EXAFSPAK – a program suite for analysis of X-ray
absorption spectroscopic data.
Graham N. George
Graham N. George
EXAFSPAK – a portable, easy to use analysis code.
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First written in Fortran and VAX Macro-11
assembler between 1983 and 1986 to run on a
VAX VMS system.
Modern code consists of a mixture of ANSI
Fortran and C.
Simple terminal-based user interface.
Incorporated several “modern” ideas – device
independent graphics (virtual address space).
Modern version of code uses X Windows
graphics.
Designed to be quick – when interface was first
designed we counted keystrokes…
Graham N. George
EXAFSPAK Portability
Operating Systems:
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Windows
Mac OS-X
Linux
Irix
Solaris
Ultrix
HPUX
Tru-64 Unix
And others…
Graham N. George
EXAFSPAK Internals
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EXAFSPAK contains little or no third party code
(Many modern programs use code “borrowed”
from others.).
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EXAFS refinement routines use analytical
derivatives (not numerical ones).
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Makes refinement robust (usually).
Graham N. George
EXAFSPAK Curve-fitting
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Stable refinement – can refine minor EXAFS components
Nickel(II) oxide (NiO) – first-shell k-space EXAFS refinement in presence of
intense outer-shell EXAFS.
Graham N. George
EXAFSPAK programs
MLIST – list information on raw data files.
MVIEW – viewing raw data.
MCALIB – energy calibration.
MAVE – average data.
PROCESS – data reduction.
OPT – curve-fitting analysis.
Feff interface – single scattering and multiple scattering.
DATFIT – least-squares fitting near-edge (and other) data
EDG_FIT – pseudo Voigt deconvolution of near-edge spectra.
PCA – principal component analysis.
TARGET – target tranformation.
MULDAT – generalized plotting (figures etc.)
Plus a number of other more minor programs (e.g. MDEAD) for more
specialized needs.
Graham N. George
MLIST
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Flexible command line interface.
Header search functions supported.
>mlist /array DHOASE-K101A_014.001
DHOASE-K101A_014.001 Hamster DHOase K101A variant. 8.5K
---------------------------------------Label
Index
Array
---------------------------------------rtc
1
Requested Energy
2
Achieved Energy
3
I
0 - 2
4 - 6
LYTLE
7
8
9
FF
1 - 30
10 - 39
ICR
1 - 30
40 - 69
--------------------------------------->
Graham N. George
MVIEW
>mview/num=10-39/den=4 DHOASE-K101A_014.001
Graham N. George
MVIEW
>mview/num=10-39/den=4 DHOASE-K101A_014.001
Graham N. George
MVIEW
>mview /help
Usage:
mview FILES [OPTIONS]
Options:
/abscissa=<arg>
/colours=<arg>
/cursors
/denominator=<arg>
/device=<arg>
/dumb
/help
/highlight
/logfile[=<arg>]
/noline
/normalize
/numerator=<arg>
/points[=<arg>]
/recover[=<arg>]
/route=<arg>
/sumdata
/takelog
/write[=<arg>]
/xmaximum=<arg>
/xminimum=<arg>
/xwindows=<arg>
/ymaximum=<arg>
/yminimum=<arg>
Options can be denoted by "-option" or "/option"
>
Graham N. George
MCALIB
>mcalib/elem=zn/edge=k/out=dho.cal DHOASE-K101A_014.001
Graham N. George
MAVE
>mave/mcalib=dho.cal/out=dho.ave
Generates averaged data file – .ave file
Options :
• Removal and weighting of individual array positions.
• detector dead-time correction.
• independent calibration of individual scans.
Graham N. George
PROCESS
Main data reduction program.
Graham N. George
OPT – EXAFS curve-fitting.
Graham N. George
Helpful features – Keystroke files…
>process/log=firstsession.log dhoase-k101a.ave
… records every keystroke and mouse action in the specified log file.
>process/rec=firstsession.log dhoase-ds2a.ave
… replays every keystroke and mouse action in the specified log file
using a different input file (useful for performing identical analysis on
lots of data).
Scripts are available to work up large numbers of files.
Graham N. George