kakarla chandu | 22 May 03:42 2015
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Re: Ifeffit Digest, Vol 147, Issue 10

Dear all

I am Dr. Chandrasekhar working on experimental condensed matter physics in NSYSU-Taiwan. As a part of my research, I am carrying XAS experiments for some multiferoic and strongly correlated systems. This is very new topic for me. As a part of my research I am studying one system. In that particular system, I face a situation where Cu2+ ions surrounded by five oxygen ligand atoms in different ligand geometries. That is CuIO5 is in square pyramid and CuIIO5 in trigonal bipyramid. So I did the EXAFS spectrum now how can I analyze the data, since XAS is element specific the Cu element scan I got one spectrum but I don’t know whether it is coming from CuIO5 or CuIIO5. So if you have any suggestion please help me

Waiting for your reply.

 

With Regards

Dr. Chandu


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Today's Topics:

   1. Plucking issue in the deglitching (Shoaib Muhammad)


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

Message: 1
Date: Fri, 22 May 2015 10:31:23 +0900
From: "Shoaib Muhammad" <mshoaibce-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
To: "'XAFS Analysis using Ifeffit'"
        <ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org>
Subject: [Ifeffit] Plucking issue in the deglitching
Message-ID: <002b01d0942f$05b44b60$111ce220$ <at> gmail.com>
Content-Type: text/plain; charset="us-ascii"



Dear all,



I am using Demeter Athena 0.9.21 on Windows 8.1 x64. Recently I measured
some XAS data in which there are some glitches. Somehow pluck tool is
working very inaccurate for me during deglitching. I can't select the point
where I click, so I have to remove several points in order to get rid of one
point. I have attached a short screen cast video along with sample XAS
dataset in which I am trying to remove a point from pre-edge for demo
purpose.



I would be thankful if you could look into it.



Regards,

/Shoaib

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End of Ifeffit Digest, Vol 147, Issue 10
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Shoaib Muhammad | 22 May 03:31 2015
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Plucking issue in the deglitching

 

Dear all,

 

I am using Demeter Athena 0.9.21 on Windows 8.1 x64. Recently I measured some XAS data in which there are some glitches. Somehow pluck tool is working very inaccurate for me during deglitching. I can’t select the point where I click, so I have to remove several points in order to get rid of one point. I have attached a short screen cast video along with sample XAS dataset in which I am trying to remove a point from pre-edge for demo purpose.

 

I would be thankful if you could look into it.

 

Regards,

/Shoaib

Attachment (deglitching.avi): video/avi, 3469 KiB
Attachment (deglitching.prj): application/octet-stream, 14 KiB
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Jagadesh K Kesavan | 12 May 16:49 2015
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help

Hi
I have windows 8 (32 bit) operating system in my laptop.
I am not able to istall the six pack software, It is not working in my pc.
What is the problem? how could i resolve this problem?
Do i get the proper six pack software for windows 8 (32 bit)?
Kindly suggest me.

Looking for your reply.

Thank you.

With Best Regards,
-----------------------------
JAGADESH KOPULA KESAVAN
PhD Research Scholar
Material Science and Nanotechnology 
Department of Science
University of Rome 3
Via della Vasca Navale 84, 
00146, Rome, Italy.
Tel: 06/57337054
Mob: +39 3207769588

-----------------------------
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Lisa Bovenkamp | 11 May 20:06 2015

Re: Ca EXAFS with Ge220 or InSb111 (Lisa Bovenkamp)

Hello.

No, the resolution is fine. I can do XANES fine with InSb111. We use those for years.
Just had problems with EXAFS because for this long range the flux has to be more stable
from the crystals.

Lisa
Lisa Bovenkamp | 11 May 17:16 2015

Ca EXAFS with Ge220 or InSb111

Hello.
After having some troubles recording a good EXAFS spectrum with some old InSb111 crystals
I started wondering if it might be better to use Ge220 instead.
Anybody have some experience with that?

Lisa
Richard Mayes | 5 May 02:16 2015
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Re: Self absorption Correction

Farzana,

I'm copying the IFEFFIT mail list, they may have the information buried in the archives somewhere.

That link points to Grant Bunker's webpage containing his XAFS tutorials and it will not open for me at the moment either. However, there are several very good books that have come out lately on XAFS that explain self absorption quite well.  If you're not interested in getting a copy of the books, there is a discussion thread from when I was a newbie to overabsorption that is found on the XAFS.org tutorials page.  I suggest going through it as several contributed substantial knowledge in that thread (http://www.xafs.org/Experiment/OverAbsorption). 

Cheers, 
-Rich

On Mon, May 4, 2015 at 7:47 PM, Farzana Nasreen <farzana6109-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Dear Rich,


I was looking at this above link to find out similar information that Jen had. Unfortunately, I couldn't open the link in the reply that you gave to her.
Do you know where I can download this paper by 
http://gbxafs.iit.edu/training/Self_Absorption_effects.pdfI am working on some PFY-XAS data on some uranium compounds.ThanksFarzana




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Shoaib Muhammad | 3 May 09:02 2015
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Scatter Plot in Athena

Dear All,

 

In Athena documentation section I can see data plotted as scatter instead of line type plot (for example the plot shown in the attached file). This feature seems to be helpful in deglitching the bad data points but I could not figure out how to do it! Can anybody guide me how to plot data as scatter in Athena? My platform is Windows8 x64.

 

Thanks,

/Shoaib

 

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ebonturim | 30 Apr 01:59 2015
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Demeter Package for mac

Hi everyone!

I would like to know if the Demeter Package is already working into the mac (2015). Someone could use it? How do install the right way files?
Thank you.

Everton Bonturim
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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
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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
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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
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Gmane