3D Visualization System VENUS

An earlier Web page giving enthusiastic publicity to VICS and VEND in Japanese is here. It is now obsolete but a valuable record of their development.

Though several good structure-drawing programs are available, no cross-platform free software is obtainable. As such, I realized a new mini-project to develop a premier system VENUS (Visualization of Electron/NUclear densities and Structures) with Ruben A. Dilanian. We designed, from the ground up, programs taking full advantage of the OpenGL technology. VENUS bears the bell in three-dimensional (3D) visualization, rendering, and manipulation of crystal structures and electron/nuclear densities determined not only by X-ray/neutron diffraction but by electronic-structure calculations with Gaussian, GAMESS, SCAT, WIEN2k, VASP (or MedeA including VASP as its component), and ABINIT. It also lets you visualize electrostatic potentials and wave functions calculated with Gaussian, GAMESS, SCAT, and ABINIT.

Furthermore, VENUS includes two programs for the Maximum-Entropy Method (MEM). They allow us to determine electron/nuclear densities and Patterson functions, which are readily displayed in three dimensions as described above.

We currently offer VENUS free of charge to each individual. However, VENUS is copyrighted with its source code not open to the public; we wish to control the development and future of the VENUS system by ourselves.

The VENUS package comprises four independent programs:

• VICS: VIsualization of Crystal Structures
• VEND: Visualization of Electron/Nuclear Densities
• 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-2000 while VEND can input 3D density files, *.pri, created by PRIMA.

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 MEM-based 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.

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!

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-2000 (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-2000. 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-2000. We must understand structural details not two-dimensionally but three-dimensionally!

VEND can input/output files storing 3D mesh data recorded with a variety of formats listed below.

1. Electron/nuclear-density files with the PRIMA format (binary).
2. Electron/nuclear-density files with the MEED format (text).
3. Patterson-function files output by ALBA for the MEP method.
4. 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), h_e(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

6.1 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 reasons, only a minor feature to convert a MEM data set binary file, *.fos, output by RIETAN-2000 into a MEM data set text file, *.mem, is currently opened to the public by giving two examples, fap and garnet, in Examples.tbz; refer to Readme_Alchemy.txt in folder 'Alchemy' before using Alchemy.exe. The resulting file, *.mem, can be analyzed by 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

Masataka Mizuno of Osaka University kindly wrote the Fortran program, contrd, to convert the binary files, F09 and F39, output by SCAT into text files storing 3D data. It is contained in an archive file, contrd.tbz (see Section 11).

6.3 wien2venus.py

With a script

• wien2venus.py

coded in Python by Masao Arai of NIMS, 3D electron densities calculated with WIEN2k are convertible into a text file, which is in turn input by VEND to display electron-density distribution in three dimensions.

6.4 Cut3D

Binary files output by ABINIT can be converted into text files having the XCrySDen format with a utility program Cut3d included in the archive file of ABINIT.

6.5 ELEN

ELEN is a utility to convert 3D electron densities into electronic-energy densities and Laplacians. It converts *.pri, *.den, *.cube, or *.rho into *.led, *.kef, *.ped, and *.ted; refer to VEND:Appendix A (ID = 6) and Subsection 3.3 in the review article described in Subsection 14.2. ELEN has already been completed. It is pendent whether or not ELEN is distributed as part of the VENUS system.

7.1 Graphic data formats

Graphic data files of the following popular formats can be exported with user-desired resolutions:

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

The features to export EPS (Encapsulated PostScript) and JPEG 2000 files are particularly attractive and useful. Users of TeX will be overjoyed at pasting EPS files directly in documents. JPEG 2000 enables reversible compression where the file size decreases to ca. 15 % in comparison with BMP files. JPEG 2000 files are convertible into files of other formats while changing image sizes and resolutions using GraphicConverter for Mac OS and IrfanView and Paint Shop Pro for Windows. The rich may prefer Adobe Photoshop CS2 to free software or shareware.

Bear in mind that video cards accelerating the OpenGL API speed up saving graphic data files.

7.2 Gallery

Please browse some JPEG files converted from high-quality TIFF files exported by VICS and VEND.

• 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/ų) for YBa₂Cu₃O₇ with (100), (001), and CuO₂ planes showing electron-density distribution (106 KB)
• Isosurfaces (0.7/ų) for MgB₂ with the z = 1/2 plane illustrating electron-density distribution (124 KB)
• Isosurfaces (1/ų) 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.

8.1 Improvements in PRIMA

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-2000 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-2000 to create a MEM data set file, *.fos. F_o(Rietveld) data in this file are analyzed by PRIMA, which creates a 3D density file, *.pri, and a feedback data file, *.fba, storing F_c(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 F_o(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 F_c(MEM) data in *.fba. Simply set NMODE at 2 and NMEM at 1 in *.ins, and then run RIETAN-2000. 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. F_o(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 R_wp) 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.

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-2000 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 improve integrated intensities obtained with them for overlapped reflections, adding value to them.

Changes in VICS, VEND, PRIMA, and ALBA since October in 2003 are listed in what follows:

10.1 VICS

• VICS-II v0.90.1, aka 1.0 beta 1 (2005/07/08): VICS was at last upgraded to VICS-II, which is obtainable from here (refer to 14.1).
• v5.6.1 (2005/06/17): Fixed a bug with the input of a symbol of element having more than two characters. Resolved an issue that data in a file, *.ics, with the ICSD format cannot be input correctly when a string that is accidentally the same as a keyword is included as a datum in *.ics.
• v5.6 (2005/06/10): Addressed an issue that changes a scale on each execution of function load_data when reading in F01 for SCAT. Added support for outputting *.ins (RIETAN-2000) containing comment lines up to 160 characters. Updated template.ins in the Programs folder.
• v5.5.8 (2005/05/17): Fixed a problem with visualization of a structural model from *.xsf (XCrySDen XSF format) containing oblique coordinates.
• v5.5.7 (2005/05/10): Modified expressions of structural models in the parts of bond radius in the Bonds and Preferences Dialog Boxes.
• v5.5.6 (2005/04/24): This version is a minor update to address four problems associated with CIF, *.cif, exported by VICS. Fixed a bug with the output of equivalent coordinate triplets. Added standard deviations in parentheses to lattice parameters. Fixed a bug with structure parameters having two-digit standard deviations in parentheses. Removed trailing blanks in lines giving structure parameters for crystallographic sites.
• v5.5.5 (2005/04/02): Removed part of the source code where the CPU time is measured and displayed in the Output Window.
• v5.5.4 (2005/03/31): Fixed a bug leading to the disappearance of a bond angle when its standard deviation falls within a definite range.
• v5.5.3 (2005/03/18): Changed [Plot range] in the Dialog Bar into [Boundary], the Plot range Dialog Box into the Boundary Dialog Box, and 'Range of fractional coordinates' in the Boundary Dialog Box into 'Ranges of fractional coordinates'.
• v5.5.2 (2005/03/12): Fixed a bug that leads to abnormal termination during reading in part of ICSD files, *.ics. Removed the last vacant lines in spgra.dat and spgri.dat; this improvement is also effective on execution of ALBA.
• v5.5.1 (2005/03/11): Fixed a problem preventing a user other than the Administrator from using VICS. Fixed a bug causing incorrect conversion of fractional coordinates in monoclinic space groups with only two settings (b- and c-axes unique) in the New and Edit Dialog Boxes.
• v5.5 (2005/02/26): Added two items, i.e., {Min. distance} for bonds, in the Search Bonds Dialog Box; this feature is indispensable for visualization of disordered structures.
• v5.4 (2005/02/23): Added the {Line width} of principal ellipses for thermal ellipsoids in the Atoms Dialog Box. A {Line width} of ca. 8.0 is appropriate when exporting an image file.
• v5.3.2 (2005/02/19): Fixed a bug in which symmetry operations displayed for each atom in the Output Window are incorrect in nonstandard settings of orthorhombic space groups. Changed check box "Show outlines of ellipsoids" into "Show principal ellipses" in the Atoms Dialog Box. Improved edges of coordination polyhedra and principal ellipses for thermal ellipsoids so that they are clearly visible on the screen.
• v5.3.1 (2005/02/05): Improved the Orientation Dialog Box in such a way that six indices, u, v, w, h, k, and l, are restored when opening it again. Fixed a minor bug with a limitation in the screen width.
• v5.3 (2005/02/03): Corrected a problem with incorrect orientation and shapes of thermal ellipsoids. Restored the feature (Baur's distortion index) implemented in v5.2. Changed a few lines in the Output Window on selection of a coordination polyhedron.
• v5.2.8 (2005/01/15): Fixed a bug with shifting the origin by specifying central coordinates in an input file, c04d, for contrd.
• v5.2.7 (2005/01/05): Changed "Polyhedra" into "Polyhedral" in the Models panel of the Dialog Bar, again (refer to v5.1.4).
• v5.2.6 (2004/12/23): Changed 'Gaussian 98' to 'Gaussian' because the Cube format remains unchanged on an upgrade from Gaussian 98 to Gaussian 03.
• v5.2.5 (2004/12/17): Fixed a bug that causes a movable lattice plane to be absent in the Graphics Window. Built VICS.exe by enabling Streaming SIMD Extensions 2 (SSE2) for PCs equipped with Pentium 4, Pentium M, parts of Celeron, Athlon 64, parts of Sempron, etc. Use VICS_P3.exe in the Programs folder if VICS.exe is aborted.
• v5.2.4 (2004/12/10): The Close button in the Export Graphics Dialog Box that appears when saving a 3D image file was changed into the Cancel button.
• v5.2.3 (2004/11/26): Fixed a bug that causes abnormal termination of VICS when clicking the OK button after inputting data in the New Data Dialog Box; this trouble is encountered only in the Linux version.
• v5.2.2 (2004/11/25): Changed "(hkl) plane on the screen" into "Project along the normal to (hkl)" in the Orientation Dialog Box. Corrected a problem with the input of Y-α-Sialon.cif.
• v5.2.1 (2004/11/22): Changed the Orientation Dialog Box appreciably. Two different modes can be used to specify the direction of projection and the upward direction on the screen: "Project along [uvw]" and "(hkl) plane on the screen". In the View direction panel, a lattice vector, [uvw], and a reciprocal lattice vector perpendicular to an (hkl) plane are input if "Manual selection" has been checked. Bear in mind that the six indices must satisfy the condition hu + kv + lw = 0.
• v5.2 (2004/11/19): On selection of a coordination polyhedron in the Graphics Window, an average bond length and a distortion index defined for bond lengths by Baur (1974) are given in the Output Window.
• v5.1.4 (2004/11/18): Fixed an issue where the same bond length may be displayed twice in the Output Window on selection of a bond in the Graphics Window. Modified several strings and inserted two vacant lines before and after a series of bond lengths for a coordination polyhedron in the Output Window. Changed "Polyhedra" into "Polyhedral" in the Models panel of the Dialog Bar in conformity with the expression "Polyhedral model." Removed unnecessary lines for an alternative setting of space group No. 152 in a database file spgri.dat.
• v5.1.3 (2004/11/03): Slightly modified the Preferences Dialog Box. Improved some lines in the Output Window; for example, added units for lattice parameters and a unit-cell volume.
• v5.1.2 (2004/10/29): Slightly modified the Preferences, New Data, and Edit Data Dialog Boxes. Corrected several lines in spgra.dat storing information about 230 space groups.
• v5.1.1 (2004/10/21): Fixed an issue where VICS is aborted while saving *.vcs with the VICS format after deleting many objects. Fixed a problem where the same bond is regarded as different objects deleted by the user.
• v5.1 (2004/10/09): Modified the source code so as not to issue warnings when compiling it with Intel C++ Compiler 8.0 or later. Fixed a bug with the click rotation mode. Modified the About Box slightly.
• v5.0.3 (2004/09/14): Fixed an issue with the New Data Dialog Box not able to create new crystal data. Some minor changes for the forthcoming Mac OS X version. Used common Vector.h in VICS and VEND.
• v5.0.2 (2004/09/11): Improved the file open/save dialog box in the Linux version using GTK+-2.4. Solved a buffer overflow problem when inputting files with the CSD and FDAT formats.
• v5.0.1 (2004/09/02): Added 'static' to global variables and functions to limit the scope of them within files including them. Restored close() in place of hide(). Solved problems with obtaining information about dialog boxes. All the dialog boxes are closed before opening a new file. Fixed a problem with a segmentation fault encountered when another file is opened after a file has been input. Added an acknowledgment in the About Box. Fixed a bug (in the Linux version) where files with the Windows format (end of each line: CR+LF) cannot be input correctly. Slightly modified the Linux version.
• v5.0 (2004/08/21): Decreased the memory size for VICS just after launching it from ca. 200 MB to ca. 20 MB; such dramatic downsizing of VICS was achieved by allocating arrays dynamically for coordination polyhedra. Fixed a bug that resulted in meaningless increases in CPU utilization. Fixed a bug with failure in animation in the "Push" mode of rotating objects.
• v4.5.2 (2004/07/30): Fixed a bug that resulted in the appearance of many extra atoms when inputting part of MDL Molfiles.
• v4.5.1 (2004/07/28): Fixed a bug with serial site numbers starting from 6 when reading in MDL Molfiles. Fixed a bug causing the generation of extra bonds on the input of MDL Molfiles.
• v4.5 (2004/07/16): Check dialog_ID when opening a glui dialog box and change glui->close() to glui->hide(), which leads to the disappearance of a warning message "GLUT: Warning in (unamed): glutSetWindow attempted on bogus window." This modification is effective only in the Linux version.
• v4.4.4 (2004/07/07): Modified the About Box.
• v4.4.3 (2004/06/17): Solved a problem with fractional coordinates in CIF's output by VICS; representations with '/', e.g., 1/2 and 1/4, for special positions were changed into decimal fractions.
• v4.4.2 (2004/06/09): Fixed a problem with calculation of estimated standard deviations (e.s.d.'s) for interatomic distances in the presence of at least one e.s.d. for lattice parameters, α, β, or γ; the unit of α, β, and γ should be radian.
• v4.4.1 (2004/06/08): Fixed a problem with calculation of estimated standard deviations (e.s.d.'s) for interatomic distances in the presence of at least one e.s.d. for lattice parameters, α, β, or γ; an incorrect formula was used to calculate the e.s.d.'s.
• v4.4 (2004/06/04): Added support for a wider variety of files with the WIEN2k struct and XCrySDen XSF formats. Increased the maximum number of bonds for each atom from 25 to 70. A minor correction of the Preferences Dialog Box.
• v4.3 (2004/05/20): Added support for text files with Windows (CR+LF), Mac OS (CR), and UNIX (LF) formats. A unit-cell volume is displayed in the Output Window just after reading in crystal data. Fixed a bug with inputting symbols of elements from *.out created by VASP.
• v4.1 (2004/05/14): On the output of an EPS file containing a vector graphic, an array storing OpenGL objects is dynamically allocated with its size adjusted appropriately.
• v4.0.1 (2004/04/29): If the memory size is too small to deal with graphic data in the main memory, the following error message appears: Insufficient memory to output an EPS file with vector data.
• v4.0 (2004/04/28): Added a feature to save EPS files storing vector data without any translucent coordination polyhedra. At least 512 MB of RAM is required to utilize this new feature.
• v3.3.5 (2004/04/09): Fixed a bug causing selected objects (atoms, bonds, or coordination polyhedra) to remain even after pressing the Delete key. Solved a similar issue where no hidden objects appear even after pressing the Esc key.
• v3.3.4 (2004/04/08): Changed 'Settings' in the Preferences Dialog box into 'Other settings'.
• v3.3.3 (2004/04/01): Fixed a bug with glide symmetry in space group P2/c (No. 13).
• v3.3.2 (2004/03/26): X coordinates are no longer exchanged for Y coordinates after reading in Cartesian coordinates of atoms in f01 for SCAT. Corrected a relevant description in Readme_contrd.txt. From now on, no source code of VICS will be distributed.
• v3.3.1 (2004/03/19): Increased the number of digits in *.vcs from 4 to 5 for translation matrices and fractional coordinates used when searching for atoms, which allows us to reproduce coordination polyhedra after saving crystal data and various settings in *.vcs.
• v3.3 (2004/03/01): Decreased the unnecessary CPU load to a certain extent while ceasing from operation.
• v3.2 (2004/02/26): Made it possible to input full space-group symbols for monoclinic space groups in CIFs.
• v3.1.5 (2004/02/23): Located "Use anisotropic atomic displacement parameters" and {Type} in the same block in the New/Edit Dialog Boxes. Added some sentences concerning atomic displacement parameters in Subsection 6.4 (VICS) in VENUS.pdf.
• v3.1.4 (2004/02/13): Modified the Projection panel in the General Dialog Box; {Perspective} was changed into {Accentuation}.
• v3.1.3 (2004/02/06): In the Parameters Panel within the Bonds Dialog Box, {Radius (B&S, poly)} was changed into {Radius (B&S, c.p.)}, where c.p. denotes coordination polyhedra.
• v3.1.2 (2004/02/04): Fixed a bug causing an error on the click of [New] if VICS.exe or VICS_P4.exe does not share the same folder with spgra.dat and spgri.dat. Solved a trouble in which bond angles are never displayed on the use of VICS_P4.exe.
• v3.1.1 (2004/02/03): Solved a trouble with the appearance of an error message "Buffer overrun detected!" during reading in *.ins with VICS_P4.exe optimized for Pentium 4 processors.
• v3.1 (2004/01/28): Modified the source code of VICS in such a way that no warnings were output by Microsoft Visual C++.NET 2003 except a warning related to JasPer. Fully optimized for Pentium 4 processors. The name of the resulting executable binary program is VICS_p4.exe.
• v3.0 (2004/01/23): Increased the maximum length of the absolute path + file name for each input/output file from 260 (in effect 80 because of a bug) to 512. Parallel projection has become the default setting. Colors of coordination polyhedra can be changed independent of colors of central atoms.
• v2.9 (2004/01/13): Added a feature to save a VICS text file, *.vcs, just by pressing function key F2. The name of *.vcs is displayed in the Save Dialog Box, if any. Increased the maximum length of the absolute path + file name for each input/output file from 256 to 260.
• v2.8.4 (2003/12/18): Fixed a bug causing the disappearance of part of cylindrical bonds.
• v2.8.3 (2003/12/17): Fixed an issue with reading in an ICSD-format file where a space group name is followed by "R" (rhombohedral lattice).
• v2.8.2 (2003/12/11): Increased the maximum number of atoms in the asymmetric unit to 3000.
• v2.8.1 (2003/12/08): Solved a trouble with CIFs created by Crystallographica. Lattice parameters, α, β, and γ, in the Edit Data Dialog Box change appropriately on a change in the crystal system, e.g., from triclinic to monoclinic.
• v2.8 (2003/11/27): In this version, file *.vasp or *.vas, output by VASP must accompany another file, *.out (a file whose name contains '/OUTCAR.out' at its tail is renamed), having the same basename in the same folder. Symbols of elements contained in the current compound are no longer input from *.vasp or *.vas because they are input from *.out. Made it possible to input GAMESS input files, *.inp, as well as surface data files, *.mmp, created by MacMolPlt from GAMESS log files, *.log. Only the origin of the 3D grid is input from *.mmp.
• v2.7 (2003/11/19): Added features to input 3D data in files with the VASP and XSF formats.
• v2.6.2 (2003/11/06): Isotropic atomic displacement parameters, 'Biso' and 'Uiso', in the Output Window were changed into 'B' and 'U', respectively.
• v2.6.1 (2003/10/31): Corrected a typographical error in the General Dialog Box, i.e., from 'Perspecive' to 'Perspective'.

10.2 VEND

• v6.7.3 (2006/01/30): Added a feature to input/output 3D density files, *.grd, created by GSAS after Fourier calculations. Fixed two bugs with the input of files with the VASP format.
• v6.7.2 (2005/04/16): Fixed a bug causing the disappearance of bonds in a ball-and-stick model input from *.vcs.
• v6.7.1 (2005/03/11): Addressed an issue preventing a user other than the Administrator from using VEND.
• v6.7 (2005/03/03): Corrected a bug with incomplete generation of equivalent positions from crystal data in *.vcs with the VICS format. Added support for minimum bond lengths recorded in *.vcs.
• v6.6.2 (2005/02/05): Improved the Orientation Dialog Box in such a way that six indices, u, v, w, h, k, and l, are restored when opening it again.
• v6.6.1 (2005/01/05): Changed "Surface", "Frame", and "Mesh" in the Models panel of the Dialog Bar into "Smooth Shading", "Wire-frame", and "Dot surface", respectively, again (refer to v6.5.4). The name of this panel was also changed from 'Models' to 'Surface type', again. Removed 'plane' in the Plane panel of the 2D Projection Dialog Box.
• v6.6 (2004/12/24): Resolved an issue with reading in part of text files with formats of other operating systems.
• v6.5.9 (2004/12/23): Fixed a trouble where a ball-and-stick model is invisible even if "Show model" has been checked after inputting a file, *.vcs, with the VICS format. Changed 'Gaussian 98' to 'Gaussian' because the Cube format remains unchanged on an upgrade from Gaussian 98 to Gaussian 03.
• v6.5.8 (2004/12/17): Changed {MAX} and {MIN} in the Contour Lines Dialog Box into {Max.} and {Min.}, respectively. Built VEND.exe by enabling Streaming SIMD Extensions 2 (SSE2) for PCs equipped with Pentium 4, Pentium M, parts of Celeron, Athlon 64, parts of Sempron, etc. Use VEND_P3.exe in the Programs folder if VEND.exe is aborted.
• v6.5.7 (2004/12/10): Fixed a bug with VEND 3D data files, *.3ed, output by VEND. The Close button in the Export Graphics Dialog Box that appears when saving a 3D image file was changed into the Cancel button.
• v6.5.6 (2004/11/25): Changed "(hkl) plane on the screen" into "Project along the normal to (hkl)" in the Orientation Dialog Box.
• v6.5.5 (2004/11/22): Changed the Orientation Dialog Box appreciably. Two different modes can be used to specify the direction of projection and the upward direction on the screen: "Project along [uvw]" and "(hkl) plane on the screen". In the View direction panel, a lattice vector, [uvw], and a reciprocal lattice vector perpendicular to an (hkl) plane are input if "Manual selection" has been checked. Bear in mind that the six indices must satisfy the condition hu + kv + lw = 0.
• v6.5.4 (2004/11/20): Changed "Surface", "Frame", and "Mesh" in the Models panel of the Dialog Bar into "Smooth Shading", "Wire-frame", and "Dot surface", respectively. The name of this panel was also changed from 'Models' to 'Surface type'.
• v6.5.3 (2004/11/03): Slightly modified the 2D Projection Dialog Box. Improved some lines in the Output Window; for example, added units for lattice parameters.
• v6.5.2 (2004/10/29): Slightly modified the Preferences Dialog Box.
• v6.5.1 (2004/10/20): Fixed a bug that resulted in inclusion of (n X n) images when saving a TIFF file of a two-dimensional map.
• v6.5 (2004/10/09): Modified the source code so as not to issue warnings when compiling it with Intel C++ Compiler 8.0 or later. Added the Smoothing panel containing [More] and [Less] buttons in the Isosurfaces Dialog Box to smooth isosurfaces by Catmull-Rom spline interpolation. Numbers of pixels along a, b, and c directions are doubled when clicking [More] and halved when clicking [Less]. Fixed a bug with the click rotation mode. Modified the About Box slightly.
• v6.4.3 (2004/09/14): Fixed a bug causing a failure in saving preferences_VEND.init. Some minor changes for the forthcoming Mac OS X version.
• v6.4.2 (2004/09/11): Improved the file open/save dialog box in the Linux version using GTK+-2.4. Slightly modified the source code.
• v6.4.1 (2004/09/02): Added 'static' to global variables and functions to limit the scope of them within files including them. Restored close () in place of hide(). Solved problems with obtaining information about dialog boxes. All the dialog boxes are closed before opening a new file. Added an acknowledgment in the About Box.
• v6.4 (2004/08/25): Decreased the memory size for VEND just after launching it from ca. 204 MB to ca. 17 MB, which was achieved by dynamic allocation of arrays in the same manner as with VICS v5.0. Increased both the maximum number of pixels on isosurfaces and the maximum number of polygons to 1 073 741 823.
• v6.3.1 (2004/08/12): Changed glui->close() in open.cpp to glui->hide(); unfortunately, this part remained unchanged in v6.3.
• v6.3 (2004/07/16): Modified the source code to avoid errors when displaying a 2D map in the 2D Map Window. Check dialog_ID when opening a dialog box and change glui->close() to glui->hide(), which leads to the disappearance of a warning message "GLUT: Warning in (unamed): glutSetWindow attempted on bogus window." Both of the modifications are effective only in the Linux version. Corrected a typographical error in the About Box, i.e., from 'whicfh' to 'which'.
• v6.2.1 (2004/07/07): Modified the About Box.
• v6.2 (2004/07/03): Changed the manner of drawing 2D maps in such a way that a full range of data are displayed even if negative data are included. The minimum value, Z(min), and the maximum value, Z(max), over a user-specified range are displayed at the upper left of the 2D Map Window.
• v6.1.1 (2004/06/04): A minor correction of the Preferences Dialog Box.
• v6.1 (2004/05/14): On the output of an EPS file containing a vector graphic, an array storing OpenGL objects is dynamically allocated with its size adjusted appropriately.
• v6.0 (2004/05/11): Supported dynamic allocation of arrays for 3D pixel data using pointers. Consequently, there is no limitation on the maximum numbers of pixels along a, b, and c directions.
• v5.0.1 (2004/04/29): If the memory size is too small to deal with graphic data in the main memory, the following error message appears: Insufficient memory to output an EPS file with vector data.
• v5.0 (2004/04/28): Added support for EPS files storing vector data without any translucent isosurfaces. At least 512 MB of RAM is required to utilize this new feature.
• v4.3.2 (2004/04/08): Changed 'Nuclear Density' in 'About VEND' into 'Nuclear Densities'. Changed 'Settings' in the Preferences Dialog Box into 'Other settings'.
• v4.3.1 (2004/03/26): X coordinates are no longer exchanged for Y coordinates after reading in 3D data files, *.sca or *.scat, output by contrd. Corrected a relevant description in Readme_contrd.txt. From now on, no source code of VEND will be distributed.
• v4.3 (2004/03/01): Decreased the unnecessary CPU load considerably while ceasing from operation.
• v4.2.2 (2004/02/13): Modified the Projection panel in the General Dialog Box; {Perspective} was changed into {Accentuation}.
• v4.2.1 (2004/02/03): Fixed an issue where parts of atoms and bonds are not drawn when reading in *.vcs with VEND_P4.exe optimized for Pentium 4 processors.
• v4.2 (2004/01/28): Modified the source code of VEND in such a way that no warnings were output by Microsoft Visual C++.NET 2003 except a warning related to JasPer. Fully optimized for Pentium 4 processors. The name of the resulting executable binary program is VEND_p4.exe.
• v4.1.5 (2004/01/23): Increased the maximum length of the absolute path + file name for each input/output file from 260 (in effect 80 because of a bug) to 512. Parallel projection has become the default setting.
• v4.1.1 (2004/01/13): Increased the maximum length of the absolute path + file name for each input/output file from 256 to 260.
• v4.1 (2004/01/05): Binary files (ID = 0), *.prim or *.pri, storing 3D densities in the unit cell can be opened. These files are output by PRIMA v3.1 or later. ID numbers assigned to all the old formats have been increased by one. Consequently, VEND script files, *.vnd, created with old versions of VEND can no longer be input by VEND v4.1 or later.
• v4.0 (2003/12/26): Added a function to colorize an isosurface to show the value of another physical quantity at each point on the surface. The shape of the surface illustrates one piece of information whereas the color indicates a different piece of data. Typically, an isosurface of electron densities is colorized to show electrostatic potentials. Text files, *.3ed, with the VEND 3D data format can be output.
• v3.2.1 (2003/12/02): Increased the maximum number of atoms in the asymmetric unit to 1 200.
• v3.2 (2003/11/27): Added a function to input surface data files, *.mmp, created by MacMolPlt from GAMESS log files, *.log.
• v3.1 (2003/11/19): Implemented features to input crystal data in files with the VASP and XSF formats. Only electron densities and electrostatic potentials can be displayed in the case of VASP files while electron densities, electrostatic potentials, and wave functions can be visualized for XSF files.
• v3.0.3 (2003/10/31): Corrected a typographical error in the General Dialog Box, i.e., from 'Perspecive' to 'Perspective'.
• v3.0.2 (2003/10/30): Corrected a typographical error in the name of a palette, i.e., from 'Invers Rainbow' to 'Inverse Rainbow'.
• v3.0.1 (2003/10/22): Added extension 'sca' for text files output by contrd in the Open Dialog Box.
• v3.0 (2003/10/03): (a) Selection of isosurfaces for positive, negative, and (both positive and negative) values with radio buttons in the Isosurfaces Dialog Box, (b) inclusion of virtual negative electron densities in *.rho, which enables us to display differences in electron densities between two datasets, and (c) specifying whether sections of isosurfaces appear or disappear (transparent sections) at drawing boundaries (Cartesian coordinates) or unit-cell edges (crystals).

10.3 PRIMA

• v3.5.6 (2006/03/23): Changed the type of a variable to adjust estimated standard deviations of |F_o|'s from INTEGER to REAL. Modified screen and file outputs slightly.
• v3.5.5 (2006/03/21): Made it possible to output 3D text data files, *.den, in the batch mode; a file name with the extension of 'den' should be described in *.prf to use this feature.
• v3.5.4 (2005/10/22): Fixed a serious bug with the G-constraint.
• v3.5.3 (2005/07/22): Corrected several improper screen and file outputs. Added batch files, *.bat, to run PRIMA.EXE by double-clicking on the icon of *.bat. With *.bat, it is no longer necessary to describe the absolute paths of input and output files in *.prf.
• v3.5.2 (2004/12/22): Fixed a bug with the input of initial electron/nuclear densities in the unit cell from a binary file, *.pri, output by PRIMA.
• v3.5.1 (2004/07/08): Corrected a typographical error in the screen output, i.e., from 'G-constaint' to 'G-constraint'.
• v3.5 (2004/06/15): Slightly modified output on the screen. Fully optimized for Pentium 4 processors with Visual Fortran for Windows v6.6C3, which decreased the size of PRIMA.exe from 612 KB to 456 KB.
• v3.4.9 (2004/06/12): Fixed a trouble with the MEM analysis of noncentrosymmetric crystals; this bug invaded PRIMA in v3.4.8.
• v3.4.8 (2004/05/29): Tried to minimize the number of GO TO statements, hoping that this is the final reformation of the source code.
• v3.4.7 (2004/04/17): Rewrote parts of the source code where OPEN and WRITE statements include ERR branch specifiers, which considerably decreased the number of awkward GO TO statements.
• v3.4.6 (2004/04/16): Rewrote many lines in conformity with the grammar of Fortran 90. There are no feature enhancements or incompatibilities with v3.4.5.
• v3.4.5 (2004/04/13): Changed 'raw file' into 'raw data file' in the screen output, where numbers of '-' (minus) in two lines were also changed.
• v3.4.4 (2004/04/06): Replaced FUNCTION ETIME (a UNIX library routine) with SUBROUTINE CPU_TIME which is a new intrinsic procedure in Fortran 95. Deleted two unnecessary lines.
• v3.4.3 (2004/02/19): Changed 'Lagrange multiplier' into 'Lagrangian multiplier' in the screen output, again, hoping that this is the final correction. Modified redundancy code.
• v3.4.2 (2004/02/13): Changed 'Lagrange multiplier' into 'Lagrangian multiplier' in the screen output, Manual.pdf, and PRIMA.pdf.
• v3.4.1 (2004/02/12): Corrected typographical errors in the screen output, i.e., from 'Langrange' to 'Lagrange'. Corrected errors in Manual.pdf and Readme.txt.
• v3.4 (2004/01/29): Corrected an error in the screen output, i.e., from 'Standard data file' to 'Standard output file'. The flag for the G-constraint is 0 (the G-constraint is not used) by default. Updated all the preferences files, *.prf. Fully optimized for Pentium 4 processors with Intel Visual Fortran Compiler 8.0 for Windows.
• v3.3.1 (2004/01/16): Modified questions displayed in the screen. Updated templates of preferences files, *.prf. Corrected several errors in Manual.pdf.
• v3.3 (2004/01/15): Added support for reading in MEM data set binary files, *.fos, output by RIETAN-2000 Rev. 1.5 or later. Hereafter, MEM data set text files, *.mem, should be used only for single-crystal diffraction data. The Lagrangian multiplier is input not by RIETAN-2000 but by PRIMA when reading in *.fos.
• v3.2.1 (2004/01/13): Increased the maximum length of the absolute path + file name for each input/output file from 256 to 512.
• v3.2 (2004/01/09): A coefficient, SCIO, to adjust |F_o|'s obtained with RIETAN-2000 is now input by PRIMA. Therefore, we no longer need to run RIETAN-2000 several times to determine the optimum value of SCIO by trial and error. MEM data set files, *.mem, output by RIETAN-2000 Rev. 1.4 or later can be input by this version of PRIMA.
• v3.1 (2004/01/05): PRIMA outputs binary files, *.pri or *.prim, storing 3D densities in the unit cell to save disk spaces considerably; text files, *.den, are no longer created. F_c(MEM) data for MPF with RIETAN-2000 Rev. 1.3 or later are also recorded in binary files, *.fba.
• v3.0.1 (2003/12/12): Fixed an issue with the analysis of neutron diffraction data of noncentrosymmetric crystals containing elements with negative coherent-scattering lengths.
• v3.0 (2003/11/05): Fixed a serious bug causing a deviation of the total number of electrons (the sum of coherent scattering lengths in neutron diffraction) in the unit cell from that specified by the user. Changed part of the screen output. Added a column for observed and calculated structure factors in the standard output, *.out.
• v2.5.2 (2003/10/25): Corrected a typographical error in the screen output, i.e., 'Langrange' --> 'Lagrange'.
• v2.5.1 (2003/10/14): Further optimization that decreases the execution time by 5-10 %.
• v2.5.0 (2003/10/09): Optimization that approximately halves execution times.

10.4 ALBA

• v1.3.3 (2005/08/06): Corrected a line in an input file output by ALBA.
• v1.3.2 (2005/05/25): Fixed a bug where space group #230 is missing in the list of Patterson symmetries. Added fail-safe code for an incorrect space group. Fixed a bug with a destination of an error message.
• v1.3.1 (2005/02/25): Removed 'including its absolute path' in two prompt lines because no absolute path is necessary when launching ALBA.exe by double-clicking batch files *.bat. Fully optimized for Pentium 4 processors with Visual Fortran for Windows v6.6C3, specifying compiler options "Maximum Optimizations" and "Generate Most-Optimized Code".
• v1.3 (2004/06/17): Changed 'amounts of substances' in output on the screen into 'numbers of atoms in the unit cell', for which real numbers are input instead of integers. Fixed problems with the output of very small values of the initial Lagrangian multiplier and the coefficient, t, to adjust the Lagrangian multiplier.
• v1.2 (2004/06/16): The first official release of ALBA.

It should be pointed out that the latest versions of RIETAN-2000, VICS, VEND, PRIMA, ALBA, Alchemy, and contrd should always be used on the combined use of them; compatibility with older versions is never considered in RIETAN-2000 and VENUS. You may encounter unforeseen trouble on the mixed use of new and old versions.

Note that the Windows, Mac OS X, and Linux versions of a next-generation structure-drawing program, VICS-II, are available in this Web page (refer to 14.1).

11.1 Windows version

Though VENUS systems for Windows and Linux have already been completed, I myself distribute only the Windows version to save labor. My excuse is that only several % of visitors of this Web site use UNIX/Linux.

The VENUS package as well as the file converter for SCAT is distributed as three archive files with the tbz (= tar.bz2) format; viruses were inspected with Norton AntiVirus. Nevertheless, you should always check the contents of the archive files by your virus checker for safety.

To download each of them, position the pointer over one of the following files:

1. VENUS system
   • VENUS: VENUS.tbz (2006/03/24; 10.8 MB)
     
   • Documents: Documents.tbz (2006/03/23; 8.9 MB)
     
   • Examples: Examples.tbz (2006/03/24; 50.5 MB)
   
   
2. File converter for SCAT
   • contrd: contrd.tbz (2006/11/10; 382 KB)

Then, right-click the link (file name) to display a pop-up menu and choose "Save Target As..." or a corresponding item (depending on your browser). Drag and drop the downloaded file, *.tbz, onto the icon of an archiver that allows us to uncompress it (refer to Archivers for Windows).

VENUS.tbz, Documents.tbz, Examples.tbz, and contrd.tbz are uncompressed to yield folders 'VENUS', 'Documents', 'Examples', and 'contrd', respectively. Note that folder 'Documents' is also contained in folder 'VENUS'; it is separately distributed for users of Linux versions.

Please read PDF files in folder 'Documents' to learn how to utilize the VENUS system.

Use VICS_P3.exe and VEND_P3.exe on PCs equipped with CPUs that do not support SSE2 if VICS.exe and VEND.exe are aborted.

Before using contrd, refer to Readme_contrd.txt (written in Japanese) in folder 'contrd' at first.

11.2 Linux version

With my permission, Hiroshi Ohki of Shinshu University has been distributing

• A Linux version of VENUS

Object files of VICS/VEND and executable binary files of PRIMA and ALBA were built with the Intel C++ and Fortran Compilers for Linux, respectively. Binary files, *.prim or *.pri, created with the Windows and Linux versions of PRIMA are compatible with each other.

Koichi Momma also distributes

• 64 bit code of PRIMA for AMD64 or EM64T platforms

built with Intel Fortran compiler 9.0 for Linux. This version is provided to deal with many reflections and/or a large number of pixels in the unit cell.

11.3 Mac OS X version

Koichi Momma of Tohoku University tried to transport VICS and VEND from Linux to Mac OS X. At present, VICS and VEND for Mac OS X have been completed except that file names have to be input in command lines in the Terminal window. No EPS (vector data) files can be obtained in proper working order. We also encounter a problem where an incomprehensible error message appears when closing parts of dialog boxes. Then, we decided to develop wxWidgets-based applications, i.e., VICS-II (refer to 14.1) and VESTA (Visualization for Electronic and STructural Analysis) that includes all the features of VICS and VEND. Mac OS X versions are developed in addition to Windows and Linux versions.

Despite the absence of PRIMA for Mac OS X, we have been distributing the Mac OS X version of Alchemy:

• Alchemy.dmg (2006/03/24; 121 KB)

Double-click Alchemy.dmg to mount a virtual drive named Alchemy. For details in this version, refer to Readme_Alchemy.txt in folder Alchemy.

MEM data set text files, *.mem, created with it can be analyzed by PRIMA on another platform, currently Windows or Linux.

In what follows, "VENUS" means a software package including not only VICS + VEND + PRIMA + ALBA + Alchemy but also successor programs to VICS and VEND, i.e., VICS-II and VESTA.

The latest license agreement described below takes priority over any previous descriptions in user's manuals and so on. Terms 12.1 and 12.2 should always be obeyed whatever program you may use.

12.1 Sale as commercial software

12.2 Usage restrictions for J-PARC

In the case of the next-generation pulsed neutron source in J-PARC, a site license is required to use (part of) VENUS for analyzing and/or visualizing data obtained directly and indirectly from time-of-flight neutron diffraction data measured there. Even outside users of J-PARC should never use VENUS without the site license or Izumi's written permission.

12.3 VICS and VEND

Drawings produced by VICS and VEND may be used in any publications provided that the following article is quoted:

• F. Izumi and R. A. Dilanian, Commission on Powder Diffraction, IUCr Newslett., No. 32 (2005) 59-63.

12.4 VICS-II

Drawings produced by VICS-II may be used in any publications provided that proper acknowledgment is given; for example,

Figure 1 was drawn with VICS-II developed by Momma and Izumi.

12.5 VESTA

Drawings produced by VESTA may be used in any publications provided that the following article is quoted:

• K. Momma and F. Izumi, Commission on Crystallographic Computing, IUCr Newslett., No. 7 (2006) in press.

On the use of both RIETAN-FP and VESTA, it is preferable to cite the following article:

• F. Izumi and K. Momma, Proc. XX Conf. Appl. Crystallogr., Solid State Phenom., in press.

12.6 PRIMA

Whenever original results acquired with PRIMA are published in journals, proceedings, facility reports, etc. or reported in meetings with abstracts, the program name PRIMA should explicitly be credited. Furthermore, cite the following review article:

• F. Izumi and R. A. Dilanian, "Recent Research Developments in Physics," Vol. 3, Part II, Transworld Research Network, Trivandrum (2002), pp. 699-726. (ISBN 81-7895-046-4)

Only giving credit to PRIMA is good enough in the cases of abstracts, short reports, and so forth with limited spaces.

12.7 ALBA

Whenever original results acquired with ALBA are published in journals, proceedings, facility reports, etc. or reported in meetings with abstracts, the program name ALBA should explicitly be credited. Furthermore, cite the following reference:

• F. Izumi, "Spectroscopy and Diffraction III," the Fifth Series of Experimental Chemistry, Vol. 11, ed. by the Chemical Society of Japan, Maruzen, Tokyo (2006), pp. 220-223. (ISBN 4-621-07310-9; in Japanese)

12.8 Alchemy

Those who are willing to use Alchemy for MEM analysis from time-of-flight neutron powder diffraction data measured with multi-detector banks should come into contact with F. Izumi. In addition, cite the following reference when publishing results obtained with this feature of Alchemy:

• F. Izumi and Y. Kawamura, Bunseki Kagaku, 55 (2006) 391-395. (in Japanese)

12.9 Warning

VENUS may still contain a fair number of bugs. VENUS is distributed in the hope that it will be useful and reliable. It is, however, provided "as is'' without any warranty. Technical service concerning it is not free.

13.1 A Web site that serves for 3D visualization from files created with SCAT

Genta Sakane of Okayama University of Science provides us with detailed information about the combined use of SCAT and VENUS:

• A tutorial for DV-Xα molecular-orbital calculations using SCAT, contrd, and VENUS
• Pleasant electronic-state calculations of complexes that appear in textbooks
• A suite of convenient utilities for the DV-Xα method
• Electronic-structure gallery of complexes
• Genta Sakane's DV-Xα and VENUS diary

13.2 Web pages for understanding how to visualize crystal structures with VICS

• Kazuki Komatsu, Tohoku University
• Kubo's page
• How to use VICS-II

14.1 VICS-II

Koichi Momma released a second-generation structure-drawing program, VICS-II, fully utilizing a C++ GUI framework, wxWidgets, to make up its GUI. VICS-II corresponds to part of a next-generation 3D visualization system, VESTA, containing all the features of VICS and VEND, offering improved scalability and performance.

Windows, Mac OS X, and Linux versions of VICS-II are available for download. Please send any comments and bug reports to Mr. Momma after testing it. Note that VICS-II is included in the VENUS system despite its distribution on his Web site JP-Mineral.

VICS is now obsolete whereas VICS-II is stable enough to be used routinely. Therefore, the use of VICS-II in place of VICS is strongly recommended.

14.2 A guide to full utilization of RIETAN: 3D visualization of electron- and nuclear-density distribution

Visualization of electron/nuclear densities from X-ray/neutron powder diffraction data with VENUS is described in detail in the following review article:

• F. Izumi, J. Crystallogr. Soc. Jpn., 44 (2002) 380-388. (in Japanese with eight color figures)

Take notice that results of benchmark tests listed in Table 1 in this article are now obsolete; those obtained with the latest version of PRIMA is presented in 10.2.

14.3 VENUS system for three-dimensional visualization of crystal structures and electronic states

A review article entitled as above was published in April in 2005:

• F. Izumi, Rigaku J., 36, No. 1 (2005) 18-27. (in Japanese with seven color figures)

At first, most parts of this Web page were translated into Japanese, and many new descriptions were added together with references.

14.4 VENUS: a 3D visualization system for crystal structures and electron/nuclear densities

A review article entitled as above was published in December in 2005:

• F. Izumi and R. A. Dilanian, Commission on Powder Diffraction, IUCr Newslett., No. 32 (2005) 59-63. (with six color figures)

14.5 Three-dimensional visualization of nuclear densities by MEM analysis from time-of-flight neutron powder diffraction data

We published a paper on Alchemy:

• F. Izumi and Y. Kawamura, Bunseki Kagaku, 55 (2006) 391-395. (in Japanese)

In this work, we established a method for determining the three-dimensional distribution of nuclear densities from time-of-flight (TOF) neutron powder diffraction data measured with multiple detector banks. At first, the observed crystal-structure factors, F_o(h), and standard deviations of |F_o(h)|'s estimated after Rietveld analysis using GSAS are output in text files, *.mem, with a file converter, Alchemy. After combining reflection data, hkl, F_o(h), σ(|F_o(h)|), in the *.mem files, so as to minimize the extinction effect in reflections with large interplanar spacings, they are analyzed by a maximum-entropy method program, PRIMA, to determine the nuclear densities in the unit cell. The resulting nuclear-density distribution is visualized in three dimensions with VEND. Such a procedure enabled us to visualize nuclear densities in Ni from TOF neutron powder diffraction data.

14.6 Cobalt oxides join the party!

Fortunately, the first paper that reported structural data obtained by combination of RIETAN-2000 and PRIMA was outstanding for the discovery of a superconducting cobalt oxide hydrate, Na_xCoO₂-yH₂O:

• K. Takada, H. Sakurai, E. Takayama-Muromachi, F. Izumi, R. A. Dilanian, and T. Sasaki, Nature (London), 422 (2003) 53-55.

This investigation is epoch-making in the respect that the superconductivity in the layered compound containing the first-transition metal, Co, other than Cu has been discovered at first. Positions of water molecules between two CoO₂ layers were easily found by MEM. With PRIMA, the MEM analysis took us only several seconds to finish!

Four color figures drawn with VICS and VEND were illustrated in a review article

• K. Takada, J. Crystallogr. Soc. Jpn., 45 (2003) 140-144. (in Japanese)

by Kazunori Takada who discovered this superconductor.

14.7 Electron-density distribution in manganese oxides

In the same issue of J. Crystallogr. Soc. Jpn., Yasuhiko Takahashi of AIST reviewed his studies on crystal and electronic structure analyses of inorganic materials by single-crystal X-ray diffraction and first-principles calculations, for which he won the Young Crystallographer Award of the Crystallographic Society of Japan in 2002. In this article, he demonstrated seven figures of 3D electron-density distribution in LiMnO₂, LiMn₂O₄, and lambda-type MnO₂:

• Y. Takahashi, J. Crystallogr. Soc. Jpn., 45 (2003) 110-118. (in Japanese)

Isosurfaces of electron densities in these figures were drawn with VEND.

14.8 Disorder and diffusion paths of oxide ions in ion conductors

Masatomo Yashima of Tokyo Institute of Technology reviewed his recent work on the positional disorder and diffusion paths of oxide ions in three oxides at high temperature:

• M. Yashima, J. Crystallogr. Soc. Jpn., 46 (2004) 232-237. (in Japanese with five color figures)

In these notable studies, he visualized nuclear densities by MPF from neutron powder diffraction data taken on HERMES, using the combination of RIETAN-2000, PRIMA, VICS, and VEND. MPF is very suitable for investigating such highly disordered systems.

I wish to thank Ruben A. Dilanian for his dedication to a great deal of programming. At my requests, Masao Arai and Masataka Mizuno kindly coded wien2venus.py and contrd, respectively. Hiroshi Ohki and Koichi Momma helped us improve VENUS. The VENUS project was financially supported by the R&D of New Superconducting Materials of NIMS and the Precursory Research for Embryonic Science and Technology of JST.

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