# Import the KohnSham module from ATK
from ATK.KohnSham import *
   
# Define function for handling molecule setup   
def waterConfiguration(angle,bondLength):
    from math import sin,cos
       
    theta = angle.inUnitsOf(radians)
    positions = [(0.0, 0.0, 0.0)*Angstrom,
                 (1.0, 0.0, 0.0)*bondLength,
                 (cos(theta), sin(theta), 0.0)*bondLength]
    elements = [Oxygen] + [Hydrogen]*2
       
    return MoleculeConfiguration(elements,positions)
    
# Setup water molecule
h2o = waterConfiguration(104.5*degrees, 0.958*Angstrom)

# Open a VNL file and add the molecule to it
vnl_file = VNLFile("h2o.vnl")
vnl_file.addToSample(h2o, "h2o")