TiO2 surface slab#
import & prepare#
[1]:
!pip install git+https://github.com/nmdl-mizo/interface_master.git@develop
!mkdir -p cif_files
!curl https://raw.githubusercontent.com/nmdl-mizo/interface_master/develop/test_files/cif_files/TiO2_mp-2657_conventional_standard.cif -o 'cif_files/TiO2_mp-2657_conventional_standard.cif'
Defaulting to user installation because normal site-packages is not writeable
Collecting git+https://github.com/nmdl-mizo/interface_master.git@develop
Cloning https://github.com/nmdl-mizo/interface_master.git (to revision develop) to /tmp/pip-req-build-uugit09c
Running command git clone --filter=blob:none --quiet https://github.com/nmdl-mizo/interface_master.git /tmp/pip-req-build-uugit09c
Resolved https://github.com/nmdl-mizo/interface_master.git to commit 2bdf96ed4835b036557ac18de82b4fa2afdabf24
Preparing metadata (setup.py) ... done
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[notice] A new release of pip available: 22.3.1 -> 23.0.1
[notice] To update, run: pip install --upgrade pip
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[2]:
from interfacemaster.interface_generator import get_surface_slab, terminates_scanner_slab_structure
from interfacemaster.cellcalc import get_primitive_hkl
from pymatgen.core.structure import Structure
from numpy import ceil
Load structures#
[3]:
primitive_unit_structure = Structure.from_file('cif_files/TiO2_mp-2657_conventional_standard.cif', \
primitive=True, sort=False, merge_tol=0.0)
[4]:
conv_unit_structure = Structure.from_file('cif_files/TiO2_mp-2657_conventional_standard.cif', \
primitive=False, sort=False, merge_tol=0.0)
[5]:
#get all the non-identical terminations
hkl_in_pri = get_primitive_hkl(hkl=[1,0,1], C_lattice=conv_unit_structure.lattice.matrix.T, \
P_lattice=primitive_unit_structure.lattice.matrix.T)
plane_list, element_list, dp_list = terminates_scanner_slab_structure(primitive_unit_structure, hkl_in_pri)
cross vector:
[[1]
[0]
[0]]
length: 2.969203
plane basis:
[[ 0 1]
[ 0 -1]
[ 1 0]]
length: 4.653272 5.519882857560747
[6]:
#height
dp_list
[6]:
[0.7623739121169246, 1.7406639121169247, 2.5030439121169246]
The function below generates a slab with its bc-plane is a specified (hkl) lattice plane#
Customerization options:#
replica — expand from primitive slab cell, default: [1,1,1]
inclination_tol — required minimum cos value of the angle between the basic crossing vector and the surface, default: gamma angle > 45 degrees
termi_shift — shift the termination of the surface, default: 0
vacuum_height — height of vaccum, default: 0
plane_normal — whether requiring the two vectors in the surface plane to be perpendicular, default: False
normal_perp — whether requiring the crossing vector to be perpendicular to the plane, default: False
normal_tol — tolerance to judge whether normal/perpendicular, default: 1e-3
lim — control the number of generated vectors to search for the crossing vectors and perpendicular vectors, default: 20
filename — name of the generated atom files, default: ‘POSCAR’
filetype — type of the generated atom files (for VASP or LAMMPS), default: ‘VASP’
[16]:
#get orthogonal cell
slab_structure = get_surface_slab(conv_unit_structure, hkl = [1,0,1], vacuum_height = 15, \
plane_normal = True, normal_perp = True, termi_shift = 1.75)
cross vector:
[[2]
[0]
[5]]
length: 17.521869837553325
plane basis:
[[ 0 1]
[-1 0]
[ 0 -1]]
length: 4.653272 5.519882857560747
[5]:
#expansion to reach a required slab size with length_a > 5, length_b > 10, length_c > 10
da, db, dc = ceil(5/6.580720371810977), ceil(10/2.969203), ceil(10/6.580720371810977)
slab_structure = get_surface_slab(unit_structure, hkl = [1,1,0], replica = [da, db, dc], vacuum_height = 20)
cross vector:
[[-1]
[-1]
[ 0]]
length: 6.580720371810977
plane basis:
[[ 0 -1]
[ 0 1]
[ 1 0]]
length: 2.969203 6.580720371810977
Try other customerization options :D