Core-Shell Mn3O4/Co3O4 Nanoparticle

import numpy as np
import czone as cz
from pymatgen.core import Structure
from cz.volume import Volume, MultiVolume, Plane, snap_plane_near_point
from cz.generator import Generator, AmorphousGenerator
from cz.transform import Rotation, Reflection, Translation, rot_vtv
from cz.scene import Scene

mn_crystal = Structure.from_file("Mn3O4_mp-18759_conventional_standard.cif")
co_crystal = Structure.from_file("Co3O4_mp-18748_conventional_standard.cif")

# correct lattice mismatch
co_100 = np.linalg.norm(co_crystal.lattice.matrix @ np.array([1,0,0]))
mn_110 = np.linalg.norm(mn_crystal.lattice.matrix @ np.array([1,1,0]))
mn_crystal.apply_strain([co_100/mn_110-1, co_100/mn_110-1, 0])

# Make Co3O4 core
co_gen = Generator(structure=co_crystal)

N_uc = 6 # stretch N unit cells from center
co_a = co_crystal.lattice.a
vecs_100 = np.array([[1,0,0],[-1,0,0],[0,1,0],[0,-1,0],[0,0,1],[0,0,-1]])
planes_100 = []
for v in vecs_100:
    planes_100.append(snap_plane_near_point(N_uc*co_a*v, co_gen, tuple(v)))

co_core = Volume(alg_objects=planes_100, generator=co_gen)

# Make unstrained Mn3O4 grain
mn_gen = Generator(structure=mn_crystal)

# rotate 45 degrees and place on top of Co core
r = Rotation(matrix=rot_v(np.array([0,0,1]), np.pi/4))
t = Translation(np.array([0,0,N_uc*co_a]))
mn_gen.transform(r)
mn_gen.transform(t)

# define top and bottom 100 surfaces
surface_point = np.array([0,0,N_uc*co_a])
mn_c = mn_crystal.lattice.c
mn_bot = snap_plane_near_point(surface_point, mn_gen, (0,0,-1))
mn_top = snap_plane_near_point(surface_point+6*mn_c*np.array([0,0,1]), mn_gen, (0,0,1))

# define 112 facets
side_vs_112 = [(1,1,-2),(1,-1,-2), (-1,1,-2), (-1,-1,-2)]
sides_112 = []
for s in side_vs_112:
    tmp_point = np.array([1,1,0]) * np.sign(s) * co_a
    tmp_plane = snap_plane_near_point(tmp_point, mn_gen, s)
    sides_112.append(tmp_plane)

# define 101 facets
mn_a = mn_crystal.lattice.a
side_vs_101 = [(1,0,1),(0,1,1),(-1,0,1),(0,-1,1)]
sides_101 = []
for s in side_vs_101:
    tmp_point = np.array([1,1,0]) * np.sign(s) * 12*mn_a + mn_top.point
    tmp_plane = snap_plane_near_point(tmp_point, mn_gen, s)
    sides_101.append(tmp_plane)

# create volume representing grain
    mn_vols = [mn_bot, mn_top] + sides_112+sides_101
    mn_grain = Volume(alg_objects=mn_vols, generator=mn_gen)
    mn_grain.priority=1

# rotate to make 5 other grains from +z shell grain
mn_grains = [mn_grain]

# get +x, -z, -x
for theta in [np.pi/2, np.pi, -np.pi/2]:
    rot = Rotation(rot_v(np.array([0,1,0]),theta))
    tmp_grain = mn_grain.from_volume(transformation=[rot])
    mn_grains.append(tmp_grain)

# get +-y
for theta in [np.pi/2, -np.pi/2]:
    rot = Rotation(rot_v(np.array([1,0,0]),theta))
    tmp_grain = mn_grain.from_volume(transformation=[rot])
    mn_grains.append(tmp_grain)

# make final core-shell NP as multivolume and save to file
core_shell_NP = MultiVolume([co_core] + mn_grains)
core_shell_NP.populate_atoms()
core_shell_NP.to_file("core_shell_NP.xyz")