EX3: LOL from Molecule and user-defined cubeΒΆ

Compute LOL and visualize it for formamide, using the inverse hyperbolic transformation.

../../_images/sphx_glr_ex003_lol_plot_001.png
from chemtools import LOL, UniformGrid, Molecule

# 1. Build Molecule, UnifromGrid and LOL model

mol = Molecule.from_file('formamide_q+0.fchk')
cub = UniformGrid.from_molecule(mol, spacing=0.1, extension=2.0)
lol = LOL.from_molecule(mol, grid=cub, trans='inverse_hyperbolic', trans_k=1, trans_a=1)

# 2. Generate cube file(s) and script for visualizing LOL
#    Files generated are chonh2-lol.cube & chonh2.vmd
#    To visualize the iso-surface, use command: $ vmd -e chonh2.vmd

lol.generate_scripts('chonh2', isosurf=0.55)

Total running time of the script: ( 0 minutes 17.227 seconds)

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