1. search interstitial sites

The menu item [Option][Search interstitials] lets you search for interstial spaces in a unit cell.

First you specify the number of divisions along each axis and some other criteria as to the desired neighbourhood. Then JSV will calculate for each of those grid nodes [x,y,x] the distance to the surface of each present atom. Thus the actual free radius around that site can be determined. If all set requirements are fullfilled that point is saved in a *.jfm file which will then be viewed with the Interstitial Viewer (which is a modification of the XRDL modul). The interstitial viewer displays each saved point as a colour coded pixel. Blue means a small free radius around that pixel, green to orange a medium free radius and red the largest found free radius. The larger you set the desired hole radius for which to search the smaller is the number of points displayed, thus narrowing down the actual interstititial positions that could accomodate other atoms.

The calculated free radii are sensitive to actual [x,y,z] and thus also to the number of divisions. It would be best to choose 100x100x100, but then the calculation is very time-consuming. I suggest to try first 50x50x50 and then adjust the divisions in response to your findings.

Before the dialog opens the cell has to be reinitialized to obtain the correct starting coordinates for the atoms and also their full radii (100% size). The cell is furthermore expanded to each side, so that also for the grid points within the cell bounding faces the free radius and the coordination can be determined.

Make sure that you selected the appropriate atom radii in your settings. If needed you can use the user-defined radii, which you can edit from within the [Option][atom radii/colors] tool.


dialog box for setting search criteria


search results for desired hole radius>=0.1A


Under [File][view file] you can see the loaded *.jfm file. Its format is as follows:

1.0000 1.0000 0.86 0.0526 Sr 96 1

1.column: x
2.column: y
3.column: z
4.column: radius = distance to nearest neighbour
5.column: symbol of nearest neighbour
6.column: serial number of nearest neighbour
7.column: coordination number (margin for distance is +/- 0.15 Angstroem)
columns 5-7 are NOT used by the viewer


2. calculate interstitial radius at [x,y,z]

The menu item [Option][hole radius at [x,y,z] ] lets you calculate the free radius at a given site. Thereby the desired location [x,y,z] must be provided in unit cell co-ordinates.