anaddb-irreps 0.1.3

anaddb_irreps: use phonopy to find the irreducible representations of the phonon modes from anaddb output. It is a simple wrapper of the Phonopy irreps module.

anaddb_irreps

A simple wrapper of the phonopy irreps module for finding irreducible representations of phonon modes in ABINIT's anaddb output.

Installation

Install from PyPI:

pip install anaddb_irreps

Or from source:

pip install .

Usage (Python API)

From anaddb PHBST (AbiPy)

Run anaddb to get the PHBST file with phonon frequencies and eigenvectors. See example in examples/MoS2_1T/anaddb_input/.

Basic Usage

from anaddb_irreps import print_irreps

# Simple usage
print_irreps("run_PHBST.nc", ind_q=0)

With Options

from anaddb_irreps import print_irreps

print_irreps(
    "run_PHBST.nc",
    ind_q=0,
    symprec=1e-8,              # Symmetry precision (default: 1e-5)
    degeneracy_tolerance=1e-4, # Frequency tolerance (default: 1e-4)
    log_level=1,               # Verbosity: 0=quiet, 1+=verbose (default: 0)
    show_verbose=True          # Show detailed phonopy output (default: False)
)

From phonopy params/YAML

If you already have a phonopy params/YAML file (e.g. phonopy_params.yaml or phonopy.yaml), you can use the phonopy-based helper:

from anaddb_irreps import print_irreps_phonopy

irr = print_irreps_phonopy(
    "phonopy_params.yaml",
    qpoint=[0.0, 0.0, 0.0],
    symprec=1e-5,
    degeneracy_tolerance=1e-4,
    log_level=0,
    show_verbose=False,
)

Parameters

For print_irreps (anaddb route):

• phbst_fname (str, required): Path to PHBST NetCDF file
• ind_q (int, required): Index of q-point in PHBST file (0-based)
• symprec (float): Symmetry precision for structure analysis (default: 1e-5)
• degeneracy_tolerance (float): Frequency tolerance for degeneracy detection (default: 1e-4)
• is_little_cogroup (bool): Use little co-group setting (default: False)
• log_level (int): Verbosity level; 0=quiet, higher=more verbose (default: 0)
• show_verbose (bool): Show detailed phonopy irreps output (default: False)

For print_irreps_phonopy (phonopy route):

• phonopy_params (str, required): Path to phonopy params/YAML file
• qpoint (sequence of 3 floats, required): q-point in fractional coordinates
• symprec (float or None): Symmetry precision for structure analysis. If None (or omitted), anaddb_irreps will try to use the symmetry tolerance recorded in the phonopy file (e.g. phonopy.symmetry_tolerance in the YAML), falling back to 1e-5 when not available.
• degeneracy_tolerance (float): Frequency tolerance for degeneracy detection (default: 1e-4)
• is_little_cogroup (bool): Use little co-group setting (default: False)
• log_level (int): Verbosity level; 0=quiet, higher=more verbose (default: 0)
• show_verbose (bool): Show detailed phonopy irreps output (default: False)

Usage (CLI)

Use the anaddb-irreps and phonopy-irreps command-line tools for quick command-line access.

Basic Example (anaddb PHBST)

anaddb-irreps --phbst run_PHBST.nc --q-index 0

With Options (anaddb PHBST)

anaddb-irreps \
  --phbst run_PHBST.nc \
  --q-index 0 \
  --symprec 1e-8 \
  --degeneracy-tolerance 1e-4 \
  --log-level 1

Basic Example (phonopy params)

phonopy-irreps \
  --params phonopy_params.yaml \
  --qpoint 0.0 0.0 0.0

CLI Options

For anaddb-irreps:

• -p, --phbst (required): Path to PHBST NetCDF file
• -q, --q-index (required): Index of q-point in PHBST file (0-based)
• -s, --symprec: Symmetry precision (default: 1e-5)
• -d, --degeneracy-tolerance: Frequency tolerance for degeneracy (default: 1e-4)
• -l, --is-little-cogroup: Use little co-group setting
• -v, --log-level: Verbosity level; 0=quiet, higher=more verbose (default: 0)

For phonopy-irreps:

• -p, --params (required): Path to phonopy params/YAML file
• --qpoint (required): Three floats for q-point in fractional coordinates
• -s, --symprec: Override symmetry precision. If omitted, anaddb_irreps will try to use the symmetry tolerance stored in the phonopy file, falling back to 1e-5.
• -d, --degeneracy-tolerance: Frequency tolerance for degeneracy (default: 1e-4)
• -l, --is-little-cogroup: Use little co-group setting
• -v, --log-level: Verbosity level; 0=quiet, higher=more verbose (default: 0)

The CLI produces the same output format as the Python API, showing q-point, point group, and a table of phonon modes with their irreducible representations and IR/Raman activity.

Output Format

The output includes:

1. Q-point coordinates in fractional coordinates
2. Point group of the structure at that q-point
3. Mode table with columns:
   • qx, qy, qz: q-point coordinates (repeated for each mode)
   • band: Mode index (0-based)
   • freq(THz): Frequency in THz
   • freq(cm-1): Frequency in cm⁻¹
   • label: Irreducible representation label (e.g., Eu, Eg, A1g)
   • IR: IR activity (Y = active, . = inactive)
   • Raman: Raman activity (Y = active, . = inactive)

Example Output

q-point: [0.0000, 0.0000, 0.0000]
Point group: -3m

# qx      qy      qz      band  freq(THz)   freq(cm-1)   label        IR  Raman
 0.0000  0.0000  0.0000     0      0.0000         0.00  -            .    .  
 0.0000  0.0000  0.0000     1      0.0000         0.00  -            .    .  
 0.0000  0.0000  0.0000     2      0.0000         0.00  -            .    .  
 0.0000  0.0000  0.0000     3      6.4001       213.49  Eu           Y    .  
 0.0000  0.0000  0.0000     4      6.4001       213.49  Eu           Y    .  
 0.0000  0.0000  0.0000     5      6.8617       228.88  Eg           .    Y  
 0.0000  0.0000  0.0000     6      6.8617       228.88  Eg           .    Y  
 0.0000  0.0000  0.0000     7     11.1626       372.34  A1g          .    Y  
 0.0000  0.0000  0.0000     8     11.3152       377.43  A2u          Y    .  

Examples

See examples/MoS2_1T/ for a complete working example with MoS2 1T structure.