dyn.run(fmax=0.00, steps=1100)
#dyn = BFGS(box)
#dyn.run(fmax=0.01, steps=200)
#dyn = BFGS(box)
#dyn.run(fmax=0.01, steps=200)
Eng = struc.get_potential_energy() * 96 / len(struc) * 3
Vol = struc.get_volume() / len(struc) * 3
stress = np.max(struc.get_stress())
struc = sort(struc)
try:
spg = get_symmetry_dataset(struc, symprec=1e-1)['number']
except:
spg = 1
struc.write(out_folder + '/' + str(i) + ".vasp", format='vasp', vasp5=True)
logging.info(
'{:4d} Spg: {:4d} Eng: {:8.4f} Vol: {:8.4f} Stress: {:5.2f}'.format(
i, spg, Eng, Vol, stress))
abc = struc.get_cell_lengths_and_angles()
abc = [int(i * 1000) / 1000 for i in abc]
#data['ID'].append(i)
data['Sym'].append(spg)
data['Eng'].append(Eng)
data['abc'].append(abc)
data['Volume'].append(Vol)
df = pd.DataFrame(data)
df = df.sort_values(['Eng', 'Volume'], ascending=[True, True])
print(df)
from utilities import relax_atoms_cell, phonons
import numpy as np
# set up cell
try:
with open("../model-{}-test-bulk_diamond-properties.json".format(
model.name)) as f:
j = json.load(f)
a0 = j["diamond_a0"]
bulk = Atoms(diamond2(a0, 14, 14))
except:
bulk = Atoms(diamond2(5.43, 14, 14))
bulk.set_calculator(model.calculator)
bulk = relax_atoms_cell(bulk, tol=1.0e-4, traj_file=None)
a0 = bulk.get_cell_lengths_and_angles()[0] * np.sqrt(2.0)
bulk = Atoms(diamond2(a0, 14, 14))
supercell = [[4, 0, 0], [0, 4, 0], [0, 0, 4]]
dx = 0.03
mesh = [16, 16, 16]
points = np.array([[0, 0, 0], [0, 0.5, 0.5], [1, 1, 1], [0.5, 0.5, 0.5]])
n_points = 50
phonon_properties = phonons(model,
bulk,
supercell=supercell,
], # NB atomic_numbers may contain ECPs
cell=[
ejp_result['final']['primitive_cell']['cell_vectors']['a']['magnitude'],
ejp_result['final']['primitive_cell']['cell_vectors']['b']['magnitude'],
ejp_result['final']['primitive_cell']['cell_vectors']['c']['magnitude']
],
positions=ejp_result['final']['primitive_cell']['ccoords']['magnitude'],
pbc=ejp_result['final']['primitive_cell']['pbc']
)
except KeyError:
logging.critical("PROBLEMATIC STRUCTURE: %s" %
ejp_result['final']['primitive_cell']['symbols'])
continue
if not all(ejp_struct.get_pbc()): # account non-periodic directions
adjust, cellpar = False, ejp_struct.get_cell_lengths_and_angles()
for n in range(3):
if cellpar[n] > CRYSTOUT.PERIODIC_LIMIT:
adjust, cellpar[n] = True, CRYSTOUT.PERIODIC_LIMIT
if adjust:
ejp_struct.set_cell(cellpar)
else:
logging.critical("CANNOT GET EJP STRUCTURE")
continue
pcy_struct = pcy_result['structures'][-1]
args = np.argsort(ejp_struct.positions[:, 2])
ejp_struct = ejp_struct[args]
args = np.argsort(pcy_struct.positions[:, 2])
pcy_struct = pcy_struct[args]
