SPM Simulator Tutorial

走査プローブ顕微鏡シミュレータ Scanning Probe Microscope Simulator チュートリアルTutorial ver.β January 27, 2017 Advanced Algorithm & Systems Co., Ltd. Tohoku University, WPI-AIMR Contents Introduction ..................................................................................................................... 5 Composition of SPM simulator ........................................................................................ 6 Chapter 1 Installation of the software and preparation ........................ 11 1 installation of the software ............................................................................. 11 Chapter 2 Operation of the software .................................................... 20 1 Overview of the GUI ........................................................................................ 20 2 Part names and functions ................................................................................ 21 3 Start up GUI ..................................................................................................... 23 4 Operations of a project file .............................................................................. 24 Create a new project ............................................................................................................... 24 Load an existing project file .................................................................................................... 25 Show a project file .................................................................................................................. 27 Save a project file .................................................................................................................... 27 Close a project......................................................................................................................... 29 5 Edit project ...................................................................................................... 30 Components ............................................................................................................................ 30 (1) Add, replace, remove ........................................................................................................ 30 (2) Initial layout setting（position, rotation, reset） ........................................................... 34 (3) Show data, modify attributes ........................................................................................... 36 Set and show a scanning area ................................................................................................. 36 Select a simulator and set parameters .................................................................................... 37 6 Simulation ....................................................................................................... 39 Calculate, replay, stop, and pause ........................................................................................... 39 Render the result .................................................................................................................... 40 7 Visualization setting ........................................................................................ 46 Show/hide a component ......................................................................................................... 46 Change viewpoint, zoom all, scaling, and perspective ............................................................ 46 View option setting ................................................................................................................. 50 8 Quit GUI .......................................................................................................... 53 9 Others ............................................................................................................. 54 Show/hide window ................................................................................................................. 54 Select a component ................................................................................................................ 55 Registration of components to the database .......................................................................... 56 1 Export image ........................................................................................................................... 57 Chapter 3 Case study ............................................................................ 58 1 Geometrical and tip-sample-image interactive AFM simulator ........................ 58 Introduction ............................................................................................................................ 58 Simulation of the AFM image, from the data of the tip and the sample ................................ 59 Simulation of the sample surface, from the tip data and the observed AFM image .............. 63 Simulation of the tip surface, from the sample data and the observed AFM image .............. 66 2 Finite Element Method AFM simulator ............................................................ 69 Introduction ............................................................................................................................ 69 Simulation of an AFM image of an organic macromolecule (non-contact mode) .................. 70 Simulation of an AFM frequency shift image of a crystalline silicon surface (frequency shift image mode) ........................................................................................................................... 74 Simulation of an AFM viscoelastic dynamics analysis of a crystalline silicon surface (viscoelastic dynamics mode) ................................................................................................. 79 3 Soft Material Liquid AFM Simulator ................................................................. 85 Introduction ............................................................................................................................ 85 Motion of the cantilever in water ........................................................................................... 86 Frequency spectrum of the cantilever .................................................................................... 96 Cantilevers having complex shapes ........................................................................................ 99 Simulation with viscoelastic dynamics .................................................................................. 102 4 Classical Force Field AFM Simulator ............................................................... 107 Introduction .......................................................................................................................... 107 Example of calculating the frequency shift image of pentacene in vacuum ......................... 107 Example of calculating force curve in aquatic environment ................................................. 109 Example of calculating force curve of chain alkane .............................................................. 111 5 Quantum Mechanical SPM Simulator ............................................................ 114 Introduction .......................................................................................................................... 114 Example of AFM (frequency shift) image simulation ............................................................ 114 Examples of STM simulation ................................................................................................. 116 (1) Simulation for a tunneling current image ................................................................... 116 (2) Calculation of Scanning Tunneling Spectroscopy ........................................................ 119 Simulation for a KPFM simulation ......................................................................................... 121 band calculation .................................................................................................................... 123 Chapter 4 Image Comparison.............................................................. 126 1 Overview ....................................................................................................... 126 2 Part names and functions .............................................................................. 127 2 3 Start up and quit Analyzer-module ................................................................ 128 4 File manipulations ......................................................................................... 129 Input the data file ................................................................................................................. 130 Save the data file ................................................................................................................... 132 Save the image ...................................................................................................................... 133 5 Fourier analyses and high-resolutionizing of images ...................................... 134 Fourier analysis of an image ................................................................................................. 134 High-resolutionize of an image ............................................................................................. 138 6 Neural-net simulator ..................................................................................... 139 Start up the Neural-net Simulator ........................................................................................

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