substrate_slab,
mat2d_slab,
max_area=40,
max_mismatch=0.05,
max_angle_diff=20,
r1r2_tol=0.01)
substrate_slab_aligned.to(fmt='poscar',
filename=address + os.sep +
'POSCAR_substrate_aligned.vasp')
mat2d_slab_aligned.to(fmt='poscar',
filename=address + os.sep +
'POSCAR_mat2d_aligned.vasp')
substrate_bulk.to(fmt='poscar',
filename=address + os.sep +
'POSCAR_substrate_bulk.vasp')
hetero_interfaces = transformations.generate_all_configs(
mat2d_slab_aligned, substrate_slab_aligned, nlayers_2d,
nlayers_substrate, separation)
for i, iface in enumerate(hetero_interfaces):
sd_flags = CalibrateSlab.set_sd_flags(interface=iface,
n_layers=nlayers_2d +
nlayers_substrate,
top=True,
bottom=False)
poscar = pymatgen.io.vasp.inputs.Poscar(
iface, selective_dynamics=sd_flags)
poscar.write_file(filename=address + os.sep +
'POSCAR_final_{}.vasp'.format(i))
counter += 1
def upload_file():
stamp = ""
if request.method == 'POST':
#request.environ['REMOTE_ADDR']
if request.environ.get('HTTP_X_FORWARDED_FOR') is None:
ip = request.environ['REMOTE_ADDR']
else:
ip = request.environ['HTTP_X_FORWARDED_FOR'] # if behind a proxy
#substrate information#
f1 = request.files['POSCAR_sub']
stamp = time.strftime("%Y%m%d-%H%M%S") + '-' + ip
poscar_sub = stamp + '-' + f1.filename
f1.save(upload_dir + os.sep + secure_filename(poscar_sub))
h_sub = int(request.form["h_sub"])
k_sub = int(request.form["k_sub"])
l_sub = int(request.form["l_sub"])
nlayers_substrate = int(request.form["nlayers_substrate"])
min_thick_sub = float(request.form["min_thick_sub"])
min_vac_sub = float(request.form["min_vac_sub"])
#is_primitive = request.form.get["is_primitive"]
hkl_sub = [h_sub, k_sub, l_sub]
#2d information#
f2 = request.files['POSCAR_2d']
poscar_2d = stamp + '-' + f2.filename
f2.save(upload_dir + os.sep + secure_filename(poscar_2d))
h_2d = int(request.form["h_2d"])
k_2d = int(request.form["k_2d"])
l_2d = int(request.form["l_2d"])
nlayers_2d = int(request.form["nlayers_2d"])
hkl_2d = [h_2d, k_2d, l_2d]
#General information#
separation = float(request.form["separation"])
max_area = float(request.form["max_area"])
max_mismatch = float(request.form["max_mismatch"])
max_angle_diff = float(request.form["max_angle_diff"])
#Matching#
try:
substrate_bulk = pymatgen.Structure.from_file(upload_dir + os.sep +
poscar_sub)
sa_sub = pymatgen.symmetry.analyzer.SpacegroupAnalyzer(
substrate_bulk)
substrate_bulk = sa_sub.get_conventional_standard_structure()
substrate_slab = Interface(substrate_bulk,
hkl=hkl_sub,
min_thick=min_thick_sub,
min_vac=min_vac_sub,
primitive=False,
from_ase=True)
mat2d_slab = utils.slab_from_file(hkl_2d,
upload_dir + os.sep + poscar_2d)
operation_dir = "static" + os.sep + "operations" + os.sep + stamp
if not os.path.exists(operation_dir):
os.makedirs(operation_dir)
mat2d_slab.to(fmt="poscar",
filename=operation_dir + "POSCAR_mat2d_slab.vasp")
sd_flags = CalibrateSlab.set_sd_flags(interface=substrate_slab,
n_layers=nlayers_substrate,
top=True,
bottom=False)
poscar = pymatgen.io.vasp.inputs.Poscar(
substrate_slab, selective_dynamics=sd_flags)
poscar.write_file(filename=operation_dir + os.sep +
"POSCAR_substrate_slab.vasp")
substrate_slab_aligned, mat2d_slab_aligned, mismatch = transformations.get_aligned_lattices(
substrate_slab,
mat2d_slab,
max_area=max_area,
max_mismatch=max_mismatch,
max_angle_diff=max_angle_diff,
r1r2_tol=0.01)
substrate_slab_aligned.to(fmt="poscar",
filename=operation_dir + os.sep +
"POSCAR_substrate_aligned.vasp")
mat2d_slab_aligned.to(fmt="poscar",
filename=operation_dir + os.sep +
"POSCAR_mat2d_aligned.vasp")
hetero_interfaces = transformations.generate_all_configs(
mat2d_slab_aligned, substrate_slab_aligned, nlayers_2d,
nlayers_substrate, separation)
for i, iface in enumerate(hetero_interfaces):
sd_flags = CalibrateSlab.set_sd_flags(interface=iface,
n_layers=nlayers_2d +
nlayers_substrate,
top=True,
bottom=False)
poscar = pymatgen.io.vasp.inputs.Poscar(
iface, selective_dynamics=sd_flags)
poscar.write_file(filename=operation_dir + os.sep +
'POSCAR_final_{}.vasp'.format(i))
p = Poscar.from_file(operation_dir + os.sep +
'POSCAR_final_{}.vasp'.format(i))
w = CifWriter(p.structure)
w.write_file(operation_dir + os.sep +
'POSCAR_final_{}.cif'.format(i))
# st = pychemia.code.vasp.read_poscar(operation_dir+os.sep+'POSCAR_final_{}.vasp'.format(i))
#rf = open("testing")
#rf.write("reading succesful")
#rf.close()
# pychemia.io.cif.save(structure=st,filename=operation_dir+os.sep+'POSCAR_final_{}.xyz'.format(i))
except:
#redirect(url_for("error",_id="matching",stamp=stamp))
return ("Error")
return redirect(url_for('result', stamp=stamp))
return render_template("matching.html",
_id="matching",
test_var="test",
stamp=stamp)
def create_heterostructure(
bulk_structure=None,
slab_structure=None,
strain_sys="overlayer", # 'support' or 'overlayer'
surface_cut=[0, 0, 1],
separation=3,
nlayers_2d=1,
nlayers_substrate=4,
# Lattice matching algorithm parameters
max_area=40,
max_mismatch=1,
max_angle_diff=0.1,
r1r2_tol=0.01,
):
"""
bulk_structure:
ase atoms object for the support material
slab_structure:
overlayer material
strain_sys:
surface_cut:
separation:
nlayers_2d:
nlayers_substrate:
max_area:
max_mismatch:
max_angle_diff:
r1r2_tol:
"""
#| - create_heterostructure
#| - Generate Heterostructures
# substrate_bulk = Structure.from_file(bulk_filename)
substrate_slab = Interface(
bulk_structure,
# substrate_bulk,
hkl=surface_cut,
min_thick=20,
min_vac=30,
primitive=False,
from_ase=True,
)
# mat2d_slab = slab_from_file([0, 0, 1], graphene_filename)
mat2d_slab = slab_structure
if strain_sys == "support":
lower_mat = mat2d_slab
upper_mat = substrate_slab
elif strain_sys == "overlayer":
lower_mat = substrate_slab
upper_mat = mat2d_slab
# mat2d_slab_aligned, substrate_slab_aligned = get_aligned_lattices(
lower_mat_aligned, upper_mat_aligned = get_aligned_lattices(
lower_mat,
upper_mat,
max_area=max_area,
max_mismatch=max_mismatch,
max_angle_diff=max_angle_diff,
r1r2_tol=r1r2_tol,
)
if strain_sys == "support":
mat2d_slab_aligned = lower_mat_aligned
substrate_slab_aligned = upper_mat_aligned
elif strain_sys == "overlayer":
mat2d_slab_aligned = upper_mat_aligned
substrate_slab_aligned = lower_mat_aligned
# Writing hetero_interfaces to pickle file
with open('aligned_latt_materials.pickle', 'wb') as fle:
pickle.dump((substrate_slab_aligned, mat2d_slab_aligned), fle)
substrate_slab_aligned.to(filename='00_substrate_opt.POSCAR')
mat2d_slab_aligned.to(filename='00_graphene_opt.POSCAR')
# merge substrate and mat2d in all possible ways
hetero_interfaces = generate_all_configs(
mat2d_slab_aligned,
substrate_slab_aligned,
nlayers_2d,
nlayers_substrate,
separation,
)
# Writing hetero_interfaces to pickle file
with open('hetero_interfaces.pickle', 'wb') as fle:
pickle.dump(hetero_interfaces, fle)
#__|
return(hetero_interfaces)
# mat2d_slab_aligned, substrate_slab_aligned = get_aligned_lattices(
lower_mat_aligned, upper_mat_aligned = get_aligned_lattices(
lower_mat,
upper_mat,
max_area=max_area,
max_mismatch=max_mismatch,
max_angle_diff=max_angle_diff,
r1r2_tol=r1r2_tol,
)
# merge substrate and mat2d in all possible ways
hetero_interfaces = generate_all_configs(
lower_mat_aligned,
upper_mat_aligned,
nlayers_2d,
nlayers_substrate,
separation,
)
out_dir = os.path.join(
'01_heterostructures',
str(surface_cut[0]) + str(surface_cut[1]) + str(surface_cut[2]))
if not os.path.exists(out_dir):
os.makedirs(out_dir)
for i, iface in enumerate(hetero_interfaces):
atoms = AseAtomsAdaptor.get_atoms(iface)
io.write(
os.path.join(