[Ifeffit] Pseudo Voigt crash Athena

[Matt Newville]

Hi Craig,

On Wed, May 1, 2019 at 10:51 AM Lawley Craig Richard (PSI) <
craig.lawley at psi.ch> wrote:

> Dear Mailing list,
>
>
>
> I have run into an issue with the peak fitting section included in Athena.
> If I include a peak that is a Pseudo-Voigt and then save the project file.
> Upon trying to reopen the same project file, Athena becomes non responsive
> with the error message “PV is not yet implemented”.
>

This may sound like a broken record, but I strongly encourage you to try
Larch and the XAS Viewer application for peak fitting of XAS spectra.  The
ifeffit library is really old (has not been updated in 5 years), not
supported, and its interface to peak fitting is primitive.

Larch (and the lmfit library it uses) and the XAS Viewer GUI are all
supported. Peak-fitting of XANES is one feature which I am confident to say
is definitely better than Athena. I'm willing to take 100% of the blame for
this, but peak-fitting does not work well in Athena. XAS Viewer has more
lineshapes including both PseudoVoigt and (true!) Voigt lineshape
functions.  It also supports better mechanisms for applying mathematical
constraints and for applying bounds on parameters which can be important
for modeling XANES with multiple peaks.    lmfit/Larch also provides more
and better fit statistics, such as reporting FWHM (and its uncertainty) for
each peak, and (for XANES) the centroid of the pre-edge peaks.  Though not
supported directly in the GUI, lmfit/Larch does allow one to do a more
thorough estimate of uncertainties and to use minimization methods other
than Levenberg-Marquardt.  My experience is that these seem to be not so
important for peak-fitting of XANES data, but I don't know that this is
always the case (and to be clear, there are certain classes of "line shape
fitting" where these are important).  Like Athena, XAS Viewer records all
the code actually run making it easy to turn a GUI session into a Larch
script or Python program to do more detailed analysis or to help write
analysis scripts for batch processing.

Hope that helps,

--Matt
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