Bruce Ravel | 28 Oct 22:00 2014

Mac support for Demeter


Hi gang,

I just heard from Frank Schima, the fellow who kindly provided
packaging of Demeter via MacPorts.  Frank is moving to a new position
at NIST Boulder and will no longer be providing IT support for the
group out there that does some XAS.  That means his availability to
maintain and update the MacPorts package will be somewhere between
slim and non-existent.  Here is what he said:

    I am no longer working for Quantum Devices as of Friday,
    10/31/2014. So I will no longer be involved in updating Demeter and
    will be unsubscribing from the Ifeffit mailing list. For updates
    please follow the Macports procedures to request an update in
    Macports by opening a Trac ticket [1]. I may actually be able to
    perform the update but I cannot guarantee anything.

    [1] <https://trac.macports.org/newticket>

I know that this support for the Mac was valued by many people in our
community, so Frank will be missed.

I am not able to provide packaging support for Mac users.  Even if I
had the time or energy to take on a new packaging responsibility, I
simply don't own a Mac.

This would be a good time for someone to step up and take over
responsibility for the Mac package.  It seems that Frank has done the
bulk of the work.  The MacPort ecosystem seems to be well supported
and well documented, so I would think that someone else could readily
(Continue reading)

Karina Mathisen | 28 Oct 17:06 2014
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Saving data as chi(E) from Athena?

To whom it might concern

 

 

The older version of Athena had the possibility to save the data as chi(E), which is sorely missed in the newer version. Is there an easy fix for this?

 

Best regards

 

Karina Mathisen

 

 -------------------------------------------------------------------------------

Karina Mathisen, PhD

Deputy Head for teaching, Department of Chemistry

NTNU - Norwegian University of Science and Technology

Associate professor

Karina.Mathisen-XuRWurlvMDs@public.gmane.org

+47 735 96218

Realfagbygget E2-106, Høgskoleringen 5, Trondheim, Norway

--------------------------------------------------------------------------------

 

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Scott Bechler | 27 Oct 22:08 2014
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Setting E0 for imported data

Hello,

I am trying to compare a sample with unknown lead bonding with some lead standards. After entering in all of the data and standard scans with reference channels, I aligned the reference channels, which shifted the data scans as well. 

My question regards the E0 of the data and standard scans. Even though the scan itself shifted, the E0 still remains where it was when I imported it, prior to aligning the reference channels. The peak itself shifted, but the program still marks the E0 at the previous peak position. Is this an issue? If so, how do I adjust the E0 of the scans the same amount that the reference channels shifted?

It does say how much the scan shifted, so I went in and manually changed the E0 of each scan so that it correlated with this shift. Would this be an effective solution? If this does solve my problem, is there a less labor-intensive way to solve it in the program?

Thanks so much for your help!
-Scott
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Bruce Ravel | 27 Oct 15:10 2014

errors importing Artemis project with quick first shell paths


Ian,

I am starting a new thread for your email.  It is only peripherally
related to the problem discussed in the other thread.

The main problem was two mistakes in how a quick first shell path was
brought back to life when importing the project file.  I'll explain,
although one of the problems is rather technical.

Mistake #1 is related to the option for auto-generating variables.
That flag was not turned off, so the auto-generated parameters got
regenerated, over writing the ones you chose.  Yikes!

Mistake #2 involved an assumption about the order of entries in a
hash data structure while bringing the QFS path back to life.  That is
extremely sloppy on my part because the order of hash entries is not
predictable.  This was leading to the intermittent aspects of the
behavior.

> Dear All,

> Sorry for resurrecting this old thread but I've been experiencing a
> bug that produces very similar symptoms and that I guess may be
> related; but that won't be solved by Bruce's fix. Details are as
> follows:

> Software: Demeter 0.9.18.2 and 0.9.20 x64 (possibly earlier releases
> too) on Windows 8.1 x64 (I've never observed this bug on Windows
> versions before 8, but I've been using Windows 8 as my main OS for a
> while now so that may be coincidental)

> Steps to reproduce: I run a fitting project using quick first shell
> fits and save it. When I re-open the project around 80% of the time
> the problem occurs.

> Symptoms: When I re-open the project around 80-90% of the time one or
> more of the following occurs:

> - One of the quick shell paths completely loses all its information
>   (including path information which isn't editable by the user,
>   parameter info etc; see attached screenshot)

I believe that I have fixed this.

> - Parameter info for one or more paths is reset to the default
>   (i.e. if I've named a path delrauau it's renamed dr_ag_au_1)

Again, I believe that I have fixed this.

> - In the GDS window starting values for parameters that have a
>   non-zero starting value are set to their previously guessed value,
>   rather than the starting value I set (ie. If I set ss as 0.003 and
>   during the fit it is guessed to be 0.001 when I reopen the project
>   the starting value will be set to 0.001) and "restrain" parameters
>   are changed to "guess".

I have examined the history of your project.  At no point is a fit
saved with a restraint.  The GDS windows is filled correctly according
to the contents of your project file.  Also, the initial guesses are
all entered into the GDS window with the values I see in the history.

Are you saying that you have made a restraint, saved the project, then
had Artemis fail to remember that you had made a restraint?

> - Phase correct fitting boxes are unticked (sometimes in an
>   "impossible fashion" where the "plot with phase correction" option
>   is set but no paths have the "use path for phase corrected plotting"
>   option set)

I don't understand how that can be a problem.  The default is not to
plot with phase correction.  I don't save the state of that button in
the project file in any case.

I need to do a bit more testing, hopefully I'll make a new trial
release package for your to test before the end of the day.

B

> Attachments:

> Noinfo.png - screenshot of Artemis when path info is lost
> Reset.png - screenshot of Artemis when parameter names are reset
> Dartemis.log - Artemis log file when opening a project that has this problem
> Artemis.fpj - Artemis project file that displays these symptoms.

> Please let me know if you need further info/files.

> Thanks,

> Ian

> Ps:
> OK, things got weird while preparing this bug report: The file in
> question stopped opening at all - Artemis loaded and went through
> loading fit x, x+1 etc., once it finished (not exactly sure what
> stage) it just closed. And then, after several attempts, started
> working again, as if by magic, before I'd saved a log file.... If I
> can figure out how to reproduce this I'll send more info...

--

-- 
  Bruce Ravel  ------------------------------------ bravel@...

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

  Homepage:    http://bruceravel.github.io/home/
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/
pushkar shejwalkar | 27 Oct 07:14 2014
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Question about using a proper model

Dear All,
            I am new to XAFS data analysis and have very limited knowledge about using modelling structures for XAS analysis. I am not sure as to if this question is directly related to Demter or XAFS analysis as such but its a part of it for sure.
     Question number one
 I am trying to analyze the sample I recently collected at SPring-8 facility. The structure I am hoping to be formed during the reaction is more of a organometallic complex at silica interface. In order to establish the structure I was told that there are two methods I could use.
1) Use a counter part compound which is exact/looks like the structure I am hoping (so basically known compound) and then do traditional comparison method to establish the structure.
      UNFORTUNATELY I cannot synthesize such compound in lab nor such material is available in literature ( including crystal structure).
2) is to use the model. 
right now for modelling such structure I am using Spartan program (again I have not used it earlier in my graduate work) So I want to know as to how to generate the models in order to get the correct crystal parameters? (atoms positions?) Is spartan good enough to do job? is there any other method for doing such fitting?
    Question number two
In order to get lower E0 values after the fitting, I read that there is a method to use in which delE value can be set to 0 intentionally and then recalibrating the spectra in athena again in order to accurately calibrate the E0. I read paper by Shelly kelly and Bruce Ravel. Also I have seen the steps in one of shelly kellys PDF formatted lecture, although I am still not sure about the exacts steps to take in order to do such calibration. Could someone explain me the steps in details (especially taking artemis files to athena and then using it as STD spectra for calibration purposes, I am confused about that)

Thank you very  much everyone in advance for your patience to go through such a long email and helping to solve my silly doubts.
Your New Bee in this fantastic group
Pushkar


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Michael Kömm | 22 Oct 15:16 2014
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Athena does not React after 2-4 steps

Dear Bruce and dear mailing list,

Athena stops working after doing a maximum of four steps (f.e. removing 
points, import data,...) when running on my PC with Windows 8. It either 
says "not responding" or just shuts down. Whenever Athena shuts down the 
errors in the .txt in the directory of the project differs. But it 
always looks like this:

          line 0: warning: Skipping unreadable file 
"C:\Users\Michael\AppData\Roaming\demeter\stash\gp_leqfnhqh"
          line 0: No data in plot

only the file name changes. But there's never a file with that name in 
that directory.

Sometimes there is as well a window opened that says: gnuplot.exe is not 
working anymore.
I've deleted the Roaming\demeter folder but it didn't end the troubles.

Hope there is a way to end this problem.

Sincerely yours

Michael Koemm

PS: There is also one of my projects in the attachment.

         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_leqfnhqh"
         line 0: No data in plot

         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_kvoazmzb"
         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_gweswxhp"
         line 0: No data in plot

         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roamingng\demeter\stash\gp_crbewhrh"
         line 0: No data in plot

         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_cjdfbtax"
         line 0: No data in plot

         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_dpzlojfz"
         line 0: No data in plot

         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_ojltkmau"
         line 0: No data in plot

         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_ovktvmqd"
         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_ghwrtgin"
         line 0: No data in plot

^C
         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_gugofvzb"
         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_ppprhupq"
         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_zuypixhz"
         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_albfrvcb"
         line 0: No data in plot

gnuplot> styles
         ^
         line 0: invalid command

         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_gugofvzb"
         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_ppprhupq"
         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_zuypixhz"
         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_albfrvcb"
         line 0: No data in plot

         line 0: Unexpected }

         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_gugofvzb"
         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_ppprhupq"
         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_zuypixhz"
         line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_albfrvcb"
         line 0: No data in plot

Attachment (A4.prj): application/octet-stream, 29 KiB
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Kurinji Krishnamoorthy | 21 Oct 05:31 2014

Artemis closes when I try to open a project file or import data

Hi,
Artemis had been working well on my laptop for a while. But today when I attempted to open a saved project file ( with a *.fpj extension), the program tried to open it for a while but then ultimately closed without any error messages. A similar thing occurred when I tried to import an Athena data file into Artemis. I was wondering if anybody had any idea how to fix this problem?

Thanks,
Kurinji 
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Samson Vallerie Ann | 20 Oct 17:08 2014
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Importing data to Athena


Hi Bruce,
I have some trouble importing data to Athena even if it's just ordinary column text file. I have attached two
sample data. These are processed data from full-field XANES images. Basically I select a region in the
image then write/output the total intensity of that region in a text file and I just iterate over several
images. I have tried deleting out the headers, putting back the headers, padding some 0's in the energy
column, checking some plugins, but to no avail. Your tips, advice is badly needed. 

Many thanks,
Vallerie    
Attachment (test3.dat): application/octet-stream, 714 bytes
Attachment (Area2.dat): application/octet-stream, 1196 bytes
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multiple absorber atoms

Hello,

This is my first message to the list so I expect to do it right.

I need to generate a path list for EXAFS fitting within ifeffit, based on a crystalline structure that has two different crystallographic positions for the absorber atom (edge K of Mo). Is there any way to do this? 

I would appreciate any information you could give me.

Thanks in advance

Jesus
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Ke Yuan | 16 Oct 15:37 2014
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XAFS Analysis using Ifeffit

Hello Drew,

Thanks for your suggestions. I just checked my original data without normalization. The edge step is about 0.7 (see pic attached). I did the measurement in fluorescence mode at APS, beamline 12-BMB. What do you think about this pic?

For the sample preparation, I think I need to mix UO2 with some other materials to dilute it. Do you have any suggestions on the matrix materials?


Best,
Ke
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Ke Yuan | 16 Oct 15:35 2014
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(no subject)

Hello Pushkar,

I think the peak value of the first derivative and the zero value of the second derivative does the same thing. My sec deriv is very noisy so it's easy for my to pick the peak value of the 1st deriv instead.

I would suggest you to watch the video from Bruce which explained HOW TO PICK Rbkg at:


Click the Athena: Data processing II

Actually all the other video lectures are very helpful, too!

Best,
Ke

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