Si/Si3N4 - Approximate#
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/Si_mp-149_conventional_standard.cif -o 'cif_files/Si_mp-149_conventional_standard.cif'
!curl https://raw.githubusercontent.com/nmdl-mizo/interface_master/develop/test_files/cif_files/Si3N4_mp-988_conventional_standard.cif -o 'cif_files/Si3N4_mp-988_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-oekxly57
Running command git clone --filter=blob:none --quiet https://github.com/nmdl-mizo/interface_master.git /tmp/pip-req-build-oekxly57
Resolved https://github.com/nmdl-mizo/interface_master.git to commit 2bdf96ed4835b036557ac18de82b4fa2afdabf24
Preparing metadata (setup.py) ... done
Requirement already satisfied: pymatgen in /home/vscode/.local/lib/python3.10/site-packages (from interfacemaster==1.1.1) (2023.1.30)
Requirement already satisfied: matplotlib in /home/vscode/.local/lib/python3.10/site-packages (from interfacemaster==1.1.1) (3.7.0)
Requirement already satisfied: gb_code in /home/vscode/.local/lib/python3.10/site-packages (from interfacemaster==1.1.1) (1.0.0)
Requirement already satisfied: numpy>=1.14.0 in /home/vscode/.local/lib/python3.10/site-packages (from gb_code->interfacemaster==1.1.1) (1.24.2)
Requirement already satisfied: contourpy>=1.0.1 in /home/vscode/.local/lib/python3.10/site-packages (from matplotlib->interfacemaster==1.1.1) (1.0.7)
Requirement already satisfied: pillow>=6.2.0 in /home/vscode/.local/lib/python3.10/site-packages (from matplotlib->interfacemaster==1.1.1) (9.4.0)
Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.10/site-packages (from matplotlib->interfacemaster==1.1.1) (23.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/vscode/.local/lib/python3.10/site-packages (from matplotlib->interfacemaster==1.1.1) (1.4.4)
Requirement already satisfied: fonttools>=4.22.0 in /home/vscode/.local/lib/python3.10/site-packages (from matplotlib->interfacemaster==1.1.1) (4.38.0)
Requirement already satisfied: cycler>=0.10 in /home/vscode/.local/lib/python3.10/site-packages (from matplotlib->interfacemaster==1.1.1) (0.11.0)
Requirement already satisfied: pyparsing>=2.3.1 in /home/vscode/.local/lib/python3.10/site-packages (from matplotlib->interfacemaster==1.1.1) (3.0.9)
Requirement already satisfied: python-dateutil>=2.7 in /usr/local/lib/python3.10/site-packages (from matplotlib->interfacemaster==1.1.1) (2.8.2)
Requirement already satisfied: tqdm in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (4.64.1)
Requirement already satisfied: plotly>=4.5.0 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (5.13.0)
Requirement already satisfied: spglib>=2.0.2 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (2.0.2)
Requirement already satisfied: networkx>=2.2 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (3.0)
Requirement already satisfied: monty>=3.0.2 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (2022.9.9)
Requirement already satisfied: sympy in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (1.11.1)
Requirement already satisfied: scipy>=1.5.0 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (1.10.1)
Requirement already satisfied: tabulate in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (0.9.0)
Requirement already satisfied: mp-api>=0.27.3 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (0.30.10)
Requirement already satisfied: ruamel.yaml>=0.17.0 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (0.17.21)
Requirement already satisfied: requests in /usr/local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (2.28.2)
Requirement already satisfied: uncertainties>=3.1.4 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (3.1.7)
Requirement already satisfied: pandas in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (1.5.3)
Requirement already satisfied: palettable>=3.1.1 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (3.3.0)
Requirement already satisfied: pybtex in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (0.24.0)
Requirement already satisfied: typing-extensions>=3.7.4.1 in /home/vscode/.local/lib/python3.10/site-packages (from mp-api>=0.27.3->pymatgen->interfacemaster==1.1.1) (4.5.0)
Requirement already satisfied: emmet-core>=0.39.8 in /home/vscode/.local/lib/python3.10/site-packages (from mp-api>=0.27.3->pymatgen->interfacemaster==1.1.1) (0.44.0)
Requirement already satisfied: msgpack in /home/vscode/.local/lib/python3.10/site-packages (from mp-api>=0.27.3->pymatgen->interfacemaster==1.1.1) (1.0.4)
Requirement already satisfied: setuptools in /usr/local/lib/python3.10/site-packages (from mp-api>=0.27.3->pymatgen->interfacemaster==1.1.1) (65.5.1)
Requirement already satisfied: tenacity>=6.2.0 in /home/vscode/.local/lib/python3.10/site-packages (from plotly>=4.5.0->pymatgen->interfacemaster==1.1.1) (8.2.1)
Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.10/site-packages (from python-dateutil>=2.7->matplotlib->interfacemaster==1.1.1) (1.16.0)
Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/site-packages (from requests->pymatgen->interfacemaster==1.1.1) (2022.12.7)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /usr/local/lib/python3.10/site-packages (from requests->pymatgen->interfacemaster==1.1.1) (1.26.14)
Requirement already satisfied: charset-normalizer<4,>=2 in /usr/local/lib/python3.10/site-packages (from requests->pymatgen->interfacemaster==1.1.1) (3.0.1)
Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/site-packages (from requests->pymatgen->interfacemaster==1.1.1) (3.4)
Requirement already satisfied: ruamel.yaml.clib>=0.2.6 in /home/vscode/.local/lib/python3.10/site-packages (from ruamel.yaml>=0.17.0->pymatgen->interfacemaster==1.1.1) (0.2.7)
Requirement already satisfied: future in /home/vscode/.local/lib/python3.10/site-packages (from uncertainties>=3.1.4->pymatgen->interfacemaster==1.1.1) (0.18.3)
Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/site-packages (from pandas->pymatgen->interfacemaster==1.1.1) (2022.7.1)
Requirement already satisfied: PyYAML>=3.01 in /usr/local/lib/python3.10/site-packages (from pybtex->pymatgen->interfacemaster==1.1.1) (6.0)
Requirement already satisfied: latexcodec>=1.0.4 in /home/vscode/.local/lib/python3.10/site-packages (from pybtex->pymatgen->interfacemaster==1.1.1) (2.0.1)
Requirement already satisfied: mpmath>=0.19 in /home/vscode/.local/lib/python3.10/site-packages (from sympy->pymatgen->interfacemaster==1.1.1) (1.2.1)
Requirement already satisfied: pydantic>=1.10.2 in /home/vscode/.local/lib/python3.10/site-packages (from emmet-core>=0.39.8->mp-api>=0.27.3->pymatgen->interfacemaster==1.1.1) (1.10.5)
[notice] A new release of pip available: 22.3.1 -> 23.0.1
[notice] To update, run: pip install --upgrade pip
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 1059 100 1059 0 0 17650 0 --:--:-- --:--:-- --:--:-- 17650
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 1371 100 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 1371 0 0 4554 0 --:--:-- --:--:-- --:--:-- 4554
Define an interface core class#
[2]:
from interfacemaster.cellcalc import get_primitive_hkl, get_pri_vec_inplane, get_normal_index, get_normal_from_MI, rot
from interfacemaster.interface_generator import core, convert_vector_index, get_disorientation
from numpy import array, dot, round, cross, eye
from numpy.linalg import inv, det, norm
[3]:
my_interface = core('cif_files/Si_mp-149_conventional_standard.cif',\
'cif_files/Si3N4_mp-988_conventional_standard.cif')
Warning!, this programme will rewrite the POSCAR file in this dir!
/Users/jasonxie/.local/lib/python3.8/site-packages/pymatgen/io/cif.py:1121: UserWarning: Issues encountered while parsing CIF: Some fractional co-ordinates rounded to ideal values to avoid issues with finite precision.
warnings.warn("Issues encountered while parsing CIF: %s" % "\n".join(self.warnings))
[4]:
#get the target disorientation
R = get_disorientation(L1 = my_interface.conv_lattice_1, L2 = my_interface.conv_lattice_2, \
v1 = [-1,1,0], hkl1 = [1, 1, 1], \
v2 = [1,0,0], hkl2 = [0, 0, 1])
R
[4]:
array([[-7.07106781e-01, -4.08248290e-01, 5.77350269e-01],
[ 7.07106781e-01, -4.08248290e-01, 5.77350269e-01],
[-3.53525080e-17, 8.16496581e-01, 5.77350269e-01]])
[8]:
#specify the two combining surfaces
hkl_1 = get_primitive_hkl([1, 1, 1], my_interface.conv_lattice_1, my_interface.lattice_1)
hkl_2 = get_primitive_hkl([0, 0, 1], my_interface.conv_lattice_2, my_interface.lattice_2)
Searching two_dimensional CSL#
[9]:
my_interface.parse_limit(du = 1e-1, S = 1e-1, sgm1=100, sgm2=100, dd = 1e-1)
#Do searching!
my_interface.search_one_position_2D(hkl_1, hkl_2, theta_range = 2, \
dtheta = 0.01, pre_R = R, match_tol = 0.01, pre_dt= True)
Congrates, we found an appx CSL!
U1 =
[[ 0 -2]
[-2 2]
[ 2 0]]; sigma_1 = 7
U2 =
[[ 0 0]
[ 1 0]
[ 1 -1]]; sigma_2 = 1
D =
[[ 1.00640892 -0.00320446 -0.00320446]
[-0.00320446 1.00640892 -0.00320446]
[-0.00320446 -0.00320446 1.00640892]]
axis = [-7.47674648 -7.47674648 -7.47674648] ; theta = 0.0
Get bicrystal#
[10]:
my_interface.compute_bicrystal_two_D(hkl_1 = hkl_1, hkl_2=hkl_2, normal_ortho = True, plane_ortho = False, lim = 50, tol_ortho = 1e-2, tol_integer=1e-3)
cell 1:
[[-1 0 -2]
[-1 -2 2]
[-1 2 0]]
cell 2:
[[-1 0 0]
[ 0 1 0]
[ 0 1 -1]]
[28]:
my_interface.get_bicrystal(two_D = True, xyz_1 = [1,1,1], xyz_2 = [1,1,1])
Please check the POSCAR file