| 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:
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
-t to specify atom type order for deepmd formats
- Multi-system: Use
--multi for directories containing multiple systems
- 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:
References
