Files needed: none (or results from peak fitting)
Learning outcomes: How to index a powder pattern in topas. See Alan’s j. appl. cryst. paper for details of the algorithms used.
Topas advantages: relatively robust to impurity peaks and (in my experience) has indexed everything that other routines have been able to index
1. Under the “Indexing” menu click on “Create Indexing File”.
2. Paste 2-theta and peak intensity values from the TiO2 peak fitting tutorial into the section of the file labelled (i.e. below where it says “paste here”!). If you haven’t done the peak fitting tutorial then either use the values below or read the data file into topas and use the “View/Search Peaks” facility.
27.4933274 1483.03892 36.1417160 600.374011 39.2491072 87.1466545 41.2995694 293.361291 44.0974357 111.974602 54.3775231 852.552752 56.6779687 263.740365 62.8179591 114.115219 64.0981291 125.848734 65.6797591 8.31017226 69.0535316 311.102223 69.8553749 142.043952 72.4689461 16.9511527 76.5935592 31.9086674 79.8803068 17.1994137 82.3774808 68.5855316 84.2921991 48.4586528 87.5124851 17.9694065 89.5947678 115.718833
3. Save the file as e.g. d5_05005_index_01.inp. Click the “Save/send to topas” icon. Launch topas and run the file.
4. Topas will then try and index in the crystal systems specified in the input file. It will produce a graph showing the best solutions. The whole run will take ~ 1 minute.
5. Openthe file d5_05005_index_01.ndx which contains the results in jedit. Topas will have found a huge number of possible cells with very high figures of merit (>100). It’s possible to view these various results graphically in topas. See the tutorial linked here on PbSO4. For this example it’s clear that best results are pseudo-tetragonal. Try running the input file again with all but cubic and tetragonal sytems excluded. i.e. the top of the input file should look like:
Bravais_Cubic_sgs 'Bravais_Trigonal_Hexagonal_sgs Bravais_Tetragonal_sgs 'Bravais_Orthorhombic_sgs 'Bravais_Monoclinic_sgs 'Bravais_Triclinic_sgs
6. The best cell should now be:
P42nm a=4.5946 c=2.9587
8. Beware. Topas gives a huge number of suggestions. Many of them are equivalent cells. You could use a package such as delred to investigate this. For complex systems lots of cells may “almost” fit the data. Only one of them would allow you to solve/refine the structure correctly. Indexing is one of the hardest stages of structure solution.
9. Extra work: if you’re interested in indexing then try the same sort of protocol on any of the other data sets in the school.