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cA_example_4.m
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% *************************************************************************
% crystalAligner.m - Crystal Alignment Tool for Electron Microscopy
% .........................................................................
% Example 4
% Extension to example E1 by adding an additional rotational stage axis to
% achieve a better alignment.
% Single alignments of the {111} and {100} plane normals in a single cubic
% crystal with the z-Axis of the microscope
% *************************************************************************
% 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
% [email protected] (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 4\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',313*degree,15*degree,137*degree, ...
crys(1).CS,crys(1).SS); %Define crystal orientation (https://mtex-toolbox.github.io/OrientationDefinition.html)
crys(1).alignAx = zvector; %Microscope axis for alignment with crystal direction/plane; Examples: zvector; [.5 .5 1]; xvector; ...
crys(1).Miller = Miller(1,1,1,crys(1).CS,crys(1).SS,'hkl'); %Define at least one crystal direction (https://mtex-toolbox.github.io/CrystalDirections.html)
crys(1).Miller.opt.useSym = true; %Apply crystal symmetry: true/false
% ******************************* Stage ***********************************
stg.rot = [xvector; yvector; -zvector]; %Stage rotation axes
stg.LB = [ 0 -45 -180 ]; %Lower bound [°]
stg.UB = [ 20 45 180 ]; %Upper bound [°]
stg.order = [ 3 1 2 ]; %Hierarchy / order of rotation: Rotation 1 before 2 before 3; Example: [3 1 2];% ************************* Genetic algorithm *****************************
%Genetic algorithm
optim.order = length(crys); %Order of optimization problem (do not change)
optim.popSz = 100; %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');