1.02

Java Structure Viewer  
© Steffen Weber 1998

Announcement of JSV1.04 The new JSV 1.04 which uses the JDK1.2 with SWING will be released after the official release of the JDK1.2 by Sun Microsystems which is expected to happen sometime in November this year. In that version I lift some restrictions. So it will support PostScript output or direct printing (for WINDOWS) as well as VRML output, GIF and JPG output. It can also calculate Xray diffraction intensities from the asymmetric unit cell data. A special Diffraction Viewer module allows the 3D/2D display of the diffraction pattern. You can view 0.layers while rotating the 3D pattern in real time or scan along some axis to see higher order layers only. (very useful for people interested in precession or electron diffraction simulations !) Also Laue patterns are possible in real time rotation. (useful for finding effect of misalignment)

 


Introduction

This page introduces JSV (Java Structure Viewer) , which I am presently developing as a stand-alone application.
In order to run it you will need some Java Virtual Machine (JVM) like the freely available JDK 1.1.3 (and higher) . Then you can use either the "java" tool or the "jre" (Java Runtime Environment) to execute JSV.  e.g:   java JSV  (inputfile)(inputfile) , where the inputfile is optional, since JSV has a file dialog to open input files.   or  jre JSV 

You might ask "why Java and not VRML?", since everybody knows that VRML gives very nice display quality for crystal structures. Well, it has some disadvantages , too. It is easy to convert a set of cartesian data into VRML data, but if you only have unit cell data, then you need some software to generate the atom positions first. Some commercial programs do that (e.g.: ATOMS).

VRML can be viewed in a Webbrowser with a VRML plug-in, which you need to install first. (I have problems finding a suitable one for LINUX's Netscape).  When viewing VRML you may not be able to measure atom distances and angles by clicking at them or switch the display of atom labels on and of. Therefore if one does not only limit oneself to simply displaying a structure a separate program becomes necessary. That's why I am writing JSV .  I also want to use it for displaying quasicrystal structures where at least 1000 atoms might be needed for a representative region. Using the WorldView VRML browser I found it annoying that I cannot switch to orthonormal projection.  With so many atoms this is a very welcome feature.

So in short, I am tailoring JSV to my own needs. I do hope, however, that some of you might  find it useful too.

To download the JDK go to  www.javasoft.com. Installation instructions are given there. For JSV1.02 please use JDK1.1.5 or higher!

For JSV1.04 you will need JDK1.2 !

 


Main Features

  • accepts input data for asymmetric unit cell, full unit cell or cartesian coordinates
  • all spacegroup symmetries included for generating atom positions
  • atom display modes: shaded spheres, discs, circles
  • stereo pairs
  • polyhedra (at present only tetrahedra)
  • real time rotations by mouse drags (if your CPU is fast enough)
  • image shifting and zooming by mouse drag
  • measuring distances and angles by clicking atoms
  • optional scrollbars for radius-factor, zoom and perspective factor
  • inputfile editor
  • periodic table for radius and atom color settings
  • output of PostSript (not screen dump; registered version only)
  • output of VRML (Virtual Reality Modelling Language)
  • output of GIF and PPM
  • help files explaining basics of the usage
  • simple bond creation (by clicking at atoms)
  • includes ICE-HTML Browser (for help files and all my applets, which are included as bonus package!)
  • -----------------------------------------------------------------------------------------------
  • (in JSV1.04) 3D/2D X-ray diffraction patterns with real time rotation and layer scanning + Laue
  • (in JSV1.04) Stereographic projections onto Wulff-net
  • (in JSV1.04) direct printing support under Windows/Solaris
  • (in JSV1.04) SWING user interface
  • (in JSV1.04) JPG output

 


How to get JSV1.02

1.  download from NETSCAPE
PRESS  [SHIFT] and CLICK HERE here to download JSV102.jar
2. download from Microsoft Internet Explorer
CLICK HERE here to download JSV102.jar
3. download by anonymous FTP
get JSV102.jar from ftp.nirim.go.jp/pub/education/java/jsv/  

 


Installation

1 download the file JSV102.jar (this is a JAR file,  Java's own compression format similar to TAR for UNIX)

2

put it in a directory on your hard disk
3 execute "jar  xvf  JSV102.jar"  (you need to have JDK1.? on your machine for the "jar" tool) which will create the directory JSV and extract all individual files including some subdirectories
4 then you may run JSV with "java JSV" or "java  JSV inputfile" (make sure your jdk1.?/bin directory is in the path)

Hint: On some systems like LINUX the JVM (Java Virtual Machine) may  use a default heap memory size of only 12-14 Mbyte. If you have more RAM then you can specify new minimum and maximum heap sizes using the -ms and -mx options (eg. java -ms24m -mx64m JSV , for using 24-64 Mbyte) As mentioned above you may also use the  jre  tool instead of the  java  tool.  

Mac: When starting the JSV-Help, which opens in fact the ICE4.0 HTML browser component the initial path is set correctly for UNIX and WINDOWS  systems. I could not check it for the MAC. So if MAC users get a message like "could not find location ...." then please modify the pathname in the textfield on the bottom-left by adding a forward slash / before the path name. That should do it.      

Performance : You need at least a 133 MHz CPU , I guess. I have a 300MHz Pentium II, and I am satisfied with the performance. But JSV is only a pseudo-3D  program and not a real 3D graphics program like the VRML browsers. The JDK seems to have problems with WINDOWS/NT4.0. Sometimes the program hangs up. I myself only work under LINUX (Redhat 5.0) and I have no problems whatsoever with that.

Restrictions : This version does not include PostScript output. JSV1.02 only allows tetrahedral coordination polyhedra. I am working on improving that feature. Please let me know your opinions on JSV, so that I see if there is any interest in it at all (which might be a motivation to speed up my efforts to improve it)

 


Screen Shots

click here for a large ScreenShot with JSV under Windows95  
 

1) example with shaded spheres  

   

2) example with discs and labels  
 

3) example with atom labels only (atom radius set to zero)  
 

4) example with polyhedra  

 

 

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