Dpdata CLI Agent Skill
> 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.
Install
one command, takes just this skill from the repositorynpx skills add https://github.com/jinzhezenggroup/computational-chemistry-agent-skills --skill dpdata-cliWhat comes with it
1 935 bytes besides the instructionThe instruction itself
22 sections, as written by the authordpdata 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
References
Other skills for the same job
different authors, same section of the catalogue
Create new skills, modify and improve existing skills, and measure skill performance. Use when users want to create a skill from scratch, edit, or optimize an existing skill, run evals to test a skill, benchmark skill performance with variance analysis, or optimize a skill's description for better triggering accuracy.
Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.
Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.
Statistical modeling toolkit. OLS, GLM, logistic, ARIMA, time series, hypothesis tests, diagnostics, AIC/BIC, for rigorous statistical inference and econometric analysis.
Add unsigned integer (uint) type support to PyTorch operators by updating AT_DISPATCH macros. Use when adding support for uint16, uint32, uint64 types to operators, kernels, or when user mentions enabling unsigned types, barebones unsigned types, or uint support.
Convert PyTorch AT_DISPATCH macros to AT_DISPATCH_V2 format in ATen C++ code. Use when porting AT_DISPATCH_ALL_TYPES_AND*, AT_DISPATCH_FLOATING_TYPES*, or other dispatch macros to the new v2 API. For ATen kernel files, CUDA kernels, and native operator implementations.
Write docstrings for PyTorch functions and methods following PyTorch conventions. Use when writing or updating docstrings in PyTorch code.
How to use it
Take jinzhezenggroup/dpdata-cli from the repository into ~/.claude/skills for personal
use, or into .claude/skills inside a project.
The agent identifies a skill by the name field in its header. Two skills with the
same name cannot sit side by side — one of them will be ignored.
The instructions reference uvx.
Without those the skill loads but fails at the first command.