from ase.visualize import view, write
from ase.calculators.vasp import *
import matplotlib.pyplot as plt
from ase.constraints import FixAtoms
from matplotlib import mlab
from numpy import *
from ase.utils.eos import EquationOfState
from ase.lattice.cubic import BodyCenteredCubic
from ase import Atom
a = 5.7885/2
cell = [[1,0,0],[0,1,0],[0,0,1]]
atoms = BodyCenteredCubic('Fe', directions=cell)
atoms.set_initial_magnetic_moments([5,5])
atoms.set_cell([a, a, a], scale_atoms=True)
carbon = Atom('C', position=(0,0.5*a,0.75*a), charge=0.4)
atoms = atoms*(2,2,2) + carbon
constraint = FixAtoms(indices=[8,10,12,14,16])
atoms.set_constraint(constraint)
atoms[-1].position = [0, 0.5*a, 0.75*a]
init = atoms.copy()
# view(init)
atoms[-1].position = [0, 0.75*a, 0.5*a]
final = atoms.copy()
# view(final)
else:
bulk = model.bulk_reference.copy()
bulk.set_calculator(model.calculator)
a0 = bulk.cell[0,0] # get lattice constant from relaxed bulk
bulk = Diamond(symbol="Si", latticeconstant=a0, directions=[[1,-1,0],[0,0,1],[1,1,0]])
bulk.set_calculator(model.calculator)
# set up supercell
bulk *= (1, 1, 10)
# flip coord system for ASE (precon minim?)
c = bulk.get_cell()
t_v = c[0,:].copy()
c[0,:] = c[1,:]
c[1,:] = t_v
bulk.set_cell(c)
ase.io.write(sys.stdout, bulk, format='extxyz')
def surface_energy(bulk, z_offset):
Nat = bulk.get_number_of_atoms()
# shift so cut is through shuffle plane
bulk.positions[:,2] += z_offset
bulk.wrap()
# relax atom positions, holding cell fixed
# vac = relax_atoms(vac, fmax=fmax)
# compute surface formation energy as difference of bulk and expanded cell
ebulk = bulk.get_potential_energy()
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
from ase.visualize import view, write
from ase.calculators.vasp import *
import matplotlib.pyplot as plt
from ase.constraints import FixAtoms
from matplotlib import mlab
from numpy import *
from ase.utils.eos import EquationOfState
from ase.lattice.cubic import BodyCenteredCubic
from ase import Atom
a = 5.7885/2
cell = [[1,0,0],[0,1,0],[0,0,1]]
atoms = BodyCenteredCubic('Fe', directions=cell)
atoms.set_initial_magnetic_moments([5,5])
atoms.set_cell([a,a,a], scale_atoms=True)
#atoms.set_cell([a,a,a])
carbon = Atom('C', position=(0,0.5*a,0.5*a), charge=0.4)
atoms = atoms*(2,2,2) + carbon
constraint = FixAtoms(indices=[8,10])
atoms.set_constraint(constraint)
init = atoms.copy()
final = atoms.copy()
final[-1].position = [0, 0.5*a, (0.5+0.25)*a]
