Lisa Bovenkamp | 20 Apr 18:01 2015

Re: energy resolution


Hello all.
I am getting confused with different comments how to determine the energy resolution
of an XAS beamline.
I think using peak fitting to determine the line width is a reasonable method.
The basis of a XAS peak is the Voigt profile (a combination of a Lorenzian and Gaussian)
The width of the Lorenzian equals the natural line width
while the width of the Gaussian represents the experimental line width and some features
Now here is question 1: 
What is the combination of the two profiles in the Athena peak fitting routine for the Pseudo-Voigt?
Question 2:
Is the sigma (Gaussian width) that delta E that represents
the resolution - (E /delta E) ?

Using a different program (Igor Pro) to determine 
the width gives different results because can only 
use a simple combination of Lorentz and Gauss (1:1).

Thanks.
Lisa
Kenneth Latham | 20 Apr 07:40 2015
Picon

Athena reporting incorrect element on import

Hi, 


I am having a number of issues with importing my data into Athema, the data that I collected was on the carbon K edge. As there is an issue with recording carbon (as it builds up on the mirrors), the synchrotron that I performed my measurments at (Australian Synchrotron) has developed software to perform a double normalization to remove these effects.


The problem comes when importing the now normalized data into Athena. As it doesn't require normalization again, I select the norm(E) data type and the correct column for energy and response which produces the correct plot of the data. When I click OK it attempts to produce the other plots, sometimes it manages to make a k-space and R-space but q-space is never displayed and other times it only manages the energy plot. Additionally, the word element is lit up red and it has selected beryllium as the element on the L2 edge. Changing this to carbon does not seem to fix the problem as it reverts back to beryllium as soon as I leave the main page.


Finally, when I go to peak fitting, any value added for peaks informs me that it is out of range.


I have attached some normalized data.


Any help with this would be greatly appreciated.


Regards, 

Ken Latham

# S Data File C1s K Edge											
#------------------
#eV	Norm
275.83	-0.001756
274.87	0.00095341
274.97	-0.0028738
275.1	-0.0014604
275.19	-0.0011729
275.29	-0.0029696
275.38	-0.0025556
275.49	-0.0023094
275.58	-0.0027391
275.68	-0.00030236
275.76	-0.00041832
275.89	-0.0030417
275.99	-0.0011031
276.09	-0.00029426
276.19	-0.0018977
276.28	-0.0013665
276.38	-0.00051702
276.49	-0.0024714
276.58	-0.0028516
276.68	0.0019144
276.77	-0.00022764
276.88	-0.0019184
276.98	0.0013644
277.08	-0.00031785
277.17	4.30E-05
277.27	0.00027229
277.37	-0.00088902
277.48	-0.00060665
277.58	-5.12E-05
277.68	0.00071247
277.78	0.0019917
277.88	-0.0019942
277.97	0.0031483
278.07	0.0021094
278.18	-0.00023179
278.26	0.0017131
278.38	-0.00048848
278.48	0.0016741
278.58	0.0020948
278.68	-0.00019404
278.77	-0.0029122
278.87	0.0012438
278.96	0.0019372
279.07	-0.0017273
279.17	0.0030833
279.28	-0.0021669
279.35	0.00053382
279.46	-0.00061272
279.58	0.0042665
279.67	-0.0010533
279.75	0.00083057
279.86	0.0014686
279.97	-0.0001052
280.06	0.0010029
280.16	0.0046544
280.27	0.001028
280.35	-4.69E-05
280.46	0.0044458
280.56	0.0022476
280.66	0.0016896
280.76	0.003431
280.86	0.0038765
280.96	0.0012344
281.05	0.003628
281.17	0.00477
281.26	0.0054546
281.35	0.0056799
281.46	0.004665
281.55	0.0055362
281.66	0.0074943
281.76	0.0065766
281.87	0.010452
281.95	0.011154
282.06	0.011888
282.14	0.013913
282.25	0.013266
282.36	0.017908
282.46	0.021512
282.56	0.023459
282.66	0.026318
282.76	0.03308
282.86	0.032041
282.94	0.03784
283.06	0.045755
283.15	0.060819
283.24	0.074274
283.34	0.098824
283.46	0.13039
283.56	0.17349
283.66	0.22834
283.75	0.28042
283.86	0.37824
283.95	0.459
284.05	0.53751
284.16	0.65769
284.26	0.74088
284.35	0.83574
284.46	0.96634
284.55	1.0362
284.64	1.0819
284.75	1.1241
284.84	1.1433
284.96	1.144
285.05	1.1094
285.14	1.0999
285.25	1.0593
285.33	1.0448
285.45	1.0344
285.54	1.0108
285.64	0.99554
285.74	1.0084
285.85	1.0681
285.94	1.1253
286.04	1.2479
286.14	1.3725
286.24	1.5017
286.34	1.614
286.45	1.7076
286.53	1.7283
286.64	1.6608
286.76	1.5938
286.84	1.5219
286.93	1.4639
287.05	1.3909
287.15	1.345
287.24	1.3199
287.33	1.31
287.44	1.3011
287.55	1.2969
287.65	1.2917
287.73	1.3108
287.84	1.3298
287.93	1.3488
288.04	1.3917
288.14	1.4285
288.24	1.467
288.35	1.4836
288.45	1.4972
288.55	1.4969
288.63	1.4918
288.75	1.5043
288.82	1.4935
288.93	1.5264
289.03	1.5349
289.13	1.5618
289.24	1.5862
289.33	1.61
289.44	1.6424
289.53	1.6765
289.64	1.714
289.73	1.7343
289.83	1.779
289.93	1.8151
290.03	1.8655
290.15	1.9197
290.24	1.9402
290.32	1.9828
290.44	2.0101
290.53	2.0391
290.62	2.0425
290.74	2.0759
290.84	2.0957
290.93	2.1161
291.03	2.1348
291.13	2.152
291.23	2.1611
291.33	2.1985
291.43	2.1957
291.53	2.2062
291.62	2.2008
291.73	2.2145
291.84	2.2294
291.93	2.2315
292.03	2.2374
292.13	2.2442
292.23	2.2412
292.33	2.2473
292.42	2.2583
292.52	2.2644
292.63	2.2629
292.73	2.266
292.84	2.2882
292.93	2.2669
293.04	2.271
293.13	2.2835
293.24	2.2782
293.31	2.2903
293.42	2.2935
293.52	2.2968
293.62	2.2953
293.73	2.2977
293.82	2.2979
293.92	2.2929
294.04	2.2907
294.13	2.2815
294.22	2.2767
294.32	2.2967
294.42	2.2907
294.53	2.2744
294.62	2.2767
294.72	2.2764
294.82	2.2818
294.92	2.2947
295.02	2.2793
295.11	2.2799
295.21	2.2703
295.32	2.2847
295.43	2.2737
295.52	2.2719
295.63	2.2785
295.73	2.2735
295.82	2.2742
295.91	2.2743
296.01	2.2682
296.11	2.2667
296.22	2.2695
296.33	2.2579
296.43	2.2507
296.53	2.2675
296.61	2.2651
296.72	2.2567
296.82	2.2529
296.91	2.2522
297.01	2.2396
297.11	2.2471
297.22	2.2329
297.32	2.232
297.42	2.2201
297.52	2.2153
297.61	2.223
297.72	2.2118
297.82	2.211
297.91	2.2069
298.01	2.1983
298.11	2.1888
298.21	2.1768
298.3	2.1762
298.41	2.1721
298.51	2.1612
298.61	2.1625
298.7	2.1492
298.8	2.1424
298.92	2.1252
299.01	2.1335
299.12	2.1199
299.21	2.1122
299.3	2.1117
299.41	2.0967
299.51	2.0838
299.6	2.0993
299.71	2.0877
299.81	2.0715
299.91	2.0745
300.02	2.0584
300.11	2.0568
300.22	2.0542
300.32	2.0417
300.41	2.0439
300.51	2.0261
300.6	2.0343
300.71	2.0153
300.83	2.006
300.91	2.0115
301	1.994
301.1	1.9908
301.2	1.9987
301.31	1.9847
301.41	1.977
301.51	1.975
301.61	1.9652
301.72	1.9585
301.82	1.9477
301.91	1.9399
302.01	1.9326
302.11	1.9368
302.22	1.9288
302.3	1.918
302.42	1.919
302.5	1.9016
302.61	1.8943
302.72	1.8981
302.81	1.8873
302.93	1.8843
303.01	1.8759
303.1	1.8627
303.2	1.861
303.29	1.8446
303.41	1.8447
303.51	1.8371
303.61	1.8213
303.71	1.8119
303.81	1.8132
303.91	1.7985
304.02	1.7978
304.1	1.7716
304.21	1.7698
304.29	1.764
304.4	1.7537
304.5	1.7518
304.61	1.7399
304.7	1.7196
304.81	1.7127
304.9	1.7023
305	1.7001
305.11	1.685
305.2	1.6751
305.31	1.6642
305.41	1.6622
305.51	1.6499
305.6	1.6332
305.7	1.6254
305.81	1.6099
305.9	1.605
306	1.5941
306.09	1.5827
306.18	1.5783
306.31	1.5706
306.41	1.5542
306.5	1.5449
306.6	1.531
306.71	1.5191
306.82	1.5128
306.91	1.5014
306.99	1.4931
307.12	1.4915
307.18	1.4876
307.31	1.4717
307.4	1.4637
307.51	1.4566
307.6	1.4491
307.71	1.439
307.81	1.4243
307.9	1.4227
307.98	1.4191
308.1	1.4
308.2	1.3958
308.3	1.392
308.41	1.3807
308.49	1.3738
308.6	1.374
308.7	1.3635
308.81	1.3497
308.89	1.3481
309	1.3428
309.1	1.328
309.21	1.3288
309.31	1.3205
309.39	1.3163
309.51	1.3063
309.61	1.2956
309.7	1.2978
309.79	1.2867
309.89	1.2883
310	1.2823
310.11	1.2771
310.21	1.2679
310.31	1.2654
310.4	1.2641
310.5	1.2572
310.59	1.2424
310.7	1.2399
310.79	1.2324
310.89	1.2354
311.01	1.2292
311.1	1.2227
311.2	1.2181
311.3	1.2187
311.41	1.2118
311.5	1.2091
311.61	1.2008
311.7	1.2014
311.79	1.2018
311.89	1.1936
311.99	1.1863
312.1	1.1853
312.2	1.1824
312.29	1.1858
312.4	1.1719
312.5	1.1719
312.59	1.1686
312.69	1.1702
312.8	1.1631
312.9	1.1622
313	1.1538
313.1	1.1552
313.2	1.1543
313.3	1.1545
313.4	1.148
313.49	1.1397
313.6	1.1375
313.68	1.1319
313.79	1.1344
313.9	1.1332
314	1.1223
314.1	1.133
314.2	1.1242
314.3	1.1253
314.4	1.1194
314.48	1.1125
314.59	1.1197
314.69	1.1077
314.8	1.1085
314.89	1.1086
314.99	1.1084
315.09	1.103
315.19	1.1012
315.31	1.094
315.41	1.0958
315.5	1.0999
315.6	1.0939
315.69	1.0899
315.8	1.0895
315.9	1.0848
315.99	1.0911
316.11	1.081
316.18	1.08
316.29	1.0763
316.4	1.0781
316.5	1.0692
316.6	1.0738
316.69	1.0685
316.8	1.0632
316.91	1.0627
317	1.0665
317.09	1.0611
317.19	1.0595
317.29	1.0623
317.41	1.0632
317.5	1.0549
317.59	1.0579
317.69	1.0524
317.79	1.053
317.89	1.0529
317.99	1.046
318.11	1.0458
318.2	1.0425
318.29	1.0427
318.39	1.0476
318.49	1.0379
318.59	1.0379
318.68	1.0412
318.8	1.0305
318.9	1.0375
319	1.0304
319.1	1.0319
319.19	1.0347
319.3	1.0308
319.39	1.0295
319.49	1.0248
319.59	1.024
319.68	1.0266
319.79	1.0252
319.89	1.0183
319.99	1.0181
320.11	1.0184
320.2	1.0195
320.28	1.0108
320.39	1.0174
320.49	1.0115
320.59	1.0148
320.67	1.0131
320.8	1.0063
320.89	1.0077
320.99	1.0035
321.09	1.0094
321.19	1.004
321.28	0.99641
321.39	1.0035
321.49	1.0021
321.59	1.0056
321.68	0.99512
321.79	0.99454
321.9	0.99336
322.01	0.99424
322.1	0.99318
322.19	0.9913
322.3	0.992
322.39	0.98923
322.48	0.98738
322.58	0.98717
322.69	0.985
322.78	0.98854
322.89	0.98828
322.99	0.98583
323.1	0.98388
323.19	0.97693
323.3	0.98501
323.41	0.98212
323.5	0.98376
323.59	0.98743
323.69	0.98058
323.79	0.97777
323.9	0.97741
323.99	0.97055
324.11	0.97174
324.18	0.97339
324.29	0.96687
324.4	0.97093
324.5	0.96809
324.59	0.96164
324.68	0.96895
_______________________________________________
Ifeffit mailing list
Ifeffit@...
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Ramiro Moreira Toja | 16 Apr 03:40 2015

Problems installing demeter in Manjaro Linux

Hi,

I'm using Manjaro 0.8.12 x64. I tried to install the demeter collection (following these instructions), but keep failing to do so. Also, I've checked to have installed all the reccomended packages, including apache and gnuplot.
When installing PGPLOT, I've had to edit the configuration to use gif instead of png, because it kept failing to install. Once I did this, it went smoothly. I add this piece of information here hoping this helps to solve later problems.
I'm having a little trouble installing dependencies. At the "sudo ./Build installdeps", it kept having trouble to find the apache/src. After a little Web search, it seems like I need to manually download the httpd sources, so I got them from here, but now it indicates I need Apache 1.3.0 version!

If I do "perl Build.PL", I get:

perl Build.PL
Checking prerequisites...
  requires:
    !  Regexp::Assemble is not installed
    !  XMLRPC::Lite is not installed

ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the versions
of the modules indicated above before proceeding with this installation

So, I guess I'm having some more problems with the dependencies, apart from the Apache ones.
What should be my next move to fix this? I've been even considering using a Ubuntu LiveUSB with persistence, just to get this working in a proven system, but really would like to get it working on my OS of choice.

Thanks in advance

Ramiro
_______________________________________________
Ifeffit mailing list
Ifeffit@...
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Eugenio Paris | 9 Apr 12:01 2015
Picon

FEFF calculation for two inequivalent absorbing sites

Hello everybody,

I'm trying to make Co K-edge EXAFS fitting for the Co3O4 compound (*.cif file is attached). The nearest neighbour of Co is oxigen at about 1.93 Angstrom distance.
Cobalt sits in two inequivalent sites in the unit cell. When I perform the FEFF calculation in Artemis for either one or the other site i get the same path with Reff = 1.93 and degeneracy = 4.
So i wonder what is the correct way to take account of the presence of both sites. At the beginning i was thinking to put 2*amp as S0^2 parameter to take account for twice the coordination number.
Then i tried to use the "Aggregate" option in Artemis. When I use this option i get exactly the same result, i.e. a SS path with Reff = 1.92 and degeneracy = 4... I was expecting to get twice the degeneracy.. (the margin and beta parameters are set to default) 

My question is:
Why do i get the same path list when I do use the "Aggregate" pathfinder and when I don't? What is wrong in my interpretation?

Thank you in advance!
Sincerely,
Eugenio
Attachment (Co3O4.cif): chemical/x-cif, 6775 bytes
_______________________________________________
Ifeffit mailing list
Ifeffit@...
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Zimina, Anna (IKFT | 8 Apr 11:47 2015

error message by import

I get the following error message when I read the txt file with two columns of data (energy and intensity):

“11:42:20: Use of uninitialized value $line in pattern match (m//) at C:/strawberry/perl/site/lib/Demeter/Files.pm line 188.”

 

Still the data can be read. What is the problem?  

 

 

Thanks in advance,

 

Anna Zimina.

______________________________________________________________________________________

 

Karlsruhe Institute of Technology (KIT)

Institute of Catalysis Research and Technology (IKFT)

 

 

Dr. Anna Zimina

Beamline scientist

 

Hermann-von-Helmholtz-Platz 1

Building 345,  Office 108

76344 Eggenstein-Leopoldshafen

Phone: +49 721 608 28673

Fax:       +49 721 608 26789

 

E-Mail anna.zimina <at> kit.edu

 

 

 

 

_______________________________________________
Ifeffit mailing list
Ifeffit@...
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Zimina, Anna (IKFT | 8 Apr 11:36 2015

Atoms

In the last version Atoms is not present as a separate program. Is it correct?

 

Mit freundlichen Grüßen,

 

Anna Zimina

______________________________________________________________________________________

 

Karlsruhe Institute of Technology (KIT)

Institut für Katalyseforschung und -technologie (IKFT)

 

Dr. Anna Zimina

Wissenschaftlerin

 

Hermann-von-Helmholtz-Platz 1

Geb. 345  Zi. 108

76344 Eggenstein-Leopoldshafen

Fon: +49 721 608 28673

Fax: +49 721 608 26789

 

E-Mail anna.zimina-Qicz5VY8OY0@public.gmane.org

 

 

 

_______________________________________________
Ifeffit mailing list
Ifeffit@...
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Ravel, Bruce | 2 Apr 17:24 2015

Re: Importing data with the new version of Athena [SEC=UNCLASSIFIED]


Zhaoming,

This conversation should be happening on the Ifeffit Mailing List.  I did not notice that last night when I replied to your first email.  Yet another reason not to answer email late at night!

I continue to be sceptical of your claims.  I have no problems with the data file you sent on either Windows or Linux once I correctly select the columns in the column selection dialog.  Once imported, the default values for normalization are set as I expect and the data is interactive in the normal manner.

Here are some hints about how to provide a useful bug report:
   http://bruceravel.github.io/demeter/pods/bugs.pod.html
Please read it carefully.

If there is more to this conversation, please use the mailing list.

B


--
 Bruce Ravel  ------------------------------------ bravel-IGkKxAqZmp0@public.gmane.org

 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

From: ZHANG, Zhaoming [zzx-miignUODZJaXcs01VSc0Sw@public.gmane.org]
Sent: Thursday, April 02, 2015 1:00 AM
To: Ravel, Bruce
Subject: RE: [Ifeffit] Importing data with the new version of Athena [SEC=UNCLASSIFIED]

Hi Bruce,

                Sorry, I did have to specify column 4 as energy, 7 as Io and 8 as It. The new version of Athena does read the .dat file in, but the default values for normalization are way wrong, and it doesn’t work by manually change them either.

                I’m happy to send you screen shots if necessary. Thanks again for your help.

Zhaoming

 

From: Ravel, Bruce [mailto:bravel-IGkKxAqZmp0@public.gmane.org]
Sent: Thursday, 2 April 2015 12:43 PM
To: ZHANG, Zhaoming
Subject: RE: [Ifeffit] Importing data with the new version of Athena [SEC=UNCLASSIFIED]

 


Zhaoming,

I'm afraid I am sceptical of your story.  I have no trouble reading this file and I don't believe that any change I've made since 0.9.20 would have affected this.  Who knows, though.  I'll take a lok on a windows machine when I get into work tomorrow morning.

It's a rather awkward file.  The first column is an index, not energy.  That's one of my pet peeves -- just a ridiculous way to present the data and kind of mean-spirited to the user.  When something is measured in energy, the first column should be energy.

That means you have to explicitly select column 2 as the energy.  Column 2 appears to be in keV, so you need to explicitly set that in the column selection dialog.  Because column 1 was not the energy, Athena had no way of figuring that out.

I have no idea which columns have data in them.  7 and 8 look rather like I0 and It.  So you need to explicitly set your data columns, as well.

I've attached a screenshot of the column selection dialog with all those settings.

When data are presented as obfuscated as they are in this data file, it is not reasonable to expect that Athena will magically know how to disentangle everything without your help.  You have to be responsible for knowing which columns to combine to turn your raw data into mu(E).

B

 

--
 Bruce Ravel  ------------------------------------ bravel-IGkKxAqZmp0@public.gmane.org

 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

From: ZHANG, Zhaoming [zzx <at> ansto.gov.au]
Sent: Wednesday, April 01, 2015 7:34 PM
To: Ravel, Bruce
Subject: [Ifeffit] Importing data with the new version of Athena [SEC=UNCLASSIFIED]

Dear Bruce,

                I’ve encountered the same problem as Sander Bruun. My data were obtained from the Australian Synchrotron. In the past, I could read the .dat file (see attached example) directly into Athena. But it doesn’t work with the new version (0.9.20), and the beamline scientist doesn’t know why either.

                I would really appreciate if you could let me know what ‘fix’ we need! Thanks so much.

Warm regards,

Zhaoming

 

_______________________________________________
Ifeffit mailing list
Ifeffit@...
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Clark, Adam | 1 Apr 15:03 2015
Picon
Picon

Possible Error on 0.9.21

Hi

I have recently encountered an error in displaying the path geometry in the latest version of artemis,
0.9.21. When running feff and then selecting a path and viewing the geometry of this path an incorrect path
is shown. This does not occur when using the same feff.inp file on the older 0.9.20 version. The problem is
limited to the numbering and showing of the path geometry in the feff calculation window.  Attached is the
feff.inp, feff.txt files and a screenshot showing the produced feff.txt ‘show geometry for this path
window’ for a selected  <at>  O.1  <at>  path (instead showing the  <at>  Zn.1  <at>  path) and ‘atoms and feff’ window
showing the discrepancy in path numbering between the feff.txt file and feff window.

Thanks
Adam

Attachment (feff.inp): application/octet-stream, 8041 bytes
# TITLE corundum

# TITLE zinc oxide

# The central atom is denoted by this token:  <at> 

# Cluster size = 6.00 A, containing 76 atoms

# 109 paths were found within 6.000 A

# Forward scattering cutoff 20.00

# TITLE O Zn

# TITLE O Zn

# TITLE Schreyer Martin

# TITLE Simultaneous determination of several crystal structures from powder

# TITLE mixtures: the combination of powder X-ray diffraction band-target

# TITLE entropy minimization and Rietveld methods

# This paths.dat file was written by Demeter 0.9.21

# Distance fuzz = 0.030 A

# Angle fuzz = 3.00 degrees

# Rmultiplier = 1.00

# Suppressing eta: yes

# Ranking criterion = feff   --   feff's curved wave amplitude ratio

# Post criterion = 3.00

# ----------------------------------------------------------------------

#  Abs   Z=30 Rmt= 1.102 Rnm= 1.410 

#  Pot 1 Z=30 Rmt= 1.089 Rnm= 1.374

#  Pot 2 Z= 8 Rmt= 0.885 Rnm= 1.121

#  Gam_ch=1.936E+00 

#  Mu=-2.610E+00 kf=2.082E+00 Vint=-1.913E+01 Rs_int= 1.742

# ----------------------------------------------------------------------

#       degen     Reff       scattering path                      I    Rank  legs   type

 0002   4.000    1.977  ---   <at>  O.1     <at>                            2  100.00  2  single scattering

 0003   6.000    3.208  ---   <at>  Zn.1    <at>                            2   46.42  2  single scattering

 0004   1.000    3.233  ---   <at>  O.3     <at>                            1    7.50  2  single scattering

 0005   6.000    3.249  ---   <at>  Zn.2    <at>                            2   45.05  2  single scattering

 0006  24.000    3.592  ---   <at>  O.2    Zn.1    <at>                     2   26.62  3  other double scattering

 0007  12.000    3.592  ---   <at>  O.1    O.2     <at>                     1   12.37  3  other double scattering

 0008   9.000    3.802  ---   <at>  O.4     <at>                            2   43.85  2  single scattering

 0009   4.000    3.955  ---   <at>  O.1           O.1     <at>              0    5.32  4  rattle

 0010  12.000    3.955  ---   <at>  O.2    Zn.1   O.2     <at>              0    4.93  4  dog-leg

 0011  12.000    3.955  ---   <at>  O.1           O.2     <at>              0    2.19  4  hinge

 0012   6.000    4.210  ---   <at>  O.2    Zn.1    <at>                     0    1.38  3  other double scattering

 0013   6.000    4.210  ---   <at>  O.2    O.3     <at>                     0    3.28  3  other double scattering

 0014   6.000    4.210  ---   <at>  Zn.1   O.3     <at>                     0    2.17  3  other double scattering

 0015  36.000    4.508  ---   <at>  O.2    Zn.1    <at>                     0    5.25  3  other double scattering

 0016  36.000    4.508  ---   <at>  O.2    O.4     <at>                     2   18.17  3  other double scattering

 0017  36.000    4.508  ---   <at>  Zn.1   O.4     <at>                     1   14.03  3  other double scattering

 0018   6.000    4.566  ---   <at>  Zn.3    <at>                            2   19.09  2  single scattering

 0019   6.000    4.582  ---   <at>  O.1    Zn.1   O.2     <at>              0    0.30  4  other triple scattering

 0020   6.000    4.582  ---   <at>  O.2    Zn.1   O.3     <at>              0    0.50  4  other triple scattering

 0021   6.000    4.583  ---   <at>  O.6     <at>                            2   17.41  2  single scattering

 0022  36.000    4.833  ---   <at>  Zn.1   Zn.1    <at>                     0    3.42  3  acute triangle

 0023  12.000    4.874  ---   <at>  Zn.2   Zn.2    <at>                     0    1.14  3  acute triangle

 0024  12.000    4.885  ---   <at>  O.2    Zn.1    <at>                     0    3.95  3  obtuse triangle

 0025  12.000    4.885  ---   <at>  O.2    O.6     <at>                     1    9.52  3  obtuse triangle

 0026  12.000    4.885  ---   <at>  Zn.1   O.6     <at>                     0    4.52  3  obtuse triangle

 0027   3.000    4.945  ---   <at>  O.7     <at>                            0    7.00  2  single scattering

 0028   6.000    5.003  ---   <at>  O.8     <at>                            1   13.53  2  single scattering

 0029   6.000    5.063  ---   <at>  O.1    Zn.1    <at>                     0    3.44  3  obtuse triangle

 0030   6.000    5.063  ---   <at>  O.1    O.7     <at>                     1    8.50  3  obtuse triangle

 0031   6.000    5.063  ---   <at>  Zn.1   O.7     <at>                     0    2.94  3  obtuse triangle

 0032  12.000    5.116  ---   <at>  O.2    Zn.2    <at>                     0    6.80  3  obtuse triangle

 0033  12.000    5.116  ---   <at>  O.2    O.8     <at>                     2   16.81  3  obtuse triangle

 0034  12.000    5.116  ---   <at>  Zn.2   O.8     <at>                     0    5.89  3  obtuse triangle

 0035  18.000    5.173  ---   <at>  O.5    Zn.3    <at>                     0    4.04  3  other double scattering

 0036  18.000    5.173  ---   <at>  O.1    Zn.3    <at>                     0    3.80  3  other double scattering

 0037  18.000    5.173  ---   <at>  O.1    O.5     <at>                     0    3.31  3  other double scattering

 0038   6.000    5.184  ---   <at>  Zn.1   O.2    Zn.1    <at>              0    0.59  4  dog-leg

 0039  12.000    5.184  ---   <at>  O.1           Zn.1    <at>              0    1.99  4  hinge

 0040   6.000    5.181  ---   <at>  O.1    O.7    Zn.1    <at>              0    1.75  4  obtuse triangle

 0041   6.000    5.181  ---   <at>  O.1    O.2    Zn.1    <at>              0    1.75  4  other triple scattering

 0042   6.000    5.181  ---   <at>  O.1           Zn.1    <at>              0    0.53  4  hinge

 0043   3.000    5.181  ---   <at>  O.1    O.7    O.1     <at>              0    3.40  4  dog-leg

 0044   3.000    5.181  ---   <at>  Zn.1   O.7    Zn.1    <at>              0    0.33  4  dog-leg

 0045   6.000    5.184  ---   <at>  O.1    O.2    O.1     <at>              0    4.05  4  dog-leg

 0046   6.000    5.187  ---   <at>  Zn.1   O.4    Zn.1    <at>              0    0.53  4  dog-leg

 0047   6.000    5.187  ---   <at>  O.2           Zn.1    <at>              0    0.22  4  hinge

 0048   3.000    5.187  ---   <at>  O.2    O.3    O.2     <at>              0    0.53  4  dog-leg

 0049   3.000    5.187  ---   <at>  Zn.1   O.3    Zn.1    <at>              0    0.42  4  dog-leg

 0050  12.000    5.187  ---   <at>  O.2           Zn.1    <at>              0    0.60  4  hinge

 0051   6.000    5.187  ---   <at>  O.2    O.6    O.2     <at>              0    2.70  4  dog-leg

 0052   6.000    5.187  ---   <at>  Zn.1   O.6    Zn.1    <at>              0    0.38  4  dog-leg

 0053  12.000    5.187  ---   <at>  O.2           Zn.1    <at>              0    0.22  4  hinge

 0054   6.000    5.187  ---   <at>  O.2    O.4    O.2     <at>              0    0.80  4  dog-leg

 0055   2.000    5.206  ---   <at>  Zn.4    <at>                            0    4.46  2  single scattering

 0056   2.000    5.206  ---   <at>  O.1    O.3     <at>                     0    2.71  3  non-forward linear

 0057   4.000    5.206  ---   <at>  O.1    Zn.4    <at>                     1   10.04  3  forward scattering

 0058   2.000    5.206  ---   <at>  O.1           O.3     <at>              0    1.00  4  forward through absorber

 0059   2.000    5.206  ---   <at>  O.1    Zn.4   O.1     <at>              0    5.65  4  double forward scattering

 0060   6.000    5.212  ---   <at>  O.2           O.3     <at>              0    0.48  4  hinge

 0061   6.000    5.212  ---   <at>  O.2    Zn.1   O.2     <at>              0    0.59  4  dog-leg

 0062  24.000    5.225  ---   <at>  O.1           Zn.2    <at>              0    0.38  4  hinge

 0063  12.000    5.225  ---   <at>  O.1    O.4    O.1     <at>              0    1.55  4  dog-leg

 0064  12.000    5.225  ---   <at>  Zn.2   O.4    Zn.2    <at>              0    1.07  4  dog-leg

 0065  22.000    5.225  ---   <at>  O.1    O.4    Zn.2    <at>              0    0.30  4  other triple scattering

 0066  12.000    5.228  ---   <at>  O.2    O.8    Zn.2    <at>              0    3.58  4  obtuse triangle

 0067   6.000    5.228  ---   <at>  Zn.2   O.2    Zn.2    <at>              0    0.59  4  dog-leg

 0068  12.000    5.228  ---   <at>  O.2           Zn.2    <at>              0    1.97  4  hinge

 0069   6.000    5.228  ---   <at>  O.2    O.2    O.2     <at>              0    4.00  4  dog-leg

 0070   8.000    5.228  ---   <at>  O.2    O.2    Zn.2    <at>              0    2.31  4  other triple scattering

 0071   6.000    5.228  ---   <at>  Zn.2   O.8    Zn.2    <at>              0    0.68  4  dog-leg

 0072  12.000    5.228  ---   <at>  O.2           Zn.2    <at>              0    1.09  4  hinge

 0073   6.000    5.228  ---   <at>  O.2    O.8    O.2     <at>              0    6.77  4  dog-leg

 0074  48.000    5.417  ---   <at>  Zn.1   O.4     <at>                     0    3.66  3  acute triangle

 0075  24.000    5.417  ---   <at>  O.4    O.5     <at>                     0    4.40  3  acute triangle

 0076  24.000    5.512  ---   <at>  Zn.1   Zn.2    <at>                     0    1.15  3  other double scattering

 0077  48.000    5.512  ---   <at>  Zn.1   Zn.3    <at>                     0    4.13  3  other double scattering

 0078  12.000    5.533  ---   <at>  O.3    Zn.2    <at>                     0    0.59  3  other double scattering

 0079  12.000    5.533  ---   <at>  O.3    O.6     <at>                     0    2.26  3  other double scattering

 0080  12.000    5.533  ---   <at>  Zn.2   O.6     <at>                     0    1.75  3  other double scattering

 0081  12.000    5.564  ---   <at>  O.2    O.6     <at>                     0    2.40  3  other double scattering

 0082  12.000    5.564  ---   <at>  O.2    Zn.3    <at>                     0    1.21  3  other double scattering

 0083  12.000    5.564  ---   <at>  Zn.3   O.6     <at>                     0    1.63  3  other double scattering

 0084  18.000    5.612  ---   <at>  Zn.5    <at>                            2   32.54  2  single scattering

 0085  18.000    5.697  ---   <at>  O.4    Zn.5    <at>                     1   13.21  3  obtuse triangle

 0086  18.000    5.697  ---   <at>  O.2    Zn.5    <at>                     2   15.26  3  obtuse triangle

 0087  18.000    5.697  ---   <at>  O.2    O.4     <at>                     1   13.85  3  obtuse triangle

 0088  36.000    5.779  ---   <at>  O.1           O.4     <at>              0    3.90  4  hinge

 0089  36.000    5.779  ---   <at>  O.1    Zn.2   O.1     <at>              0    3.57  4  dog-leg

 0090  18.000    5.779  ---   <at>  O.5    Zn.3   O.5     <at>              0    1.36  4  dog-leg

 0091  18.000    5.779  ---   <at>  O.1           O.5     <at>              0    0.45  4  hinge

 0092  18.000    5.781  ---   <at>  O.4    Zn.5   O.4     <at>              1    8.01  4  dog-leg

 0093  18.000    5.781  ---   <at>  O.2           O.4     <at>              0    2.61  4  hinge

 0094   1.000    5.783  ---   <at>  O.2    Zn.2   O.5     <at>              0    0.03  4  other triple scattering

 0095   1.000    5.783  ---   <at>  O.5    Zn.2   O.2     <at>              0    0.03  4  other triple scattering

 0096  18.000    5.799  ---   <at>  Zn.1   O.6     <at>                     0    1.76  3  other double scattering

 0097  12.000    5.798  ---   <at>  O.5    O.6     <at>                     0    1.69  3  other double scattering

 0098  12.000    5.798  ---   <at>  Zn.1   O.5     <at>                     0    0.39  3  other double scattering

 0099   6.000    5.802  ---   <at>  O.3    O.5     <at>                     0    0.60  3  other double scattering

 0100   6.000    5.802  ---   <at>  O.5    Zn.3    <at>                     0    0.43  3  other double scattering

 0101   6.000    5.811  ---   <at>  Zn.1   Zn.1    <at>                     0    0.46  3  other double scattering

 0102   6.000    5.811  ---   <at>  Zn.1   O.2    Zn.1    <at>              0    0.51  4  other triple scattering

 0103  12.000    5.811  ---   <at>  Zn.1   Zn.4    <at>                     0    1.07  3  other double scattering

 0104   6.000    5.811  ---   <at>  O.1    O.2    O.3     <at>              0    1.18  4  other triple scattering

 0105  12.000    5.811  ---   <at>  O.1    Zn.4   Zn.1    <at>              0    1.18  4  other triple scattering

 0106   3.000    5.917  ---   <at>  O.9     <at>                            0    4.11  2  single scattering

 0107   6.000    5.964  ---   <at>  O.10    <at>                            1    8.02  2  single scattering

 0108  12.000    5.978  ---   <at>  Zn.1   O.7     <at>                     0    1.21  3  other double scattering

 0109  12.000    5.978  ---   <at>  Zn.1   O.4     <at>                     0    0.40  3  other double scattering

 0110  12.000    5.978  ---   <at>  O.4    O.7     <at>                     0    1.61  3  other double scattering

_______________________________________________
Ifeffit mailing list
Ifeffit@...
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
George Sterbinsky | 25 Mar 22:38 2015

Artemis on Yosemite

Hello,

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

Thanks,
George

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



_______________________________________________
Ifeffit mailing list
Ifeffit@...
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Johan Nilsson | 24 Mar 17:05 2015
Picon
Picon

Incomplete source tarballs for larch?

Dear all,

Today I helped a colleague install larch on OSX Yosemite but we ran into some problems using the source tarball from CARS (larch-0.9.24.tar.gz). It was a bit of a learning curve for me as a linux user but we managed to install the prerequisites (exept for epics) using macports and then ran the larch installer without noticing any warnings or errors. The problem after that was that we could not locate the larch binary. The source tarball does not include a 'bin' directory and some other things that are found in the github source so we went ahead and installed larch from the github source instead. After that we could locate the binery and start the interpreter. Did we make some mistake here or are there things missing in the source tarballs?

Best regards,
Johan Nilsson


_______________________________________________
Ifeffit mailing list
Ifeffit@...
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Rana, Jatinkumar Kantilal | 21 Mar 14:06 2015
Picon

Breaking down correlationships between parameters

Dear All,

I have stumbled upon a question regarding correlationships between various parameters in EXAFS fitting. As we know, the parameters S02*N and sigma2 are highly correlated (where N is the number of nearest neighbors).

I would like to determine the number of nearest neighbors for a series of sample subjected to some treatment. I can do this by simply setting S02 to a value for a given absorber (based on the literature or my own measurements of some reference compounds) and letting N and sigma2 vary in a fit. However, the problem is the physical process which changes the number of nearest neighbors, also introduces structural disorder in samples. Thus, I always get the values of N overestimated due to its correlationship with sigma2. 

I know of a method which can be used to breakdown the correlationship between S02 and sigma2 by setting a series of S02 values at different k-weights and refining the corresponding sigma2 as discussed in several literature. However, in this approach the explicit assumption is, S02 is the property of absorbing atoms and thus is independent of changes occurring inside the sample. In my case, however, both sigma2 and N vary with changes inside samples. Is there any way to break this correlationship ?

I look forward to your valuable suggestions and comments.

Best regards,
Jatin






Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de
_______________________________________________
Ifeffit mailing list
Ifeffit@...
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Gmane