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1. Inrtoduction

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

  • Deal with structural models and volumetric data at 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.
  • MUCH better performance than VICS and VEND. For example, bonds search speed in VESTA is several to thousands times faster than that in VICS. Algorithm for calculation of isosurface geometry is more than six times efficient than that in VEND.

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. 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
  12. GEOMETRY.OUT output by the Elk FP-LAPW Code
  13. ICSD (Inorganic Crystal Structure Database)
  14. ICSD-CRYSTIN
  15. MDL Molfile
  16. MINCRYST (Crystallographic Database for Minerals)
  17. MOLDA
  18. PDB (Protein Data Bank)
  19. Input files of RIETAN-FP (*.ins)
  20. Output files of RIETAN-FP (*.lst)
  21. Output files of STRUCTURE TIDY (*.sto)
  22. WIEN2k (*.struct)
  23. XMol XYZ (*.xyz)
  24. F01 for SCAT and C04D for contrd
  25. MXDORTO/MXDTRICL FILE06.DAT, FILE07.DAT
  26. XTL file (*.xtl)
Volumetric data
  1. PRIMA (*.pri; *.prim)
  2. MEED/PRIMA text data (*.den)
  3. Energy Band (*.eb)
  4. General volumetric-data format (*.?ed)
  5. Periodic volumetric-data format (*.grd)
  6. SCAT volumetric-data files (*.sca, *.scat)
  7. WIEN2k (*.rho) obtained with wien2venus.py
  8. WinGX 3D Fourier (*.fou)
  9. 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. VRML (*.wrl)
  9. Input files of MADEL (*.pme)
  10. Input files of STRUCTURE TIDY (*.sto)
  11. P1 structure (*.p1)
  12. Fractional coordinates (*.xtl)
Volumetric data
  1. General volumetric-data format (*.3ed)
  2. Periodic volumetric-data format (*.grd)
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
3. 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.

4. Change Log
  • Aug. 17 2009 ver. 2.1.1
    • Fixed an issue that latter part of data may not be exported when exporting 2D map data in a text file.
    • When output files of RIETAN-FP/2000 (*.lst) are opened, VESTA now checks if standard uncertainty (s.u.) of lattice parameters are consistent with the Bravais lattice type. When opening data of a cubic crystal in previous versions, for example, only s.u. of a axis is read while those of b and c axes are set at 0, since those are not written in the *.lst files. It results in underestimation of s.u. for interatomic distances and bond angles calculated by VESTA.
    • In the "Orientation" dialog, upward direction on the screen is now calculated by the Gram-Schmidt process when the "Projection vector" and "Upward vector" are not mutually orthogonal.
  • Aug. 8 2009 ver. 2.1.0
    • Enabled to read CASTEP files *.cell and *.charg_frm formats.
    • Enabled to read VASP files with only structural data, POSCAR and CONTCAR, again.
    • Length of vectors on atoms are now treated in the unit of Angstrom.
    • Recompiled madel so that the Madelung energy and site potential can be calculated for crystals with larger unit cell.
    • A path to rietan.exe written in the default setting file is updated.
    • Updated wxWidgets library to 2.8.10.
    • Updated user's manual.
  • Feb. 12 2009 ver. 2.0.3
    • This is a quick fix for a bug in ver. 2.0.2 that prevents users from importing volumetric data after opening structure data.
  • Feb. 11 2009 ver. 2.0.2
    • Enabled to set the default isosurface level in Preference dialog.
    • Fixed a bug where division of a volumetric data set by another data set was calculated as multiplication of the two data sets.
    • Fixed many bugs specific to certain platforms, including crash of the Linux version on Mesa 7.x software driver and crash of the Windows version in combination with Windows Vista and Intel made video chips. As a regression caused by this fix, full scene anti-alias would be temporarily disabled on some platforms.
  • Sep. 28 2008 ver. 2.0.1
    • Fixed crash when proceeding "Standardization of Crystal Data" for data having both structural and volumetric information.
    • Runs on Mac OS X 10.3 series again.
    • Fixed an issue of reading some of Gaussian cube format.
    • Fixed a bug where the first atom in FEFF format files is ignored.
    • Updated wxWidgets library to 2.8.9.
  • Jul. 11 2008 ver. 2.0
    • Information of site multiplicities, Wyckoff letters, and site symmetries is added for output of atoms' information.
    • Supported standardization of crystal data and determination of the Niggli-reduced cell by calling STRUCTURE TIDY internally.
    • Supported export of 2D data from 2D Data Display window.
    • When site occupation factors are smaller than 1, the atoms are rendered as circular chart.
    • By polishing the use of OpenGL technology, memory usage was significantly reduced when rendering huge structural models.
    • The site occupation factors are now taken into account when calculating the charge distribution.
    • Fixed a fault in space group database, spgra.dat (symmetry operation of No. 144, P31 was wrong).
    • Anisotropic atomic displacement parameters Uij or betaij will not be set from isotopic atomic displacement parameters any more.
    • Fixed a bug that no coordination polyhedra can be made for aperiodic data.
    • Fixed an issue that only atoms in the asymmetric unit are displayed for some of Wien2k *.struct files.
    • Fixed a typo in MADEL (the unit of Madelung energy: mJ/mol -> MJ/mol).
  • May. 18 2008 ver. 1.4.4
    • Changed the license agreement. (Changed the reference to be cited.)
    • Added a tool to set display magnification in the unit of Angstrom in "Overall appearance" dialog.
    • Fix a bug in 64-bit version that causes a crash of the program when searching peaks in volumetric data.
    • Fix a crash when reading some files with FEFF format.
    • Corrected the unit of laplacian of electron densities where laplacians were 4 times smaller than the unit of e/a.u.-5 in previous versions.
    • Check of effective digits of special positions was improved.
  • Apr. 21 2008 ver. 1.4.3
    • Fixed a bug introduced in v1.2b that conversions of fractional coordinates between different origin choices were incorrect in tetragonal and cubic space groups.
    • Fixed an issue where the setting files of VESTA were stored in wrong place when an environment variable "VESTA_PREF" is set.
    • Fixed a bug where some polyhedra were still shown even when "Show polyhedra" option is disabled in the "Bonds" dialog.
    • When changing lattice settings of orthorhombic space groups, now standard deviations of lattice parameters are also transformed.
    • Files used for simulation of powder diffraction patterns will not be automatically deleted any more.
    • Added license statements in "About" dialog.
  • Apr. 8 2008 ver. 1.4.2
    • Fixed a bug where isotropic atomic displacement parameters are not correctly read from *.vesta files.
    • Tweaked a parameter for determination of polyhedral faces again.
  • Apr. 6 2008 ver. 1.4.1
    • Fixed an issue in 2D Data Display window where numerical values displayed in the status bar do not match with the cursor position. This bug exists in versions between 1.2b to 1.4.
    • Tweaked a parameter used to determine whether or not an atom lies on a polyhedral face.
    • Changed some labels of user interfaces from "surface colorization" to "surface coloring".
  • Mar. 27 2008 ver. 1.4 (stable)
    • Conversion of space-group settings was broken for orthorhombic space groups having only one origin choice. This bug was introduced with a change in ver. 1.2b.
    • Fixed incorrect conversions between anisotropic atomic displacement parameters (Uij or betaij) and equivalent isotropic atomic displacement parameters (U or B).
    • Do not draw principal ellipses of thermal ellipsoids when anisotropic displacement parameters are "isotropic."
    • Fixed a bug where translucent isosurfaces are drawn with incorrect opacity when "Antialiasing" option is enabled.
    • File import of American Mineralogist Crystal Structure Database (*.amc) format has been improved.
    • When exporting a line profile, the exported file now has information about distances from the first position in Angstrom.


Version history of VESTA prior to 1.4

Version history of VICS-II

Copyright © 2007-2009 by Koichi Momma.