OpenMX (v3.9-focused)

Use this skill when you need to run OpenMX calculations or prepare/inspect OpenMX inputs/outputs. The examples and notes here are aligned with the OpenMX v3.9 manual (openmx3.9.pdf) and this repo’s openmx_example/ library.

Example Library (This Repo)

This repository includes many ready-to-run OpenMX inputs under openmx_example/. Prefer starting from the closest example, then editing:

• System.Name (unique per run)
• DATA.PATH (points to DFT_DATA19 / basis+pseudopotential directory on your system)
• Atoms.* and <Definition.of.Atomic.Species ...> (structure + basis/pseudo choices)

Example index: references/examples.md (NEB/ESM/work-function/NEGF/unfolding/SOC+U/etc.).

To search examples by feature:

python scripts/find_examples.py --pattern "MD\\.Type\\s+NEB"

If you run it from outside this repo, pass --root /path/to/openmx_example or set OPENMX_EXAMPLE_DIR.

Quick Start (Run a Calculation)

1. Create an input file work/<name>.dat (see template below).
2. Run OpenMX (serial or MPI):
   • Serial: openmx work/<name>.dat > work/<name>.std
   • MPI: mpirun -np <N> openmx work/<name>.dat > work/<name>.std
3. Check results in work/<System.Name>.out.

If you need binary matrices for post-processing, set HS.fileout=ON to write work/<System.Name>.scfout.

Input File Template (Minimal)

OpenMX input is keyword-based; order is flexible. A minimal, common structure:

System.CurrrentDirectory   ./      # note the spelling in the manual
System.Name                mycalc

Species.Number  2
<Definition.of.Atomic.Species
H  H5.0-s1   H_PBE19
C  C5.0-s1p1 C_PBE19
Definition.of.Atomic.Species>

Atoms.Number  5
Atoms.SpeciesAndCoordinates.Unit  Ang
<Atoms.SpeciesAndCoordinates
1 C   0.000  0.000  0.000  2.0  0.5 0.5 0.5
2 H  -0.890 -0.629  0.000  0.5  0.5 0.5 0.5
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit  Ang
<Atoms.UnitVectors
10.0 0.0  0.0
0.0  10.0 0.0
0.0  0.0  10.0
Atoms.UnitVectors>

scf.XcType            GGA-PBE
scf.SpinPolarization  off        # off|on|nc
scf.Kgrid             1 1 1
scf.maxIter           100
scf.criterion         1.0e-10

HS.fileout            ON         # writes System.Name.scfout

Outputs to Expect

Common outputs (controlled by level.of.fileout in the input):

• work/<System.Name>.out: main log (SCF history, energies, charges, geometry optimization history).
• work/<System.Name> rst/: restart directory.
• work/<System.Name>.scfout: binary Hamiltonian/overlap/density matrices when HS.fileout=ON.

Reference

• Keyword cheat sheet: references/keywords.md
• Example catalog (this repo): references/examples.md