Just like most other days, I have started the day by addressing the comments that my mentors have made on the PRs. A good amount of the comments discussed how the functions should be implemented – and this feedback cycle has been helping me improve computational thinking a lot. Another few comments dealt with the coding style, including small issues like listing modules in alphabetical order to formatting. I haven’t really thought much about properly formatting code and how it can greatly affect readability as most of my previous work had been done alone. My mentors’ comments and the experience of editing my initial code is building the capacity to collaborate for bigger codebase.

I have spent some of time today preparing the material that would eventually be included in the documentation and will fulfill the motivation for building the bridge to horton. Based on horton documentation, I have a draft version of example code for calculating Becke charges. For now, I am writing the code here before I confirm the details:

import cclib

from cclib.method.density import Density
from cclib.bridge import cclib2horton
from horton import BeckeMolGrid
from horton import getgobasis
from horton.matrix.dense import DenseTwoIndex

# First load ccData object
filename = "/some/path/to/cclib/data/Gaussian/basicGaussian16/dvb_un_sp.log"
data = cclib.io.ccread(filename)

# Use bridge function to generate horton IOData object
ht = cclib2horton.makehorton(data)

# Calculate density matrix using cclib then convert this into horton's DenseTwoIndex object
d = Density(data)
d.calculate()
den = d.density

dsty = DenseTwoIndex(len(ht.orb_alpha))
dsty._array = den[0] + den[1] # if unrestricted

# Create integration grid for Becke Charges
grid = BeckeMolGrid(ht.coordinates, ht.numbers, ht.pseudo_numbers, mode='only')

# Define Gaussian basis set
gob = get_gobasis(ht.coordinates, ht.numbers, default = 'STO-3G') # loaded file in this example was generated on STO-3G basis set

# Calculate grid density
moldens = gob.compute_grid_density_dm(dsty, grid.points)

# Partition charges
wpart = BeckeWPart(ht.coordinates, ht.numbers, ht.pseudo_numbers, grid, moldens, local=True)
wpart.do_charges()

print(wpart['charges'])

Some of the points I need to confirm before including this into docs:

  1. fchk files are not parsed with mocoeffs in cclib.
  2. Does this need testing?
  3. Any wrappers?