Dpdata CLI

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dpdata-cli

Dpdata CLI is an Agent Skill for documents published in the deepmodeling/dpdata repository on GitHub: a SKILL.md instruction file an AI agent can load to do this task.

Convert and manipulate atomic simulation data formats using dpdata CLI. Use when converting between DFT/MD output formats (VASP, LAMMPS, QE, CP2K, Gaussian, ABACUS, etc.), preparing training data for DeePMD-kit, or working with DeePMD formats. Supports 50+ formats including deepmd/raw, deepmd/comp, deepmd/npy, deepmd/hdf5.

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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`	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