# Dpdata CLI

> 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.

- Skill: `jinzhezenggroup/dpdata-cli` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds@latest add jinzhezenggroup/dpdata-cli`
- Raw SKILL.md: https://api.skillmd.com/api/skills/jinzhezenggroup/dpdata-cli/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: jinzhezenggroup (https://skillmd.com/u/jinzhezenggroup)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/jinzhezenggroup/dpdata-cli

---


# 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)