Graham N. George

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.

• 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:

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

Graham N. George

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).

Graham N. George

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.

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) dataEDG_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

>mlist /array DHOASE-K101A_014.001DHOASE-K101A_014.001 Hamster DHOase K101A variant. 8.5K----------------------------------------Label Index Array----------------------------------------rtc 1Requested Energy 2Achieved Energy 3I 0 - 2 4 - 6LYTLE 7 8 9FF 1 - 30 10 - 39ICR 1 - 30 40 - 69---------------------------------------- >

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

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 fileOptions :

• 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.