def decorate_interface():
ats = Atoms('interface.xyz')
dataset = spglib.get_symmetry_dataset(ats, symprec=1e-5)
with open('unique_lattice_sites.json', 'w') as f:
json.dump([
list(ats[site_num].position)
for site_num in np.unique(dataset['equivalent_atoms'])
], f)
unique_atoms = []
for at in ats:
unique_atoms.append(at.position)
voronoi = Voronoi(limits=tuple(np.diag(ats.cell)),
periodic=(True, True, False))
cntr = voronoi.compute_voronoi(unique_atoms)
ints_list = []
for site_num in np.unique(dataset['equivalent_atoms']):
for vert in voronoi.get_vertices(site_num, cntr):
ints_list.append(vert.tolist())
for unique in ints_list:
ats.add_atoms(unique, 1)
for i in range(len(ats)):
ats.id[i] = i
#remove voronoi duplicates
print 'Fe_H atoms', len(ats)
ats.wrap()
del_ats = aseAtoms()
for at in ats:
del_ats.append(at)
geometry.get_duplicate_atoms(del_ats, cutoff=0.2, delete=True)
ats = del_ats.copy()
print 'Fe_H atoms remove duplicates', len(ats)
#select unique hydrogens
#for i in range(len(ats)):
# ats.id[i] = i
ints_list = [at.position for at in ats if at.number == 1]
with open('unique_h_sites.json', 'w') as f:
json.dump([list(u) for u in ints_list], f)
ats.write('hydrogenated_grain.xyz')
args = parser.parse_args()
DOUBLE_CELL = args.double_cell
ats = Atoms('crack.xyz')
if DOUBLE_CELL:
ats = ats*(1,1,2)
ats.info['adsorbate_info']=None
with open('crack_info.pckl','r') as f:
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)
from quippy import Atoms
from imeall.calc_inter_ener import get_interface_bounds
with open('unique_h_sites.json','r') as f:
h_sites = json.load(f)
print 'There are ', len(h_sites), 'H interstitials'
ats = Atoms('output.xyz')
gb_min, gb_max, z_width, at_min = get_interface_bounds(ats)
h_ats = ats.copy()
for h_site in h_sites:
h_site_tmp = list(h_site)
#remove vacuum restore min position
h_site_tmp[2] += gb_min - 1.0 + at_min
h_ats.add_atoms(h_site_tmp, 1)
h_int_ats = Atoms('interface.xyz')
for h_site in h_sites:
h_site_tmp = list(h_site)
h_int_ats.add_atoms(h_site_tmp, 1)
for i in range(0,len(h_ats)):
h_ats.id[i] = i
for i in range(0, len(h_int_ats)):
h_int_ats.id[i] = i
h_ats.write('decorated.xyz')
h_int_ats.write('int_decorated.xyz')
r'\[\s+([\-0-9\.]+)\s+([\-0-9\.]+)\s+([\-0-9\.]+)\s?\s?\]\s+([\-0-9\.]+)\s+([\-0-9\.]+)',
re.S)
with open(args.input_file) as f:
lines = h_line_re.findall(f.read())
interstitials = []
for line in lines:
site = map(float, [line[0], line[1], line[2]])
energy = float(line[4])
interstitials.append(Particle(site, 'H', energy))
interstitials.sort(key=lambda x: x.energy)
for int_ in interstitials:
print int_.site, int_.energy
ats = Atoms('output.xyz')
num_fe = len(ats)
for int_ in interstitials:
ats.add_atoms(np.array(int_.site), 1)
for i in range(len(ats)):
ats.id[i] = i
ats.add_property('locen', 0.0)
for i, at in enumerate(interstitials):
ats.properties['locen'][i + num_fe] = at.energy
ats.write('h_energetics.xyz')