dpdata-cli v1.0A

Immutable. This exact content is served forever at /api/v1/blob/c0091ada417d2414.

---
name: dpdata-cli
description: Convert and manipulate atomic simulation data formats using dpdata CLI. Use when converting between DFT/MD output formats (VASP, LAMMPS, QE, CP2K, Gaussian, ABACUS, etc.), preparing training data for DeePMD-kit, or working with DeePMD formats. Supports 50+ formats including deepmd/raw, deepmd/comp, deepmd/npy, deepmd/hdf5.
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
2. **Type mapping**: Use `-t` to specify atom type order for deepmd formats
3. **Multi-system**: Use `--multi` for directories containing multiple systems
4. **Compressed output**: Use `deepmd/npy` or `deepmd/hdf5` for smaller file sizes

## References

- [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)