Displaying molecular orbitals with chemlab and chemview

In [1]:

    

from chemlab.io import remotefile

df = remotefile('https://raw.githubusercontent.com/cclib/cclib/master/data/GAMESS/basicGAMESS-US2012/water_mp2.out', 'gamess')

molecule = df.read('molecule')
mocoeffs = df.read('mocoeffs')
gbasis = df.read('gbasis')


    

In [2]:

    

from chemlab.qc import molecular_orbital

coefficients = mocoeffs[0][2]
f = molecular_orbital(molecule.r_array, coefficients, gbasis)
print(f(0, 1, 0))


    

    




[[ 0.         -0.00666785  0.        ]
 [ 0.07906491  0.05291183  0.        ]
 [-0.07906491  0.05291183  0.        ]]
0.0

In [3]:

    

from chemview import enable_notebook, MolecularViewer
enable_notebook()

import numpy as np

mv = MolecularViewer(molecule.r_array, { 'atom_types': molecule.type_array })
mv.ball_and_sticks(ball_radius=0.01)
mv.add_isosurface(f, isolevel=0.3, color=0xff0000, resolution=64)
mv.add_isosurface(f, isolevel=-0.3, color=0x0000ff, resolution=64)

mv


    

    















    















    















    




/home/gabriele/miniconda/envs/test_install/lib/python2.7/site-packages/IPython/utils/traitlets.py:364: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  silent = bool(old_value == new_value)

In [ ]: