdata-cli, ready for a manual X post.
dpdata-cli: A command-line utility for converting and manipulating over 50 atomic simulation data formats... 135 stars https://www.openagentskill.com/skills/jinzhezenggroup-dpdata-cli?ref=x
Listing + install path for dpdata-cli: https://www.openagentskill.com/skills/jinzhezenggroup-dpdata-cli?ref=x Install: npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdat...
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Install targets
Codex install prompt
Install the "dpdata-cli" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/dpdata-cli. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {"event_id":"install_<unique-id>","skill_slug":"jinzhezenggroup-dpdata-cli","task":"Install dpdata-cli","agent":"codex","outcome":"success","install_used":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.Supply asset profile
Code review, repo analysis, testing, CI, GitHub, DevOps, and developer workflow skills.
Scenario
GitHub automation
I need my agent to triage GitHub issues, review pull requests, and summarize repository changes.
Agent fit
Claude Code + CLI + Codex
Codex, Claude Code, Cursor, CLI, or custom agents.
Install
Ready
npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli
Maintenance
fresh
1d since push
Risk
Needs review
Financial research output is not financial advice; require human review before any live investment decision
GitHub quality
135
68/100 Quality · 78/100 Trust
Coverage tags
Review notes
Financial research output is not financial advice; require human review before any live investment decision · Financial research output is not financial advice; require human review before any live investment decision.
Agent adoption scorecard
These scores combine public repository metadata, OpenAgentSkill review signals, maintenance freshness, and install readiness. They are a shortlist signal, not a replacement for human review.
Quality
PromisingUseful candidate, but compare it with alternatives before adopting.
Trust
Sandbox onlyUseful candidate with missing or mixed trust signals. Keep it in an isolated workspace until the outcome loop proves task fit.
Audit
Needs reviewA machine-readable review of install readiness, security metadata, maintenance, and adoption risk.
OpenAgentSkill Trust Score v5
Run only in a sandbox and compare close alternatives before using it for real work.
Stars
135 GitHub stars
Repo activity
135 stars, 27 forks
Maintenance
1d since push
License
LGPL-3.0
Install
npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli
Install safety
Agent-readable metadata
Use this block or the embedded JSON to decide whether an agent should install this skill, choose an alternative, or ask for human review first.
Suited tasks
Suited agents
Install decision
Trust and risk
Outcome loop
Install command
npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cliDo not use when
Agent safety v2
Sparse or mixed signals. Useful for discovery, but not for autonomous installation.
Test manually in an isolated workspace and compare against safer alternatives.
high
Skill metadata references terminal, CLI, shell, subprocess, or command execution workflows.
medium
Skill likely fetches remote pages, APIs, repositories, or external services.
medium
Skill may read or write project files, documents, generated artifacts, or local workspace state.
Agent resolve plan
The Resolve API returns the selected skill, alternatives, safety policy, audit notes, install target, and copy-paste prompt an agent can follow without scraping this page.
Open JSON
/api/agent/resolve?task=Use%20dpdata-cli%20for%20an%20agent%20workflow&agent=codex&max_risk=medium
Resolve text
/api/agent/resolve?task=Use%20dpdata-cli%20for%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text
Install handoff
/api/skills/jinzhezenggroup-dpdata-cli/install
Agent should check
Copy prompt
Task: Use dpdata-cli in this workspace.
Resolve first: https://www.openagentskill.com/api/agent/resolve?task=Use%20dpdata-cli%20for%20an%20agent%20workflow&agent=codex&max_risk=medium
Review install handoff: https://www.openagentskill.com/api/skills/jinzhezenggroup-dpdata-cli/install
Install command: npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli
Before running it, summarize audit warnings, required permissions, and the fallback skill if install is risky.Agent handoff
Use the public install endpoint to fetch the command, safety checklist, target prompts, and canonical links for this skill.
Install handoff
/api/skills/jinzhezenggroup-dpdata-cli/install
LLM text format
/api/skills/jinzhezenggroup-dpdata-cli/install?format=text
Find alternatives
/api/skills/search?q=dpdata-cli&limit=3
Agent prompt
Use dpdata-cli for this task. Review https://www.openagentskill.com/api/skills/jinzhezenggroup-dpdata-cli/install, then install with: npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cliRegistry metadata
This page exposes the same decision, trust, audit, use-case, and install signals through the Registry API, so agents can rank this skill without scraping the UI.
Manifest
/api/registry/manifest/jinzhezenggroup-dpdata-cli
LLM text
/api/registry/manifest/jinzhezenggroup-dpdata-cli?format=text
Install alias
/api/registry/install/jinzhezenggroup-dpdata-cli
Recommend
/api/registry/recommend?task=Use%20dpdata-cli%20in%20an%20agent%20workflow&limit=3
Agent fit
GitHub automation
Use-case tags
Platforms
Claude Code
Audit report
A machine-readable review of install readiness, security metadata, maintenance, and adoption risk.
Agent decision cockpit
Prototype with this skill first; keep a fallback candidate ready.
Role in stack
Fallback candidate
Primary fit
GitHub automation
Trust label
Prototype first
Install path
Command ready
Use when
Evidence
review first
Implementation path
Trust profile
Useful candidate with missing or mixed trust signals. Keep it in an isolated workspace until the outcome loop proves task fit.
GitHub adoption
INFO135 GitHub stars
Stars/forks activity
CHECK135 stars, 27 forks; issue activity unavailable in current metadata
Recent maintenance
PASS1d since push
License clarity
PASSLGPL-3.0
Good signals
Review before install
Recommended action
Run only in a sandbox and compare close alternatives before using it for real work.
Quality profile
Useful candidate, but compare it with alternatives before adopting.
Workflow fit
Manage repositories
I need my agent to triage GitHub issues, review pull requests, and summarize repository changes.
Operate web apps
I need my agent to control a browser, fill forms, and verify web app workflows.
Build and ship code
I need a coding agent that can understand a repository, edit code, and review pull requests.
Workflow fit
Operate and verify web apps
A workflow for agents that navigate products, fill forms, take screenshots, and verify real user flows across web applications.
Inspect, patch, and verify code
A workflow for software agents that inspect repositories, review pull requests, generate tests, and turn findings into shippable patches.
Scrape, clean, and reuse web data
A practical workflow for agents that crawl public pages, extract clean content, normalize data, and hand it to downstream research or RAG workflows.
Alternative shortlist
Similar skills that may fit this task.
Apache ECharts is a powerful, interactive charting and data visualization library for browser
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Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 160,000+ scientists worldwide. 140 ready-to-use skills plus 100+ scientific databases covering biology, chemistry, medicine, and drug discovery. Compatible with Cursor, Claude Code, Codex, Pi, Antigravity, and the open Agent Skills standard.
Apache Superset is a Data Visualization and Data Exploration Platform
--- 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 version: '1.0' 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
| 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
```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:
- [Formats Reference (stable)](https://docs.deepmodeling.com/projects/dpdata/en/stable/formats.html)
### 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 |
## Tips
1. **Auto-detection**: Use `-i auto` (default) to let dpdata detect format automatically 1. **Type mapping**: Use `-t` to specify atom type order for deepmd formats 1. **Multi-system**: Use `--multi` for directories containing multiple systems 1. **Compressed output**: Use `deepmd/npy` or `deepmd/hdf5` for smaller file sizes
## References
- [dpdata Documentation](https://docs.deepmodeling.com/projects/dpdata/) - [CLI Reference](https://docs.deepmodeling.com/projects/dpdata/en/stable/cli.html) - [Formats Reference](https://docs.deepmodeling.com/projects/dpdata/en/stable/formats.html) - [GitHub Repository](https://github.com/deepmodeling/dpdata)
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No agent outcome data yet. The first agent run can report success, setup needs, risk blocks, failure, or not-relevant through /api/agent/outcome.
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dpdata-cli: A command-line utility for converting and manipulating over 50 atomic simulation data formats... 135 stars https://www.openagentskill.com/skills/jinzhezenggroup-dpdata-cli?ref=x
Listing + install path for dpdata-cli: https://www.openagentskill.com/skills/jinzhezenggroup-dpdata-cli?ref=x Install: npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdat...
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Install targets
Codex install prompt
Install the "dpdata-cli" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/dpdata-cli. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {"event_id":"install_<unique-id>","skill_slug":"jinzhezenggroup-dpdata-cli","task":"Install dpdata-cli","agent":"codex","outcome":"success","install_used":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.Supply asset profile
Code review, repo analysis, testing, CI, GitHub, DevOps, and developer workflow skills.
Scenario
GitHub automation
I need my agent to triage GitHub issues, review pull requests, and summarize repository changes.
Agent fit
Claude Code + CLI + Codex
Codex, Claude Code, Cursor, CLI, or custom agents.
Install
Ready
npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli
Maintenance
fresh
1d since push
Risk
Needs review
Financial research output is not financial advice; require human review before any live investment decision
GitHub quality
135
68/100 Quality · 78/100 Trust
Coverage tags
Review notes
Financial research output is not financial advice; require human review before any live investment decision · Financial research output is not financial advice; require human review before any live investment decision.
Agent adoption scorecard
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Quality
PromisingUseful candidate, but compare it with alternatives before adopting.
Trust
Sandbox onlyUseful candidate with missing or mixed trust signals. Keep it in an isolated workspace until the outcome loop proves task fit.
Audit
Needs reviewA machine-readable review of install readiness, security metadata, maintenance, and adoption risk.
OpenAgentSkill Trust Score v5
Run only in a sandbox and compare close alternatives before using it for real work.
Stars
135 GitHub stars
Repo activity
135 stars, 27 forks
Maintenance
1d since push
License
LGPL-3.0
Install
npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli
Install safety
Agent-readable metadata
Use this block or the embedded JSON to decide whether an agent should install this skill, choose an alternative, or ask for human review first.
Suited tasks
Suited agents
Install decision
Trust and risk
Outcome loop
Install command
npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cliDo not use when
Agent safety v2
Sparse or mixed signals. Useful for discovery, but not for autonomous installation.
Test manually in an isolated workspace and compare against safer alternatives.
high
Skill metadata references terminal, CLI, shell, subprocess, or command execution workflows.
medium
Skill likely fetches remote pages, APIs, repositories, or external services.
medium
Skill may read or write project files, documents, generated artifacts, or local workspace state.
Agent resolve plan
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Open JSON
/api/agent/resolve?task=Use%20dpdata-cli%20for%20an%20agent%20workflow&agent=codex&max_risk=medium
Resolve text
/api/agent/resolve?task=Use%20dpdata-cli%20for%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text
Install handoff
/api/skills/jinzhezenggroup-dpdata-cli/install
Agent should check
Copy prompt
Task: Use dpdata-cli in this workspace.
Resolve first: https://www.openagentskill.com/api/agent/resolve?task=Use%20dpdata-cli%20for%20an%20agent%20workflow&agent=codex&max_risk=medium
Review install handoff: https://www.openagentskill.com/api/skills/jinzhezenggroup-dpdata-cli/install
Install command: npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli
Before running it, summarize audit warnings, required permissions, and the fallback skill if install is risky.Agent handoff
Use the public install endpoint to fetch the command, safety checklist, target prompts, and canonical links for this skill.
Install handoff
/api/skills/jinzhezenggroup-dpdata-cli/install
LLM text format
/api/skills/jinzhezenggroup-dpdata-cli/install?format=text
Find alternatives
/api/skills/search?q=dpdata-cli&limit=3
Agent prompt
Use dpdata-cli for this task. Review https://www.openagentskill.com/api/skills/jinzhezenggroup-dpdata-cli/install, then install with: npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cliRegistry metadata
This page exposes the same decision, trust, audit, use-case, and install signals through the Registry API, so agents can rank this skill without scraping the UI.
Manifest
/api/registry/manifest/jinzhezenggroup-dpdata-cli
LLM text
/api/registry/manifest/jinzhezenggroup-dpdata-cli?format=text
Install alias
/api/registry/install/jinzhezenggroup-dpdata-cli
Recommend
/api/registry/recommend?task=Use%20dpdata-cli%20in%20an%20agent%20workflow&limit=3
Agent fit
GitHub automation
Use-case tags
Platforms
Claude Code
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A machine-readable review of install readiness, security metadata, maintenance, and adoption risk.
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Command ready
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Evidence
review first
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Trust profile
Useful candidate with missing or mixed trust signals. Keep it in an isolated workspace until the outcome loop proves task fit.
GitHub adoption
INFO135 GitHub stars
Stars/forks activity
CHECK135 stars, 27 forks; issue activity unavailable in current metadata
Recent maintenance
PASS1d since push
License clarity
PASSLGPL-3.0
Good signals
Review before install
Recommended action
Run only in a sandbox and compare close alternatives before using it for real work.
Quality profile
Useful candidate, but compare it with alternatives before adopting.
Workflow fit
Manage repositories
I need my agent to triage GitHub issues, review pull requests, and summarize repository changes.
Operate web apps
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I need a coding agent that can understand a repository, edit code, and review pull requests.
Workflow fit
Operate and verify web apps
A workflow for agents that navigate products, fill forms, take screenshots, and verify real user flows across web applications.
Inspect, patch, and verify code
A workflow for software agents that inspect repositories, review pull requests, generate tests, and turn findings into shippable patches.
Scrape, clean, and reuse web data
A practical workflow for agents that crawl public pages, extract clean content, normalize data, and hand it to downstream research or RAG workflows.
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--- 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 version: '1.0' 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
| 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
```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:
- [Formats Reference (stable)](https://docs.deepmodeling.com/projects/dpdata/en/stable/formats.html)
### 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 |
## Tips
1. **Auto-detection**: Use `-i auto` (default) to let dpdata detect format automatically 1. **Type mapping**: Use `-t` to specify atom type order for deepmd formats 1. **Multi-system**: Use `--multi` for directories containing multiple systems 1. **Compressed output**: Use `deepmd/npy` or `deepmd/hdf5` for smaller file sizes
## References
- [dpdata Documentation](https://docs.deepmodeling.com/projects/dpdata/) - [CLI Reference](https://docs.deepmodeling.com/projects/dpdata/en/stable/cli.html) - [Formats Reference](https://docs.deepmodeling.com/projects/dpdata/en/stable/formats.html) - [GitHub Repository](https://github.com/deepmodeling/dpdata)
Source provenance
Decision snapshot
recent repository activity
Audit
Install and adoption review
Agent-proven evidence
Outcome reports after resolve, review, install, and one narrow run.
No agent outcome data yet. The first agent run can report success, setup needs, risk blocks, failure, or not-relevant through /api/agent/outcome.
Install
Free and open source. Review the report before installing into production agents.
Growth loop
Scenario-led draft for dpdata-cli, ready for a manual X post.
dpdata-cli: A command-line utility for converting and manipulating over 50 atomic simulation data formats... 135 stars https://www.openagentskill.com/skills/jinzhezenggroup-dpdata-cli?ref=x
Listing + install path for dpdata-cli: https://www.openagentskill.com/skills/jinzhezenggroup-dpdata-cli?ref=x Install: npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdat...
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Install targets
Codex install prompt
Install the "dpdata-cli" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/dpdata-cli. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: 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. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {"event_id":"install_<unique-id>","skill_slug":"jinzhezenggroup-dpdata-cli","task":"Install dpdata-cli","agent":"codex","outcome":"success","install_used":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.Supply asset profile
Code review, repo analysis, testing, CI, GitHub, DevOps, and developer workflow skills.
Scenario
GitHub automation
I need my agent to triage GitHub issues, review pull requests, and summarize repository changes.
Agent fit
Claude Code + CLI + Codex
Codex, Claude Code, Cursor, CLI, or custom agents.
Install
Ready
npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli
Maintenance
fresh
1d since push
Risk
Needs review
Financial research output is not financial advice; require human review before any live investment decision
GitHub quality
135
68/100 Quality · 78/100 Trust
Coverage tags
Review notes
Financial research output is not financial advice; require human review before any live investment decision · Financial research output is not financial advice; require human review before any live investment decision.
Agent adoption scorecard
These scores combine public repository metadata, OpenAgentSkill review signals, maintenance freshness, and install readiness. They are a shortlist signal, not a replacement for human review.
Quality
PromisingUseful candidate, but compare it with alternatives before adopting.
Trust
Sandbox onlyUseful candidate with missing or mixed trust signals. Keep it in an isolated workspace until the outcome loop proves task fit.
Audit
Needs reviewA machine-readable review of install readiness, security metadata, maintenance, and adoption risk.
OpenAgentSkill Trust Score v5
Run only in a sandbox and compare close alternatives before using it for real work.
Stars
135 GitHub stars
Repo activity
135 stars, 27 forks
Maintenance
1d since push
License
LGPL-3.0
Install
npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli
Install safety
Agent-readable metadata
Use this block or the embedded JSON to decide whether an agent should install this skill, choose an alternative, or ask for human review first.
Suited tasks
Suited agents
Install decision
Trust and risk
Outcome loop
Install command
npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cliDo not use when
Agent safety v2
Sparse or mixed signals. Useful for discovery, but not for autonomous installation.
Test manually in an isolated workspace and compare against safer alternatives.
high
Skill metadata references terminal, CLI, shell, subprocess, or command execution workflows.
medium
Skill likely fetches remote pages, APIs, repositories, or external services.
medium
Skill may read or write project files, documents, generated artifacts, or local workspace state.
Agent resolve plan
The Resolve API returns the selected skill, alternatives, safety policy, audit notes, install target, and copy-paste prompt an agent can follow without scraping this page.
Open JSON
/api/agent/resolve?task=Use%20dpdata-cli%20for%20an%20agent%20workflow&agent=codex&max_risk=medium
Resolve text
/api/agent/resolve?task=Use%20dpdata-cli%20for%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text
Install handoff
/api/skills/jinzhezenggroup-dpdata-cli/install
Agent should check
Copy prompt
Task: Use dpdata-cli in this workspace.
Resolve first: https://www.openagentskill.com/api/agent/resolve?task=Use%20dpdata-cli%20for%20an%20agent%20workflow&agent=codex&max_risk=medium
Review install handoff: https://www.openagentskill.com/api/skills/jinzhezenggroup-dpdata-cli/install
Install command: npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cli
Before running it, summarize audit warnings, required permissions, and the fallback skill if install is risky.Agent handoff
Use the public install endpoint to fetch the command, safety checklist, target prompts, and canonical links for this skill.
Install handoff
/api/skills/jinzhezenggroup-dpdata-cli/install
LLM text format
/api/skills/jinzhezenggroup-dpdata-cli/install?format=text
Find alternatives
/api/skills/search?q=dpdata-cli&limit=3
Agent prompt
Use dpdata-cli for this task. Review https://www.openagentskill.com/api/skills/jinzhezenggroup-dpdata-cli/install, then install with: npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cliRegistry metadata
This page exposes the same decision, trust, audit, use-case, and install signals through the Registry API, so agents can rank this skill without scraping the UI.
Manifest
/api/registry/manifest/jinzhezenggroup-dpdata-cli
LLM text
/api/registry/manifest/jinzhezenggroup-dpdata-cli?format=text
Install alias
/api/registry/install/jinzhezenggroup-dpdata-cli
Recommend
/api/registry/recommend?task=Use%20dpdata-cli%20in%20an%20agent%20workflow&limit=3
Agent fit
GitHub automation
Use-case tags
Platforms
Claude Code
Audit report
A machine-readable review of install readiness, security metadata, maintenance, and adoption risk.
Agent decision cockpit
Prototype with this skill first; keep a fallback candidate ready.
Role in stack
Fallback candidate
Primary fit
GitHub automation
Trust label
Prototype first
Install path
Command ready
Use when
Evidence
review first
Implementation path
Trust profile
Useful candidate with missing or mixed trust signals. Keep it in an isolated workspace until the outcome loop proves task fit.
GitHub adoption
INFO135 GitHub stars
Stars/forks activity
CHECK135 stars, 27 forks; issue activity unavailable in current metadata
Recent maintenance
PASS1d since push
License clarity
PASSLGPL-3.0
Good signals
Review before install
Recommended action
Run only in a sandbox and compare close alternatives before using it for real work.
Quality profile
Useful candidate, but compare it with alternatives before adopting.
Workflow fit
Manage repositories
I need my agent to triage GitHub issues, review pull requests, and summarize repository changes.
Operate web apps
I need my agent to control a browser, fill forms, and verify web app workflows.
Build and ship code
I need a coding agent that can understand a repository, edit code, and review pull requests.
Workflow fit
Operate and verify web apps
A workflow for agents that navigate products, fill forms, take screenshots, and verify real user flows across web applications.
Inspect, patch, and verify code
A workflow for software agents that inspect repositories, review pull requests, generate tests, and turn findings into shippable patches.
Scrape, clean, and reuse web data
A practical workflow for agents that crawl public pages, extract clean content, normalize data, and hand it to downstream research or RAG workflows.
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--- 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 version: '1.0' 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
| 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
```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:
- [Formats Reference (stable)](https://docs.deepmodeling.com/projects/dpdata/en/stable/formats.html)
### 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 |
## Tips
1. **Auto-detection**: Use `-i auto` (default) to let dpdata detect format automatically 1. **Type mapping**: Use `-t` to specify atom type order for deepmd formats 1. **Multi-system**: Use `--multi` for directories containing multiple systems 1. **Compressed output**: Use `deepmd/npy` or `deepmd/hdf5` for smaller file sizes
## References
- [dpdata Documentation](https://docs.deepmodeling.com/projects/dpdata/) - [CLI Reference](https://docs.deepmodeling.com/projects/dpdata/en/stable/cli.html) - [Formats Reference](https://docs.deepmodeling.com/projects/dpdata/en/stable/formats.html) - [GitHub Repository](https://github.com/deepmodeling/dpdata)
Source provenance
Decision snapshot
recent repository activity
Audit
Install and adoption review
Agent-proven evidence
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No agent outcome data yet. The first agent run can report success, setup needs, risk blocks, failure, or not-relevant through /api/agent/outcome.
Install
Free and open source. Review the report before installing into production agents.
Growth loop
Scenario-led draft for dpdata-cli, ready for a manual X post.
dpdata-cli: A command-line utility for converting and manipulating over 50 atomic simulation data formats... 135 stars https://www.openagentskill.com/skills/jinzhezenggroup-dpdata-cli?ref=x
Listing + install path for dpdata-cli: https://www.openagentskill.com/skills/jinzhezenggroup-dpdata-cli?ref=x Install: npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill dpdat...
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