Obtaining and installing CRYSFIRE(free for academic usage)NOTE: A graphical program for MS-Windows that links into CRYSFIRE to help check trial cells and determine spacegroups is the Chekcell software - part of the LMGP suite for Windows by Jean Laugier and Bernard Bochu.
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Note: The following is just a single example of using CRYSFIRE. There are other methods of interacting with the program and doing the following. The assumption is that you have got your peaks / observations into a Crysfire CDT file (via some of the other tutorials). This run through will use the peak list file obtained in the Lithium Titanate Fundamental Parameters Peak Profiling Tutorial. (I.E. Grey, L. M. D. Cranswick, C. Li, L. A. Bursill, and J. L. Peng, "New Phases Formed in the Li-Ti-O System under Reducing Conditions", Journal of Solid State Chemistry, 138, 74-86 (1998)) The strategy here is INdex using all the available programs by using the IN command. By using all the programs, we will then obtain a good idea at the range of possible solutions the data will support. Hopefully one or two of those solutions will appear superior compared to the great mass of other trial cells. The following assumes you have already created a Crysfire CDT file. Example tutorials for importing data into Crysfire are:
A comment from Robin Shirley about filenames and descriptive textFrom: Robin Shirley [R.Shirley@surrey.ac.uk] Organization: Psychology Dept, Surrey Univ. U.K. To: Lachlan Cranswick [l.m.d.cranswick@dl.ac.uk] Date: Mon, 22 Jul 2002 18:43:55 GMT Incidentally, in this context, could you please emphasise in your tutorials the importance of spending the few seconds that it takes to give each new dataset a well-chosen name and some helpful brief descriptive text in its description field, seeing that whatever is used there will remain the default throughout the rest of the analysis? Careful dataset naming really is important for keeping track of progress in any serious study that can involve several dataset variants, and such distinctive names have been assumed throughout Crysfire as the basis of its data organisation. Users shouldn't rely just on having kept each problem separate within its own data directory (folder). While that's important, it's *not* sufficient, because (a) doing that only identifies the directory, not the files within it, and (b) as the study progresses, it's likely that several datasets and dataset variants will be required, for example after recalibration, applying estimated Z2theta or specimen-displacement corrections, rescaling, etc. These will all need to be kept in the same directory so that, for example, their trial cells can easily be loaded and examined (LC, M1, etc), but if they aren't given different names (and preferably also different description fields - see below) then complete confusion will quickly result. Since the description field gets appended to every summary-file solution line, an important opportunity is lost if its contents can't act as an aide memoire of the characteristics of the particular dataset or dataset variant that was used for that trial solution. This becomes particularly relevant when datasets are merged and/or rescaling/unscaling is used, as was discussed above and as is increasingly likely to happen in response to the new volume estimates and rescaling prompts in CF2002. I'm already regretting that I short-sightedly left it far too easy in WF2crys and XF2crys for users to default to an undistinctive and meaningless dataset name like Crys.cdt (I've noticed that you are yourself a frequent offender in this regard!), and I may well look at ways to prevent this in the next revisions of those programs. As things stand, it's too easy for a moment's impatience on the part of the user at this basic choice point to handicap all subsequent work on that sample with a basically null name (and description) - I really should have had the foresight to protect users from this pitfall. (A bit of a rant, perhaps, but I do think the point needs making.) With best wishes Robin |
TaupWe may as well start indexing using the Crysfire recommended sequence. Using the INdex command, select Taup (TP) and go with all the defaults. Crysfire will tell you which programs have been run already based on the present output files.
Continue on to then view the a) Taup output, b) the Crysfire summary file and c) the LePage reduced cell summary file.
Crysfire summary file so Far. - Taup
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Dicvol - high symmetry modeAfter viewing the LePage summary file, Crysfire will return to the main menu ready to index again. Using the INdex command, select Dicvol high symmetry mode (D1) and go with all the defaults. This gets around some problems with Dicvol searching out in volume shells and not terminating before reporting the highest symmetry solutions. Unless you have a lot of time, it could be best to avoid trying to using the Triclinic option in Dicvol.
In this example, Dicvol finds no high symmetry solutions, so Crysfire does not show the Crysfire summary file or Le Page output. |
ITOWhen no solutions are found, Crysfire continues on, in this case, we will run ITO.Crysfire tries to gives smart defaults. However, other people may give different hints. Based on advice from Armel Le Bail, he suggested to not use more than 25 peaks when starting out. (in this example, there are a total of 34 peaks and Crysfire will recommend we use all of these for Ito) But for more complicated samples, you may have to interact at a deeper level, entering the "possible number" of spurious peaks, etc). (If prompted, do not apply an extra two-theta offset correction as this has already been included using the self-calibration technique.) Using the INdex command, select Ito (IT) and go with all the defaults. Keep pressing [Enter] at the point Crysfire will spawn and run ITO after which it will prompt you to continue on.
Continue on to then view the ITO output, the Crysfire summary file and the LePage reduced cell summary file.
Crysfire summary file so Far. - Taup, Dicvol - high symmetry, ITO
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FJZNAgain, after viewing the LePage summary file, Crysfire will return to the main menu ready to index again. Using the INdex command, select FJZN (FJ) and go with all the defaults.
Continue on to then view the a) FJZN output, b) the Crysfire summary file and c) the LePage reduced cell summary file.
Crysfire summary file so Far. - Taup, Dicvol - high symmetry, ITO, Fjzn
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TreorAgain, after viewing the LePage summary file, Crysfire will return to the main menu ready to index again. Using the INdex command, select Treor (TR) and go with all the defaults.
Continue on to then view the a) Treor output, b) the Crysfire summary file and c) the LePage reduced cell summary file.
Crysfire summary file so Far. - Taup, Dicvol - high symmetry, ITO, Fjzn, Treor
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KohlAgain, after viewing the LePage summary file, Crysfire will return to the main menu ready to index again. Using the INdex command, select Kohl (KL) and go with all the defaults. When prompted, go for the the default of indexing all 3 systems (orthorhombic, monoclinic, triclinic)
Continue on to then view the a) Kohl output, b) the Crysfire summary file and c) the LePage reduced cell summary file.
Crysfire summary file so Far. - Taup, Dicvol - high symmetry, ITO, Fjzn, Treor, Kohl
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Dicvol - low symmetry modeAgain, after viewing the LePage summary file, Crysfire will return to the main menu ready to index again. Using the INdex command, select Dicvol (high symmetry) (D2) and go with all the defaults. (if prompted to over-write an existing Dicvol file - just type Y for yes) (Unless you have a lot of time, it could be best to avoid trying to using the Triclinic option in Dicvol - which is one of the non-default options).
Continue on to then view the a) Dicvol output, b) the Crysfire summary file and c) the LePage reduced cell summary file.
Crysfire summary file so Far. - Taup, Dicvol - high symmetry, ITO, Fjzn, Treor, Kohl, Dicvol - low symmetry
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LzonAgain, after viewing the LePage summary file, Crysfire will return to the main menu ready to index again. Using the INdex command, select Lzon (LZ) and go with all the defaults.
Continue on to then view the a) Lzon output, b) the Crysfire summary file and c) the LePage reduced cell summary file.
Crysfire summary file so Far. - Taup, Dicvol - high symmetry, ITO, Fjzn, Treor, Kohl, Dicvol - low symmetry, Lzon
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As can be seen from the following screen image, the following monoclinic cell is quite popular near
the top of the FOM (Figure of Merit):
14.0875 2.9476 4.8992 90.000 92.212 90.000 14.0876 2.9475 4.8992 90.000 92.212 90.000 14.0876 2.9475 4.8992 90.000 92.212 90.000 14.0876 2.9475 4.8992 90.000 92.212 90.000 14.0876 2.9475 4.8992 90.000 92.212 90.000 14.0876 2.9475 4.8992 90.000 92.212 90.000 14.0876 2.9475 4.8992 90.000 92.212 90.000 14.0876 2.9475 4.8992 90.000 92.212 90.000 14.0876 2.9475 4.8992 90.000 92.212 90.000 14.0876 2.9475 4.8992 90.000 92.212 90.000 14.1047 2.9511 4.9051 90.000 92.210 90.000 14.0890 2.9474 4.8988 90.000 92.209 90.000 14.0879 2.9469 4.8988 90.000 92.213 90.000 14.1050 2.9508 4.9054 90.000 92.216 90.000 14.1050 2.9508 4.9054 90.000 92.216 90.000 Thus by getting an overall view of what all the indexing programs are outputting, you can get a better idea of the possible solutions, and possibly focus in on some worth pursuing with Le Bail fitting or with Chekcell graphical indexing helper tool. A new option in Crysfire 2002 is to try and evaluate solutions is MMAP. The following gives an idea of how to make use of it. |
Analyse your resultsMMapToo evalute solutions with MMAP, first make sure you have the relevant CDT file loaded into memory (using the LO command). Then use the Load Cell command (LC) to load a trial cell into Crysfire's memory. The following screen dump gives the type of prompt you will encounter.
Tell Crysfire you wish to load a cell from the Crysfire summary file on which you will be given the Summary file list.
Select Cell the top FOM solution by typing 1. After accepting this and the various Crysfire information, you will be prompted to Display the 3 principal M1-map sections for this cell. Type Y for Yes.
Following is a MMAP Merit Map from solution 12 (a triclinic cell) it shows two main features and a verticle ridge connecting them - not a good sign of a correct solution. But examining "good" solutions like the above might show interesting MMAP landscape features that should put you on your guard.
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Crysfire Log fileCrysfire creates a Log file of all the major functions you run, opening the relevant *.LOG file will display what you did.
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Analyse your resultsNow try ChekcellNow might be a good time to pass the results over to the Chekcell graphical indexing helper tool by Jean Laugier and Bernard Bochu.
Make sure you peruse the following tutorial: Using Ton Spek's Lepage within Chekcell to find super-cells and better trial cell solutions
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