EX3: ELF from Molecule and user-defined cubeΒΆ

Compute ELF and visualize it for formamide.

../../_images/sphx_glr_ex003_elf_plot_001.png
from chemtools import ELF, UniformGrid, Molecule

# 1. Build Molecule, UnifromGrid and ELF model

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

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

elf.generate_scripts('chonh2', isosurf=0.8)

Total running time of the script: ( 0 minutes 20.940 seconds)

Generated by Sphinx-Gallery