def calc_elast_dipole_dft(input_file, vasp_calc=True):
"""Reads OUTCAR file in the same directory with one shot forces
induced by removal of defect. Reads defect position
from .xyz file (which contains the defect) defined by `input_file`
calculates and returns the elastic dipole tensor of the defect.
Args:
input_file(str): name of input .xyz file containing defect cell.
Returns:
Elastic Dipole Tensor 3x3 numpy array.
"""
elastic = ElasticDipole()
ats_def = Atoms(input_file)
defect = find_h_atom(ats_def)
if vasp_calc:
import ase.io.vasp as vasp
ats_pos = vasp.read_vasp()
ats = vasp.read_vasp_out()
ats = Atoms(ats)
else:
pass
print 'Defect index', defect.index, 'Position', defect.position, 'Type: ', defect.number
f = ats.get_forces()
ats.add_property('force', f.T)
ats.write('force.xyz')
return elastic.compute_vacancy_dipole(defect,
ats_pos.copy(),
forces=ats.get_forces())
rem = []
for atom in at:
if atom.position[0] <= 0.00 and atom.position[1] <= 100.0:
rem.append(atom.index + 1)
print 'Removing ', len(rem), ' atoms.'
if len(rem) > 0:
at.remove_atoms(rem)
else:
print 'No atoms displaced from unitcell'
pot = Potential('IP EAM_ErcolAd do_rescale_r=T r_scale={0}'.format(r_scale),
param_filename=eam_pot)
at.set_calculator(pot)
at.write('unrelaxed.xyz')
print 'Running Relaxation'
opt = FIRE(at)
opt.run(fmax=0.1)
print 'Calculating connectivity and Nye Tensor'
ref_slab = Atoms('ref_slab.xyz')
ref_slab.set_cutoff(3.0)
ref_slab.calc_connect()
at.set_cutoff(3.0)
at.calc_connect()
alpha = calc_nye_tensor(at, ref_slab, 3, 3, at.n)
at.add_property('screw', alpha[2, 2, :])
at.add_property('edgex', alpha[2, 0, :])
at.add_property('edgey', alpha[2, 1, :])
at.write('e{0}.xyz'.format(name))
def NetCDFReader(source, frame=None, start=0, stop=None, step=1, format=None):
opened = False
if isinstance(source, str):
opened = True
source = netcdf_file(source)
from quippy import Atoms
DEG_TO_RAD = pi/180.0
remap_names = {'coordinates': 'pos',
'velocities': 'velo',
'cell_lengths': None,
'cell_angles': None,
'cell_lattice': None,
'cell_rotated': None}
prop_type_to_value = {PROPERTY_INT: 0,
PROPERTY_REAL: 0.0,
PROPERTY_STR: "",
PROPERTY_LOGICAL: False}
prop_dim_to_ncols = {('frame','atom','spatial'): 3,
('frame','atom','label'): 1,
('frame', 'atom'): 1}
if frame is not None:
start = frame
stop = frame+1
step = 1
else:
if stop is None:
stop = source.variables['cell_lengths'].shape[0]
for frame in range(start, stop, step):
cl = source.variables['cell_lengths'][frame]
ca = source.variables['cell_angles'][frame]
lattice = make_lattice(cl[0],cl[1],cl[2],ca[0]*DEG_TO_RAD,ca[1]*DEG_TO_RAD,ca[2]*DEG_TO_RAD)
at = Atoms(n=netcdf_dimlen(source, 'atom'), lattice=lattice, properties={})
for name, var in source.variables.iteritems():
name = remap_names.get(name, name)
if name is None:
continue
name = str(name) # in case it's a unicode string
if 'frame' in var.dimensions:
if 'atom' in var.dimensions:
# It's a property
value = var[frame]
if value.dtype.kind != 'S': value = value.T
at.add_property(name, value)
else:
# It's a param
if var.dimensions == ('frame','string'):
# if it's a single string, join it and strip it
at.params[name] = ''.join(var[frame]).strip()
else:
if name == 'cutoff':
at.cutoff = var[frame]
elif name == 'cutoff_skin':
at.cutoff_skin = var[frame]
elif name == 'nneightol':
at.nneightol = var[frame]
elif name == 'pbc':
at.pbc = var[frame]
else:
at.params[name] = var[frame].T
if 'cell_rotated' in source.variables:
cell_rotated = source.variables['cell_rotated'][frame]
orig_lattice = source.variables['cell_lattice'][frame]
#if cell_rotated == 1:
at.set_lattice(orig_lattice, True)
yield at
def close(self):
if self.opened: source.close()
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')