Re: [Ifeffit] Constraining values in Artemis fit

2018-08-23 Thread Bruce Ravel

On 08/23/2018 10:55 AM, Thomas, Andrew (AGW) wrote:

Hello,


Does anyone have any suggestions for breaking the correlation between 
the coordination number and sigma^2? Specifically, is there a way to set 
a maximum or minimum value for parameters in a fit?


Matt is, of course, correct when he says that this correlation is 
inherent to EXAFS analysis and cannot be "broken".  I would like to 
suggest a broader way of thinking about this sort of issue.


When you have a very well behaved analysis problem -- that is, something 
like my teaching example of FeS2, something for which the structure is 
pretty well known -- then your EXAFS analysis will yield defensible 
values for CN and sigma^2 without too much effort.  They will still be 
correlated, but sensible numbers will tend to just fall out.


In a harder problem -- y'know something you are doing actual research on 
-- you often run into the situation where these correlations preclude a 
"fall right out" analysis.  It is tempting to assert that the CN must be 
SOMETHING and the ss must be SOMETHING.  That's true in a sense, but you 
have made a real measurement and are doing a real analysis with real 
measurement uncertainties.  And you have to respect that.


When you are running into trouble in your EXAFS analysis -- big 
uncertainties, indefensible values, that sort of thing -- that is 
usually the program trying to tell you something about your analysis. 
Usually, that would mean that you want to know something that the data 
do not support (or do not support beyond some level of precision or 
accuracy).  Or it might mean that your fitting model is not realized in 
the data -- that is, your model is missing some important feature and 
the bad fit results are the result of missing that important feature.


To summarize, I want to encourage you not to assert that you need to 
find a way to break the correlations.  i want to encourage you think 
about what the wonky fit results are trying to tell you about your data 
or your fitting model.



That was kind of rambling, I admit.  Hopefully it was helpful 
nonetheless....


B


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

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Lead Beamline Scientist, 06BM (BMM)
 Building 743, Room 114
 Upton NY, 11973

 Homepage:http://bruceravel.github.io/home/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Ifeff calculation

2018-08-15 Thread Bruce Ravel
more about your skepticism of the
robustness of EXAFS LCF, Matt?

To be fair, it suffers from many of the same drawbacks of XANES LCF,
plus others. But I'm curious about your thoughts on it since yours seems to
be what amounts to a "strong opinion" on the subject.




I would not say that no one should ever do linear combination fitting for
EXAFS.  For sure, linear analysis of XANES is quite robust and verified
many times to give good results, at least at level of a few percent.
Linear analysis of EXAFS suffers more data processing challenges and
conceptual problems that limit its robustness.  For sure, there are cases
for which it can work well.

Longer answer:
Any linear analysis (LCF, PCA, MCR-ALS, etc) of XANES works reasonably
well (typically to a few percent) because:
a) the processing needed is minimal.  Data need to have a common
energy calibration better than the intrinsic energy resolution -- typically
energy calibration of 0.25 eV or better will be OK.  Data need to have a
consistent normalization of mu(E), typically to a few percent.   Variations
in these processing steps will have a direct and negative effect on the
results.

b) conceptually, the assumption is that there exists a nearly 1 to 1
correspondence between "local chemical configuration" and "measured XANES",
and that the "local chemical configurations" that are being investigated
are discrete and well-defined (ie "iron carbonate") and not continuous.
  That is, if you determine that your Fe XANES spectra is "50% iron
carbonate and 50% iron sulfate" then implicit conclusion is that 50% of the
iron atoms are iron carbonate and 50 percent are iron sulfate, not that all
irons are 50% carbonate and 50% sulfate.

To be clear, linear analysis of XANES does not work well to ppm levels,
partly due to the poor experimental contrast (that is, mu(E) tend to all
look alike and features are intrinsically broadened to the ~eV level), but
also conceptually, because at the ppm level, local chemical configurations
are not always limited to 3 to 10 discrete states.

Linear Combination EXAFS is more challenging from both the processing and
conceptual point of view.

For Processing, EXAFS requires more data processing than XANES.  The
selection of E0 and the background mu0(E) will have an effect on linear
analysis of EXAFS if not done consistently.  It is not really obvious how
E0 or mu0(E) can be selected consistently for very different spectra.

Conceptually, EXAFS is much more sensitive to disorder and subtle
variations in the bond lengths (thermal or static disorder) and can have
significant variation in its sensitivity to second and further neighbors.
  In that sense, EXAFS is much less discrete and much more continuous in its
variability across different kinds of local structures.

Again, this is not to say that linear analysis of EXAFS cannot ever work,
just that is probably more limited in applicability and absolute accuracy
than linear analysis of XANES.  Of course, for EXAFS you can also do an
actual fit of structural parameters.  The information content is somewhat
limited so that refining multiple overlapping components may not always be
possible, and linear combinations of end-member spectra may look
attractive

Hopefully, anyone who has other insights or experiences will be able to
correct any of my misunderstandings.

--Matt


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit



___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit






___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




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

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Lead Beamline Scientist, 06BM (BMM)
 Building 743, Room 114
 Upton NY, 11973

 Homepage:http://bruceravel.github.io/home/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Demeter on ubuntu 14.04

2018-08-08 Thread Bruce Ravel


Is larch up to date?  Or even installed?  It would seem that $larch_exe 
is not being evaluated properly and is undefined when you get to line 
288 in Larch.pm.


B


On 08/08/2018 10:07 AM, Edmund Welter wrote:

Dear all,
I am hitting a wall trying to install the latest Demeter version on my 
ubuntu laptop.

System: Ubuntu 14.04
Demeter: 0.9.26
perl: 5.18.2
pdl and pdl::stats from repositories. (I tried a newer versions from 
cpan, but ot no avail)

moose: initially from repositories, than vs. 2.2011  from cpan

I did follow the installation instructions on
https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.html 


and tried to install demeter in ~/perl5
and also the instructions in:
https://bruceravel.github.io/demeter/documents/SinglePage/installation.html
to install Demeter as sudo

Both attempts ended with the same result when I start dathena in a 
terminal the image of the goddess appears briefly and I get the 
following error messages in the terminal:

-
Invalid version format (non-numeric data) at 
/usr/local/lib/perl/5.18.2/Moose/Exporter.pm line 11,  line 90.
BEGIN failed--compilation aborted at 
/usr/local/lib/perl/5.18.2/Moose/Exporter.pm line 11,  line 90.
Compilation failed in require at /usr/local/lib/perl/5.18.2/Moose.pm 
line 15,  line 90.
BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Moose.pm 
line 15,  line 90.
Compilation failed in require at /usr/local/lib/perl/5.18.2/Demeter.pm 
line 123,  line 90.
BEGIN failed--compilation aborted at 
/usr/local/lib/perl/5.18.2/Demeter.pm line 123,  line 90.
Compilation failed in require at 
/usr/local/lib/perl/5.18.2/Demeter/UI/Athena.pm line 24,  line 90.
BEGIN failed--compilation aborted at 
/usr/local/lib/perl/5.18.2/Demeter/UI/Athena.pm line 24,  line 90.
Compilation failed in require at /usr/local/bin/dathena line 31,  
line 90.
BEGIN failed--compilation aborted at /usr/local/bin/dathena line 31, 
 line 90.
Use of uninitialized value $Larch::larch_exe in concatenation (.) or 
string at /usr/local/lib/perl/5.18.2/Larch.pm line 288,  line 90.
Can't exec "-q": No such file or directory at 
/usr/local/lib/perl/5.18.2/Larch.pm line 288,  line 90.



When i try to start denv to create the nice overview of installed 
components I only get the following errors:


[PDL->Version: 10 PDL_CORE_VERSION: 8 XS_VERSION: ] PDL::Stats::Distr 
needs to be recompiled against the newly installed PDL at 
/usr/lib/perl/5.18/DynaLoader.pm line 207.

Compilation failed in require at (eval 1130) line 5.
BEGIN failed--compilation aborted at (eval 1130) line 5.
BEGIN failed--compilation aborted at /usr/local/bin/denv line 24.
Use of uninitialized value $Larch::larch_exe in concatenation (.) or 
string at /usr/local/lib/perl/5.18.2/Larch.pm line 288.
Can't exec "-q": No such file or directory at 
/usr/local/lib/perl/5.18.2/Larch.pm line 288.

--
This is insofar interesting as I got the same error about PDL when I 
tried to start dathena before I installed the pdl::stats module from 
cpan, that means when both, pdl and pdl::stats were installed from 
repositories.


Any hint would be welcome, upgrading ubuntu to a newer LTS version might 
be useful (It is absolutely possible that something is weird with this 
installation after a lot of playing around) but I am currently reluctant 
to do so, because it will for sure break other things...


Best regards,
Edmund
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit



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

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Lead Beamline Scientist, 06BM (BMM)
 Building 743, Room 114
 Upton NY, 11973

 Homepage:http://bruceravel.github.io/home/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Find white line position

2018-08-02 Thread Bruce Ravel



It's not very sophisticated.

Starting with the "flattened" spectrum (see 
http://bruceravel.github.io/demeter/documents/Athena/bkg/norm.html#the-flattening-algorithm), 
it simply finds the highest point in the spectrum.  Literally just the 
ceiling function.


The flattened spectrum is used rather than the normalized spectrum 
because the curvature of the post-edge (or even the curvature of the 
pre-edge in fluorescence data with a energy dispersive detector) could 
result in other regions being higher in value than the white line.


This is a pretty horrible algorithm.  It is, I think, guaranteed to find 
an obviously wrong point for a metal.  Basically it works for spectra 
with a white line and it will almost certainly fail for spectra without 
a white line.


Use with caution!

HTH,
B


On 08/02/2018 01:28 AM, Hiroshi OJI wrote:

Dear all,

I have a question about one of the useful function, "find white line
position" in Athena.

Could anyone tell me how Athena find the white line position by this
function? In other words, I would like to know the algorithm to find the
white line position in Athena.

Thank you very much for your help, in advance.

Best regards,

Hiroshi Oji





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

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Lead Beamline Scientist, 06BM (BMM)
 Building 743, Room 114
 Upton NY, 11973

 Homepage:http://bruceravel.github.io/home/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Basic questions about the preliminary data processing in Athena

2018-07-27 Thread Bruce Ravel

On 07/27/2018 01:32 PM, Haifeng Li wrote:
What is the real difference between calibration and alignment? Do they 
have specific meaning?



In Athena, calibration means to determine a value for e0 shift such that 
a particular point in the data is specified to be a particular energy. 
Then the value for E0 is set to that particular energy.  Thus, 
calibration changes both e0 and e0 shift for the group being calibrated.


For example, set the E0 shift such that the first inflection point in 
copper is made to be 8979 eV.  Then set the value for E0 in the 
background removal to 8979.


In Athena alignment is the process by which one data group is given an 
e0 shift value such that it lines up with another data group.  This is 
to compensate for some scan-to-scan variability in the behavior of the 
monochromator.  Often, but not always, alignment is done using a 
zero-valent (or some other) reference which is measured simultaneously 
with the actual sample.  In Athena, the alignment tool DOES NOT change 
the value of e0, but certainly does change the value of e0 shift for the 
group being aligned.  The alignment tool does not change either e0 or e0 
shift for the alignment standard.


Whether you want to do one, the other, both, or neither depends upon the 
beamline and the type of data ensemble you have measured.


This /is/ explained in the user manual.

B


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

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Lead Beamline Scientist, 06BM (BMM)
 Building 743, Room 114
 Upton NY, 11973

 Homepage:http://bruceravel.github.io/home/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] window 10

2018-07-11 Thread Bruce Ravel



One of the values of a mailing list is that past posts are archived and 
can be searched.  This particular problem has -- I think -- been 
discussed many times in recent months.


https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06031.html

You should go to the preferences and make sure the settings for the 
feff6 and gnuplot executables are set correctly for your new machine.



I am sorry this continues to be a problem.  I am not with a lot of time 
for software development these days.



Also, an email that simply says "the program crashed" is not at all 
helpful.  There is no way that you can expect me to understand the 
nature of the problem with such an insubstantial bug report.  As I have 
asked many times, please consult this page for hints on how to write an 
actionable bug report.


http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html

B


On 07/11/2018 10:12 AM, dien...@srnl.doe.gov wrote:

Hi, Bruce and Matt

We just transitioned to Window 10 yesterday. I just found that as I ran 
Artemis for EXAFS data fitting, it constantly crashed (stopped running) 
my computer, I am using Demeter 9:24 I believe, is it possible I need a 
new version, where is the link for latest version? Thanks.


Dien Li

Savannah River National Laboratory



___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




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

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Lead Beamline Scientist, 06BM (BMM)
 Building 743, Room 114
 Upton NY, 11973

 Homepage:http://bruceravel.github.io/home/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


[Ifeffit] copper fluoride

2018-07-10 Thread Bruce Ravel



Hi all,

I wonder if anyone has a spectrum of copper fluoride, CuF2, that they 
are willing to share.  This would be a big help for my undergraduate 
student's summer research project.


Thanks!
B


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

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Lead Beamline Scientist, 06BM (BMM)
 Building 743, Room 114
 Upton NY, 11973

 Homepage:http://bruceravel.github.io/home/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Artemis Error

2018-04-19 Thread Bruce Ravel


Hi Chính,

First off, I have to apologize for the very slow response.  For the last 
month, I have been busy with the first few user groups to visit our 
newly commissioned beamline here at NSLS-II.  I haven't had much time to 
manage software issues.


I haven't forgotten about your post to the mailing list, though, and I 
would like to look into the problem.  The picture you posted with your 
bug report is useful, but not quite sufficient.  It would be helpful to 
me to see both the project file that triggered the problem and the log 
file 
(http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html#capturing-error-messages) 
that gets written when Artemis crashes.


B


On 03/29/2018 12:36 AM, Lê Ngọc Chính wrote:

Dear Demeter developer

I have some trouble when using artemis. I have used artemis normally on 
windows 10, but recently I can't use it anymore. The error message 
appears after I click "FIT" button.
I also have tried re-install the software, but nothing happened. Please 
provide me the way to fix it. Thank you so much

--
Chính


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] install for mac error

2018-04-03 Thread Bruce Ravel

On 04/03/2018 01:47 PM, Luke Higgins wrote:

I see this error too. This is a bit of a bodge job, but if you replace:

/opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm

With the attached template.pm from p5.24, it seems to work fine. I’d 
just rename the old Template.pm in the same directory, rather than 
deleting it – since another program may end up needing the most recent one.




Luke,

It's better than a bodge.  It seems to be a good idea.  It seems there 
was a big change in Text::Template at version 1.48.  Your attachment was 
version 1.47 -- i.e. before this significant change.


This confuses me.  I've read the relevant code and I don't understand 
why it's a problem.  Even more, I don't understand how it can be a 
problem only on the Mac and not everywhere.  Weird.


Anyway, I think replacing Text::Template as Luke suggests is a good idea 
for anyone seeing this problem on the Mac.


B


--
 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/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] install for mac error

2018-04-03 Thread Bruce Ravel

On 04/03/2018 12:52 PM, Matt Newville wrote:


I see the same problem with athena from demeter 0.9.25. I think the 
warnings about "Demeter::Templates::F" and so forth are meant to be 
warnings only -- I think they may not be related to the crash of 
athena.   For me, hephaestus gives the same sort of warnings, but runs fine.


Those are only warnings and should not be related to whatever is causing 
Athena to crash.


I am confused why those warnings get reported.  I am using the same 
version of perl as Chris (5.26), so presumably the same version of 
Text::Template.  I don't see those warnings and don't understand why 
they would show up on a different system.


That said, I can think of a couple ways to suppress those warnings, but 
it is something someone would have to volunteer to test for me.


B

--
 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/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Problem building latest demeter on Debian 32bit Stretch

2018-03-30 Thread Bruce Ravel

On 03/30/2018 01:47 PM, Matthew Newville wrote:

Hi Al, Bruce,

Is there a need to run analysis codes running 32-bit Linux?  I haven't 
seen one of those in a long time, and don't plan on testing or 
supporting any codes on that platform.

I'm not even excited about supporting 32-bit Windows.


Well... neither am I, but that's what the question was

B


--
 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/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Problem building latest demeter on Debian 32bit Stretch

2018-03-30 Thread Bruce Ravel


Still puzzling.  I sort of understand what you are seeing, but it makes 
little sense, isn't consistent with my understanding of how package 
loading in perl works, and certainly is not something I have seen before.


Try putting

use Graphics::GnuplotIF;

somewhere near the top of lib/Demeter/Plot/Gnuplot.pm.  Doesn't much 
matter where.  After line 57 would be fine.


If that works -- great!  Both of my suggestions do no harm, so I'll just 
commit them to github


B


On 03/30/2018 12:49 PM, Al Kwiatkowski wrote:

Hm, we're getting somewhere.  Putting the 'use Carp;' line now has dathena
come up, but delivering this error:

Use of uninitialized value in subroutine entry at 
/usr/local/lib/i386-linux-gnu/perl/5.24.1/Demeter/Plot/Gnuplot.pm line 29.


and when you exit, it pops up a dialogue box with this error:

Use of uninitialized value in stat at 
/usr/local/lib/i386-linux-gnu/perl/5.24.1/Demeter/Plot/Gnuplot.pm line 270.


The program seems to behave ok otherwise, but I don't know what operations
would have problems with an uninitialized gnuplot module variable or 
subroutine.  Why would it have issues initializing in the first place 
(or not finding the Carp module)?


Thanks for the help so far!



--
 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/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Problem building latest demeter on Debian 32bit Stretch

2018-03-30 Thread Bruce Ravel


Well ... the beam just dumped, so let's see if I can figure this out

Demeter does not use Carp::Clan, so the version number of 
libcarp-clan-perl is irrelevant.


This is a puzzler for me.  I have never seen this problem over many, 
many versions of perl.  So there is something I don't understand about 
your system.  I cannot reproduce this problem, so it's going to be 
difficult to resolve.




Try this:

Put

use Carp;

just after line 257 of lib/Demeter/Plot/Gnuplot.pm.  Line 257 is the one 
that says


{ no warnings 'redefine';


No guarantees, but maybe that'll help  Let me know.
B


On 03/30/2018 10:19 AM, Al Kwiatkowski wrote:

Hello -

We're trying to install demeter on a 32-bit system running Debian 9.2 
Stretch.  The 'perl Build.PL' and 'Build' run into no issues, but when 
we try running 'Build test' we get the following error messages:


t/001_base.t  String found where operator expected at
/home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line
273, near "croak "Couldn't unlink $self->{__error_log}: $!""
     (Do you need to predeclare croak?)
syntax error at
/home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line
273, near "croak "Couldn't unlink $self->{__error_log}: $!""
Compilation failed in require at
/home/kwiatal/sources/demeter-master/blib/lib/Demeter.pm line 244.
Compilation failed in require at t/001_base.t line 22.
BEGIN failed--compilation aborted at t/001_base.t line 22.
# Looks like your test exited with 255 before it could output anything.
t/001_base.t  Failed 24/24 subtests
t/002_types.t ... String found where operator expected at
/home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line
273, near "croak "Couldn't unlink $self->{__error_log}: $!""
     (Do you need to predeclare croak?)
syntax error at
/home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line
273, near "croak "Couldn't unlink $self->{__error_log}: $!""
Compilation failed in require at
/home/kwiatal/sources/demeter-master/blib/lib/Demeter.pm line 244.

The "croak" command not getting found appears to come from the "Carp" 
perl module - we have version 6.06-1 of the 'libcarp-clan-perl' package 
installed.  Any suggestions as to what's causing this error?  Again, the 
'perl Build.PL' command shows no issues with the installed modules, but 
since most of them were installed from the Debian repository, maybe 
there's a discrepancy with the modules installed when we run './Build 
installdeps'?


Thanks for any assistance -

Al Kwiatkowski
kwia...@phys.iit.edu
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit



--
 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/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Athena crashes on windows10

2018-03-28 Thread Bruce Ravel


Thanks, Lisa,

I have been seeing a similar problem this week at the beamline.  Some 
tests on my own computer make it clear that LCF is not working correctly 
in the current release.


I will work on this as soon as possible, however, I am with users for a 
while


B


On 03/28/2018 01:56 PM, Lisa Bovenkamp-Langlois wrote:

Hello.
Me and other people running windows 10 have problems with Athena
(demeter version 0.9.26). when switching to the LCF window the program
crashes.
I tested that indeed sometimes this happens when the list of data sets 
is long.

However, it recently happened with only 3 data sets in the list.
In one case Athena crashes at this same spot repeatedly.
In other cases if works after restarting Athena or the PC.

Is there a fix in sight or do I have to go back to windows7?

Thanks,
Lisa


Lisa Bovenkamp-Langlois, PhD
CAMD/LSU
6980 Jefferson Hwy
Baton Rouge, LA 70806
Email: lbovenk...@lsu.edu <mailto:lbovenk...@lsu.edu>
website: http://www.camd.lsu.edu/



___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Report a bug

2018-03-19 Thread Bruce Ravel


Once again, the fine manual is your friend:

http://bruceravel.github.io/demeter/documents/Athena/import/columns.html#data-types-and-energy-units


B


On 03/19/2018 12:17 PM, Matt Noerpel wrote:

Hello Zhengrui,

It looks like you may be importing the data as XANES instead of u(E).  
There's a pulldown menu about halfway down the import screen labelled 
"Data type" where you can change that.  Or you can hold down alt+ctrl 
and left click on the blue text near the top of the home screen that 
says "Datatype:XANES" to change it to "Datatype: xmu".  I was able to 
plot it in k once the datatype was changed.


I hope that helps,

Matt

On Mon, Mar 19, 2018 at 11:59 AM, Zhengrui Xu <z...@vt.edu 
<mailto:z...@vt.edu>> wrote:


To whom it may concern,

I found a bug when I am dealing with my data. I am using Windows
system, and the software version is 0.9.26.

I can plot my data in E, however, not in k, R and q. This problem
happen to all of my data. My other three group members also have
this problem.

My raw data is attached for your review.

We really appreciate your help.




Best,
Zhengrui Xu

First-year PhD student
Department of Chemistry
Virginia Tech




___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
<mailto:Ifeffit@millenia.cars.aps.anl.gov>
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
<http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>
Unsubscribe:
http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
<http://millenia.cars.aps.anl.gov/mailman/options/ifeffit>





___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Error in Atoms output

2018-02-27 Thread Bruce Ravel

On 02/19/2018 06:23 AM, Kaustubh Priolkar wrote:
We are trying to fit low temperature V K edge EXAFS data in V2O3. As per 
the cif files available (attached herewith – V2O3_10K data.cif) the 
structure is described by I2/a space group. When this file is read by 
ATOMS it gives an erroneous output ( attached herewith - feff.inp). In 
particular the values of V-O and V-V bond distances are not correct and 
do not match with bond distances reported in literature (Phys. Rev. B 2 
(1970) 3771).


Could anyone tell me where am I making a mistake. I am aware that I2/a 
is a non standard space group but I am not sure if I need to take any 
precaution while reading the cif file in ATOMS.


Thanks and regards,


Hi Kaustubh,

Thanks for this bug report.  This uncovered not one but two bugs in how 
Atoms handles monoclinic space groups.  How economical!  I will be 
pushing a fix to github soon and I will try to find some time to make a 
new windows installer.


I should point out that, even with the bug fix, the distances using the 
CIF file you attached will not match Phys. Rev. B 2 (1970) 3771.


The CIF file that you supplied is from 
doi:10.1016/S0022-4596(03)00295-0, which reports slightly different 
numbers for the undoped V2O3 compared to the 1970 paper.  I have 
attached a feff.inp file that I think is correct.


B





--
 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/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/


V2O3_feff.inp
Description: chemical/gamess-input
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Artemis having trouble

2018-02-09 Thread Bruce Ravel

On 02/04/2018 12:50 PM, Sheraz Gul wrote:
             Thank you for the suggestions. I have other project files 
in the same folder and they open fine. Anyways, I  upgraded to Demeter 
version 0.9.26 pre 2 and somehow every project file opens fine now. 
Although, in the ini file,  I had to correct the paths corresponding to 
exe files for gunplot and feff; otherwise, Athena/Artemis will crash 
before opening.


Yesterday, I posted a new version of the Windows installer that should 
address the exe paths problem.  I am pretty sure it is done correctly in 
the new installer.  I was able to reproduce that problem on our beamline 
windows computer and I was able to verify that the new installer works 
(at least on that one computer).


This installer also addresses a number of other issues that have come up 
in the last year.  Details are in the change log on the Demeter website.


I also made a new tag and new release on Demeter's github page.

B


--
 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/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] How to use Artemis with feff85L

2018-01-12 Thread Bruce Ravel


Jose,

I am unclear what you are sad about.  The version of Feff has little to 
do with the quality of the analysis.  See our recent paper:


  https://doi.org/10.1107/S1600577517011651

It is true that feff8l would simplify and streamline the code, making it 
easier to write and maintain.  That's a bit incentive /for/ /me/ to do 
that work.


But I think you are overstating the impact on the analysis you and 
others do with Artemis.


B


On 01/12/2018 07:15 AM, José Carlos Conesa wrote:

OK Bruce, I understand. (Sigh)

Good luck in your actual job.

JC


El 12/01/2018 a las 12:35, Bruce Ravel escribió:


Yes.  But I am pretty busy these with my new beamline.

"Beamline scientist" is my actual job.  "Software guy" is a side 
project.  So the software work gets done when it gets done.


B



On 01/12/2018 05:25 AM, José Carlos Conesa wrote:

Dear Bruce,

Do you foresee that (in a not far future) Artemis may be adapted so 
that it can use the results of feff8.5L?


All the best,


El 12/09/2017 a las 19:11, Bruce Ravel escribió:


Feff8L is not properly integrated into Artemis yet.  Sorry.  I have 
a new beamline these days.  It's hard to find time to work on the 
software.


This is on my to do list, but it's going to take a while.

B


On 09/12/2017 12:54 PM, José Carlos Conesa wrote:

Hi,

I should like to use feff85L within Artemis (from Demeter 0.9.25), 
just to check in my system whether selfconsistency has a role in 
unifying E0 values (with feff 6, allowing different E0 for each 
scatterer leads to E0 differences >10 eV, which seems too much to 
me). I find that after loading the EXAFS data (from Athena) and a 
model (a .cif file containing Cu, Ce and O atoms), if I click Run 
Atoms and then Run Feff with feff6 as executable I get the usual 
set of paths that allow me doing a fit of the data, but if I try to 
use the feff85L.exe that comes with the Demeter software (by 
changing the feff executable in the File/Edit preferences menu), 
after clicking the Run Feff button (without including the SCF card) 
a bit of computation happens and after finishing it the path list 
is empty.


¿Any idea of the possible reason why I get no path list?

Thanks in advance














--
 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/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] How to use Artemis with feff85L

2018-01-12 Thread Bruce Ravel


Yes.  But I am pretty busy these with my new beamline.

"Beamline scientist" is my actual job.  "Software guy" is a side 
project.  So the software work gets done when it gets done.


B



On 01/12/2018 05:25 AM, José Carlos Conesa wrote:

Dear Bruce,

Do you foresee that (in a not far future) Artemis may be adapted so that 
it can use the results of feff8.5L?


All the best,


El 12/09/2017 a las 19:11, Bruce Ravel escribió:


Feff8L is not properly integrated into Artemis yet.  Sorry.  I have a 
new beamline these days.  It's hard to find time to work on the software.


This is on my to do list, but it's going to take a while.

B


On 09/12/2017 12:54 PM, José Carlos Conesa wrote:

Hi,

I should like to use feff85L within Artemis (from Demeter 0.9.25), 
just to check in my system whether selfconsistency has a role in 
unifying E0 values (with feff 6, allowing different E0 for each 
scatterer leads to E0 differences >10 eV, which seems too much to 
me). I find that after loading the EXAFS data (from Athena) and a 
model (a .cif file containing Cu, Ce and O atoms), if I click Run 
Atoms and then Run Feff with feff6 as executable I get the usual set 
of paths that allow me doing a fit of the data, but if I try to use 
the feff85L.exe that comes with the Demeter software (by changing the 
feff executable in the File/Edit preferences menu), after clicking 
the Run Feff button (without including the SCF card) a bit of 
computation happens and after finishing it the path list is empty.


¿Any idea of the possible reason why I get no path list?

Thanks in advance









--
 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/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] data table for larch data group

2017-12-22 Thread Bruce Ravel


On 12/22/2017 04:53 PM, Matthew Newville wrote:
>
> At the moment, No.  But that should be easy and a very good idea to 
separate reading headers plus the data table from naming of the 1d 
arrays...  Like, I often run into cases where I want to rename arrays 
after reading the file.  I'll work on that.


Cool.  I was working on it this morning, but didn't like my solution. 
Hence the question.




> I'd also like to be able to sensibly handle columns of non numeric 
data.  Maybe that's too separate a topic


Not this topic but a very good idea nonetheless.

B

--
 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/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


[Ifeffit] data table for larch data group

2017-12-22 Thread Bruce Ravel


Matt,

If I read an ascii file with read_ascii() like so:

  a = read_ascii(file)

The "a" group has a data attribute which contains the entire data table 
as a 2D array.  It also has 1D arrays for each column from the data 
table.  Those 1D arrays have attribute names taken from the column labels.


If I do something to change the data table, is there a function that I 
can call that repopulates the 1D arrays with the columns of the altered 
data table?


For example:

  a = read_ascii(file)

a.data is, say, 

Re: [Ifeffit] current-amp recommendation

2017-11-14 Thread Bruce Ravel

Hi Matthew,

At NSLS-II, we use a solution developed here at BNL for quad BPMs and 
other current-measurement operations.  (I am using it for ion chambers 
at my beam line.)


It is a box developed in the Instrumentation Division with a current 
amplifier, an A2D converter, and a microprocessor all inside a box 
that's about the size of a box of Pop Tarts.  It has 4 SMA input 
channels and a single gain for all four channels.  SMA to BNC cables are 
readily available from all the standard vendors.  The output is an 
ethernet cable.  The microprocessor runs a small debian system and 
starts an EPICS IOC and a DHCP client on boot.  the 4 current get 
exposed as 4 PVs and the IOC does a lot of useful statistics on the fly.


Seems to work pretty well.

You could contact Pete Siddons.  (Search for Siddons at the BNL website. 
 When I tried it, the second hit was his staff page.)


B

On 11/14/2017 03:16 PM, Matthew Marcus wrote:
I've gotten involved with a project in which stabilization of the 
position of a monochromatic, soft X-ray beam is needed.  The
offending frequencies seem to be vibration frequencies like 57 and 
116Hz.  We have in mind to use a thin Au film with a gap in the
middle, measuring the drain current from the films, much as people 
normally use the jaws of slits.  Now, I'd like to find a couple
of current amplifiers which are small enough so that they can be 
connected with very short cables to the BNC connectors on the
air-side of this detector, and which would have decent frequency 
response and low noise with inputs of the order of 0.1-1nA.
Although this topic is outside the realm of XAFS analysis with IFEFFIT, 
I figure that people on this group might have some

good experience.

 mam
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit



--
 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/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Hephaestus: Absorption Data Source

2017-11-13 Thread Bruce Ravel

On 11/13/2017 11:15 AM, Daniel Przyrembel wrote:

Still I can't see any reference to 'Keski-Rahkonen and Krause' in



http://bruceravel.github.io/demeter/documents/Athena/hephaestus.html#absorption


Here is the relevant bit from Feff:

https://github.com/xraypy/feff85exafs/blob/master/src/COMMON/setgam.f

Note that that bit in Feff is less sophisticated than you might think. 
My memory (Matt or John might remember better) is that Steve Zabinski 
(main author of Feff6) "interpolated" those values from the plots in the 
K paper.  This was done with a ruler back in the days before we had 
software tools for such chores.  I am not saying that the values in 
setgam.f are wrong -- just not as precise as you might imagine.


B



--
 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/
 Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] How to use Artemis with feff85L

2017-09-13 Thread Bruce Ravel

On 09/13/2017 09:35 PM, Matt Newville wrote:
Then again, maybe Demeter does come with a working feff8l, and I just 
wasn't aware of it.


Not yet. :(
B

--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Ifeffit Digest, Vol 174, Issue 8

2017-08-17 Thread Bruce Ravel

On 08/17/2017 05:16 PM, Bruce Ravel wrote:
That's a thumbs-up from me, Hiroyuki.  Carmelo set out to use Larch 
specifically to address the problem of processing many MANY files.  I 
think Athena and PrestoPronto could both have a good place in anyone's 
toolbox.



Although I was thrilled to hear that you got Larch+Demeter+Windows 
working, Hiroyuki.  It is very gratifying that a third party -- not me, 
not Matt -- was able to do so.  Whew!


B

--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Ifeffit Digest, Vol 174, Issue 8

2017-08-17 Thread Bruce Ravel


That's a thumbs-up from me, Hiroyuki.  Carmelo set out to use Larch 
specifically to address the problem of processing many MANY files.  I 
think Athena and PrestoPronto could both have a good place in anyone's 
toolbox.


B


On 08/17/2017 04:29 PM, Carmelo Prestipino wrote:

Hi Hiroyuki,
I done a small interface to Larch to work with a lot of files 
http://soonready.github.io/PrestoPronto/
It is not nice as Athena and it has not all its possibility but if you 
are used to  Athena  you should not get lost (the name of parameter is 
the same).

It is not fast how it should be but give a try, maybe could be useful
Carmelo


On Thu, Aug 17, 2017 at 7:00 PM, 
<ifeffit-requ...@millenia.cars.aps.anl.gov 
<mailto:ifeffit-requ...@millenia.cars.aps.anl.gov>> wrote:


Send Ifeffit mailing list submissions to
ifeffit@millenia.cars.aps.anl.gov
<mailto: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
<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
<mailto:ifeffit-requ...@millenia.cars.aps.anl.gov>

You can reach the person managing the list at
ifeffit-ow...@millenia.cars.aps.anl.gov
<mailto: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. Re: How to use Larch as backend for Athena and Artemis on
   Windows (Bruce Ravel)
2. Re: How to use Larch as backend for Athena and Artemis on
   Windows (ASAKURA, Hiroyuki)


--

Message: 1
Date: Wed, 16 Aug 2017 13:17:13 -0400
From: Bruce Ravel <bra...@bnl.gov <mailto:bra...@bnl.gov>>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov
<mailto:ifeffit@millenia.cars.aps.anl.gov>>
Subject: Re: [Ifeffit] How to use Larch as backend for Athena and
 Artemis on Windows
Message-ID: <1956f39f-85f4-7a92-a989-24a5436df...@bnl.gov
<mailto:1956f39f-85f4-7a92-a989-24a5436df...@bnl.gov>>
Content-Type: text/plain; charset=utf-8; format=flowed


Hi Hiroyuki,

Sorry I didn't respond yesterday.  Yesterday was a bit of crazy day...

I suppose that this is still a work in progress.  I believe that Demeter
works with Larch on Windows, but it is certainly not as easy or
convenient yet as it should be.

In the place where Demeter got installed on your computer, there is a
folder called \perl\site\bin -- you can look at the properties of the
Athena desktop icon to see where that is.  In that folder is the
"dathena.bat" file which the Athena desktop icon points at.

You should also find a file called "lathena.bat".  Try running that or
pointing your desktop icon at it instead.

The difference between "lathena.bat" and "dathena.bat" is line 25 that
sets an environment variable that Demeter uses to decide which of
ifeffit or larch to use.

Obviously, there are number of other ways to get this environment
variable set.  The bottom line is, yes, there is a switch.  The switch
is the DEMETER_BACKEND environment variable.

Unfortunately, that switch cannot be in the configuration files,
although what you tired in item 2 of your email was a sensible guess.
It turns out that the choice of larch/ifeffit has to made long before
the configuration files are read.

Do let me know how you get on.  While Demeter + larch should work, there
are still almost certainly problems.  I need to get a new version of the
Demeter installer out soon, so it would be nice to get some feedback in
this area.

As for using Demeter + larch + 100s of file -- it should work after a
fashion.  But I worry that Athena's performance might not be what you
are hoping for.  Athena does a lot of things that are more user-friendly
than performance-friendly


Cheers,
B


On 08/15/2017 06:10 AM, ASAKURA, Hiroyuki wrote:
 > Dear all,
 >
 > I would like to use the latest Larch as backend for Athena and
Artemis
 > on Windows to handle hundreds of XAS data (, hopefully).
 > But, I'm stuck. I would appreciate any comments and suggestions.
 >
 > Matt announced it is now possible on this list, but I still
cannot do it
 > on Windows.
 >
 > [Ifeffit] Larch 0.9.33
 >
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017-April/009091.html
<http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017-April/009091.html>
 >
 >> The "serve

Re: [Ifeffit] How to use Larch as backend for Athena and Artemis on Windows

2017-08-16 Thread Bruce Ravel


Hi Hiroyuki,

Sorry I didn't respond yesterday.  Yesterday was a bit of crazy day...

I suppose that this is still a work in progress.  I believe that Demeter 
works with Larch on Windows, but it is certainly not as easy or 
convenient yet as it should be.


In the place where Demeter got installed on your computer, there is a 
folder called \perl\site\bin -- you can look at the properties of the 
Athena desktop icon to see where that is.  In that folder is the 
"dathena.bat" file which the Athena desktop icon points at.


You should also find a file called "lathena.bat".  Try running that or 
pointing your desktop icon at it instead.


The difference between "lathena.bat" and "dathena.bat" is line 25 that 
sets an environment variable that Demeter uses to decide which of 
ifeffit or larch to use.


Obviously, there are number of other ways to get this environment 
variable set.  The bottom line is, yes, there is a switch.  The switch 
is the DEMETER_BACKEND environment variable.


Unfortunately, that switch cannot be in the configuration files, 
although what you tired in item 2 of your email was a sensible guess. 
It turns out that the choice of larch/ifeffit has to made long before 
the configuration files are read.


Do let me know how you get on.  While Demeter + larch should work, there 
are still almost certainly problems.  I need to get a new version of the 
Demeter installer out soon, so it would be nice to get some feedback in 
this area.


As for using Demeter + larch + 100s of file -- it should work after a 
fashion.  But I worry that Athena's performance might not be what you 
are hoping for.  Athena does a lot of things that are more user-friendly 
than performance-friendly



Cheers,
B


On 08/15/2017 06:10 AM, ASAKURA, Hiroyuki wrote:

Dear all,

I would like to use the latest Larch as backend for Athena and Artemis 
on Windows to handle hundreds of XAS data (, hopefully).

But, I'm stuck. I would appreciate any comments and suggestions.

Matt announced it is now possible on this list, but I still cannot do it 
on Windows.


[Ifeffit] Larch 0.9.33
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017-April/009091.html


The "server mode" for Athena and Artemis now works on all platforms and I
strongly encourage everyone to use this over the ifeffit back end.


Here is what I did.

Environment:
Windows 10 Pro (Japanese)
Demeter 0.9.25 (via official website)
Python 3.6 (official distribution)

1. Installation of the latest Larch

git clone https://github.com/xraypy/xraylarch.git (sha1: 
5a372cfe1368a8ac10c2ebfc5bef4e9a9a325f6d)

cd xraylarch
python setup.py install

# Some dependency related to XRD is not fulfilled.

2. Start Larch server


cd %LOCALAPPDATA%\Programs\Python\Python36\Scripts
python larch_server start

larch_server port=4966: started

I found a parameter of peakfit backend in demeter.ini and changed to 
larch, but did not work (as expected).


In the dathena.log, Athena still uses ifeffit as backend.


perl version: v5.18.2
backend: ifeffit


Should I compile Demeter package by myself to use the Larch backend?
Or, is there any "switch" to use Larch?

Thanks in advance,

ASAKURA, Hiroyuki





--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


[Ifeffit] Demeter on Windows with Inkscape (and possibly other programs)

2017-08-10 Thread Bruce Ravel


Windows users:

I got an interesting bug report today from a fellow who develops a 
popular open source program for vector graphics editing (Inkscape).


Apparently, there is a problem in Demeter's installer that has an impact 
on the ability of that program (and possibly others) in accessing system 
font files.  The issue with Inkscape is described here: 
https://github.com/bruceravel/demeter/issues/51


I mention this here on the mailing list in an effort to help the folks 
who maintain Inkscape.


If you use Demeter and Inkscape on your Windows machine, there is a 
problem and it is my fault :(


The simplest solution is to uninstall Demeter, then continue using Inkscape.

If that's not true or if someone needs a better solution right now, post 
here and I will help you work out a solution.


I think the real fix to the problem is simple and I will work on a new 
installer this month.


Cheers,
B



--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Exporting Curves (as Data rather than Images)

2017-06-26 Thread Bruce Ravel

On 06/26/2017 09:08 AM, Zhang, Guanghui wrote:

Felix,
After you finish the fitting, you can go to the "Data" window, data-> 
save data and fits as.

There are also other save options you can try.


relevant document page:

http://bruceravel.github.io/demeter/documents/Artemis/data.html#the-data-menu

Also relevant to this thread:

http://bruceravel.github.io/demeter/documents/Athena/plot/other.html#single-file-output

That single-file output option is available in both A & A.

B



--
Regards,
Guanghui





At 2017-06-26 02:36:16, "Felix E. Feiten" <fei...@cat.hokudai.ac.jp> wrote:

Dear all,

I think the title is almost enough explanation.

I would like to export the data corresponding to fits, chi(k), 
fourier-transform and back-transform to plot them with a different software.


I couldn't figure out how, can someone please help me?

With kind regards

Felix


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] FEFF8/FEFF9 in Demeter​

2017-06-16 Thread Bruce Ravel


My standard response to the feff9 question:

http://bruceravel.github.io/SCFtests/scf.html

B

On 06/15/2017 02:55 AM, 이국승(에너지환경소재연구팀) wrote:

​Dear Ifeffit users,


I remember that one of you have posted the method how we can use 
FEFF8/FEFF9 in Demeter​ program.


But I cannot find the posting in the archives.

Could you please kindly  let me know how can I find it or directly write 
again?



Best,

Kug-Seung Lee


Kug-Seung Lee, Ph.D.
Staff Scientist
Manager, 8C Nano Probe XAFS Beamline
Pohang Accelerator Laboratory

Pohang 790-784, Republic of Korea

Office: +82-54-279-1522
Fax: +82-54-279-1599
C. P.: +82-10-6419-7801
Researcher ID: http://www.researcherid.com/rid/D-7088-2011



___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] nonsensical negative values / restrictions

2017-06-16 Thread Bruce Ravel

Felix,

When you fit your EXAFS data using Artemis + Ifeffit or Larch, you are 
using a Levenberg-Marquardt non-llinear, steepest descent algorithm. The 
fit does kn ow anything /at all/ about what you are trying to do. It 
doesn't know what a sensible value for sigma^2 or any other parameter 
is.  All it knows is that you have data and a model that you are 
throwing at the data.


Armed with data and model, the algorithm optimizes the parameters that 
you have flagged as the variables.  It changes those values until it 
makes the sum of the paths look as much like the data as possible.  It's 
goal is to make the red line look like the blue line.  That's it. That's 
all it does.  That's how sigma^2 can come out as a negative number.


A negative sigma^2 or any other nonsensical parameter doesn't represent 
a failure of Artemis.  It is information that is useful to you, the 
person doing the fit.


A nonsense parameter is trying to tell you about a way that the model 
you have proposed does not represent the data that you have measured. 
And it is a hint about what changes you need to explore in your model to 
more properly represent the data.


An example: suppose you have an unknown oxide phase and you have reason 
to believe it is some sort of highly disordered phase.  Just to pull an 
example out of the air, you might think that your sample is filled with 
FeO(OH) when in fact it is filled with FeO.  FeO(OH) is pretty 
disordered, whereas FeO is rocksalt.  If you run Feff on Feo(OH), you 
will get a spread of paths at several distances for the first shell. 
When you make the fit with the FeO(OH) model, the structural 
contribution to the disorder is MUCH higher than in the actual sample. 
The fit is likely to use a negative sigma^2 to counteract that effect.


That's a simple and contrived "explaining example", but it makes the 
point (I hope).  Artemis didn't fail.  The fit is trying to tell you 
that you assumptions were not realized in the data.


In short, I agree that your results make no sense, but I suggest that 
the problem is that you are making a poor assumption in your fitting model.


It also might be the case that there is a problem with the measurement 
of your data that introduces a systematic error that the fit compensates 
for by applying a weird parameter value.


Or maybe you have a sulfide instead of the oxide you were expecting.

Or maybe you ran Feff for the Pt K edge rather than the Pt L3 edge. 
(Oops! I actually do that with embarrassing frequency)


Or something else I haven't thought of

HTH,
B


On 06/16/2017 02:09 AM, Felix E. Feiten wrote:

Dear all,

I have the following problem:

In some fits using Artemis (Demeter 0.9.25) I will get negative values 
for parameters where it makes no sense at all.
For example, when trying to fit two first shell paths, Pt-Pt and Pt-O, 
for a Pt nanoparticle,

sigma^2 for the Pt-O path becomes negative.

Obviously, sigma^2 has to be a positive number.

My questions:

1. Why does the fit algorithm do this?

2. What can I do to avoid this?

I know that there are most likely significant problems with my fit if 
this behaviour occurs.
As far as I know it's possible to impose restrictions in Artemis and if 
anyone could point me
towards a tutorial explaining how to implement restrictions that might 
be a first step in the right direction.
Currently, the chapter "Constraints and restraints" in the Artemis 
documentation is "Coming soon..".


With kind regards,

Felix


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit



--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Calculating Ce oxidation state at the L3 edge

2017-05-16 Thread Bruce Ravel

On 05/16/2017 01:31 PM, Stephanie Laga wrote:


I have a (hopefully) quick question about calculating oxidation state of
CeO2 at the L3 edge.

When calculating ox state by taking the ratio of peak areas, is the
pre-edge feature for Ce included in this calculation? This point isn't
clear to me from looking at various papers.

I've attached an image from Bernardi 2015, which shows that the %Ce III
calculation doesn't include the fitted pre-edge feature A. I'm not sure
why this would not be included? Is this because we only consider 2p > 5d
transitions and the pre-edge is 2p > 4f (forbidden) transition?




I am not sufficiently knowledgeable about CeO2 specifically to answer 
your question specifically.  However, there are some general principles 
that apply.


The concept here is to come up with a set of peak shapes that describe 
the shapes of the end member spectra.  Those two sets of peaks, taken 
together, represent the contribution to the spectra from each end 
member.  Sum the areas of each set of peaks, that represents the 
contribution.


You then fit all of both sets of peaks to an unknown spectrum and sum up 
each set.  You now have enough information to quantify the amount of 
each end member.


So, in general, yes, you would include the fitted peak A because that is 
part of your quantification metric.  So, I disagree with the formula in 
the figure you attached.  But peak A is small, so neglecting it has 
scant impact on the result.


Some caveats:

1. You must be very careful about normalization.  If you do not 
normalize consistently, then you will introduce systematic error in the 
phase quantification.


2. You must use the same step-like function for both end members and for 
the unknowns.  If the step function changes, then the areas under the 
peaks will change, introducing systematic error.


It would be interesting to compare this to linear combination analysis 
to see if you get the same answers


HTH,
B

--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Error importing data into Athena

2017-05-03 Thread Bruce Ravel

Sharon,

It's pretty important to ask questions in a way that aids and encourages 
answers.  In this case, it's basically impossible to help given that you 
shared neither the error message nor an example of the data that 
triggered the error.


/Good/ questions get good answers.

B


On 05/01/2017 02:18 PM, Bone, Sharon Elizabeth wrote:

Hi,



I’m running the current version of Athena on a windows 10 machine. It
had been working fine, but now I get an error whenever I try to import
new data (.dat file from SSRL). The error tells me the program can’t
read the file and asks whether I need a plugin.



Do I need a plugin?



How do I uninstall and reinstall the program? I’m guessing this might be
the best fix?



Thanks!

Sharon



___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Silent Oxygen

2017-04-18 Thread Bruce Ravel

On 04/18/2017 11:10 AM, Fuxiang Zhang wrote:

Hi, all,
I am in studying the EXAFS of perovskite and clearly see the split of
the first peak after ion irradiation. It should come from a symmetry
change, so I use a tetragonal model (instead the original cubic) which
contains two independent O sites. However, after running Atoms and
Feff, all paths are contributed by only one O atom and nothing related
to another Oxygen atoms (see attached file). As a result it may
be difficult to get a good fit of the first split Ta-O peaks. I am not
sure if it is true or something wrong.
Thank you very much


A fairly common question here on the mailing list.  This is a *feature* 
of Artemis, not a bug.


http://bruceravel.github.io/demeter/documents/Artemis/extended/fuzzy.html

If you want to /model/ a split in distance, you can drag that path into 
the path list twice and adjust the delta R and amplitude parameters 
accordingly.


B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Information content from Athena for Hamilton test?

2017-04-11 Thread Bruce Ravel

On 04/09/2017 11:59 PM, Will Bennett wrote:

How is this value of "Information Content" determined in Athena?


This is not explained well in the manual.

The number Athena reports is the fitting range of the data divided by 
the core-hole lifetime of the edge measured.  I am not certain that is 
especially well-justified, but it seems like a reasonable approximation.


B

--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Conflicting FEFF calculation

2017-04-04 Thread Bruce Ravel

On 04/04/2017 11:58 AM, Robert Gordon wrote:

Seems to be looking for gnuplot in the wrong location. Gnuplot was
installed to:
C:\Users\ragordon\AppData\Roaming\DemeterPerl\c\bin\gnuplot
not
C:\Strawberry...


Drat!  I thought I had that working correctly.

You can manually fix that in the preferences.  Change Gnuplot-->program 
the the fully resolved path where it is installed.




also, log has this:
C:/Users/ragordon/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Artemis.pm
line 26

Which has the slashes in the wrong direction for windows...just
something from the log writing
or a linux-typo in the program somewhere?


Don't know.  Was there any context?

B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Conflicting FEFF calculation

2017-04-04 Thread Bruce Ravel

On 04/04/2017 01:42 PM, Ashis Biswas wrote:

In the new pre-release version of Artemis I am getting similar paths
for TAA regardless of the order of import. Therefore, the problem
does not exist anymore. Thank you very much for your time and help.


Whew!  I was getting worried about that one!

B

--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Conflicting FEFF calculation

2017-03-28 Thread Bruce Ravel

On 03/27/2017 11:02 AM, Ashis Biswas wrote:

Thank you very much for your reply. Here I am attaching two Artemis
projects files (TAA_TPA and TPA_TAA), named according to their order of
import. In my computer the paths for *TAA* are different in two project
files. For example, i) in TAA_TPA project the Reff for three single
scattering paths of O (@O1.1; @O3.1, and @O5.1) are different to that in
TPA_TAA project, ii) the single scattering path @C5.1 (path number 6) at
Reff of 2.682 A0 in TAA_TPA project is missing in TPA_TAA project, and
so on.

I am also attaching the papers from where the coordinates for TAA and
TPA are obtained: TAA (Kamenar et al., 1993: tables 1 & 2; Fig. 1) and
TPA (Pappalardo et al., 1983: Table 1; Fig. 1).



I agree that the TPA_TAA.fpj project file that you sent me has incorrect 
data in the Feff tab for TAA.


I have not, however, been able to reproduce that here.  And not for want 
of trying -- I spent the last half hour trying to find a way to 
replicate what you are showing in the TPA_TAA file.  Regardless of the 
order in which I import the two structures and regardless of whether I 
have discarded and reimported Feff calculations, when I click the "Run 
Atoms" button on the TAA cif file, I /always/ get the structure from 
Table 4 in the Kamenar paper.  I cannot reproduce the Feff tab that you 
show in your TPA_TAA project file.


I have no idea how you got into the state you show in the TPA_TAA 
project.  It is clear that something went awry, but I don't know if it 
is an error of the program or of the user.  I can't fix a problem I 
can't observe.


I understand that this is not the answer you were looking for.  I am 
simply not seeing the problem you are reporting.


B



--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Multiple data set fit limit

2017-03-24 Thread Bruce Ravel


Victor,

I now believe that you are seeing the problem you claim to be seeing, 
but it's going to take a lot of work for me to understand how you got there.


When I import the Artemis project files you sent, I see that you have 24 
copies of the FeS2 data in the project and you seem to be including 3 of 
them in the fit.


I suspect the central problem here is that Demeter is making an ifeffit 
group for each copy of the data, even the ones you are excluding from 
the fit.  This exceeds the normal compiled-in limit of 16.  From a user 
interface perspective, I suspect that the sin is that Demeter blithely 
does this without warning you about Ifeffit's limit of 16 data sets.


It is going to take me a long time to really track down all the things 
you have done to push at the boundaries of what Artemis + Ifeffit can 
do.  I have not done much testing beyond a handful of data sets 
(neighborhood of 6).  It's possible I have done no testing in double 
digits and I have clearly not done much testing up against Ifeffit's 
compiled-in limitation on number of data sets.




Some suggestions:

1. Don't exceed 16 data sets, even if you are planning on clicking off 
the "include" button for some of them.  In earlier email, when I said I 
do not see what you are observing, what I really meant was that if I do 
a fit with a handful of data sets, all of which are included in the fit, 
I see no such problem.


2. Try using Larch.  Larch, not being a Fortran program, does not have 
Ifeffit's compiled in limits.  That is not to say that Artemis+Larch 
will certainly work correctly with a large number of data sets (some of 
which are excluded from the fit) -- there most certainly could still be 
bugs in this untested regime.




In any case, there are things that could be done to make it easier to 
identify the exact problem you are uncovering.  I can see from examining 
your project files that you added a large number of copies of the data 
then hit the Fit button a couple dozen times before finally saving and 
sending me the project file.  From my perspective as developer and 
bug-squisher, it is always better to see an example that is as minimal 
as possible.  The more data you add after seeing a problem, the more 
times you hit the fit button after seeing a problem, the harder it is 
for me to track down the actual proximate cause of problems.


I acknowledge that this was likely not the answer you were hoping for. 
I guess I am saying, take small steps as you build up a big, complex 
fitting model.  It is true that a program written by a competent 
programmer should be able to take whatever you throw at it.  Alas, 
Artemis was written by a dilettante.


B

On 03/18/2017 10:59 PM, Victor Streltsov wrote:

Hi Bruce,
Sorry for delayed reply. I didn't want to take up too much of your time and I 
have attempted to run more tests to reproduce the problem with other data and 
models.

First, I thought that you were able to reproduce the problem (maybe partially) 
since you wrote:

On 03/08/2017 10:53 AM, Bruce Ravel wrote:
Well . a multiple data set fit using larch runs to completion and
reports sensible values for parameters, but does not manage the data
sets correctly.  One obvious sign that something has gone wrong is the
after-fit plot attached.  Yikes!


Similar behaviour I observed in my refinement using Ubuntu version of 
Demeter/Artemis/Ifeffit. Windows version works fine. (Switching to Linux 
version is related to my previous bug report about user input of epsilon which 
is still not available under Windows (until next release), but fixed in the 
latest Linux version(s))

The task I was running included 3 data sets and a model with 55 paths. However, the 
"Monitor/Debug options/Show mode status" in Demeter/Artemis shows content with 
330 paths instead of expected 3x55= 165, if I understand correctly this option. It seems 
that it counts all added and previous replaced/removed data sets (extra 3 datasets which 
were not included and even removed). It doesn't effect Windows based run, however, 
creates the problem I mentioned before using the same project file under Linux. Is number 
of paths a compiled-in limit (less than ~300 or so) in Linux/Ifeffit?

To avoid any possible problems caused by my model and data I used available for 
Artemis example FeS2 data for test runs.  I have simply added many the same 
FeS2 data sets in the Artemis but included only 3 data sets to actual fit. 
Extra unused data sets did not affect at all the fit of 3 data sets under 
Windows, however, the problem reproduced using Linux version. I have attached 
(zip) project files, log files and contents file (mode status) for both runs 
under Windows and Linux.

I hope it is more helpful.

Victor

-Original Message-
From: Ifeffit [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of 
Bruce Ravel
Sent: Saturday, 11 March 2017 1:17 AM
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.a

Re: [Ifeffit] Conflicting FEFF calculation

2017-03-24 Thread Bruce Ravel

On 03/21/2017 09:10 AM, Ashis Biswas wrote:

I have a problem of conflicting FEFF calculation for
tris(acetate-O)arsenic [As(OCOCH3)3] (TAA) and tris(phenyl thio)arsenic
[As(SC6H5)3] (TPA); respective cif and atom input files are attached. In
Artemis, when I import TAA after TPA, the paths obtained for TAA from
FEFF calculation are different compared to the scenario when I import
and calculate the path for TAA at first. The problem is similar in both
computers with Windows 7 home premium 64 bit operating system and 0.9.24
version of Demeter and Windows 7 professional 32 bit operating system
and 0.9.25 version of Demeter.

I have even tried a scenario, where I discarded both FEFF objects after
getting inconsistent results for TAA and then imported TAA at first
without restarting Artemis and I got wrong paths again, indicating
software can remember from last calculation. Any explanation for this
problem will be deeply appreciated.



I don't observe this using the input data you supplied and the recipes 
you describe.


I have no idea what TAA is supposed to look like, but the atoms list and 
the path list are identical regardless of the order in which I import 
your two files.


You will need to find a way to demonstrate to me better how to see what 
you are seeing.  Perhaps if you saved Artemis project files that I could 
then open on my own computer


B

--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] [Question about XANES] Hello I'm a graduate student in Korea

2017-03-17 Thread Bruce Ravel


Doyoub's question is a common enough one that I added a section to the 
Athena user manual:


http://bruceravel.github.io/demeter/documents/Athena/bkg/short.html

My answer to Doyoub's question is much the same as Matt's.

B

On 03/17/2017 09:18 AM, Matt Newville wrote:

Dear Doyoub,



On Thu, Mar 16, 2017 at 10:59 PM, 김도엽(신소재공학과)
<mdyk...@postech.ac.kr <mailto:mdyk...@postech.ac.kr>> wrote:

Hello



I'm a graduate student at POSTECH in Korea.

Currently, I obtained XANES spectra over a narrow energy range and
looked through the Athena manual


But, I'm kind of lost as to how exactly I'm supposed to normalize
raw data

which only has XANES spectra.


It would be very generous of you if you help me figure this out


It's hard for us to answer questions that are so vague.

Generally, it is recommended to collect XANES spectra out to at least
100 eV (and better 300 eV) above the edge in order to get a decent
normalization.  Well, for "normal" hard X-ray spectra: for edges below
about 3000 eV, you can often get by with less energy range.

If you don't have that, it is sometimes OK to pick an energy as far
above the edge as possible and pick an edge step so that all the spectra
is 1.0 at that energy.  That is definitely prone to systematic biases in
normalization.   Furthermore, if your data is particularly noisy, it can
add a lot of variation in the normalization to use just a single energy.

Which just brings me back to the original point: it's hard to say in
general how to best handle XANES with a short energy range.

--Matt


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Ifeffit Digest, Vol 169, Issue 9

2017-03-15 Thread Bruce Ravel

On 03/14/2017 06:15 AM, Abhinav Prabhakar wrote:

Attached is the CIF file in question. The crystal is Tobermorite 14A,
taken from COD website.



Abhinav,

I don't understand the contents of the CIF file in the context of the 
copy of the International Tables that I have in front of me.  The list 
of equivalent positions given in the CIF file just doesn't seem to be 
right for space group 9.


The CIF file is clearly using the C axis as the unique axis since the z 
coordinate is the negated coordinate.  But the list of positions does 
not correspond to any of the three cell choices.


While this could be a problem in Artemis, I am inclined to think that 
the authors of the paper cited in the CIF file made some kind of 
non-standard choice for the setting of their crystal.


As I said before, Artemis does what the International Tables tell it to 
do.  If the author of a crystallography paper makes some non-standard 
choice, Artemis won't know how to deal with it.


B



--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Data export and coordination number

2017-03-13 Thread Bruce Ravel

On 03/13/2017 09:48 AM, Abhinav Prabhakar wrote:

i) Is it possible to extract the normalized/background corrected data
from Athena (in E-,k- and R- space) and export it as numbers (to Excel
perhaps)?


This is explained in the manual.


ii) Using Artemis, how can coordination numbers (N) be expressed as
'guess' parameters (Artemis allows only numerical values for N)?


This has been discussed many times on this mailing list.  You cn find 
that by searching the archives.


B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Space group type in Artemis

2017-03-13 Thread Bruce Ravel

On 03/11/2017 05:56 AM, Abhinav Prabhakar wrote:

Hello,

I have a question about the working of Artemis as a new user.

Artemis does not recognize the space group B11b. When importing a cif
file of a crystal with this symmetry, it sends a prompt message that the
space group symbol cannot be recognized. As a result, I changed it to
P11b and it works. But would this change any crystal information (for
eg. Degen, Reff values) significantly?


I am not a crystallography expert in any sense.  When I wrote Artemis, I 
meticulously followed what I found in the fourth edition of the 
International Tables for Crystallography, Volume A.  Every symbol 
defined in there is recognized by Artemis.  (Well, I guess I should say 
that every symbol is /supposed to be/ recognized by Artemis.  If one is 
missing,  that's a bug and should be reported.)


"B11b" is not a symbol that I found in my copy of ITC volume A.  As 
Robert suggested, there may be a way to rotate group 9 so that "B11b" is 
an interpretable symbol in the abstract.  But Artemis does not know how 
to do that.  (Nor do I.)


"P11b" is a setting for space group #7.  If, as Robert suggests, your 
CIF file is for space group #9, then the answer to your last question is 
yes.  It is plainly obvious that using a different space group will 
change the degeneracies and distances.



Of course, you did not bother to include a copy of the CIF file in 
question to your original email, so it is not actually possible for 
Robert or I or anyone else to actually help you effectively.


At the risk of sounding like an annoyingly broken record, everyone 
should take the time to ask a good question or write an actionable bug 
report:


  http://bruceravel.github.io/demeter/documents/SinglePage/help.html
  http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html

B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Multiple data set fit limit

2017-03-10 Thread Bruce Ravel


On 03/09/2017 05:15 AM, Victor Streltsov wrote:

3 data set refined to completion with sensible refined parameter, however,

R-factor for 3^rd data set is 1. (overall R for 3 data set is huge
too) and after-fit plot for 3^rd data set is missing, only experimental
one shown. I am using latest versions of programs.



Again, I don't see this behavior on my own computer.

It is always better to /show/ something to me than to /explain/ 
something to me.  If you are unwilling or unable to make an actionable 
bug report, then there isn't anything that I am going to be able to do 
for you.


It is not my intent to be difficult.  You are telling me about things 
that I cannot reproduce on my own computer.  Despite my explicit request 
for a more useful bug report, you are not showing me how to see what you 
are seeing.


If you cannot do something to make this conversation more productive, 
then I am just going to stop responding.


http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html

B




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Multiple data set fit limit

2017-03-08 Thread Bruce Ravel

On 03/08/2017 10:53 AM, Bruce Ravel wrote:




Well . a multiple data set fit using larch runs to completion and
reports sensible values for parameters, but does not manage the data
sets correctly.  One obvious sign that something has gone wrong is the
after-fit plot attached.  Yikes!


This turned out to be a few Larch syntax problems.  I just checked a fix 
into github.


As far as I know, the head of github has an Artemis that works for 
single and multiple data set fits with Larch or Ifeffit.


B

--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Multiple data set fit limit

2017-03-08 Thread Bruce Ravel

On 03/08/2017 09:37 AM, Bruce Ravel wrote:

On 03/08/2017 09:31 AM, Matt Newville wrote:

Can Artemis use Larch?

Yes.
B



Well . a multiple data set fit using larch runs to completion and 
reports sensible values for parameters, but does not manage the data 
sets correctly.  One obvious sign that something has gone wrong is the 
after-fit plot attached.  Yikes!


Shouldn't be too hard to fix.  A single data set fit with larch or any 
fit with ifeffit works as I expect.


B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Multiple data set fit limit

2017-03-08 Thread Bruce Ravel

On 03/08/2017 09:31 AM, Matt Newville wrote:

Can Artemis use Larch?

Yes.
B

--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Multiple data set fit limit

2017-03-08 Thread Bruce Ravel

On 03/08/2017 03:46 AM, Victor Streltsov wrote:

The Linux latest version of Artemis limits multiple data set fit to 2
data sets.

The input takes any number of data sets but 2 sets is used in the fit only.

I’ve tried latest available windows version it uses more than 2 in fit
(e.g. I used 3).



That does not seem to be true.  I just ran a three-data-set fit on my 
Ubuntu 16.04 machine.


If you need to me to do something, you will need to submit a more 
informative bug report.


B

--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


[Ifeffit] downloading Demeter

2017-03-01 Thread Bruce Ravel


To those who have noticed that Demeter has not been available for 
download in the last day or so:


I use Amazon's S3 service to distribute the large installer files.  You 
may have seen the news in the last 12 hours about a massive outage of 
that service, or you may have noticed that other internet resources that 
you use are unresponsive.


There is nothing I can do to resolve this problem.  Eventually Amazon S3 
will come back on line and you will again be able to download Demeter.


Please be patient and try again later.

Regards,
B

Example news article: 
https://techcrunch.com/2017/02/28/amazon-aws-s3-outage-is-breaking-things-for-a-lot-of-websites-and-apps/




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Limitations of maximum number of points in a data file in Athena

2017-03-01 Thread Bruce Ravel

On 02/28/2017 08:17 PM, Harishchandra Singh wrote:

Hi All,

I have a query regarding limitation of maximum number of data points
(or maximum size) of data file in to be imported in Athena.
It would be great to hear form you all.


It would be helpful to tell us what you are trying to do.  Your 
questions, as asked, is vague and open-ended.


B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Units for various parameters of ‘feffNNNN.dat’ file

2017-02-28 Thread Bruce Ravel

On 02/28/2017 11:09 AM, Samy Ould-Chikh wrote:

I am a bit surprised about φc and φeff.
I was expecting radian unit...


Sorry, as Matt said, phase is intended to be interpreted as radians.  I 
suppose that was stated unclearly.  Phi is added to 2*k*R.  k*R is 
[Ang^-1]*[Ang], which is unitless and interpreted as radians.


And I forgot about that page in the Larch manual.  It's great that Matt 
captured that in the modern documentation.


B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Units for various parameters of ‘feffNNNN.dat’ file

2017-02-28 Thread Bruce Ravel


On 02/28/2017 10:10 AM, Samy Ould-Chikh wrote:

Dear Ifeffit mailing list,



I have a question which concern units and I can’t find the answer in the
Feff manual.

In a FeffNNN.dat output file, what are the unit of the numbers (if any)
corresponding to

φc,

|Feff|,

φeff,

the reduction factor,

λ,

Re(p)


Samy,

This is a peculiar reference, but I think the clearest written 
explanation of this is in the manual for the ancient "feffit" program. 
Here is a copy of its manual:


http://cars.uchicago.edu/~newville/feffit/feffit.pdf

You will want to look at page 22.  While the rest of the manual is not 
so useful anymore (in the sense that there are very few users of the old 
feffit remaining), it's explanation of how the feff.dat files are 
used is excellent.


Eq. 6.1 should clarify how each term is used and what the units are. 
Column 1 is, of course, inverse Angstroms.  Columns 2, 3, and 4 are 
unitless.  The two phase terms go into the argument of the sine, thus 
must be unitless.  The amplitude term is multiplied by N and S02, thus 
is also unitless.  The reduction factor, as well, is unitless -- it is 
used in the computation of the amplitude term in equation 6.1.


Lambda has units of angstroms, the real part of p (which is the complex 
wavenumber used in the Feff calculation) has units of inverse Angstrom.


I am pretty certain I got all that right.

I think it would be a good idea to capture all of this information as 
well as eq. 6.1 in the Artemis manual.


HTH,
B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] command buffer input

2017-02-22 Thread Bruce Ravel


I still don't really understand the problem.  You are describing 
something I haven't seen before but you're not giving me any way to 
visualize or reproduce the problem.


Are you telling me that the command buffer window does not look like 
this on certain Windows computers?


http://bruceravel.github.io/demeter/documents/Artemis/monitor.html#the-command-buffer

Does it help to resize the window?

B


On 02/21/2017 03:03 PM, Karl-Michael Schindler wrote:



Am 21.02.2017 um 20:17 schrieb Bruce Ravel <bra...@bnl.gov>:

OK   you didn't tell us exactly what you tried to do, you didn't tell us 
what you expected to happen, and you didn't tell us what actually happened.  I 
don't know if this a bug report or a question or something else?

B


OK, I try again.

In Artemis I select the menu Monitor → Show command buffer and the corresponding 
panel Ifeffit & Plot Buffer opens. In this panel i use the command prompt to 
enter commands like write_data or others. The problems is that unter Windows Server 
I do not get an active cursor in the text filed of the command prompt and i cannot 
enter any character, what ever i try and yesterday it also happened under Mac OS X 
→ VirtualBox → Windows XP. Today the latter works again, but the trouble with the 
Windows Server is permanent. So, what could be the reason, why I cannot use the 
command prompt and how can i fix it?

My main use of this is to export data for further processing in IgorPro. My 
current workaround is to check the files in the folder Stash and load the data 
from there.

Michael.
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] command buffer input

2017-02-21 Thread Bruce Ravel


OK   you didn't tell us exactly what you tried to do, you didn't 
tell us what you expected to happen, and you didn't tell us what 
actually happened.  I don't know if this a bug report or a question or 
something else?


B


On 02/20/2017 07:22 AM, Schindler Karl-Michael wrote:

Hi.

I used to issue some commands in the command field of the command buffer panel, 
mainly to export arrays with data with write_data. At least i thought so. 
However, now i cannot enter commands any longer. Can someone give me a hint?

Michael.
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Calculation of metal concentration (and hence density) from Edge Jump

2017-02-21 Thread Bruce Ravel



This might help: https://doi.org/10.1107/S1600577514001283

Note that we measured a sequence of standards of known thickness and 
concentration /prior/ to the rest of the experiment, so the methodology 
in that paper might not be useful after the fact in the absence of that 
prep work.


B

On 02/20/2017 10:19 PM, pushkar shejwalkar wrote:

Dear All,
First of all, is it possible to calculate the concentration of metal
(loading, therefore) from just the edge jump? Is there a simpler
equation like knowing the Flux values or some basic instrumental
information we can calculate the concentration term using Io and It
values of beamline (the simplest form of Beer-lambert law)? if so what
formula should we use.
I searched in the mailing list archive and have found one such archive
but it discusses how to use calculation to find out how much sample
would be needed to get the edge jump. I am rather interested in the
reverse way. I have an experimental edge jump and want to calculate (if
possible with as much accuracy as possible) the concentration of metal.
I know with only edge jump it will be difficult and XRF will be a better
and more reliable way. But for better understanding and cross checking
between different samples, I wish to do such calculations.
Can anyone guide me to the right direction and equations to do such
calculations?
Thank you all in advance
Warmest regards
Pushkar

--
Best Regards,
Pushkar Shejwalkar.
Post-doctoral -Researcher,
Tokyo Engineering University,
Tokyo-to
Japan



___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Trigonometric Function in GDS

2017-02-06 Thread Bruce Ravel


I've never seen that before.  You have provided no context.  Without 
some context, I cannot be expected to provide an answer.


http://bruceravel.github.io/demeter/documents/SinglePage/help.html

B

On 02/06/2017 10:36 AM, Mikhail Solovyev wrote:

Hello to all.

I am encountering an issue when trying to input a trigonometric function
in my GDS window. When trying to fit the data, i get what appears to be
an error

GDS: 'FeN0'
 function_2

And it applies to every GDS that has the trig function in it.
What exactly does the function_2 mean?

Thank you.




___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] XEAFS fitting problems

2017-01-31 Thread Bruce Ravel

On 01/30/2017 04:31 PM, Fuxiang Zhang wrote:

Dear all,
I am new for XAS analysis and now working on solid solution alloys with
EXAFS measurements. Here are some general questions about EXAFS fitting
that may need your help.

1. In NiCoCr alloys, I always get obvious smaller ss for the pairs of
Ni-Cr or Co-Cr than Ni-Co (0.002 vs 0.008-0.011), when measuring the
K-edge of Ni and Co, does it suggest that Cr is favorably bonded with Ni
and Co?


Possibly, but I'd be skeptical.  That sort of alloy is not one of the 
strengths of XAFS.  The backscattering amplitudes of elements close in Z 
number are pretty similar, making it difficult in a numerical sense to 
distinguish them.  Z-numbers that differ by only 3 or 4 are very hard to 
distinguish in XAFS.


As a result, I would expect uncertainties on your sigma2 values to be 
rather large.  I would also expect correlations between the various 
amplitude and sigma2 parameters to be high.


As a result, I think you would have trouble making a strong and 
defensible argument.  I would certainly be a skeptical reviewer of a 
manuscript claiming this unless it had a very compelling argument backed 
up by strong data from another measurement or from theory.



2. In order to get the bond length of different pairs in binary AB
system, can I use formula alpha1*Reff and alpha2*Reff to refine the
length of pairs of A-A, A-B (simple cubic symmetry)?


The "alpha*reff" thing is a way of expressing all the DeltaR parameters 
of a purely cubic crystals using a single parameter.  That is the only 
situation in which that formula is, strictly speaking, applicable.


https://speakerdeck.com/bruceravel/discussion-of-the-fes2-exafs-analysis-example?slide=9

It is a mistake to think that there are magical formulas that can be 
memorized to make EXAFS analysis easy.  No such things exist.


Every way of parameterizing the terms in your EXAFS analysis in Artemis 
must be defensible in the context of the model you are using to try to 
understand your data.


What I mean by defensible is that you can explain to the reviewer of a 
paper or to a member of your thesis defense jury why the fitting model 
is reasonable, why you chose to use that parameterization, and how that 
model helps to answer the scientific question without introducing an 
unsupportable approximation or some other form of systematic uncertainty.


So, the answer to your specific question is "Maybe".


3. The selection of k range in Fourier transformation Parameters seems
to have some effect on the fitting results, how to select the range in
order to get reasonable results.


This has been discussed plenty in recent months on this mailing list and 
Scott discussed it at some length in his book.


Executive summary: include /data/ in the FT range, not noise.  If the 
measurement is dominated by statistical or systematic uncertainty after 
some value of k, don't use that part of the measurement.


HTH,
B


Many thanks

Fuxiang Zhang


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] GNU plot crashes

2017-01-31 Thread Bruce Ravel


Marcus,

Without a reproducible recipe, I cannot observe this problem in action. 
So I don't know how I can help.


A bit of googling quickly turned up a situation involving a conflict 
between libgtk versions.  Since you didn't offer any information about 
the environment in which you are running the software, there is, again, 
nothing I can do to help.


B


On 01/31/2017 06:07 AM, mfehse wrote:

Hi everyone

while working in athena project gnu plot sometimes crashes and gives the
following error:


Gdk:ERROR:/build/gtk+2.0-KsZKkB/gtk+2.0-2.24.30/gdk/gdkregion-generic.c:337:miSetExtents:
assertion failed: (pExtents->y1 < pExtents->y2)
Aborted (core dumped)


Its a bit strange because I have not observed this error when working
with other athena projects before and it also does not happen every time
I want to plot something, only sometimes. It seems quite random to me.

I have attached the athena project file so you can try yourself

many thanks

marcus



___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] delR and sigma2 models for multiple Scattering Paths

2017-01-18 Thread Bruce Ravel

On 01/18/2017 01:27 PM, Mikhail Solovyev wrote:

I'm currently trying to Artemis fit a molecule that is highly symmetric
with multiple scattering paths playing a large role.
delR and sigma2 have been handled rather well for all of the single paths.
I am, however, confused as to how to handle it for multiple scattering
paths.
Reff for them seems to be close to the value of the furthest atom, but
is always ~5-10% off. (which would be my second question, how is Reff
determined for multiple scattering paths)
I've looked at the presentation and examples, such as FeS2.
I am trying to incorporate all of the same variables used in single
scattering paths for multiple scattering paths the best i can.


Mikhail,

The definition of Reff is /always/ "half-path-length".

For a single scattering path, this is trivial.  It's simply the 
inter-atomic distance.


For a multiple scattering path, you add up the length of each leg, then 
divide by 2.  For the case of strictly collinear multiple scattering 
path, Reff is the distance between the two atoms farthest apart. 
However, if there are scattering angle that are something other than 0 
or 180 degrees, Reff will be related to interatomic distances via some 
kind of trigonometric relationship that has to do with scattering angles.


You are wise to try to build constraints between SS and MS paths in your 
fit.  For DeltaR parameters, trigonometry helps, but may only be an 
approximation.  Possibly a good approximation, but an approximation 
nonetheless.



Scott discusses how to parameterize sigma^2 in his book:

https://www.amazon.com/XAFS-Everyone-Scott-Calvin/dp/1439878633

There are some situations (see https://doi.org/10.1103/PhysRevB.54.156) 
where MS sigma^2 can be related exactly to SS.  In general, though, MS 
sigma^2s usually can only be approximated by constraint with the SS 
sigma^2s.


https://speakerdeck.com/bruceravel/discussion-of-the-fes2-exafs-analysis-example?slide=6

HTH,
B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] error when fitting in Artemis

2017-01-04 Thread Bruce Ravel

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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 2

2017-01-03 Thread Bruce Ravel

On 01/03/2017 03:32 PM, Raj kumar wrote:

From XRD, it is confirmed that there is no side phase formation and
contamination. Hence, i guess the heavier element role could be avoided
here.


Raj,

While this might be true for your sample, in general, a statement like 
this always concerns me.


From XRD, you can say is that there is no /crystalline/ side phase 
formation and that there is no contamination in the /diffracting/ 
/portion/ of the sample.


It is very common when preparing nanoparticulate matter for there to be 
non- or poorly-diffracting content in the sample.  If that content 
contains the absorbing element, then it will have an impact on the XAS data.


B



--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12

2016-12-22 Thread Bruce Ravel


Robert,

It seems you are sort of cherry picking through the code.

When I first wrote Xray::Crystal, I spent a lot of time pouring over 
chapter 5 of ITC volume A.  I am mostly confident that the various 
transformations are applied correctly in response to space group symbol 
choices.  Demeter does that by applying a transformation to place the 
positions under the alternate symbol onto the setting of the standard 
symbol (*) then transforms back after applying symmetry operations.


Again, my goal was to build the cluster correctly but without concern 
for alignment to a particular set of axes.


None of this is to say that I do not welcome actionable bug reports, but 
emphasis is on the "actionable".


B

(*) "Standard" means "has an entry in chapter 7 of ITC Volume A", as 
opposed to being tabulated in Chapter 4.  Atoms tried to recognize all 
the symbols in Chapter 4, but it transforms coordinates to the standard 
settings before applying symmetry operations.


Obviously, a program like Atoms need not work that way.  It could simply 
apply symmetries encoded in any symbol from Chapter 4.  But Atoms does 
what I described.



On 12/21/2016 08:22 PM, Robert Gordon wrote:

Hi Bruce,

I looked at Site.pm and Cell.pm as well (and I don't program in perl, so
please forgive
any naivete).

In Site.pm, lines 188 - 191, it says:
#-- rotate from F or C settings to P or I
  if ($is_tetr) {
($x, $y) = ($x-$y, $x+$y);
  };

and this looks like a 45 degree rotation to me, and I can understand why if
someone specified a cell that was "c-centred tetragonal" which is really P
or face-centred tetragonal being I, but is it being applied to all
tetragonal systems?

In Cell.pm, lines 516 - 521, it says:
  ## rotate a tetragonal group to the standard setting
  if (($crystal_class eq "tetragonal" ) and ($setting ne 'positions')) {
my ($a, $b) = $self->get(qw(a b));
$self->a($a/sqrt(2));
$self->b($b/sqrt(2));
  };

but I see a re-scaling, not a rotation.

Possibly related: When I look at Site.pm on my linux box, from line 134
on, it is almost all
purple. z and utag are highlighted in red, as is $self on line 138. The
file looks normal
on github, but if I copy it, these colour changes manifest. I normally
associate
blue with comments, purple with text strings, green for $self...

thanks,
-R.

On 12/21/2016 12:58 PM, Bruce Ravel wrote:

On 12/21/2016 02:50 PM, Robert Gordon wrote:

So, for all but tetragonal, the orientation of the cluster can be
identified with the
orientation of the crystal axes. Does it not seem more logical to
preserve the
apparent orientation with respect to the crystal axes so that, when
using POLARIZATION
(issues in FEFF6 aside), confusion is less-likely?


Hmm ... I think I understand your point.

I think you may be ascribing too much agency and intelligence to the
the Atoms algorithm.  The way Atoms works these days is to use this
tabulation of chapter 7 of volume A of the International Tables:

https://github.com/bruceravel/demeter/blob/master/lib/Xray/Crystal/share/space_groups.db.PL


It selects the symmetry operations appropriate to the specified space
group and applies them to the list of unique coordinates. In the case
of a space group with multiple settings, it uses some heuristics to
try to guess the correct setting.  (That's what things like "b_unique"
and so on are all about.  Those heuristics often fail.)  It expands
out a unit cell and weeds through the unit cell to identify duplicates
(i.e. high symmetry positions that repeatedly generate the same
location when the symmetry operations are applied).  It then stacks up
enough unit cells to contain the cluster, then translates fractional
coordinates to Cartesian coordinates.

At no point in that operation does the program make any decisions on
the basis of the definitions of the Cartesian axes.

None of this is a value judgment on what you have said or on Raj's
original question -- I'm simply explaining how the program works.
There just isn't an obvious mechanism in the code to let the user
orient the cluster in a certain way.  That's an interesting idea, but
not something available at this time.

To use Feff's polarization, you have to choose a polarization vector
appropriate to the cluster as written.  Or, I suppose, write your own
tool to rotate the cluster to a more convenient orientation.

B





___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit



--
 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://gi

Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12

2016-12-21 Thread Bruce Ravel

On 12/21/2016 02:50 PM, Robert Gordon wrote:

So, for all but tetragonal, the orientation of the cluster can be
identified with the
orientation of the crystal axes. Does it not seem more logical to
preserve the
apparent orientation with respect to the crystal axes so that, when
using POLARIZATION
(issues in FEFF6 aside), confusion is less-likely?


Hmm ... I think I understand your point.

I think you may be ascribing too much agency and intelligence to the the 
Atoms algorithm.  The way Atoms works these days is to use this 
tabulation of chapter 7 of volume A of the International Tables:


https://github.com/bruceravel/demeter/blob/master/lib/Xray/Crystal/share/space_groups.db.PL

It selects the symmetry operations appropriate to the specified space 
group and applies them to the list of unique coordinates.  In the case 
of a space group with multiple settings, it uses some heuristics to try 
to guess the correct setting.  (That's what things like "b_unique" and 
so on are all about.  Those heuristics often fail.)  It expands out a 
unit cell and weeds through the unit cell to identify duplicates (i.e. 
high symmetry positions that repeatedly generate the same location when 
the symmetry operations are applied).  It then stacks up enough unit 
cells to contain the cluster, then translates fractional coordinates to 
Cartesian coordinates.


At no point in that operation does the program make any decisions on the 
basis of the definitions of the Cartesian axes.


None of this is a value judgment on what you have said or on Raj's 
original question -- I'm simply explaining how the program works.  There 
just isn't an obvious mechanism in the code to let the user orient the 
cluster in a certain way.  That's an interesting idea, but not something 
available at this time.


To use Feff's polarization, you have to choose a polarization vector 
appropriate to the cluster as written.  Or, I suppose, write your own 
tool to rotate the cluster to a more convenient orientation.


B



--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12

2016-12-21 Thread Bruce Ravel


Robert,

You have me confused.  You seem to be saying that using the correct 
space group symbol is important.  I couldn't possibly disagree.


Raj's original question had to do with the fact that two different 
versions of atoms, which used different algorithms for interpreting the 
crystal data, resulted in clusters that were rotated relative to one 
another.  My answer, appropriate (I think) in that case, was to shrug.


You seem to be commenting on something unrelated to the original 
question, but I'm not understanding the point.


B

On 12/21/2016 01:13 PM, Robert Gordon wrote:

Hi Bruce,

The atoms.inp file attached is for bct Fe. In symmetry I4/mmm, the
resulting feff input has the coordinates
rotated, while in Immm the resulting coordinates are not rotated
relative to the crystal axes (i.e. in Immm
the 2nd near neighbour is obvious as a lattice constant away in each
direction).

So, with no polarization, the results for scattering paths are the same
(using CRITERIA default), as expected
Path #
Degen
Reff
Scattering Path
Type
Rank I4/mmm
Rank Immm
1
8
2.48
fe1
ss
100
100
2
4
2.835
fe2
ss
37.56
37.56
3
2
2.92
fe3
ss
17.59
17.59
4
16
3.897
fe1-fe1
ms
3.42
3.42
5
32
3.897
fe1-fe2
ms
12.83
12.83
7
16
3.94
fe1-fe3
ms
6.37
6.37


Now consider with  POLARIZATION 1 0 0 (and 1 1 0 for I4/mmm)

#
Degen
Reff
Scatt. Path
Type
I4 1 0 0
I4 1 1 0
Im 1 0 0

4
2.48
fe1
ss
100



4
2.48
fe1
ss
7.89



8
2.48
fe1
ss

100
100

4
2.835
fe2
ss
55.45



2
2.835
fe2
ss

62.05
62.05

16
3.897
fe1-fe1
ms
4.41
9.90
15.43

16
3.897
fe1- fe2
ms
19.03
21.58
21.59



For that first multiple scattering path, the scattering angles are
36.1/90 for I4(1 0 0), 55.1/55.1
for I4(110) and for Im(100) they are 55.1/124.9. The ranking of this
path is not the same,
and the plots for this path differ as well - in shape as well as amplitude.

Conceptually, the Immm model calculation has the atoms aligned with the
crystal lattice
and the I4/mmm has the atoms rotated. FEFF sees a difference, and I
would take
the Immm result as the correct one based on the positions of the atoms
in the cluster
relative to the axes.

-R.


On 12/21/2016 6:49 AM, Bruce Ravel wrote:

On 12/19/2016 11:01 PM, Robert Gordon wrote:

What if one were to do this FEFF calculation using the POLARIZATION
card?
1 0 0 means something different if the atom positions have been rotated
by 45 degrees relative to the crystal axes along which the polarization
is defined.


Well ... you could rotate the polarization vector by 45 degrees ...

I guess I have always considered FEFF's polarization card to be an a
posteriori addition to the feff.inp file -- i.e. a decision that the
user makes after using Atoms to convert crystal data to a cluster in
feff.inp.

B





___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12

2016-12-21 Thread Bruce Ravel

On 12/19/2016 11:01 PM, Robert Gordon wrote:

What if one were to do this FEFF calculation using the POLARIZATION card?
1 0 0 means something different if the atom positions have been rotated
by 45 degrees relative to the crystal axes along which the polarization
is defined.


Well ... you could rotate the polarization vector by 45 degrees ...

I guess I have always considered FEFF's polarization card to be an a 
posteriori addition to the feff.inp file -- i.e. a decision that the 
user makes after using Atoms to convert crystal data to a cluster in 
feff.inp.


B

--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Web Atoms 1.8 vs Demeter 0.9.26: feff output are not same

2016-12-16 Thread Bruce Ravel

On 12/16/2016 10:34 AM, Raj kumar wrote:

Recently, i found out that feff.inp generated by web atoms and Demeter
0.9.26 are not the same. My main worry is in the position of atoms. For
evidence, i am attaching YbVO4 (*feff.inp*) files generated by both web
atoms and Demeter. With this kind of zircon type structure, one would
except V1_2 at position *x/2+c/4* (3.85250). In web atoms generated
file, i could see this relation clearly, while in Demeter generated file
the relation reads like *x/2+y/2+c/4* instead of earlier condition.
Furthermore, all atoms (except few) are represented with three
coordinated position for Demeter generated file instead of two
coordinated position.



Hi Raj,

I don't acknowledge that there is a problem.  It is certainly true that 
the two files have the atoms list rotated by 45 degrees relative to one 
another, but all the distances are the same.  Although I only 
investigated at the level of running feff on each one and examining the 
first few dozen items in the path list, it seems these two feff input 
files yield identical results.


So ... what's the problem?

B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Problems with gnuplot graphics on Mac OS 10.12.1

2016-12-09 Thread Bruce Ravel

On 12/08/2016 10:19 PM, Paul Fons wrote:

Hi All,

I just wanted to give an update to my earlier problems with the
mysterious gnuplot errors. After editing the file Matt mentioned
earlier, I decided to uninstall and install demeter to no avail. I
then realized that I had been relying on the latest version of
xquartz (the x11 system) and installed x11 using macports.  After a
bit of trouble with installation (I had to break the installation
into pieces — but this is a typical macports problem), the x11
installation completed and athena worked fine. Thus my conclusion is
that there was some sort of weird interference between x11
subsystems.  In any case, all is well now.


Hi Paul,

Glad it worked out.  I don't quite understand what happened.  If you 
have any suggestions for what I can add to the Mac installation 
instructions to help the next poor soul, that would be great.


http://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.html

B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] error message when trying to reopen Artemis file

2016-12-02 Thread Bruce Ravel

On 12/02/2016 09:01 AM, Bruce Ravel wrote:


Your cif file triggered a very specific bug in my software that has
nothing to do with your recent difficulties.

Had you picked almost any other cif file for any other material, you
would have been fine.

I am guessing you chose this one:

  http://www.crystallography.net/cod/cod/cif/7/20/60/7206075.cif

or something very similar.  Demeter makes a mistake parsing the space
group symbol in that file.

Try this:

  http://cars9.uchicago.edu/atomsdb/TiO2-ana.inp

It seems to work correctly without triggering the specific problem that
the cif file triggers which, again, has to do with the specific symbol
used and how Demeter parses it.


Thanks for reporting this.  I'll work on it.



I just pushed a fix for this to github.

The project file you sent me is not fixable (well ... not easily).  The 
best thing to do is to discard it and start again.


Thanks again for uncovering a fairly obscure bug!

B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] error message when trying to reopen Artemis file

2016-12-02 Thread Bruce Ravel


Marcus,

Your cif file triggered a very specific bug in my software that has 
nothing to do with your recent difficulties.


Had you picked almost any other cif file for any other material, you 
would have been fine.


I am guessing you chose this one:

  http://www.crystallography.net/cod/cod/cif/7/20/60/7206075.cif

or something very similar.  Demeter makes a mistake parsing the space 
group symbol in that file.


Try this:

  http://cars9.uchicago.edu/atomsdb/TiO2-ana.inp

It seems to work correctly without triggering the specific problem that 
the cif file triggers which, again, has to do with the specific symbol 
used and how Demeter parses it.



Thanks for reporting this.  I'll work on it.

B

On 12/02/2016 06:07 AM, mfehse wrote:

Hi

so i have created a little Artemis project to practice. Its tio2 data
file with anatase cif file, i just included teh first path but havent
done any fitting yet. When i close artemis and want to reopen it I get
the following error:

"You must define a method name at
/usr/lib/i386-linux-gnu/perl5/5.22/Class/MOP/Mixin/HasMethods.pm line 96

Class::MOP::Mixin::HasMethods::has_method('Class::MOP::Class::Immutable::Moose::Meta::Class::__ANON__::SERIAL::1=HASH(0xe06c454)',
'') called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm
line 442
Demeter::Atoms::parse_line('Demeter::Atoms=HASH(0x106b5394)', ' :')
called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm
line 465
Demeter::Atoms::parse_line('Demeter::Atoms=HASH(0x106b5394)', 'space
= I 41/a m d :1') called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm
line 390
Demeter::Atoms::read_inp('Demeter::Atoms=HASH(0x106b5394)') called
at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm
line 200
Demeter::Atoms::__ANON__('Demeter::Atoms=HASH(0x106b5394)',
'/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp', '')
called at accessor Demeter::Atoms::file (defined at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm
line 204) line 10
Demeter::Atoms::file('Demeter::Atoms=HASH(0x106b5394)',
'/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp')
called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Atoms/Xtal.pm
line 667

Demeter::UI::Atoms::Xtal::open_file('Demeter::UI::Atoms::Xtal=HASH(0x1312b8e0)',
'/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp')
called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis.pm
line 1388
Demeter::UI::Artemis::make_feff_frame('Wx::Frame=HASH(0x127f5b3c)',
'/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp',
1010942) called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis/Project.pm
line 351
Demeter::UI::Artemis::Project::read_project('HASH(0x102e8084)',
'/home/marquinhos/Desktop/TIO2_tryout.fpj') called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis.pm
line 1026
Demeter::UI::Artemis::OnMenuClick('Wx::Frame=HASH(0x127f5b3c)',
'Wx::CommandEvent=SCALAR(0x12ab14cc)') called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis.pm
line 440
Demeter::UI::Artemis::__ANON__('Wx::Frame=HASH(0x127f5b3c)',
'Wx::CommandEvent=SCALAR(0x12ab14cc)') called at demeter/bin/dartemis
line 31
eval {...} at demeter/bin/dartemis line 31
"

i have attached the project so you can try if you can open it on your
artemis

many thanks

marcus

On 01/12/2016 19:26, Bruce Ravel wrote:

On 12/01/2016 01:20 PM, mfehse wrote:


and am now able to launch the athena and it seems to work, however i
still get the error message:
"Could not find Larch Server -- falling back to Ifeffit"
is this something i should care about?


Nope.

It's a message that will eventually go away.  Right now, Matt and I
are working on migrating to Larch.  This week we have been figuring
out how to make Athena's interaction with Larch work reliably.  That
message is there so that I know what is going on while I am working on
the code. In this case, it is Demeter telling you that it is
gracefully recognizing that you do not have Larch installed.

If you don't want to be looking at the head of the main branch, then
you could download the zip file for the most recently tagged release:
https://github.com/bruceravel/demeter/tree/0.9.25

B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.c

Re: [Ifeffit] problems installing athena et al under ubuntu 16.04 LTS

2016-12-01 Thread Bruce Ravel
I just checked a fix into github that addresses the problem Juan 
identified.  Matt's assessment at 
https://github.com/bruceravel/demeter/issues/42 was exactly right.  I 
adopted his second solution.


Thanks to all of you for this discussion.
B



On 11/25/2016 05:23 AM, Juan de la figuera wrote:

Hi,

I send one of the data files we are currently acquiring (SPLINE beamline
at ESRF).

I have checked that my compiled 0.9.24 version works with the examples
cu10k.dat file, but it is true, as Robert confirmed, that strange things
happen if you mark ev instead of kev.

With our data files like the one enclosed, dathena chokes on the scale.
Actually it opens the window but it has x10^9 scale. On the other hand,
the 0.9.24 for Windows opens the files ok. Now, the files are
MSDOS-ended files, I tried converting them to Linux-ending, but same
result. I also tried putting a # comment on the first line.

I stress that Athena 0.8.061 (included in the horae package in ubuntu)
opens the file like a charm.

One additional detail (just in case), I have Ubuntu 16.04 LTS 64-bit.

Best,
Juan


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] struggling to install demeter under ubuntu 16.04

2016-12-01 Thread Bruce Ravel

On 12/01/2016 01:20 PM, mfehse wrote:


and am now able to launch the athena and it seems to work, however i
still get the error message:
"Could not find Larch Server -- falling back to Ifeffit"
is this something i should care about?


Nope.

It's a message that will eventually go away.  Right now, Matt and I are 
working on migrating to Larch.  This week we have been figuring out how 
to make Athena's interaction with Larch work reliably.  That message is 
there so that I know what is going on while I am working on the code. 
In this case, it is Demeter telling you that it is gracefully 
recognizing that you do not have Larch installed.


If you don't want to be looking at the head of the main branch, then you 
could download the zip file for the most recently tagged release:

https://github.com/bruceravel/demeter/tree/0.9.25

B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] struggling to install demeter under ubuntu 16.04

2016-12-01 Thread Bruce Ravel

Sorry.  That wasn't quite right.

At the command line:

  DEMETER_FORCE_IFEFFIT=1 dathena

to force the use of Ifeffit in that instance of Athena.

Or,

  export DEMETER_FORCE_IFEFFIT=1

later,

  dathena

That forces the use of Ifeffit in that instance of the shell so that, 
later, when you fire up Athena, it uses Ifeffit.


Or put the "export" line in your .bashrc to make it persist the next 
time you log in.


B


On 12/01/2016 01:18 PM, Bruce Ravel wrote:

On 12/01/2016 12:57 PM, Juan de la figuera wrote:


Is there a switch in demeter to select the backend? Or in other words,
to go back to ifeffit, should I delete the larch binaries?


At the command line:

   export DEMETER_FORCE_IFEFFIT=1 dathena

or put

   export DEMETER_FORCE_IFEFFIT=1

in your ~/.bashrc file

B





--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] struggling to install demeter under ubuntu 16.04

2016-12-01 Thread Bruce Ravel

On 12/01/2016 12:57 PM, Juan de la figuera wrote:


Is there a switch in demeter to select the backend? Or in other words,
to go back to ifeffit, should I delete the larch binaries?


At the command line:

   export DEMETER_FORCE_IFEFFIT=1 dathena

or put

   export DEMETER_FORCE_IFEFFIT=1

in your ~/.bashrc file

B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] struggling to install demeter under ubuntu 16.04

2016-12-01 Thread Bruce Ravel

On 12/01/2016 09:12 AM, mfehse wrote:

In my struggle to install demeter under ubuntu 16.04 I'm slowly
advancing. I think some of the packages that were supposed to be
installed following the first line of the protocol were incomplete. I
have redone this and have now managed to build the dathena and other
files, but when I want to start it I get the following error message:


"marquinhos@marquinhos-Lapi:~/demeter$ bin/dathena

Could not find Larch Server -- falling back to Ifeffit
Can't locate object method "new" via package "Graphics::GnuplotIF" at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter.pm
line 239.
Compilation failed in require at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Athena.pm
line 24.
BEGIN failed--compilation aborted at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Athena.pm
line 24.
Compilation failed in require at bin/dathena line 27.
BEGIN failed--compilation aborted at bin/dathena line 27.
Can't exec "-p": No such file or directory at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Larch.pm
line 270.
"

any ideas what might be the problem?



That seems to be saying that Graphics::GnuplotIF is not installed.

It should have been installed when you did the "./Build installdeps" step.

B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] your mail to the ifeffit mailing list

2016-11-30 Thread Bruce Ravel


So, where did the dathena script get installed on your computer?

B


On 11/30/2016 10:49 AM, mfehse wrote:

thanks for the quick reply. I just registered with the mailing list
today, i didnt add any address.

Concerning your remarks for my installation problem your two hints
resulted in this:

marquinhos@marquinhos-Lapi:~/demeter$ echo $PATH".  "./Build
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin.
./Build
marquinhos@marquinhos-Lapi:~/demeter$ hash -r
marquinhos@marquinhos-Lapi:~/demeter$ dathena
No command 'dathena' found, did you mean:
 Command 'athena' from package 'horae' (multiverse)
dathena: command not found
marquinhos@marquinhos-Lapi:~/demeter$

hash -r didnt do much im afraid and about the path im not sure what this
is supposed to tell me.
As you might have noticed im not a frequent terminal user and I think
this cpan/ perl/ demeter installation is probably the trickiest thing i
have ever done, so please excuse my lack of experience



--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Athena bug

2016-11-29 Thread Bruce Ravel

On 11/29/2016 08:11 AM, S.Rowe wrote:

I have been experiencing a bug in Athena, this is occurring in the most
recent version 0.9.25, as well as the older versions I have used.

The big is occurring when using the difference spectra window to produce
difference spectra for a set of data.

When I use the 'Plot difference spectra for all marked groups' function
it will produce the plot but if I change any parameters in the main
window and want to check how this has changed the difference spectra it
will only plot the original difference spectra. To see the new
difference spectra after the changes have been made I need to close
Athena down completely and open it up again. If I just close the project
and load in new data and try to plot the difference spectra for this
new set of data it will still only plot the difference spectra for the
old data.

I have attached an Athena project file, please let me know if there is
something different I need to do to change the difference spectra plot.

Kind regards,

Sinead Rowe



Sinead,

I am having trouble reproducing this problem, but I am suspicious that 
Athena might be getting confused if the Standard is also one of the 
marked spectra.  Athena should exclude the Standard from the list of 
marked groups, but clearly is not doing so.


When you observe this behavior, what group from the file is selected as 
the Standard?  Is it "BiFeO3_410C"?  Does the problem get better if you 
unmark that group (i.e. unclick its checkbutton in the groups list)?


Since I am having trouble reproducing the problem, it would help if you 
could give me a click-by-click recipe for reproducing the problem.


B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Athena bug

2016-11-29 Thread Bruce Ravel

Hi Sinead,

I have a long list of chores waiting for me after the holiday that just 
finished here in the States, but I will get to your difference spectrum 
issue just as soon as I can.


B

On 11/29/2016 08:11 AM, S.Rowe wrote:

Dear all,

I have been experiencing a bug in Athena, this is occurring in the most
recent version 0.9.25, as well as the older versions I have used.

The big is occurring when using the difference spectra window to produce
difference spectra for a set of data.

When I use the 'Plot difference spectra for all marked groups' function
it will produce the plot but if I change any parameters in the main
window and want to check how this has changed the difference spectra it
will only plot the original difference spectra. To see the new
difference spectra after the changes have been made I need to close
Athena down completely and open it up again. If I just close the project
and load in new data and try to plot the difference spectra for this
new set of data it will still only plot the difference spectra for the
old data.

I have attached an Athena project file, please let me know if there is
something different I need to do to change the difference spectra plot.

Kind regards,

Sinead Rowe



___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Problems with gnuplot graphics on Mac OS 10.12.1

2016-11-29 Thread Bruce Ravel


Hi Paul,

I have a hard time understanding how that happens, but I have a couple 
ideas.  Let's look into the simpler one first.


In the installation location of Demeter, there is a file called 
lib/Demeter/templates/plot/gnuplot/marker.tmpl


It should look exactly like this:

https://github.com/bruceravel/demeter/blob/master/lib/Demeter/templates/plot/gnuplot/marker.tmpl

Could you check to verify that that file has not been altered in any way?

If that file is ok, then we'll dig deeper.

B


On 11/28/2016 02:35 PM, Paul Fons wrote:

Hi All,
  I have installed demeter using Macports on 10.12.1 and while
hephaestus seems to run normally, athena has some trouble with graphics.
 The usual athena perl based panel shows up just fine, but upon loading
some data, there is always an error when gnuplot is invoked to plot
graphics (as reproduced below).  It would seem that the command “set” is
missing the first letter.  Does anyone have a suggestion as to what to
check to fix this?


Axion:perl5.24 $ use_macports.sh athena

gnuplot> et label '{/Symbol \305}' at 400.7,853.0387 center front
textcolor ls 12
 ^
 line 0: invalid command


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] error on installing demeter on MacOSX 10.9.5

2016-11-24 Thread Bruce Ravel


Y'know, this mailing list isn't only a place where you can ask 
questions.  It is also a place where you can search and /find/ answers.


From less than three weeks ago: 
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2016-November/008866.html


B


On 11/23/2016 11:54 AM, christophe den auwer wrote:

Dear all,

I am trying to install Demeter on OS 10.9.5 and I am stuck!

I installed Xcode 6.2 fine with the licence agreement and everything.
Then I installed MacPort 2.3.5 fine as well. I also checked updated
version and everything worked fine.
Then I tried to install Demeter and got stuck with the following lines :

Error: org.macports.archivefetch for port libcxx returned: archivefetch
failed for libcxx @3.9.0_0+universalError: Failed to install libcxx
Please see the log file for port libcxx for details:
Error: Processing of port demeter failed

I attached to my message, if of any use, the full procedure and feedback
from terminal window.

If someone could help that would be really great!!!

Thanks a lot

Christophe







-
Christophe Den Auwer
Professeur
Institut de Chimie de Nice
Université de Nice Sophia Antipolis
06108 Nice, France
0492076362
christophe.denau...@unice.fr <mailto:christophe.denau...@unice.fr>
--







--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Athena crashing with "Larch_Server not found"

2016-11-14 Thread Bruce Ravel

On 11/14/2016 03:29 PM, Frederik Eistrup wrote:


Now, followed again the instructions and ran into new problems. Can't
get over the "./Build test" (terminal output:
screen_message_Frederik_test.txt) and "./Build install" gives error
(terminal output: screen_message_Frederik_install.txt).


What is the problem now? Im very sorry for not being able to solve it
myself!



Frederik,

Not sure.  At the command line, in the directory where you are running 
"./Build test" could you do the following command instead:


prove -bv

and capture /all/ the screen output.

B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Athena crashing with "Larch_Server not found"

2016-11-14 Thread Bruce Ravel
rederik/perl5/bin/dathena line 31/

So, where is the problem? Can anyone helo with this?

Made sure larch was installed through sudo apt-get install, but all
stays the same.


Thanks for any help!


Frederik

David Hughes' guide to Demeter Installation on Ubuntu ...
<https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.html>
bruceravel.github.io
David Hughes' guide to Demeter Installation on Ubuntu¶ These
instructions cover a non-root manual build of Bruce Ravel's Demeter
package under Ubuntu 12.04.

Found out that Athena



___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] athena LCF issue

2016-11-08 Thread Bruce Ravel


Thanks Fred.  Simple enough to fix.  As you said, it is mostly a bit of 
a nuisance message.  In any case, it will be fixed in the next release 
(whenever that is...).


B

On 10/28/2016 12:16 PM, fred.mosselm...@diamond.ac.uk wrote:

Dear Bruce,

I realise you may be travelling soon ,

This is not a very serious bug as I have work rounds.

I was demonstrating linear combination fitting in Athena using the gold
thiobacteria example this week.

I am using 9.25 on a windows 7 computer.

I read in all the data from the cynaobacteria project file

I mark  5 or 6 standards

In the LCF tab

I  use marked groups, untick the sum weights to 1 option leaving just
the all weights between 0 and 1 option selected.

I pick a sample spectrum eg 4.73

I select fit all combinations

It rolls through them  and reports the apparently correct results but an
error message is reported:

Redundant argument in sprint at C:/…
/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Athena/LCF.prm
line 780,  line 122



Clicking any of the answers in the combinatorics tab brings up this
error again.



If I  do a fit of lot of spectra using  the same set of standards, I get
a similar  error message except this time it is line 906 and some of the
combined spectra don’t plot properly until you refit them as a single
spectra in the standards tab



I attach a log file but not a project as I assume you can find that on
github!



Regards

Fred





J.F.W. Mosselmans

Prinicipal Beamline Scientist I18

Diamond Light Source Ltd

Diamond House

Harwell Campus

Didcot

OX11 0DE



P + 44 1235 778568

M + 44 7785510211

E fred.mosselm...@diamond.ac.uk





--

This e-mail and any attachments may contain confidential, copyright and
or privileged material, and are for the use of the intended addressee
only. If you are not the intended addressee or an authorised recipient
of the addressee please notify us of receipt by returning the e-mail and
do not use, copy, retain, distribute or disclose the information in or
attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual
and not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any
attachments are free from viruses and we cannot accept liability for any
damage which you may sustain as a result of software viruses which may
be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in
England and Wales with its registered office at Diamond House, Harwell
Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Athena and "norm" file groups

2016-10-17 Thread Bruce Ravel


Read these:

http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html
http://bruceravel.github.io/demeter/documents/SinglePage/help.html

You "question" isn't one that I can realistically answer.  I have no 
idea what the problem is and you have not provided enough information to 
replicate your problem on my own computer.  I can only give a good 
answer when asked a good question.


B


On 10/15/2016 04:06 PM, Mike Massey wrote:

Hi everyone,


Apologies if this has been covered before, I'm just getting around to
upgrading to Demeter. I have a bunch of old project files with a
mishmash of data from different sources, and I'm having trouble
getting them to work fully with the new software.

Any group with a data type of "xmu" (energy space) seems to work as
expected, but any group with a data type of "norm" (normalized data)
doesn't seem to work properly when it comes to spline or post-edge
background subtraction (which is handy if I want to do LCF, for
example). Is this a bug or a feature? Has anybody yet developed a
workaround?

Any thoughts or advice would be greatly appreciated. The ultimate
workaround is to use different data, but I'd like to use existing
projects if possible (saves a lot of time and brain damage).


Cheers, and thanks!


Mike





___ Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe:
http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] General question

2016-10-14 Thread Bruce Ravel

On 10/13/2016 05:17 PM, Dimitar Popmintchev wrote:

I would like to ask, after a fit (in Artemis) which column in the output
file gives the uncertainty for peaks position dR (R+/-dR  i.e. 3+/-0.02
Angstroms)  ?


Error bars are not propagated in Artemis currently.  That's something 
you, the user, has to do using the math expression that relates your 
variable(s) to the delta R in question.


The simplest common case is one where you have

   guess delr = 0

then later, for some path,

   reff   = 3.0
   deltaR = delr

In that case, delr is varied and the path length is 3.0 + delr.

Propagating the uncertainty in this case is trivial:

   delta( 3.0 + delr) = delta(3.0) + delta(delr)

3.0 is a constant, so the error bar in the path length is the same as 
the error bar in the variable.


HTH,
B



--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Artemis crash on import

2016-10-13 Thread Bruce Ravel
ata
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 create
global data
Oct 13 14:52:38  perl5.24[20180] : Window Server is not available.
Oct 13 14:52:38  perl5.24[20180] : Window Server is not available.
Segmentation fault: 11


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Smoothing aligned data in Athena

2016-09-29 Thread Bruce Ravel


Hi Ian,

Thank you for a very clear and well articulated bug report.  It is much 
appreciated.


This was a simple one to fix.  When I implemented the boxcar filter in 
Athena, I neglected to copy the energy shift value from the noisy group 
to the smoothed group.  Oops!  I just pushed a fix to github which will 
be included in the next windows installer.


If you would like to mend the copy of Athena on your computer, it's a 
small edit, as shown here:


https://github.com/bruceravel/demeter/commit/a84e5fb605cef26dd4be42bba46924264d941900

Thanks,
B


On 09/28/2016 11:33 AM, Godfrey, Ian wrote:

Dear All,


I have a bug to report when using the Athena data smoothing feature with
aligned data. Exemplar project and log files are attached, along with a
screenshot. I am running Windows 10 x64 with Athena 0.9.25 x64.


Summary:

When using the data smoothing feature in Athena with data that has
previously been aligned using the alignment feature, the smoothing is
performed on the non-aligned data, and the resulting, processed dataset
is shifted in E.


Recipe:


Open Athena

Import a dataset that has a reference channel

Import a second dataset with reference

Import a standard dataset, with a slightly off alignment wrt to the
first two datasets (I imported all three from Athena projects, rather
than raw datafiles)

Use the alignment tool to align the reference channel of one of the
datasets to the standard (I used the automatic alignment)

Go to the smoothing tool. You can immediately see that the smoothed
curve is in the wrong place for the aligned dataset.

The dataset that wasn't aligned will appear correctly


Many thanks,


Ian





Ian Godfrey



PhD Student,

UCL/JAIST Programme


Industrial Doctorate Centre in Molecular Modelling and Materials Science,

Department of Chemistry,

University College London



and



School of Materials Science,

Japan Advanced Institute of Science and Technology



i.godf...@ucl.ac.uk <mailto:i.godf...@ucl.ac.uk> i.godf...@jaist.ac.jp
<mailto:i.godf...@jaist.ac.jp>



___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Ni(I), Ni(II), and Ni(III) Reference XAS required

2016-09-20 Thread Bruce Ravel

On 09/19/2016 02:49 AM, mazhar iqbal wrote:

Hello

Can some please provide me the standard XAS of Ni(I), Ni(II), and Ni(III).


Mazhar,

You probably need to be more specific about what you want.  There are 
/lots/ of Ni compounds.  No one here knows what you work on, so no one 
here can possibly know which standards you are looking for.


As always, vague, open ended questions are unlikely to get a response. 
Clear, concise questions usually do.  Please read:


   http://bruceravel.github.io/demeter/documents/SinglePage/help.html

B



--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] artemis doesn't read user's epsilon(k)

2016-09-16 Thread Bruce Ravel


This has been fixed and pushed to the head of the GitHub repository. 
The fix will be included in the next Windows installer.


B


On 08/29/2016 09:55 AM, Bruce Ravel wrote:


Victor,

You are correct.  That is shockingly broken.  I'll let you know when and
how it gets fixed.

B

On 08/28/2016 04:20 AM, Victor Streltsov wrote:

Hi Bruce,



Epsilon(k) input “A user specified values for measurement uncertainty”
in Artemis does not change the default value determined by Ifeffit.

It assumes that input is a value of 0. I’ve tried the latest Artemis
versions for Windows and Linus and they both behave the same.



Best regards,

Victor Streltsov



___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit







--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Saving Bug

2016-09-12 Thread Bruce Ravel

On 09/10/2016 07:03 PM, Matteo Busi wrote:


It occurs when I try to save groups to files, it seems that the saving
option change the output while it shouldn't. When I save using the "Save
current group as ..." option I get the full log with many columns,
whereas when I save using the "Save marked group as ..." option I only
get 2 columns.
(I saved only as xmu and norm but I guess it is occuring for every
extension)


I do not see this behavior.  It's not that I don't believe you, it is 
that you have not provided enough information for me to see the problem 
on my own computer.


I need to know things about the state of Athena that should be contained 
in the project file.  Specifically, I want to know that you have 
actually marked groups before trying to "Save marked groups as ..."


So, post a project file that displays this behavior AND provide an 
explicit recipe of mouse clicks so I can reproduce it on my computer.


B

--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Help in background removal with Athena

2016-09-06 Thread Bruce Ravel

On 09/06/2016 10:55 AM, Irina Pi wrote:

Thank you for the quick answer. Which range should I have for the EXAFS
analysis to be meaningful? Like 200eV above the edge?


I am always uncomfortable when newcomers ask for "rules".  Having a rule 
without understanding when and why it might apply seems counter-productive.


Firstly, lets discuss the relation ship between "energy above the edge" 
and photoelectron wave number.  The conversion constant between energy 
and wavenumber is


   k = sqrt( ETOK * (E-E0) )

where ETOK is the appropriate combination of fundamental constants (2m_e 
/ hbar^2, where m_e is the mass of the electron and hbar is Planck's 
constant) about equal to 1 / 3.81.  So, 10 inverse Angstroms is about 
381 volts above the edge.


The extent of the signal in k determines how well you can interpret an 
EXAFS signal in a quantitative sense.  See this page in the Athena manual:


   http://bruceravel.github.io/demeter/documents/Athena/plot/krange.html

Scott Calvin discusses this in his book.  There is more information 
about EXAFS data reduction among the tutorials at http://xafs.org/Tutorials.


As Fred and Robert have said, you need "enough" data range to make a 
useful interpretation of the EXAFS.  200 eV is not a lot -- that will 
leave you with only a small handful of independent measurements in your 
data, possibly not even enough to reliably determine a first shell bond 
length.


B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Phase correction not working in Athena

2016-08-31 Thread Bruce Ravel

On 08/31/2016 09:05 AM, Sebastian George wrote:

I hope that I am writing this in the correct place, and if I am not, I
apologize. The problem I'm having is pretty much summed up in the
Subject line. I'm analyzing some experimental EXAFS data in Athena, and
it seems that ticking the "phase correction" box has no effect on my
Forward Fourier transform. Has anybody run into this problem, and if so,
were you able to fix it? The material I'm studying is amorphous SmCo.
Could it be that having multiple backscattering species or a lack of
crystalline structure causing problems for the phase correction?


You didn't think to say so, but I am assuming you are using a Windows
computer.

The phase correction has been broken for a while in the Windows
installer.  I noticed that last week.  Happily, I noticed it in time
for the recently posted 0.9.25 release of the Windows installer.  If
you got to the Demeter homepage and grab the latest, you should find
that phase correction now works.

If any of my assumptions were wrong (understandable given that you
provided little information), let me know and I will continue to look
into the problem.



More generally, I'm wondering how exactly this phase correction is
determined anyway. If used, is it the sort of thing that can put the
first peak in my FT fairly close to the true nearest neighbor distance?


In Athena, nothing is known about the scatterers, so the phase
correction is only for the central atom part of the phase shift in the
EXAFS equation.  The central atom phase shift data used by Athena is
simply a static tabulation computed using Feff6.



Perhaps a better phrased question is: when can the phase transformation
be expected to give a quantitatively accurate radial distribution (in
terms of peak positions),


Basically never.

In rare situations, it might be possible that the first peak of a
phase-corrected FT might approximate an RDF for the first neighbor in
some sense.  But I caution you against thinking about it that way.  You
are more likely to be wrong than right.

Here's a dose of wisdom from Shelly from many moons ago:


http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg00171.html


and when is it more likely to only be qualitatively useful?


Always.

The Fourier transform of chi(k) is not a radial distribution function.

I am going to say that again all caps because this point is so
important that I want to yell it at you.

THE FOURIER TRANSFORM OF CHI(K) IS NOT A RADIAL DISTRIBUTION FUNCTION.

 * chi(k) includes multiple scattering

 * chi(k) includes a complex scattering factor

 * For heavy elements, the magnitude of the complex scattering factor
   has a lot of structure, resulting in a sort of Ramsauer-Townsend
   effect -- see

https://speakerdeck.com/bruceravel/the-ramsauer-townsend-effect-in-x-ray-absorption-spectroscopy

 * chi(k) can have scattering atoms at very close distances and the
   contributions from those scatterers can overlap in surprising ways

 * chi(k) has a sigma^2 term

 * chi(k) has a mean-free-path term

For all of these reasons, the FT of chi(k) is just chi(R).  It is not
a radial distribution function.

That said, when we analyze chi(R) in Artemis, we extract information
from the fit that can be used to reconstruct partial pair distribution
functions.




Also, I would have assumed that a backscattering
species would need to be given in order to calculate the phase shift,
but I haven't found anywhere to do that. Have I missed something?


Nope.  But in Athena, nothing is yet known about the scatterers.
Correcting the FT for the full phase shift is a chore that cannot be
done until something is known about them.

B

--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] artemis doesn't read user's epsilon(k)

2016-08-29 Thread Bruce Ravel


Victor,

You are correct.  That is shockingly broken.  I'll let you know when and 
how it gets fixed.


B

On 08/28/2016 04:20 AM, Victor Streltsov wrote:

Hi Bruce,



Epsilon(k) input “A user specified values for measurement uncertainty”
in Artemis does not change the default value determined by Ifeffit.

It assumes that input is a value of 0. I’ve tried the latest Artemis
versions for Windows and Linus and they both behave the same.



Best regards,

Victor Streltsov



___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] pgplot and ifeffit installation on current linux systems

2016-08-26 Thread Bruce Ravel


Hi Anselm,

Things change over time and there are a lot of slightly different linux 
distributions out there.


If you get to a point where you can build correctly on Arch and would 
like to contribute an how to or some modifications to build scripts, 
that would be great.  I would be more than happy to see that your 
contributions get used or linked to as appropriate.


B


On 08/26/2016 07:33 AM, Loges, Anselm G wrote:

Dear all,


I hope this is the right platform for my question. If not, sorry to
bother anyone. The question:

Has anyone successfully installed pgplot and ifeffit on a recent Arch
Linux system and could provide a quick how-to guide (also for the
Demeter website maybe)? Although I have not yet tested it, my problem
may also be relevant for current Debian/Ubuntu systems. Here's the
situation:


I am trying to install ifeffit on a current Arch Linux machine and
therefore need to install pgplot first. The PGPLOT_install script on the
respective GitHub page (as linked by a tutorial on the Demeter page, see
links below) does not work because it relies on several outdated paths
to dependencies. The one culprit I was able to isolate and fix was the
path to the X11 libraries, which the script looks for here:

/usr/X11or /usr/X11R6

but in current Arch Linux (at least in mine, which is Manjaro to be
precise, link below) is here:

/usr/share/X11

This alone does not fix all problems, there are several dependencies
missing in the X11 directory and I could not find out what the actual
relevant package names are in Arch (Debian/Ubuntu names cannot be
found). Also the config files of pgplot seem to have a bunch of similar
problems that (at least partially) seem to stem from use of an old
fortran-to-c translator (f2c) instead of the gcc fortran frontend
and missing dependencies for that.


If I am not mistaken, the latest Ubuntu LTS (16.04.) also has the
/usr/share/X11 path, so the script should not work there either.


I'd be happy to provide an updated installation script if I ever get it
running but I thought I'd ask if someone has done that already or has
solved the related problems so as not to invent the wheel anew.


Links:

<https://bruceravel.github.io/demeter/documents/SinglePage/installation.html>https://bruceravel.github.io/demeter/documents/SinglePage/installation.html

https://github.com/newville/ifeffit

<https://manjaro.github.io/>https://manjaro.github.io/


Best regards,

Anselm



___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Demeter Installation issues

2016-08-22 Thread Bruce Ravel


So, there is not really enough information to go on in this email.  I 
don't know what system you are one, although I'd guess it is some kind 
of linux.


I don't really know what is meant by "so I installed pgplot separately". 
 Installed from source?  From the package manager?


I don't know why ifeffit's PGPLOT_install script failed for you.  It has 
always worked just fine for me.


Anyway, when I did not find a file called "libgcc_path.sh" on my own 
computer, I turned to good ol' Google.  As near as I can tell, 
cpg/libgcc_path.sh is a script that compiles a simple C program, then 
probes the result to figure out what libraries it is compiled against. 
In short, it seems to be a way to figure out how to put the right 
collection of default -L command line directives into the compilation 
command so that program compiled against the pgplot library isn't 
missing anything.


Or some such.

I don't know how to resolve this problem either and it seems beyond the 
scope of what I can reasonably support given that went off-script to get 
pgplot installed on your computer.  Doing that sort of thing presumes a 
certain level of independent spirit


In the absence of other information, I would recommend that you figure 
out where libgcc_path.sh got installed on your machine then figure out 
how to make sure that it gets resolved at Build time.


One fragile way to do that would be to "sudo mkdir /cpg" if it doesn't 
exist.  Then make a symlink in /cpg to wherever your copy of 
libgcc_path.sh resides.  Make sure it is accessible and executable by a 
normal user.


B


On 08/19/2016 01:26 PM, Gaurab Rimal wrote:

Hello,
I have been trying to install demeter in my archlinux machine but
have issues in the build process. I had issues installing pgplot from
ifeffit git source so I installed pgplot separately (as outlined in the
original pgplot instructions). After installing ifeffit and after all
dependencies were met, I ran ./Build and got an error about
'cpg/libgcc_path.sh'. Below is the full output from ./Build. I am unsure
of this error because it seems to be related to ifeffit and pgplot and
do not know how to resolve this.

$ ./Build
Ifeffit's installations directory is /usr/local/share/ifeffit
(found by capturing `ifeffit -i`)
Compilation flags (from /usr/local/share/ifeffit/config/Config.mak):
 -L/usr/local/lib -lifeffit  -L/usr/local/pgplot/ -lpgplot -lX11
`/cpg/libgcc_path.sh` -lgcc -lm -lc
-L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1
-L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../../../lib -L/lib/../lib
-L/usr/lib/../lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../..
-lgfortran -lm -lgcc_s -lquadmath
cc -I/usr/lib/perl5/core_perl/CORE -fPIC -L/usr/local/lib -lifeffit
-L/usr/local/pgplot/ -lpgplot -lX11 `/cpg/libgcc_path.sh` -lgcc -lm -lc
-L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1
-L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../../../lib -L/lib/../lib
-L/usr/lib/../lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../..
-lgfortran -lm -lgcc_s -lquadmath -c -D_REENTRANT -D_GNU_SOURCE -fwrapv
-fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -march=x86-64 -mtune=generic
-O2 -pipe -fstack-protector-strong -o src/ifeffit_wrap.o src/ifeffit_wrap.c
cc: error: `/cpg/libgcc_path.sh`: No such file or directory
error building src/ifeffit_wrap.o from 'src/ifeffit_wrap.c' at
/usr/share/perl5/core_perl/ExtUtils/CBuilder/Base.pm line 174,  line 11.

Gaurab
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit



--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Athena interpolation when removing mono glitches

2016-08-12 Thread Bruce Ravel
mbers of the Ifeffit list,

I recently collected some EXAFS data with some significant monochromator
glitches that I am looking to remove. I have used a python script
graciously written by the beamline scientist to remove the offending
regions, but when I import the data into Athena, Athena does some funny
business in an attempt to join together the regions outside of the data
gap. (See the bending away in the dataset and/or attached image.) I have
confirmed by plotting with other software that the strange step-like
behaviour in the mu(E) is present only after importing into Athena (the
raw data is fine).

I have looked through the mailing list archives and also the user
manual, but can't seem to find anything that explains it, or other
people who have experienced this problem in the past. From what I can
determine, Athena joins together the segments to obtain a linear
interpolation in the norm(E)? This leads to a warping in the mu(E).
==How does Athena try to treat this data?==

I was wondering if other people have had similar issues, and what steps
can be taken to remedy the problem. For example, replacing removed data
points with artificial points along a linear interpolation would be
possible, but the act of adding artificial points that don't exist is
concerning to me.
==What is the best way to treat data with mono glitches to reduce
spurious features not intrinsic to the sample?==

If you are interested, I have included links to .prj datasets and images
to highlight these problems below.

With thanks for your time,
Michael

--
.prj file with 4 ways of working up the same data:
http://bit.ly/2bnfNZ5

1) raw data
2) mono glitches removed
3) rebinned data
4) rebinned and manually removed points (This leads to some
strange-looking features in k-space, and this would be less than
desireable on the many datasets we have collected)

images to highlight these problems:
a) mu(E)
http://bit.ly/2aYaJIf

b) norm(E)
http://bit.ly/2aYaX27

c) k
http://bit.ly/2baWh0h


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Statistical errors in linear combination fits

2016-08-11 Thread Bruce Ravel

On 08/11/2016 04:31 PM, Joshua Kas wrote:

I was wondering if it is possible to pass a value for the uncertainty in
the data to Athena when doing linear combination fits. We have
calculated chi^2 values using a simple estimate of the statistical
uncertainty, and find that our values differ by several factors of 10
when compared to the reported values from Athena. I assume that this has
to do with value of the uncertainty that Athena is using, but I
certainly could be mistaken. In any case, the reduced chi^2 reported by
Athena is much smaller than 1, while the fit is off by fairly large
amounts compared to any reasonable estimate of the statistical error.


Not so easy with Ifeffit, quite easier with larch.  It's on my to do 
list, but has not yet been implemented in Athena.


B

--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Converting PDF files to CIF files for usage in Artemis

2016-08-09 Thread Bruce Ravel

On 08/09/2016 01:50 PM, Matthew Marcus wrote:

This actually results in a bit of inconvenience - if you want to use
ATOMS, you have to load some data into Artemis and pretend you want to
analyze it.


There is a "Stand-alone Atoms" item in the frickin' Start Menu.  How 
does that constitute an inconvenience?  If that's too many clicks for 
you, drag and drop a shortcut to the desktop.


You can use atoms from the command line to read an input or CIF file and 
write to a file or to standard output.  You can use atoms from the 
command line with the "--wx" switch to fire up the stand-alone GUI app.


I acknowledge that the web app that died last January was widely used 
and that I am an unredeemable lay-about for not recreating it.  But your 
criticism is a bit unfair, Matthew.


B

--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Converting PDF files to CIF files for usage in Artemis

2016-08-08 Thread Bruce Ravel


Have you read the Colinet & Pasturel paper?  Skimming through it, it 
seems like section III.b along with Fig 1 gives enough information to 
fill in the Atoms window 
(http://bruceravel.github.io/demeter/documents/Artemis/feff/index.html) 
by hand.


B


On 08/08/2016 05:02 PM, Ed Han wrote:

Dear All,

In the upcoming fall, my research group plans on performing XAS studies
observing the Hf L3-edge for various Hf-Al intermetallic samples.

In preparation for the experiments, I am looking for CIF files of the
various Hf-Al intermetallic systems, including HfAl3, HfAl2, Hf4Al3, etc.

Upon scavenging through a multitude of crystallographic databases, I was
not able to find any CIF files of Hf-Al intermetallics. However, I have
acquired powder diffraction files (PDF) for said intermetallics.

Seeing as how PDFs cannot be used in Artemis for EXAFS data analysis (to
my knowledge), is there a way to convert PDFs into CIFs? I have attached
one of the PDF files to demonstrate what information it contains.

I would really appreciate your help!

Regards,
Edmund Han





___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit




--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


Re: [Ifeffit] Amorphous

2016-08-08 Thread Bruce Ravel

On 08/08/2016 11:19 AM, Carlos Triana Estupinan wrote:

I want to know if it is possible to obtain a 3D structure (.cif file) of
an amorphous material from the EXAFS fitting carried out from artemis. I
mean, there is a way to extract a .cif file with the structural data
obtained from the refined spectra.


No.

EXAFS is basically a one-dimensional measurement.  You measure R. 
Multiple scattering gives you limited information about the 3D 
arrangement of atoms, but mostly EXAFS is just R.


Unless I am misunderstanding the question, I don't think you can do what 
you are asking even for a well-ordered crystal, much less an amorphous 
material.



Also, in amorphous materials there
must be a distribution of interatomic bond distances and coordination,
and so, how can I address such a structural distribitions.


Well, sure.

There is a while literature on the use X-ray or neutron scattering along 
with EXAFS and molecular dynamics and monte carlo methods to study 
amorphous materials.  It seems that the most successful approaches 
involve forward modeling -- i.e. testing structures against the EXAFS data.


There simply isn't enough information in EXAFS to invert the EXAFS and 
extract a 3d configuration.  Artemis does not even try to do that.


B


--
 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/
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


  1   2   3   4   5   6   7   8   9   >