Re: [Ifeffit] SO2 for samples with non-planar geometry

[Joel Brugger]

Thanks Rob.,

Good thought, but definitively Cu++; we get the right energy shift and the 
right shape for XANES (linear Cu+ is very distinctive). We actually maintain 
nice oxidising conditions (4 bar of air applied to the capillary), and the 
spectra were stable over time (slew scan mode, with ~5 minutes per scan, and 10 
scans collected). 

Note that Cu+ is not stable in solution unless you give it a ligand such as 
chloride; reduction to Cu+ in our solution most likely would result in 
precipitation of Cu(0) via disproportionation. No evidence for this at all.


> On 22 Apr 2023, at 12:14 pm, Robert Gordon  wrote:
> 
> Hi Joel,
> 
> How much edge shift are you seeing between your foil and the solution?
> Cu+2 is about 4.5 eV up from Cu metal...you seeing about that much?
> 
> Cu+2 can photoreduce...I know Cu+(aq) isn't stable, but maybe some complex is 
> forming?
> Just a thought...CN=2 and I think linear Cu+
> 
> -R.
> 
> On 2023-04-21 6:58 p.m., Joel Brugger wrote:
>> Capillary is silica glass :-)
>> 
>>> On 22 Apr 2023, at 11:57 am, Anatoly Frenkel 
>>> mailto:anatoly.fren...@stonybrook.edu>> 
>>> wrote:
>>> 
>>> Capillary made or what?
>>> 
>>> Anatoly
>>> 
>>>> On Apr 21, 2023, at 9:52 PM, Joel Brugger >>> <mailto:joel.brug...@monash.edu>> wrote:
>>>> 
>>>>  Fluo, 0.5 wt% Cu.
>>>> 
>>>>> On 22 Apr 2023, at 11:41 am, Anatoly Frenkel 
>>>>> mailto:anatoly.fren...@stonybrook.edu>> 
>>>>> wrote:
>>>>> 
>>>>> Fluorescence or transmission?
>>>>> What is the Cu concentration? Could be self absorption. 
>>>>> 
>>>>> Anatoly
>>>>> 
>>>>>> On Apr 21, 2023, at 9:31 PM, Joel Brugger >>>>> <mailto:joel.brug...@monash.edu>> wrote:
>>>>>> 
>>>>>>  Dear list,
>>>>>> 
>>>>>> We are trying to fit EXAFS from data collected on solutions within a 
>>>>>> capillary. The capillary has OD 1mm, ID 0.8mm, and was placed 
>>>>>> horizontally. The beam is 1x2 mm (VxH).
>>>>>> 
>>>>>> Fitting the copper reference foil, we get the expected SO2 value of ~0.7.
>>>>>> 
>>>>>> However, the solution containing the Cu(II) aqua ion gives a 
>>>>>> coordination of 2, instead of the expected 5-6. So our SO2 for this 
>>>>>> solution is apparently ~0.25. 
>>>>>> 
>>>>>> I couldn’t find a discussion of the effect of geometry (in our case 
>>>>>> cylindrical rather than planar) on SO2. Is it possible that the low SO2 
>>>>>> is a result of the odd geometry?
>>>>>> 
>>>>>> Confused as ever,
>>>>>> 
>>>>>> JOEL
>>>>>> 
>>>>>> 
>>>>>> Joël Brugger
>>>>>> Professor of Synchrotron Geosciences
>>>>>> 
>>>>>> Monash University
>>>>>> School of Earth, Atmosphere and Environment 
>>>>>> Room 257A, Level 2, 9 Rainforest Walk 
>>>>>> Clayton, Victoria 3800 
>>>>>> Australia 
>>>>>> 
>>>>>> T: +61 3 9905 4898 
>>>>>> E: joel.brug...@monash.edu <mailto:andrew.mackint...@monash.edu> 
>>>>>> Twitter: @JoelBrugger
>>>>>> 
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Re: [Ifeffit] SO2 for samples with non-planar geometry

[Joel Brugger]

Capillary is silica glass :-)

> On 22 Apr 2023, at 11:57 am, Anatoly Frenkel  
> wrote:
> 
> Capillary made or what?
> 
> Anatoly
> 
>> On Apr 21, 2023, at 9:52 PM, Joel Brugger  wrote:
>> 
>> Fluo, 0.5 wt% Cu.
>> 
>>> On 22 Apr 2023, at 11:41 am, Anatoly Frenkel 
>>> mailto:anatoly.fren...@stonybrook.edu>> 
>>> wrote:
>>> 
>>> Fluorescence or transmission?
>>> What is the Cu concentration? Could be self absorption. 
>>> 
>>> Anatoly
>>> 
>>>> On Apr 21, 2023, at 9:31 PM, Joel Brugger >>> <mailto:joel.brug...@monash.edu>> wrote:
>>>> 
>>>> Dear list,
>>>> 
>>>> We are trying to fit EXAFS from data collected on solutions within a 
>>>> capillary. The capillary has OD 1mm, ID 0.8mm, and was placed 
>>>> horizontally. The beam is 1x2 mm (VxH).
>>>> 
>>>> Fitting the copper reference foil, we get the expected SO2 value of ~0.7.
>>>> 
>>>> However, the solution containing the Cu(II) aqua ion gives a coordination 
>>>> of 2, instead of the expected 5-6. So our SO2 for this solution is 
>>>> apparently ~0.25. 
>>>> 
>>>> I couldn’t find a discussion of the effect of geometry (in our case 
>>>> cylindrical rather than planar) on SO2. Is it possible that the low SO2 is 
>>>> a result of the odd geometry?
>>>> 
>>>> Confused as ever,
>>>> 
>>>> JOEL
>>>> 
>>>> 
>>>> Joël Brugger
>>>> Professor of Synchrotron Geosciences
>>>> 
>>>> Monash University
>>>> School of Earth, Atmosphere and Environment 
>>>> Room 257A, Level 2, 9 Rainforest Walk 
>>>> Clayton, Victoria 3800 
>>>> Australia 
>>>> 
>>>> T: +61 3 9905 4898 
>>>> E: joel.brug...@monash.edu <mailto:andrew.mackint...@monash.edu> 
>>>> Twitter: @JoelBrugger
>>>> 
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Re: [Ifeffit] SO2 for samples with non-planar geometry

[Joel Brugger]

Fluo, 0.5 wt% Cu.

> On 22 Apr 2023, at 11:41 am, Anatoly Frenkel  <mailto:anatoly.fren...@stonybrook.edu>> wrote:
> 
> Fluorescence or transmission?
> What is the Cu concentration? Could be self absorption. 
> 
> Anatoly
> 
>> On Apr 21, 2023, at 9:31 PM, Joel Brugger > <mailto:joel.brug...@monash.edu>> wrote:
>> 
>> Dear list,
>> 
>> We are trying to fit EXAFS from data collected on solutions within a 
>> capillary. The capillary has OD 1mm, ID 0.8mm, and was placed horizontally. 
>> The beam is 1x2 mm (VxH).
>> 
>> Fitting the copper reference foil, we get the expected SO2 value of ~0.7.
>> 
>> However, the solution containing the Cu(II) aqua ion gives a coordination of 
>> 2, instead of the expected 5-6. So our SO2 for this solution is apparently 
>> ~0.25. 
>> 
>> I couldn’t find a discussion of the effect of geometry (in our case 
>> cylindrical rather than planar) on SO2. Is it possible that the low SO2 is a 
>> result of the odd geometry?
>> 
>> Confused as ever,
>> 
>> JOEL
>> 
>> 
>> Joël Brugger
>> Professor of Synchrotron Geosciences
>> 
>> Monash University
>> School of Earth, Atmosphere and Environment 
>> Room 257A, Level 2, 9 Rainforest Walk 
>> Clayton, Victoria 3800 
>> Australia 
>> 
>> T: +61 3 9905 4898 
>> E: joel.brug...@monash.edu <mailto:andrew.mackint...@monash.edu> 
>> Twitter: @JoelBrugger
>> 
>> ___
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[Ifeffit] SO2 for samples with non-planar geometry

[Joel Brugger]

Dear list,

We are trying to fit EXAFS from data collected on solutions within a capillary. 
The capillary has OD 1mm, ID 0.8mm, and was placed horizontally. The beam is 
1x2 mm (VxH).

Fitting the copper reference foil, we get the expected SO2 value of ~0.7.

However, the solution containing the Cu(II) aqua ion gives a coordination of 2, 
instead of the expected 5-6. So our SO2 for this solution is apparently ~0.25. 

I couldn’t find a discussion of the effect of geometry (in our case cylindrical 
rather than planar) on SO2. Is it possible that the low SO2 is a result of the 
odd geometry?

Confused as ever,

JOEL


Joël Brugger
Professor of Synchrotron Geosciences

Monash University
School of Earth, Atmosphere and Environment 
Room 257A, Level 2, 9 Rainforest Walk 
Clayton, Victoria 3800 
Australia 

T: +61 3 9905 4898 
E: joel.brug...@monash.edu  
Twitter: @JoelBrugger



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[Ifeffit] using the mail list archive for mac install

[Joel Brugger SAM]

I ran into the problem that some people seem to have with Demeter on mac
while upgrading to High Sierra. I found a fix on this mail list, butŠ
1) I can¹t download Template.pm from the archive (bin file that uncompresses
to cpgz file that uncompresses back to a bin fileŠ)
2) Matt mentions that he installed 0.9.26 from macports, but I see only
0.9.25 (stable & develop).
Sorry for the trivial questions :-)
All the best, JOEL

[Ifeffit] install for mac error
Luke Higgins pmljrh at leeds.ac.uk

Tue Apr 3 12:47:31 CDT 2018

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Hi All,

I see this error too. This is a bit of a bodge job, but if you replace:

/opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm

With the attached template.pm from p5.24, it seems to work fine. I¹d just
rename the old Template.pm in the same directory, rather than deleting it ­
since another program may end up needing the most recent one.

Cheers,

Luke

From: Ifeffit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > on behalf of
Chris Patridge http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> >
Reply-To: XAFS Analysis using Ifeffit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> >
Date: Tuesday, 3 April 2018 at 19:22
To: XAFS Analysis using Ifeffit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> >
Subject: Re: [Ifeffit] install for mac error

Thank you for the input Matt. I am glad to hear that it is not ³user error².
I tried it again and I need to correct my earlier statement because Artemis
GUI will stay open after the warning however Athena closes/crashes.
I will try on a different system.

Thanks again,

Chris
Sent from my iPhone

On Apr 3, 2018, at 11:52 AM, Matt Newville http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>  >> wrote:
Hi Chris,

On Mon, Apr 2, 2018 at 4:15 PM, Christopher Patridge http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>
 >> wrote:
Hello everyone,

I tried to install demeter on my mac (running high Sierra) and it appeared
everything went well.  However when I run either Athena or Artemis I get an
error shown below about Demeter::Templates: showing a error and I am not
sure how I can correct this error.  Any help would be appreciated.

Thanks in advanced,

I can confirm this.  I just did a fresh install of Macports on 10.13.3 (high
sierra).  The MacPorts install was not super easy, but once it got to the
demeter install, that part went fine.
I see the same problem with athena from demeter 0.9.25. I think the warnings
about "Demeter::Templates::F" and so forth are meant to be warnings only --
I think they may not be related to the crash of athena.   For me, hephaestus
gives the same sort of warnings, but runs fine.
I can install and run Demeter 0.9.26 (including using Larch as a backend)
using Macports, though there are definitely some Mac-specific weirdness.
Anyway, I do not believe that "install from source" is a feasible approach
for demeter on OSX. I do not know enough about Macports to update the
existing package.  I don't know that using some other system would be an
improvement.

We keep seeing problems with demeter on OSX.   I'm not sure what the right
answer is.  Anyone have any suggestions?

--Matt
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