/
cA_example_3.m
86 lines (82 loc) · 7.04 KB
/
cA_example_3.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
% *************************************************************************
% crystalAligner.m - Crystal Alignment Tool for Electron Microscopy
% .........................................................................
% Example 3
% Concurrent alignment of the <011> and [001] directions in a cubic and
% an orthorhombic crystal with the x-Axis and z-Axis of the microscope,
% respectively.
% *************************************************************************
% If you use this script for research and find it useful I would appreciate a
% citation of the associated article:
% [crystalAligner: a computer program to align crystal directions in a scanning
% electron microscope by global optimization, F. Niessen, Journal of Applied
% Crystallography, 2020, doi: 10.1107/S1600576719017345]
% *************************************************************************
% Dr. Frank Niessen, University of Wollongong, Australia, 2018
% contactnospam@fniessen.com (remove the nospam to make this email address
% work)
% 2021/04, Improvements implemented by Dr. Vivian Tong, NPL
% *************************************************************************
% Execution of the software requires installation of
% * mtex (http://mtex-toolbox.github.io/)
% * MATLAB Optimization toolbox
% * MATLAB Global optimization toolbox
% * Optional: MATLAB Parallel Computing Toolbox
% Compatibility tested with MATLAB R2104a - R2016b and MTEX 4.2.1 to 5.6
% *************************************************************************
% Copyright 2018 Frank Niessen (see attached MIT license file)
%% Initialization
clear variables; close all; home;
fprintf('\n*************************************************************');
fprintf('\n crystalAligner Example 3\n');
fprintf('*************************************************************\n\n');
fprintf('-> Starting up MTEX ...\n'); %ScreenPrint
currentFolder; %Add subfolder to path
iniExtLibs; %Initialize MTEX and check for MATLAB toolboxes
%% Definition of alignment problem
% ****************************** Crystals *********************************
% *** Crystal Alignment Objective 1
crys(1).SS = specimenSymmetry('triclinic'); %Define specimen symmetry ['triclinic'|'orthorhombic']
crys(1).CS = crystalSymmetry('m-3m','mineral','cubicPhase'); %Define crystal symmetry (https://mtex-toolbox.github.io/CrystalSymmetries.html)
crys(1).ori = orientation('Euler',261*degree,43*degree,28*degree, ...
crys(1).CS,crys(1).SS); %Define crystal orientation (https://mtex-toolbox.github.io/OrientationDefinition.html)
crys(1).alignAx = xvector; %Microscope axis for alignment with crystal direction/plane; Examples: zvector; [.5 .5 1]; xvector; ...
crys(1).Miller = Miller(0,1,1,crys(1).CS,crys(1).SS,'uvw'); %Define at least one crystal direction (https://mtex-toolbox.github.io/CrystalDirections.html)
crys(1).Miller.opt.useSym = true; %Apply crystal symmetry: true/false
% *** Crystal Alignment Objective 2
crys(2).SS = specimenSymmetry('triclinic'); %Define specimen symmetry ['triclinic'|'orthorhombic']
crys(2).CS = crystalSymmetry('222',[3.0, 4.9, 4.6],...
'mineral','orthorhombicPhase'); %Define crystal symmetry (https://mtex-toolbox.github.io/CrystalSymmetries.html)
crys(2).ori = orientation('Euler',175*degree,20*degree,102*degree, ...
crys(2).CS,crys(2).SS); %Define crystal orientation (https://mtex-toolbox.github.io/OrientationDefinition.html)
crys(2).alignAx = zvector; %Microscope axis for alignment with crystal direction/plane; Examples: zvector; [.5 .5 1]; xvector; ...
crys(2).Miller = Miller(0,0,1,crys(2).CS,crys(2).SS,'uvw'); %Define one crystal direction (https://mtex-toolbox.github.io/CrystalDirections.html)
crys(2).Miller.opt.useSym = false; %Apply crystal symmetry: true/false
% ******************************* Stage ***********************************
stg.rot = [xvector; -zvector]; %Stage rotation axes
stg.LB = [ 0 -180 ]; %Lower bound [°]
stg.UB = [ 20 180 ]; %Upper bound [°]
stg.order = [ 2 1 ]; %Hierarchy / order of rotation: Rotation 1 before 2 before 3; Example: [3 1 2];
%Genetic algorithm
optim.order = length(crys); %Order of optimization problem (do not change)
optim.popSz = 500; %Population size
optim.funcTol = 0.1; %FunctionTolerance
optim.maxStallGen = 10; %Maximum stall generations
optim.iterOut = false; %Writing output for each iteration in subFolder 'iterOut': true/false
%Multiobjective genetic algorithm settings
optim.wghtFac = [1,1]; %Weighting factors for TOPSIS multiobjective decision making method
optim.multiCore = false; %Utilization of parallel processing (switch off if errors ocur): true/false
optim.hybridFcn = false; %Flag: Use a hybrid function to (may speed op convergence but compromise diversity of solution space): true/false
optim.autoSol = true; %Flag: Pick optimum solution automatically by distance of Pareto solution from the optimal solution: true/false
% ***************************** Optional **********************************
%FIB liftout calculations
FIB.mode = false; %Flag: FIB liftout output: true/false
FIB.trench.ang = 52; %Trenching - or look-in - angle of Trench [°]
FIB.trench.z = 15; %Trench depth 'z' [µm]
FIB.axs.tilt = 1; %Index of tilt axis in 'axs.rot'
FIB.axs.rot = 2; %Index of rotation axis in 'axs.rot'
%Output
optim.plot = true; %Plotting 1: true/false
%% Run crystalAligner
[oNew,stgRot,x,eps] = crystalAligner(crys,stg,optim,FIB);
fprintf('\n -> All done!\n');