runstruct_abacus is a lightweight interface script connecting ATAT (Alloy Theoretic Automated Toolkit) with ABACUS (Atomic-orbital Based Ab-initio Computation at UStc). It automatically converts ATAT's str.out structure files into ABACUS INPUT/STRU input files, runs the DFT calculation, and extracts results back into ATAT-compatible formats (energy, str_relax.out).

• Seamless ATAT Integration: Works within ATAT's multi-directory enumeration workflow (1/, 2/, 3/...)
• Template-Based Input: Uses abacus.wrap as a template—nearly a native ABACUS INPUT file with minimal script-specific annotations
• Automatic File Discovery: Searches abacus.wrap upward through parent directories (./ → ../ → ../../...)
• Smart Pseudopotential/Orbital Matching: Auto-detects files in pseudo_dir/orbital_dir by element prefix; explicit override available for ambiguous cases
• Flexible Execution Modes: Supports full pipeline, input-only generation, and post-calculation extraction
• Parallel Ready: Accepts mpirun/srun prefixes for HPC environments

No installation is required. Simply place runstruct_abacus in your $PATH (or in the same directory as other ATAT runstruct_* scripts) and ensure it is executable:

chmod +x runstruct_abacus

• ATAT toolkit (cellcvrt, kmesh etc.) must be in $PATH
• ABACUS executable path must be set in ~/.abacus.rc

Create this file in your home directory to tell the interface where ABACUS lives:

#!/bin/bash
ABACUSCMD="abacus"                    # or "mpirun -np 4 abacus"

The script will auto-generate a template if this file does not exist.

abacus.wrap is almost a standard ABACUS INPUT file. The script copies nearly every line verbatim into INPUT, except for species lines which are consumed by the script to build the STRU file.

INPUT_PARAMETERS
calculation    vc-relax
ecutwfc        50
basis_type     lcao
kspacing       0.15
pseudo_dir     /path/to/pseudopotentials
orbital_dir    /path/to/numerical_orbitals

species  Al  26.982  Al_ONCV_PBE-1.0.upf  Al_gga_7au_60Ry_2s2p1d.orb
species  Fe  55.845  Fe_ONCV_PBE-1.0.upf  Fe_gga_8au_100Ry_2s2p2d1f.orb

species  <Element>  <Mass>  <PP_File>  [<Orb_File>]

If auto-search finds zero or more than one match for an element, the script aborts and prints a helpful message asking you to add an explicit species line.

runstruct_abacus [-w file] [-nr] [-ex] [-clean] [cmdprefix]

The optional cmdprefix argument lets you prepend any launch command—most commonly MPI wrappers:

# Run with 4 MPI ranks
runstruct_abacus "mpirun -np 4"

# Run with srun (SLURM)
runstruct_abacus "srun -n 8"

# Run on a specific node (similar to Abinit's node-prefix syntax)
runstruct_abacus "ssh node02 mpirun -np 16"

The prefix is inserted directly before $ABACUSCMD:

$CMDPREFIX $ABACUSCMD > log.out 2>&1

runstruct_abacus -w my_custom.wrap

If the specified file is not found in the current directory, the script searches upward (../, ../../, ../../../) exactly like the default abacus.wrap.

# Inside a numbered ATAT subdirectory, e.g., 1/, 2/, ...
cd 1/

# 1. Generate inputs and run
runstruct_abacus

# 2. Or generate only, then submit to cluster manually
runstruct_abacus -nr
# ... user submits job via qsub/sbatch ...
runstruct_abacus -ex   # extract after job finishes

# 3. Clean and restart if needed
runstruct_abacus -clean
runstruct_abacus

Both abacus.wrap and str.out follow ATAT's upward-search convention:

This allows a single abacus.wrap (and optionally a shared ~/.abacus.rc) to serve an entire ATAT enumeration tree.

• Shengjun Chen (陈胜君) @ Peking University

[Fill in according to your project license]

For issues related to the ABACUS engine itself, please visit:

• GitHub: deepmodeling/abacus-develop