if hasattr(params, 'surface'):
surface = params.surface
else:
# Make a surface unit cell by repllcating and adding some vaccum along y
surface = unit_slab * [1, params.surf_ny, 1]
surface.center(params.vacuum, axis=1)
# ********** Surface energy ************
# Calculate surface energy per unit area
surface.set_calculator(params.calc)
if hasattr(params, 'relax_bulk') and params.relax_bulk:
print('Minimising surface unit cell...')
surface = relax_structure(surface)
E_surf = surface.get_potential_energy()
E_per_atom_bulk = a.get_potential_energy() / len(a)
# volume is not get_volume() because it's not a solid 3D system!
volume = np.prod([np.ptp(vect) for vect in a.get_positions().T])
area = volume / np.ptp(a.get_positions()[:,1])
gamma = ((E_surf - E_per_atom_bulk * len(surface)) /
(2.0 * area))
print('Surface energy of %s surface %.4f J/m^2\n' %
(params.cleavage_plane, gamma / (units.J / units.m ** 2)))
# ***** Setup crack slab supercell *****
crack_slab = unit_slab
buffer_hops = 8
deltay_tip = 1.05
##### OTHER STUFF, LEAVE UNCHANGED UNLESS NECESSARY #####
cluster_vacuum = 12.0
crack_slab = ase.io.read('crack.xyz', format='extxyz')
ring_size = int(raw_input('Size of ring at crack tip:'))
pre_optim = True
try:
pre_optim = (sys.argv[1] in [' ', 't', 'T', 'True', 'true', 'y', 'yes'])
except:
print("") # it's alright
if pre_optim:
crack_slab = relax_structure(crack_slab)
folder = 'ring%1d_strain%.03f' % (ring_size, strain)
try:
os.mkdir(folder)
except:
print("Folder already existing. Overwrite?")
sig = raw_input()
if sig not in ['y', 'yes']:
exit
core_ring = np.loadtxt('tip_4ring.csv', dtype='int')
try:
xy_ring = np.loadtxt('xy_ring.csv', dtype='int')
temp = set(xy_ring)
for idx in xy_ring: