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VESTA: a Three-Dimensional Visualization System for Electronic and Structural Analysis

Koichi MOMMA
National Museum of Nature and Science,
4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan

Fujio IZUMI

August 10, 2022

E-mail: vesta.dev@gmail.com
LICENSE AGREEMENT
1 INTRODUCTION AND BACKGROUND
 1.1 Understanding Crystal and Electronic Structures in Three Dimensions
 1.2 Circumstances behind the Development of VESTA
 1.3 What’s New in VESTA 3
 1.4 Notes on this Manual
2 OVERVIEW OF THE PROGRAM
 2.1 General Features
 2.2 Visualization of Structural Models
 2.3 Visualization of Volumetric Data
 2.4 Visualization of Crystal Morphologies
 2.5 Cooperation with External Programs
 2.6 Input and Output Files
 2.7 Programming Concept
3 GETTING STARTED
 3.1 Minimum requirements of hardware
 3.2 Windows
 3.3 macOS
 3.4 Linux
 3.5 Trouble Shooting
 3.6 Loading Files
4 MAIN WINDOW
 4.1 Components of the Main Window
 4.2 Menus
 4.3 Tools in the Horizontal Toolbar
 4.4 Tools in the Vertical Toolbar
 4.5 Text Area
5 DISPLAY STYLES
 5.1 Structural Models
 5.2 Volumetric Data
 5.3 Crystal Shapes
6 GIVING PHASE DATA
 6.1 Defining Phases
 6.2 Symmetry and Unit Cell
 6.3 Structure Parameters
 6.4 Volumetric Data
 6.5 Crystal Shape
7 OVERLAYING MULTIPLE DATA
 7.1 Positioning of Phases
 7.2 Relative Orientation of Phases
 7.3 Examples
8 CREATING BONDS AND POLYHEDRA
 8.1 Specifications of Searching for Bonds
 8.2 Operating Instructions
9 ADDITIONAL OBJECTS
 9.1 Vectors on Atoms
 9.2 Lattice Planes
10 DEFINING DRAWING BOUNDARIES AND VIEW DIRECTIONS
 10.1 Drawing Boundaries
 10.2 View Direction
11 INTERACTIVE MANIPULATIONS
 11.1 Rotate
 11.2 Magnify
 11.3 Translate
 11.4 Select
 11.5 Distance
 11.6 Bond angle
 11.7 Dihedral angle
 11.8 Interfacial angle
12 PROPERTIES OF OBJECTS
 12.1 Properties Dialog Box
 12.2 Objects Tab in the Side Panel
13 OVERALL APPEARANCE
 13.1 Background
 13.2 Lighting
 13.3 Projection Mode
 13.4 Depth-Cueing
14 UTILITIES
 14.1 Equivalent Positions
 14.2 Geometrical Parameters
 14.3 Standardization of Crystal Data
 14.4 Niggli-Reduced Cell
 14.5 Site Potentials and Madelung Energy
 14.6 Powder Diffraction Pattern
 14.7 Structure Factors
 14.8 Fourier Synthesis
 14.9 Model Electron Densities
 14.10 Model Nuclear Densities
 14.11 Patterson Densities
 14.12 2D Data Display
 14.13 Line Profile
 14.14 Peak Search
 14.15 Conversion of Electron Densities
15 TWO-DIMENSIONAL DATA DISPLAY
 15.1 Components of the 2D Data Display Window
 15.2 Menus
 15.3 Tools in the Toolbar
 15.4 Tools in the Vertical Toolbar
 15.5 Create and Edit a 2D Image
 15.6 Controlling Properties of a 2D Image
 15.7 Exporting 2D data
16 PREFERENCES
 16.1 Settings for RIETAN
 16.2 Font for Text Area
 16.3 Open a New File in
 16.4 Animation
 16.5 Start-up Search for Bonds
 16.6 A Setting for Raster Image Export
 16.7 Default isosurface level
 16.8 History level
17 COMMAND LINE INTERFACE
 17.1 How to use
 17.2 Commands that only work with -nogui mode
 17.3 Commands that work with/without GUI window
 17.4 Commands that only work with GUI window
18 INPUT AND OUTPUT FILES
 18.1 Files Used by VESTA
 18.2 Directories for User Settings
 18.3 File Formats of Volumetric Data
 18.4 File Format of *.pgrid and *.ggrid
 18.5 Supported File Formats
CLOSING REMARKS
 Feedback and Suggestions
 Acknowledgments
APPENDIX
A Keyboard Shortcuts
Bibliography
Index

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