Re: [Ifeffit] synthesis of EXAFS via larch

[Katy Smith]

That's Fantastic.
Thanks for swift reply, Matt.
Best regards,
Kate

On 20 March 2018 at 18:35, Matt Newville  wrote:

> Hi Katy,
>
>
> On Tue, Mar 20, 2018 at 11:34 AM, Katy Smith 
> wrote:
>
>> I seem to be able to make some progress in using Larch, thanks to the
>> developers. I wish to produce a plot in R rather than k, what would be the
>> equivalent commands to ff2chi, path.k etc as per the
>> /examples/feffit/doc_feffdat3.lar?
>>
>
>
> The sum with `ff2chi` only sums in k-space.  But the output is ready to do
> a Fourier transform with `xftf` (short for "XAFS Fourier Transform
> Forward").  So, building on doc_feffdat3.lar,  you could do
>
># sum of paths (assumed to be defined already), writing chi(k) to
> "mysum":
>ff2chi([path1, path2, path3, path4, path5], group=mysum)
>
># now do an XAFS Fourier transform on that group to go from k to R
> space:
>xftf(mysum,   kweight=2,  kmin=3, kmax=15, window='kaiser', dk=4)
>
>   # plot of |chir(R)| for this sum
>   plot(mysum.r,  mysum.chir_mag, label='sum of paths', xlabel=r'$R
> \rm\,(\AA)$',ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$')
>
> We're working to release the next version of Larch very soon, which
> includes common xafs plotting commands so that the
> last line there could be written as "plot_chir(mysum, label='sum of
> paths')".
>
> --Matt
>
>
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Re: [Ifeffit] synthesis of EXAFS via larch

[Matt Newville]

Hi Katy,


On Tue, Mar 20, 2018 at 11:34 AM, Katy Smith  wrote:

> I seem to be able to make some progress in using Larch, thanks to the
> developers. I wish to produce a plot in R rather than k, what would be the
> equivalent commands to ff2chi, path.k etc as per the
> /examples/feffit/doc_feffdat3.lar?
>


The sum with `ff2chi` only sums in k-space.  But the output is ready to do
a Fourier transform with `xftf` (short for "XAFS Fourier Transform
Forward").  So, building on doc_feffdat3.lar,  you could do

   # sum of paths (assumed to be defined already), writing chi(k) to
"mysum":
   ff2chi([path1, path2, path3, path4, path5], group=mysum)

   # now do an XAFS Fourier transform on that group to go from k to R space:
   xftf(mysum,   kweight=2,  kmin=3, kmax=15, window='kaiser', dk=4)

  # plot of |chir(R)| for this sum
  plot(mysum.r,  mysum.chir_mag, label='sum of paths', xlabel=r'$R
\rm\,(\AA)$',ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$')

We're working to release the next version of Larch very soon, which
includes common xafs plotting commands so that the
last line there could be written as "plot_chir(mysum, label='sum of
paths')".

--Matt
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Re: [Ifeffit] synthesis of EXAFS via larch

[Katy Smith]

I seem to be able to make some progress in using Larch, thanks to the
developers. I wish to produce a plot in R rather than k, what would be the
equivalent commands to ff2chi, path.k etc as per the
/examples/feffit/doc_feffdat3.lar?

Thanks, K






On 19 March 2018 at 18:53, Matt Newville  wrote:

> Hi Katy,
>
> On Mon, Mar 19, 2018 at 12:39 PM, Katy Smith 
> wrote:
>
>> Dear Colleagues,
>>
>> I am aiming to use Larch to synthesise EXAFS spectra for metal oxides and
>> I wonder if that would be the right way. I can synthesise the paths in
>> Demeter/Artemis but I have no idea how to sum them in order to obtain a
>> single EXAFS spectrum. Hence, the interest in Larch hoping that it can do
>> what I am looking for.
>>
>>
> You might find the examples at
>   http://xraypy.github.io/xraylarch/xafs/feffpaths.html
>
> helpful.  In particular,
>   http://xraypy.github.io/xraylarch/xafs/feffpaths.html#
> example-adding-feff-files
>
> shows how to sum paths together.  The Artemis GUI can help you do this,
> but being able to do this at the scripting level (aka "the hard way") is
> really not that hard, and can give you much more power.
>
> --Matt Newville
>
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Re: [Ifeffit] synthesis of EXAFS via larch

[Jesús Eduardo Vega Castillo]

El lun., 19 de mar. de 2018 20:15, Katy Smith 
escribió:

> Thank you so much, Matt. These examples seems a good starting point, I'll
> try it soon.
> Best wishes, Kate
>
> On 19 March 2018 at 18:53, Matt Newville 
> wrote:
>
>> Hi Katy,
>>
>> On Mon, Mar 19, 2018 at 12:39 PM, Katy Smith 
>> wrote:
>>
>>> Dear Colleagues,
>>>
>>> I am aiming to use Larch to synthesise EXAFS spectra for metal oxides
>>> and I wonder if that would be the right way. I can synthesise the paths in
>>> Demeter/Artemis but I have no idea how to sum them in order to obtain a
>>> single EXAFS spectrum. Hence, the interest in Larch hoping that it can do
>>> what I am looking for.
>>>
>>>
>> You might find the examples at
>>   http://xraypy.github.io/xraylarch/xafs/feffpaths.html
>>
>> helpful.  In particular,
>>
>> http://xraypy.github.io/xraylarch/xafs/feffpaths.html#example-adding-feff-files
>>
>> shows how to sum paths together.  The Artemis GUI can help you do this,
>> but being able to do this at the scripting level (aka "the hard way") is
>> really not that hard, and can give you much more power.
>>
>> --Matt Newville
>>
>> ___
>> Ifeffit mailing list
>> Ifeffit@millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>>
>>
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Re: [Ifeffit] synthesis of EXAFS via larch

[Katy Smith]

Thank you so much, Matt. These examples seems a good starting point, I'll
try it soon.
Best wishes, Kate

On 19 March 2018 at 18:53, Matt Newville  wrote:

> Hi Katy,
>
> On Mon, Mar 19, 2018 at 12:39 PM, Katy Smith 
> wrote:
>
>> Dear Colleagues,
>>
>> I am aiming to use Larch to synthesise EXAFS spectra for metal oxides and
>> I wonder if that would be the right way. I can synthesise the paths in
>> Demeter/Artemis but I have no idea how to sum them in order to obtain a
>> single EXAFS spectrum. Hence, the interest in Larch hoping that it can do
>> what I am looking for.
>>
>>
> You might find the examples at
>   http://xraypy.github.io/xraylarch/xafs/feffpaths.html
>
> helpful.  In particular,
>   http://xraypy.github.io/xraylarch/xafs/feffpaths.html#
> example-adding-feff-files
>
> shows how to sum paths together.  The Artemis GUI can help you do this,
> but being able to do this at the scripting level (aka "the hard way") is
> really not that hard, and can give you much more power.
>
> --Matt Newville
>
> ___
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>
>
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Re: [Ifeffit] synthesis of EXAFS via larch

[Katy Smith]

Thanks Raul. I am familiar with the instructions in the Demeter video
series but there seems no option in Artemis that allows summing the paths
generated from atoms. I think Larch would be more capable than Artemis here.
Best regards, Kate

On 19 March 2018 at 17:49, Acevedo-Esteves, Raul  wrote:

> Hello
>
>
>
> I think this is what you are looking for, in Artemis:
>
>
>
> https://vimeo.com/8954845
>
>
>
>
>
> https://player.vimeo.com/video/8957754
>
>
>
>
>
> https://vimeo.com/channels/exafs/9469738
>
>
>
>
>
> https://player.vimeo.com/video/9473249
>
>
>
> https://vimeo.com/channels/exafs/9628956
>
>
>
>
>
> Regards,
>
>
>
> Raul Acevedo-Esteves, PhD
> Post-Doctoral Research Associate/ 8-ID (ISS) beamline
> NSLS-II, Bldg. 743 C08U
> Brookhaven National Laboratory
> Upton, NY 11973-5000
> 631 344 4181 <(631)%20344-4181>
>
> 787 940 4023 <(787)%20940-4023>
> racev...@bnl.gov
>
>
>
> *From: *Ifeffit  on behalf of
> Katy Smith 
> *Reply-To: *XAFS Analysis using Ifeffit  >
> *Date: *ADMonday, March 19, 2018 at 1:39 PM
> *To: *"ifeffit@millenia.cars.aps.anl.gov"  anl.gov>
> *Subject: *[Ifeffit] synthesis of EXAFS via larch
>
>
>
> Dear Colleagues,
>
>
>
> I am aiming to use Larch to synthesise EXAFS spectra for metal oxides and
> I wonder if that would be the right way. I can synthesise the paths in
> Demeter/Artemis but I have no idea how to sum them in order to obtain a
> single EXAFS spectrum. Hence, the interest in Larch hoping that it can do
> what I am looking for.
>
>
>
> Best regards,
>
> Kate
>
> ___
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>
>
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Re: [Ifeffit] synthesis of EXAFS via larch

[Matt Newville]

Hi Katy,

On Mon, Mar 19, 2018 at 12:39 PM, Katy Smith  wrote:

> Dear Colleagues,
>
> I am aiming to use Larch to synthesise EXAFS spectra for metal oxides and
> I wonder if that would be the right way. I can synthesise the paths in
> Demeter/Artemis but I have no idea how to sum them in order to obtain a
> single EXAFS spectrum. Hence, the interest in Larch hoping that it can do
> what I am looking for.
>
>
You might find the examples at
  http://xraypy.github.io/xraylarch/xafs/feffpaths.html

helpful.  In particular,

http://xraypy.github.io/xraylarch/xafs/feffpaths.html#example-adding-feff-files

shows how to sum paths together.  The Artemis GUI can help you do this, but
being able to do this at the scripting level (aka "the hard way") is really
not that hard, and can give you much more power.

--Matt Newville
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Re: [Ifeffit] synthesis of EXAFS via larch

[Acevedo-Esteves, Raul]

Hello

I think this is what you are looking for, in Artemis:

https://vimeo.com/8954845


https://player.vimeo.com/video/8957754


https://vimeo.com/channels/exafs/9469738


https://player.vimeo.com/video/9473249

https://vimeo.com/channels/exafs/9628956


Regards,

Raul Acevedo-Esteves, PhD
Post-Doctoral Research Associate/ 8-ID (ISS) beamline
NSLS-II, Bldg. 743 C08U
Brookhaven National Laboratory
Upton, NY 11973-5000
631 344 4181
787 940 4023
racev...@bnl.gov

From: Ifeffit  on behalf of Katy 
Smith 
Reply-To: XAFS Analysis using Ifeffit 
Date: ADMonday, March 19, 2018 at 1:39 PM
To: "ifeffit@millenia.cars.aps.anl.gov" 
Subject: [Ifeffit] synthesis of EXAFS via larch

Dear Colleagues,

I am aiming to use Larch to synthesise EXAFS spectra for metal oxides and I 
wonder if that would be the right way. I can synthesise the paths in 
Demeter/Artemis but I have no idea how to sum them in order to obtain a single 
EXAFS spectrum. Hence, the interest in Larch hoping that it can do what I am 
looking for.

Best regards,
Kate
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