Index of /LFK/software/gsas_tools
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gsas_tools.tar.Z 14-Dec-1995 01:44 18k
gsas_tools.zip 14-Dec-1995 01:44 13k
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gsas_tools/ 07-Jun-2001 10:22 -
gsas_raw: a simple tool to build GSAS raw files
gsas_fwhm: a simple tool to extract GSAS FWHM
fixrec80: convert text files to GSAS .raw or .inst files
fixrec80.c: Unix machines
fixrec80.for: VMS machines (maybe there is a better
way to do the job of fixrec80 on VMS machines,
but this was the fastest solution for me. any
hints welcome)
read_phh.f: tool to convert EXPNAM.Phh files to ascii files
read_refnnp: tool to convert EXPNAM.REFnnP files to ascii files
The following applies to Unix machines and maybe to DOS
machines. On VMS machines I use to redirect the output by
issuing, e.g., "define/user sys$output buffer_file".
Quickly added remark:
I've just found out, that fixrec80 and fold are not really necessary.
You might want to know that:
convstod = fixrec80
convdtos = fold
Both conv* programs came with the GSAS distribution for SGI.
I don't know about the packages for other platforms.
In case of problems don't delay to contact me:
Ralf Grosse-Kunstleve: [email protected]
Using "gsas_raw":
X-ray, without ESD's:
- Setup a file which contains the counts only.
Any format is legal.
Say, the file name is "collected_data".
- Run: "gsas_raw collected_data > buffer_file"
- Edit the first two lines of "buffer_file". An
example: The header produced by gsas_raw is:
Put your Title here
BANK 1 7997 800 CONST 0.0000 0.0000 0 0 STD
Given your scan range starts at 5 deg, step with
0.02 deg, change the header to:
Exciting new material
BANK 1 7997 800 CONST 500.0000 2.0000 0 0 STD
- Run: "fixrec80 buffer_file > exciting_new_material.raw"
Done.
X-ray, with ESD's:
- Setup a file which contains pairs of counts and esd's.
Any format is legal.
- Run: "gsas_raw -ESD collected_data > buffer_file"
- Continue with the "Edit" step above.
Rutherford TOF data:
- Setup a file which contains a sequence of TOF's, counts,
and esd's.
Any format is legal.
- Run: "gsas_raw -RALF collected_data > buffer_file"
- Continue with the "Edit" step above.
Using some standard Unix tools it's easy to pre-process the
original files. E.g., given a file with 2-theta, counts on
each line, this two lines script will do the job:
#! /bin/sh
sed 's/^ *//' $1 | sed 's/ */ /g' | cut -f2 -d' ' | gsas_raw
Or for files with 2-theta, counts, esd's on each line:
#! /bin/sh
sed 's/^ *//' $1 | sed 's/ */ /g' | cut -f2-3 -d' ' | gsas_raw -ESD
Also, by using the Unix fold command it's easy to convert the
.raw files back to a standard text file, just run:
fold exciting_new_material.raw > buffer_file
Thus, there is no need to keep the buffer_file.
A caveat: There is no provision to scale the the counts and esd's.
Since I use an external tool to do this (just one more filter in
the pipeline) I don't need this feature. If there is a demand,
please let me know and I will add something like
"gsas_raw -Scale=100".
Using "gsas_fwhm":
Before you start using gsas_fwhm please notice: this tool is
limited to the "CW Profile Function 2" with this 12 refineable
parameters:
GU, GV, GW
LX, LY, trns
asym, shft, GP
stec, ptec, sfec
BUT makes use of GU, GV, GW, LX, LY, GP, stec, ptec only.
Parameters trns, asym, shft, sfec are IGNORED!
This tool works for me. And that's all I claim it's
doing. I hope, the developers of GSAS will make gsas_fwhm
obsolete one day.
At the end of your extraction or refinement, leave GSAS
and rename your .LST file temporarily. Enter GSAS again
and issue:
convdtos EXPNAM.EXP texp
Next, call "reflist" and, after choosing your histogram,
use "L" to write the hkl data to the list file.
Leave GSAS again and rename the .LST file to, e.g.,
reflist. Now you can re-rename your original .LST file.
If you want a file containing 2-theta, FWHM, run:
gsas_fwhm -ACEgr 1 1 texp reflist > fwhm.xmgr
ACEgr alias xmgr is a comprehensive freeware XY plotting
tool (ftp.ccalmr.ogi.edu). But the format is simple text
and I assume you can use any XY plotting program to
visualize the FWHM.
XTAL users who want to work with extracted Fobs may like:
gsas_fwhm -Xtal 1 1 texp reflist > addref.inp
A sample output:
: gsas_fwhm -xtal 1 1 texp reflist
: UnitCell 9.8946 9.8946 36.8715 90.000 90.000 90.000
: Lambda 0.94734
: GU GV GW 56.6 -14.0 3.6
: LX LY trns 0.888 10.282 0.00
: asym shft GP 0.0000 0.0000 0.0
: stec ptec sfec 0.00 0.00 0.00
0 0 2 2.945 0.04894 8.491+06 1.0
0 0 4 5.891 0.04888 2.105+07 1.0
1 0 2 6.229 0.04890 2.562+07 1.0
...
This is hkl, 2-theta, FWHM, Fosq, esd's are set to unity. GSAS does
not provide esd's.
If one wants to have the GSAS Fosq reduced to Fobs, the "-focus"
option might be interesting. "gsas_fwhm -focus" produces input for
an in-house program:
# gsas_fwhm -focus 1 1 texp reflist
# UnitCell 9.8946 9.8946 36.8715 90.000 90.000 90.000
# Lambda 0.94734
# GU GV GW 56.6 -14.0 3.6
# LX LY trns 0.888 10.282 0.00
# asym shft GP 0.0000 0.0000 0.0
# stec ptec sfec 0.00 0.00 0.00
0 0 2 2913.93 * 0.04894
0 0 4 4588.03 * 0.04888
1 0 2 5061.62 * 0.04890
...
This is hkl, Fobs, *, FWHM.
read_phh.f:
c
c Tool to convert EXPNAM.Phh files (histogram files)
c to ascii files
c
c usage: link or copy the EXPNAM.Phh file you want to convert
c to "gsas.Phh", then type read_phh.
c Redirection of the output is recommended.
c
c Caveat: Sometimes there are bogous records at the end
c of the file. Delete them with your editor.
c
read_refnnp.f:
c
c Tool to convert EXPNAM.REFnnP files (reflection files)
c to ascii files
c
c usage: link or copy the EXPNAM.REFnnP file you want to convert
c to "gsas.REFnnP", then type read_refnnp.
c Redirection of the output is recommended.
c
c Besides converting gsas.REFnnP to an ascii file,
c read_refnnp also writes a new direct access
c file "gsas.REFnnP_new", with all of the data
c items 9-13 (Fosq, esd_Fosq, FoTsq, Fcsq, FcTsq)
c set to 1.
c This is very useful for starting a LeBail extraction:
c - Set up the experiment file as usual
c - powpref
c - 1 cycle genles
c - copy EXPNAM.REFnnP to gsas.REFnnP
c - read_refnnp
c - copy gsas.REFnnP_new to EXPNAM.REFnnP
c - continue with genles
c This procedure is necessary after each use of
c powpref.
c
c Caveat: Sometimes there are bogous records at the end
c of the file. However, since gsas knows how many
c records to read this should not hurt.
c