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 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 14. PRIMA binary format (*.pri) 15. General volumetric-data (text format) (*.?ed) 16. Periodic volumetric-data (text format) (*.grd) 17. General volumetric-data (binary format) (*.ggrid) 18. Periodic volumetric-data (binary format) (*.pgrid) 19. Compressed volumetricdata format (*.m3d) Graphic formats (raster image)

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. WIEN2k (*.struct) 26. XMol XYZ (*.xyz) 27. F01 for SCAT and C04D for contrd 28. MXDORTO/MXDTRICL FILE06.DAT, FILE07.DAT 29. XTL file (*.xtl)

Volumetric data 30. PRIMA binary format (*.pri; *.prim) 31. MEED/PRIMA text data (*.den) 32. Energy Band (*.eb) 33. General volumetric-data (text format) (*.?ed) 34. Periodic volumetric-data (text format) (*.grd) 35. General volumetric-data (binary format) (*.ggrid) 36. Periodic volumetric-data (binary format) (*.pgrid) 37. Compressed volumetric-data format (*.m3d) 38. SCAT volumetric-data files (*.sca, *.scat) 39. WIEN2k (*.rho) obtained with wien2venus.py 40. WinGX 3D Fourier (*.fou) 41. X-PLOR/CNX (*.xplor) Structure & volumetric data 42. CASTEP (*.cell, *.charg_frm) 43. GAMESS input and 3D surface data files output by MacMolPlt 44. Gaussian Cube format 45. VASP

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

46. XCrySDen XSF format 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 userfriendly 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.

3D Visualization System VENUS

2. Components of VENUS
The VENUS package contains five independent applications:

VICS: VIsualization of Crystal Structures VEND: Visualization of Electron/Nuclear Densities VESTA: Visualization for Electronic and STructural Analysis PRIMA: PRactice Iterative MEM Analyses ALBA: After Le Bail Analysis

That is, VICS and VEND visualize crystal structures and electron/nuclear densities, respectively. VICS delivers a feature to input/output standard input files, *.ins, of RIETAN-FP while VEND can input 3D density files, *.pri, created by PRIMA. Koichi Momma has integrated VICS and VEND into a single application VESTA, adopting a cross-platform application framework wxWidgets and adding many new features. The processing speed, scalability, and quality of 3D images in VESTA have been considerably improved in comparison with VICS and VEND. Please use VESTA in place of VICS and VESTA. VESTA is separately distributed at JP-Mineral, where detailed information about VESTA is also obtainable. PRIMA is a MEM analysis program to calculate electron densities from X-ray diffraction data and nuclear densities from neutron diffraction data. It was designed with MEMbased Pattern Fitting (MPF) in mind, as can be inferred from its name. ALBA is a program for the Maximum-Entropy Patterson (MEP) method, whereby Patterson functions in the unit cell can be determined from observed integrated intensities.

3. 3D visualization programs, VICS and VEND

VICS and VEND have been written in ANSI C for cross-platform portability, which allows us to port them from Microsoft Windows (hereafter abbreviated to Windows) to UNIX/Linux including Mac OS X. With VICS, crystal structures are represented with ball-and-stick, space-filling, polyhedral, wireframe, stick, dot-surface, and thermal-ellipsoid models. Ball-and-stick and stick models may be enclosed in dot surface spheres with van der Waals radii. You will recognize that VICS is capable of representing anisotropic thermal motion better than ORTEP-III, which has no 3D-graphic capability. Boundaries for drawing structures are specified in sophisticated ways similar to convoluting sphere and reiterative convoluting sphere in ORTEP-III.

Selection of objects (atoms, bonds, and coordination polyhedra) makes it possible to obtain fractional coordinates, translation vectors, equivalent positions, interatomic distances, bond angles, torsion angles, and information on coordination polyhedra (volumes, quadratic elongations, bond angle variances, and bond valence sums of central metals). Arrows indicating magnetic moments and positional shifts may be added to any selected atoms. With VEND, electron/nuclear densities as well as wave functions and electrostatic potentials obtained by molecular-orbital methods are visualized as isosurfaces, bird's-eye views, and two-dimensional maps. Translucent isosurfaces and/or slices can overlap a ball-and-stick/stick model created by VICS. Objects are rotated, expanded, shrunken, and translated fast in three dimensions, particularly in the presence of video cards accelerating the OpenGL API, e.g., those powered by the GeForce and RADEON graphic processing units (GPUs). Four different modes of rotating objects are supported: drag, push, click, and rotate automatically. In addition to crystallographic and electronic-state studies and education, we will take pleasure in manipulating 3D objects on personal computers. The development of VENUS was motivated by a desire to present the poor with the advanced graphic software. Neither graphics workstations nor commercial programs are now necessary for 3D visualization!

4. Structural data files for VICS

VICS can input and/or output files with the following formats: 1. Original format of VICS (input & output) 2. American Mineralogist Crystal Structure Database 3. Chem3D 4. CIF (Crystallographic Information File; input & output) 5. CrystalMaker text file 6. ICSD-CRYSTIN 7. CSSR (Crystal Structure Search and Retrieval) 8. CSD/FDAT 9. GAMESS input and 3D surface data files output by MacMolPlt 10. Gaussian Cube format 11. ICSD (Inorganic Crystal Structure Database) 12. MDL Molfile 13. MINCRYST (Crystallographic Database for Minerals) 14. MOLDA 15. PDB (Protein Data Bank; input & output) 16. User input file, *.ins, of RIETAN-FP (input & output) 17. VASP 18. WIEN2k struct 19. XCrySDen XSF format

20. XMol XYZ (input & output) 21. asse 22. F01 for SCAT and C04D for contrd 23. MXDORTO FILE07.DAT The feature of outputting *.ins allows us to read in crystal data files of various formats with VICS, simulate powder diffraction patterns, and carry out subsequent Rietveld refinements with RIETAN-FP. Heavy users of RIETAN will be very happy to input and output *.ins. After releasing VENUS, such a 3D visualization software package will be regarded as an indispensable tool for those who utilize a Rietveld-analysis program like RIETAN-FP. We must understand structural details not two-dimensionally but threedimensionally!

5. 3D data files for VEND

VEND can input/output files storing 3D mesh data recorded with a variety of formats listed below. 1. 2. 3. 4. Electron/nuclear-density files with the PRIMA format (binary). Electron/nuclear-density files with the MEED format (text). Patterson-function files output by ALBA for the MEP method. Electron-density, electrostatic-potential, and wave function files with the Gaussian Cube format 5. 3D surface data files obtained by MacMolPlt from GAMESS log files 6. Electron-density, electrostatic-potential, and wave function files obtained with contrd from files F09 and F39 output by SCAT 7. Electron-density and electrostatic-potential files output by VASP 8. VEND 3D data files storing g(r), nu(r), he(r), Laplacian of electron densities, etc. 9. Electron-density files obtained with WIEN2k plus wien2venus.py 10. Electron-density, electrostatic-potential, and wave function files with the XSF format of XCrySDen 11. Files storing energy eigenvalues resulting from band-structure calculations with, e.g., WIEN2k

6. File converters
6.1 Alchemy
A file converter, Alchemy, for PRIMA was developed by Yukihiko Kawamura and Fujio Izumi. The Windows version of Alchemy, Alchemy.exe, is contained in folder 'Programs' as part of the VENUS system. For political and technical reasons, only a minor feature to convert a MEM data set binary file, *.fos, output by RIETAN-FP into a MEM data set text file, *.mem, is currently opened to the public by giving two examples, fap and garnet, in Examples.zip; refer to Readme_Alchemy.txt in folder 'Alchemy' before using

Alchemy.exe. The resulting file, *.mem, can be analyzed with PRIMA.exe to give a feedback data file, *.fba, and a 3D densities file, *.pri or *.den. The Mac OS X version of Alchemy is also distributed; go to Subsection 11.3 to get it.

6.2 contrd and makec04d

Masataka Mizuno of Osaka University kindly wrote a Fortran program, contrd, to convert binary files, F09 and F39, output by SCAT for the DV-X method; method into text files storing 3D data. It is contained in an archive file, dvxa_v1_0*.zip, together with makec04d to create a template file of an input file, C04d, for contrd. The two programs, contrd and makec04d, can be conveniently launched from an assistance environment for the DV-X method. It consists of many Hidemaru macros, helping us to launch a series of programs for DV-X molecular-orbital calculations and 3D visualization with VESTA. Its GUI enables us to utilize pulldown and pop-up menus, buttons, and shortcut keys. Note that this environment must be used in combination with the latest versions of dvscat programs and a molecular-orbital calculation system, eduDV, for education. To download the archive file of the above assistance environment, go to Ball & stick model of double carbon nanotubes (99 KB) Coordination polyhedra in YBa2Cu4O8 (237 KB) Thermal ellipsoids in YBa2Cu3O7 with Cu-O bonds and the translucent (101) plane (97 KB) SiO4 tetrahedra in an SiO2 melt (Calculated with MXDORTO. 167 KB) Co sites with arrows denoting magnetic moments in CoAl2O4 (151 KB) Electron-density image and a wave function of a Ti6C cluster (calculated with SCAT; PDF: 1.7 MB) Isosurfaces (3/3) for YBa2Cu3O7 with (100), (001), and CuO2 planes showing electron-density distribution (106 KB) Isosurfaces (0.7/3) for MgB2 with the z = 1/2 plane illustrating electron-density distribution (124 KB) Isosurfaces (1/3) for electron densities determined by MPF from synchrotron X-ray powder diffraction data of anthraquinone (174 KB) At my request, Masao Arai kindly calculated the 3D electron densities in the second and third files outputted by VEND, using WIEN2k.

8. Super-fast program, PRIMA, for MEM analysis

8.1 Improvements in PRIMA
The award-winning technology of MPF is an alternative to a traditional approach, i.e., Rietveld analysis, to structure refinement from powder diffraction data. Crystal structures are represented not with structure parameters in Rietveld analysis but with electron/nuclear densities in MPF. A fast MEM analysis program is desired in MPF where MEM analysis and whole-pattern fitting are alternately iterated until convergence. Till lately, we had been utilizing MEED for the MEM analysis of structure factors obtained experimentally from X-ray and neutron diffraction data. After making every effort to speed up MEM analysis, we at last completed our own Fortran 90 program PRIMA, the state of the art in MEM analysis. MEED is now obsolete because of its serious bug and sluggish speed. PRIMA has been written from the ground up in Fortran 90, which enables us to create storage for allocatable arrays dynamically. It is thoroughly optimized for personal computers equipped with Intel Pentium 4 processors and operated with Windows. Nonlinear single-pixel approximation (never use this for a small number of reflections), full use of space-group symmetry, and adjustment of Lagrangian multipliers further accelerate MEM analysis. PRIMA is applicable to MEM analysis from neutron diffraction data of compounds containing elements whose coherent-scattering lengths are negative, e.g., H, Li, Ti, and Mn.

8.2 How to use PRIMA in combination with RIETAN-FP and VEND

PRIMA makes it easier to modify a structural model in the course of Rietveld analysis. In a user input file, *.ins, set NMODE at 0 and NMEM at 1, and input various parameters for MEM analysis. Run RIETAN-FP to create a MEM data set file, *.fos. Fo(Rietveld) data in this file are analyzed by PRIMA, which creates a 3D density file, *.pri, and a feedback data file, *.fba, storing Fc(MEM)'s. VEND serves to input *.pri to visualize 3D electron/nuclear-density distribution. Your structural model is rebuild after close checking of the density image, if necessary (so-called MEM/Rietveld method). Thus, PRIMA is now regarded as a must-have item for Rietveld analysis on PCs. The MEM/Rietveld method is a halfway approach to determination of electron/nuclear densities from X-ray/neutron powder diffraction data because the Fo(Rietveld)'s are more or less biased toward the structural model in the Rietveld analysis. For this purpose, MPF is far superior to the MEM/Rietveld method. Nothing is so difficult as MPF. At first, whole-pattern fitting (w.p.f.) is carried out from the Fc(MEM) data in *.fba. Simply set NMODE at 2 and NMEM at 1 in *.ins, and then run RIETAN-FP. Note that all the structure parameters in *.ins must have been updated on the analysis of X-ray diffraction data because contributions of anomalous scattering to structure factors are calculated from them. Of course, we should change the ID(I)'s of the

structure parameters into zero and comment out linear constraints, if any. On repartition of observed diffraction intensities after the w.p.f., structural information contained in (nearly) isolated reflections effectively reduces the bias toward the structural model in the Rietveld analysis. Fo(w.p.f.) data in the resultant binary file, *.fos, or a text file, *.mem, converted from it are analyzed by PRIMA to get *.fba as well as a 3D densities file, *.pri (binary file) or *.den (text file). In such a way, w.p.f. and MEM analysis are alternately repeated until R factors (usually Rwp) in the former no longer decrease (REMEDY cycles). The bias to the structural model reduces with increasing number of cycles. Throughout the REMEDY cycles, the total number of electrons (X-ray diffraction) or the total coherent-scattering lengths (neutron diffraction) in the unit cell is fixed at that obtained from the chemical formula and Z. Thus, electron/nuclear-density distribution affording the best fit to the observed diffraction pattern can be determined by MPF. Refer to a PDF file, PRIMA.pdf, entitled "Super-fast Program, PRIMA, for the Maximum-Entropy Method" to learn further details in PRIMA.

9. ALBA for the MEP method

ALBA is a Fortran 90 program for the MEP analysis of observed integrated intensities (1) estimated by the Le Bail method from powder diffraction data and (2) determined from single-crystal diffraction data. The name of the program originates from the most significant feature of the program; that is, MEP analysis is carried out After Le Bail Analysis. Only a program for MEP analysis from integrated intensities obtained by the Pawley method has hitherto been developed by David of RAL. No MEP analysis program has yet been distributed on the Web. Therefore, we built a powerful MEM engine into ALBA, making alterations to that of PRIMA. Thus, ultra-fast MEP analysis is possible with ALBA. Integrated intensities of overlapped reflections in powder diffraction data are, more or less, improved by the sophisticated MEP method, which is favorable for ab initio structure analysis from powder diffraction data. ALBA is used in combination with a multi-purpose pattern-fitting system RIETAN-FP or EXPO for ab initio structure analysis from powder diffraction data by a direct method. ALBA outputs a binary file, *.pri, storing 3D Patterson functions, which are, in turn, visualized with VEND, as described in Section 5. The resulting 3D images in the unit cell serve for construction of an initial structural model by the heavy-atom method. Most Rietveld-analysis programs incorporate the feature of Le Bail analysis because of the ease with which it can be implemented in this type of software. ALBA allows us to

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