Re: [Ifeffit] Artemis crash upon empirical standard import.

[George Sterbinsky]

Hi Mismel,

Unfortunately, I do not have a solution, but there are some potential
workarounds. In the end, I used the log-ratio method for the analysis I was
doing, which can give the same information and is built into Athena. In the
past I have also taken the phase and amplitude functions extracted from a
standard, formatted them like the output of a FEFF file, and then imported
them into Artemis as if they were a FEFF calculation. That approach works
fine, but is a bit more effortful.

HTH,
George



On Thu, May 21, 2020 at 12:49 PM Mismel Ruiz  wrote:

> Hello George:
>
> Did you finally solved this problem? I´m having the same situation when
> trying to import an empirical standard.
>
> Thank you,
>
> Mismel.
>
>
> El lun., 13 de abr. de 2020 a la(s) 11:04, George Sterbinsky (
> georgesterbin...@u.northwestern.edu) escribió:
>
>> Hello,
>>
>> I am trying to import an empirical standard (.es file created in Athena)
>> into Artemis. Upon import, Artemis crashes. This occurs with both the
>> latest mac and windows releases (0.9.25 on mac and 0.9.26 on windows). I
>> have attached an Athena project file containing the data used to generate
>> the .es file (Co1-13C-std) and the data to be fit (Co1-57C-toFit). I have
>> also attached the .es file. Following the instructions at
>> https://bruceravel.github.io/demeter/documents/Artemis/extended/empirical.html,
>> I import Co1-57C-toFit into Artemis and the choose "import an empirical
>> standard" in the data window. When I choose the .es file from the file
>> selection dialog, Artemis crashes.
>>
>> Thank you,
>> George
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[Ifeffit] Change in fixed baseline after fit in XAS Viewer

[George Sterbinsky]

Hello,

I have observed changes in fixed parameters while running a pre-edge peak
fit in XAS Viewer. I first run a baseline fit. This provides a good match
to the data in the baseline fitting region. I would like to subtract the
baseline from the data and then numerically integrate the data. In order to
export the baseline fit and data, I fix all of the fitting parameters for
bline and bpeak and then click "fit model". This generates a baseline and
fit that no longer match the data well in the baseline fitting region.
Additionally, in the "Fit Results" window, the reported best-fit values of
the fixed parameters are slightly different from the values reported in the
"Value" field after the baseline fit, to which they were fixed. This
appears to be the result of rounding of the baseline fit parameters at some
point after the baseline fit. For example bline_slope was fixed to
"-0.0024752483" but the best-fit value is "-0.00247500". I realize I am
using XAS Viewer in a way that it was not exactly designed for, and perhaps
no one anticipated someone fixing a parameter out to 10 decimal places.
However, what I am doing still seems reasonable, and I would greatly
appreciate it if XAS Viewer could be updated so that all digits entered in
the Value field for a fixed parameter will be maintained for the fit. I am
happy to provide a project file and instructions to reproduce my
observation if they would be helpful.

Thank you,
George
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Re: [Ifeffit] unable to export xdi file in xas viewer

[George Sterbinsky]

Hi Matt,

Thanks for the explanation, I now see what you meant.

George

On Fri, May 1, 2020 at 6:28 PM Matt Newville 
wrote:

> Hi George,
>
>
> On Thu, Apr 30, 2020 at 11:39 PM George Sterbinsky <
> georgesterbin...@u.northwestern.edu> wrote:
>
>> Hi Matt,
>>
>> Thank you, it is now working for me too. In your previous email, you
>> said, "It probably should not even be trying to estimate the uncertainty in
>> the model." Why do you say that? Having the uncertainty in the fit
>> parameters, and therefore the centroid, could seemingly be useful.
>>
>>
> Sorry for the delay in answering...
>
> I think the problem you were seeing was because uncertainties in fitted
> parameters were not estimated.  Sometimes that happens, say if some
> parameter doesn't actually alter the fit or gets stuck at a boundary or
> something like that. That case is not ideal, but it should be
> acceptable - and definitely not cause problems.
>
> After a fit is done, the code tries to evaluate the uncertainties in the
> best-fit, per point `delta_fit` so that one would be able to plot bands of
> uncertainty (such as
> https://lmfit.github.io/lmfit-py/examples/documentation/model_uncertainty.html).
>  Of course, to calculate that `delta_fit`, it needs uncertainties in the
> parameters.  The error you were seeing wat that it could not do this
> calculation because, for some reason, it did not have those uncertainties.
> So, what I meant was that the code should not be trying to estimate that
> `delta_fit` if it doesn't have uncertainties in the parameters.
>
> --Matt
>
>
>
>
>
>
>
>
> George
>>
>> On Wed, Apr 29, 2020 at 12:05 PM Matt Newville <
>> newvi...@cars.uchicago.edu> wrote:
>>
>>> Hi George,
>>>
>>> Very sorry, that should have been
>>>  delta_fit = 0.0*result.best_fit
>>> It's now fixed in github master, and I verified that I could actually
>>> export a model from pre-edge peak fitting in XAS_Viewer.
>>>
>>>
>>>
>>> On Wed, Apr 29, 2020 at 10:31 AM George Sterbinsky <
>>> georgesterbin...@u.northwestern.edu> wrote:
>>>
>>>> Hi Matt and all,
>>>>
>>>> Unfortunately, after a clean install of larch following the source
>>>> installation instructions, I am not able export any fits to xdi files, and
>>>> a different error, shown below, is now printed in the terminal. Please let
>>>> me know if any additional information would be helpful in solving this
>>>> issue.
>>>>
>>>> Thank you,
>>>> George
>>>>
>>>>
>>>> Traceback (most recent call last):
>>>>   File
>>>> "/opt/anaconda3/lib/python3.7/site-packages/xraylarch-0.9.47-py3.7.egg/larch/wxxas/prepeak_panel.py",
>>>> line 366, in onExportFitResult
>>>> yerr=yerr, x=x)
>>>>   File
>>>> "/opt/anaconda3/lib/python3.7/site-packages/xraylarch-0.9.47-py3.7.egg/larch/io/export_modelresult.py",
>>>> line 59, in export_modelresult
>>>> delta_fit = 0.0*result_best_fit
>>>> NameError: name 'result_best_fit' is not defined
>>>>
>>>>
>>>>
>>>>
>>>> On Tue, Apr 21, 2020 at 9:25 AM Matt Newville <
>>>> newvi...@cars.uchicago.edu> wrote:
>>>>
>>>>> Hi George,
>>>>>
>>>>> Hm, sorry about that.  It seems to be saying that the parameter
>>>>> uncertainties weren't calculated correctly.  It probably should not even 
>>>>> be
>>>>> trying to estimate the uncertainty in the model.  I believe it should be
>>>>> fixed in git master for larch, and I'll see about looking for this in 
>>>>> lmfit
>>>>> too.
>>>>>
>>>>> On Mon, Apr 20, 2020 at 4:00 PM George Sterbinsky <
>>>>> georgesterbin...@u.northwestern.edu> wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> When attempting to export an xdi file for a pre-edge peak fit in XAS
>>>>>> viewer, the error message below prints to the terminal and the xdi file 
>>>>>> is
>>>>>> not generated. I can provide the project file and instructions for
>>>>>> generating the error message if that would be helpful.
>>>>>>
>>>>>> Thank you,
>>>>>> George
>>>>>>
>>>>>&g

Re: [Ifeffit] unable to export xdi file in xas viewer

[George Sterbinsky]

Hi Matt,

Thank you, it is now working for me too. In your previous email, you said,
"It probably should not even be trying to estimate the uncertainty in the
model." Why do you say that? Having the uncertainty in the fit parameters,
and therefore the centroid, could seemingly be useful.

George

On Wed, Apr 29, 2020 at 12:05 PM Matt Newville 
wrote:

> Hi George,
>
> Very sorry, that should have been
>  delta_fit = 0.0*result.best_fit
> It's now fixed in github master, and I verified that I could actually
> export a model from pre-edge peak fitting in XAS_Viewer.
>
>
>
> On Wed, Apr 29, 2020 at 10:31 AM George Sterbinsky <
> georgesterbin...@u.northwestern.edu> wrote:
>
>> Hi Matt and all,
>>
>> Unfortunately, after a clean install of larch following the source
>> installation instructions, I am not able export any fits to xdi files, and
>> a different error, shown below, is now printed in the terminal. Please let
>> me know if any additional information would be helpful in solving this
>> issue.
>>
>> Thank you,
>> George
>>
>>
>> Traceback (most recent call last):
>>   File
>> "/opt/anaconda3/lib/python3.7/site-packages/xraylarch-0.9.47-py3.7.egg/larch/wxxas/prepeak_panel.py",
>> line 366, in onExportFitResult
>> yerr=yerr, x=x)
>>   File
>> "/opt/anaconda3/lib/python3.7/site-packages/xraylarch-0.9.47-py3.7.egg/larch/io/export_modelresult.py",
>> line 59, in export_modelresult
>> delta_fit = 0.0*result_best_fit
>> NameError: name 'result_best_fit' is not defined
>>
>>
>>
>>
>> On Tue, Apr 21, 2020 at 9:25 AM Matt Newville 
>> wrote:
>>
>>> Hi George,
>>>
>>> Hm, sorry about that.  It seems to be saying that the parameter
>>> uncertainties weren't calculated correctly.  It probably should not even be
>>> trying to estimate the uncertainty in the model.  I believe it should be
>>> fixed in git master for larch, and I'll see about looking for this in lmfit
>>> too.
>>>
>>> On Mon, Apr 20, 2020 at 4:00 PM George Sterbinsky <
>>> georgesterbin...@u.northwestern.edu> wrote:
>>>
>>>> Hello,
>>>>
>>>> When attempting to export an xdi file for a pre-edge peak fit in XAS
>>>> viewer, the error message below prints to the terminal and the xdi file is
>>>> not generated. I can provide the project file and instructions for
>>>> generating the error message if that would be helpful.
>>>>
>>>> Thank you,
>>>> George
>>>>
>>>>
>>>> Traceback (most recent call last):
>>>>   File
>>>> "/anaconda3/lib/python3.7/site-packages/larch/wxxas/prepeak_panel.py", line
>>>> 369, in onExportFitResult
>>>> yerr=yerr, x=x)
>>>>   File
>>>> "/anaconda3/lib/python3.7/site-packages/larch/io/export_modelresult.py",
>>>> line 60, in export_modelresult
>>>> delta_fit = result.eval_uncertainty(result.params, **kwargs)
>>>>   File "/anaconda3/lib/python3.7/site-packages/lmfit/model.py", line
>>>> 1488, in eval_uncertainty
>>>> dval = pars[pname].stderr/3.0
>>>> TypeError: unsupported operand type(s) for /: 'NoneType' and 'float'
>>>> ___
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>>>
>>>
>>> --
>>> --Matt Newville  630-252-0431
>>> ___
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>
>
> --
> --Matt Newville  630-252-0431
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Re: [Ifeffit] unable to export xdi file in xas viewer

[George Sterbinsky]

Hi Matt and all,

Unfortunately, after a clean install of larch following the source
installation instructions, I am not able export any fits to xdi files, and
a different error, shown below, is now printed in the terminal. Please let
me know if any additional information would be helpful in solving this
issue.

Thank you,
George


Traceback (most recent call last):
  File
"/opt/anaconda3/lib/python3.7/site-packages/xraylarch-0.9.47-py3.7.egg/larch/wxxas/prepeak_panel.py",
line 366, in onExportFitResult
yerr=yerr, x=x)
  File
"/opt/anaconda3/lib/python3.7/site-packages/xraylarch-0.9.47-py3.7.egg/larch/io/export_modelresult.py",
line 59, in export_modelresult
delta_fit = 0.0*result_best_fit
NameError: name 'result_best_fit' is not defined




On Tue, Apr 21, 2020 at 9:25 AM Matt Newville 
wrote:

> Hi George,
>
> Hm, sorry about that.  It seems to be saying that the parameter
> uncertainties weren't calculated correctly.  It probably should not even be
> trying to estimate the uncertainty in the model.  I believe it should be
> fixed in git master for larch, and I'll see about looking for this in lmfit
> too.
>
> On Mon, Apr 20, 2020 at 4:00 PM George Sterbinsky <
> georgesterbin...@u.northwestern.edu> wrote:
>
>> Hello,
>>
>> When attempting to export an xdi file for a pre-edge peak fit in XAS
>> viewer, the error message below prints to the terminal and the xdi file is
>> not generated. I can provide the project file and instructions for
>> generating the error message if that would be helpful.
>>
>> Thank you,
>> George
>>
>>
>> Traceback (most recent call last):
>>   File
>> "/anaconda3/lib/python3.7/site-packages/larch/wxxas/prepeak_panel.py", line
>> 369, in onExportFitResult
>> yerr=yerr, x=x)
>>   File
>> "/anaconda3/lib/python3.7/site-packages/larch/io/export_modelresult.py",
>> line 60, in export_modelresult
>> delta_fit = result.eval_uncertainty(result.params, **kwargs)
>>   File "/anaconda3/lib/python3.7/site-packages/lmfit/model.py", line
>> 1488, in eval_uncertainty
>> dval = pars[pname].stderr/3.0
>> TypeError: unsupported operand type(s) for /: 'NoneType' and 'float'
>> ___
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>
>
> --
> --Matt Newville  630-252-0431
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[Ifeffit] unable to export xdi file in xas viewer

[George Sterbinsky]

Hello,

When attempting to export an xdi file for a pre-edge peak fit in XAS
viewer, the error message below prints to the terminal and the xdi file is
not generated. I can provide the project file and instructions for
generating the error message if that would be helpful.

Thank you,
George


Traceback (most recent call last):
  File
"/anaconda3/lib/python3.7/site-packages/larch/wxxas/prepeak_panel.py", line
369, in onExportFitResult
yerr=yerr, x=x)
  File
"/anaconda3/lib/python3.7/site-packages/larch/io/export_modelresult.py",
line 60, in export_modelresult
delta_fit = result.eval_uncertainty(result.params, **kwargs)
  File "/anaconda3/lib/python3.7/site-packages/lmfit/model.py", line 1488,
in eval_uncertainty
dval = pars[pname].stderr/3.0
TypeError: unsupported operand type(s) for /: 'NoneType' and 'float'
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Re: [Ifeffit] Larch 0.9.47

[George Sterbinsky]

Hi Matt,

Thanks, that worked. I got an error that said something about 'asteval' on
my first try, so I also deleted that package.

George

On Sat, Apr 18, 2020 at 11:24 AM Matt Newville 
wrote:

> Hi George,
>
> Sorry for the trouble.  I think a fresh install is not the only option,
> but it might be the simplest ;).  It seems there were some challenges with
> using conda to update, including that it sometimes just seems to take
> forever.   I'm not sure what to do about that.
>
> I think pip install should work, but you may need to manually blow away
> some of the installed folders in "python3.7/site-packages", as there can be
> confusion about where the newly installed packages go based on the
> installation method (that this, there might be a folder called 'larch' and
> there might be one called 'xraylarch-0.9.45-py3.7.egg', and similarly for
> other packages.   You could just blow away (a partial list, and maybe not
> exhaustive, but ones that I know were changed between 0.9.45. and 0.947 and
> potentially causing confusion), these folders under
> python3.7/site-packages/  in your installation:
>larch
>xraylarch*
>pyepics*
>epics
>pyshortcuts*
>wxmplot*
>lmfit*
>silx*
>uncertainties*
>
> Then a fresh `pip install xraylarch` should work.  If you try that and
> still run into problems, please let me know what you see.
>
> --Matt
>
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Re: [Ifeffit] Larch 0.9.47

[George Sterbinsky]

Hi All,

I am trying to upgrade larch from 0.9.45. Neither "conda update --all" nor
"pip install xraylarch" are updating to 0.9.47. Is a complete reinstall of
anaconda my only option?

Thank you,
George

On Tue, Mar 3, 2020 at 11:22 AM Matt Newville 
wrote:

> Hi Garret,
>
>
> On Tue, Mar 3, 2020 at 8:01 AM Garret Bland  wrote:
>
>> Hi All,
>> I tried to reinstall anaconda (Windows 10) and create a new environment
>> to install the newest version of larch. It gave me the following error:
>>
>> conda install -yc GSECARS xraylarch
>> Collecting package metadata (current_repodata.json): done
>> Solving environment: failed with initial frozen solve. Retrying with
>> flexible solve.
>> Solving environment: failed with repodata from current_repodata.json,
>> will retry with next repodata source.
>> Collecting package metadata (repodata.json): done
>> Solving environment: failed with initial frozen solve. Retrying with
>> flexible solve.
>> Solving environment: -
>> Found conflicts! Looking for incompatible packages.
>> This can take several minutes.  Press CTRL-C to abort.
>> failed
>>
>
> Sorry for the trouble.  It seems like updating from a previous release is
> not working as well as I hoped.  I'm not sure what that error *really*
> means, but I have also seen some Anaconda environments be either very, very
> slow to "solve environment" or fail when I'm pretty sure it really should
> succeed.
>
> Slightly conda-specific, but: It should definitely be the case that doing
> an "conda update --all" or making a completely new environment and
> installing into that should work too.  I'm reluctant to expect most users
> to have to install / update with conda, but I also think it should work.
>
>>
>> I then installed pip on my virtual environment and used pip install
>> xraylarch. That seemed to work for me.
>>
>
> OK, yes.  For the Python-enabled users, `pip install xraylarch` should
> work for most work (including all the XAFS functionality).  It will not
> install some optional packages (notably tomopy), but that should be OK
> unless you're doing fluorescence tomography.
>
> Just for completeness and to prove that all three systems have their own
> challenges, `pip install xraylarch` will work on Windows and MacOS, but
> will work on Linux only if wxPython has already somehow been installed.  A
> binary package is not available for "Linux" and compiling from source on
> Linux is not trivial (these two things are related).
>
> Anyway, I'm glad to hear you've got something working.
>
> --Matt
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[Ifeffit] Artemis crash upon empirical standard import.

[George Sterbinsky]

Hello,

I am trying to import an empirical standard (.es file created in Athena)
into Artemis. Upon import, Artemis crashes. This occurs with both the
latest mac and windows releases (0.9.25 on mac and 0.9.26 on windows). I
have attached an Athena project file containing the data used to generate
the .es file (Co1-13C-std) and the data to be fit (Co1-57C-toFit). I have
also attached the .es file. Following the instructions at
https://bruceravel.github.io/demeter/documents/Artemis/extended/empirical.html,
I import Co1-57C-toFit into Artemis and the choose "import an empirical
standard" in the data window. When I choose the .es file from the file
selection dialog, Artemis crashes.

Thank you,
George


Co1-13C.es
Description: Binary data


Co1-exafs-2T.prj
Description: Binary data
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Re: [Ifeffit] errors in bond lengths

[George Sterbinsky]

Matthew, Matt, and Anatoly,

Thanks for your replies and some good suggestions. You have convinced me
that the best thing for me to do here is to try multiple analysis methods
and see how well the results, and uncertainties, compare, as was done in
the previously referenced PRL.

Thanks again,
George

On Sun, Apr 12, 2020 at 11:45 PM Matthew Marcus  wrote:

> Something I've done for analyzing DWF on data taken at several
> temperatures is what I called 'consensus amplitude' fitting.  Here, I
> fitted shells to
> k^n*chi[i](k) = exp(-2 dsig2[i] k^2) A(k) sin(phi(k)+2 dr[i]k)
>
> where i is the index to temperature, and the fit parameters are A(k),
> phi(k), dr[i] and dsig2[i].  The obvious ambiguity is solved by
> arbitrarily picking one i, say i=0, to have dsig2[0]=0 and dr[0]=0.
> This was done iteratively, starting with A and phi obtained by
> back-transforming the filtered shells.  You can do this with multiple
> shells.  In at least one case, this helped me separate two shells by
> their differing temperature dependence.
>
> Doing this treats the data 'democratically', not taking one of the
> spectra as a reference to which all others are fit.  Also, it doesn't
> overemphasis the low-amplitude parts of the signal, which the log-ratio
> method could do.
>
> Refs: M. A. Marcus, M. P. Andrews, J. Zegenhagen, A. S. Bommannavar, P.
> Montano, "Structure and vibrations of chemically produced Au55 clusters",
> PRB 42,3312 (1990)
>
> M. Marcus (that was before I started using my middle initial), "Siting
> and dynamics of Cu impurity in Ti lattice", Solid State Commun. 38, 251
> (1981)
>
> Not a lot of detail in those papers, I'm afraid.  I did do more with
> this method way back when, but it doesn't seem to have made its way into
> the literature.   Back then, I was so naive that I considered a
> conference proceeding to be as good as a PRL, so lost a lot of impact.
>
> mam
>
> On 4/12/2020 8:15 PM, Matt Newville wrote:
> > Hi George,
> >
> > I think this will not be a different answer from Matthew's or Anatoly's
> > answers, but just reiterate their points.  The Purans et al 2008 PRL
> > from 2008 appears to use both non-linear fitting with Feff and EDA
> > (which should give basically the same results as Artemis/Ifeffit/Larch,
> > though I do not know in detail what error analysis is done), and the
> > log-ratio method.  I think they also fit the resulting sigma2 (derived
> > from the non-linear fit) to an Einstein model.
> >
> > The log-ratio method can only determine relative changes in distance,
> > coordination number, and sigma2.  The main motivation for using this
> > method is that scattering factors in the EXAFS equation will cancel out
> > (or mostly cancel out) when comparing two similar experimental spectra.
> > In addition, it is often argued that data extraction errors (energy
> > scale, background subtraction, etc) would tend to be the same for two
> > experimental spectra and so would also mostly cancel out.  There usually
> > isn't much analysis of what residual systematic errors happen with the
> > log-ratio method.   The working idea is that the ratio of the log of
> > isolated single-shell EXAFS chi(k) (or what we would call chi(q) in
> > Artemis/Ifeffit/Larch)  amplitudes vs k**2 should be linear (intercept =
> > Delta N, slope=Delta sigma2) and the phase difference vs k should also
> > be linear (intercept=0 if E0 is truly unchanged, and slope = Delta R).
> >   For anyone who actually plots those (even for spectra on the same
> > sample), you will probably find that these are "linear-ish", clearly
> > showing both "yeah, that could work" and also "maybe not perfectly".
> >
> > But, if I'm reading this PRL correctly, it looks like they use the
> > log-ratio method to compare sigma2 and R of spectra at the same
> > temperature but with different isotopes. That does seem like a fine way
> > to better determine the subtle differences between those spectra.
> >
> > --Matt
> >
> >
> > On Sat, Apr 11, 2020 at 12:41 PM George Sterbinsky
> >  > <mailto:georgesterbin...@u.northwestern.edu>> wrote:
> >
> > Hello,
> >
> > As is well known, EXAFS is more accurate at determining relative
> > changes in bond lengths than absolute changes in bond lengths due to
> > cancelation of systematic errors in relative comparisons. When
> > comparing the relative changes in bond lengths determined from EXAFS
> > fits, as one might for a temperature series for example, is it
> > appropriate to use the uncertainties returned by Artemis?
> >

[Ifeffit] errors in bond lengths

[George Sterbinsky]

Hello,

As is well known, EXAFS is more accurate at determining relative changes in
bond lengths than absolute changes in bond lengths due to cancelation of
systematic errors in relative comparisons. When comparing the relative
changes in bond lengths determined from EXAFS fits, as one might for a
temperature series for example, is it appropriate to use the uncertainties
returned by Artemis?

My question arises in part from Phys Rev Lett vol. 100 pg. 055901 (2008),
where the authors state that errors for changes in bond length in a
temperature series were determined by empirical means rather than
statistical means. This then raises the question as to if the authors
believe that statistical means would overestimate the error. My inclination
is to think that the uncertainties reported by Artemis would be appropriate
because of the scaling by the square root of reduced chi squared. However,
I want to see what others think about this before committing to it.

Thank you,
George
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[Ifeffit] Fe 4+ reference

[George Sterbinsky]

Hello,

Does anyone have Fe K-edge XANES from an Fe4+ reference or sample (for
example SrFeO3) that they can share?

Thank you,
George
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Re: [Ifeffit] color of fonts in demeter

[George Sterbinsky]

Hi Ricardo,

Are you using dark mode? If you turn it off, does that fix the problem?

George

On Mon, Jan 27, 2020 at 9:36 AM Ricardo Faccio  wrote:

> Dear all
>
> After installing Demeter in MacOS I am having some problems related to
> the color of fonts and background. Since they look identical is diffcult
> to see and read.
>
> How could be possible to change the color of fonts?
>
> I am attaching an example.
>
> Best regards
>
> Ricardo
>
> --
> -
>Dr. Ricardo Faccio
>Prof. Agregado de Física (Assoc. Prof.)
>Mail: Área Física, DETEMA, Facultad de Química,
>Universidad de la República
> Av. Gral. Flores 2124, C.C. 1157
> C.P. 11800, Montevideo, Uruguay.
>E-mail: rfac...@fq.edu.uy
>Phone: (+598) 2924 9859
>   (+598) 2929 0648
>Fax:   (+598) 2924 1906
>Web:  http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
>
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Re: [Ifeffit] Installation problems on MacOS catalina, macports

[George Sterbinsky]

Thanks for following up Ricardo. I find the same issue when doing a fresh
install of macports and demeter on MacOS Mojave (10.14.6), so it seems the
issue is not unique to Catalina.

George



On Sat, Jan 25, 2020 at 12:23 PM Ricardo Faccio  wrote:

> Dear all
>
> This is just a comment how to suceed installing demeter from a fresh
> installation in MacOS Catalina.
>
> After doing:
>
> sudo port install xorg-server demeter
>
> the perl5 install seems to be not activated nor correctly installed, so
> just type:
>
> sudo port install perl5
>
> If everything is going ok, maybe some other error could apper, such as the
> previously commented and resolved issue on the list.
>
>
> https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06698.html
>
> Best regards
>
> Ricardo
>
> El 7/1/20 a las 19:23, Ravel, Bruce escribió:
>
> Dear all
> I followed al the instructions in 
> https://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.html.In
>  principle, I got a clean installation without errors.
>
> But when running athena I get:
>
> MacBook-Pro-de-Ricardo:~ rfaccio$ athenaCan't locate Demeter/Here.pm in @INC 
> (you may need to install the Demeter::Here module) (@INC contains: 
> /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 
> /Network/Library/Perl/5.18/darwin-thread-multi-2level 
> /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.4 
> /System/Library/Perl/5.18/darwin-thread-multi-2level 
> /System/Library/Perl/5.18 
> /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level 
> /System/Library/Perl/Extras/5.18 .) at /opt/local/bin/athena line 7.BEGIN 
> failed--compilation aborted at /opt/local/bin/athena line 7.
>
>
> Any hint will be appreciated.
>
> Best regards
>
> Ricardo
>
>
> --
> -
>   Dr. Ricardo Faccio
>   Prof. Agregado de Física (Assoc. Prof.)
>   Mail: Área Física, DETEMA, Facultad de Química,
>   Universidad de la República
>Av. Gral. Flores 2124, C.C. 1157
>C.P. 11800, Montevideo, Uruguay.
>   E-mail: rfac...@fq.edu.uy
>   Phone: (+598) 2924 9859
>  (+598) 2929 0648
>   Fax:   (+598) 2924 1906
>   Web:  http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
>
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Re: [Ifeffit] Hephaestus ion chamber absorption

[George Sterbinsky]

Thank you Matt.

George

On Mon, May 29, 2017 at 10:02 PM, Matt Newville <newvi...@cars.uchicago.edu>
wrote:

> Hi George,
>
> On Mon, May 29, 2017 at 5:57 PM, George Sterbinsky <GeorgeSterbinsky@u.
> northwestern.edu> wrote:
>
>> Hello,
>>
>> Can anyone explain why the values given by the ion chamber utility in
>> Hephaestus differ from those given for a 10 cm He filled ion chamber in
>> figure 3.14 of Grant Bunker's Intro to XAFS book at high energy? For
>> instance, figure 3.14 indicates an absorption fraction of ~3E-7 at 40 keV,
>> whereas Hephaestus indicates 2E-4 at the same energy.
>>
>>
> I believe the difference is probably in whether one considers only the
> photo-electric cross-section or also includes the incoherent  and coherent
> scattering.   For very light elements at high enough energy, the incoherent
> scattering becomes much more likely than the photo-electric absorption,
>
> Using the Elam et al tables, give (with mu in cm^2/gr):
>
> larch> mu_elam('He', 4.0, kind='total')
> 0.1763091369476893
> larch> mu_elam('He', 4.0, kind='photo')
> 0.00025649564143021724
>
> The question then becomes how are you using this value.   To estimate what
> fraction of the 40 keV X-ray intensity will exit a 10 cm ion chamber filled
> with He, use the total attenuation.  But to estimate the photo-current
> generated in the ion chamber from that beam, I think you should use the
> photo-electric cross-section only.
>
> Hope that helps, or that someone else has better insight,
>
> --Matt
>
>
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[Ifeffit] Hephaestus ion chamber absorption

[George Sterbinsky]

Hello,

Can anyone explain why the values given by the ion chamber utility in
Hephaestus differ from those given for a 10 cm He filled ion chamber in
figure 3.14 of Grant Bunker's Intro to XAFS book at high energy? For
instance, figure 3.14 indicates an absorption fraction of ~3E-7 at 40 keV,
whereas Hephaestus indicates 2E-4 at the same energy.

Thank you,
George
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Re: [Ifeffit] error when fitting in Artemis

[George Sterbinsky]

Hi Robert and Bruce,

Thank you for your replies and, Robert, for providing a work-around. I too
apologize for taking so long to respond. I was hoping to investigate the
problem a bit further as to provide a more actionable bug report before
responding to Robert, but in light of Bruce's message that no longer seems
as necessary. I also do not see a "phase.bin" file on my computer, and I do
see "0_Warning.txt". I will try to figure out when, in the history of the
file, it became damaged and report back to the list if that information
will help others prevent the problem or indicates a fix.

Thanks again,
George



On Wed, Jan 4, 2017 at 10:05 AM, Bruce Ravel <bra...@bnl.gov> wrote:

> On 12/22/2016 12:11 PM, George Sterbinsky wrote:
>
>> I have attached an Artemis project. Upon opening the project, and
>> clicking the fit button the error in the attached log file is generated
>> and the fit is not run. Looking at the history, fits have been run
>> previously without error. The error message indicates Feff may need to
>> be run again, but upon opening the Atoms and Feff window and then
>> clicking on the Feff tab, I see the Run Feff button is grey and cannot
>> be clicked. What steps are necessary in order to run a fit?
>>
>
> Hi George,
>
> Sorry it has taken so long to respond.  Partly holidays, partly that I
> have been doing a bunch of work on Demeter that needed to get finished.
>
> So, the problem here does not seem to be a problem with Artemis.  It seems
> to be an issue with someone's antivirus software.
>
> The artemis.fpj is simply a zip file with a different file extension.
> Opening it up, one finds a folder called "feff".  In the case of your
> project file, the relevant subfolder is "azxqc" (that's a randomly
> generated 5-character string, which is how Demeter names most things
> internally).  In that folder, there should be a "phase.bin" file from the
> Feff run.  It's absent.  Instead, I see a file called "0_Warning.txt", the
> contents of which read:
>
> BLOCKED FILE ALERT
>
> A file has been blocked due to the 'Blocked for exchange' rule.
> Context: 'phase.bin'
> Disallowed due to
> Ticket Number: '09e8-5852-0da2-0001'
> See your system administrator for further information. Copyright 1999-2013
> McAfee, Inc.All Rights Reserved.http://www.mcafee.com
>
> Now, I do not know if this happened when you mailed the project file to
> the list or if it happened at some other time.  While the error message is
> certainly misleading in this case, I think that it is Artemis' way of
> complaining about the missing phase.bin file.
>
> Perhaps there is some other problem at play.  I don't know.  But I cannot
> possibly troubleshoot that other problem given that an anti-virus package
> has, at some point, irretrievably damaged this project file.
>
> I think that the only plausible work-around is Robert's suggestion.
> Reimport the feff.inp file, rerun Feff, exclude the existing path,
> drag-and-drop the replacement path, then push path parameter values from
> the old path to the new one.  Awkward, but I don't know what else to
> suggest.
>
> B
>
> PS: If anyone has any kind of working knowledge of McAfee or any other AV
> software, I would be open to a suggestion for how to fix this.  Is it a
> file /name/ problem -- should phase.bin be called something else?  Is there
> something in the phase.bin file that triggered McAfee?  Any wisdom would be
> welcome.
>
>
> --
>  Bruce Ravel   bra...@bnl.gov
>
>  National Institute of Standards and Technology
>  Synchrotron Science Group at NSLS-II
>  Building 743, Room 114
>  Upton NY, 11973
>
>  Homepage:http://bruceravel.github.io/home/
>  Software:https://github.com/bruceravel
>  Demeter: http://bruceravel.github.io/demeter/
>
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[Ifeffit] Artemis crash on import

[George Sterbinsky]

Hello,

I am using Demeter on Mac OS X 10.11.6. I recently updated Demeter to
version 0.9.25 using the command "sudo port upgrade demeter". In Artemis,
choosing the menu item "open project or data" causes Artemis to crash. I've
pasted the information printed to the terminal below. This includes
everything printed to the terminal from the point at which Artemis was
started. Please let me know if any additional information would help in
resolving this issue.

Thank you,
George


$ Artemis
2016-10-13 14:51:18.097 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data

gnuplot: unable to open display
'/private/tmp/com.apple.launchd.U9mQNzlNS1/org.macosforge.xquartz:0'
gnuplot: X11 aborted.
2016-10-13 14:51:22.884 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:23.096 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:23.097 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:23.443 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:23.443 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:25.277 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:25.278 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:26.809 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:26.809 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:27.278 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:27.278 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:28.221 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:28.221 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:28.555 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:28.555 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:34.322 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:51:34.322 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:52:30.445 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:52:30.446 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:52:32.009 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:52:32.009 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:52:34.926 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:52:34.926 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:52:35.148 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:52:35.148 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:52:38.016 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global
data
2016-10-13 14:52:38.017 perl5.24[20180:991862] CFPasteboardRef
CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to 

Re: [Ifeffit] Athena crash on mac on import

[George Sterbinsky]

Bruce,

I could not find that particular bit of code in the file. Instead I added
the line you suggested (delete $r_attributes->{bkg_funnorm};) at the end of
this block of code (lines 1488 to 1496)

foreach my $d (@$r_data) {

#print ">>>>>>> $d\n";

my $yaml = ($args{file}) ? $zip->contents("$d.yaml")

: $self->slurp(File::Spec->catfile($args{folder}, "$d.yaml"));

my ($r_attributes, $r_x, $r_y) = YAML::Tiny::Load($yaml);

## the current implementation of XDI support has the xdifile attribute
read-only if Xray::XDI is not available

delete $r_attributes->{xdifile} if (not $INC{'Xray/XDI.pm'});

delete $r_attributes->{fit_pcpath}; # correct an early

delete $r_attributes->{fit_do_pcpath}; # design mistake...

delete $r_attributes->{bkg_funnorm};


and this block (lines 1230 to 1239)

foreach my $which ('', '_standard') {

my $yaml = ($args{file}) ? $zip->contents("$d$which.yaml")

: $self->slurp(File::Spec->catfile($args{folder}, "$d$which.yaml"));

my ($r_attributes, $r_x, $r_y) = YAML::Tiny::Load($yaml);


## the current implementation of XDI support has the xdifile attribute
read-only if Xray::XDI is not available

delete $r_attributes->{xdifile} if (not $INC{'Xray/XDI.pm'});


delete $r_attributes->{fit_pcpath}; # correct an early

delete $r_attributes->{fit_do_pcpath}; # design mistake...

delete $r_attributes->{bkg_funnorm};


I am now able to open the project file without crashing Artemis.

Thank you again for your help.

George

On Fri, Jul 8, 2016 at 8:36 AM, Bruce Ravel <bra...@bnl.gov> wrote:

>
> George,
>
> You can do a similar work-around as before.  In
> /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/Fit.pm,
> near line 1263 (as the traceback indicates) you will find this:
>
>   ## correct for change in energy-dependent normalization
>   delete $r_attributes->{bkg_fnorm};
>
> add
>
>   delete $r_attributes->{bkg_funnorm};
>
>
> B
>
>
>
>
> On 07/05/2016 02:57 PM, George Sterbinsky wrote:
>
>> Bruce,
>>
>> I am seeing a similar issue with Artemis. Upon trying to open a .fpj
>> file created elsewhere, Artemis crashes and the following message is
>> printed to the terminal. Any suggestions as to a possible fix? I have
>> not attached the file since it is not mine to share, but if you need it
>> or anything else please let me know.
>>
>> Thank you,
>> George
>>
>>
>> [!!!] bkg_funnorm is not an attribute to set for
>> Demeter::Data=HASH(0x7fdb97cd4810) at
>>
>> /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/MooseX/SetGet.pm
>> line 9.
>>  MooseX::SetGet::set(Demeter::Data=HASH(0x7fdb97cd4810), "bkg_pre1",
>> -205, "multiplier", 1, "energy_string", "", "name", "merge 4", ...)
>> called at
>>
>> /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/Fit.pm
>> line 1263
>>  Demeter::Fit::grab(Demeter::Fit=HASH(0x7fdb79280ba0), "folder",
>> "/Users/.../.horae/stash/_dem_nsqtbpqj/fits/iaple", "regenerate", 0)
>> called at
>>
>> /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Artemis/Project.pm
>> line 397
>>  Demeter::UI::Artemis::Project::read_project(HASH(0x7fdb93be5ff0))
>> called at
>>
>> /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Artemis.pm
>> line 990
>>  Demeter::UI::Artemis::OnMenuClick(Wx::Frame=HASH(0x7fdb96c547c0),
>> Wx::CommandEvent=SCALAR(0x7fdb96c576a0)) called at
>>
>> /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Artemis.pm
>> line 434
>>  Demeter::UI::Artemis::__ANON__(Wx::Frame=HASH(0x7fdb96c547c0),
>> Wx::CommandEvent=SCALAR(0x7fdb96c576a0)) called at
>> /opt/local/bin/Artemis line 47
>>  eval {...} called at /opt/local/bin/Artemis line 47
>>
>> On Fri, Jul 1, 2016 at 4:26 PM, Bruce Ravel <bra...@bnl.gov
>> <mailto:bra...@bnl.gov>> wrote:
>>
>>
>> That was the right thing to do.  Glad it worked.
>>
>> B
>>
>> On 07/01/2016 04:19 PM, George Sterbinsky wrote:
>>
>> Hi Bruce,
>>
>> Thanks for providing a fix. The Prj.pm file on my system does
>> not look
>> exactly like what you describe. Lines 260 to 268 looked like this:
>>
>> next if any { $k eq $_ } qw(
>>
>> bindtag deg_tol denominator detectors
>>
>> en_str file frozen line mu_st

Re: [Ifeffit] Athena crash on mac on import

[George Sterbinsky]

Bruce,

I am seeing a similar issue with Artemis. Upon trying to open a .fpj file
created elsewhere, Artemis crashes and the following message is printed to
the terminal. Any suggestions as to a possible fix? I have not attached the
file since it is not mine to share, but if you need it or anything else
please let me know.

Thank you,
George


[!!!] bkg_funnorm is not an attribute to set for
Demeter::Data=HASH(0x7fdb97cd4810) at
/opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/MooseX/SetGet.pm
line 9.
MooseX::SetGet::set(Demeter::Data=HASH(0x7fdb97cd4810), "bkg_pre1",
-205, "multiplier", 1, "energy_string", "", "name", "merge 4", ...) called
at
/opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/Fit.pm
line 1263
Demeter::Fit::grab(Demeter::Fit=HASH(0x7fdb79280ba0), "folder",
"/Users/.../.horae/stash/_dem_nsqtbpqj/fits/iaple", "regenerate", 0) called
at
/opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Artemis/Project.pm
line 397
Demeter::UI::Artemis::Project::read_project(HASH(0x7fdb93be5ff0))
called at
/opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Artemis.pm
line 990
Demeter::UI::Artemis::OnMenuClick(Wx::Frame=HASH(0x7fdb96c547c0),
Wx::CommandEvent=SCALAR(0x7fdb96c576a0)) called at
/opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Artemis.pm
line 434
Demeter::UI::Artemis::__ANON__(Wx::Frame=HASH(0x7fdb96c547c0),
Wx::CommandEvent=SCALAR(0x7fdb96c576a0)) called at /opt/local/bin/Artemis
line 47
eval {...} called at /opt/local/bin/Artemis line 47

On Fri, Jul 1, 2016 at 4:26 PM, Bruce Ravel <bra...@bnl.gov> wrote:

>
> That was the right thing to do.  Glad it worked.
>
> B
>
> On 07/01/2016 04:19 PM, George Sterbinsky wrote:
>
>> Hi Bruce,
>>
>> Thanks for providing a fix. The Prj.pm file on my system does not look
>> exactly like what you describe. Lines 260 to 268 looked like this:
>>
>> next if any { $k eq $_ } qw(
>>
>> bindtag deg_tol denominator detectors
>>
>> en_str file frozen line mu_str
>>
>> numerator old_group original_label
>>
>> peak refsame not_data
>>
>> bkg_switch bkg_switch2
>>
>> is_xmu is_chi is_xanes is_xmudat
>>
>> bkg_stan_lab bkg_flatten_was
>>
>> );
>>
>>
>> After line 267, I added a new line that reads "bkg_fnorm bkg_funnorm" as
>> you suggested, and now I am able to open the prj file.
>>
>> Thanks again,
>> George
>>
>>
>>
>> On Fri, Jul 1, 2016 at 3:17 PM, Bruce Ravel <bra...@bnl.gov
>> <mailto:bra...@bnl.gov>> wrote:
>>
>> On 07/01/2016 03:00 PM, Bruce Ravel wrote:
>>
>> There is probably a simple-ish work-around.  Let me think about
>> it and
>> I'll get back to you.
>>
>>
>> There's not a way to simply fix this that does not involve you
>> upgrading Demeter.  However, if you don't mind a bit of hands on
>> effort, try this:
>>
>>   * Open the file
>>
>> /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/Data/Prj.pm
>> in a text editor (not Word!).
>>
>>   * Go to line 308.  Here's what the surrounding lines lines look
>> like:
>>
>>  next if any { $k eq $_ } qw(
>>   bindtag deg_tol denominator
>> detectors
>>   en_str file frozen line mu_str
>>   numerator old_group original_label
>>   peak refsame not_data
>>   bkg_switch bkg_switch2
>>   is_xmu is_chi is_xanes is_xmudat
>>   bkg_stan_lab bkg_flatten_was
>>   bkg_fnorm
>>);
>> Line 308 is the one that says "bkg_fnorm".  Edit this to read
>> "bkg_fnorm bkg_funnorm".  Save.
>>
>> Try reading in the project file again.  I tested this and I think it
>> will work.  Let me see the error message if this idea doesn't.
>>
>> B
>>
>> P.S. The Prj.pm file might be in a different location on someone
>> else's computer.
>>
>>
>>
>>
>> --
>>   Bruce Ravel   bra...@bnl.gov
>> <mailto:bra...@bnl.gov>
>>
>>   National Institute of Standards and Technology
>>

Re: [Ifeffit] Athena crash on mac on import

[George Sterbinsky]

Hi Bruce,

Thanks for providing a fix. The Prj.pm file on my system does not look
exactly like what you describe. Lines 260 to 268 looked like this:

next if any { $k eq $_ } qw(

bindtag deg_tol denominator detectors

en_str file frozen line mu_str

numerator old_group original_label

peak refsame not_data

bkg_switch bkg_switch2

is_xmu is_chi is_xanes is_xmudat

bkg_stan_lab bkg_flatten_was

);

After line 267, I added a new line that reads "bkg_fnorm bkg_funnorm" as
you suggested, and now I am able to open the prj file.

Thanks again,
George



On Fri, Jul 1, 2016 at 3:17 PM, Bruce Ravel  wrote:

> On 07/01/2016 03:00 PM, Bruce Ravel wrote:
>
>> There is probably a simple-ish work-around.  Let me think about it and
>> I'll get back to you.
>>
>
> There's not a way to simply fix this that does not involve you upgrading
> Demeter.  However, if you don't mind a bit of hands on effort, try this:
>
>  * Open the file
> /opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/Data/Prj.pm
> in a text editor (not Word!).
>
>  * Go to line 308.  Here's what the surrounding lines lines look like:
>
> next if any { $k eq $_ } qw(
>  bindtag deg_tol denominator detectors
>  en_str file frozen line mu_str
>  numerator old_group original_label
>  peak refsame not_data
>  bkg_switch bkg_switch2
>  is_xmu is_chi is_xanes is_xmudat
>  bkg_stan_lab bkg_flatten_was
>  bkg_fnorm
>   );
>Line 308 is the one that says "bkg_fnorm".  Edit this to read
> "bkg_fnorm bkg_funnorm".  Save.
>
> Try reading in the project file again.  I tested this and I think it will
> work.  Let me see the error message if this idea doesn't.
>
> B
>
> P.S. The Prj.pm file might be in a different location on someone else's
> computer.
>
>
>
>
> --
>  Bruce Ravel   bra...@bnl.gov
>
>  National Institute of Standards and Technology
>  Synchrotron Science Group at NSLS-II
>  Building 743, Room 114
>  Upton NY, 11973
>
>  Homepage:http://bruceravel.github.io/home/
>  Software:https://github.com/bruceravel
>  Demeter: http://bruceravel.github.io/demeter/
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[Ifeffit] Athena crash on mac on import

[George Sterbinsky]

Hello,

Athena crashes upon import of the attached project file. I am using the
latest release of Athena for mac (0.9.22) on OSX 10.10.5. I am able to open
the file on windows. The message that is printed to the terminal when
Athena crashes is pasted below. Please let me know if any further
information would be helpful.

Thank you,
George


[!!!] bkg_funnorm is not an attribute to set for
Demeter::Data=HASH(0x7fe2e57967c8) at
/opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/MooseX/SetGet.pm
line 9.
MooseX::SetGet::set(Demeter::Data=HASH(0x7fe2e57967c8), "bkg_spl2e",
110.195726042215, "y_offset", 0, "bft_rwindow", "hanning", "fft_kwindow",
"hanning", ...) called at
/opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/Data/Prj.pm
line 411
Demeter::Data::Prj::_record(Demeter::Data::Prj=HASH(0x7fe2e5785c70), 5,
"psmtj") called at
/opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/Data/Prj.pm
line 197
Demeter::Data::Prj::record(Demeter::Data::Prj=HASH(0x7fe2e5785c70), 1)
called at
/opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena/IO.pm
line 802
Demeter::UI::Athena::IO::_prj(Demeter::UI::Athena=HASH(0x7fe2dc0226a8),
"/Users...sta"..., "/Users...sta"..., 1, "") called at
/opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena/IO.pm
line 164

Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x7fe2dc0226a8))
called at
/opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena.pm
line 859
Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0x7fe2e28ff570),
Wx::CommandEvent=SCALAR(0x7fe2e5781840),
Demeter::UI::Athena=HASH(0x7fe2dc0226a8)) called at
/opt/local/lib/perl5/site_perl/5.22/darwin-thread-multi-2level/Demeter/UI/Athena.pm
line 782
Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0x7fe2e28ff570),
Wx::CommandEvent=SCALAR(0x7fe2e5781840)) called at /opt/local/bin/athena
line 44
eval {...} called at /opt/local/bin/athena line 44


standard.prj
Description: Binary data
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Re: [Ifeffit] Demeter under El Capitan

[George Sterbinsky]

Hi Matt,

Thanks for explaining. I didn't realize all of the differences between what
you and Zack had done. You mention that the instructions say to install
xorg-server. Even so, it is not necessary if you have xQuartz installed.
Hopefully this can at least save some people 8 hours!

George

On Thu, Nov 12, 2015 at 8:37 PM, Matt Newville <newvi...@cars.uchicago.edu>
wrote:

> Hi George,
>
>
>
> On Thu, Nov 12, 2015 at 7:59 PM, George Sterbinsky <
> georgesterbin...@u.northwestern.edu> wrote:
>
>> Hi Matt,
>>
>> I am just guessing here, but Zack and Manuel both mention installing
>> XQuartz, whereas you mention installing xorg-server. While Demeter should
>> work with either, perhaps on the new OS there is a problem installing
>> Demeter with xorg-server and one has to go with xQuartz.
>>
>
> I do have XQuartz installed, from before starting to build MacPorts.  The
> installation instructions for demeter say to install xorg-server.
>
> Have you tried installing xQuartz or following Zack's instructions
>> exactly?
>>
>
> Depends on what "exactly" means. ;).  I did not "migrate", I built
> MacPorts from scratch, after completely erasing any trace of MacPorts as
> described in their own uninstalling description.
> This was my second attempt at a completely fresh install on El Capitan,
> and I've installed Demeter with MacPorts on several machines using previous
> OS / MacPorts / Demeter versions.  Something is definitely broken.
>
>
>> That is installing xQuartz and not installing xorg-server at all?
>>
>
> The problem I see is not related to X.  It's that Perl's PDL does not
> compile with GSL.   I submitted a ticket about this to the MacPorts site.
>
> --Matt
>
>
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Re: [Ifeffit] Demeter under El Capitan

[George Sterbinsky]

Hi Matt,

I am just guessing here, but Zack and Manuel both mention installing
XQuartz, whereas you mention installing xorg-server. While Demeter should
work with either, perhaps on the new OS there is a problem installing
Demeter with xorg-server and one has to go with xQuartz. Have you tried
installing xQuartz or following Zack's instructions exactly? That is
installing xQuartz and not installing xorg-server at all?

George

On Thu, Nov 12, 2015 at 2:00 PM, Zack Gainsforth  wrote:

> Hi Matt,
>
> I have to agree it is a real annoyance to have to rebuild from scratch —
> and no there isn’t any great reason why that is better.  I’ve always chimed
> to myself “a macports version is better than no version” whenever I get an
> arcane fail message from macports.
>
> In the worst case, mac users can always run demeter from within a virtual
> machine (VMware, Parallels or VirtualBox).
>
> On the other hand, there is a method of using macports to produce a dmg
> (mac install file).  I have never used it, but the command goes like:
>
> sudo port mdmg demeter
>
> https://guide.macports.org/chunked/using.binaries.html
>
> My guess is that there would be a bit of development to make that work,
> but it is worth looking into.  Then, we build it once for each new version
> and release a dmg.
>
> Zack
>
> On Nov 12, 2015, at 10:53 AM, Matt Newville 
> wrote:
>
> Hi Manuel,
>
>
> On Thu, Nov 12, 2015 at 3:45 AM, Muñoz Manuel <
> manuel.mu...@ujf-grenoble.fr> wrote:
>
>> Dear all,
>>
>> Thank you for your feedbacks.
>>
>> After several attempts, I was finally successful with the installation of
>> Demeter. I attach a log file summarizing the different steps I experienced
>> (and a screenshot of the main window). I guess step 2 and 5 would have been
>> enough:
>> xcode-select --install
>> sudo port install demeter
>>
>> Indeed, several hours were required for the whole installation procedure
>> (more than 9 hours, but my internet connection is quite slow at home...).
>>
>> I can now execute athena from the terminal, and apparently it works fine.
>> However, I observe a strange behavior : After athena is running, I must
>> click once on the terminal window before the main menus are active in
>> Demeter (File, Group, Energy, etc.). But when we know that, it’s ok.
>>
>> And the most important, I don’t have any graphical window to display the
>> spectra. Would you have any suggestion? (Xquartz and Aquaterm are already
>> installed on my computer).
>>
>> Thank you again for your help!
>> Manuel
>>
>>
>
> That's great that it worked for you.
>
> I tried again with a completely fresh install of MacPorts, starting a few
> days ago, and again, it did not work for me.  To be clear, I have Xcode and
> command-line tools (as from  xcode-select --install ) installed, and can
> compile and build many programs.
>
> Starting with installing the latest MacPorts package, the initial
>
>   ~> sudo port -v selfupdate
>
> works fine. Similar to what you saw,
>
>   ~> sudo port install xorg-server
>
> also works, but takes at least 8 hours.  Really.For me
>
>   ~> sudo port install demeter
>
> took about two days of running close to full time,  And it failed.  As I
> mentioned earlier, the demeter package depends on llvm, libgcc, gcc4.9 and
> gcc5.2 all of which must be built FROM SOURCE, which is completely, utterly
> stupid.  Really, this alone pretty much convinces me that MacPorts is not a
> good solution for distributing Athena for Mac OS X.  More later.   Anyway
> building all these compilers and effectively building an isolated BSD
> user-space from source did work, and most of the dependencies and perl
> modules correctly installed.
>
> What failed to install was perl-5.22-pdl.  This gave a compilation error
> using some GSL component.  I uninstalled the gsl port, successfully
> installed the rest of the perl modules, and got the point where
>
>   ~> sudo port -v install demeter
>
> reports
>   --->  Computing dependencies for demeter
>   --->  Dependencies to be installed: p5.22-pdl gsl p5.22-pdl-stats
>
> That is, all other required components (including the wxPerl package) were
> installed.   GSL (2.0) does install, but p5.22-pdl fails with with
>
> ==
> ...
> /usr/bin/clang -c
> "-I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-pdl/p5.22-pdl/work/PDL-2.013/Basic/Core"
> -I/opt/local/include -pipe -Os -fno-common -DPERL_DARWIN
> -I/opt/local/include -fno-strict-aliasing -fstack-protector-strong
> -I/opt/local/include -arch x86_64 -O3   -DVERSION=\"2.013\"
> -DXS_VERSION=\"2.013\"
> "-I/opt/local/lib/perl5/5.22/darwin-thread-multi-2level/CORE"   ELLINT.c
> ELLINT.xs:1736:159: error: too many arguments to function call, expected
> 4, have 5
> GSLERR(gsl_sf_ellint_D_e,((phi_datap)[0] PDL_COMMENT("ACCESS()")
> ,(k_datap)[0] PDL_COMMENT("ACCESS()") ,(n_datap)[0] PDL_COMMENT("ACCESS()")
> 

Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X Yosemite

[George Sterbinsky]

In the Athena preferences menu, the "gnuplot-->terminal" parameter is set
to "x11" on my system. If yours is set to something else you might try
changing it to x11.

George

On Tue, Sep 22, 2015 at 4:18 PM, Bruce Ravel  wrote:

> On 09/22/2015 05:03 PM, Raimundo Lora Serrano wrote:
>
>>   * Can you make a plot?  To find out, plot a sine wave at the gnuplot
>>> >command line with "plot sin(x)”
>>>
>> Yes. I just tested and left the gnuplot window opened and ran “athena” in
>> another terminal, but there is no communication with gnuplot. Still, no
>> data is plotted.
>>
>>
>>
> That's not how the communication works.  Demeter needs to start its own
> instance of gnuplot.
>
> I'm afraid I don't know where to go from there.  Perhaps Joe or someone
> else can advise.
>
> B
>
>
> --
>  Bruce Ravel   bra...@bnl.gov
>
>  National Institute of Standards and Technology
>  Synchrotron Science Group at NSLS-II
>  Building 535A
>  Upton NY, 11973
>
>  Homepage:http://bruceravel.github.io/home/
>  Software:https://github.com/bruceravel
>  Demeter: http://bruceravel.github.io/demeter/
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Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X Yosemite

[George Sterbinsky]

I've found that if the terminal value is set to wxt, it is reset to qt upon
restarting Athena, and Athena will not plot. This does not happen if the
terminal value is set to x11 or aqua.

George

On Tue, Sep 22, 2015 at 9:32 PM, Matt Newville 
wrote:

> Sorry for not keeping up with the "Athena on OS X" details.  Here's my
> experience (OS X 10.10.5, up to date patches from Apple) which might be
> helpful to some.
>
> Athena from macports was working fine for me, but was many months old.
> This evening I did
>
>   sudo port -v selfupdate
>   sudo port install xorg-server
>
> This installed many updates -- it had been awhile. I then did
>   sudo port uninstall demeter
>   sudo port install demeter
>
> athena ran, but would not plot, in the way many had seen.  The gnuplot
> program was set to "gnuplot", but terminal was "qt".  Setting this to
> "wxt", plotting worked fine.
>
> Not sure why that happened (I'm pretty sure it had been "wxt" previously),
> but it was easy to fix.   And I'm still very impressed that the macports
> solution works so well!
>
> --Matt
>
>
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Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X Yosemite

[George Sterbinsky]

Hi All,

The result I get is
/private/tmp/com.apple.launchd.a2i2wnuP2l/org.macosforge.xquartz:0 and
Athena is working fine on my system.

George

On Tue, Sep 22, 2015 at 6:50 AM, Alison Tebo  wrote:

> Hi Raimundo (and Rémi),
>
> I'm not a pro here but, have you installed xorg-server? It seems like your
> $DISPLAY variables are not being set correctly. The problem might be
> XQuartz. The demeter build from Macports doesn't know to use that X windows
> server (everything is installed in different places) and is looking for the
> macports version. Your $DISPLAY variable should be something with
> org.macports rather than org.macosforge.xquartz:0. FWIW, xorg-server is
> maintained by and updated with XQuartz.
>
> Good luck,
>
> Alison
>
> On Mon, Sep 21, 2015 at 10:15 PM, Raimundo Lora Serrano <
> rloraserr...@infis.ufu.br> wrote:
>
>> Dear all,
>>
>> I have the same problems installing Athena/Demeter on Yosemite (10.10.5)
>> as Remi.
>> Also in my case (as for Rémi) - I use the Rémi’s message edited as
>> required to my softwares’ versions:
>>
>> > Athena launches well from the Terminal, I have the
>> > main window (perl5.22), I can import data or load former athena projects
>> > etc, but there is no plot window. No error message shows up in the
>> > terminal.
>>
>>
>> > I’ve *carefully* installed Macports 2.3.3, i.e., installed Xcode Version 
>> > 7.0 (7A220),
>> > agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite.
>> > I runned the "sudo port -v selfupdate" command
>> > Then "sudo port install demeter-devel”
>>
>> > And port upgrade outdated to ensure everything is up to date
>> > Plus, I have XQuartz 2.7.7 installed.
>>
>>
>> I also uninstalled and reinstalled macports (and Xcode, xquartz) but the
>> problem remains.
>>
>> By typing
>> echo $DISPLAY
>> /private/tmp/com.apple.launchd.RgzrDheMAp/org.macosforge.xquartz:0
>>
>> Any guess?
>> Many thanks in advance.
>> Raimundo
>>
>>
>>
>>
>> Em 21/09/2015, à(s) 14:00, ifeffit-requ...@millenia.cars.aps.anl.gov
>> escreveu:
>>
>> Send Ifeffit mailing list submissions to
>> ifeffit@millenia.cars.aps.anl.gov
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> or, via email, send a message with subject or body 'help' to
>> ifeffit-requ...@millenia.cars.aps.anl.gov
>>
>> You can reach the person managing the list at
>> ifeffit-ow...@millenia.cars.aps.anl.gov
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Ifeffit digest..."
>>
>>
>> Today's Topics:
>>
>>   1. No plot window in Athena/Demeter on Mac OS X Yosemite
>>  (R?mi BELISSONT)
>>
>>
>> --
>>
>> Message: 1
>> Date: Mon, 21 Sep 2015 14:57:34 +0200
>> From: R?mi BELISSONT 
>> To: ifeffit@millenia.cars.aps.anl.gov
>> Subject: [Ifeffit] No plot window in Athena/Demeter on Mac OS X
>> Yosemite
>> Message-ID: <6d35429a-8b4f-42fa-ba4d-92407447f...@univ-lorraine.fr>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hello,
>>
>> I?m currently using Athena using the iXAFS 3.0.3 application, which is ?
>> if I?ve well understood ? an old version no longer updated (
>> http://cars9.uchicago.edu/ifeffit/Downloads <
>> http://cars9.uchicago.edu/ifeffit/Downloads>).
>>
>> So, today I tried to install the current version by installing Demeter,
>> following the procedure detailed at http://bruceravel.github.io/demeter/
>> .
>>
>> I?ve *carefully* installed Macports 2.3.3, i.e., installed Xcode 6.4,
>> agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite.
>> I runned the sudo port -v self update command
>> Then sudo port install xorg-server demeter
>> And port upgrade outdated to ensure everything is up to date
>> Plus, I have XQuartz 2.7.7 installed.
>>
>> Here is my problem.
>> Athena launches well from the Terminal (in home directory), I have the
>> main window (pearl5.22), I can import data or load former athena projects
>> etc, but there is no plot window. No error message shows up in the
>> terminal. However I can still produce a PNG of the plot I?m desperately
>> trying to see via Plots/Save last plot as...
>>
>> I?ve seen a similar thread concerning such an issue in OS X Mavericks but
>> couldn?t solve it from what was explained there (
>> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html
>> <
>> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html>).
>> I guess the issue comes from the DISPLAY environment but I don?t have any
>> clue to solve that.
>>
>> Thank you in advance for your help,
>> I think it may be useful for other users,
>>
>> Kind regards,
>>
>> R?mi
>>
>>
>> ???
>> R?mi Belissont
>> Ph.D. Student | Universit? de Lorraine ? Labex R21
>>
>> GeoRessources
>> CNRS-UMR 7359, Facult? des Sciences
>> BP 

Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X Yosemite

[George Sterbinsky]

Hi Remi,

I noticed a typo in the commands you used. "selfupdate" should be one word,
not two. Perhaps this was just a typo in your email, but if not then you
may want to try running it again. Also, I noticed that the instructions at
the Demeter website say to log out and log back in after installation, so
you may want to try that if you have not.

If that is not the problem, here is the sequence I used to get Demeter
working on my system:

1. install XQuartz 2.7.7 (xorg-server 1.15.2).
2. install Xcode
3. install command line tools by typing "xcode-select --install" in the
terminal.
4. install macports:
https://distfiles.macports.org/MacPorts/MacPorts-2.3.3-10.10-Yosemite.pkg
5. ensure macports is working by typing "sudo port -v selfupdate" in the
terminal.
6. run "sudo port upgrade outdated".
7. install Demeter using the command "sudo port install demeter-devel".
8. log out and log back in (I didn't need to do this, but the instructions
say that it may be necessary in some cases).

You mentioned you already have Xcode and XQuartz installed. I don't know if
this will fix your problem, but you could try uninstalling macports (
http://guide.macports.org/#installing.macports.uninstalling), then follow
steps 3 through 8 above. I hope that helps.


George

On Thu, Sep 10, 2015 at 9:18 AM, Rémi BELISSONT 
wrote:

> Hello,
>
> I’m currently using Athena using the iXAFS 3.0.3 application, which is –
> if I’ve well understood – an old version no longer updated (
> http://cars9.uchicago.edu/ifeffit/Downloads).
>
> So, today I tried to install the current version by installing Demeter,
> following the procedure detailed at http://bruceravel.github.io/demeter/.
>
> I’ve *carefully* installed Macports 2.3.3, i.e., installed Xcode 6.4,
> agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite.
> I runned the sudo port -v self update command
> Then sudo port install xorg-server demeter
> And port upgrade outdated to ensure everything is up to date
> Plus, I have XQuartz 2.7.7 installed.
>
> Here is my problem.
> Athena launches well from the Terminal (in home directory), I have the
> main window (pearl5.22), I can import data or load former athena projects
> etc, but there is no plot window. No error message shows up in the
> terminal. However I can still produce a PNG of the plot I’m
> desperately trying to see via Plots/Save last plot as...
>
> I’ve seen a similar thread concerning such an issue in OS X Mavericks
> but couldn’t solve it from what was explained there (
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html).
> I guess the issue comes from the DISPLAY environment but I don’t have any
> clue to solve that.
>
> Thank you in advance for your help,
> I think it may be useful for other users,
>
> Kind regards,
>
> Rémi
>
>
>
>
>
>
>
>
>
> ___
> Ifeffit mailing list
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>
>
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Re: [Ifeffit] MacPorts now contains Demeter 0.9.22 (and requires Perl 5.22)

[George Sterbinsky]

Hi Joe,

I am now able to update without errors.

Thanks,
George

On Wed, Aug 12, 2015 at 9:22 AM, Fowler, Joseph W. joe.fow...@nist.gov
wrote:

 Dear George,


 I'm afraid that you've uncovered a silly and known problem. (See
 https://trac.macports.org/ticket/48517 )


 This bug is fixed in principle but not committed to the MacPorts
 repository. Last week there was some activity on this. Unfortunately, we'll
 need a MacPorts person with the right privileges to commit this change. I
 don't know how to push this forward.


 If you are a MacPorts expert, then you can certainly grab the patch found
 at that ticket and apply it.  I'm afraid that's something that I don't know
 how to do without an hour of research, though.


 I'm sorry about that, but we might have to be patient. I will investigate
 how one pushes the MacPorts committer group to commit their changes. Or, I
 mean, other people's changes.


 Joe


 --
 *From:* George Sterbinsky georgesterbin...@u.northwestern.edu
 *Sent:* Tuesday, August 11, 2015 8:27 PM
 *To:* XAFS Analysis using Ifeffit
 *Subject:* Re: [Ifeffit] MacPorts now contains Demeter 0.9.22 (and
 requires Perl 5.22)

 Hi Joe,

 Thanks for updating the package! I tried updating, first running sudo
 port selfupdate and then sudo port update demeter-devel. I get the
 following error when I try the latter command:

 bash-3.2$ sudo port upgrade demeter-devel
 Password:
 ---  Computing dependencies for ifeffit
 ---  Verifying checksums for ifeffit
 Error: Checksum (rmd160) mismatch for 1.2.final.tar.gz
 Error: Checksum (sha256) mismatch for 1.2.final.tar.gz
 Error: org.macports.checksum for port ifeffit returned: Unable to verify
 file checksums
 Please see the log file for port ifeffit for details:

 /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_ifeffit/ifeffit/main.log
 Error: Unable to upgrade port: 1
 To report a bug, follow the instructions in the guide:
 http://guide.macports.org/#project.tickets
 bash-3.2$

 I've attached the log file as well. Any suggestions as to what else I
 might try?

 Thank you,
 George



 On Tue, Aug 11, 2015 at 3:49 PM, Fowler, Joseph W. joe.fow...@nist.gov
 wrote:

 Dear Bruce:


 Wait a minute! In fact, I updated the Mac Ports package *demeter* within
 the last two weeks to use Demeter version 0.9.22. Mac users might want to
 use the latest version and should consider doing a port self update 
 port upgrade demeter.

 Users who installed the development version port called *demeter-devel* will
 also land on 0.9.22 if they upgrade to the latest.

 Note that the latest Mac Ports version is known as 0.9.22_1, where the
 revision number _1 corresponds to the upgrade from Perl 5.16 to 5.22 (which
 the MacPorts team is pushing on). For many users, there will be numerous
 dependency upgrades when you upgrade to 0.9.22_1, but I found they took
 only a few minutes in my particular case. This change in Perl versions
 could conceivably cause problems, but I haven't heard of any.

 Best wishes,
 Joe Fowler
 (MacPorts maintainer for demeter)

 --
 *From:* Bruce Ravel bra...@bnl.gov
 *Sent:* Tuesday, August 11, 2015 6:55 AM
 *To:* XAFS Analysis using Ifeffit
 *Subject:* Re: [Ifeffit] Energy shift after deglitch


 I don't see the behavior you describe when I follow your recipe.
 Perhaps it got fixed when I fixed this fellow's issue...?

 http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-May/012496.html

 Of course, the Mac package is a fair bit behind at this point.

 B

 On 08/06/2015 06:10 PM, George Sterbinsky wrote:
  Hello,
 
  I am writing to report a bug in Athena running on OSX 10.10.4. Here are
  the steps to reproduce the problem. I'm not sure that all steps are
  necessary.
 
  1. Open Athena and import the attached project, which contains two
  groups that are both marked.
  2. Change plot range to plot from -30 to 30 eV.
  3. Select the deglitch and truncate window.
  4. Select group Ref data.merge.
  5. In deglitch many points, set margin to 0.05, Emin to -24, and Emax to
  -20.
  6. Click replot margins.
  7. Click remove points.
  8. Click return to main window.
  9. Click the derivative check box to plot marked groups as normalized
  derivative.
  10. Click mu(E) button to plot marked groups as derivative of mu(E).
 
  When the last step is done the groups appear to shift with respect to
  each other. One can switch between Normalized and mu(E) and see the
  shift come and go.
 
  Thank you,
  George
 
 
 
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 --
   Bruce Ravel   bra...@bnl.gov

   National Institute of Standards and Technology
   Synchrotron Science Group at NSLS-II
   Building 535A
   Upton NY, 11973

   Homepage:http://bruceravel.github.io/home

Re: [Ifeffit] Energy shift after deglitch

[George Sterbinsky]

Hi Bruce,

Thanks for your reply. Are there any plans to update the macports package
in the future?

Thanks,
George

On Tue, Aug 11, 2015 at 7:55 AM, Bruce Ravel bra...@bnl.gov wrote:


 I don't see the behavior you describe when I follow your recipe. Perhaps
 it got fixed when I fixed this fellow's issue...?

 http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-May/012496.html

 Of course, the Mac package is a fair bit behind at this point.

 B


 On 08/06/2015 06:10 PM, George Sterbinsky wrote:

 Hello,

 I am writing to report a bug in Athena running on OSX 10.10.4. Here are
 the steps to reproduce the problem. I'm not sure that all steps are
 necessary.

 1. Open Athena and import the attached project, which contains two
 groups that are both marked.
 2. Change plot range to plot from -30 to 30 eV.
 3. Select the deglitch and truncate window.
 4. Select group Ref data.merge.
 5. In deglitch many points, set margin to 0.05, Emin to -24, and Emax to
 -20.
 6. Click replot margins.
 7. Click remove points.
 8. Click return to main window.
 9. Click the derivative check box to plot marked groups as normalized
 derivative.
 10. Click mu(E) button to plot marked groups as derivative of mu(E).

 When the last step is done the groups appear to shift with respect to
 each other. One can switch between Normalized and mu(E) and see the
 shift come and go.

 Thank you,
 George



 ___
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 http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit



 --
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Building 535A
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/
 ___
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 http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: [Ifeffit] MacPorts now contains Demeter 0.9.22 (and requires Perl 5.22)

[George Sterbinsky]

Hi Joe,

Thanks for updating the package! I tried updating, first running sudo port
selfupdate and then sudo port update demeter-devel. I get the following
error when I try the latter command:

bash-3.2$ sudo port upgrade demeter-devel
Password:
---  Computing dependencies for ifeffit
---  Verifying checksums for ifeffit
Error: Checksum (rmd160) mismatch for 1.2.final.tar.gz
Error: Checksum (sha256) mismatch for 1.2.final.tar.gz
Error: org.macports.checksum for port ifeffit returned: Unable to verify
file checksums
Please see the log file for port ifeffit for details:

/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_ifeffit/ifeffit/main.log
Error: Unable to upgrade port: 1
To report a bug, follow the instructions in the guide:
http://guide.macports.org/#project.tickets
bash-3.2$

I've attached the log file as well. Any suggestions as to what else I might
try?

Thank you,
George



On Tue, Aug 11, 2015 at 3:49 PM, Fowler, Joseph W. joe.fow...@nist.gov
wrote:

 Dear Bruce:


 Wait a minute! In fact, I updated the Mac Ports package *demeter* within
 the last two weeks to use Demeter version 0.9.22. Mac users might want to
 use the latest version and should consider doing a port self update 
 port upgrade demeter.

 Users who installed the development version port called *demeter-devel* will
 also land on 0.9.22 if they upgrade to the latest.

 Note that the latest Mac Ports version is known as 0.9.22_1, where the
 revision number _1 corresponds to the upgrade from Perl 5.16 to 5.22 (which
 the MacPorts team is pushing on). For many users, there will be numerous
 dependency upgrades when you upgrade to 0.9.22_1, but I found they took
 only a few minutes in my particular case. This change in Perl versions
 could conceivably cause problems, but I haven't heard of any.

 Best wishes,
 Joe Fowler
 (MacPorts maintainer for demeter)

 --
 *From:* Bruce Ravel bra...@bnl.gov
 *Sent:* Tuesday, August 11, 2015 6:55 AM
 *To:* XAFS Analysis using Ifeffit
 *Subject:* Re: [Ifeffit] Energy shift after deglitch


 I don't see the behavior you describe when I follow your recipe.
 Perhaps it got fixed when I fixed this fellow's issue...?

 http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-May/012496.html

 Of course, the Mac package is a fair bit behind at this point.

 B

 On 08/06/2015 06:10 PM, George Sterbinsky wrote:
  Hello,
 
  I am writing to report a bug in Athena running on OSX 10.10.4. Here are
  the steps to reproduce the problem. I'm not sure that all steps are
  necessary.
 
  1. Open Athena and import the attached project, which contains two
  groups that are both marked.
  2. Change plot range to plot from -30 to 30 eV.
  3. Select the deglitch and truncate window.
  4. Select group Ref data.merge.
  5. In deglitch many points, set margin to 0.05, Emin to -24, and Emax to
  -20.
  6. Click replot margins.
  7. Click remove points.
  8. Click return to main window.
  9. Click the derivative check box to plot marked groups as normalized
  derivative.
  10. Click mu(E) button to plot marked groups as derivative of mu(E).
 
  When the last step is done the groups appear to shift with respect to
  each other. One can switch between Normalized and mu(E) and see the
  shift come and go.
 
  Thank you,
  George
 
 
 
  ___
  Ifeffit mailing list
  Ifeffit@millenia.cars.aps.anl.gov
  http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
 


 --
   Bruce Ravel   bra...@bnl.gov

   National Institute of Standards and Technology
   Synchrotron Science Group at NSLS-II
   Building 535A
   Upton NY, 11973

   Homepage:http://bruceravel.github.io/home/
   Software:https://github.com/bruceravel
   Demeter: http://bruceravel.github.io/demeter/


 ___
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main.log
Description: Binary data
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[Ifeffit] Energy shift after deglitch

[George Sterbinsky]

Hello,

I am writing to report a bug in Athena running on OSX 10.10.4. Here are the
steps to reproduce the problem. I'm not sure that all steps are necessary.

1. Open Athena and import the attached project, which contains two groups
that are both marked.
2. Change plot range to plot from -30 to 30 eV.
3. Select the deglitch and truncate window.
4. Select group Ref data.merge.
5. In deglitch many points, set margin to 0.05, Emin to -24, and Emax to
-20.
6. Click replot margins.
7. Click remove points.
8. Click return to main window.
9. Click the derivative check box to plot marked groups as normalized
derivative.
10. Click mu(E) button to plot marked groups as derivative of mu(E).

When the last step is done the groups appear to shift with respect to each
other. One can switch between Normalized and mu(E) and see the shift come
and go.

Thank you,
George


BugDemo.prj
Description: Binary data
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[Ifeffit] Artemis on Yosemite

[George Sterbinsky]

Hello,

When I attempt to open Artemis on OSX Yosemite (10.10.2) the error message
copied below prints to the terminal. The initial image that indicates
Artemis is opening does appear, although Artemis fails to open. Athena and
Hephaestus open without error. Any suggestions as to how this could be
resolved would be appreciated.

Thanks,
George

$ artemis
Can't locate Math/Round.pm in @INC (@INC contains:
/opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level
/opt/local/lib/perl5/site_perl/5.16.3
/opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level
/opt/local/lib/perl5/vendor_perl/5.16.3
/opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level
/opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl
/opt/local/lib/perl5/vendor_perl .) at
/opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/ScatteringPath.pm
line 44.
BEGIN failed--compilation aborted at
/opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/ScatteringPath.pm
line 44.
Compilation failed in require at
/opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter.pm
line 306.
BEGIN failed--compilation aborted at
/opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/UI/Artemis.pm
line 26.
Compilation failed in require at /opt/local/bin/artemis line 34.
BEGIN failed--compilation aborted at /opt/local/bin/artemis line 34.
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[Ifeffit] Athena crash report

[George Sterbinsky]

Hello,

I am running Athena 0.9.20 on OSX 10.8.5. Selecting the difference spectra
tool from the drop-down menu causes Athena to crash and the following
message to print to the terminal.

Usage: Wx::ComboBox::GetClientData(THIS, n) at
/opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/UI/Athena/Difference.pm
line 215, F line 339.

I've tried this with several different projects and it appears to be
general behavior. If I can provide any additional information please let me
know.

Thank you,
George
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Re: [Ifeffit] Rendering of windows in Artemis and transferring paths from feff calculation

[George Sterbinsky]

Hi Bruce and Alison,

I am able to confirm the behavior reported by Alison (both bigger and
lesser problems) on OSX 10.8.5. Pressing the transfer displayed path
button causes Artemis to crash and the message below to print to the
terminal.

2014-04-18 11:18:26.309 perl5.16[1309:707] *** WARNING: -[NSImage
compositeToPoint:fromRect:operation:] is deprecated in MacOSX 10.8 and
later. Please use -[NSImage drawAtPoint:fromRect:operation:fraction:]
instead.
Can't locate object method transfer via package Wx::Panel at
/opt/local/lib/perl5/site_perl/5.16.1/darwin-thread-multi-2level/Demeter/UI/Artemis/Data.pm
line 1126, F line 9.


Best,
George



On Thu, Apr 17, 2014 at 3:30 PM, Bruce Ravel bra...@bnl.gov wrote:

 On 03/24/2014 03:21 PM, Alison Tebo wrote:

 I am running Demeter 0.9.18 installed on a Mac 10.6.8 via the (very
 helpful!) Macports port. I've had nearly no problems with processing my
 data, but Artemis appears very strange. Most of the button can't be seen
 and are black instead (I've attached a screenshot). The bigger problem
 is that once I run a Feff calculation, I can't seem to transfer the
 paths from the Feff Window into the Data Window (see second screenshot).
 The program seems to think it's doing it--there are no error messages in
 the log and it even makes the little graphic as it 'grabs' the path--but
 it never transfers it over to the Data Window.

 I have attached a project file where I get this error, the feff input
 file that I run the calculation on, and two screenshots of what Artemis
 looks like for me. I don't think the input and project file matter much
 since this happens for me even with examples from the various courses
 Bruce has given.

 Any advice would be greatly appreciated.


 Hi Alison,

 First off, I apologize that it has taken me so long to respond to this.
  Busy time.

 I don't quite understand the bigger problem.  This is certainly  not a
 problem I have on other platforms.  Do other Mac users observe the same
 behavior?

 As for the lesser problem, looking at the icons across the top in your
 screenshots, it would seem that you are using some kind of color theme that
 is different from a Mac out of the box.  Is that right?  If so, how does
 the software behave if you change the theme back to the default?

 Cheers,
 B


 --
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973

  Homepage:http://xafs.org/BruceRavel
  Software:https://github.com/bruceravel
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Re: [Ifeffit] Demeter: Problem closing communication to gnuplot

[George Sterbinsky]

Hi Bruce,

Thanks for your help. I made the changes you suggested and now get a
different message:

Global symbol $data_object requires explicit package name at LoadData.pl
line 8.
Execution of LoadData.pl aborted due to compilation errors.

The script follows.

#!/usr/bin/perl

use Demeter qw(:ui=screen);


my $data = Demeter::Data - new(file = data/fe.060,

name = 'test',

);

$data - plot('E');

$data_object - pause;


Any further help is appreciated.


Thanks,

George


On Sat, Apr 12, 2014 at 4:40 PM, Bruce Ravel bra...@bnl.gov wrote:


 It would, of course, help to see the script, but I can guess what the
 issue is.

 Try doing

   use Demeter qw(:ui=screen);

 at the top of the script, and

   $data_object - pause;

 before it exits.

 The specific message is issued because the perl script ended while the
 pipe to the gnuplot process was still open.  That doesn't happen if you put
 in a pause.  And you get to look at the plot before it vanishes!

 B


 On 04/11/2014 06:45 PM, George Sterbinsky wrote:

 Hello,

 I am trying to learn to use Demeter following The Demeter Programmer
 Guide. When I attempt to run the first example script in the importing
 data section I get the following error message:

 Graphics::GnuplotIF (object 1): problem closing communication to gnuplot

 I also see the plot window flash open and then closed on my screen.

 I am using  perl 5.16.1 on  mac OSX 10.8.5. If anyone can provide any
 suggestions as to how I might correct this please let me know.

 Thank you,
 George


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 --
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973

  Homepage:http://xafs.org/BruceRavel
  Software:https://github.com/bruceravel
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[Ifeffit] Demeter: Problem closing communication to gnuplot

[George Sterbinsky]

Hello,

I am trying to learn to use Demeter following The Demeter Programmer Guide.
When I attempt to run the first example script in the importing data
section I get the following error message:

Graphics::GnuplotIF (object 1): problem closing communication to gnuplot

I also see the plot window flash open and then closed on my screen.

I am using  perl 5.16.1 on  mac OSX 10.8.5. If anyone can provide any
suggestions as to how I might correct this please let me know.

Thank you,
George
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Re: [Ifeffit] Peaks in MCA spectra

[George Sterbinsky]

Matt and Matthew,

Thanks for your suggestions. I will try to collect some spectra well above
the Co L-edge and see if they provide additional insight.

Best,
George


On Tue, Apr 1, 2014 at 6:07 PM, Matthew Marcus mamar...@lbl.gov wrote:

 I don't think so.  This may be a better question for M. Newville, or
 whoever wrote the program.
 mam


 On 4/1/2014 9:56 AM, George Sterbinsky wrote:

 Hi Matthew,

 Hephaestus shows the strength of the Ll emission to be about 10% of the
 La2 emission. When fitting the spectrum as a sum of Gaussians, I find that
 the area of of the Gaussian used to fit the Ll is 24% of that used to fit
 the La2. What would cause the ratio determined from tabulated data to
 differ from that found in the data I collected? Am I misunderstanding the
 meaning of the strength value in Hephaestus?

 Thanks,
 George


 On Tue, Apr 1, 2014 at 11:45 AM, Matthew Marcus mamar...@lbl.govmailto:
 mamar...@lbl.gov wrote:

 OK, I think the other Matt has solved it - it's the L1 peak.  I was
 confused by an inaccurate attempt at reading the energy scale.
 Also, I somehow didn't read correctly the branching ratio from
 Hephaestus.
  mam


 On 3/31/2014 8:57 PM, George Sterbinsky wrote:

 Hi Matt,

 Thanks for your reply. Please see below.

 On Mon, Mar 31, 2014 at 8:10 PM, Matt Newville 
 newvi...@cars.uchicago.edu mailto:newvi...@cars.uchicago.edu mailto:
 newville@cars.__uchicago.edu mailto:newvi...@cars.uchicago.edu wrote:

  Hi George,

  Calibrated spectra would help, but if we guess the
 calibration is 0.56
  bins/ eV, then we'd have


 I've attached a plot of the data showing the x-axis in keV. Also,
 as requested by Zack, I've attached a two column data file.


 line E (eV)   bin #
  --__---

  Co La1,2   775  434
  O Ka1,2 525  294
  C Ka1,2 277  155

  which looks  pretty good. This puts the the unknown peak
 near
  380/0.56 which is 678 eV.   Tthat's very close to Co Ll
 (M1-L3),
  which is at 677 eV, and should be a bit less than 10%  of Co
 La1 and
  La2, which is roughly right.


 Based on fitting the spectrum with Gaussians, the Co LI is 24% of
 the La2. As you mention, a value of roughly 10% is expected. What could
 cause such a discrepancy?


  So, I think it's Co Ll.  That says the sample is just Co, C,
 and O.
  Is that reasonable?


 Yes, it is. I think maybe a little fluorine too, but it is very
 weak as I mention in my response to Matthew.


  What surprises me is that there is no signal from the
 elastic peak.
  Was that somehow filtered out?


 No, if there is an elastic peak it is probably lost under the Co
 La2.


 Thanks,
 George

  The fact that the counts don't go to
  zero between C and O could be many factors, including
 incomplete
  charge collection.  This (and Compton scattering) generally
 make peaks
  have a slightly non-Gaussian shape, with a low-energy tail.






  Cheers,

  --Matt

  On Mon, Mar 31, 2014 at 5:01 PM, George Sterbinsky
  GeorgeSterbinsky@u.__northwestern.edu mailto:
 georgesterbin...@u.northwestern.edu mailto:GeorgeSterbinsky@u.__n
 orthwestern.edu mailto:georgesterbin...@u.northwestern.edu wrote:
Hello,
   
I am writing with a general XAS question. It does not
 necessarily pertain to
Ifeffit, however, I think the topic is something some,
 maybe most, list
members will be knowledgeable about. So it seems like
 this list is a good
place to post this question.
   
On to the question. I have attached a plot of a MCA
 spectrum collected with
a vortex silicon drift detector. The spectrum is actually
 the average of
several spectra, all collected in the post edge region of
 the Co L-edge. The
spectra were averaged to reduce noise. The three peaks
 result from
fluorescence from carbon, oxygen, and cobalt. Low-energy
 shoulders on the Co
and O peaks are also observed. These can be seen as the
 regions of the
spectrum that are not well reproduced by the fit. The
 main reason I included
the fit in the plot is to illustrate the presence of
 these shoulders,
particularly in the oxygen florescence, where the
 additional intensity is
not so obvious.
   
I am writing to see if anyone has any suggestion as to
 what the origins of
these peaks might be. They are not due

Re: [Ifeffit] Peaks in MCA spectra

[George Sterbinsky]

Hi Matthew,

Hephaestus shows the strength of the Ll emission to be about 10% of the La2
emission. When fitting the spectrum as a sum of Gaussians, I find that the
area of of the Gaussian used to fit the Ll is 24% of that used to fit the
La2. What would cause the ratio determined from tabulated data to differ
from that found in the data I collected? Am I misunderstanding the meaning
of the strength value in Hephaestus?

Thanks,
George


On Tue, Apr 1, 2014 at 11:45 AM, Matthew Marcus mamar...@lbl.gov wrote:

 OK, I think the other Matt has solved it - it's the L1 peak.  I was
 confused by an inaccurate attempt at reading the energy scale.
 Also, I somehow didn't read correctly the branching ratio from Hephaestus.
 mam


 On 3/31/2014 8:57 PM, George Sterbinsky wrote:

 Hi Matt,

 Thanks for your reply. Please see below.

 On Mon, Mar 31, 2014 at 8:10 PM, Matt Newville 
 newvi...@cars.uchicago.edu mailto:newvi...@cars.uchicago.edu wrote:

 Hi George,

 Calibrated spectra would help, but if we guess the calibration is 0.56
 bins/ eV, then we'd have


 I've attached a plot of the data showing the x-axis in keV. Also, as
 requested by Zack, I've attached a two column data file.


line E (eV)   bin #
 -
 Co La1,2   775  434
 O Ka1,2 525  294
 C Ka1,2 277  155

 which looks  pretty good. This puts the the unknown peak near
 380/0.56 which is 678 eV.   Tthat's very close to Co Ll (M1-L3),
 which is at 677 eV, and should be a bit less than 10%  of Co La1 and
 La2, which is roughly right.


 Based on fitting the spectrum with Gaussians, the Co LI is 24% of the
 La2. As you mention, a value of roughly 10% is expected. What could cause
 such a discrepancy?


 So, I think it's Co Ll.  That says the sample is just Co, C, and O.
 Is that reasonable?


 Yes, it is. I think maybe a little fluorine too, but it is very weak as I
 mention in my response to Matthew.


 What surprises me is that there is no signal from the elastic peak.
 Was that somehow filtered out?


 No, if there is an elastic peak it is probably lost under the Co La2.


 Thanks,
 George

 The fact that the counts don't go to
 zero between C and O could be many factors, including incomplete
 charge collection.  This (and Compton scattering) generally make peaks
 have a slightly non-Gaussian shape, with a low-energy tail.






 Cheers,

 --Matt

 On Mon, Mar 31, 2014 at 5:01 PM, George Sterbinsky
 georgesterbin...@u.northwestern.edu mailto:GeorgeSterbinsky@u.
 northwestern.edu wrote:
   Hello,
  
   I am writing with a general XAS question. It does not necessarily
 pertain to
   Ifeffit, however, I think the topic is something some, maybe most,
 list
   members will be knowledgeable about. So it seems like this list is
 a good
   place to post this question.
  
   On to the question. I have attached a plot of a MCA spectrum
 collected with
   a vortex silicon drift detector. The spectrum is actually the
 average of
   several spectra, all collected in the post edge region of the Co
 L-edge. The
   spectra were averaged to reduce noise. The three peaks result from
   fluorescence from carbon, oxygen, and cobalt. Low-energy shoulders
 on the Co
   and O peaks are also observed. These can be seen as the regions of
 the
   spectrum that are not well reproduced by the fit. The main reason
 I included
   the fit in the plot is to illustrate the presence of these
 shoulders,
   particularly in the oxygen florescence, where the additional
 intensity is
   not so obvious.
  
   I am writing to see if anyone has any suggestion as to what the
 origins of
   these peaks might be. They are not due to additional elements, as
 they
   appear at the same incident energies as the main florescence
 peaks, i.e. the
   Co shoulder appears at the same incident energies as the main Co
 peak, and
   the O shoulder appears at the same incident energies as the main O
 peak. It
   is possible that the peaks result form other transitions.
 Considering Co,
   the main peak is due to L3/L2-M4 transitions, and the shoulder is
 in a
   position that could be consistent with L3/L2-M1 transitions.
 However, by
   fitting the peaks with Gaussians, one finds an area for the
 shoulder that is
   about 25% of the area of the main peak. This is significantly
 larger than
   what one might expect from tabulated transition strengths like
 those given
   in Hephaestus.
  
   To summarize, does anyone know what these shoulders might result
 from if not
   lower energy transitions? If they are low energy transitions, why
 would the
   relative transition strengths differ from tabulated values?
  
   Thank you,
   George

[Ifeffit] Peaks in MCA spectra

[George Sterbinsky]

Hello,

I am writing with a general XAS question. It does not necessarily pertain
to Ifeffit, however, I think the topic is something some, maybe most, list
members will be knowledgeable about. So it seems like this list is a good
place to post this question.

On to the question. I have attached a plot of a MCA spectrum collected with
a vortex silicon drift detector. The spectrum is actually the average of
several spectra, all collected in the post edge region of the Co L-edge.
The spectra were averaged to reduce noise. The three peaks result from
fluorescence from carbon, oxygen, and cobalt. Low-energy shoulders on the
Co and O peaks are also observed. These can be seen as the regions of the
spectrum that are not well reproduced by the fit. The main reason I
included the fit in the plot is to illustrate the presence of these
shoulders, particularly in the oxygen florescence, where the additional
intensity is not so obvious.

I am writing to see if anyone has any suggestion as to what the origins of
these peaks might be. They are not due to additional elements, as they
appear at the same incident energies as the main florescence peaks, i.e.
the Co shoulder appears at the same incident energies as the main Co peak,
and the O shoulder appears at the same incident energies as the main O
peak. It is possible that the peaks result form other transitions.
Considering Co, the main peak is due to L3/L2-M4 transitions, and the
shoulder is in a position that could be consistent with L3/L2-M1
transitions. However, by fitting the peaks with Gaussians, one finds an
area for the shoulder that is about 25% of the area of the main peak. This
is significantly larger than what one might expect from tabulated
transition strengths like those given in Hephaestus.

To summarize, does anyone know what these shoulders might result from if
not lower energy transitions? If they are low energy transitions, why would
the relative transition strengths differ from tabulated values?

Thank you,
George
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Re: [Ifeffit] Peaks in MCA spectra

[George Sterbinsky]

Hi Matthew,

Thanks for your reply. see below.

On Mon, Mar 31, 2014 at 6:30 PM, Matthew Marcus mamar...@lbl.gov wrote:

 Hmmm.  An interesting brain-teaser.  Scaling very roughly from the graph,
 the mystery peak shows up at about 715eV.  This is consistent with Fe.
 Could there be a background from Fe somewhere in the detection systen?


I don't think so. The shoulder appears when the incident energy corresponds
to the Co L-edge, at the same time as the main Co peak. Also, MCA spectra
collected above and below the Fe L-edge are pretty much identical.


 The intensity between the O and Co peaks doesn't really look like
 a peak, but just like a background tail, perhaps from the strong Co peak.
  It seems to be a little to the right of where N (from, for instance,
 a kapton window) would be.  I could be wrong, in which case my Fe theory
 goes away.


I'm assuming you mean the intensity between C and O. I've attached a plot
of a MCA spectrum from the Co L pre-edge. This is again the sum of several
spectra collected in the pre-edge region to reduce noise.The intensity
between C and O is still present, so I don't think it is due to a tail from
the Co peak. I also agree that is to the right of where one expects N.


 Now, I thought about an escape peak from Si, but I suspect that
 this is really small down here and anyway, the Si L-fluorescence energy is
 92eV or so, and the extra peak is about 55eV below the main peak.

 Did you duck below the Fe edge to see if the peak to the L of Co goes away?


Yes, as noted above, the attached MCA spectrum from the Co pre-edge is
pretty much identical to spectra collected below the Fe L-edge. A peak is
seen at energies consistent with Fe and/or Co florescence. I think it is
actually a combination of 2nd order cobalt, a small amount of fluorine, and
maybe some elastic scatter. However regardless of its origin, it is much
weaker than the Co L3/L2-M4 and the shoulder on that peak, so I don't think
they are related.


 The peaks in the fit seem to be consistently to the left of the ones in
 the data.  Any idea why?  Was the energy scale not a fit parameter?


My guess is that they are shifted because they are trying to fit the
intensity of the shoulders.

In order to analyze the 'extra' peaks, it may be useful to optimize the fit
 to the main peaks, then subtract to get the residual, including
 the 'extras'.  What would happen if you added Fe and maybe N to the fit?


Yes, I do get a good fit when I do that. In fact, that is what I originally
thought before I started to look at the data a little more closely and
ruled out Fe in the ways explained above. I'll take a look at the
residuals, but I need to play around with the fit to get rid of the
shifting to left of the peaks.


Thanks,
George



 I admit that I've never done soft X-ray fluorescence, so my ideas come
 from hard X-ray experience, which may not totally apply.
 mam


 On 3/31/2014 3:01 PM, George Sterbinsky wrote:

 Hello,

 I am writing with a general XAS question. It does not necessarily pertain
 to Ifeffit, however, I think the topic is something some, maybe most, list
 members will be knowledgeable about. So it seems like this list is a good
 place to post this question.

 On to the question. I have attached a plot of a MCA spectrum collected
 with a vortex silicon drift detector. The spectrum is actually the average
 of several spectra, all collected in the post edge region of the Co L-edge.
 The spectra were averaged to reduce noise. The three peaks result from
 fluorescence from carbon, oxygen, and cobalt. Low-energy shoulders on the
 Co and O peaks are also observed. These can be seen as the regions of the
 spectrum that are not well reproduced by the fit. The main reason I
 included the fit in the plot is to illustrate the presence of these
 shoulders, particularly in the oxygen florescence, where the additional
 intensity is not so obvious.

 I am writing to see if anyone has any suggestion as to what the origins
 of these peaks might be. They are not due to additional elements, as they
 appear at the same incident energies as the main florescence peaks, i.e.
 the Co shoulder appears at the same incident energies as the main Co peak,
 and the O shoulder appears at the same incident energies as the main O
 peak. It is possible that the peaks result form other transitions.
 Considering Co, the main peak is due to L3/L2-M4 transitions, and the
 shoulder is in a position that could be consistent with L3/L2-M1
 transitions. However, by fitting the peaks with Gaussians, one finds an
 area for the shoulder that is about 25% of the area of the main peak. This
 is significantly larger than what one might expect from tabulated
 transition strengths like those given in Hephaestus.

 To summarize, does anyone know what these shoulders might result from if
 not lower energy transitions? If they are low energy transitions, why would
 the relative transition strengths differ from tabulated values?

 Thank you

Re: [Ifeffit] Demeter on Mac OS X via Macports

[George Sterbinsky]

Hi Frank,

I installed Athena on OSX 10.8.5 using Macports. The error given below
prints to the terminal when I run Athena, and Athena does not generate any
plots. If there is any further information I can provide that would be
helpful, let me know.

Graphics::GnuplotIF : cannot find environment variable DISPLAY

Best,
George





On Fri, Jan 24, 2014 at 3:22 PM, Schima, Frank frank.sch...@nist.govwrote:

  Hello Mac users,


  I finally have launched a Mac OS X version of Demeter 0.9.18.2 on
 Macports. I have not tested it very much because I’m not actually a Demeter
 user. It builds, launches and opens some example data but beyond that, it
 is untested. If the Mac version interests you, fire up your Terminal and
 follow these instructions:

  1. *Carefully* follow the steps to install Macports. 
 http://www.macports.org/install.php
 2. Open a new Terminal window and type the following. It will take a while
 depending on your computer and network speed.

  sudo port install demeter

  3. When it is done, launch Athena by typing the following in Terminal.
 Note: Make sure you are in a directory you have write permission to (like
 your home directory) because it creates hidden log files at launch time.

  athena

  It is a known issue that artemis and hephaestus do not launch right now,
 but Bruce is working on a fix that will be added soon. I'm not going to
 have time to debug people's Macports issues when installing Demeter with
 Macports, but tech support is available on the Macports Users mailing list
 [1]. You should not need any help installing if you correctly follow the
 intructions. Please let Bruce and I know if it works for you or not after
 you have it installed. I have only tested on OS X Mavericks and Mountain
 Lion so far. Keep in mind that this is the first working release candidate
 of Demeter on Mac OS X, so problems are going to be expected.


  Cheers!
 Frank

  [1] https://lists.macosforge.org/mailman/listinfo/macports-users


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Re: [Ifeffit] Header information data Lepidocrocite

[George Sterbinsky]

Hi Florian,

The acronyms stand for

Scan Region Boundary
Scan Region Step Size
Seconds Per Point

Best,
George



On Tue, Nov 5, 2013 at 6:51 AM, daltonabd...@gmail.com 
daltonabd...@gmail.com wrote:

 Hello, Florian.

 Welcome to the list!

 I watched Bruce's video a while ago and I can not remember what those
 acronyms stand for.

 As for the 15k, that means how far in k (k A-1) he collected his EXAFS
 data. You're missing an important information: E (eV) ~ 3.81 k2. Now, do
 the math! Hope that'll make things more clear to you :)

 As for the k steps, 0.05k, that was the way he collected his data, in
 k-steps, instead of energy steps. I usually collect XANES data in E-steps
 and switch to k-steps to collect EXAFS data.

 I'm not sure if this is a proper venue to make advertisements but Scott
 Calvin has recently published an excellent book on XAFS, XAFS for Everyone,
 and I would suggest you to refer to it at your earliest convenience, so you
 can work on your backgrounds more effectively :)


 Good luck!


  - Dalton


 On Tue, Nov 5, 2013 at 9:27 AM, Florian Werner 
 florian.wer...@wzw.tum.dewrote:

  Hi All,

 I'm trying to find my way into XAFS data processing with Athena, but I'm
 new to the topic. I hope someone can help me out with my questions. As
 background information: Currently I'm planning my beamtime experiment for
 XANES spectra about phosphorus speciation at SLRI in Thailand.

 I have made a tutorial with data from Bruce Ravel from scans of
 Lepidocrocite. I have a question regarding this data. For example in the
 header information of file Fe_lepidocrocite.000 (from Bruce Ravel's github
 site) there can be found the abbreviations SRB, SRSS and SPP. So my first
 question is: What do this abbreviations stand for? SRB is the sampling
 range (SR..?!), i guess, so what does 15k stand for (data ends at
 7971.35723 keV, but how is this connected to 15k?)? SRSS manages the step
 size (..SS?), but how does 0.05k result in the given steps?

 I assume that this kind of k-settings may be limited to X-23A2 beamline
 (or BNL), but still I'm anxious to know how the data has been collected.

 Best regards,

 Florian

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Re: [Ifeffit] Athena crash report

[George Sterbinsky]

Hi Bruce,

The output from 'denv' is below.

Thanks,
George



Demeter 0.9.18 with perl 5.014002 on linux
using Ifeffit 1.2.11d

 Major modules   version
==
 Ifeffit ... 3.0.1
 Moose . 2.1005
 MooseX::Aliases ... 0.11
 MooseX::Singleton . 0.29
 MooseX::Types . 0.38
 Archive::Zip .. 1.30
 Capture::Tiny . 0.23
 Chemistry::Elements ... 1.07
 Config::INI ... 0.021
 Const::Fast ... 0.014
 DateTime .. 1.03
 Graph . 0.96
 Graphics::GnuplotIF ... 1.7
 Math::Round ... 0.06
 Pod::POM .. 0.28
 PDL ... 2.007
 PDL::Stats  0.6.3
 Regexp::Assemble .. 0.35
 Regexp::Common  2011121001
 Heap::Fibonacci ... 0.80
 String::Random  0.22
 Text::Template  1.45
 Tree::Simple .. 1.22
 YAML::Tiny  1.50



On Mon, Oct 28, 2013 at 8:48 AM, Bruce Ravel bra...@bnl.gov wrote:

 On 10/27/2013 02:43 PM, George Sterbinsky wrote:

 Hello,

 I am writing to report a crash of Athena 0.9.18 running on Ubuntu 12.04
 as a virtual machine. The terminal output is below. Let me know if I can
 provide any additional information.


 At the command line, type denv and capture the output.

 I am worried that your virtual machine has a very old version of perl
 or perhaps an old version of something Demeter depends upon.  The
 error message seems really surprising to me

 B



 --
  Bruce Ravel  --**-- bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973

  Homepage:http://xafs.org/BruceRavel
  Software:https://github.com/bruceravel
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Re: [Ifeffit] Athena crash report

[George Sterbinsky]

Hi Bruce,

I checked the demeter.ini file and nor1 is set to 150. In fact, I don't see
any values ending in a trailing decimal point in this file.

I have found however that I can reliably crash Athena by opening up a
project, and trying to manually type a value (seemingly any value) for the
start of the normalization range.

Thanks,
George


On Mon, Oct 28, 2013 at 10:47 AM, Bruce Ravel bra...@bnl.gov wrote:


 Hi George,

 I now know what is causing the problem.  For one of the main libraries
 that Demeter depends upon that, your computer has a version that is
 actually ahead of any of my computers.  One of the things that library
 does is manage parameters, including type constraints.  That means
 that it does early checking that, for example, a numerica parameter is
 being set to a numeric value.

 A recent version of that library changed its definition of what
 constitutes a number.

 Apparently, your initialization file (~/.horae/demeter.ini) has a
 value for the default of the lower bound of the normalization range of
 15..  That value, with the trailing dot, is causing the problem.
 That is, I can replicate your problem by setting that parameter to
 that value.

 I know how to fix Demeter to do the right thing given the current
 state of that library and such a perfectly reasonable numeric value as
 15.  That fix will make it into the next release.

 The immediate work-around is to edit the file ~/.horae/demeter.ini and
 search for this section:

 [bkg]
 e0_fraction = 0.5
 spl2 = 0
 nor2 = -100
 clamp2 = 24
 e0 = derivative
 kwindow = hanning
 pre1 = -150
 dk = 0
 fnorm = true
 nor1 = 150
 nnorm = 3
 kw = 2
 nclamp = 5
 spl1 = 0.0
 clamp1 = 0
 rbkg = 1.0
 flatten = true
 pre2 = -30

 You will have a line like

 nor1 = 15.

 Edit that to read

 nor1 = 15

 and try restarting Athena.  If you get a similar error message, search
 through that section or elsewhere in the .ini file for numeric values
 that have a trailing dot.

 Thanks for finding and reporting this!

 B


 --
  Bruce Ravel  --**-- bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973

  Homepage:http://xafs.org/BruceRavel
  Software:https://github.com/bruceravel
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[Ifeffit] Athena crash report

[George Sterbinsky]

Hello,

I am writing to report a crash of Athena 0.9.18 running on Ubuntu 12.04 as
a virtual machine. The terminal output is below. Let me know if I can
provide any additional information.

Thanks,
George

parallels@parallels-Parallels-Virtual-Platform:~$ dathena
Attribute (bkg_nor1) does not pass the type constraint because: Validation
failed for 'Num' with value 15. at accessor Demeter::Data::bkg_nor1
(defined at
/home/parallels/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm
line 264) line 12, F line 1.
Demeter::Data::bkg_nor1(Demeter::Data=HASH(0xd26a1b0), 15.) called at
/home/parallels/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/Main.pm
line 843

Demeter::UI::Athena::Main::OnParameter(Demeter::UI::Athena::Main=HASH(0xaf7f780),
Wx::CommandEvent=SCALAR(0xc130520), Demeter::UI::Athena=HASH(0x186fad0),
bkg_nor1) called at
/home/parallels/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/Main.pm
line 341

Demeter::UI::Athena::Main::__ANON__(Demeter::UI::Athena::Main=HASH(0xaf7f780),
Wx::CommandEvent=SCALAR(0xc130520)) called at
/home/parallels/perl5/bin/dathena line 47
eval {...} called at /home/parallels/perl5/bin/dathena line 47
parallels@parallels-Parallels-Virtual-Platform:~$
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[Ifeffit] Renaming groups in Athena

[George Sterbinsky]

Hello,

I am writing to report what I believe to be a bug in Athena. In the
attached project, there are two groups, a main group and a reference group.
Changing the name of the first group does not change the name of the
reference group. Changing the name of the reference group separately
doesn't work well either. This results in an extra Ref being added to the
beginning of the group name, which cannot be deleted. This happens every
time one changes the name of the reference group, which can result in quite
a long name for the reference. Let me know if any further information would
be helpful.

Thank you,
George


Example.prj
Description: Binary data
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Re: [Ifeffit] Athena fix edge step

[George Sterbinsky]

Hi Bruce,

That seems to do the trick for me as well. Thanks!

George


On Tue, Sep 24, 2013 at 5:44 PM, Bruce Ravel bra...@bnl.gov wrote:

 On 09/20/2013 11:53 AM, George Sterbinsky wrote:

 Hello,

 I am writing to report what I believe to be a bug in Athena. I am using
 Demeter 0.9.18 and windows 8.

 To reproduce the behavior, open the attached project, and press the
 button to plot normalized marked groups in energy. One will observe that
 the fix edge step box is checked for the first group. Changing the edge
 step value for this group and pressing the button to replot the
 normalized data has no effect on the plot.


 George,

 Didn't find a time to look at this until today.

 Could you replace


 C:\strawberry\perl\site\lib\**Demeter\templates\process\**
 ifeffit\normalize.tmpl

 with the attached text file.  Make sure it is called normalize.tmpl.
 Sometimes the mailer will add .txt or some such to a file.

 That seems to do the trick.  Let me know if that fixes the problem to
 your satisfaction and I will push the fix into the next release.

 B


 --
  Bruce Ravel  --**-- bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973

  Homepage:http://xafs.org/BruceRavel
  Software:https://github.com/bruceravel

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Re: [Ifeffit] normalization methods

[George Sterbinsky]

The question of whether it is appropriate to use flattened data for
quantitative analysis is something I've been thinking about a lot recently.
In my specific case, I am analyzing XMCD data at the Co L-edge. To obtain
the XMCD, I measure XAS with total electron yield detection using a ~70%
left or right circularly polarized beam and flip the magnetic field on the
sample at every data point. The goal then, is to subtract the XAS measured
in a positive field (p-XAS) from XAS measured in a negative field (n-XAS)
and get something (the XMCD) that is zero in the pre-edge and post-edge
regions. I often find that after removal of a linear pre-edge, the spectra
still have a linearly increasing post edge (with EXAFS oscillations
superimposed on it), and the slope of the n-XAS and p-XAS post-edge lines
are different. In this case simply multiplying the n-XAS and p-XAS by
constants will never give an XMCD spectrum that is zero in the post edge
region. There is then some component of the XAS background that is not
accounted for by linear subtraction and multiplication by a constant. It
seems to me that flattening could be a good way to account for such a
background. So is flattening a reasonable thing to do in a case such as
this, or is there a better way to account for such a background?

Thanks,
George


On Wed, May 15, 2013 at 11:41 AM, Matthew Marcus mamar...@lbl.gov wrote:

 The way I commonly do pre-edge is to fit with some form plus a power-law
 singularity representing the initial rise of the edge, then
 subtract out that some form.  Now, that form can be either linear,
 linear+E^(-2.7) (for transmission), or linear+ another power-law
 singularity centered at the center passband energy of the fluorescence
 detector.  That latter is for fluorescence data which is affected by
 the tail of the elastic/Compton peak from the incident energy.  Whichever
 form is taken gets subtraccted from the whole data range, resulting
 in data which is pre-edge-subtracted but not yet post-edge normalized.
  The path then splits; for EXAFS, the usual conversion to k-space, spline
 fitting in the post-edge, subtraction and division is done, all
 interactively.  Tensioned spline is also available due to request of a
 prominent user.
 For XANES, the post-edge is fit as previously described.  Thus, there's no
 distinction made between data above and below E0 in XANES, whereas
 there is such a distinction in EXAFS.
 mam


 On 5/15/2013 8:25 AM, Matt Newville wrote:

 Hi Matthew,

 On Wed, May 15, 2013 at 9:57 AM, Matthew Marcus mamar...@lbl.gov wrote:

 What I typically do for XANES is divide mu-mu_pre_edge_line by a linear
 function which goes through the post-edge oscillations.
 This division goes over the whole data range, including pre-edge.  If the
 data has obvious curvature in the post-edge, I'll use a higher-order
 polynomial.  For transmission data, what sometimes linearizes the
 background
 is to change the abscissa to 1/E^2.7 (the rule-of-thumb absorption
 shape) and change it back afterward.  All this is, of course, highly
 subjective and one of the reasons for taking extended XANES data (300eV,
 for instance).  For short-range XANES, there isn't enough info to do more
 than divide by a constant.  Once this is done, my LCF programs allow
 a slope adjustment as a free parameter, thus muNorm(E) =
 (1+a*(E-E0))*Sum_on_ref{x[ref]***muNorm[ref](E)}.  A sign that this
 degree of
 freedom
 may be being abused is if the sum of the x[ref] is far from 1 or if
 a*(Emax-E0) is large.  Don't get me started on overabsorption :-)
  mam


 Thanks -- I should have said that pre_edge() can now do a
 victoreen-ish fit, regressing a line to mu*E^nvict (nvict can be any
 real value).

 Still, it seems that the current flattening is somewhere between
 better and worse, which is unsettling...  Applying the
 flattening polynomial to the pre-edge range definitely seems to give
 poor results, but maybe some energy-dependent compromise is possible.

 And, of course, over-absorption is next on the list!

 --Matt
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Re: [Ifeffit] normalization methods

[George Sterbinsky]

By standard normalization, I meant subtraction of a linear pre-edge and
multiplication by a constant. If this treatment is applied to the XAS
spectra before subtraction, one does not obtain an XMCD spectrum that goes
to zero in the post edge region for the data I described. As you noted,
that is what would be expected given the p-XAS and n-XAS have different
slopes in the post-edge region.

On the other hand, standard normalization + flattening does result in pre
and post-edge regions that go to zero, again as one might expect. So
perhaps, the background modeled by standard normalization + flattening is
an accurate representation of the real background in some cases and can be
used in quantitative analysis. Is there reason to believe that cannot be
the case?

Thanks,
George




On Wed, May 15, 2013 at 3:04 PM, Matthew Marcus mamar...@lbl.gov wrote:

 OK, I guess I don't know what 'standard normalization' is.  It looks from
 the quotient that you'll need some sort of curved post-edge.
 I guess the division didn't work because the electron energy distribution
 is different pre- and post-edge, so the magnetic effects are
 different and vary across the edge.  Thus, the shapes of the MCD peaks
 will be at least a little corrupted even if the pre- and post-edge
 spectra are taken into account.  I don't know what to do about this.  Did
 you try asking Elke?
 mam


 On 5/15/2013 11:52 AM, George Sterbinsky wrote:

 Hi Matthew,



 On Wed, May 15, 2013 at 1:20 PM, Matthew Marcus mamar...@lbl.govmailto:
 mamar...@lbl.gov wrote:

 You say that the flipping difference (p - n) is 0 in pre-edge and far
 post-edge regions, which is as it should be, but then say that the
 slopes of p- and n- post-edges, considered separately, are different.
  I must be misunderstanding because those two statements would seem to be
 inconsistent.



 Sorry, I think my wording wasn't particularly clear here. What I should
 have said is:

 The goal then is to subtract the /normalized/ XAS measured in a positive
 field (p-XAS) from /normalized/ XAS measured in a negative field (n-XAS)
 and get something (the XMCD) that is zero in the pre-edge and post-edge
 regions. /However, standard normalization does not give this result/


 Italics indicate new text.

 I wonder if the sensitivity of the TEY changes with magnetic field
 because of the effect of the field on the trajectories of
 the outgoing electrons, which would explain the differing curves.


 I would agree, I think the effect of the magnetic field on the electrons
 is the likely source of the differences in background.

 A possibility - if you divide the p-XAS by n-XAS, do you get something
 which is a smooth curve everywhere but where MCD is expected?  Does
 that curve match in pre- and far post-edge regions?


 No, after division of the p-XAS by the n-XAS (before any normalization),
 both the pre and post-edge regions are smooth, but one would need a
 step-like function to connect them. I've attached a plot showing the result
 of division.


 If that miracle occurs,
 then perhaps you could fit that to a polynomial, except in the MCD
 region, then divide the p-XAS by that polynomial, to remove the effect of
 the differing sensitivities.

 There are people here at ALS, such as Elke Arenholz 
 earenh...@lbl.gov mailto:earenh...@lbl.gov, who do this sort of
 spectroscopy.  I suggest asking her.

  mam


 Thanks for the suggestion and your reply.

 George








 On 5/15/2013 9:58 AM, George Sterbinsky wrote:

 The question of whether it is appropriate to use flattened
 data for quantitative analysis is something I've been thinking about a lot
 recently. In my specific case, I am analyzing XMCD data at the Co L-edge.
 To obtain the XMCD, I measure XAS with total electron yield detection using
 a ~70% left or right circularly polarized beam and flip the magnetic field
 on the sample at every data point. The goal then, is to subtract the XAS
 measured in a positive field (p-XAS) from XAS measured in a negative field
 (n-XAS) and get something (the XMCD) that is zero in the pre-edge and
 post-edge regions. I often find that after removal of a linear pre-edge,
 the spectra still have a linearly increasing post edge (with EXAFS
 oscillations superimposed on it), and the slope of the n-XAS and p-XAS
 post-edge lines are different. In this case simply multiplying the n-XAS
 and p-XAS by constants will never give an XMCD spectrum that is zero in the
 post edge region. There is then some
 component of the

 XAS background that is not accounted for by linear
 subtraction and multiplication by a constant. It seems to me that
 flattening could be a good way to account for such a background. So is
 flattening a reasonable thing to do in a case such as this, or is there a
 better way to account for such a background?

 Thanks,
 George


 On Wed, May 15, 2013

[Ifeffit] Shifted data in Athena

[George Sterbinsky]

Hello,

I have attached an (D)Athena project with containing two groups, imported
as a primary data set and a reference. The groups were therefore imported
on the same energy grid. However, when plotted, the energy values of the
data points for the two groups are clearly shifted with respect to each
other. Can someone please explain the origin of this shift?

Thank you,
George


ShiftedData.prj
Description: Binary data
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Re: [Ifeffit] Merging data in Athena

[George Sterbinsky]

Hi Chris,

The reason that I have spectra with different point spacings is because I
felt that a given range of the spectrum was oversampled. That is to say,
all of the spectral features could be captured with less points. It is not
clear to me why merging two spectra, where one has more data points than
necessary, would not still reduce the noise and uncertainty of the
measurement. Could you elaborate on your concern?

Thank you,
George




On Wed, Feb 27, 2013 at 8:24 AM, Christopher Patridge
patri...@buffalo.eduwrote:

  George,

 It seems rather unconventional to try and merge data which has different
 energy grid spacing?  I thought the main point of merging data is to reduce
 the noise and uncertainty of a measurement.  I am not sure how the exact
 method of merging data is implemented but I don't think it is fair to call
 this a bug as a result of a unique situation.  Could you or have you
 reinterpolate one spectrum?

 Chris Patridge

 
 Christopher J. Patridge, PhD
 NRC Post Doctoral Research Associate
 Naval Research Laboratory
 Washington, DC 20375
 Cell: 315-529-0501

 On 2/26/2013 6:55 PM, George Sterbinsky wrote:

  I am writing to make you aware of what I believe to be a bug in
 (D)Athena.  To demonstrate the problem, I have attached a project file
 containing two groups. Both groups have the same energy range but were
 measured with slightly different point spacings. Attempting to merge the
 two groups results in Athena excluding one of the groups from the merge
 for being too short.

  Thank you,
 George


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Re: [Ifeffit] Merging data in Athena

[George Sterbinsky]

Thanks Bruce


On Wed, Feb 27, 2013 at 8:28 AM, Bruce Ravel bra...@bnl.gov wrote:

 On Tuesday, February 26, 2013 06:55:21 PM George Sterbinsky wrote:
  I am writing to make you aware of what I believe to be a bug in
 (D)Athena.
  To demonstrate the problem, I have attached a project file containing two
  groups. Both groups have the same energy range but were measured with
  slightly different point spacings. Attempting to merge the two groups
  results in Athena excluding one of the groups from the merge for being
 too
  short.

 Look at the merge preferences.

 B


 --

  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973

  Homepage:http://xafs.org/BruceRavel
  Software:https://github.com/bruceravel
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[Ifeffit] Merging data in Athena

[George Sterbinsky]

I am writing to make you aware of what I believe to be a bug in (D)Athena.
To demonstrate the problem, I have attached a project file containing two
groups. Both groups have the same energy range but were measured with
slightly different point spacings. Attempting to merge the two groups
results in Athena excluding one of the groups from the merge for being too
short.

Thank you,
George


athena.prj
Description: Binary data
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Re: [Ifeffit] merging data

[George Sterbinsky]

The unexpected result I demonstrated persists for real step-like XAS data.
The data in the project I attached are actually just monitor counts, and
are only being used here to illustrate the unexpected behavior. It is not
actually data that I am trying to analyze.

George


On Fri, Dec 14, 2012 at 12:12 PM, Bruce Ravel bra...@bnl.gov wrote:


 I agree that you have uncovered an edge case where my merging
 algorithm does something unexpected.  Figuring this out and fixing it
 is nowhere near the top of my list of priorities.  I think I would be
 happier flagging an error when the user sets a zero-length range for
 the pre- or post-edge lines.

 Athena is not intended to be a generic data processing tool.  Its
 algorithms are fairly well tested and expected to work when you have
 data that nominally resembles XAS data -- that is, some kind of
 step-like function, possibly with wiggles above the step.  It has an
 algorithm for normalization that makes those same assumptions.

 We all eventually go to the beamline and measure something that needs
 interpretation, but which is not a step-like function with wiggles.
 The solution to that problem is not to expect Athena to miraculously
 do what you want.  The solution is to go find the find the right tool
 for the job.  Or, if it doesn't exist, write it yourself.

 B

 On Thursday, December 06, 2012 10:59:55 AM George Sterbinsky wrote:
  Hello,
 
  I am observing some behavior in (D)Athena that I do not understand, and I
  was hoping someone could explain it to me. I have attached a project file
  to illustrate my question. The first two groups in the file have been
  normalized such that mu(E) and norm(E) are identical. I then merged these
  groups in mu(E) and norm(E), also in the file. Since mu(E) and norm(E)
 are
  the same for the groups, I would expect the data merged in mu(E) and
  norm(E) to also be identical, but it is not. While it is clear that
 merging
  in mu(E) is averaging the groups, it seems merging in norm(E) is not. So
  what is merging in norm(E) doing?
 
  Thank you,
  George


 --

  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973

  Homepage:http://xafs.org/BruceRavel
  Software:https://github.com/bruceravel
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[Ifeffit] merging data

[George Sterbinsky]

Hello,

I am observing some behavior in (D)Athena that I do not understand, and I
was hoping someone could explain it to me. I have attached a project file
to illustrate my question. The first two groups in the file have been
normalized such that mu(E) and norm(E) are identical. I then merged these
groups in mu(E) and norm(E), also in the file. Since mu(E) and norm(E) are
the same for the groups, I would expect the data merged in mu(E) and
norm(E) to also be identical, but it is not. While it is clear that merging
in mu(E) is averaging the groups, it seems merging in norm(E) is not. So
what is merging in norm(E) doing?

Thank you,
George


Example.prj
Description: Binary data
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[Ifeffit] Demeter on windows 8

[George Sterbinsky]

Hello,

Has anyone been able to install Demeter on windows8?

When I try to open Athena I get the message in attached screen shot.

I tried reinstalling as suggested by the message, which did not help. One
thing I noticed however was that Perl was not removed by the built in
Demeter uninstaller.

Any suggestions appreciated.

Thank you,
George
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Re: [Ifeffit] Demeter on windows 8

[George Sterbinsky]

Hi All,

Athena seems to be running now. It may have just been necessary to reboot
the system, though I also reinstalled again, so I'm not certain exactly
what fixed it.

Thank you,
George


On Tue, Nov 13, 2012 at 5:58 PM, George Sterbinsky 
georgesterbin...@u.northwestern.edu wrote:

 Hello,

 Has anyone been able to install Demeter on windows8?

 When I try to open Athena I get the message in attached screen shot.

 I tried reinstalling as suggested by the message, which did not help. One
 thing I noticed however was that Perl was not removed by the built in
 Demeter uninstaller.

 Any suggestions appreciated.

 Thank you,
 George


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[Ifeffit] ifeffit on Lion

[George Sterbinsky]

Hi list members,

I am attempting to install ifeffit on mac book running Lion (10.7.4). I
have downloaded and installed xcode and gfortran. I downloaded the iffeffit
package from github. I then cd into .../Downloads/newville-ifeffit-30644e
and run

sudo ./PGPLOT_install

I get the following error:

 = = = = = = = = = = = = = = = = = = = = = = = = = =
 = PGPLOT installation script
 =
 system =  linux  ==  linux g77_gcc
 prefix =  /usr/local/
 = Looking for PGPLOT file: pgplot5.2.tar.gz
 = PGPLOT file not found
 = I'll try to download it for you...
  trying with regular old ftp
  you may have to hit return here for this to work --
  Really, you won't need to enter 'anonymous' or a valid
  username --- just hit return
ftp: Can't connect to `131.215.193.54': Connection refused
ftp: Can't connect to `ftp.astro.caltech.edu'
./PGPLOT_install: line 176:  1407 Segmentation fault: 11  $ftp
$pgp_ftpsite  EOF
anonymous
ifef...@cars.uchicago.edu
cd  $pgp_ftpdir
hash
get $pgp_file
exit
EOF

 = Sorry, I couldn't download the PGPLOT tar file.
 = You'll have to download it yourself. Try this:
 =   ftp ftp.astro.caltech.edu
 =   cd  pub/pgplot/
 =   get pgplot5.2.tar.gz
 = then run this script again

I then downloaded pgplot5.2.tar.gz, dropped this into newville...e and
ran ./PGPLOT_install again. This gives the following message, which
comes after numerous warnings:

= = = = = = = = = = = = = = = = = = = = = = = = = =
 = Uh-oh.  PGPLOT is missing some important files!
 = It looks like PGPLOT failed during building or
 = is only partially installed.
 =
 = Please consult the PGPLOT installation instructions
 = in the subdirectory  pgplot/, and the log file:
 =/Users/gsterbinsky/Downloads/newville-ifeffit-306444e/PGPLOT_install.log
 = which contains a full list of commands run.
 =
 = You may want to repeat these steps by hand or
 = consult the PGPLOT installations instructions
 = in install-unix.txt
 = = = = = = = = = = = = = = = = = = = = = = = = = =

I did some googling and found this explanation of what might be going
on: http://mingus.as.arizona.edu/~bjw/software/pgplot_fix.html

However, the iffefit INSTALL file says pgplot must be installed with
the PGPLOT_install command, which these directions do not use.
Furthermore, since iXAFS runs on Lion, it seems to me that someone may
have already found a solution to this problem.
So rather than trying more random solutions, I thought it might be
pertinent to check with the list so see if that is the case.
If anyone can provide any suggestions or a known solution to this
problem, I would appreciate it.

Thanks,
George
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Re: [Ifeffit] Sudden Difficulty with Importing Data into Athena

[George Sterbinsky]

Tony, You ask are there hidden files I should remove as well that aren't
removed...? I do find a Perl folder in my Library folder. I'm not sure
if this was installed by iXAFS or affects iXAFS...

George




On Thu, Feb 2, 2012 at 8:18 PM, Tony Kelly tkell...@gmail.com wrote:

 This will make me seem pretty dense, but I'm still trying to figure
 out how to reply to specific threads in the list-serve from my gmail,
 and I keep seeming to create new threads... for which I wholeheartedly
 apologize if it's becoming annoying.  But I really do thank everyone
 for their help and patience thus far.

 What I've attempted since earlier today:
 1.  Completely reinstalling from older versions and newer versions of
 IFEFFIT onto the Mac.  Didn't work.
 2.  I went to two other Macs, did a clean install of the newest iXAFS
 software and it worked fine... which can only mean something really
 crazy is going on with the Mac I am trying to use for my work.  I'd
 like to mention again that I was able to import data just fine last
 night, and it was only this morning that things started breaking.
 3.  I've reinstalled X11 and XQuartz.
 4.  I've checked the data files on the other Mac machines (and Dr.
 Zając checked them) and the files were fine.
 5.  I attempted to run from the command line and found some errors
 that weren't there at one time.
 6.  I then checked my version of perl, and it is version 5

 bash-3.2$ perl -v

 This is perl, v5.10.0 built for darwin-thread-multi-2level
 (with 2 registered patches, see perl -V for more detail)

 6.  Something that MAY shed light on the situation... when I open
 iXAFS from the Application menu in the Dock (I'll try attaching an
 image), it seems that iXAFS is broken or not installing correctly.
 However, I can then open iXAFS up in the FINDER window, it looks
 okay and can be opened... it just doesn't function correctly.  What
 I don't understand is why a clean install doesn't fit the problem...
 are there hidden files I should remove as well that aren't removed
 when I uninstall iXAFS from the application directory with (rm -rf ) ?

 7.  George mentions that his build is different than my own, so now I
 am looking at my structure (modified for more pleasant viewing), but
 the directory does seem to exist.:

 bash-3.2$ ls /Applications/iXAFS.app/
 Contents

 ls /Applications/iXAFS.app/Contents/
 Info.plist  MacOS   PkgInfo Resources

 ls /Applications/iXAFS.app/Contents/Resources/
 Artemis.icnsAthena.icns English.lproj
 Hephaestus.icns Horae   iXAFS Shell.icns
 iXAFS Shell.sh  iXAFS.icns

 ls /Applications/iXAFS.app/Contents/Resources/Horae/bin/
 Aquaterm.appatoms   crc32
  feffit
 ifeffit libpng-config   perlindex
 tkpod
 artemis autobk  diffkk
  findatp
 ifeffit_shell.pllibpng12-config rdaj
 athena  chartex feff6
 hephaestus  ixafs-env   lsprj
 tkmore


 Tony Kelly, M.Sc.
 DTRA PhD Student
 Air Force Institute of Technology
 Nuclear Physics and Engineering



 On Thu, Feb 2, 2012 at 5:15 PM,
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  When replying, please edit your Subject line so it is more specific
  than Re: Contents of Ifeffit digest...
 
 
  Today's Topics:
 
1. Re: Sudden Difficulty with Importing Data into Athena
   (Dr. Dariusz A. Zaj?c)
2.  Sudden Difficulty with Importing Data into Athena (Tony Kelly)
3. Re: Sudden Difficulty with Importing Data into Athena
   (Bruce Ravel)
4. Re: Sudden Difficulty with Importing Data into Athena (Tony Kelly)
5. Re: Sudden Difficulty with Importing Data into Athena
   (Dr. Dariusz A. Zaj?c)
6. Re: Sudden Difficulty with Importing Data into Athena
   (Dr. Dariusz A. Zaj?c)
 
 
  --
 
  Message: 1
  Date: Thu, 02 Feb 2012 19:07:32 +0100
  From: Dr. Dariusz A. Zaj?c ki...@ifj.edu.pl
  To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
  Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into
 Athena
  Message-ID: 4f2ad0e4.3010...@ifj.edu.pl
  Content-Type: text/plain; charset=UTF-8; format=flowed
 
  check the data, if at the end of  files are some zeros or strange
  numbers or even empty line(maybe). That what you described can be
  exactly caused by problem with the data in file, eg. injection during
  measurements
 
  W dniu 12-02-02 

Re: [Ifeffit] Sudden Difficulty with Importing Data into Athena

[George Sterbinsky]

Tony,

Have you checked to see if the directories referenced in your error
messages actually exist?

I am running iXAFS (according to the about iXAFS menu it is version 2
(2.2)) on mac OSX 10.5.8. One thing I noticed is that the directory
referenced in your error message,
/Applications/iXAFS.app/Contents/Resources/Horae/bin/ifeffit, does not
exist on my computer. Instead ifeffit is found in
/Applications/iXAFS.app/Contents/Resources/local/bin/ifeffit


George


2012/2/2 Dr. Dariusz A. Zając ki...@ifj.edu.pl

 Hmm,
 under Win XP I had no problems to open files, together with the reference.
 For Tony's data as well as downloaded from internet's one.
 I'm just thinking - this maybe is some problem with the settings in open
 window, or with compilation of Athena.
 About second case I have not to much to say,
 About first - maybe some option for opening file and processing data? I
 tried to see each counter separately and I had no problems, also with
 negate function...
 any ideas?
 darek

 W dniu 12-02-02 20:23, Tony Kelly pisze:

 1.  I made sure to check the data files for strange behavior,
 definitely a good idea.  I know when I use other software such as
 ROOT, file structure and pat names can become problems.  This didn't
 fix the problem, however :-/

 2.  I then ran Athena from the command line as was suggested, and it
 seems that there is a major problem there:

 bash-3.2$ athena
 Can't load '/Applications/iXAFS.app/**Contents/Resources/local/lib/**
 perl5/site_perl/5.12.1/darwin-**multi-2level/auto/Ifeffit/**
 Ifeffit.bundle'
 for module Ifeffit:
 dlopen(/Applications/iXAFS.**app/Contents/Resources/local/**
 lib/perl5/site_perl/5.12.1/**darwin-multi-2level/auto/**
 Ifeffit/Ifeffit.bundle,
 1): Library not loaded: libifeffit.so
  Referenced from:
 /Applications/iXAFS.app/**Contents/Resources/local/lib/**
 perl5/site_perl/5.12.1/darwin-**multi-2level/auto/Ifeffit/**
 Ifeffit.bundle
  Reason: image not found at
 /Applications/iXAFS.app/**Contents/Resources/local/lib/**
 perl5/5.12.1/darwin-multi-**2level/DynaLoader.pm
 line 204.
  at /Applications/iXAFS.app/**Contents/Resources/local/bin/**athena line
 67
 Compilation failed in require at
 /Applications/iXAFS.app/**Contents/Resources/local/bin/**athena line 67.
 BEGIN failed--compilation aborted at
 /Applications/iXAFS.app/**Contents/Resources/local/bin/**athena line 67.


 3.  Then I became more curious and attempted ifeffit itself:

 bash-3.2$ ifeffit
 dyld: Library not loaded: libpgplot.dylib
   Referenced from: /Applications/iXAFS.app/**
 Contents/Resources/Horae/bin/**ifeffit
   Reason: image not found
 Trace/BPT trap


 I am using Max OSX 10.6.8.
 Intel Core i5.

 Any other Mac users out there have ideas?

 Thanks much,

 Tony Kelly
 Air Force Institute of Technology
 Nuclear Physics and Engineering
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[Ifeffit] number of independent points

[George Sterbinsky]

Hello,

Since I haven't received a response to my previous question, I just wanted
to make sure I asked it clearly. To elaborate, I am attaching a log from
Athena. The log file lists:

 Independent points  =  27.057617188

If I attempt to reproduce this result using the equation in the feffit
document, I find

Nidp = { [2*(kmax - kmin)*(Rmax-Rmin) / pi] + 2} = { [2*(14 - 0.5)*(4.2 -
1.0) / pi] + 2} = 29.50197417,

where I have used the k-range and R-range in the log file as kmax, kmin,
Rmax, and Rmin.

Can someone explain to me why may calculation does not reproduce the number
given for independent points in the log fie?

Thank you,
George

On Fri, Oct 7, 2011 at 1:04 PM, George Sterbinsky 
georgesterbin...@u.northwestern.edu wrote:

 Hello,

 I am wondering what values Artemis/feffit use for kmax and kmin when
 calculating the number of independent points (Nidp) for a fit done in
 R-space, where according the feffit document, Nidp = { [2*(kmax -
 kmin)*(Rmax-Rmin) / pi] + 2}, and kmax and kmin define the fitting range. I
 have tried using the Fourier transform range for kmax and kmin, but this
 does not give agreement with the value of Nidp reported by Artermis.

 Thank you,
 George



LaCoO3_pow_2.log
Description: Binary data
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Re: [Ifeffit] number of independent points

[George Sterbinsky]

Sorry, the log file is from Artemis, not Athena...

On Mon, Oct 10, 2011 at 10:35 AM, George Sterbinsky 
georgesterbin...@u.northwestern.edu wrote:

 Hello,

 Since I haven't received a response to my previous question, I just wanted
 to make sure I asked it clearly. To elaborate, I am attaching a log from
 Athena. The log file lists:

  Independent points  =  27.057617188

 If I attempt to reproduce this result using the equation in the feffit
 document, I find

 Nidp = { [2*(kmax - kmin)*(Rmax-Rmin) / pi] + 2} = { [2*(14 - 0.5)*(4.2 -
 1.0) / pi] + 2} = 29.50197417,

 where I have used the k-range and R-range in the log file as kmax, kmin,
 Rmax, and Rmin.

 Can someone explain to me why may calculation does not reproduce the number
 given for independent points in the log fie?

 Thank you,
 George

 On Fri, Oct 7, 2011 at 1:04 PM, George Sterbinsky 
 georgesterbin...@u.northwestern.edu wrote:

 Hello,

 I am wondering what values Artemis/feffit use for kmax and kmin when
 calculating the number of independent points (Nidp) for a fit done in
 R-space, where according the feffit document, Nidp = { [2*(kmax -
 kmin)*(Rmax-Rmin) / pi] + 2}, and kmax and kmin define the fitting range. I
 have tried using the Fourier transform range for kmax and kmin, but this
 does not give agreement with the value of Nidp reported by Artermis.

 Thank you,
 George



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Re: [Ifeffit] number of independent points

[George Sterbinsky]

Bruce, Matt, and Jeremy,

Thank you for explaining this. Your responses are much appreciated.

George

On Mon, Oct 10, 2011 at 11:35 AM, Bruce Ravel bra...@bnl.gov wrote:

 On Monday, October 10, 2011 10:35:12 am George Sterbinsky wrote:
  Since I haven't received a response to my previous question, I just
 wanted
  to make sure I asked it clearly.

 I suspect the lack of response had more to do with it being a
 non-trivial question asked on a Friday afternoon :)

  To elaborate, I am attaching a log from
  Athena. The log file lists:
 
   Independent points  =  27.057617188
 
  If I attempt to reproduce this result using the equation in the feffit
  document, I find
 
  Nidp = { [2*(kmax - kmin)*(Rmax-Rmin) / pi] + 2} = { [2*(14 - 0.5)*(4.2 -
  1.0) / pi] + 2} = 29.50197417,
 
  where I have used the k-range and R-range in the log file as kmax, kmin,
  Rmax, and Rmin.
 
  Can someone explain to me why may calculation does not reproduce the
 number
  given for independent points in the log fie?

 George,

 A quick examination of the ifeffit source code shows that there are
 two issues:

  1. Regardless of what it may say in the document, Ifeffit uses +0
rather than +2.  See line 345 of
http://cars9.uchicago.edu/svn/ifeffit/trunk/src/lib/iff_feffit.f

A bit of history: Ed Stern wrote this paper back in 1993:
   http://dx.doi.org/10.1103/PhysRevB.48.9825

Over the years, many have expressed scepticism of his conclusion.
The Bayesian work I mentioned earlier suggests quibbling over the
value of N in the +N term misses the bigger issue.  Ifeffit's
use of +0 provides a conservative yet easily stated estimate of
Nidp.

  2. The difference to the left of the decimal point has to do with the
fact that Artemis allows you to pick any value for kmin, kmax,
rmin, and rmax.  When Ifeffit evaluates Nidp (and anything else)
is actually takes the nearest grid points to those four values.
The grid in k-space is 0.05 inv. Angstroms.  This sets the grid in
R space to be about 0.03 Angstroms, but not exactly.  So the
values of Rmax and Rmin used by Ifeffit to compute Nidp (and other
things) are not quite what you specified.

 At some point, George, you may want to bite the bullet and look at
 source code.  Details are not unknowable, they just might not be
 written down anywhere beside the source code.

 Here is the top of Ifeffit:
   http://cars9.uchicago.edu/svn/ifeffit/trunk/

 B


 --

  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973

  My homepage:http://xafs.org/BruceRavel
  EXAFS software:  http://cars9.uchicago.edu/ifeffit/Demeter
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[Ifeffit] number of independent points

[George Sterbinsky]

Hello,

I am wondering what values Artemis/feffit use for kmax and kmin when
calculating the number of independent points (Nidp) for a fit done in
R-space, where according the feffit document, Nidp = { [2*(kmax -
kmin)*(Rmax-Rmin) / pi] + 2}, and kmax and kmin define the fitting range. I
have tried using the Fourier transform range for kmax and kmin, but this
does not give agreement with the value of Nidp reported by Artermis.

Thank you,
George
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Re: [Ifeffit] Artemis fitting k-weight

[George Sterbinsky]

Thanks Bruce.

George

On Tue, Sep 20, 2011 at 3:48 PM, Bruce Ravel bra...@bnl.gov wrote:

 On Tuesday, September 20, 2011 03:44:55 pm Bruce Ravel wrote:
  I have not explored this issue in the new Artemis, but if is exists it
  will be fixed before the next Demeter release.

 FWIW, I tested this in the the new version of Artemis and it seems to
 be done correctly.

 B

 --

  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973

  My homepage:http://xafs.org/BruceRavel
  EXAFS software:  http://cars9.uchicago.edu/ifeffit/Demeter
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[Ifeffit] Artemis fitting k-weight

[George Sterbinsky]

Hello,

When fitting data in Artemis with the other k weight box checked and the
kw = 1, 2, or 3 boxes unchecked, I find that the log file lists k-weight =
1, kw, where kw is the value I entered into the other k weight text box.
If I choose 0 as the other k weight, then the log file lists k-weight = 1.
Is it possible to run a fit in Artemis using only a k-weight of something
other than 1, 2, or 3?

Thank you,
George
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Re: [Ifeffit] more bugs in atoms?

[George Sterbinsky]

Hi Lisa,

The typo in the core atom does not affect the result if run in Artemis. I
think I now have a better grasp of why atoms cannot run my structure
correctly. The standard i2/c setting has a unique axis a, but the structure
in the input file below has a unique axis b. This appears to through atoms
off. If I convert to an I2/a setting, then I get the correct results without
a shift vector.

George



On Fri, May 27, 2011 at 1:40 PM, Gudrun Lisa Bovenkamp 
bovenk...@physik.uni-bonn.de wrote:

 Hi George,

 I cannot understand how you got this atoms.inp file where the core is
 stated to be Co1 and there is only Fe. So, I cannot confirm the crystal
 structure from a database.
 My problem is solved. I understood that the ATOMS program implemented in
 Arthemis and ATOMS 2.5 have some bugs that are corrected in ATOMS 3.0 and
 WebATOMS. When I use those two programs I get a correct crystal structure
 xyz table in feff.inp.
 the only reason that I can think of, why your shifting seem to work better
 is that the atoms.inp file was not representing the correct structure in the
 first place. This can happen when the situation you wnat to describe is not
 the situation that was measured by somebody else. Or there is a mistake in
 the paper.
 Anyway. Thanks for sharing this idea.

 Lisa



  Date: Thu, 26 May 2011 11:41:08 -0400
 From: George Sterbinsky georgesterbin...@u.northwestern.edu
 To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov

 Subject: Re: [Ifeffit] more bugs in atoms?
 Message-ID: BANLkTi=OH=ncjjmwhke5vlmnteao8k3...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1


 Hi Lisa,

 Let me just mention one situation I have encountered using atoms, and how
 I
 resolved it. I am not sure if this is the result of a bug or not, but
 perhaps you can try applying the approach I took to your own situation and
 see if it can resolve your problem.

 The issue I encountered was running atoms for a monoclinic I2/c structure,
 space group 15.

 Here is the atoms input file:

 ! This atoms input file was generated by Artemis 0.8.014
 ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001
 title = ...
 space = i 2/c 1 1
 a =  5.51120b =  5.51120c =  7.79410
 alpha = 90.0beta = 90.740gamma = 90.0
 core =Co1edge =Krmax =  6.0
 !shift   0.25000   0.25000   0.25000
 atoms
 ! elem   x  y  z tag   occ.
  Fe0.00.00.0  Fe1   1.0

 If one calculates the Fe-Fe distance between the atom at (0,0,0) and the
 atom at (0, 0, 0.5), from application of the (x, -y, -z+0.5) lattice
 translation, one finds a Fe-Fe distance of 3.9705. However, if one runs
 the
 above atoms input file, this Fe-Fe distance is not found. Instead, a shift
 vector of (0.25, 0.25, 0.25) is needed to get the correct Fe-Fe distance.
 Note, the i2/c space group is listed with only one origin in the
 international tables. I determined the necessary shift vector from trail
 and
 error. It is still unclear to me why it was necessary to include a shift
 vector. So the best suggestion I have is that you can try including
 different shift vectors in your own atoms.inp file and see if you can get
 agreement with the crystallography program that way. Since, as I said, it
 isn't clear to me why this fixed my problem, its hard to say if this is
 the
 same issue you are having, but it may be worth a try.

 It may also be worth while to calculate some atomic distances from the
 lattice positions given in the international tables, and see if atoms or
 the
 crystallography program is giving you the same thing.

 Finally, let me add on another question for the list here since it is
 somewhat related. When one runs the above atoms.inp file with the (0.25,
 0.25, 0.25) shift vector one finds four Fe1_1 atoms at 3.9701 and two Fe_2
 atoms at 3.9705. When one then runs Feff, it combines these into a single
 Fe1_1 scattering path with N=6. Is there a command can be placed in the
 Feff
 input file to tell Feff not to combine identical paths like this?

 Best,
 George


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Re: [Ifeffit] more bugs in atoms?

[George Sterbinsky]

Hi Lisa,

Let me just mention one situation I have encountered using atoms, and how I
resolved it. I am not sure if this is the result of a bug or not, but
perhaps you can try applying the approach I took to your own situation and
see if it can resolve your problem.

The issue I encountered was running atoms for a monoclinic I2/c structure,
space group 15.

Here is the atoms input file:

! This atoms input file was generated by Artemis 0.8.014
! Atoms written by and copyright (c) Bruce Ravel, 1998-2001
title = ...
space = i 2/c 1 1
a =  5.51120b =  5.51120c =  7.79410
alpha = 90.0beta = 90.740gamma = 90.0
core =Co1edge =Krmax =  6.0
!shift   0.25000   0.25000   0.25000
atoms
! elem   x  y  z tag   occ.
  Fe0.00.00.0  Fe1   1.0

If one calculates the Fe-Fe distance between the atom at (0,0,0) and the
atom at (0, 0, 0.5), from application of the (x, -y, -z+0.5) lattice
translation, one finds a Fe-Fe distance of 3.9705. However, if one runs the
above atoms input file, this Fe-Fe distance is not found. Instead, a shift
vector of (0.25, 0.25, 0.25) is needed to get the correct Fe-Fe distance.
Note, the i2/c space group is listed with only one origin in the
international tables. I determined the necessary shift vector from trail and
error. It is still unclear to me why it was necessary to include a shift
vector. So the best suggestion I have is that you can try including
different shift vectors in your own atoms.inp file and see if you can get
agreement with the crystallography program that way. Since, as I said, it
isn't clear to me why this fixed my problem, its hard to say if this is the
same issue you are having, but it may be worth a try.

It may also be worth while to calculate some atomic distances from the
lattice positions given in the international tables, and see if atoms or the
crystallography program is giving you the same thing.

Finally, let me add on another question for the list here since it is
somewhat related. When one runs the above atoms.inp file with the (0.25,
0.25, 0.25) shift vector one finds four Fe1_1 atoms at 3.9701 and two Fe_2
atoms at 3.9705. When one then runs Feff, it combines these into a single
Fe1_1 scattering path with N=6. Is there a command can be placed in the Feff
input file to tell Feff not to combine identical paths like this?

Best,
George


On Fri, May 13, 2011 at 5:00 PM, Gudrun Lisa Bovenkamp 
bovenk...@physik.uni-bonn.de wrote:

 Hi George,

 thanks for responding. I sure imported the same structural information into
 atoms and the crystal structure program.

 Lisa



 Hi Lisa,

 I'm not very familiar with PbSO4, so I'm not sure if I can help, but your
 email immediately brought some questions to mind.

 First, did you import the same information into atoms and the crystal
 structure program? The way you worded your message made me think that the
 crystal structure program already knew the structure of PbSO4, in which
 case perhaps it is using a structure that is slightly different from the
 one
 you import into atoms.

 Second, what is the source of the structure data you are feeding into
 atoms?
 In my experience, errors and inconsistencies in the reporting of structure
 data in the literature can lead to unusual results in atoms.

 Best,
 George




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Re: [Ifeffit] Athena Artemis

[George Sterbinsky]

Also, for anyone who just wants to see the difference in the two data sets
I've attached a figure.

George

On Thu, May 12, 2011 at 1:23 PM, George Sterbinsky 
georgesterbin...@u.northwestern.edu wrote:

 Hello,

 I've noticed an odd behavior in Athena and Artemis and I was hoping someone
 could explain it to me.

 I've attached an Artemis file Data3.apj and an Athena file Data4.prj.

 First open Data3.apj. Then from the Artemis file menu choose open, then
 open Data4.prj and import the Data4.xmu file. Now plot the data in k-space
 you will see a slight difference between the two spectra, most noticeably
 above 15 k, so plotting in k^3 is best to see the difference.

 Now close Artemis and don't save. Open Data4.prj with athena and choose to
 import only the file Data4.xmu. Save the project as something else. I saved
 as Data4C.prj, which I have also attached.

 Close Athena and don't save. Open Data3.apj again. Then from the Artemis
 file menu choose open, then open Data4C.prj or whatever you may have named
 the file and import the Data4.xmu file, which should now be the only data
 file in the project. Now plot the data in k-space and you will find that the
 two data sets are now the same. The differences at high k are no longer
 present. Can anyone explain what is going on here?

 Thank you,
 George



DataDiff.pdf
Description: Adobe PDF document
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Re: [Ifeffit] more bugs in atoms?

[George Sterbinsky]

Hi Lisa,

I'm not very familiar with PbSO4, so I'm not sure if I can help, but your
email immediately brought some questions to mind.

First, did you import the same information into atoms and the crystal
structure program? The way you worded your message made me think that the
crystal structure program already knew the structure of PbSO4, in which
case perhaps it is using a structure that is slightly different from the one
you import into atoms.

Second, what is the source of the structure data you are feeding into atoms?
In my experience, errors and inconsistencies in the reporting of structure
data in the literature can lead to unusual results in atoms.

Best,
George



On Wed, May 11, 2011 at 3:07 PM, Gudrun Lisa Bovenkamp 
bovenk...@physik.uni-bonn.de wrote:

 Hey everybody,

 For a while I was wondering why I could not get a proper XANES simulation
 using FEFF (8 or 9). Recently I realized that the xyz list which is created
 in atoms from the crystal structure is not the same as from a crystal
 structure program for PbSO4. Can somebody please check this. I attached my
 feff.imp file including the atoms.imp (which was created by arthemis).

 Thanks,
 Lisa


  * input file was generated by Artemis 0.8.014
  * Atoms written by and copyright (c) Bruce Ravel, 1998-2001

  * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
  *   total mu*x=1:13.94 microns,  unit edge step:24.69 microns
  *   specific gravity =  5.382
  * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
  *   Normalization correction:0.00039 ang^2
  * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *

  * -
  * The following crystallographic data were used:
  *
  * title*-PbSO4 -[PNMA] Anglesite - orthorhombic
  * title'James, R W'
  * titleProceedings of the Royal Society of London, Series A:
 Mathematical and Physical Sciences (76,1906-)
  * space = P n m a
  * a =8.450 b =   5.380 c =   6.930
  * alpha =   90.0   beta =   90.0   gamma =  90.0
  * core =   Pb  edge =  L3
  * atoms
  * ! elem   x  y  z   tagocc
  *   Pb0.315300.250000.337501.0
  *   S 0.443000.25000   -0.194701.0
  *   O-1.0   -1.0   -1.01.0
  * -

  EDGE  L3
  S02   1.0
   CONTROL   1  1 1 1 1  1
  PRINT 1  0 0 0 0  0
   SCF   5.16556   0  15 0.1
  EXCHANGE  0  0   0
   XANES 6.0 0.07 0.5
  FMS   6

  *LDOS  -2020   0.1
   POTENTIALS
  *   ipot   z [ label   l_scmt  l_fms  stoichiometry ]
   0   82Pb -1  -1   0
   18O  -1  -1   1
   2   16S  -1  -1   1
   3   82Pb -1  -1   1


  ATOMS  * this list contains 156 atoms
  *   x  y  z  ipot  tag  distance
0.00.00.0  0 Pb  0.0
1.560721.345001.12613  3 O_1 2.34799
1.56072   -1.345001.12613  3 O_1 2.34799
1.079060.03.24185  2 S_1 3.41672
   -2.182632.69000   -0.22315  2 S_2 3.47128
   -2.18263   -2.69000   -0.22315  2 S_2 3.47128
2.042372.69000   -0.98960  2 S_3 3.51947
2.04237   -2.69000   -0.98960  2 S_3 3.51947
   -2.664291.34500   -2.33887  3 O_2 3.79180
   -2.66429   -1.34500   -2.33887  3 O_2 3.79180
1.079060.0   -3.68815  2 S_4 3.84276
   -3.145940.02.47540  2 S_5 4.00307
4.225000.0   -1.21275  1 Pb_14.39561
   -4.225000.0   -1.21275  1 Pb_14.39561
1.560724.035001.12613  3 O_3 4.47049
1.56072   -4.035001.12613  3 O_3 4.47049
   -1.103572.690003.46500  1 Pb_24.52329
   -1.10357   -2.690003.46500  1 Pb_24.52329
   -1.103572.69000   -3.46500  1 Pb_24.52329
   -1.10357   -2.69000   -3.46500  1 Pb_24.52329
3.121432.690002.25225  1 Pb_34.69596
3.12143   -2.690002.25225  1 Pb_34.69596
   -2.664294.03500   -2.33887  3 O_4 5.37122
   -2.66429   -4.03500   -2.33887  3 O_4 5.37122
0.05.380000.0  1 Pb_45.38000
0.0   -5.380000.0  1 Pb_45.38000
   -3.145940.0   -4.45460  2 S_6 5.45348
   -2.664291.345004.59112  3 O_5 5.47593
   -2.66429   -1.345004.59112  3 O_5 5.47593
5.304060.02.47540  2 S_7 5.85326
1.560721.34500   -5.80387  3 O_6

[Ifeffit] iXAFS

[George Sterbinsky]

Hi, I am wondering what is the best way to uninstall iXAFS version 2.1.1 for
Leopard before installing the new version. Is it sufficient to just drag
iXAFS.app to the trash or is there a better way to make sure everything gets
removed?

Thank you,
George
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Re: [Ifeffit] iXAFS

[George Sterbinsky]

After downloading the iXAFS3.0.3.dmg from 
http://cars9.uchicago.edu/ifeffit/Downloads; and installing iXAFS, I find
that if I open iXAFS look at about iXAFS, it tells me that I have version
2. Is this just a case of confusing labeling, or has some aspect of my
installation gone awry?

Thank you,
George

On Mon, Nov 29, 2010 at 10:37 AM, Jeff Terry ter...@iit.edu wrote:

 That should work fine. Alternately, you the new version should overwrite
 the old if you drag it to the Applications folder.

 Sent from my iPhone

 On Nov 29, 2010, at 9:05 AM, George Sterbinsky 
 georgesterbin...@u.northwestern.edu wrote:

  Hi, I am wondering what is the best way to uninstall iXAFS version 2.1.1
 for Leopard before installing the new version. Is it sufficient to just drag
 iXAFS.app to the trash or is there a better way to make sure everything gets
 removed?
 
  Thank you,
  George
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Re: [Ifeffit] feff question

[George Sterbinsky]

Josh,

That seems to have done the trick!

thank you,
George

On Wed, Nov 3, 2010 at 7:22 PM, Joshua Kas joshua.j@gmail.com wrote:

 Hi George,
 The obsolete warning is probably not a big deal, however, the compilation
 should be tested since compiling with gfortran has not been well tested for
 feff7.  If you can get an old version of g77, you won't have issues.
 Otherwise, I would use the following command when running gfortran.

 gfortran -finit-local-zero -o feff702 feff702.f

 This may not work with your version of gfortran (-finit-local-zero is not
 in the manual) but if it does, the compiled feff will be less likely to have
 runtime errors.
 Cheers,
 Josh Kas

 I installed gfortran-4.2.3.dmg file on top of the gfortran-42-5577.pkg and
 can now see gfortran in '/usr/local/bin'. I am also able to compile
 simple
 fortran code, but when I attempt to run Feff7 I get the following message:

 bash-3.2$ /usr/local/bin/gfortran -o feff702 feff702.f
 feff702.f:12161.72:

if (den.eq.0) pause 'failure in polint'
   1
 Warning: Obsolete: PAUSE statement at (1)
 feff702.f:12226.72:

if (den.eq.0) pause 'failure in polint'
   1
 Warning: Obsolete: PAUSE statement at (1)
 bash-3.2$

 Any idea as to what the problem is now?

 Thank you,
 George



 On Wed, Nov 3, 2010 at 3:45 PM, Matt Newville newvi...@cars.uchicago.edu
 wrote:

  Hi George,
 
  On Wed, Nov 3, 2010 at 2:37 PM, George Sterbinsky

  georgesterbin...@u.northwestern.edu wrote:
   I've also noticed that there is not a file or directory called
 gfortran
  in
   '/usr/local/bin'. This is what made me think I may also need to
 install
  the

   gfortran-4.2.3.dmg file. If I do not see a file or directory called
  gfortran
   in '/usr/local/bin' does this indicate that gfortran is not installed?
 Is
  it
   possible that gfortran-42-5577.pkg placed it somewhere else?
 
  Yes, those are all possible.   You need to install gfortran, find out
  where it is, and then run it to compile and link feff702 into an
  executable.It sounds like you might want to get a local unix-savvy
  person who can help you
 
  --Matt
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Re: [Ifeffit] feff question

[George Sterbinsky]

Is it possible that I need to download and install the gfortran-4.2.3.dmg
file in addition to gfortran-42-5577.pkg file? Any suggestions as to what to
try would be appreciated.

thanks,
George

On Tue, Nov 2, 2010 at 1:59 PM, George Sterbinsky 
georgesterbin...@u.northwestern.edu wrote:

 Matt, Jeff and List members,

 It took me some time to find a download for version of Xcode that was
 compatible with my OS and gfortran. I installed Xcode 3.1.4 and the
 gfortran-42-5577.pkg file from the link Matt sent. I put the feff702.f file
 and the feff.inp file in the same folder. I used the x11 terminal to cd into
 that folder and the tried the commands that you suggested, but neither
 worked. When I try gfortran -o feff702 feff702.f I get the message
 gfortran: command not found and when I type ./feff702 I get the message
 ./feff702: No such file or directory. Any idea as to what I am doing wrong
 or suggestions as to what to try next?

 Also, to answer Matt's question: I want to use Feff7 because I am trying to
 compare my results to fits done my someone else, who used Feff7, and I want
 to change as little as possible for my analysis.

 Thank you,
 George


 On Wed, Oct 27, 2010 at 2:29 PM, Jeff Terry ter...@iit.edu wrote:

 Following Matt's example, you would go to the directory where you build
 the program. You need to have a valid feff.inp file inside that directory.

 At the prompt (%), could be different depending on what shell you are
 running, type:

 ./feff702

 It should run.

 Jeff

 On Oct 27, 2010, at 1:19 PM, Matt Newville wrote:

  Hi George,
 
  Feff6 comes built in with the Mac distributions of Ifeffit
  (iXAFS.app), and is at
  /Applications/iXAFS.app/Contents/Resources/local/bin/feff6.
 
  Is that OK or do you really need Feff7?  There's not much in Feff7
  that's not in Feff6 (or a whole lot better in Feff8).
  FWIW, that version was built with gfortran 4.2,  downloaded from
  http://r.research.att.com/tools/.I believe you'll need xcode
  installed.
  Once installed
  gfortran -o feff702 feff702.f
  should work.
 
  Cheers,
 
  --Matt
 
 
  On Wed, Oct 27, 2010 at 12:43 PM, George Sterbinsky
  georgesterbin...@u.northwestern.edu wrote:
  Hi, I am hoping someone can explain to me how to run Feff 7 on a mac
 (OSX
  version 10.5.8) starting from the feff702.f file.
 
  Thank you,
  George
 
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Re: [Ifeffit] feff question

[George Sterbinsky]

I've also noticed that there is not a file or directory called gfortran in
'/usr/local/bin'. This is what made me think I may also need to install the
gfortran-4.2.3.dmg file. If I do not see a file or directory called gfortran
in '/usr/local/bin' does this indicate that gfortran is not installed? Is it
possible that gfortran-42-5577.pkg placed it somewhere else?

George

On Wed, Nov 3, 2010 at 3:12 PM, Matt Newville newvi...@cars.uchicago.eduwrote:

 Hi George,

 On Wed, Nov 3, 2010 at 2:07 PM, George Sterbinsky
 georgesterbin...@u.northwestern.edu wrote:

  Is it possible that I need to download and install the gfortran-4.2.3.dmg
  file in addition to gfortran-42-5577.pkg file? Any suggestions as to what
 to
  try would be appreciated.

 I doubt it.

  It took me some time to find a download for version of Xcode that was
  compatible with my OS and gfortran. I installed Xcode 3.1.4 and the
  gfortran-42-5577.pkg file from the link Matt sent. I put the feff702.f
 file
  and the feff.inp file in the same folder. I used the x11 terminal to cd
 into
  that folder and the tried the commands that you suggested, but neither
  worked. When I try gfortran -o feff702 feff702.f I get the message
  gfortran: command not found and when I type ./feff702 I get the
 message
  ./feff702: No such file or directory. Any idea as to what I am doing
 wrong
  or suggestions as to what to try next?


 ./feff702 didn't work because, as reported, there is no file named
 feff702.

 That file would have been created by gfortran -o feff702 feff702.f,
 but was not created because the gfortran program was not found, also
 as reported.

 What you probably need to do is either add '/usr/local/bin' to your
 path before running
gfortran -o feff702  feff702.f

 or be explicit and run
   /usr/local/bin/gfortran -o feff702 feff702.f

 Then, check that there is a file feff702, and try to run it:
   ./feff702

  Also, to answer Matt's question: I want to use Feff7 because I am trying
  to compare my results to fits done my someone else, who used Feff7, and
 I
  want to change as little as possible for my analysis.

 OK.


 --Matt
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Re: [Ifeffit] feff question

[George Sterbinsky]

Matt, Jeff and List members,

It took me some time to find a download for version of Xcode that was
compatible with my OS and gfortran. I installed Xcode 3.1.4 and the
gfortran-42-5577.pkg file from the link Matt sent. I put the feff702.f file
and the feff.inp file in the same folder. I used the x11 terminal to cd into
that folder and the tried the commands that you suggested, but neither
worked. When I try gfortran -o feff702 feff702.f I get the message
gfortran: command not found and when I type ./feff702 I get the message
./feff702: No such file or directory. Any idea as to what I am doing wrong
or suggestions as to what to try next?

Also, to answer Matt's question: I want to use Feff7 because I am trying to
compare my results to fits done my someone else, who used Feff7, and I want
to change as little as possible for my analysis.

Thank you,
George

On Wed, Oct 27, 2010 at 2:29 PM, Jeff Terry ter...@iit.edu wrote:

 Following Matt's example, you would go to the directory where you build the
 program. You need to have a valid feff.inp file inside that directory.

 At the prompt (%), could be different depending on what shell you are
 running, type:

 ./feff702

 It should run.

 Jeff

 On Oct 27, 2010, at 1:19 PM, Matt Newville wrote:

  Hi George,
 
  Feff6 comes built in with the Mac distributions of Ifeffit
  (iXAFS.app), and is at
  /Applications/iXAFS.app/Contents/Resources/local/bin/feff6.
 
  Is that OK or do you really need Feff7?  There's not much in Feff7
  that's not in Feff6 (or a whole lot better in Feff8).
  FWIW, that version was built with gfortran 4.2,  downloaded from
  http://r.research.att.com/tools/.I believe you'll need xcode
  installed.
  Once installed
  gfortran -o feff702 feff702.f
  should work.
 
  Cheers,
 
  --Matt
 
 
  On Wed, Oct 27, 2010 at 12:43 PM, George Sterbinsky
  georgesterbin...@u.northwestern.edu wrote:
  Hi, I am hoping someone can explain to me how to run Feff 7 on a mac
 (OSX
  version 10.5.8) starting from the feff702.f file.
 
  Thank you,
  George
 
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[Ifeffit] feff question

[George Sterbinsky]

Hi, I am hoping someone can explain to me how to run Feff 7 on a mac (OSX
version 10.5.8) starting from the feff702.f file.

Thank you,
George
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Re: [Ifeffit] feff question

[George Sterbinsky]

Jeff, Thanks, could you please tell me specifically what to type at the
command prompt or direct me to some instructions on this part? I've never
run Feff before (other than with the help of Artemis).

thanks,
George

On Wed, Oct 27, 2010 at 2:05 PM, Jeff Terry ter...@iit.edu wrote:

 Hi George,

 You need to have a fortran compiler installed on your Mac. You can find
 information on Mac OS X fortran compilers here:
 http://hpc.sourceforge.net/

 Once you have the compilers installed, you compile the feff702.f file. You
 can run it from the command line using any feff.inp file.

 Jeff


 On Oct 27, 2010, at 12:43 PM, George Sterbinsky wrote:

  Hi, I am hoping someone can explain to me how to run Feff 7 on a mac (OSX
 version 10.5.8) starting from the feff702.f file.
 
  Thank you,
  George
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