EXAFSPAK

1
EXAFSPAK a program suite for analysis of X-ray
absorption spectroscopic data.
Graham N. George
2
EXAFSPAK a portable, easy to use analysis code.

• 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

3
EXAFSPAK Portability

• Operating Systems
• Windows
• Mac OS-X
• Linux
• Irix
• Solaris
• Ultrix
• HPUX
• Tru-64 Unix
• And others

4
EXAFSPAK Internals

• EXAFSPAK contains little or no third party code
  (Many modern programs use code borrowed from
  others.).
• EXAFS refinement routines use analytical
  derivatives (not numerical ones).
• Makes refinement robust (usually).

5
EXAFSPAK Curve-fitting

• Stable refinement can refine minor EXAFS
  components

Nickel(II) oxide (NiO) first-shell k-space
EXAFS refinement in presence of intense
outer-shell EXAFS.
6
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.

7
MLIST

• Flexible command line interface.
• Header search functions supported.

gtmlist /array DHOASE-K101A_014.001 DHOASE-K101A_0
14.001 Hamster DHOase K101A variant.
8.5K ---------------------------------------- Labe
l 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 ------------------------------
---------- gt
8
MVIEW
gtmview/num10-39/den4 DHOASE-K101A_014.001
9
MVIEW
gtmview/num10-39/den4 DHOASE-K101A_014.001
10
MVIEW
gtmview /help Usage mview FILES
OPTIONS Options /abscissaltarggt
/coloursltarggt /cursors /denominatorltarggt
/deviceltarggt /dumb /help /highlight
/logfileltarggt /noline /normalize
/numeratorltarggt /pointsltarggt
/recoverltarggt /routeltarggt /sumdata
/takelog /writeltarggt /xmaximumltarggt
/xminimumltarggt /xwindowsltarggt
/ymaximumltarggt /yminimumltarggt Options can be
denoted by "-option" or "/option" gt
11
MCALIB
gtmcalib/elemzn/edgek/outdho.cal
DHOASE-K101A_014.001
12
MAVE
gtmave/mcalibdho.cal/outdho.ave

• Generates averaged data file .ave file
• Options
• Removal and weighting of individual array
  positions.
• detector dead-time correction.
• independent calibration of individual scans.

13
PROCESS
Main data reduction program.
14
OPT EXAFS curve-fitting.
15
Helpful features Keystroke files
gtprocess/logfirstsession.log dhoase-k101a.ave
records every keystroke and mouse action in the
specified log file.
gtprocess/recfirstsession.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.