# Import the KohnSham module from ATK
from ATK.KohnSham import *

# Set up elements and positions
elm = [ Hydrogen, Hydrogen ]
pos = [ ( +0.4, 0.0, 0.0)*Angstrom,
        ( -0.4, 0.0, 0.0)*Angstrom ]

# Add them to a configuration
h2 = MoleculeConfiguration(elm,pos)

# Setup Kohn-Sham method
dft_method = KohnShamMethod()

# Set name of check point file
params = runtimeParameters(
    verbosity_level=10,
    checkpoint_filename='h2.nc'
    )

# Calculate the optimized atomic geometry
h2_opt = calculateOptimizedAtomicGeometry(
    atomic_configuration=h2,
    method=dft_method,
    runtime_parameters=params
    )

# Print the coordinates of the individual atoms
print '\nAtom coordinates\n---------------------------'
for coord in h2_opt.cartesianCoordinates():
    for c in coord:
        print '%7.4f' % (c.inUnitsOf(Angstrom)),
    print