# 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`). ## 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 | ```bash # 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 ``` ## 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. ### 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. ### Single file ```bash 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 ``` ### 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. ```bash # 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.