Hi!
I’d like to create (1,1,1) surface of the oxides of some elements like Pt, Co and so on. I get different results from pymatgen and ASE packages. Do I use these functions incorrectly or is there something else about slab generation that I’m missing?
I share the structures below and the code to reproduce them.
PtO2 (1,1,1) generated by pymatgen:
PtO2 (1,1,1) generated by ase:
Code for generating the surface by pymatgen:
# import structure by Material Project ID
mp_id = 'mp-1285'
structure = mpr.get_structure_by_material_id(mp_id)
formula = structure.composition.reduced_formula
# get conventional cell
conv_cell = SpacegroupAnalyzer(structure).get_conventional_standard_structure()
# generate all possible slabs of planes with maximum index of 1 and other parameters
all_slabs = generate_all_slabs(conv_cell, max_index=2, min_slab_size=2.0,
min_vacuum_size=5,symmetrize=True,
in_unit_planes = True,
center_slab=True,max_normal_search=5, primitive=False)
# take the most dense slab
slabs_111 = [a for a in all_slabs if a.miller_index==(1,1,1)]
slabs_111_dense = [a.density for a in slabs_111]
slab = slabs_111[slabs_111_dense.index(max(slabs_111_dense))]
from pymatgen.io.ase import AseAtomsAdaptor
# convert slab to ASE object from pymatgen object
slab_ase = AseAtomsAdaptor.get_atoms(slab)\
# visualize top and front view
fig, axs = plt.subplots(1, 2)
plot_atoms(slab_ase, axs[0]);
plot_atoms(slab_ase, axs[1], rotation=('-90x, -30y'))
axs[0].set_axis_off()
axs[1].set_axis_off()
Code for generating the surface by ase:
# read the structure file
structure = read('PtO2.cif')
# slab parameters
plane = (1,1,1)
n_layers = 5
vacuum = 10
# create surface of the structure
slab = surface(structure, plane, n_layers, vacuum=vacuum)
# visualize top and front view
fig, axs = plt.subplots(1, 2)
plot_atoms(slab, axs[0]);
plot_atoms(slab, axs[1], rotation=('-90x, -30y'))
axs[0].set_axis_off()
axs[1].set_axis_off()