SDPD Internet Course
Indexing powder patterns, part 1.
Read deeply chapters 2.2 to 2.3, included, of the SDPD tutorial (CD). Another way is to access to the Kunming Workshop (CD) conference text (beginning of part 2). Some examples of indexation are given, with solutions. You should play with those data (CD: Na2C2O4, [Pd(NH3)4]Cr2O7, t-AlF3, beta-BaAlF5 and cimetidine C10H16N6S) before to try to solve the exercise given below.
Remember : indexing is more art than science. That step is frequently qualified of "bottleneck". Many people cannot even think to do invest time in something which has not a unique solution, which supposes that the compound under study is pure, that purity being uncertain, etc. If you can survive to that session of the course, you should be able to finish the whole course.
You may also consider to look at (see the full book references given at the first session of the course) :
B5 : Chapter 6 (pages 419-504). This will allow you to measure the change in indexing techniques, 25 years later.
B7 : Chapter 7 (pages 118-135). The more recent views of Per-Erik Werner (author of TREOR) about autoindexing.
Software to download
Most indexing programs use the peak positions extracted from a powder pattern. So, you need first (having recorded the powder pattern) to extract these peak positions.
Most diffractometers are delivered with their own commercial system for peak position extraction (for instance EVA with the Bruker/Siemens powder diffractometers). But you may want to try some others.
- You may find more details on some of the peak position extraction programs at the CCP14 page on that topic (CD). You may already have downloaded some of them the previous week for data conversion purpose. Those programs can even do much more.
- Indexing software may be found in several places. The most up to date versions should always be obtained from the authors themselves. However, the latest versions may also be found at some repository places. The versions below were compiled by A. Le Bail, they are distributed with Fortran sources, and TREOR and DICVOL were modified for accepting a zeropoint value.
You may have a look at the full list (CD) of indexing programs (and other programs) that were used in successful SDPD, and verify that few others are really in use, and also look at the CCP14 page on indexing (CD). Note that the Crysfire program will be used next week -so wait before using it.
Very recent approaches make use of Monte Carlo, genetic algorithm (CD: see paper in PDF), for indexing, either on the raw data or applied to extracted peak positions. The problem with this approach is calculation time which can be prohibitive in low symmetries. One simple software in this new category is :
Other useful software
- Other software that you may need at this time are those who can generate the whole list of reflections for a given cell. For instance, if you choose to add a standard compound like NAC (Na2Ca3Al2F14) to your sample, in order to calibrate, then you need the full list of the NAC reflections.
In fact, many programs can deliver such hkl list of reflections together with angular positions (for instance some Rietveld codes, etc), but you will have hyperlinks to them in a few weeks.
Space groups - systematic extinctions
Cell parameters refinement
Next week, you will have other software
to download on the same indexing topic. So that, even if you find other quite
interesting software, please wait for next week before to inform us.
Software for future use
Some software are free for non-commercial use but cannot be obtained without contacting their authors. You will need some of these softwares during the SDPD Internet Course, so that we suggest that it could be time already for trying now to obtain them. Here is the list :
We expect from you here an exact result, because a wrong one is simply false. You should produce your unique cell proposition (we do not want 200 hypothetical cells, only one).
A compound was synthesized in the NaF/CrF3 system. Although some data exist in the JCPDS-ICDD PDF-2 database, the proposed indexation seems to be wrong (verify if this is correct). Two patterns were recorded on a D8 diffractometer (CuKalpha), one with the pure sample (na5.raw, na5.uxd, na5.dat, na5.udf) and one with the sample mixed with a standard (NAC, cubic a=10.2533A, space group I213) (na5+nac.raw, na5+nac.uxd, na5+nac.dat, na5+nac.udf).
- Propose a zeropoint for both powder
patterns (to be added, so care to the sign).
The solutions must be returned by email.
Copy-paste the condensed results (should not exceed 50-100 lines for each
of the 3 indexing programs, including figures of merit and direct cell parameters,
together with the list of dobs/dcalc and 2theta-obs/calc). At this stage,
we do not ask you for more (do not give space group).
The next week will be reserved for
indexing, part 2.