deepmodeling/dpdata-cli
skills/dpdata-cli/SKILL.md
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.
$ install --global
skillsauthnpx skillsauth add deepmodeling/dpdata dpdata-cliInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- 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
- 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:
uvx dpdata <from_file> [options]
Command Line Usage
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
uvx dpdata OUTCAR -i vasp/outcar -O deepmd_data -o deepmd/raw
Convert LAMMPS dump to VASP POSCAR
uvx dpdata dump.lammps -i lammps/dump -O POSCAR -o vasp/poscar
Convert with type map
uvx dpdata OUTCAR -i vasp/outcar -O deepmd_data -o deepmd/raw -t C H O N
Convert multiple systems
uvx dpdata data_dir -i vasp/outcar -O output_dir -o deepmd/comp --multi
Convert to deepmd/npy (compressed format)
uvx dpdata OUTCAR -i vasp/outcar -O deepmd_npy -o deepmd/npy
Convert to deepmd/hdf5
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)
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
- Auto-detection: Use
-i auto(default) to let dpdata detect format automatically - Type mapping: Use
-tto specify atom type order for deepmd formats - Multi-system: Use
--multifor directories containing multiple systems - Compressed output: Use
deepmd/npyordeepmd/hdf5for smaller file sizes
References
- dpdata Documentation
- CLI Reference
- Formats Reference
- GitHub Repository
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