def calc_elast_dipole_eam(input_file, force_tol, relax_cell):
"""
Calculate elastic dipole using an Embedded Atom Potential.
Args:
input_file (str): Name of .xyz file contains unitcell with defect.
force_tol (float): Force tolerance to stop relaxation.
relax_cell (bool): Relax lattice vectors.
Returns:
Elastic Dipole Tensor 3x3 numpy array.
"""
try:
POT_DIR = os.environ['POTDIR']
except KeyError:
sys.exit("PLEASE SET export POTDIR='path/to/potfiles/'")
elastic = ElasticDipole()
eam_pot = os.path.join(POT_DIR, 'PotBH.xml')
pot = Potential(
'IP EAM_ErcolAd do_rescale_r=T r_scale={0}'.format(1.00894848312),
param_filename=eam_pot)
ats = Atoms(input_file)
ats.set_calculator(pot)
init_vol = ats.get_volume()
print 'Initial Vol.', init_vol
elastic.relax_defect_cell(ats, force_tol=force_tol, relax_cell=relax_cell)
final_vol = ats.get_volume()
print 'Final Vol.', final_vol
print 'Volume Diff.', final_vol - init_vol
ats = Atoms('defect_cell_relaxed.xyz')
defect = find_h_atom(ats)
print 'Defect index', defect.index, 'Position', defect.position, 'Type: ', defect.number
ats.set_calculator(pot)
return elastic.compute_vacancy_dipole(defect, ats.copy(), pot)
else:
print ("Using PURE EAM POTENTIAL")
qm_pot = Potential('IP EAM_ErcolAd do_rescale_r=T r_scale={0}'.format(1.00894848312), param_filename=eam_pot)
nebpath = NEBPaths()
nebanalysis = NEBAnalysis()
if args.auto_gen:
disloc_ini, disloc_fin = nebpath.build_h_nebpath(neb_path=np.array(args.neb_path), fmax = args.fmax, sup_cell=args.sup_cell)
else:
disloc_ini = Atoms('disloc_0.xyz')
disloc_fin = Atoms('disloc_1.xyz')
n_knots = args.knots
images = [disloc_ini] + \
[disloc_ini.copy() for i in range(n_knots)] + \
[disloc_fin]
#copied this from Tom's scripts: need to check and understand
#Will turn these on after the initial run throughs to check the difference.
#alpha = dft_alat/eam_alat
#eam_bulk_mod = (eam_C11 + 2.0*eam_C12)/3.0
#dft_bulk_mod = (dft_C11 + 2.0*dft_C12)/3.0
#beta = eam_bulk_mod/dft_bulk_mod/alpha/alpha/alpha
qmmm_pot = ForceMixingCarvingCalculator(disloc_ini, qm_region_mask,
mm_pot, qm_pot,
buffer_width=buff,
alpha=1.0, beta=1.0,
vacuum=5.0,
pbc_type=[False, False, True])
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)
if __name__ == '__main__':
gen_interface()
decorate_interface()
with open('unique_h_sites.json', 'r') as f:
h_sites = json.load(f)
g = open('h_site_ener_{}_{}.txt'.format(mode, str(num)), 'w')
ats = Atoms('output.xyz')
gb_min, gb_max, z_width, at_min = get_interface_bounds(ats)
with open('subgb.json', 'r') as f:
subgb_dict = json.load(f)
s_ats = ats.copy()
s_ats = apply_strain(s_ats, mode, num)
s_ats.set_calculator(pot)
E_gb = s_ats.get_potential_energy()
for h_site in h_sites[:50]:
h_ats = s_ats.copy()
h_site_tmp = list(h_site)
#-1.0 to subtract vacuum added in calc_eseg.py at_min to account for diff between gb_min and lowest atom.
h_site_tmp[2] += gb_min - 1.0 + at_min
h_ats.add_atoms(h_site_tmp, 1)
h_ats.set_calculator(pot)
opt = FIRE(h_ats)
opt.run(fmax=force_tol)
E_gbh = h_ats.get_potential_energy()
h_at_rel = filter(lambda x: x.number == 1, h_ats)
#print position of relaxed h atom and the interstitial energies.
help='Force Tolerance',
default=0.05,
type=float)
args = parser.parse_args()
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)
with open('subgb.json', 'r') as f:
subgb_dict = json.load(f)
force_tol = args.force_tol
E_h2 = -4.73831215121
#E_gb = subgb_dict['E_gb']
all_h_ats = ats.copy()
for mode in args.modes:
for num in args.nums:
g = open('h_site_ener_{}_{}.txt'.format(mode, str(num)), 'w')
s_ats = ats.copy()
s_ats = apply_strain(s_ats, mode, num)
s_ats.set_calculator(pot)
E_gb = s_ats.get_potential_energy()
for h_site in h_sites:
h_ats = s_ats.copy()
h_site_tmp = list(h_site)
#-1.0 to subtract vacuum added in calc_eseg.py at_min to account for diff between gb_min and lowest atom.
h_site_tmp[2] += gb_min - 1.0 + at_min
h_ats.add_atoms(h_site_tmp, 1)
h_ats.set_calculator(pot)
opt = FIRE(h_ats)
