Nate Turner | 19 Aug 20:07 2014
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Artemis and FEFF interaction in fit process

Hello All,

I have a question about Artemis' interaction with FEFF.

I know you can either run FEFF6L in Artemis to populate a paths list or externally create the FEFFnnnn.dat files in FEFF and import them into Artemis. We currently do the later using FEFF9, the use of the SCF card gives a better Eo initial guess and our compound has fractional occupancy/disorder that requires us to do some altering of the atoms list after its populated in ATOMS, which we find best to do outside of Artemis.

My question is once these external FEFF9 paths are brought in does Artemis use FEFF6L in the fit process or is FEFF in Artemis only to populate the paths list? 

If Artemis doesn't use FEFF in the fit process then there's no issue but while I've read the mailing list and seen that many do not believe there is any improvement in the EXAFS results from FEFF6L to FEFF9, I'd rather be consistent in which version of FEFF we use throughout the analysis. I would have Artemis calling to FEFF9 instead of FEFF6L if in fact Artemis does use FEFF in the fit. 

The reason I haven't gone ahead with having Artemis call to FEFF9 making this a non issue is I'm not sure how. I know you can direct Artemis to whatever version of FEFF you want under preferences, but then I'm not sure what file I need to direct to specifically for FEFF9.

So to summarize, 

Does Artemis use FEFF in the fitting process or is its only function in Artemis to create the paths for the fit?
If it does use FEFF in the fitting, how do you/is it possible to have Artemis call to FEFF9 instead of FEFF6L?

Thanks all for your time,

Nate Turner
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Bruce Ravel | 18 Aug 20:22 2014

importing larch functionality


This:

    use_plugin_path('xafs')
    from feffdat import feffpath

works as expected.  It adds the path to larch's xafs plugins into the
search path and imports "feffdat" such that it can be used in the
namespace of the plugin I am working on.

This fails

    use_plugin_path('wx')
    from plotter import newplot, plot

with this error message:

    file <stdin>, line 0
    ImportError: cannot import name newplot
        add_plugin('f85ut')

What am I not understanding?  newplot (and plot) seem to be exported
by wx/plotter.py the same way that feffpath is exported by
xafs/feffdat.py.

B

--

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

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

  Homepage:    http://bruceravel.github.io/home/
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/
Jens Kruse | 18 Aug 16:12 2014
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Meaning of linear combination fit reports

Hi everyone,

I doing LCF on my XANES data. I wonder if someone can tell me the meaning of the values in parentheses following the weight value in the Fit results window?. I looked into the respective document section of the Manuel but could not find the answer, yet.

I am asking because I did a Fitting with over 20 standards (STD) to find all combination of max 4 standards which describe my unknown sample spectra. This results in a lot of combination with similar chi-square(reduced) and R-values. I know a relative changes between these values are more probably meaningful than absolute values.
A lot of the possible combinations provided by after the fit yieled combinations with at lest on STD having a weight of 0.000. (Fit 1). I thought that this would mean, that 3 standards are sufficient to describe the system. However, repeating the fit with only the three standards with weight > 0.0 yielded a complete different proportions (Fit 2).  How can this be explain and how should I deal with combinations or standards having  a weight of 0.000?

Thanks a lot for your thoughts and suggesting,

Cheers Paul

Results Fit  1:

  3: STD3           0.324(0.025)
  7: STD7             0.686(0.021)
  20:  STD2O       0.127(0.016)
  27: STD27         0.000(0.036)

vs.

Results Fit 2:
  3: STD3           0.473(0.019)
  7: STD7             0.620(0.023)
  20:  STD20       0.000(0.030)
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이국승 | 18 Aug 09:55 2014
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Questions for Artemis fit

Dear,

I am a biginer in this area and I have two stupid questions.

 

I met a problem while I was trying to fit a Au foil data using Artemis following the process of 'Artemis instruction videos' which (I guess) was made by Bruce.

I followed exactly the same procedure as the 'Artemis instruction video'. But, when I click the Fit button, a popup window appeared with some error messages. The image of the popup window is attached.

 

Before I met this problem, I could not load the 'atoms.inp' when I clicked the 'Import crystal data or a Feff calculation' button. The atoms.inp file does not exist in any place of my PC. I installed demeter again, and nothing different. Does demeter installer file not contain atoms.inp file?

 

Your kind instruction or explanation will be deeply appreciated.

Thank you.

 

Kug-Seung Lee

Attachment (Fit error.PNG): application/octet-stream, 56 KiB
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ZHAN Fei | 14 Aug 19:46 2014
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problem of normalization of feff calculation and experimental spectrum

Hellow,everyone:

 When the energy range is too short (for instance 60 70 eV,this moment normal normalization in Athena may not be perfect),how to do the normalization of both the feff calculation and experimental spectrum?I want to let feff calculation fit the experiment , so spectrum normalization had better can be express a parameter to be fited,I'm not sure normal edge jump works,anyone have good idea about it ?

Thanks,

Sincerely,

zhanfei

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史乾涛 | 14 Aug 10:45 2014
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The missing feff paths



Hi,

I have a problem when I used Demeter 9.18 or 9.20. The Artemis window only show parts of the calculated feff paths such as the followed figure (only 0, 4, 5, 6, 7, 10 paths of the first 10 paths were shown, and where is the other paths?).

 

Did anyone meet this problem and how did you treat it?

Many thanks!

best regards,

Qiantao Shi

Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences




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Yuanyuan Li | 10 Aug 05:28 2014
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help with XAFS spectrum of NbS2

Hi,

We have measured some Nb doped MoS2 samples and want to compare Nb edges of these samples with standard NbS2. If someone has it and would like to share it, it would be great help to us.
Thank you very much!

Best,

Yuanyuan Li
Physics Department
Yeshiva University
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Bruce Ravel | 8 Aug 21:52 2014

Re: space group P 4/mmc ?

On 08/08/2014 03:33 PM, Marinkovic, Nebojsa wrote:
> Bruce,
> I found the PtO strucutre (WJ Moore, JACS 63 (1941) 1392) reported as P
> 4/m m c , but Atoms says "invalid space group".   Any clues?
> Thanks,
> Ned
>

Hi Ned,

I am CCing my answer to the Ifeffit Mailing List since I think this 
question of general interest.

The author is using archaic notation, which is a common problem with 
crystallography references from the early decades of the 20th century. 
"P 4/m m c" does not exist in the modern International Tables of 
Crystallography.  See
     http://en.wikipedia.org/wiki/List_of_space_groups

Happily the author also gives the Schoenflies notation.  "D^9_4h" is "P 
42/m m c" in modern notation.

The majority of the symbols Artemis recognizes are given in the Artemis 
Users' Guide:
    http://bruceravel.github.io/demeter/artug/atoms/space.html
although perhaps not in the most useful manner.  The wikipedia page is 
also useful for resolving a Schoenflies symbol to the corresponding 
Hermann-Maguin symbol.

You can also simply use the Schoenflies symbol in Artemis.  The string 
"D^9_4h" should be recognized by Atoms as the same as "P 42/m m c".

B

--

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

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

  Homepage:    http://bruceravel.github.io/home/
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/
Peng Liu | 1 Aug 18:29 2014
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Picon

Undo in Athena

Hello everyone,

I have one more question about undo in Athena, e.g. I accidentally 
deleted one of the good spectra, how I can get it back. In word, I can 
go to Edit and click undo, but I haven't found it in Athena.

Thanks for your time,

Peng

--

-- 
Ph.D. Candidate
Earth and Environmental Sciences, CEIT Bldg. Rm. 2026
University of Waterloo        Ph: 519-888-4567 ext. 37232
200 University Avenue West
Waterloo, Ontario  N2L 3G1    Fax:519-746-3882
p26liu@...
Johan Nilsson | 1 Aug 17:30 2014
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larch warning about epics plugin

Hello,

Today I reinstalled larch after upgrading my computer to Ubuntu 14.04. I downloaded the latest source and installed all the recommended dependencies except PyEpics and then continued with the install. Everything went smoothly and larch appears to be working as it should. However when I start the program I get warning messages about the epics plugin

$ larch
  Larch 0.9.23 (8-Apr-2014) M. Newville, T. Trainor
  using python 2.7.6, numpy 1.8.1, wx-enabled, wx version 2.8.12.1
Warning: /usr/share/larch/plugins/epics/xrfcontrol.py is not a valid plugin
   error:  ImportError('cannot import name ROI',)
Warning: /usr/share/larch/plugins/epics/xrf_detectors.py is not a valid plugin
   error:  ImportError('cannot import name ROI',)
Warning: /usr/share/larch/plugins/epics/xspress3.py is not a valid plugin
   error:  ImportError('cannot import name ROI',)

I have no plans to use this plugin but I tried to install PyEpics to see if anything would change but it did not. Is this a bug or is there some configuration I can change to get rid of the warnings?

--Johan


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Peng Liu | 31 Jul 04:54 2014
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http://ixs.iit.edu/database/)

Hi all,

I searched the Farel Lytle Database and looked like I found chalcopyrite spectra for Cu from http://ixs.iit.edu/database/data/Farrel_Lytle_data/RAW/Cu/index.html.

I downloaded the data, but I can not import into Athena. I looked into the data, it looked wired for me. The first column doesn't look like energy for Cu.

I am wondering if anyone have any idea how to import or transfer the data. I attached the data file.

Regards,

Peng
-- Ph.D. Candidate Earth and Environmental Sciences, CEIT Bldg. Rm. 2026 University of Waterloo Ph: 519-888-4567 ext. 37232 200 University Avenue West Waterloo, Ontario N2L 3G1 Fax:519-746-3882 p26liu-QFUY5ocGksJFJ04o6PK0Fg@public.gmane.org
 NPTS  NS CUEDGE  CUHITE   DSPACE  STPDEG  STEPMM  START    STOP     SCALE
  468   3  84294. 200000. 1.92017   4000.   3150.  85290.  75506.    2.000
  DELTA:     50.      5.     22.     36.     48.
 DELEND:  84788.  83804.  81216.  76752.  71076.
    SEC:   2.000   2.000   2.000   2.000   2.000
 OFFSET: 1140. 1608.  401.    4.    4.    6.  137.    4.    6.   18.  641.    3.    2.    5.   61.   20.   93.  232.    0.    0.    0.    0.    0.    0.
SINGLE XTAL CUINSE2 CHALCOPYRITE                                  7   7  5-30-83
    85290. 2.62740E+05 2.69329E+05 1.37453E+04
    85240. 2.63329E+05 2.69903E+05 1.32863E+04
    85190. 2.62699E+05 2.69422E+05 1.31963E+04
    85140. 2.61994E+05 2.68895E+05 1.31268E+04
    85090. 2.61453E+05 2.68538E+05 1.30418E+04
    85040. 2.60785E+05 2.68062E+05 1.29858E+04
    84990. 2.60028E+05 2.67461E+05 1.28778E+04
    84940. 2.59236E+05 2.66832E+05 1.28148E+04
    84890. 2.58560E+05 2.66316E+05 1.27378E+04
    84840. 2.57993E+05 2.65934E+05 1.26993E+04
    84790. 2.57192E+05 2.65293E+05 1.27238E+04
    84740. 2.56507E+05 2.64779E+05 1.26123E+04
    84735. 2.56674E+05 2.65012E+05 1.27078E+04
    84730. 2.56887E+05 2.65249E+05 1.27523E+04
    84725. 2.56154E+05 2.64440E+05 1.26368E+04
    84720. 2.56329E+05 2.64673E+05 1.26843E+04
    84715. 2.56113E+05 2.64444E+05 1.27128E+04
    84710. 2.56446E+05 2.64826E+05 1.27273E+04
    84705. 2.55947E+05 2.64302E+05 1.27208E+04
    84700. 2.56291E+05 2.64673E+05 1.27248E+04
    84695. 2.55780E+05 2.64124E+05 1.26613E+04
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    84670. 2.55303E+05 2.63702E+05 1.26383E+04
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    84635. 2.55268E+05 2.63751E+05 1.27593E+04
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    84620. 2.54470E+05 2.62934E+05 1.27748E+04
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    84600. 2.53850E+05 2.62341E+05 1.26843E+04
    84595. 2.53891E+05 2.62446E+05 1.27378E+04
    84590. 2.54576E+05 2.63216E+05 1.29453E+04
    84585. 2.54663E+05 2.63329E+05 1.29638E+04
    84580. 2.54231E+05 2.62850E+05 1.28738E+04
    84575. 2.54398E+05 2.63065E+05 1.29358E+04
    84570. 2.54572E+05 2.63252E+05 1.30038E+04
    84565. 2.54527E+05 2.63225E+05 1.30218E+04
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    84530. 2.53443E+05 2.62177E+05 1.31223E+04
    84525. 2.53673E+05 2.62465E+05 1.31653E+04
    84520. 2.53002E+05 2.61739E+05 1.30518E+04
    84515. 2.53242E+05 2.62024E+05 1.30948E+04
    84510. 2.52940E+05 2.61718E+05 1.31593E+04
    84505. 2.53206E+05 2.62026E+05 1.32078E+04
    84500. 2.54107E+05 2.63049E+05 1.34943E+04
    84495. 2.54317E+05 2.63286E+05 1.35813E+04
    84490. 2.52789E+05 2.61595E+05 1.32793E+04
    84485. 2.52997E+05 2.61858E+05 1.33278E+04
    84480. 2.50979E+05 2.59652E+05 1.29903E+04
    84475. 2.51198E+05 2.59921E+05 1.30453E+04
    84470. 2.51339E+05 2.60108E+05 1.32198E+04
    84465. 2.51797E+05 2.60612E+05 1.32753E+04
    84460. 2.51716E+05 2.60529E+05 1.34003E+04
    84455. 2.51748E+05 2.60576E+05 1.34403E+04
    84450. 2.52445E+05 2.61346E+05 1.36928E+04
    84445. 2.52573E+05 2.61517E+05 1.37278E+04
    84440. 2.51574E+05 2.60421E+05 1.36693E+04
    84435. 2.51689E+05 2.60599E+05 1.36873E+04
    84430. 2.51963E+05 2.60922E+05 1.38693E+04
    84425. 2.52106E+05 2.61099E+05 1.39708E+04
    84420. 2.50991E+05 2.59896E+05 1.39283E+04
    84415. 2.51205E+05 2.60151E+05 1.39608E+04
    84410. 2.51709E+05 2.60726E+05 1.41528E+04
    84405. 2.51660E+05 2.60700E+05 1.42468E+04
    84400. 2.51470E+05 2.60489E+05 1.43853E+04
    84395. 2.51864E+05 2.60887E+05 1.45548E+04
    84390. 2.49928E+05 2.58771E+05 1.42703E+04
    84385. 2.50040E+05 2.58935E+05 1.44408E+04
    84380. 2.50029E+05 2.58943E+05 1.46093E+04
    84375. 2.50348E+05 2.59314E+05 1.47668E+04
    84370. 2.51470E+05 2.60558E+05 1.52528E+04
    84365. 2.51704E+05 2.60858E+05 1.54398E+04
    84360. 2.50432E+05 2.59461E+05 1.54388E+04
    84355. 2.50551E+05 2.59619E+05 1.56348E+04
    84350. 2.50747E+05 2.59853E+05 1.60613E+04
    84345. 2.50891E+05 2.60029E+05 1.63008E+04
    84340. 2.50463E+05 2.59563E+05 1.66128E+04
    84335. 2.50609E+05 2.59757E+05 1.68973E+04
    84330. 2.49165E+05 2.58212E+05 1.71793E+04
    84325. 2.49428E+05 2.58521E+05 1.75208E+04
    84320. 2.49664E+05 2.58802E+05 1.83013E+04
    84315. 2.49780E+05 2.58969E+05 1.88503E+04
    84310. 2.49104E+05 2.58223E+05 1.96293E+04
    84305. 2.49514E+05 2.58715E+05 2.05448E+04
    84300. 2.50507E+05 2.59815E+05 2.21398E+04
    84295. 2.50668E+05 2.60028E+05 2.35713E+04
    84290. 2.49512E+05 2.58776E+05 2.58373E+04
    84285. 2.49699E+05 2.58998E+05 2.85503E+04
    84280. 2.50206E+05 2.59571E+05 3.43628E+04
    84275. 2.50372E+05 2.59772E+05 4.22278E+04
    84270. 2.48729E+05 2.57983E+05 5.60163E+04
    84265. 2.48859E+05 2.58139E+05 6.90043E+04
    84260. 2.50532E+05 2.60006E+05 8.37428E+04
    84255. 2.50905E+05 2.60426E+05 9.30623E+04
    84250. 2.49640E+05 2.59061E+05 1.02885E+05
    84245. 2.49756E+05 2.59231E+05 1.13400E+05
    84240. 2.47923E+05 2.57273E+05 1.30315E+05
    84235. 2.48177E+05 2.57631E+05 1.48519E+05
    84230. 2.47706E+05 2.57351E+05 1.69783E+05
    84225. 2.47486E+05 2.57321E+05 1.81379E+05
    84220. 2.46507E+05 2.56325E+05 1.85952E+05
    84215. 2.46653E+05 2.56361E+05 1.83662E+05
    84210. 2.45808E+05 2.55068E+05 1.75544E+05
    84205. 2.45510E+05 2.54460E+05 1.69388E+05
    84200. 2.47379E+05 2.56409E+05 1.68255E+05
    84195. 2.47851E+05 2.56966E+05 1.67940E+05
    84190. 2.46780E+05 2.55954E+05 1.67538E+05
    84185. 2.47243E+05 2.56553E+05 1.68100E+05
    84180. 2.47468E+05 2.56890E+05 1.67826E+05
    84175. 2.47473E+05 2.56958E+05 1.68112E+05
    84170. 2.47751E+05 2.57292E+05 1.71370E+05
    84165. 2.47675E+05 2.57238E+05 1.78118E+05
    84160. 2.47903E+05 2.57499E+05 1.83812E+05
    84155. 2.47337E+05 2.56896E+05 1.89260E+05
    84150. 2.46936E+05 2.56478E+05 1.91718E+05
    84145. 2.47393E+05 2.56977E+05 1.92195E+05
    84140. 2.47461E+05 2.57083E+05 1.90046E+05
    84135. 2.47259E+05 2.56882E+05 1.85391E+05
    84130. 2.47694E+05 2.57360E+05 1.82660E+05
    84125. 2.47580E+05 2.57262E+05 1.79064E+05
    84120. 2.47646E+05 2.57374E+05 1.78275E+05
    84115. 2.46353E+05 2.55949E+05 1.76955E+05
    84110. 2.46485E+05 2.56134E+05 1.77123E+05
    84105. 2.45995E+05 2.55645E+05 1.76134E+05
    84100. 2.46045E+05 2.55809E+05 1.75237E+05
    84095. 2.45237E+05 2.55115E+05 1.72985E+05
    84090. 2.45312E+05 2.55451E+05 1.71555E+05
    84085. 2.45391E+05 2.55743E+05 1.70577E+05
    84080. 2.45339E+05 2.55614E+05 1.71091E+05
    84075. 2.44076E+05 2.53767E+05 1.71775E+05
    84070. 2.44261E+05 2.53574E+05 1.73692E+05
    84065. 2.43646E+05 2.52555E+05 1.74442E+05
    84060. 2.44319E+05 2.53287E+05 1.75594E+05
    84055. 2.46247E+05 2.55592E+05 1.77957E+05
    84050. 2.47067E+05 2.56717E+05 1.79167E+05
    84045. 2.47696E+05 2.57614E+05 1.80541E+05
    84040. 2.47709E+05 2.57750E+05 1.81363E+05
    84035. 2.47335E+05 2.57378E+05 1.82033E+05
    84030. 2.47469E+05 2.57557E+05 1.83158E+05
    84025. 2.47566E+05 2.57681E+05 1.83738E+05
    84020. 2.47878E+05 2.58023E+05 1.84556E+05
    84015. 2.47394E+05 2.57494E+05 1.84455E+05
    84010. 2.47595E+05 2.57740E+05 1.84722E+05
    84005. 2.46876E+05 2.56966E+05 1.83930E+05
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    76020. 1.22353E+05 1.40247E+05 1.02013E+05
    75972. 1.21587E+05 1.39483E+05 1.01160E+05
    75924. 1.20602E+05 1.38305E+05 1.00927E+05
    75876. 1.20118E+05 1.37814E+05 1.00571E+05
    75828. 1.19033E+05 1.36588E+05 9.98553E+04
    75780. 1.18166E+05 1.35655E+05 9.93158E+04
    75732. 1.16845E+05 1.33990E+05 9.89728E+04
    75684. 1.16519E+05 1.33847E+05 9.80803E+04
    75636. 1.14068E+05 1.30614E+05 9.71368E+04
    75588. 1.16220E+05 1.33612E+05 9.80908E+04
    75540. 1.14880E+05 1.32535E+05 9.57318E+04
    75492. 1.14183E+05 1.31423E+05 9.64503E+04

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