def pmg_surfer(mpid='', vacuum=15, mat=None, max_index=1, min_slab_size=15):
if mat == None:
with MPRester() as mp:
mat = mp.get_structure_by_material_id(mpid)
if mpid == '':
print('Provide structure')
sg_mat = SpacegroupAnalyzer(mat)
mat_cvn = sg_mat.get_conventional_standard_structure()
mat_cvn.sort()
indices = get_symmetrically_distinct_miller_indices(mat_cvn, max_index)
#ase_atoms = AseAtomsAdaptor().get_atoms(mat_cvn)
structures = []
pos = Poscar(mat_cvn)
try:
pos.comment = str('sbulk') + str('@') + str('vac') + str(vacuum) + str(
'@') + str('size') + str(min_slab_size)
except:
pass
structures.append(pos)
mat_cvn.to(fmt='poscar',
filename=str('POSCAR-') + str('cvn') + str('.vasp'))
for i in indices:
slab = SlabGenerator(initial_structure=mat_cvn,
miller_index=i,
min_slab_size=min_slab_size,
min_vacuum_size=vacuum,
lll_reduce=False,
center_slab=True,
primitive=False).get_slab()
normal_slab = slab.get_orthogonal_c_slab()
slab_pymatgen = Poscar(normal_slab).structure
#ase_slab.center(vacuum=vacuum, axis=2)
#slab_pymatgen = AseAtomsAdaptor().get_structure(ase_slab)
xy_size = min_slab_size
dim1 = int((float(xy_size) /
float(max(abs(slab_pymatgen.lattice.matrix[0]))))) + 1
dim2 = int(
float(xy_size) /
float(max(abs(slab_pymatgen.lattice.matrix[1])))) + 1
slab_pymatgen.make_supercell([dim1, dim2, 1])
slab_pymatgen.sort()
surf_name = '_'.join(map(str, i))
pos = Poscar(slab_pymatgen)
try:
pos.comment = str("Surf-") + str(surf_name) + str('@') + str(
'vac') + str(vacuum) + str('@') + str('size') + str(
min_slab_size)
except:
pass
pos.write_file(filename=str('POSCAR-') + str("Surf-") +
str(surf_name) + str('.vasp'))
structures.append(pos)
return structures
def pmg_surfer(vacuum=15,
mat=None,
max_index=1,
min_slab_size=15,
write_file=True):
"""
Pymatgen surface builder for a Poscar
Args:
vacuum: vacuum region
mat: Structure object
max_index: maximum miller index
min_slab_size: minimum slab size
Returns:
structures: list of surface Structure objects
"""
if mat == None:
print("Provide structure")
sg_mat = SpacegroupAnalyzer(mat)
mat_cvn = sg_mat.get_conventional_standard_structure()
mat_cvn.sort()
indices = get_symmetrically_distinct_miller_indices(mat_cvn, max_index)
structures = []
pos = Poscar(mat_cvn)
try:
pos.comment = (str("sbulk") + str("@") + str("vac") + str(vacuum) +
str("@") + str("size") + str(min_slab_size))
except:
pass
structures.append(pos)
if write_file == True:
mat_cvn.to(fmt="poscar",
filename=str("POSCAR-") + str("cvn") + str(".vasp"))
for i in indices:
slab = SlabGenerator(
initial_structure=mat_cvn,
miller_index=i,
min_slab_size=min_slab_size,
min_vacuum_size=vacuum,
lll_reduce=False,
center_slab=True,
primitive=False,
).get_slab()
normal_slab = slab.get_orthogonal_c_slab()
slab_pymatgen = Poscar(normal_slab).structure
xy_size = min_slab_size
dim1 = (int((float(xy_size) /
float(max(abs(slab_pymatgen.lattice.matrix[0]))))) + 1)
dim2 = (int(
float(xy_size) / float(max(abs(slab_pymatgen.lattice.matrix[1]))))
+ 1)
slab_pymatgen.make_supercell([dim1, dim2, 1])
slab_pymatgen.sort()
surf_name = "_".join(map(str, i))
pos = Poscar(slab_pymatgen)
try:
pos.comment = (str("Surf-") + str(surf_name) + str("@") +
str("vac") + str(vacuum) + str("@") + str("size") +
str(min_slab_size))
except:
pass
if write_file == True:
pos.write_file(filename=str("POSCAR-") + str("Surf-") +
str(surf_name) + str(".vasp"))
structures.append(pos)
return structures