Strain tests in low dimensional materials: Geometrical Phase Analysis

Abstract

In the last decades there has been an increasing interest in computing the local strain at the atomic scale of materials. By knowing aspects of the local strain in a lattice, one has information about measurements of distortions of lattice parameters concerning shifts, deformations and defects computed with respect to a smooth, defect-free reference region. Multiple methods have been implemented so far in order to map the strain of two-dimensional lattice patterns, which are obtained through means of a High Resolution Electron Microscope (HRTEM). The functioning of a HRTEM is based on the same principles as an optical microscope, but it uses a beam of electrons instead of visible light. One of the computational methods which then processes the obtained two-dimensional images is called the Geometrical Phase Analysis (GPA) and makes use of a very important mathematical tool, the Fourier transform. The GPA method lies at the center of this project and consists of several steps. First, the Fourier transform of the lattice image is plotted and two Bragg peaks corresponding to two linearly independent frequency vectors in the power spectrum are chosen. Next, a mask is applied around these peaks, separately. In my project I have chosen to apply the Hann smoothing filter. Then, the inverse Fourier transform is applied to the masked image and the phase (also called the raw phase) is plotted. The next step is to compute the reduced phase, which is defined at a local pixel as being the raw phase from which the following product is subtracted: 2𝜋 ⃗𝑔 ⋅ ⃗𝑟, where ⃗𝑟 is the vector corresponding to a pixel in the real space and ⃗𝑔 the frequency vector corresponding to the Bragg peak around which one has applied the mask. At this point the reference region is computed by choosing a smooth, homogeneous area in the reduced phase image. In order to obtain the strain, one needs an optimal frequency vector ⃗𝑔 defined at every pixel of lattice. In order to do so, a minimization process defined in the context of a computer algorithm in the programming language Python has been implemented. These computations should lead to obtaining the lattice strain, which is calculated by taking the symmetric part of the derivation of the displacement obtained from the two linearly independent Fourier components, which is in turn called the distortion. The antisymmetric part of the distortion is the rotation component and serves as a check for the correctness of the computational method. The goal of my project is not only to provide a solid theoretical background for the GPA method and to discuss the strain at atomic level in several lattice patterns, but to also provide a rigorous computer algorithm that makes these computations reality. This algorithm, opposed to pre-existing software, facilitates the reader’s process immensely by the large amount of detail which is given at every step, detail which easily motivates and supports the reader in potential side-steps they would want to take in order to make the method their own.