9.2. Input Formats

Project/package name: dpa-adapt Python import: dpa_adapt Main CLI: dpa-adapt Optional short alias: dpaad Display name: DPA-ADAPT — Atomistic DPA Adaptation for Property Tasks

dpa-adapt data convert and the Python dpa_adapt.convert() helper auto-detect the input type and route it to the correct pipeline: SMILES table → RDKit 3D conformer generation, structure files → dpdata (auto-detect or explicit --fmt).

9.2.1. SMILES Tables (CSV)

Trigger: file extension .csv and a SMILES column. By default, the converter reads SMILES/smiles; use --smiles-col for other column names such as smi or mol. Or pass --fmt smiles explicitly.

Parameter	Default	Description
--smiles-col	SMILES	Column name for SMILES strings
--property-col	Property	Input table column to read target values from; also used as the output label name
--train-ratio	0.9	Fraction of samples used for training set
--mol-dir	—	Directory of pre-generated .mol, .sdf, .xyz, or .pdb structure files (skips RDKit 3D conformer generation)
--mol-template	id{row}.mol	Filename template under --mol-dir; use {row} for the CSV row index
--split-seed	42	Random seed for train/valid splitting
--conformer-seed	42	Random seed for RDKit 3D conformer generation

# Auto-detected via SMILES column
dpa-adapt data convert --input molecules.csv --output ./npy \
    --property-col homo
# Short alias
dpaad data convert --input molecules.csv --output ./npy \
    --property-col homo

# Explicit fmt + custom column names
dpa-adapt data convert --input data.csv --output ./npy --fmt smiles \
    --smiles-col smi --property-col GAP --train-ratio 0.85 \
    --split-seed 42 --conformer-seed 43
# Short alias
dpaad data convert --input data.csv --output ./npy --fmt smiles \
    --smiles-col smi --property-col GAP --train-ratio 0.85 \
    --split-seed 42 --conformer-seed 43

9.2.2. Structure Files via dpdata

Trigger: inputs not routed to the SMILES pipeline. This means --fmt is not smiles; when --fmt is omitted, CSV inputs are routed here only if they do not contain a recognized SMILES column. Calls dpdata for format auto-detection or explicit conversion.

9.2.2.1. Common Formats

--fmt value	Typical file(s)	Notes
xyz	*.xyz	Plain XYZ
vasp/poscar / vasp/contcar	POSCAR, CONTCAR	VASP input/final structure
vasp/outcar	OUTCAR	VASP output (energies, forces, stress)
vasp/xml	vasprun.xml	VASP XML output
vasp/string	VASP structure string	VASP structure from a string
abacus/stru / stru	STRU	ABACUS input structure
abacus/scf / abacus/pw/scf / abacus/lcao/scf	SCF output	ABACUS SCF calculation
abacus/md / abacus/pw/md / abacus/lcao/md	MD output	ABACUS molecular dynamics
abacus/relax / abacus/pw/relax / abacus/lcao/relax	Relax output	ABACUS relaxation
cp2k/aimd_output	CP2K MD output	CP2K AIMD output file
cp2k/output	CP2K SCF output	CP2K single-point output
deepmd/raw	set.*/ dirs	DeePMD-kit raw format
deepmd/comp / deepmd/npy	set.*/ dirs	DeePMD-kit compressed/npy format
deepmd/npy/mixed	mixed deepmd/npy dir	DeePMD-kit mixed npy format
deepmd/hdf5	*.hdf5	DeePMD-kit HDF5 format
lammps/dump / dump	dump.*	LAMMPS dump trajectory
lammps/lmp / lmp	*.lmp	LAMMPS data file
qe/cp/traj	CP trajectory	Quantum ESPRESSO Car-Parrinello MD
qe/pw/scf	PWscf output	Quantum ESPRESSO PWscf
siesta/output	Siesta output	SIESTA SCF output
siesta/aimd_output	Siesta MD output	SIESTA AIMD output
gaussian/log	*.log	Gaussian log file
gaussian/fchk	*.fchk	Gaussian formatted checkpoint
gaussian/md	Gaussian MD output	Gaussian MD trajectory
gaussian/gjf	*.gjf	Gaussian input file
amber/md	Amber MD output	Amber MD trajectory
gromacs/gro / gro	*.gro	GROMACS coordinate file
pwmat/output / pwmat/movement / pwmat/mlmd	REPORT, MOVEMENT, MLMD	PWmat output / movement / MLMD
pwmat/final.config / pwmat/atom.config	final.config, atom.config	PWmat final/input structure
fhi_aims/output / fhi_aims/md	FHI-aims output/MD	FHI-aims calculation or MD trajectory
fhi_aims/scf	FHI-aims SCF output	FHI-aims SCF
psi4/out	Psi4 output	Psi4 calculation output
psi4/inp	Psi4 input	Psi4 input file
orca/spout	ORCA output	ORCA single-point output
sqm/out	SQM output	SQM output
sqm/in	SQM input	SQM input
openmx/md	OpenMX MD output	OpenMX MD trajectory
n2p2	n2p2 output	n2p2/NNPack output
dftbplus	DFTB+ output	DFTB+ detailed.xml
mol / mol_file	*.mol	MDL Molfile
sdf / sdf_file	*.sdf	MDL SDFile
ase/structure	Any ASE format	ASE structure (single frame)
ase/traj	Any ASE trajectory	ASE trajectory (multi-frame)
pymatgen/structure	pymatgen objects	pymatgen Structure
pymatgen/molecule	pymatgen objects	pymatgen Molecule
pymatgen/computedstructureentry	pymatgen objects	pymatgen ComputedStructureEntry
lmdb	LMDB dir	DeePMD-kit LMDB format
list	List-format dir	List of system directories
3dmol	3Dmol format	3Dmol.js format

You can omit --fmt and let dpdata infer the input format from the file name or content. For example, files named POSCAR, OUTCAR, or *.xyz are often recognized automatically. Use --fmt when the file name is ambiguous or auto-detection fails.

9.2.2.2. Single file

dpa-adapt data convert --input POSCAR --output ./npy
dpaad data convert --input POSCAR --output ./npy

dpa-adapt data convert --input OUTCAR --output ./npy --fmt vasp/outcar
dpaad data convert --input OUTCAR --output ./npy --fmt vasp/outcar

dpa-adapt data convert --input traj.xyz --output ./npy --fmt xyz
dpaad data convert --input traj.xyz --output ./npy --fmt xyz

9.2.2.3. Glob patterns

When --input contains wildcards (*, ?, [), conversion uses mirrored batch output:

• 1 or more matches → each matched file is converted into an output directory that mirrors its path relative to the non-wildcard prefix.

• 0 matches → FileNotFoundError.

• A manifest.json is written into the output root, recording converted and skipped files.

# Glob output mirrors the input tree under ./npy_root
dpa-adapt data convert --input "calcs/**/OUTCAR" --output ./npy_root --fmt vasp/outcar
dpaad data convert --input "calcs/**/OUTCAR" --output ./npy_root --fmt vasp/outcar

For example, calcs/run1/OUTCAR is written as npy_root/run1/OUTCAR/. When --strict is set, the first conversion error fails immediately. Without it, errors are skipped and logged in the manifest.