1 Introduction
VICS-II is the next generation of VICS, which was originally developed by
Fujio Izumi and
Ruben A. Dilanian as a part of
VENUS.
VENUS stands for
Visualization of
Electron/
NUclear densities and
Structures. They started VENUS project in mid 2001.
Although basic features were almost completed when I first knew about VENUS at the end of 2003, early version of VICS/VEND had serious performance issues and could not run well on my PC. So I started checking the sources and tried to fix it. I committed some fixes to them but could not fix all issues because some of them are originated in programing model and some are originated in toolkit itself.
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 new programs from scratch using some of original code and new toolkit called
wxWidgets.
VICS-II runs on Windows, Mac OS X, Linux, and is contributed free of charge for non-commercial users.
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
Please refer to
Home Page of Fujio Izumi for the further information about VENUS.
2 Features
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. 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.
Some of novel features:
- Open multiple files with tab without consuming system resources.
- Support multi window with single process.
- Virtually unlimited number of atoms, bonds, polyhedra. (Theoretical limit on 32bit system is 1,073,741,823)
- Transformation of General equivalent positions (GEPs) from conventional to non-conventional setting.
- Export high-resolution graphic images exceeding Video card limitation.
Note:
File format of VICS-II is slightly changed from original VICS for enhancement. Following data are incompatible with each other.
- Hidden objects.
- Lattice planes.
- Vectors.
- Transformation matrix (only supported by VICS-II).
- Depth-cueing.
Both old and new formats can be read by VEND correctly.
3 Supported file types
Supported input files
- Original format of VICS (*.vcs)
- American Mineralogist Crystal Structure Database
- Chem3D
- CIF (Crystallographic Information File)
- CrystalMaker text file
- ICSD-CRYSTIN
- CSSR (Crystal Structure Search and Retrieval)
- CSD/FDAT
- GAMESS input and 3D surface data files output by MacMolPlt
- Gaussian Cube format
- ICSD (Inorganic Crystal Structure Database)
- MDL Molfile
- MINCRYST (Crystallographic Database for Minerals)
- MOLDA
- PDB (Protein Data Bank)
- User input file, *.ins, of RIETAN-2000
- VASP
- WIEN2k struct
- XCrySDen XSF format
- XMol XYZ
- asse
- F01 for SCAT and C04D for contrd
- MXDORTO FILE07.DAT
- FEFF input file
Supported output files
- Original format of VICS (*.vcs)
- Chem3D
- CIF (Crystallographic Information File)
- PDB (Protein Data Bank)
- User input file, *.ins, of RIETAN-2000
- XMol XYZ
- VRML
Pixel based graphic formats
- BMP
- EPS
- JPEG
- JPEG 2000
- PNG
- PPM
- RAW
- RGB (SGI)
- TGA
- TIFF
Vector based graphic formats
- EPS
- PDF
- PS
- Aug. 10 2006 v0.92.6
- Backported a new feature from VESTA to remove symmetry operation and to treat structure as "P 1".
- Added a feature to remove duplicate atoms. (Useful when converting a space group from "P 1" to higher symmetry one.)
- Enabled to treat complex lattice such as "C 1" and "F 1" for space group "P 1" and "P -1".
- Fixed a problem where CIF formats with rhombohedral lattice settings were treaded as hexagonal lattice.
- Read space group information properly from Wien2K formats.
- Fixed a bug where lattice plane was not properly displayed in a certain case.
- Apr. 7 2006 v0.92.5
- Bug fix on v0.92.4 was insufficient. Fixed CIF input problem again.
- Enabled to read origin shift written in AMC (American Mineralogist Crystal Database) files.
- Mar. 26 2006 v0.92.4
- Fixed a problem with input of CIF format. (Monoclinic space group with second or higher setting number was treated as first setting or P1.)
- Feb. 23 2006 v0.92.3
- Fixed a problem where lattice plane (hk0) with h+k=0 cannot be displayed.
- Jan. 25 2006 v0.92.2
- Improved support for VASP format.
- Minor improvements on UI.
- Dec. 18 2005 v0.92.1
- Enabled to sort list items in "Geometrical Parameters" dialog
- Disabled to edit texts in "Equivalent Positions" dialog.
- Fixed lots of typo and improper expressions.
- Nov. 27 2005 v0.92
- Implemented "Geometrical Parameters" dialog. It enables you to visualize pair of atoms used as restraints on interatomic distance and bond angle in RIETAN-2000.
- Replaced atoms and bonds search algorithm to super fast one. It reduces cpu times from O(N2) to O(N).
- Enabled to sort list items in "Structure" dialog.
- Changed sequence of equivalent positions to make it consistent with RIETAN-2000.
- Removed assignment of shortcut key "Ctrl + Click (select)" to "Vectors" dialog. If "Vectors" dialog is open when user selected atoms in Graphic window, corresponding list items in "Vectors" dialog are now automatically selected.
- Windows version now uses Unicode (UTF8) for internal character set.
- Nov. 14 2005 v0.91 (aka. 1.0 beta 2)
- Drag & Drop files to program icons and double clicking associated files are finally supported on Mac OS X Version!
- Fixed some regressions related to Lattice Plane settings, and file save behavior on Mac and Linux.
- Improved rendering quality on Stick Model View.
- Oct. 8 2005 v0.90.9
- Fixed a bug specific to Mac OS X and Linux versions where VICS-II doesn't run when user doesn't have write permission to program directory.
- Read title of FEFF input files.
- Oct. 4 2005 v0.90.8
- Fixed a serious bug introduced in v0.90.7 where invalid transformation matrix were written when saving files.
- If you already have files saved by v0.90.7, reset "Transformation matrix" to unit matrix from Edit -> Structure -> Option.
- Oct. 2 2005 v0.90.7
- Version 0.90.5 and 0.90.6 of VICS-II didn't fix bugs enough. Fixed problems related to object selection and execution from symbolic link again.
- Added support for FEFF input files.
- Fixed a bug with VRML export.
- Aug. 31 2005 v0.90.6
- VICS-II now remembers the latest file format used to export a file.
- Fixed an issue where full path of the program location should be specified to execute it even when environment variable "PATH" is set to point the program directory.
- Fixed an issue specific to Mac OS X where "Return" key should be pressed to apply changes in Properties dialog.
- Aug. 2 2005 v0.90.5
- Selection of bonds and/or polyhedra was disabled when "Manipulations" is "Distance" or "Angle" mode.
- Jul. 24 2005 v0.90.4
- Fixed a bug where VICS-II aborts after selecting more than 5 atoms with "Shift + Click".
- Fixed an issue where specification of projection orientation distort structure when inner product of "Projection vector" and "Upward vector" is not zero.
- Fixed an issue specific to Mac OS X where input of "-" (minus) in a dialog was impossible.
- Improved support for CIF and CrystalMaker text file. Some other fixes related to Mac OS X.
- Jul. 19 2005 v0.90.3
- Enabled to handle non ASCII characters on Mac OS X.
- In case a file is saved without an extension, an extension is now automatically added to a file (Mac OS X & Linux version).
- Fixed a potential risk of endless loop when reading invalid file format. Some other minor fixes.
- Jul. 10 2005 v0.90.2
- Fixed an issue where original file format is over written with VICS-II file format when closing an edited file with "Save changes" option.
- Fixed a bug causing an error when exporting raster image with TIFF format.
- Removed some extra character at the end of *.ins format.
- Jul. 8 2005 v0.90.1 (aka. 1.0 beta 1)
- First release of VICS-II.