gpumdkit-format-conversion

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Use when converting structure files between computational materials science formats. Supports VASP (POSCAR/OUTCAR/XDATCAR), LAMMPS, CP2K, ABACUS, CIF, MTP, ASE trajectory, and extxyz. Use when user asks about: format conversion, file conversion, structure conversion, POSCAR to xyz, OUTCAR to extxyz, LAMMPS dump conversion, or adding group labels.

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GPUMDkit Format Conversion

Supported Formats

Format	Extensions	Description
VASP	POSCAR, OUTCAR, XDATCAR	Vienna Ab initio Simulation Package
LAMMPS	.data, dump.*	Large-scale Atomic/Molecular Massively Parallel Simulator
CP2K	.log, pos.xyz, frc.xyz, cell.cell	Quantum chemistry and solid state physics
ABACUS	running_scf.log, running_md.log	Atomic-orbital Based Ab-initio Computation at UStc
CIF	.cif	Crystallographic Information File
MTP	.cfg	Moment Tensor Potential format
ASE	.traj	Atomic Simulation Environment trajectory
extxyz	.xyz	Extended XYZ (primary working format)

Command Reference

VASP Conversions

# OUTCAR to extxyz (directory, shell version)
gpumdkit.sh -out2xyz <directory>

# OUTCAR to extxyz (Python version)
gpumdkit.sh -out2exyz <directory>

# XDATCAR to extxyz
gpumdkit.sh -xdat2exyz XDATCAR output.xyz

# POSCAR to extxyz
gpumdkit.sh -pos2exyz POSCAR model.xyz

# extxyz to POSCAR (all frames)
gpumdkit.sh -exyz2pos structures.xyz

LAMMPS Conversions

# LAMMPS dump to extxyz
# IMPORTANT: Element symbols must match atom type IDs in dump file
gpumdkit.sh -lmp2exyz dump.lammpstrj Li Y Cl

# POSCAR to LAMMPS data
gpumdkit.sh -pos2lmp POSCAR lammps.data

CIF Conversions

# CIF to POSCAR
gpumdkit.sh -cif2pos input.cif POSCAR.vasp

# CIF to extxyz
gpumdkit.sh -cif2exyz input.cif model.xyz

Other Conversions

# ASE trajectory to extxyz
gpumdkit.sh -traj2exyz input.traj output.xyz

dp2xyz

Converts DeepMD npy datasets to extxyz format. Recursively scans a directory for datasets containing type.raw, type_map.raw, and set.000/.

Usage:

gpumdkit.sh -dp2xyz database train.xyz

Dependencies: dpdata, ase. Requires conda activate gpumd environment. Author: Denan LI (lidenan@westlake.edu.cn)

Structure Manipulation

# Add group labels (required for GPUMD/NEP)
gpumdkit.sh -addgroup POSCAR Li Y Cl

# Add weights to structures
gpumdkit.sh -addweight input.xyz output.xyz 2.0

# Replicate structure (by factors)
gpumdkit.sh -replicate POSCAR supercell.vasp 2 2 2

# Replicate structure (by target atom count)
gpumdkit.sh -replicate POSCAR supercell.vasp 256

# Extract specific frame (0-based index)
gpumdkit.sh -get_frame trajectory.xyz 1000

# Clean extxyz metadata
gpumdkit.sh -clean_xyz input.xyz clean.xyz

Detailed CLI Flag Reference

CLI Flag	Conversion	Syntax
`-out2xyz`	OUTCAR -> extxyz (shell)	`gpumdkit.sh -out2xyz <dir>`
`-out2exyz`	OUTCAR -> extxyz (python)	`gpumdkit.sh -out2exyz <dir>`
`-pos2exyz`	POSCAR -> extxyz	`gpumdkit.sh -pos2exyz <poscar> <xyz>`
`-exyz2pos`	extxyz -> POSCAR	`gpumdkit.sh -exyz2pos <xyz>`
`-pos2lmp`	POSCAR -> LAMMPS data	`gpumdkit.sh -pos2lmp <poscar> <lmp>`
`-lmp2exyz`	LAMMPS dump -> extxyz	`gpumdkit.sh -lmp2exyz <dump> <elem...>`
`-cif2pos`	CIF -> POSCAR	`gpumdkit.sh -cif2pos <cif> <output>`
`-cif2exyz`	CIF -> extxyz	`gpumdkit.sh -cif2exyz <cif> <output>`
`-xdat2exyz`	XDATCAR -> extxyz	`gpumdkit.sh -xdat2exyz XDATCAR dump.xyz`
`-traj2exyz`	ASE traj -> extxyz	`gpumdkit.sh -traj2exyz <traj> <xyz>`
`-dp2xyz`	DeepMD npy → extxyz (via dpdata)	`gpumdkit.sh -dp2xyz <input_dir/> [output.xyz]`
`-addgroup`	Add group labels	`gpumdkit.sh -addgroup <poscar> <elem...>`
`-addweight`	Add weight	`gpumdkit.sh -addweight <in> <out> <weight>`
`-replicate`	Replicate structure	`gpumdkit.sh -replicate <in> <out> a b c`
`-get_frame`	Extract frame	`gpumdkit.sh -get_frame <xyz> <index>`
`-clean_xyz`	Clean extxyz info	`gpumdkit.sh -clean_xyz <in> <out>`

Examples

Example 1: Convert VASP MD Output

# Convert all OUTCAR files in current directory
gpumdkit.sh -out2xyz .

# Add group labels for NEP training
gpumdkit.sh -addgroup POSCAR Pb Ti O

# Result: model.xyz ready for NEP training

Example 2: Prepare LAMMPS Simulation

# Convert POSCAR to LAMMPS data
gpumdkit.sh -pos2lmp POSCAR system.data

# After LAMMPS simulation, convert dump back
gpumdkit.sh -lmp2exyz dump.lammpstrj Li P S

Example 3: Batch Conversion

# Convert multiple OUTCAR files
for dir in run_*; do
    gpumdkit.sh -out2xyz "$dir"
    mv "$dir"/model.xyz "$dir"/trajectory.xyz
done

Example 4: Structure Replication

# Replicate to 2x2x2 supercell
gpumdkit.sh -replicate POSCAR supercell_222.vasp 2 2 2

# Replicate to target ~256 atoms
gpumdkit.sh -replicate POSCAR supercell_256.vasp 256

Notes

extxyz is the primary format: Most GPUMDkit tools work with extxyz files
Group labels are essential: Required for GPUMD/NEP to identify atom types
Frame indexing is 0-based: First frame is index 0
Element ordering matters for LAMMPS: Must match atom type IDs in dump file
exyz2pos exports all frames: Creates separate POSCAR for each frame

Dependencies

Most Python scripts require:

ase (Atomic Simulation Environment)
numpy

Detailed Documentation

See format_conversion.md for comprehensive guide.