v1.0 to v1.0

70 added, 69 removed. Audit A to A.

---

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"

+ 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 |

+ | 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 |

+ | 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 |

+ | `deepmd/npy/mixed` | DeePMD-kit mixed type format |

+ | `deepmd/hdf5` | DeePMD-kit HDF5 format |

### VASP Formats

- | Format Name | Description |

- |-------------|-------------|

+ | 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 |

+ | `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 |

+ | 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 |

+ | 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 |

- |-------------|-------------|

+ | Format Name | Description |

+ | ------------ | ---------------- |

| `qe/cp/traj` | QE CP trajectory |

- | `qe/pw/scf` | QE PWscf output |

+ | `qe/pw/scf` | QE PWscf output |

### CP2K Formats

- | Format Name | Description |

- |-------------|-------------|

- | `cp2k/output` | CP2K output |

+ | Format Name | Description |

+ | ------------------ | ---------------- |

+ | `cp2k/output` | CP2K output |

| `cp2k/aimd_output` | CP2K AIMD output |

### Gaussian Formats

- | Format Name | Description |

- |-------------|-------------|

- | `gaussian/log` | Gaussian log file |

+ | Format Name | Description |

+ | --------------- | ----------------------------- |

+ | `gaussian/log` | Gaussian log file |

| `gaussian/fchk` | Gaussian formatted checkpoint |

- | `gaussian/md` | Gaussian MD output |

- | `gaussian/gjf` | Gaussian input file |

+ | `gaussian/md` | Gaussian MD output |

+ | `gaussian/gjf` | Gaussian input file |

### Other Formats

- | Format Name | Description |

- |-------------|-------------|

- | `xyz` | XYZ format |

+ | 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 |

+ | `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

+ 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)