| name | dpdata-cli |
| description | Convert and manipulate atomic simulation data formats using dpdata CLI. Use when converting between DFT/MD output formats or preparing DeePMD-kit training data. Supports 50+ formats including deepmd, xyz or extxyz, ABACUS, VASP, LAMMPS, CP2K, etc. |
| compatibility | Requires uvx (uv) for running dpdata |
| 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 |
Extended XYZ (extxyz) Format Details
The following format names are all equivalent and invoke the same reader/writer:
extxyz — general-purpose extended XYZquip/gap/xyz / quip/gap/xyz_file — QUIP/GAP framework datasetsmace/xyz — MACE model training datanequip/xyz — NequIP model training datagpumd/xyz — GPUMD simulation data
Important: Plain xyz is a different, simpler format that stores atom species and coordinates but does not provide per-frame properties such as energies, forces, cell information, or periodic boundary conditions. Do not confuse xyz with extxyz.
CLI Examples for extxyz
uvx dpdata data.xyz -i extxyz -O deepmd_data -o deepmd/npy --multi
uvx dpdata data.xyz -i extxyz -O deepmd_data -o deepmd/npy/mixed --multi
uvx dpdata data.xyz -i extxyz -O POSCAR -o vasp/poscar
uvx dpdata data.xyz -i extxyz -O deepmd_data -o deepmd/npy -t H C N O
Tips for extxyz
- Use
-i extxyz explicitly when working with .xyz files that contain extended XYZ data. Using -i xyz retains only atom species and coordinates, omitting per-frame properties such as energies, forces, and cell information.
- Use
--multi for any multi-frame extxyz file. Without --multi, the CLI constructs a LabeledSystem that keeps only the first frame. This applies to all multi-frame trajectories, not just heterogeneous (mixed-composition) files. dpdata groups frames by chemical formula internally.
- All alias names behave identically —
-i mace/xyz, -i nequip/xyz, -i gpumd/xyz, -i quip/gap/xyz, -i quip/gap/xyz_file, and -i extxyz produce the same result.
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
References
