Computational Chemistry Agent Skills
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dpdata-cli

data-processing
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.
v1.0 Requires uvx (uv) for running dpdata repository source

Installation

Install folder: dpdata-cli · Repo path: data-processing/dpdata-cli
Copy/paste this message to your OpenClaw agent. 
Please install the OpenClaw skill "dpdata-cli" on the OpenClaw host.

Steps:
- Download: https://skills.computchem.cn/skill-zips/dpdata-cli.zip
- Unzip it to get dpdata-cli/
- Copy dpdata-cli/ into the workspace skills directory (<workspace>/skills/)
- Start a NEW OpenClaw session so the skill is loaded

Then verify:
openclaw skills list --eligible
openclaw skills info dpdata-cli
Prerequisites: Requires uvx (uv) for running 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

ArgumentDescription
from_fileRead data from a file (positional)
--to_file, -ODump data to a file
--from_format, -iFormat of from_file (default: “auto”)
--to_format, -oFormat of to_file
--no-labeled, -nLabels aren’t provided (default: False)
--multi, -mSystem contains multiple directories (default: False)
--type-map, -tType map for atom types
--versionShow 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:

DeePMD-kit Formats

Format NameDescription
deepmd/rawDeePMD-kit raw text format
deepmd/comp / deepmd/npyDeePMD-kit compressed numpy format
deepmd/npy/mixedDeePMD-kit mixed type format
deepmd/hdf5DeePMD-kit HDF5 format

VASP Formats

Format NameDescription
vasp/poscar / vasp/contcar / poscar / contcarVASP structure files
vasp/outcar / outcarVASP OUTCAR output
vasp/xml / xmlVASP XML output
vasp/stringVASP string format

LAMMPS Formats

Format NameDescription
lammps/lmp / lmpLAMMPS data file
lammps/dump / dumpLAMMPS dump file

ABACUS Formats

Format NameDescription
stru / abacus/struABACUS structure file
abacus/lcao/scf / abacus/pw/scf / abacus/scfABACUS SCF output
abacus/lcao/md / abacus/pw/md / abacus/mdABACUS MD output
abacus/lcao/relax / abacus/pw/relax / abacus/relaxABACUS relax output

Quantum ESPRESSO Formats

Format NameDescription
qe/cp/trajQE CP trajectory
qe/pw/scfQE PWscf output

CP2K Formats

Format NameDescription
cp2k/outputCP2K output
cp2k/aimd_outputCP2K AIMD output

Gaussian Formats

Format NameDescription
gaussian/logGaussian log file
gaussian/fchkGaussian formatted checkpoint
gaussian/mdGaussian MD output
gaussian/gjfGaussian input file

Other Formats

Format NameDescription
xyzXYZ format
mace/xyz / nequip/xyz / gpumd/xyz / extxyz / quip/gap/xyzExtended XYZ variants
ase/structureASE structure format
ase/trajASE trajectory
pymatgen/structurepymatgen structure
pymatgen/moleculepymatgen molecule
gromacs/gro / groGROMACS gro file
siesta/outputSIESTA output
siesta/aimd_outputSIESTA AIMD output
pwmat/output / pwmat/mlmd / pwmat/movementPWmat output
pwmat/final.config / pwmat/atom.configPWmat config
orca/spoutORCA output
psi4/outPSI4 output
dftbplusDFTB+ output
fhi_aims/output / fhi_aims/mdFHI-aims output
amber/mdAMBER MD
n2p2n2p2 format
mol_file / molMOL file
sdf_file / sdfSDF file
openmx/mdOpenMX MD
sqm/outSQM output
sqm/inSQM input
listList format
3dmol3Dmol 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