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Software > VESTA
1. Inrtoduction

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 files of RIETAN-FP (*.ins)
  22. Output files 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.

5. Change Log
  • Feb. 26 2013 ver. 3.1.5
    • Rebuilt the Windows versions using the latest development snapshot of wxWidgets to address a crash problem. On Windows, versions 3.1.3 and 3.1.4 crash on simulation of powder diffraction pattern. The cause of the problem is a recently introduced regression in wxWidgets, and it seems to be fixed with the latest version.
  • Feb. 22 2013 ver. 3.1.4
    • Fixed a regression of version 3.1.3 on Linux that text output were not displayed when the text contained non ASCII characters.
    • Minor changes to a data selection dialog box, which appears when reading files containing multiple phase data.
    • Improved support for an upcoming change in USPEX format.
    • On OSX, do not save users data in the application bundle.
  • Jan. 30 2013 ver. 3.1.3
    • Fixed a regression in v3.1.2 in input of VASP files.
    • Fixed a bug in input of rhombohedral lattice from Wien2k *.struc files.
    • Fixed interprocess communications on Mac OS X.
    • In the "Fourier Synthesis" dialog box, enabled to import structure factors from *.fcf files output by SHELXL with "list 3" command.
  • Dec. 28 2012 ver. 3.1.2
    • Enabled to select data to read when opening CIF files with more than two structure data.
    • Added an option to mark enantiomorphic sites. This feature enables you to draw general position diagrams similar to those in International Tables for Crystallography Vol. A.
    • Added an option to disable lighting on structural models.
    • Updated the database file of bond valence parameters to bvparm2011.cif.
    • Improved support for various file formats, including support for USPEX structure data files.
    • Fixed incompatibility with the latest version of RIETAN-FP.
    • Fixed a bug related to import of second phase.
    • Fixed a typo in asfdc file. (It was harmless for VESTA anyway.)
  • Jul. 29 2012 ver. 3.1.1
    • Fixed a bug in a feature of "Fourier Synthesis" dialog box that the result of calculation changes every time the "Calculate" button is pressed.
    • Fixed a bug that cell parameters are not read correctly from some of CASTEP *.cell files.
    • Miscellaneous fixes for GUI.
    • Updated STRUCTURE TIDY.
  • Apr. 8 2012 ver. 3.1.0
    • Fixed a bug that ver. 3.0.9 crashes on Windows when calculating an interatomic distance.
    • Updated the template file of RIETAN-FP.
  • Mar. 15 2012 ver. 3.0.9
    • Fixed a bug that VESTA 3.0.8 crashes on Linux when adding new bonds and lattice planes.
    • Windows version of PowderPlot included in ver. 3.0.8 does not run correctly when it is set as default program to open powder diffraction data.
  • Mar. 11 2012 ver. 3.0.8
    • Support transformation of triclinic unit cells between primitive and complex lattices.
    • When changing space group settings or transforming lattices by a matrix, Miller indices of crystal faces (forms) and lattice planes can now be transformed automatically in addition to structural parameters.
    • Added support for FHI-AIMS *.in file format.
    • Improved support for Gaussian cube format.
    • Changed number of significant digits of standard uncertainties in a range from 2 to 19 in concordance with IUCr guidelines.
    • Fixed a performance issue of the side panel when number of sites per asymmetric unit is huge.
    • Fixed a bug that parts of crystal faces are not drawn under certain conditions.
    • Fixed a bug that some redundant digits are written in CIF files output by VESTA. Also fixed a problem inputting CIF files with some non-standard space-group settings.
    • Fixed a typo in afsdc.dat file (it was harmless for VESTA anyway).
  • Dec. 15 2011 ver. 3.0.7
    • Fixed: Import of volumetric data didn't work in the "Phase" tab in "Edit Data" dialog box.
    • Fixed: On creation of super-lattice by a matrix, additional atoms are searched in wrong positions when the translation vector q is not zero.
    • In the "Conversion of Electron Densities" menu, added an option to select the unit of electron densities (Å-3 or a0-3).
    • Read space group information correctly for CIF files with multiple phase data.
    • Read structure data from *.ins when opening electron density data with PRIMA format (*.pri). (This behavior was broken since ver. 3.0.5 or so.)
    • Fixed some other minor bugs and issues.
  • Dec. 8 2011 ver. 3.0.6
    • Fixed a serious bug introduced in ver. 3.0.4: Atomic displacement parameters are overwritten to strange values when the "Edit Data" dialog box are opened, and also when it is closed by OK button. There are possibly other operations that are influenced by this bug.
    • Fixed a rendering bug of planar polyhedra. This bug was also introduced in ver. 3.0.4.
    • Changed a directory for saving settings on Mac from ~/.VESTA to ~/Library/Application Support/VESTA.
  • Dec. 5 2011 ver. 3.0.5
    • Added a feature to calculate an angle between two faces (planes).
    • Added two types of binary volumetric data formats.
    • Fixed a bug introduced in ver. 3.0.4. This bug prevents opening files with no extensions (e.g. CONTCAR, POSCAR, etc.) when they are placed under a directory containing "." in the name.
  • Nov. 27 2011 ver. 3.0.4
    • Added support for non-standard settings of monoclinic space groups with unique axis a.
    • Fixed a bug that the sign of determinant may not be correctly calculated when setting a matrix for lattice transformation. This bug does not exist in v2.x series or older versions.
    • Workaround a problem on some Windows 7 PCs that the depth buffering of OpenGL canvas was disabled.
    • Updated the license agreement to refer a paper of VESTA 3 as a reference.
  • Nov. 7 2011 ver. 3.0.3
    • Fixed: On some Linux distributions, VESTA still didn't run on a locale setting where comma is used as a decimal separator.
    • Added support for input and output of VASP POSCAR files with the Cartesian coordinate format.
  • Oct. 6 2011 ver. 3.0.1
    • New: "Fourier Synthesis" dialog box to import structure factors from an external file to carry out Fourier synthesis from them.
    • Fixed: surface area of crystal faces were calculated as doubled value.
    • Fixed: "apply symmetry operations" for cutoff planes could not be saved in *.vesta format (this bug exists in v2.90.2b and v3.0).
    • Miscellaneous bug fixes.
  • Aug. 27 2011 ver. 3.0
    • Support SHELXL *.ins format.
    • Miscellaneous bug fixes.