[Ifeffit] Ifeffit Digest, Vol 67, Issue 12

Zajac, Dariusz dariusz.zajac at desy.de
Tue Sep 9 09:22:39 CDT 2008


Hi,
AFIK, in Athena it is not possible - you can do it quickly in other
programs, like excel, origin etc... and save/export it in the same
format you have in file
in Athena you can only choose E0
cheers
kicaj

>-----Original Message-----
>From: ifeffit-bounces at millenia.cars.aps.anl.gov 
>[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf 
>Of Khalid, Syed
>Sent: Tuesday, September 09, 2008 4:08 PM
>To: ifeffit at millenia.cars.aps.anl.gov
>Subject: Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 12
>
>
>That is correct: It is a QEXAFS scan of Ni foil as a 
>function of time.
> 
>Please see the data attached as a .txt file.
>The first column is time, second I0, and third It.
>I can plot this in Athena, time appears at energy axis.
>I can set the first derivative to 8333.0 eV ( changing X-axis 
>from time to energy ). If I have another known energy point of 
>Ni scan ( which is not a problem ) then I can convert the time 
>axis to correct energy axis and proceed with normal analysis.
>Is that possible?   
>
>-----Original Message-----
>From: ifeffit-bounces at millenia.cars.aps.anl.gov
>[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov]On Behalf Of 
>ifeffit-request at millenia.cars.aps.anl.gov
>Sent: Tuesday, September 09, 2008 9:23 AM
>To: ifeffit at millenia.cars.aps.anl.gov
>Subject: Ifeffit Digest, Vol 67, Issue 12
>
>
>Send Ifeffit mailing list submissions to
>	ifeffit at millenia.cars.aps.anl.gov
>
>To subscribe or unsubscribe via the World Wide Web, visit
>	http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>or, via email, send a message with subject or body 'help' to
>	ifeffit-request at millenia.cars.aps.anl.gov
>
>You can reach the person managing the list at
>	ifeffit-owner at 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: ODP:  enrgy-axis-expansion (Bruce Ravel)
>   2. Re: ODP: enrgy-axis-expansion (Matt Newville)
>   3. Re: Bugs in Athena under Windows (Matt Newville)
>   4. Noise level in XANES spectrum (Pushan Shah)
>   5. Re: ODP:  enrgy-axis-expansion (Zajac, Dariusz)
>   6. Re: Noise level in XANES spectrum (Zajac, Dariusz)
>   7. Re: Ifeffit Digest, Vol 67, Issue 11 (Khalid, Syed)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Mon, 8 Sep 2008 16:59:08 -0400
>From: Bruce Ravel <bravel at bnl.gov>
>Subject: Re: [Ifeffit] ODP:  enrgy-axis-expansion
>To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
>Message-ID: <200809081659.08948.bravel at bnl.gov>
>Content-Type: text/plain;  charset="utf-8"
>
>On Monday 08 September 2008 16:40:47 Zajac, Dariusz wrote:
>> I do not clearly understood what you mean. could you explain it more 
>> precisely? do you want to replace the x scale from energy to 
>time? if 
>> you want only set the edge energy use E0
>
>
>Apparently (and Khalid or Anatoly should correct me if I am 
>wrong), they are collecting data as a function of time in 
>quick scan mode.  They then have the problem of converting 
>time to energy.  If the mono speed is recorded somehow 
>incorrectly, then there is an accordian effect throughout the 
>data. I think that Khalid wants to be able to adjust this 
>accordian effect to correct the energy scale of teh data.
>
>B
>
>
>-- 
> Bruce Ravel  ------------------------------------ bravel at bnl.gov
>
> National Institute of Standards and Technology
> Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, 
>X23A2  Building 535A  Upton NY, 11973
>
> My homepage:    http://xafs.org/BruceRavel
> EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
>
>
>
>------------------------------
>
>Message: 2
>Date: Mon, 8 Sep 2008 16:18:55 -0500
>From: "Matt Newville" <newville at cars.uchicago.edu>
>Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion
>To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
>Message-ID:
>	<b8522e3d0809081418h564560d4n2fed4de0223e227 at mail.gmail.com>
>Content-Type: text/plain; charset=ISO-8859-1
>
>Hi Khalid,
>
>I agree with Dariusz: I do not understand the question.  I 
>have a hard time believing it is "the beamline cannot provide 
>data as a function of energy, can Athena do this for me 
>automatically?" (if it is, the
>answer is definitely 'No!').    Could you explain what you're trying
>to do?
>
>--Matt
>
>
>------------------------------
>
>Message: 3
>Date: Mon, 8 Sep 2008 16:24:45 -0500
>From: "Matt Newville" <newville at cars.uchicago.edu>
>Subject: Re: [Ifeffit] Bugs in Athena under Windows
>To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
>Message-ID:
>	<b8522e3d0809081424x5a6135dfk3aefb0e4a13c3bce at mail.gmail.com>
>Content-Type: text/plain; charset=ISO-8859-1
>
>Timna,
>
>Posting a project would definitely help here, as would clarify 
>"since the last two versions ..." to say explicitly which 
>versions do and do not work.  My suspicion is that this 
>related to the bug noted last week (and possibly another 
>recent vague report of "not working") that is due to the 
>latest version of athena -for-windows being hard-linked to 
>pre-final-release of the ifeffit dll which is making athena's 
>ifeffit session get stuck in an unresponsive state.
>
>I believe the only cure is a new version of athena.  Again, if 
>you could post a project that demonstrates the problem, that 
>would be most helpful.
>
>--Matt
>
>
>------------------------------
>
>Message: 4
>Date: Tue, 09 Sep 2008 15:48:51 +1000
>From: "Pushan Shah" <pshah at gse.mq.edu.au>
>Subject: [Ifeffit] Noise level in XANES spectrum
>To: <ifeffit at millenia.cars.aps.anl.gov>
>Message-ID: <48C69AE2.0BBD.0060.0 at gse.mq.edu.au>
>Content-Type: text/plain; charset=US-ASCII
>
>Hello Everyone,
>
>I have a general question regarding noise level of XANES 
>spectrum. I have collected XANES data for an element which is 
>present in ppm level in my samples.
>
>Some samples are exhibiting varying degree of noise in XANES 
>spectrum.  
>
>Is the noise level of XANES spectrum would be proportional or 
>consistent with the concentration of the sample? As XANES 
>spectra for some of my samples with relatively higher 
>concentration of this element are exhibiting greater level of 
>noise than those with relatively lower concentrations.   Will 
>sample matrix play any role in the noise level? 
>
>Thanks and I appreciate your help.
>
>regards,
>Pushan
>
>
>
>
>
>------------------------------
>
>Message: 5
>Date: Tue, 9 Sep 2008 10:03:46 +0200
>From: "Zajac, Dariusz" <dariusz.zajac at desy.de>
>Subject: Re: [Ifeffit] ODP:  enrgy-axis-expansion
>To: "Bruce Ravel" <bravel at bnl.gov>,	"XAFS Analysis using Ifeffit"
>	<ifeffit at millenia.cars.aps.anl.gov>
>Message-ID: <35E004AD6290A7438FCA34BBF325F4161148AA at ADXV2.win.desy.de>
>Content-Type: text/plain;	charset="us-ascii"
>
>hi
>so, I think, in case of converting time scale to energy - this 
>should be supported by beamline (beamline scientist) 
>somehow... if there is any nonlinearity of the converion 
>factor (Anatoly  - what whould happened if D parameter is 
>time/energy dependent?) I think only reference spectra can 
>help -  do you have it Syed? if you have all needed parameters 
>the calibration can be relatively quickly done in some other 
>programs, also in macro (for many files) but that's my 
>speculations kicaj
>
>>-----Original Message-----
>>From: ifeffit-bounces at millenia.cars.aps.anl.gov
>>[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf 
>>Of Bruce Ravel
>>Sent: Monday, September 08, 2008 10:59 PM
>>To: XAFS Analysis using Ifeffit
>>Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion
>>
>>
>>On Monday 08 September 2008 16:40:47 Zajac, Dariusz wrote:
>>> I do not clearly understood what you mean. could you explain it more
>>> precisely? do you want to replace the x scale from energy to 
>>time? if
>>> you want only set the edge energy use E0
>>
>>
>>Apparently (and Khalid or Anatoly should correct me if I am
>>wrong), they are collecting data as a function of time in 
>>quick scan mode.  They then have the problem of converting 
>>time to energy.  If the mono speed is recorded somehow 
>>incorrectly, then there is an accordian effect throughout the 
>>data. I think that Khalid wants to be able to adjust this 
>>accordian effect to correct the energy scale of teh data.
>>
>>B
>>
>>
>>--
>> Bruce Ravel  ------------------------------------ bravel at bnl.gov
>>
>> National Institute of Standards and Technology
>> Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A,
>>X23A2  Building 535A  Upton NY, 11973
>>
>> My homepage:    http://xafs.org/BruceRavel
>> EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
>>
>>_______________________________________________
>>Ifeffit mailing list
>>Ifeffit at millenia.cars.aps.anl.gov
>>http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>
>
>
>
>------------------------------
>
>Message: 6
>Date: Tue, 9 Sep 2008 10:12:42 +0200
>From: "Zajac, Dariusz" <dariusz.zajac at desy.de>
>Subject: Re: [Ifeffit] Noise level in XANES spectrum
>To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
>Message-ID: <35E004AD6290A7438FCA34BBF325F4161148AB at ADXV2.win.desy.de>
>Content-Type: text/plain;	charset="us-ascii"
>
>Hi Pushan,
>can you tell more about the experiment and the way of data collecting?
>how did you measure your samples? which method did you use? 
>what kind of
>samples do you have?
>the answer of your question is not stricted, but generaly I would say
>that the noise level should be independent of the samples, did you
>change something on the beamline or program between
>samples/measurements? e.g. sample time, no. of repeats, you moved in
>/out detector, amplification gain, etc....
>kicaj
>
>>-----Original Message-----
>>From: ifeffit-bounces at millenia.cars.aps.anl.gov 
>>[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf 
>>Of Pushan Shah
>>Sent: Tuesday, September 09, 2008 7:49 AM
>>To: ifeffit at millenia.cars.aps.anl.gov
>>Subject: [Ifeffit] Noise level in XANES spectrum
>>
>>
>>Hello Everyone,
>>
>>I have a general question regarding noise level of XANES 
>>spectrum. I have collected XANES data for an element which is 
>>present in ppm level in my samples.
>>
>>Some samples are exhibiting varying degree of noise in XANES 
>>spectrum.  
>>
>>Is the noise level of XANES spectrum would be proportional or 
>>consistent with the concentration of the sample? As XANES 
>>spectra for some of my samples with relatively higher 
>>concentration of this element are exhibiting greater level of 
>>noise than those with relatively lower concentrations.   Will 
>>sample matrix play any role in the noise level? 
>>
>>Thanks and I appreciate your help.
>>
>>regards,
>>Pushan
>>
>>
>>
>>_______________________________________________
>>Ifeffit mailing list
>>Ifeffit at millenia.cars.aps.anl.gov 
>>http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>
>
>
>
>------------------------------
>
>Message: 7
>Date: Tue, 9 Sep 2008 09:22:14 -0400
>From: "Khalid, Syed" <khalid at bnl.gov>
>Subject: Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 11
>To: <ifeffit at millenia.cars.aps.anl.gov>
>Message-ID:
>	<55C249AA18FE564E86564FEB2412D45BEFD18B at exchangemb1.bnl.gov>
>Content-Type: text/plain;	charset="iso-8859-1"
>
>Anatoly: I will try your approach:
>
>Same problem I can address in a different way.
>Suppose the energy is not linear in case of a Pt-L3 scan.
>We can set Pt-L3 edge at known 11564 eV. Scanning all the way to
>L2 edge and say we find it 200 eV off (exaggerating), can we set
>in Athena the L2 edge at known 13273 eV, while the L3 edge is still 
>at 11564 eV?
>
>-----Original Message-----
>From: ifeffit-bounces at millenia.cars.aps.anl.gov
>[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov]On Behalf Of
>ifeffit-request at millenia.cars.aps.anl.gov
>Sent: Monday, September 08, 2008 4:44 PM
>To: ifeffit at millenia.cars.aps.anl.gov
>Subject: Ifeffit Digest, Vol 67, Issue 11
>
>
>Send Ifeffit mailing list submissions to
>	ifeffit at millenia.cars.aps.anl.gov
>
>To subscribe or unsubscribe via the World Wide Web, visit
>	http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>or, via email, send a message with subject or body 'help' to
>	ifeffit-request at millenia.cars.aps.anl.gov
>
>You can reach the person managing the list at
>	ifeffit-owner at 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. FW: enrgy-axis-expansion (Khalid, Syed)
>   2. Re: enrgy-axis-expansion (Bruce Ravel)
>   3. Re: enrgy-axis-expansion (Anatoly Frenkel)
>   4. Re: enrgy-axis-expansion (Bruce Ravel)
>   5. ODP:  enrgy-axis-expansion (Zajac, Dariusz)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Mon, 8 Sep 2008 13:46:47 -0400
>From: "Khalid, Syed" <khalid at bnl.gov>
>Subject: [Ifeffit] FW: enrgy-axis-expansion
>To: <ifeffit at millenia.cars.aps.anl.gov>
>Message-ID:
>	<55C249AA18FE564E86564FEB2412D45BEFD187 at exchangemb1.bnl.gov>
>Content-Type: text/plain;	charset="iso-8859-1"
>
>
>
>-----Original Message-----
>From: Khalid, Syed 
>Sent: Monday, September 08, 2008 12:21 PM
>To: 'ifeffit at millenia.cars.aps.anl.gov'
>Subject: enrgy-axis-expansion
>
>It is X-axis, sorry my typo. How to expand or shrink
>in an EXAFS spectrum, using Athena.
> 
>
>Syed Khalid
>725D, National Synchrotron Light Source
>Brookhaven National Laboratory
>Upton, NY 11973
>
>Ph: 631-344-7496
>FAX: 631-344-3238
>e-mail: khalid at bnl.gov
>
>
>
>------------------------------
>
>Message: 2
>Date: Mon, 8 Sep 2008 13:51:12 -0400
>From: Bruce Ravel <bravel at bnl.gov>
>Subject: Re: [Ifeffit] enrgy-axis-expansion
>To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>Message-ID: <200809081351.12614.bravel at bnl.gov>
>Content-Type: text/plain;  charset="iso-8859-1"
>
>On Monday 08 September 2008 12:20:47 Khalid, Syed wrote:
>> Is it possible in Athena to change the y-axis (energy
>> scale) at two different energy points of an EXAFS scan?
>>
>> I have a Ni foil spectrum as a function of time.
>> The edge can be set at 8333.0 eV, and I want to
>> to assign higher energy to a known feature in the Ni scan.
>
>I am not 100% certain I understand the question, but I think the
>question is about the calibration dialog.  That is, you want to assign
>an energy shift, but not referenced to the edge energy position.
>
>Why can't you just set the energy shift by hand on Athena's main page?
>
>B
>
>
>
>
>-- 
> Bruce Ravel  ------------------------------------ bravel at bnl.gov
>
> National Institute of Standards and Technology
> Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
> Building 535A
> Upton NY, 11973
>
> My homepage:    http://xafs.org/BruceRavel
> EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
>
>
>
>------------------------------
>
>Message: 3
>Date: Mon, 8 Sep 2008 13:59:42 -0400
>From: "Anatoly Frenkel" <frenkel at bnl.gov>
>Subject: Re: [Ifeffit] enrgy-axis-expansion
>To: "'XAFS Analysis using Ifeffit'"
>	<ifeffit at millenia.cars.aps.anl.gov>
>Message-ID: <20080908175744.9B7E429C12 at fe6.prod.mis.yu.edu>
>Content-Type: text/plain; charset="us-ascii"
>
>Khalid, what you can do is to note how much the higher energy 
>(at energy E1)
>feature is shifted from what you think it should be (let's say 
>by the amount
>of D eV), provided that you fixed the lower energy point to 
>what you wanted
>(say, E0). Then, you should transfer the data into a 
>spreadsheet and apply
>linear scaling:
>
> 
>
>E --> E0 + (E-E0)*D
>
> 
>
>It will ensure that in the range between E0 and E1 the data 
>are linearly
>stretched or compressed, depending on the sign of D.
>
> 
>
>Anatoly
>
> 
>
>=
>
>  _____  
>
>From: Khalid, Syed [mailto:khalid at bnl.gov] 
>Sent: Monday, September 08, 2008 12:21 PM
>To: ifeffit at millenia.cars.aps.anl.gov
>Subject: [Ifeffit] enrgy-axis-expansion
>
> 
>
>Is it possible in Athena to change the y-axis (energy
>scale) at two different energy points of an EXAFS scan?
>
>I have a Ni foil spectrum as a function of time.
>The edge can be set at 8333.0 eV, and I want to
>to assign higher energy to a known feature in the Ni scan.
>
>
>Syed Khalid
>725D, National Synchrotron Light Source
>Brookhaven National Laboratory
>Upton, NY 11973
>
>Ph: 631-344-7496
>FAX: 631-344-3238
>e-mail: khalid at bnl.gov
>
>_______________________________________________
>Ifeffit mailing list
>Ifeffit at millenia.cars.aps.anl.gov
>http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
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>------------------------------
>
>Message: 4
>Date: Mon, 8 Sep 2008 14:13:37 -0400
>From: Bruce Ravel <bravel at bnl.gov>
>Subject: Re: [Ifeffit] enrgy-axis-expansion
>To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>Message-ID: <200809081413.37559.bravel at bnl.gov>
>Content-Type: text/plain;  charset="utf-8"
>
>
>
>On Monday 08 September 2008 14:03:05 Carlo Segre wrote:
>> It sounds to me like the question is a bit more complex than that.  I
>> believe that with their continuous scan electronics, they 
>get absorption
>> as a function of time, not energy.  If I am not mistaken, he 
>is asking to
>> have a conversion to energy built in somehow.
>
>>From this, I finally understand the question.
>
>Athena does not currently provide a mechanism for expanding the energy
>axis.  I could be convinced to code that up, but I would need a
>clearer statement of what you actually want done and several clear
>examples of how to process the data correctly.
>
>B
>
>
>
>
>On Monday 08 September 2008 13:59:42 Anatoly Frenkel wrote:
>> Khalid, what you can do is to note how much the higher 
>energy (at energy
>> E1) feature is shifted from what you think it should be 
>(let's say by the
>> amount of D eV), provided that you fixed the lower energy 
>point to what you
>> wanted (say, E0). Then, you should transfer the data into a 
>spreadsheet and
>> apply linear scaling:
>>
>>
>>
>> E --> E0 + (E-E0)*D
>>
>>
>>
>> It will ensure that in the range between E0 and E1 the data 
>are linearly
>> stretched or compressed, depending on the sign of D.
>>
>>
>>
>> Anatoly
>>
>>
>>
>> =
>>
>>   _____
>>
>> From: Khalid, Syed [mailto:khalid at bnl.gov]
>> Sent: Monday, September 08, 2008 12:21 PM
>> To: ifeffit at millenia.cars.aps.anl.gov
>> Subject: [Ifeffit] enrgy-axis-expansion
>>
>>
>>
>> Is it possible in Athena to change the y-axis (energy
>> scale) at two different energy points of an EXAFS scan?
>>
>> I have a Ni foil spectrum as a function of time.
>> The edge can be set at 8333.0 eV, and I want to
>> to assign higher energy to a known feature in the Ni scan.
>>
>>
>> Syed Khalid
>> 725D, National Synchrotron Light Source
>> Brookhaven National Laboratory
>> Upton, NY 11973
>>
>> Ph: 631-344-7496
>> FAX: 631-344-3238
>> e-mail: khalid at bnl.gov
>>
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
>
>-- 
> Bruce Ravel  ------------------------------------ bravel at bnl.gov
>
> National Institute of Standards and Technology
> Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
> Building 535A
> Upton NY, 11973
>
> My homepage:    http://xafs.org/BruceRavel
> EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
>
>
>
>
>------------------------------
>
>Message: 5
>Date: Mon, 8 Sep 2008 22:40:47 +0200
>From: "Zajac, Dariusz" <dariusz.zajac at desy.de>
>Subject: [Ifeffit] ODP:  enrgy-axis-expansion
>To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
>Message-ID: <35E004AD6290A7438FCA34BBF325F4160C56CB at ADXV2.win.desy.de>
>Content-Type: text/plain; charset="iso-8859-2"
>
>I do not clearly understood what you mean. could you explain 
>it more precisely? do you want to replace the x scale from 
>energy to time?
>if you want only set the edge energy use E0
>kicaj
>
>________________________________
>
>Od: ifeffit-bounces at millenia.cars.aps.anl.gov w imieniu Khalid, Syed
>Wys?ano: Pn 2008-09-08 18:20
>Do: ifeffit at millenia.cars.aps.anl.gov
>Temat: [Ifeffit] enrgy-axis-expansion
>
>
>
>Is it possible in Athena to change the y-axis (energy
>scale) at two different energy points of an EXAFS scan?
>
>I have a Ni foil spectrum as a function of time.
>The edge can be set at 8333.0 eV, and I want to
>to assign higher energy to a known feature in the Ni scan.
>
>
>Syed Khalid
>725D, National Synchrotron Light Source
>Brookhaven National Laboratory
>Upton, NY 11973
>
>Ph: 631-344-7496
>FAX: 631-344-3238
>e-mail: khalid at bnl.gov
>
>_______________________________________________
>Ifeffit mailing list
>Ifeffit at millenia.cars.aps.anl.gov
>http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
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End of Ifeffit Digest, Vol 67, Issue 11
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End of Ifeffit Digest, Vol 67, Issue 12
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