Indexing using Treor


Treor90 is a well-known program for indexing powder diffraction patterns (P.-E. Werner, "Trial-and-error computer methods for the indexing of unknown powder patterns", Z. Krist. 120, 375-387 (1964); P.-E. Werner, L. Eriksson and M. Westdahl, "Treor, a semi-exhaustive trial-and-error powder indexing program for all symmetries", J. Appl. Cryst. 18, 367-370 (1985).).

Treor can be used by Match! to derive unit cell parameters from the peak positions of marked experimental peaks. As an alternative to Treor, Dicvol can also be used for this purpose.

Setting up and running Treor90 indexing calculations

All that is required to run an indexing calculation are either experimental peaks or raw diffraction data. If only raw (profile) but no peak data are present when the indexing command is run, Match! will automatically execute the raw data processing before the actual indexing calculation is started.

Before running the "Indexing" command, you should mark the peaks to be taken into account in the indexing calculation. If you do not mark any peaks, Match! will automatically use the 20 strongest peaks (if present) that are not yet covered by selected phases and whose relative intensity is larger than the corresponding minimum value (which can e.g. be adjusted using the red bar on the y-axis of the diffraction pattern graphics) for indexing. You can also adjust the corresponding parameter “minimum relative intensity for automatic peak usage” on the Indexing tab or the parameter "minimum relative intensity for peak correlations" on the Search-Match tab of the “Options” dialog.

You can run indexing either using the corresponding command from the "Tools" menu, or simply by pressing the corresponding button in the main toolbar. Depending on the current settings and situation, this will either bring up a dialog asking which indexing method (Treor or Dicvol) you would like to use, run the default indexing program, or display the table of indexing results that are already present (and from which also new calculations can be run).

Once you have run the indexing command and selected Treor as the indexing program to be used, the Treor90 parameter settings dialog will be displayed. The following parameters are available:

Crystal system(s) to be checked

You can select if you would like to investigate either triclinic or non-triclinic crystal systems. If you mark "non-triclinic", you can include or exclude cubic, tetragonal/hexagonal, orthorhombic and/or monoclinic cells.

Unit cell parameter restrictions

In this sectionm you can define maximum value for the cell lengths as well as the maximum unit cell volume.

Additional limits

You can define the minimum figure-of-merit as well as the maximum number of unindexed peaks for a solution to be accepted. Increasing the maximum number of unindexed peaks will increase the probability to get a solution (unit cell), so this may be a way out if you do not get a reasonable result with the standard settings. You should keep in mind though that you have to check afterwards why the unindexed peaks are present in your pattern (maybe they belong to an impurity phase or are just artifacts). Note that by ignoring unindexed peaks it is quite easy to get artificial unit cells that have nothing to do with reality!

Known formula weight and density

If you know the arbitrary formula weight and density of your compound, and if the expected number of molecules or formula units in the unit cell is integer, you can enter the corresponding values as well as the max. density deviation as additional criteria to restrict the cell volume and hence the search space of the program. The value for the max. density deviation should be the maximum expected density deviation plus about 5-10%. The choice of the value should also take the quality of your diffraction data into account.

Results viewing

When the calculation has finished, Treor will select the most promising indexing result (unit cell) automatically. Match! will display the result and ask you to confirm or reject this solution. You will then be taken to the indexing results dialog where you can evaluate the solutions (i.e. unit cells) that you have found up to now, inspect peak data, select crystal system and space group, and finally export the solution or add it as a new manual entry to the match list (e.g. in order to proceed with structure solution).

If you would like to take a look at the original Treor90 output file, you can do so by marking the corresponding solution in the solution list and clicking the View output button on the upper right-hand side.

Some general hints on indexing pitfalls and strategies

The following hints on indexing have been taken from the Treor documentation: