OpenMX (openmx) workflows with emphasis on OpenMX v3.9: write and validate input .dat files (System.Name, Atoms.SpeciesAndCoordinates, scf.Kgrid, Band.kpath), run SCF/geometry optimization/band/DOS/NEB/ESM/SOC(+U)/unfolding/Wannier90/NEGF examples, and interpret outputs (.out/.scfout/restart). Trigger this skill whenever the user mentions OpenMX/openmx.
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.
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.
work/<name>.dat (see template below).openmx work/<name>.dat > work/<name>.stdmpirun -np <N> openmx work/<name>.dat > work/<name>.stdwork/<System.Name>.out.If you need binary matrices for post-processing, set HS.fileout=ON to write work/<System.Name>.scfout.
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
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.references/keywords.mdreferences/examples.md