def gen_edge_dislocation(self):
screw_slab_unit = BodyCenteredCubic(directions = [self.x, self.y, self.z],
size = (1,1,1), symbol='Fe', pbc=(1,1,1),
latticeconstant = 2.83)
screw_slab_unit = Atoms(screw_slab_unit)
n_x = int(self.l_x/screw_slab_unit.get_cell()[0,0])
n_y = int(self.l_y/screw_slab_unit.get_cell()[1,1])
n_z = 1
screw_slab_super = supercell(screw_slab_unit, n_x, n_y, n_z)
screw_slab_unit.write('ref_slab.xyz')
b = screw_slab_unit.get_cell()[0,0]
brg_vec = b*np.array([1,0,0])
vacuum = 70.
screw_slab_super.lattice[1,1] += vacuum
disloc_l = np.array([0,0,1])
screw_slab_super.set_lattice(screw_slab_super.get_cell(), scale_positions=False)
super_slab = screw_slab_super.copy()
L_x = screw_slab_super.lattice[0,0]
L_y = screw_slab_super.lattice[1,1]
L_z = screw_slab_super.lattice[2,2]
#Maintain Periodicity along x and z for an edge dislocation:
core = np.array([(L_x)/2., (L_y-vacuum)/2., (L_z)/2.])
screw_slab_super.set_cutoff(3.0)
screw_slab_super.calc_connect()
disloc_noam(screw_slab_super, core, disloc_l, brg_vec)
screw_slab_super.info['core'] = core
screw_slab_super.write('e{0}.xyz'.format(self.name))
POT_DIR = os.environ['POTDIR']
eam_pot = os.path.join(POT_DIR, 'PotBH.xml')
r_scale = 1.00894848312
pot = Potential('IP EAM_ErcolAd do_rescale_r=T r_scale={0}'.format(r_scale), param_filename=eam_pot)
#alat = 2.82893
#could just use the proper one as well....
alat = 2.837666
sup_cell = args.supercellsize
tetra_pos = alat*np.array([0.5, 0.0, 0.75])
octa_pos = alat*np.array([0.5, 0.5, 0.0])
#Structures
gb = BodyCenteredCubic(directions = [[1,0,0], [0,1,0], [0,0,1]],
size = (sup_cell[0],sup_cell[1],sup_cell[2]), symbol='Fe', pbc=(1,1,1),
latticeconstant = alat)
mid_point = 0.5*(np.diag(gb.get_cell()))
mid_point = [((sup_cell[0]-1)/2.)*alat for sp in sup_cell]
gb = Atoms(gb)
if args.tetra:
print 'Tetrahedral Defect'
tetra_pos += mid_point
gb.add_atoms(tetra_pos, 1)
gb.write('bcc_h.xyz')
elif args.octa:
print 'Octahedral Defect'
octa_pos += mid_point
gb.add_atoms(octa_pos, 1)
gb.write('bcc_h.xyz')
else:
gb.write('bcc.xyz')
#screw_slab_unit.add_atoms(center_cell*0.76, 6)
screw_slab_unit.set_atoms(screw_slab_unit.Z)
print len(screw_slab_unit)
tb.write_control_file('ctrl.fe', screw_slab_unit)
pot = Potential('IP LMTO_TBE',
param_str="""
<params>
<LMTO_TBE_params n_types="2" control_file="ctrl.fe">
<per_type_data type="1" atomic_num="26"/>
<per_type_data type="2" atomic_num="1"/>
</LMTO_TBE_params>
</params>""")
#If there is an initial strain energy increment that here:
pot.print_()
screw_slab_unit.write('screw_unitcell.xyz')
screw_slab_unit.set_calculator(pot)
#Elastic constants are disabled until we have tight binding operational.
if calc_elastic_constants and dyn_type != 'LOTF':
cij = pot.get_elastic_constants(screw_slab_unit)
print 'ELASTIC CONSTANTS'
print((cij / units.GPa).round(2))
E = youngs_modulus(cij, y)
nu = poisson_ratio(cij, y, x)
print 'Youngs Modulus: ', E / units.GPa, 'Poisson Ratio: ', nu
print 'Effective elastic modulus E: ', E / (1. - nu**2)
print 'Loading Structure File:', '{0}.xyz'.format(input_file)
defect = Atoms('{0}.xyz'.format(input_file))
top = defect.positions[:, 1].max()
bottom = defect.positions[:, 1].min()
screw_slab_unit.add_atoms(center_cell,1)
#screw_slab_unit.add_atoms(center_cell*0.76, 6)
screw_slab_unit.set_atoms(screw_slab_unit.Z)
print len(screw_slab_unit)
tb.write_control_file('ctrl.fe', screw_slab_unit)
pot = Potential('IP LMTO_TBE', param_str="""
<params>
<LMTO_TBE_params n_types="2" control_file="ctrl.fe">
<per_type_data type="1" atomic_num="26"/>
<per_type_data type="2" atomic_num="1"/>
</LMTO_TBE_params>
</params>""")
#If there is an initial strain energy increment that here:
pot.print_()
screw_slab_unit.write('screw_unitcell.xyz')
screw_slab_unit.set_calculator(pot)
#Elastic constants are disabled until we have tight binding operational.
if calc_elastic_constants and dyn_type != 'LOTF':
cij = pot.get_elastic_constants(screw_slab_unit)
print 'ELASTIC CONSTANTS'
print ((cij / units.GPa).round(2))
E = youngs_modulus(cij, y)
nu = poisson_ratio(cij, y, x)
print 'Youngs Modulus: ', E/units.GPa,'Poisson Ratio: ', nu
print 'Effective elastic modulus E: ', E/(1.-nu**2)
print 'Loading Structure File:', '{0}.xyz'.format(input_file)
defect = Atoms('{0}.xyz'.format(input_file))
top = defect.positions[:,1].max()
bottom = defect.positions[:,1].min()
def calc_bulk_dissolution(args):
"""Calculate the bulk dissolution energy for hydrogen
in a tetrahedral position in bcc iron.
Args:
args(list): determine applied strain to unit cell.
"""
POT_DIR = os.path.join(app.root_path, 'potentials')
eam_pot = os.path.join(POT_DIR, 'PotBH.xml')
r_scale = 1.00894848312
pot = Potential(
'IP EAM_ErcolAd do_rescale_r=T r_scale={0}'.format(r_scale),
param_filename=eam_pot)
alat = 2.83
gb = BodyCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
size=(6, 6, 6),
symbol='Fe',
pbc=(1, 1, 1),
latticeconstant=alat)
cell = gb.get_cell()
print 'Fe Cell', cell
e1 = np.array([1, 0, 0])
e2 = np.array([0, 1, 0])
e3 = np.array([0, 0, 1])
if args.hydrostatic != 0.0:
strain_tensor = np.eye(3) + args.hydrostatic * np.eye(3)
cell = cell * strain_tensor
gb.set_cell(cell, scale_atoms=True)
print 'Hydrostatic strain', args.hydrostatic
print 'strain tensor', strain_tensor
print gb.get_cell()
elif args.stretch != 0.0:
strain_tensor = np.tensordot(e2, e2, axes=0)
strain_tensor = np.eye(3) + args.stretch * strain_tensor
cell = strain_tensor * cell
print 'Stretch strain'
print 'Cell:', cell
gb.set_cell(cell, scale_atoms=True)
elif args.shear != 0.0:
strain_tensor = np.tensordot(e1, e2, axes=0)
strain_tensor = np.eye(3) + args.shear * strain_tensor
cell = strain_tensor.dot(cell)
print 'Shear Strain', strain_tensor
print 'Cell:', cell
gb.set_cell(cell, scale_atoms=True)
gb.write('sheared.xyz')
else:
print 'No strain applied.'
tetra_pos = alat * np.array([0.25, 0.0, 0.5])
h2 = aseAtoms('H2', positions=[[0, 0, 0], [0, 0, 0.7]])
h2 = Atoms(h2)
gb = Atoms(gb)
gb_h = gb.copy()
gb_h.add_atoms(tetra_pos, 1)
#caclulators
gb.set_calculator(pot)
h2.set_calculator(pot)
gb_h.set_calculator(pot)
gb_h.write('hydrogen_bcc.xyz')
#Calc Hydrogen molecule energy
opt = BFGS(h2)
opt.run(fmax=0.0001)
E_h2 = h2.get_potential_energy()
h2.write('h2mol.xyz')
#strain_mask = [1,1,1,0,0,0]
strain_mask = [0, 0, 0, 0, 0, 0]
ucf = UnitCellFilter(gb_h, strain_mask)
#opt = BFGS(gb_h)
opt = FIRE(ucf)
opt.run(fmax=0.0001)
E_gb = gb.get_potential_energy()
E_gbh = gb_h.get_potential_energy()
E_dis = E_gbh - E_gb - 0.5 * E_h2
print 'E_gb', E_gb
print 'E_gbh', E_gbh
print 'H2 Formation Energy', E_h2
print 'Dissolution Energy', E_dis
