Specification of Structural Viewer and Analytical Tool
(JECP/SVAT)
by X.Z. Li
Specification of Structural Viewer and Analytical Tool
(JECP/SVAT)
by X.Z. Li
1. Purpose
2. Graphic user interface
3. Features
4. Installation
5. Basic operation
6. Contact the author
7. References
Java Electron Crystallography Package (JECP) is a collection of programs for crystallography and electron diffraction analysis. The package is designed and written by Dr. X.Z. Li. The software can be used as a research tool as well as a teaching aid.
The need of a structural viewer/an analytical tool, using the same input data format as the JECP and proJECT software, becomes obvious with the growth of the JECP and proJECT programs and users.
There exist many programs for structural design and/or display in various levels developed by individual, research group or software company. Some of them are expensive software with multi-purpose and advanced graphics, which maybe not be suitable for beginners. Others are simply programs for building/dislaying crystal structures. The motivation for the development of JECP/SVAT is to provide a structure viewer and also working as a analytical tool.
JECP/SVAT provides mouse/arrow-key drived real-time 3D display of crystal structure
in a unit-cell, including the chemical bonds and magnetic moments. The structure can also
be displayed in animated modes including rotation or wobble.
The structure can be analyzed (i) as a projection in a user selected [uvw] direction
or layer by layer, (ii) as a local structure (or polyhedral cluters) by defining
a center atom, and a radius of spherical range. Tools for calculate the bond length/angle
are included. One important feature is that user's work on the structure can be saved
to a file, which can be reloaded for a quick display next time or continue on
an unfinished work. The display of a structure can be sent directely to printer for
printing or saved as JECP and TIFF image files. More details of the features are
described below.
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The GUI of JECP/SVAT consists of a drop-down menu, a menu bar, a display panel and several operational panels. The drop-down menu provides all the options and the menu bar provides more frequently used ones. The display panel and control operational panel are always on, while other operational panels can be turned on and off as needed.
Figure 1 shows the GUI of JECP/SVAT with the Bi2Pt structure as example.
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Figure 2 shows all the operational panels.
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Crystal structure file can be prepared using a built-in template of the input file.
All JECP and proJECT software use the same jecp format of input files.
Figure 3. shows (a) the template for creating crystal structure file (the jecp format),
(b) the existed crystal structure files in jecp format and other formats (e.g, CIF, JEMS,
PowderCell)can be edited and saved in the jecp format.
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Crystal structure can be displayed in 3D view with an adjustable perspective constant. Various options for the atomic label and atomic appearance are available. Chemical bonds and magnetic moments can be added on for numeric atomic labels.
Figure 4 shows the structure of Bi2Pt with various appearance, atom as (a) solid ball,
(b) transparent ball, (c) disk and (d) circle; atomic label as (a) off, (b) numerical,(c) element
and (d) atom label.
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For a computer with a relatively slow speed CPU, it is suggested firstly to manipulate
the structure using the atomic appearance of disk or circle and then reset the atomic
appearance of solid ball.
Figure 5 shows the structure of Si with chemical bonds.
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Figure 6. shows the structure of FePt L10 phase with magnetic moments on Fe atoms.
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The software provides the data sets of calcualted and empirical measured atomic radii in the periodic table of the elements. Both atomic radius and atom display color can be customized.
Figure 7. shows the periodic table of the elements with the calculated atomic radii.
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Crystal structures can be displayed with lattice only or 3D structure in the unit-cell. Crystal structures can also be displayed/analyzed using projection/layer and local structure/polyhedral cluster. This is an important way to display/analyze complex structures.
Figure 8. shows the structure of the Al3Mn phase, a crystalline approximant of
the Al-Mn decagonal quasicrystal.
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Figure 9. shows the polyhedral cluster marked in Figure 8 viewed at four different angles.
Figure 10. shows a structural projection of the Al3Mn structure (the lower part)
for a specifically selected the layer, as shown in the upper part.
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As shown in Figure 2(g), JECP/SVAT can show the structure in animated rotation or wobble. Besides an operational panel in Figure 2(h) is for calculating bond length and bond angle, the other operational dialog is for calculating the shortest bond length and a bond list within a given bond length.
Java virtual machine, i.e., J2RE, must be installed for running JECP/SVAT. The 3D vision is generated using 3D geometical calucation and Java2D functions, so Java3D library is not needed.
The executable bytecodes, together with the data files for testing and this specification file is available in compressed form (jecp_svat.rar) at http://www.unl.edu/CMRAcfem/programs.htm.
Uncompress jecp_svat.rar in a user defined directory, e.g. c:\jecp_svat\ and execute jecp_svat.jar (double click in window or type 'java -jar jecp_svat.jar in command line).
The software works in two levels, basic (trial) level and full level.
A license file is required for running in the full level. Without the license file,
the software can be run in the basic level. The software is fully operational
at basic level, but all fuctions for save and print are blocked.
A coded structure file is required for the software in basic level.
The code is free avaiable for the first-time users and continue available
if the users provides a picture of the structure created
by JECP/SVAT together with a link to JECP/SVAT site in their webpages.
Both normal and coded structure file can be used in the full mode.
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i) As mentioned above, new crystal files can be prepared using the editing panel. Crystal structures can be loaded using the menu bar or the drop-down menu.
ii)In addition to the structure file, there is a second type of input file, which contains the information of previous work on a structure. A work file of the same crystal file can be loaded subsequently to display the work done previously or to continue an unfinished work. The work file can be loaded in both modes, but can only saved in the software with a license.
iii) Most operations are self-explainatory but some may need guidance. For example,
atom radius and atom displayed color can be edited by users for current work
and can also be saved into a work file and reloaded as a custumized data set for later works.
A user manual for the detials for all operation is in preparation now.
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For the license file and the code of a structure file, please contact the author
(xli2@unl.edu). Suggestion and bug reports are welcome.
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http://en.wikipedia.org/wiki/Atomic_radius.
http://en.wikipedia.org/wiki/Perspective_(graphical).
Edward Angel, Computer Graphics, Addison-Wesley Publishing Company (1990).
Leen Ammeraal and Kang Zhang, Computer Graphics for Java Programmers, John Wiley & Sons Ltd. (2007).
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