def gen_super(self, grain=None, rbt=None, sup_v=6, sup_bxv=2, rcut=2.0):
""" :method:`gen_super` Creates a :class:SubGrainBoundary super cell according to
conventions described in Rittner and Seidman (PRB 54 6999).
Args:
grain(:class:`ase.Atoms`): atoms object passed from gen_super_rbt.
rbt (list): rigid body translation as fractional translations of the supercell.
sup_v(int): Size of supercell along v.
sup_bxv(int): Size of supercell along boundary_plane_normal crossed with v.
rcut(float): Atom deletion criterion in angstrom.
"""
io = ImeallIO()
if rbt == None:
x = Atoms('{0}.xyz'.format(os.path.join(self.grain_dir, self.gbid)))
else:
x = Atoms(grain)
struct_dir = os.path.join(self.grain_dir, 'structs')
self.name = '{0}_v{1}bxv{2}_tv{3}bxv{4}_d{5}z'.format(self.gbid,
str(sup_v), str(sup_bxv), '0.0', '0.0', str(rcut))
#TODO fix this so it is more transparent.
#if rcut = 0 then only a super cell is generated with no deletion of atoms.
if rcut > 0.0:
x.set_cutoff(2.4)
x.calc_connect()
x.calc_dists()
rem = []
u = np.zeros(3)
for i in range(x.n):
for n in range(x.n_neighbours(i)):
j = x.neighbour(i, n, distance=3.0, diff=u)
if x.distance_min_image(i,j) < rcut and j != i:
rem.append(sorted([j,i]))
rem = list(set([a[0] for a in rem]))
if len(rem) > 0:
x.remove_atoms(rem)
else:
print 'No duplicate atoms in list.'
else:
x = x*(sup_v, sup_bxv, 1)
x.set_scaled_positions(x.get_scaled_positions())
if rbt == None:
self.struct_file = self.name
self.subgrain_dir = io.make_dir(self.calc_dir, self.name)
try:
with open('{0}/subgb.json'.format(self.subgrain_dir), 'r') as f:
j_dict = json.load(f)
except IOError:
j_dict = {}
j_dict['name'] = self.name
j_dict['param_file'] = self.param_file
j_dict['rbt'] = [0.0, 0.0]
j_dict['rcut'] = rcut
with open('{0}/subgb.json'.format(self.subgrain_dir), 'w') as f:
json.dump(j_dict, f, indent=2)
else:
return sup_v, sup_bxv, x
def del_atoms(x=None):
rcut = 2.0
#x = Atoms('crack.xyz')
if x == None:
x = Atoms('1109337334_frac.xyz')
else:
pass
x.set_cutoff(3.0)
x.calc_connect()
x.calc_dists()
rem=[]
r = farray(0.0)
u = fzeros(3)
print len(x)
for i in frange(x.n):
for n in frange(x.n_neighbours(i)):
j = x.neighbour(i, n, distance=3.0, diff=u)
if x.distance_min_image(i, j) < rcut and j!=i:
rem.append(sorted([j,i]))
if i%10000==0: print i
rem = list(set([a[0] for a in rem]))
if len(rem) > 0:
print rem
x.remove_atoms(rem)
else:
print 'No duplicate atoms in list.'
x.write('crack_nodup.xyz')
return x
def delete_atoms(self, grain=None, rcut=2.0):
"""
Delete atoms below a certain distance threshold.
Args:
grain(:class:`quippy.Atoms`): Atoms object of the grain.
rcut(float): Atom deletion criterion.
Returns:
:class:`quippy.Atoms` object with atoms nearer than deletion criterion removed.
"""
io = ImeallIO()
if grain == None:
x = Atoms('{0}.xyz'.format(os.path.join(self.grain_dir,
self.gbid)))
else:
x = Atoms(grain)
x.set_cutoff(2.4)
x.calc_connect()
x.calc_dists()
rem = []
u = fzeros(3)
for i in frange(x.n):
for n in frange(x.n_neighbours(i)):
j = x.neighbour(i, n, distance=3.0, diff=u)
if x.distance_min_image(i, j) < rcut and j != i:
rem.append(sorted([j, i]))
rem = list(set([a[0] for a in rem]))
if len(rem) > 0:
x.remove_atoms(rem)
else:
print 'No duplicate atoms in list.'
if grain == None:
self.name = '{0}_d{1}'.format(self.gbid, str(rcut))
self.subgrain_dir = io.make_dir(self.calc_dir, self.name)
self.struct_file = gbid + '_' + 'n' + str(
len(rem)) + 'd' + str(rcut)
x.write('{0}.xyz'.format(
os.path.join(self.subgrain_dir, self.struct_file)))
return len(rem)
else:
return x
#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:
print 'No H atoms closer than threshold.'
#Now a little housekeeping. In the vicinity of a cracktip
#Delaunay can go a little haywire. We remove any H that is far too close to an Fe atom
# |h-fe| < 1.1. and we remove the vacuum Hs
ats.write('crackH.xyz')
h_atoms = sum((ats.get_atomic_numbers() ==1))
zlen = ats.get_cell()[2,2]