ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
We are going to use the ASE interface to the siesta calculator, for the official SIESTA documentation see here.
Part 1: Standard basis sets
In the following script you will relax the structure of the H2O molecule to find its equilibrium structure.
import time
import numpy as np
from ase import Atoms, units
from ase.optimize import QuasiNewton
from ase.calculators.siesta import Siesta
# Set up a H2O molecule by specifying atomic positions
h2o = Atoms(symbols=’H2O’,
positions=[( 0.776070, 0.590459, 0.00000),
(-0.776070, 0.590459, 0.00000),
(0.000000, -0.007702, -0.000001)],
pbc=(1,1,1))
# Center the molecule in the cell with some vacuum around
h2o.center(vacuum=6.0)
# Select some energy-shifts for the basis orbitals
e_shifts = [0.01,0.1,0.2,0.3,0.4,0.5]
# Run the relaxation for each energy shift, and print out the
# corresponding total energy, bond length and angle
for e_s in e_shifts:
starttime = time.time()
calc = Siesta(’h2o’,meshcutoff=200.0 * units.Ry, mix=0.5, pulay=4)
calc.set_fdf(’PAO.EnergyShift’, e_s * units.eV)
calc.set_fdf(’PAO.SplitNorm’, 0.15)
calc.set_fdf(’PAO.BasisSize’, ’SZ’)
h2o.set_calculator(calc)
# Make a -traj file named h2o_current_shift.traj:
dyn = QuasiNewton(h2o, trajectory=’h2o_%s.traj’ % e_s)
dyn.run(fmax=0.02) # Perform the relaxation
E = h2o.get_potential_energy()
print # Make the output more readable
print "E_shift: %.2f" %e_s
print "----------------"
print "Total Energy: %.4f" % E # Print total energy
d = h2o.get_distance(0,2)
print "Bond length: %.4f" % d # Print bond length
p = h2o.positions
d1 = p[0] - p[2]
d2 = p[1] - p[2]
r = np.dot(d1, d2) / (np.linalg.norm(d1) * np.linalg.norm(d2))
angle = np.arccos(r) / pi * 180
print "Bond angle: %.4f" % angle # Print bond angle
endtime = time.time()
walltime = endtime - starttime
print ’Wall time: %.5f’ % walltime
print # Make the output more readable
Run the script using three different basis sets: single-Z (SZ), double-Z (DZ) and double-Z plus polarization (DZP).
Run it in different directories for each basis set, since the run will produce a large amount of output files. The
bases are defined in the script through these three lines:
6.4. Further reading 47