def gen_interface():
"""Selects an interfacial region of a bicrystal
based on common neighbour analysis. The width of the interfacial region
is equal to 2*(gb_max-gb_min) where gb_max is the z-coordinate of the highest
non-bcc atom, and gb_min is the lowest non-bcc atom.
The method creates a file `interface.xyz` in the working directory,
with the interface centered in a unit cell with 1 angstrom vacuum
on each side.
Returns:
:class:`ase.Atoms`: Atoms object of the interfacial slab in same
coordinates as original bicrystal.
"""
#output.xyz must have structure_type property attached.
ats = Atoms('output.xyz')
cell_midpoint = ats.get_cell()[2,2]/2.0
#select non-BCC sites are 0 otherwise 3.
struct_type = np.array(ats.properties['structure_type'])
struct_mask = [not struct for struct in struct_type]
interface = ats.select(struct_mask)
#select upper interface to decorate.
interface = interface.select([at.position[2] > cell_midpoint for at in interface])
z_vals = [at.position[2] for at in interface]
z_min = min(z_vals)
z_max = max(z_vals)
#take slice of interface max uncoordinated with min uncoordinated.
z_width = (z_max-z_min)/2.0
z_center = z_width + z_min
gb_max = z_max + 1.0*z_width
gb_min = z_min - 1.0*z_width
zint = ats.select([(gb_min <= at.position[2] <= gb_max) for at in ats])
#make a copy to return
int_ats = zint.copy()
zint.center(vacuum=1.0, axis=2)
zint.write('interface.xyz')
#Write POSCAR to use interstitial site generator:
ats = Atoms('interface.xyz')
#vasp_args=dict(xc='PBE', amix=0.01, amin=0.001, bmix=0.001, amix_mag=0.01, bmix_mag=0.001,
# kpts=[3, 3, 3], kpar=9, lreal='auto', ibrion=-1, nsw=0, nelmdl=-15, ispin=2,
# nelm=100, algo='VeryFast', npar=24, lplane=False, lwave=False, lcharg=False, istart=0,
# voskown=0, ismear=1, sigma=0.1, isym=2)
#vasp = Vasp(**vasp_args)
#vasp.initialize(ats)
#write_vasp('POSCAR', vasp.atoms_sorted, symbol_count=vasp.symbol_count, vasp5=True)
return int_ats
crack_dict= pickle.load(f)
print 'G: {}, H_d: {}, sim_T {}'.format(crack_dict['initial_G']*(units.m**2/units.J),
crack_dict['H_d'], crack_dict['sim_T']/units.kB)
h_list = hydrify.hydrogenate_gb(ats, mode='CrackTip', d_H=crack_dict['H_d'][0], tetrahedral=True, crackpos_fix=ats.params['CrackPos'])
for h in h_list:
ats.add_atoms(h,1)
#ats.wrap()
ats.write('crackH.xyz')
ats = None
ats = Atoms('crackH.xyz')
ats.set_cutoff(2.4)
ats.calc_connect()
ats.calc_dists()
filter_mask = (ats.get_atomic_numbers()==1)
h_atoms = ats.select(filter_mask, orig_index=True)
rem=[]
u = np.zeros(3)
for i in h_atoms.orig_index:
print 'hindex', i
print 'nneighbs', ats.n_neighbours(i)
for n in range(ats.n_neighbours(i)):
j = ats.neighbour(i, n+1, distance=2.4, diff=u)
print 'neighb index', j
if ats.distance_min_image(i,j) < 1.1 and j!=i:
rem.append(i)
rem = list(set(rem))
if len(rem) > 0:
print 'Removing {} H atoms'.format(len(rem))
ats.remove_atoms(rem)
else:
