def build_surface(self, bp=[-1,1,12], v=[1,1,0]):
'''
Build Surface unit cell
'''
bpxv = [(bp[1]*v[2]-v[1]*bp[2]), (bp[2]*v[0]-bp[0]*v[2]), (bp[0]*v[1]- v[0]*bp[1])]
surf_cell = BodyCenteredCubic(directions = [v, bpxv, bp],
size = (1,1,1), symbol='Fe', pbc=(1,1,1),
latticeconstant = 2.85)
n = 2
while(surf_cell.get_cell()[2,2]< 20.0 ):
surf_cell = BodyCenteredCubic(directions = [v, bpxv, bp],
size = (1,1,n), symbol='Fe', pbc=(1,1,1),
latticeconstant = 2.85)
n += 1
surf_cell.center(vacuum=20.0, axis=2)
return surf_cell
def gamma_surf(h_pos=np.array([1.41, 1.500, 22.48])):
"""
:method:`gamma_surf` generates a set of directories with the upper
half unit cell displaced along a certain distance
along a particular lattice vector. Hydrogens can be added by
setting vector in h_pos.
TODO:
h_pos should be a list of vectors and atom type for this to be more general.
"""
vasp_exe = '/projects/SiO2_Fracture/iron/vasp.bgq'
crack_geom = {
'cleavage_plane': (1, 1, 0),
'crack_front': (1, -1, 0),
'crack_direction': (0, 0, 1)
}
crack_direction = crack_geom['crack_direction']
crack_front = crack_geom['crack_front']
cleavage_plane = crack_geom['cleavage_plane']
fe_unit = BodyCenteredCubic(
directions=[crack_direction, crack_front, cleavage_plane],
size=(1, 1, 1),
symbol='Fe',
pbc=(1, 1, 1),
latticeconstant=2.83)
nunits = 8
fe_bulk = BodyCenteredCubic(
directions=[crack_direction, crack_front, cleavage_plane],
size=(2, 2, nunits),
symbol='Fe',
pbc=(1, 1, 1),
latticeconstant=2.83)
fe_unit = Atoms(fe_unit)
fe_bulk = Atoms(fe_bulk)
ycut = 5.0 + float(nunits) / 2.0 * fe_unit.lattice[2, 2]
fe_bulk.center(vacuum=5.0, axis=2)
print 'lattice', fe_bulk.lattice[1, 1]
print 'ycut', ycut
a1 = fe_unit.lattice[0, 0]
a2 = fe_unit.lattice[1, 1]
POT_DIR = os.environ['POTDIR']
eam_pot = os.path.join(POT_DIR, 'PotBH.xml')
r_scale = 1.00894848312
#eam_pot = os.path.join(POT_DIR, 'iron_mish.xml')
#r_scale = 1.0129007626
pot = Potential(
'IP EAM_ErcolAd do_rescale_r=T r_scale={0}'.format(r_scale),
param_filename=eam_pot)
fe_bulk.set_calculator(pot)
print 'Bulk Energy', fe_bulk.get_potential_energy()
refen = fe_bulk.get_potential_energy()
A = fe_bulk.get_volume() / fe_bulk.lattice[2, 2]
vasp_args = dict(
xc='PBE',
amix=0.01,
amin=0.001,
bmix=0.001,
amix_mag=0.01,
bmix_mag=0.001,
kpts=[8, 8, 1],
kpar=32,
lreal='auto',
ibrion=2,
nsw=40,
nelmdl=-15,
ispin=2,
nelm=100,
algo='VeryFast',
npar=8,
lplane=False,
lwave=False,
lcharg=False,
istart=0,
voskown=1,
ismear=1,
sigma=0.1,
isym=2) # possibly try iwavpr=12, should be faster if it works
dir_name = 'b111shiftsym'
#dir_name = 'b001shiftsym'
f = open('_patdon123{0}H1.dat'.format(dir_name), 'w')
WRITEVASP = True
a0 = 2.83
for inum, ashift in enumerate(np.arange(0, 1.10, 0.10)):
try:
os.mkdir('{0}{1}'.format(dir_name, ashift))
except:
pass
print 'Directory already exists'
os.chdir('{0}{1}'.format(dir_name, ashift))
fe_shift = fe_bulk.copy()
fe_shift.set_calculator(pot)
for at in fe_shift:
if at.position[2] > ycut:
#[00-1](110)
# at.position += ashift*np.array([-a1,0,0])
#[1-11](110)
at.position += 0.5 * ashift * np.array([a1, a2, 0])
# print >> fil1, ashift, (units.m**2/units.J)*(fe_shift.get_potential_energy()-refen)/A
line = []
for at in fe_shift:
line.append(FixedLine(at.index, (0, 0, 1)))
#Now add Hydrogen
# fe_shift.add_atoms(np.array([0.53*a0, 0.53*a0, 21.0+a0/2]),1)
# at relaxed position:
fe_shift.add_atoms(h_pos, 1)
fix_atoms_mask = [at.number == 1 for at in fe_shift]
fixedatoms = FixAtoms(mask=fix_atoms_mask)
fe_shift.set_constraint(line + [fixedatoms])
opt = LBFGS(fe_shift)
opt.run(fmax=0.1, steps=1000)
if inum == 0:
print 'Setting Reference Energy'
refen = fe_shift.get_potential_energy()
print >> f, ashift, (units.m**2 / units.J) * (
fe_shift.get_potential_energy() - refen) / A
fe_shift.write('feb{0}.xyz'.format(ashift))
if WRITEVASP:
vasp = Vasp(**vasp_args)
vasp.initialize(fe_shift)
write_vasp('POSCAR',
vasp.atoms_sorted,
symbol_count=vasp.symbol_count,
vasp5=True)
vasp.write_incar(fe_shift)
vasp.write_potcar()
vasp.write_kpoints()
os.chdir('../')
f.close()
