v0.0.3 workflow scripts
aenet_env provides reusable APIs and environment/workflow utilities, a set of composable stages. The following scripts are v0.0.3 examples. Edit the constants at the top of each script and run python script.py. The structure-generation scripts provide alternative methods selected for the calculation under study.
b00 — b00_make_poscar.py
Set WORK_DIR, ELEMENTS, and optional CELL. The script calls aenet_env.xyz.convert_xyz_tree(WORK_DIR, WORK_DIR, elements=ELEMENTS, cell=CELL) to convert numbered periodic XYZ structures to VASP5 POSCAR files with grouped elements. The supplied example uses SiO2, ('Si','O'), and CELL=None. Check periodic cells, element order, and output paths before running.
b01 — b01_stage_structures.py
Set WORK_DIR. aenet_env.structures.discover_flat_cases discovers and reports calculation cases and checks for POSCAR files. The supplied v0.0.3 script only inspects cases; it does not copy or relocate structures.
b02 — b02_prepare_vasp.py
Set CALCULATIONS_DIR, POTCAR_ROOT, ELEMENTS, KPOINT_GRID, and INCAR_TAGS. load_or_discover_cases finds cases, and vasp_inputs.prepare_vasp_inputs prepares INCAR, KPOINTS, and POTCAR. The example uses ENCUT=520 eV, EDIFF=1e-5, NSW=0, IBRION=-1, ISMEAR=0, SIGMA=0.1, ISPIN=1, and a Gamma-only (1,1,1) mesh. These are example single-point settings, not converged settings for all materials. Verify PAW datasets, cutoff, k-mesh, spin, and convergence. The example ~/potpaw_PBE.64 is site-specific.
b03 — b03_submit_vasp_jobs.py
Set WORK_DIR, CALCULATIONS_DIR, JOB_FILE, SUBMIT_COMMAND, and SUBMIT. The script verifies POSCAR, INCAR, KPOINTS, and POTCAR, reuses or copies a job script, and optionally submits each case. The example uses job_hpcs2024_node1.sh, ('qsub',), and SUBMIT=True. Set SUBMIT=False for a preliminary check; inspect queue settings, resource requests, and existing outputs. Site-specific scheduler logic belongs in the example script, not the reusable package.
c00 — c00_collect_references.py
Set VASP_CASES_DIR and REFERENCES_DIR. aenet_env.references.collect_reference_xsf collects training XSF references from VASP results (vasprun.xml). Verify SCF convergence, cells, element ordering, energies, forces, units, and missing/failed jobs before accepting references.
c01 — c01_train_ann.py
The script collects *.xsf under REFERENCES=ROOT/'references' and delegates to aenet_env.training. Enable exactly one of fortran_legacy, fortran_normal, aenet_python_torch, and separate_aenet_pytorch in main(). The attached v0.0.3 example enables fortran_normal(refs). See Training parameters for configuration and model-specific caveats.
Stage boundaries
b00 → b01 → b02 → b03 → c00 → c01 is a representative workflow, not a required package execution order. Validate structure construction, DFT input validity, completed calculations, reference labels, ML accuracy, and any RMC_POT application separately. SiO₂ paths and constants correspond to the v0.0.3 example.