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name dpdata-cli
description 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.
compatibility Requires uvx (uv) for running dpdata
metadata
author version repository
njzjz-bot
1.0

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:

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
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