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Methods, Problems and Solutions

GSAS (General Structure Analysis System) Rietveld powder diffraction and Single Crystal software

GSAS and CYCLIC refinements/Batch mode multiple refinements on related samples

The CCP14 Homepage is at http://www.ccp14.ac.uk

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[The reference to use for GSAS in any resulting publications is: A.C. Larson and R.B. Von Dreele, "General Structure Analysis System (GSAS)", Los Alamos National Laboratory Report LAUR 86-748 (1994).]

Also Refer:

GSAS-BATCH - Duan Qiang (David) Wang

Via Rietveld Mailing List

Date: Fri, 02 Jun 2000 17:12:55 +0300
From: Alexandros Lappas [lappas@iesl.forth.gr]
X-Mailer: Mozilla 4.5 [en] (Win98; I)
To: rietveld_l@ill.fr
Subject: GSAS and CYCLIC refeinements ?

Dear all

I have collected a large number of neutron diffraction data (1650 in
total) in various temperature scans!

I would like to use GSAS to do Rietveld refinements, but it will take
for ever if I start refinining them one by one!

Has anybody got a script file (or other ?) that will work either with
the MS-DOS/Windows or Linux versions of GSAS so that I can do some kind
of CYCLIC refinements after the first temperature if fully refined?  

I know that FULLPROF has a CYCLIC mode, but for the type of magnetic
structure analysis I wish to do I trust more to use GSAS.

Thank you.


  Dr. Alexandros Lappas
  Foundation for Research and Technology-Hellas (FORTH)
  Institute of Electronic Structure and Laser (IESL)
  P.O.Box 1527
  Heraklion 711 10
  Tel:+30 81 391344, Fax:+30 81 391305, E-mail:lappas@iesl.forth.gr
Date: Fri, 2 Jun 2000 15:35:04 +0100 (BST) 
From: Jon Wright [jpw22@cus.cam.ac.uk] 
To: RIETVELD_L Distribution List [rietveld_l@ill.fr] 
Subject: Re: GSAS and CYCLIC refeinements ? 


There's something below which might help you. You'd need to set up a
refinement with a .exp file and a .raw file with the same root name (eg
fit.raw and fit.exp). The batch file then takes two arguments, the data
file name (eg run1.raw) and the root of name of the .exp file (eg. fit for
fit.exp). It just copies the appropriate data onto fit.raw and does a
powpref, genles and pubtable. I used it to follow a cell parameter as a
function of temperature. Use the 'for' command to apply this to multiple
files as explained below. See alt.msdos.batch for further info, it should
be possible to customise it to do just about whatever you want. If you
have windows NT I think you need to remove the /Y from the copy commands.

Hope this helps,


         Dept. of Chemistry, Lensfield Road, Cambridge, CB2 1EW
   Phone-Office 01223 (3)36396; Lab 01223 (3)36305; Home 01223 462024


rem - Batch file for fitting multiple gsas files
rem - Type the following to use it.....
rem - "for %1 in (scan*.raw) do call ramp %1 something"
rem - where scan*.raw is a wildcard list of filenames
rem - and  'something' is your .exp/.raw file
rem - Copy the data of interest over the data in the dummy/inital fit
copy /Y %1 %2.raw
rem - write to a list file the name of the data file (%1, which is the
rem - first argument given to ramp.bat)
echo %1 >> %2.lis
rem - Fit the data and get some results (%2, the second argument to ramp
rem - it should be the name of a .exp file) 
powpref %2
genles %2
pubtable %2
rem - use the find command to get the cell parameter from the .tbl file
find "a =" < %2.tbl >> %2.lis
rem - save the results from this fit
copy /Y %2.tbl %1.tbl

Lachlan's Lame DOS/Windows Batch Refinement Scripts for GSAS

(Mainly for mass-Unit-cell refinements)

From the readme file.

Lachlan's Lame GSAS Batch Processing Scripts for Mass Unit Cell Refinement.
  - 29th November 2003.

Lachlan M. D. Cranswick
Neutron Program for Materials Research (NPMR),
National Research Council (NRC),
  Postal Address:
    NPMR, NRC,
    Building 459, Station 18,
    Chalk River Laboratories,
    Chalk River, Ontario,
    Canada, K0J 1J0                  Fax: (613) 584-4040
Tel (work): (613) 584-8811  Office:  ext 3719 ; C2 diff: ext 3039
Email: lachlan.cranswick@nrc.gc.ca   WWW: http://neutron.nrc.ca/
Tel (home): (613) 584-4226           WWW: http://lachlan.bluehaze.com.au/
Home Email:  lachlan@melbpc.org.au  Mobile/Cell phone: 613 401 3433

These DOS/Windows batch files are optimised for peforming mass structure
based unit cell refinement, by using previous GSAS EXP file and applying
it to the next file. The scripts go inside the EXP file and substitute
in the new file name. It should be relatively easy to change them to do
other things and for other types of analysis.

Be very careful on how you use batch scripting as it is very easy to
do something dodgy that is not caught by blindly running the batch
scripts - affect of spurious peaks or impurity peaks are an example
of this.  Routine graphical spot checking at least some of the datasets
at each temperature is important.  As well as perusing the GSAS EXP
files to make sure nothing too beserk has happened.  Normally, routine
graphing up of the results will show most problems, but it will not
show all problems.

callkall.bat  (has list of gsas data files to use when running
               the kall.bat file.  These can be generated in Excel or
               another spreadsheet.  Just use a text editor such as PFE
               to replace TAB and "0." with spaces prior to running).

kall.bat      (runs GSAS using the parameters provided by callkall)
              (to work properly with "mtr" and "grep", the first thing it
               does is rename the GSAS data file to be within a 8 x 3
               filename)  mtr is used to substitute the data file name
               within the GSAS EXP file.

filter.bat    (obtain the unit cell, volume, and offset values with esds
               from the GSAS *.lst output file using Grep.  kall.bat deletes
               the lst file prior to doing a single cycle of refinement, thus
               you only have a single cycle of results in the lst file.)
              (use an editor such as PFE to get rid of surrounding text
               prior to inserting into a spreadsheet)

clean.bat     (remove some of the GSAS output files)
cleaner.bat   (remove all of the GSAS output files)

Data Collection and Refinement strategy:

One thing to consider is that 2-theta offset should be a constant for a PSD
detector as is being used here (neutron diffraction in capillary geometry).
(and if you are using a good, reproducable scanning point detector)

Thus do the refinement in two stages:

  -  Collect lots of short datasets at each temperature rather than
       a single long one.  (data can be merged on the scans where the
       sample has reached thermal equilibrium if counting stats need to
       be improved).  This will allow you to determine when the sample
       has reached thermal equilibrium by plotting the unit-cell results
       as a function of scan number.   You should do this on some initial
       expendable samples so you can find out this information in advance.

       Consider collecting both going up in temperature and down in
       temperature to make sure the data-point at each temperature at
       the same (if they are not, you have not reached thermal equilibrium -
       or some other effect is going on).  If expecting to go through a
       non-reversable phase transition, you can using the following type
       of data collection strategy:
          start at   25 C
           up to    40 C
           up to    60 C
           down to  40 C
           up to    80 C
           down to  60 C
           up to   100 C
           down to  80 C
           up to   120 C
           down to 100 C, 
           up to   140 C
           down to 120 C, etc, etc.  (you get each temperature on the up and down)

       If time is valuable and you don't want to collect at the same temperature
        twice, you can use a "hop-scotch" method.  E.g.,
         start at   25 C
           up to    60 C
           down to  40 C
           up to   100 C
           down to  80 C
           up to   140 C
           down to 120 C,
           up to   180 C
           down to 160 C, etc, etc.

  -  Refine the 2-theta offset with all the other parameters.
     Use the varience in the 2-theta offset as a function of
     temperature (or whatever you are measuring) to indicate if the
     sample is moving in the beam.  There will be some scatter due
     to correlation between 2-theta offset and unit-cell (especially
     with poor counting stats).   Be wary that big jumps in 2-theta
     could be indicating that your furnace mounts and/or sample are
     annealing and moving in the beam.

     Graphically spot-check refinements using Brian Toby's EXPGUI
      and LIVEPLOT.

  -  Using the average "2-theta offset" value for the ambient data,
      fix the 2-theta offset at this value and re-refine the data.

     Graphically spot-check refinements using Brian Toby's EXPGUI
      and LIVEPLOT.

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