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
References
