jinzhezenggroup 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
-tto specify atom type order for deepmd formats - Multi-system: Use
--multifor directories containing multiple systems - Compressed output: Use
deepmd/npyordeepmd/hdf5for smaller file sizes