EX3: NCI from Molecule and user-defined cubeΒΆ

Compute NCI and visualize it for formic acid dimer.

../../_images/sphx_glr_ex003_nci_plot_001.png
from chemtools import NCI, UniformGrid, Molecule


# 1. Build UniformGrid and NCI model

mol = Molecule.from_file('formic_acid_dimer.fchk')
cub = UniformGrid.from_molecule(mol, spacing=0.1, extension=0.5)
nci = NCI.from_molecule(mol, grid=cub)

# 2. Generate plot, cube file(s) and script for visualizing NCI
#    Files generated are formic_acid_dimer-dens.cube, formic_acid_dimer-grad.cube,
#    & formic_acid_dimer.vmd
#    To visualize the iso-surface, use command: $ vmd -e formic_acid_dimer.vmd

nci.generate_plot('formic_acid_dimer', denslim=(-0.15, 0.15))
nci.generate_scripts('formic_acid_dimer')

Total running time of the script: ( 0 minutes 12.734 seconds)

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