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

# Read self consistent calculation from NetCDF file
scf = restoreSelfConsistentCalculation('h2.nc')

# Set the force tolerance
opt = geometricOptimizationParameters(
    force_tolerance=0.00001*electronVolt/Angstrom
    )

# Set name of check point file
params = runtimeParameters(
    verbosity_level=10
    )

# Calculate the optimized atomic geometry
h2_opt = calculateOptimizedAtomicGeometry(
    self_consistent_calculation=scf,
    optimization_parameters=opt,
    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