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

VESTA format (*.vesta)
VICS format (*.vcs)
American Mineralogist Crystal Structure Database (*.amc)
asse (*.asse)
Chem3D
CIF (Crystallographic Information File)
CrystalMaker text file (*.cmt)
CSSR (Crystal Structure Search and Retrieval)
CSD/FDAT
DL_POLY CONFIG
FEFF input file (feff.inp)
FHI-AIMS input file (*.in)
GEOMETRY.OUT output by the Elk FP-LAPW Code
GSAS format (*.EXP)
ICSD (Inorganic Crystal Structure Database)
ICSD-CRYSTIN
MDL Molfile
MINCRYST (Crystallographic Database for Minerals)
MOLDA
PDB (Protein Data Bank)
Input file of RIETAN-FP (*.ins)
Output file of RIETAN-FP (*.lst)
Input file of SHELXL (*.ins, *.res)
Output files of STRUCTURE TIDY (*.sto)
Structure data files output by USPEX.
WIEN2k (*.struct)
XMol XYZ (*.xyz)
F01 for SCAT and C04D for contrd
MXDORTO/MXDTRICL FILE06.DAT, FILE07.DAT
XTL file (*.xtl)

Volumetric data

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

Structure & volumetric data

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

Output

Structure data

Original format of VESTA (*.vesta)
CIF (Crystallographic Information File)
PDB (Protein Data Bank)
SHELXL (*.ins)
Standard input file of RIETAN-FP (*.ins)
XMol XYZ
Chem3D (*.cc1)
STL file (*.stl)
VRML (*.wrl)
DL_POLY CONFIG
Input files of MADEL (*.pme)
Input files of STRUCTURE TIDY (*.stin)
P1 structure (*.p1)
VASP POSCAR format
Fractional coordinates (*.xtl)

Volumetric data

PRIMA binary format (*.pri)
General volumetric-data (text format) (*.?ed)
Periodic volumetric-data (text format) (*.grd)
General volumetric-data (binary format) (*.ggrid)
Periodic volumetric-data (binary format) (*.pgrid)
Compressed volumetric-data format (*.m3d)

Graphic formats (raster image)

BMP
EPS
JPEG
JPEG 2000
PNG
PPM
RAW
RGB (SGI)
TGA
TIFF

Graphic formats (vector image)

4. Circumstances behind the development of VESTA

VESTA is originated from two GLUT- and GLUI-based applications, VICS and VEND, developed by Dr. Ruben A. Dilanian and Dr. Fujio 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

Aug. 11 2022 ver. 3.5.8
- Fixed a bug that deleted objects reappeared when reopening *.vesta files since v3.5.6.
- Fixed a bug that wrong structure factors were calculated in some cases due to erroneous multi-threading control.
- Fixed a bug in the Windows version that some of states in the 2D Data Display didn't reproduce when reopening *.vesta files.
- Fixed a bug that sites with huge s.u. were interpreted to overlap with another site and weren't displayed since v3.5.4.
- Fixed a bug that B_ij in CIF files were interpreted as beta_ij.
- When selecting a polyhedron, bond distances are now listed in ascending order.
- Improved support for SHELX format and *.fcf format.
Jan. 9 2021 ver. 3.5.7
- Fixed a bug that breaks geometry of structural models after calculating dihedral angles.
- Fixed a bug that d-spacing of hkl plane was not updated correctly, again.
- Updated the wxWidgets library to the latest version.
Dec. 20 2020 ver. 3.5.6
- Fixed crash when reading some of PDB, XSF, and VASP files.
- Fixed a bug that the sign of electronic potential-energy densities v(r) was flipped.
- Fixed crash on Linux when specifying a transformation matrix with its determinant 0.
- Changed the default value of U_iso/B_iso to 0 and the default type to U_iso.
- When exporting cif files, write '?' instead of values of U_iso/B_iso if they are not changed from their default value 0.
- Enabled to read 2nd and subsequent volumetric data in the XSF files.
- Fixed an issue that calculation of site potentials and Madelung energy failed on Linux since ver. 3.4.8. (Restored the MADEL program missing since ver. 3.4.8.)
Sep. 26 2020 ver. 3.5.5
- Fixed a regression in v3.5.3 and v3.5.4 that d-spacing of lattice planes were not correctly shown in dialog boxes.
Sep. 24 2020 ver. 3.5.4
- Enabled to use cyclic color scheme when coloring isosurfaces by phases.
- Enabled to export coordination polyhedra, crystal shape, and isosurfaces to *.stl file.
- Fixed a regression in v3.5.3 that wrong (larger) value of multiplicity of a site was displayed due to too strict comparison of coordinates.
Aug. 23 2020 ver. 3.5.3
- Fixed a bug specific to Windows versions after v3.4.8 that calculation of bond distances was wrong. To address these compiler related bugs, revert the build setting to monolithic executable file.
- Fixed a regression since v3.5.1 that sorted structure factors might have wrong phases, resulted in strange output when calculating model electron/nuclear densities.
May. 6 2020 ver. 3.5.2
- Fixed a regression in v3.5.0 and 3.5.1 that incorrect keywords "_cell_length_alpha" etc. are recorded instead of "_cell_angle_alpha" etc. when exporting CIF files.
- Fixed a regression in v3.5.1 that the program crashes when displaying non-periodic structures.
May. 4 2020 ver. 3.5.1
- Really fix a bug that crystal morphology was not rendered correctly by v3.4.8 and v3.5.0 on Windows.
- Among equivalent indices of structure factors, indices shown in "Structure Factors" and "Powder Diffraction" dialog boxes are changed.
- When saving *.vesta files, also save volumetric data in *.pgrind automatically if the volumetric data was generated by VESTA.
- Enabled to export volumetric data in VASP format.
- Enabled to export structure and volumetric data in Cube file.
Apr. 29 2020 ver. 3.5.0
- Fixed a bug in ver.3.4.8 that some of VASP files could not be opened correctly.
- Fixed a bug that conversion to the Niggli reduced cell sometimes fails.
- Added an option to convert to a primitive cell when exporting VASP files.
- Fixed a couple of bugs when exporting VRML files.
- Fixed a bug in ver.3.4.8 that crystal morphology were sometimes rendered incorrectly on Windows. (It was actually a bug of compiler used to build the Windows versions.)
- Automatically set environment variable GDK_BACKEND=x11 on start-up to prevent segmentation fault of GTK3 version on Wayland.
- Enabled to draw contour lines on isosurfaces' sections and lattice planes in 3D view.
- Enabled to set cutoff levels of isosurfaces' sections and lattice planes more flexibly.
- Enabled to export multiple phase data in a CIF file.
- Enabled to set background color transparent when exporting images to PNG or TIFF formats.
- Enabled to move an item upper or lower in a list control, such as a list of crystallographic sites, bond specifications, lattice planes etc.
- Added output information about internal Cartesian coordinates when atoms are selected.
Dec. 30 2019 ver. 3.4.8
- Fixed a bug in the Structure Factors dialog box where intensities (I) are multiplied by X-ray polarization factor (of non-polarized X-ray source) even when the source is set as neutron.
- Tuned internal parameters again to address a remaining 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 external file paths weren't correctly saved in *.vesta format when the external files were two or more directory above where *.vesta placed.
- Enabled to select POSCAR/CONTCAR from the Open dialog box.
- Enabled to read multiple data set in VASP files regardless of file names. (Previously only the first data set was read unless the file name is POSCARS.)
- Improved support for pdb file format.
- Supported HiDPI on Windows and Linux GTK3 versions (Per Monitor DPI is still not supported).
- Improved support for dark mode.
- Various internal changes including update of wxWidgets library and build options.
Jun. 15 2019 ver. 3.4.7
- Fixed a bug that graphics isn't displayed correctly on macOS 10.14.4 or later.
- Enabled to keep labels and selection status when editing structure and/or drawing boundary.
Jan. 27 2019 ver. 3.4.6
- Fixed a bug that multi-line comments in CIF files were not correctly recognized.
- Fixed a bug for calculation of site potentials and Madelung energy for structures having partially occupied sites.
- Fixed a few glitches of GUI on macOS 10.14 Mojave.
- Dropped support of the 32 bit Linux version.
- Removed dependency of the Linux version on libpng12.so.0.
Nov. 22 2018 ver. 3.4.5
- Fixed a bug in conversion of structure parameters when changing setting of the space group P b a n (No. 50).
- Enabled conversion of structure parameters to keep geometry when changing space group settings, even when transformation matrix is set.
- Updated orthorhombic space group symbols containing symmetry element "e" to comply with the latest standards, e.g., A e m 2 instead of A b m 2. Files with old symbols are still supported.
- Fixed crash on Ubuntu Linux.
- Enabled to run on macOS 10.14 Mojave, and dropped support for OS X 10.6-10.8. The minimum supported version is OS X 10.9.
- Related to the above change, hardware anti-aliasing (OpenGL sample buffers) is disabled by default on macOS to work around a regression on some platforms.
- Enabled to edit colors from objects list on macOS version.
- Enabled to run simulation of powder diffraction patterns using the latest RIETAN-FP.
- Updated a file bvparm2013.cif to bvparm2016.cif, which contains a list of bond valence parameters.
Mar. 28 2018 ver. 3.4.4
- Fixed a few bugs regarding calculation of polyhedra.
- Fixed a regression since ver. 3.4.1 that some of atoms at borders of unit cell were missing when exporting data as VASP or DL_POLY formats.