dpdata-cli

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
license	GPL-3.0-only
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:

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

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

GPUMD / NEP integration

dpdata natively supports gpumd/xyz and extxyz formats. Key workflows:

• DFT → NEP training data:

  uvx dpdata OUTCAR -i vasp/outcar -O train.xyz -o extxyz
  

• GPUMD trajectory conversion:

  uvx dpdata movie.xyz -i extxyz -O output.data -o lammps/lmp
  

• Virial convention warning: after conversion to extxyz, verify the virial sign matches the NEP convention (total cell virial in eV) before training.
• Species ordering: the -t type-map flag controls element order. Ensure this matches the type line in nep.in.

References

• dpdata Documentation
• CLI Reference
• Formats Reference
• GitHub Repository