abacus-data-processing

name	abacus-data-processing
description	Prepare ABACUS calculation inputs from CIF/POSCAR with default settings and generate per-structure INPUT/KPT/STRU run directories.

ABACUS Data Processing

Reference usage policy:

• Do not bulk-read reference/* during normal execution.
• Before finalizing generated config files, quickly scan reference/ROUTING.md for strong intent matches.
• If a very close route is found, open only the mapped markdown(s) (and minimal companion example files if needed), then adapt parameters to that pattern instead of blindly keeping defaults.
• If no strong route is found, keep the template/script defaults.
• When discussing setup choices with the user, you may reference relevant files under reference/* as supporting evidence.
• Keep reference loading minimal and targeted; do not ingest unrelated documents.

1. Prepare one split-local ABACUS workdir per dataset split. Do not run train and test generation in one shared mutable directory.
2. Seed each split-local workdir from <skill_root>/templates/abacus/:

• abacus_input_gen.yaml
• run_abacus.sh

3. Render the copied template into the split-local workdir. Do not edit skill-owned templates in place.
4. In abacus_input_gen.yaml, render split-specific fields only:

• structure_glob
• output_root
• optional system_name

5. In run_abacus.sh, only render split-specific values such as SYSTEM_NAME, INPUT_ROOT, and DATASET_ROOT. Preserve the runtime environment contract.
6. Keep default settings unless the user explicitly requests overrides. Default baseline:

• calculation=scf
• basis_type=lcao
• ecutwfc=100, scf_thr=1e-7, scf_nmax=200
• out_mat_hs2=1 (export sparse H/S matrices for downstream graph generation)
• kpt=Gamma 4x4x4

7. Runtime environment policy:

• run via <skill_root>/scripts/data_processing.sh
• for input generation, default conda env is ${ABACUS_CONDA_ENV:-OpenMX} (contains pymatgen and pyyaml); if unavailable, fall back to base
• for ABACUS execution via run_abacus.sh, default conda env is ${ABACUS_CONDA_ENV:-abacus_env}
• only override ABACUS_CONDA_ENV or PYTHON_BIN when explicitly needed
• logs are written to <workdir>/logs/abacus_input_gen.log

8. Use the split-local entry command:

• <skill_root>/scripts/data_processing.sh --workdir <abacus_split_root> --config abacus_input_gen.yaml

9. For ABACUS batch execution against generated case directories, use:

• bash ./run_abacus.sh [jobs] [omp_threads]
• default command is ABACUS_CMD=${ABACUS_CMD:-${ABACUS_BIN}} and can be overridden for site-specific launchers.

10. Input policy:

• CIF input is first-class
• POSCAR/CONTCAR/vasp-like files are also allowed when readable by pymatgen
• fail fast when structure_glob resolves to zero files
• placeholders like __CIF_GLOB__ / __ABACUS_INPUT_ROOT__ must be rendered before execution

11. Generation policy:

• output is one run folder per structure under output_root
• each run folder contains INPUT, KPT, STRU, and source.* for traceability
• default naming is index_stem
• default overwrite=false; existing run dirs must fail instead of silent overwrite
• default copy_source_file=true
• default move_flags=[1,1,1]

12. Mapping and safety guardrails:

• validate pseudopotential mapping (PP_DICT) for all species
• when basis_type=lcao, validate orbital mapping (ORB_DICT) for all species
• if any element mapping is missing, stop and report missing symbols; do not guess

13. Multi-split isolation:

• train/test (or other splits) must use independent output_root
• do not let one split overwrite another split's generated run folders

14. Returnables for downstream stages:

• generated output_root per split
• generated run-folder list
• generation log path (logs/abacus_input_gen.log)
• when run_abacus.sh is executed, return ABACUS run log path (logs/run_abacus_*.log)
• clear failure reason when generation stops