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Software > VESTA
1. Introduction

VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies. Some of the novel features of VESTA are listed below.

  • Deal with multiple structural models, volumetric data, and crystal morphologies in the same window.
  • Support multiple tabs corresponding to files.
  • Support multiple windows with more than two tabs in the same process.
  • Deal with virtually unlimited number of objects such as atoms, bonds polyhedra, and polygons on isosurfaces (theoretical limit on 32bit operating system is 1,073,741,823)
  • Support lattice transformation from conventional to non-conventional lattice by using matrix. The transformation matrix is also used to create superlattice and sublattice.
  • Visualize interatomic distances and bond angles that are restrained in Rietveld analysis with RIETAN-FP.
  • Transparent isosurfaces can be overlap with structural models.
  • Isosurface can be colored on the basis of another physical quantity.
  • Arithmetic operations among multiple volumetric data files.
  • High quality smooth rendering of isosurfaces and sections.
  • Export high-resolution graphic images exceeding Video card limitation.

VESTA is a successor to two 3D visualization programs, VICS and VEND, in the VENUS (Visualization of Electron/NUclear and Structures) software package.

VESTA runs on Windows, Mac OS X, and Linux. It is contributed free of charge for non-commercial users.

2. New features in VESTA 3
  • Visualization of crystal morphologies
  • Superimposition of multiple structural models, volumetric data, and crystal faces on the same Graphic Area
  • Visualization of isosurfaces with multiple levels
  • An extended bond-search algorithm to allow more sophisticated search in complex molecules, cage-like structures, etc.
  • Calculations of electron and nuclear densities from structure parameters
  • Calculations of Patterson-function densities from structure parameters or volumetric data
  • Integration of electron and nuclear densities by Voronoi tessellation
  • Significant performance improvements in rendering of isosurfaces and calculation of slices
  • Output information about principal axes and mean square displacements for anisotropic thermal motion
  • Determination of the best plane for selected atoms
  • Displaying labels of atoms
  • Customization of styles per sites or bond types
  • Customization of symmetry operations
  • Improvements in inputting files with various formats
  • Support of undo and redo in GUI operations
3. Supported file formats
Input

Structure data

  1. VESTA format (*.vesta)
  2. VICS format (*.vcs)
  3. American Mineralogist Crystal Structure Database (*.amc)
  4. asse (*.asse)
  5. Chem3D
  6. CIF (Crystallographic Information File)
  7. CrystalMaker text file (*.cmt)
  8. CSSR (Crystal Structure Search and Retrieval)
  9. CSD/FDAT
  10. DL_POLY CONFIG
  11. FEFF input file (feff.inp)
  12. FHI-AIMS input file (*.in)
  13. GEOMETRY.OUT output by the Elk FP-LAPW Code
  14. GSAS format (*.EXP)
  15. ICSD (Inorganic Crystal Structure Database)
  16. ICSD-CRYSTIN
  17. MDL Molfile
  18. MINCRYST (Crystallographic Database for Minerals)
  19. MOLDA
  20. PDB (Protein Data Bank)
  21. Input file of RIETAN-FP (*.ins)
  22. Output file of RIETAN-FP (*.lst)
  23. Input file of SHELXL (*.ins, *.res)
  24. Output files of STRUCTURE TIDY (*.sto)
  25. Structure data files output by USPEX.
  26. WIEN2k (*.struct)
  27. XMol XYZ (*.xyz)
  28. F01 for SCAT and C04D for contrd
  29. MXDORTO/MXDTRICL FILE06.DAT, FILE07.DAT
  30. XTL file (*.xtl)

Volumetric data

  1. PRIMA binary format (*.pri; *.prim)
  2. MEED/PRIMA text data (*.den)
  3. Energy Band (*.eb)
  4. General volumetric-data (text format) (*.?ed)
  5. Periodic volumetric-data (text format) (*.grd)
  6. General volumetric-data (binary format) (*.ggrid)
  7. Periodic volumetric-data (binary format) (*.pgrid)
  8. Compressed volumetric-data format (*.m3d)
  9. SCAT volumetric-data files (*.sca, *.scat)
  10. WIEN2k (*.rho) obtained with wien2venus.py
  11. WinGX 3D Fourier (*.fou)
  12. X-PLOR/CNX (*.xplor)

Structure & volumetric data

  1. CASTEP (*.cell, *.charg_frm)
  2. GAMESS input and 3D surface data files output by MacMolPlt
  3. Gaussian Cube format
  4. VASP
  5. XCrySDen XSF format
Output

Structure data

  1. Original format of VESTA (*.vesta)
  2. Chem3D
  3. CIF (Crystallographic Information File)
  4. DL_POLY CONFIG
  5. PDB (Protein Data Bank)
  6. Standard input file of RIETAN-FP (*.ins)
  7. XMol XYZ
  8. VASP POSCAR format
  9. VRML (*.wrl)
  10. Input files of MADEL (*.pme)
  11. Input files of STRUCTURE TIDY (*.sto)
  12. P1 structure (*.p1)
  13. Fractional coordinates (*.xtl)

Volumetric data

  1. PRIMA binary format (*.pri)
  2. General volumetric-data (text format) (*.?ed)
  3. Periodic volumetric-data (text format) (*.grd)
  4. General volumetric-data (binary format) (*.ggrid)
  5. Periodic volumetric-data (binary format) (*.pgrid)
  6. Compressed volumetric-data format (*.m3d)

Graphic formats (raster image)

  1. BMP
  2. EPS
  3. JPEG
  4. JPEG 2000
  5. PNG
  6. PPM
  7. RAW
  8. RGB (SGI)
  9. TGA
  10. TIFF

Graphic formats (vector image)

  1. EPS
  2. PDF
  3. PS
  4. SVG
4. Circumstances behind the development of VESTA
VESTA is originated from two GLUT- and GLUI-based applications, VICS and VEND, developed by R. A. Dilanian and F. Izumi during 2001-2004. They saw the light of day at the end of 2002 and, since then, continued their growth to be used widely in a variety of studies. However, we never get full satisfaction from their usability and performance. First, the combined use of VICS and VEND to visualize both crystal and electronic structures via text files is rather troublesome; on-the-fly visualization of these two kinds of images is highly desired. Second, their graphical user interface (GUI) is not very user-friendly because they are based on the old-fashioned toolkits, GLUT and GLUI, which have been no longer upgraded. Above all things, they require large system resources and source codes written in C language lack scalability owing to unrefined programming.

At the end of June 2004, one of the main developer Dilanian leaved the project and both VICS and VEND became unlikely to continue its progress. Then I decided to create a new program employing a modern C++ GUI framework wxWidgets. We at first upgraded VICS to VICS-II with a new state-of-art GUI and further integrated VICS-II and VEND into the next-generation 3D visualization system VESTA, adding new capabilities.

Please refer to Home Page of Fujio Izumi for the further information about the VENUS package.

  • Oct. 19 2017 ver. 3.4.1
    • Fixed an occasional crash when searching bonds.
    • Fixed a bug where calculation of bond distances and angles occasionally reports wrong values on ver. 3.4.0.
    • Fixed a long-standing bug where a part of faces of coordination polyhedron is missing when more than four atoms are aligned on the same plane.
    • Fixed a bug where some of monoclinic space group settings with the unique axis "a" (e.g., #9 Cc) could not be read from files.
    • When exporting data to VASP or DL_POLY format, now the entire phases will be merged if the data contains more than two phases.
    • Fixed a bug that VESTA could not read the fixed-format PDB and MXDORTHO format having no spaces between two digits.
    • Preliminary support of reading the macromoleuclar CIF (mmCIF) format.
    • Enabled to export the ball-and-stick model to the STL format.
  • Jan. 5 2017 ver. 3.4.0
    • Reimplemented routines for calculation of bond distances, angles, and dihedral angles so that calculation of standard uncertainty (s.u.) takes into account of crystal symmetry.
    • Updated a code for reading magCIF to support the final specification of magCIF 1.0.
    • Fixed a bug that may crash the application when reading some data of flat molecules.
    • Fixed a minor bug when reading PDB and Xcrysden files.
    • Minor improvements in a window for simulation of X-ray powder diffraction pattern.
  • Oct. 4 2016 ver. 3.3.9
    • Refined automatic bond search behavior further.
    • Fixed broken conversion from Uij to beta_ij when exporting RIETAN *.ins file.
    • Fixed broken text encoding when exporting structure factors and/or powder diffraction peak table on Windows.
  • Jun. 18 2016 ver. 3.3.8
    • Fixed automatic bond search feature, which was somewhat broken in ver. 3,3,7. (Bonds were searched by the "Search atoms bonded to A1" mode.)
  • Jun. 18 2016 ver. 3.3.7
    • Fixed a bug in ver. 3.3.6 that results in a crash on selection of a polyhedron.
    • Fixed unit cell dimensions of GEOMETRY.OUT from the atomic unit to Angstrom.
  • Jun. 7 2016 ver. 3.3.6
    • Allow showing/hiding morphology data per each phase.
    • Added Si-Si and Ge-Ge pairs as default bonds.
  • Jun. 6 2016 ver. 3.3.5
    • Improved automatic bond search behaviors.
    • Added new "Summary" tab in the main window for output of phase summary.
    • Fixed performance issue when opening large data and toggling between large number of phase data.
  • Jun. 4 2016 ver. 3.3.4
    • Allow disabling automatic bond search when opening files by turning off the option "Start-up search for bonds" in the Preferences dialog box.
    • Enabled to toggle data by specifying data number.
    • Fixed a bug when reading VASP files having space characters before keyword strings.
  • May 29 2016 ver. 3.3.3
    • Enabled to export volumetric and morphology data in the VRML format.
    • Enabled to toggle data by buttons in the side panel.
    • In the built-in "Powder Diffraction" window, enabled to export a list of diffraction peaks to a text file.
    • Fixed a bug in ver. 3.3.2 that incorrect intensities were output when exporting structure factors to a text file. (Intensities displayed on the "Structure Factors" dialog box were correct.)
    • Fixed crash when selecting a polyhedron in aperiodic (molecular) data with non-zero charge assigned to each site.
    • Fixed crash when executing the "Standardization of Crsytal Data" menu.