Difference between revisions of "Sequential GSAS"
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===Sequential GSAS Hints=== | ===Sequential GSAS Hints=== | ||
* Data sets must be in a proper GSAS format. | |||
* The datasets must have sequential numeric file names. File names should be renamed (if necessary) before starting. An example of appropriate names would be: | |||
file0.raw, file1.raw, file2.raw, ... file11.raw, file12.raw... file100.raw | file0.raw, file1.raw, file2.raw, ... file11.raw, file12.raw... file100.raw | ||
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long files names will cause problems, for this reason, the format in the later example is recommended. | long files names will cause problems, for this reason, the format in the later example is recommended. | ||
* Give your initial (manually performed) refinement a '''short''' name like ''seq.exe'', then set up the refinement using the dataset "0.fxye" | |||
* Program is command line only, but can be accessed from the EXPGUI interface, look in the '''CALC''' menu for '''seqgsas''' and '''seqplot'''. | |||
Revision as of 01:27, 11 July 2011
Sequential GSAS
Sequential GSAS (using the programs SEQGSAS & SEQPLOT) can automatically perform multiple Rietveld refinements from a sequence of powder data sets using GSAS/EXPGUI. The first refinement must be performed manually, but subsequent related datasets can then be refined automatically. Each subsequent refinement uses the values and parameters of the previous refinement as a starting point.
As an example, this might be used to obtain refined lattice parameters (or atomic positions, particle strain, etc..) from a series of diffraction datasets collected while varying the temperature of the sample. This works well if changes between datasets are minor (i.e. no changes in symmetry etc)
SEQGSAS & SEQPLOT were written by Robert Von Dreele and added to GSAS in ~ 2005. This is no GUI (command line only), but EXPGUI has shortcuts to launch the routines. The programs are not documented in the GSAS manual; limited info can be found in the Rietveld mailing list archive.
The hints below should help get you started...
Sequential GSAS Hints
- Data sets must be in a proper GSAS format.
- The datasets must have sequential numeric file names. File names should be renamed (if necessary) before starting. An example of appropriate names would be:
file0.raw, file1.raw, file2.raw, ... file11.raw, file12.raw... file100.raw
or just
0.fxye, 1.fxye, 2.fxye, ... 11.fxye, 12.fxye... 100.fxye
long files names will cause problems, for this reason, the format in the later example is recommended.
- Give your initial (manually performed) refinement a short name like seq.exe, then set up the refinement using the dataset "0.fxye"
- Program is command line only, but can be accessed from the EXPGUI interface, look in the CALC menu for seqgsas and seqplot.
To facilitate extraction of the results the parameter name, value & esd list file print option (option "V" in L-S print option menu) should be set. SeqGSAS will copy the current EXP file changing the raw data file names for all powder histograms to the next ones in their series to a new EXP file named in numerical sequence. Two sets of POWPREF & GENLES are run by SeqGSAS to refine to this data set. It then repeats this process for the next data set; it stops when it has exhausted the sequence of raw file names.
Hints:
- Data file names must be sequential. You will likely need to rename your files before starting. (for example, this type of batch conversion can be simply done using Automater on a Mac)
- Once your refinement is 'complete'; then turn on (EXPGUI tick boxes) ONLY the parameter flag you wish to sequential refine from the subsequent data sets (e.g. lattice, LX, and atom XYZ etc...)
- Also, turn on the flags ______________ to # 256 ???????????
- Launch SEQGSAS, follow instructions
- SEQPLOT will read 1000 PVE files; limited to 200 parameters.
- Note there is an option to refine "live" data....
- makes .pve files...
- SEQPLOT, plot or export to csv file...
1. SeqPLOT has been enhanced. It now can accept alternative values for the X-axis (i.e. temperatures) and a new X-axis label. It will output an ascii file with a table of all parameters (limit 200) found with esds for all the runs processed suitable for input to some other graphics program (e.g. Excel). The plots now show error bars (1 sigma) for all values.
1. Enhancements of SEQGSAS & SEQPLOT: SEQGSAS now will read raw data files until it runs out and then ask if "there are more". This is to allow SEQGSAS to run in a live data acquisition pipeline where one does Rietveld refinement on data as it is produced in an experiment varying temperature. SEQPLOT now has an "update" mode where new PVE files are read on demand ("U" option). GENLES has been modified so that profile R values (Rp & Rpw) are put in the PVE file and the lattice parameters (a, b, c, etc.) with esds are also put in this file when varied. ASCII table output tweaked a bit to give 6 sig(?) figures; used to be 4. Raw data file names still must be in numerical sequence but no longer require any leading characters (although this is a good idea anyway) before the number (e.g. 25.dat, 26.dat, etc. is OK). Please note that SEQGSAS does not work for raw data sets that are not in "proper" GSAS format. Use CNVFILE to fix them if needed.
