Troubleshooting#

Use this page to diagnose common issues when running moldenViz.

Parser Exceptions#

  • ValueError: Unsupported basis functions – the parser only accepts spherical Gaussian functions. Re-export your Molden file with spherical GTOs enabled.

  • ValueError: Invalid shell label – occurs when the [GTO] section contains unexpected angular momentum labels. Confirm the file adheres to the Molden format specification.

  • RuntimeError: Grid creation is not allowed when `only_molecule` is set to `True`. – raised if you request grids or exports while skipping orbitals. Re-run without --only-molecule.

File Not Found#

from moldenViz import Parser

try:
    Parser('missing-file.inp')
except FileNotFoundError:
    print('Molden file not found')

Invalid Molden Format#

from moldenViz import Parser

try:
    Parser('invalid.inp')
except ValueError as exc:
    print(f'Invalid molden file: {exc}')

Grids With only_molecule=True#

Tabulator cannot build grids when you skip molecular orbital data:

from moldenViz import Tabulator

tab = Tabulator('molden.inp', only_molecule=True)

try:
    tab.cartesian_grid(x, y, z)
except RuntimeError:
    print('Cannot create grids when only_molecule=True')

Configuration Errors#

Invalid entries in ~/.config/moldenViz/config.toml raise ValueError the next time you import plotting classes:

from moldenViz import Plotter

try:
    Plotter('molden.inp')
except ValueError as exc:
    print(f'Configuration error: {exc}')
    print('Review your TOML configuration and try again')

Export Errors#

  • ValueError: Orbital selection out of bounds – ensure the indices passed to --orbitals or Tabulator.export_* fall within the available range reported by Parser.mos.

  • RuntimeError: Tabulator grid is undefined – create a grid (cartesian or spherical) before calling an export method.

  • RuntimeError: Cube export requires a cartesian grid – Gaussian cube files expect a rectilinear grid; re-run the export with --grid cartesian or --export-cube only.

If a problem persists, run moldenViz -h to confirm the CLI supports the options you are using and check the Configuration Reference for grid defaults.