Re: [Ifeffit] Matthew Marcus Ifeffit Digest, Vol 137, Issue 5

To: Matthew Marcus Hi Matthew, would you be able to send me the executable file and manual for PCA? My spectra files are in .dat form . Thanks and kind regards. Teck Kwang Choo PhD Candidate Department of Chemical Engineering Room 225, Building 36 Monash University Mobile No.: 04-11489904 On 3 July 2014 16:19, Teck Kwang Choo wrote:

Thanks everyone for the suggestions! I will give Six pack a go first since I have that software. If that doesn't work, I'll send another message.

I wish you all a pleasant day.

Teck Kwang Choo PhD Candidate Department of Chemical Engineering Room 225, Building 36 Monash University Mobile No.: 04-11489904

On 3 July 2014 01:33, wrote:

...

Send Ifeffit mailing list submissions to ifeffit@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@millenia.cars.aps.anl.gov

You can reach the person managing the list at ifeffit-owner@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: Principal Component Analysis (PCA) for XANES (fred.mosselmans@diamond.ac.uk) 2. Re: Principal Component Analysis (PCA) for XANES (Matthew Marcus) 3. Re: Ifeffit Digest, Vol 137, Issue 4 (Abhijeet Gaur)

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

Message: 1 Date: Wed, 2 Jul 2014 07:48:29 +0000 From: To: Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES Message-ID: < CF65047C5B0562499EAFF9FBBC542D64757859A1@EXCHMBX01.fed.cclrc.ac.uk> Content-Type: text/plain; charset="us-ascii"

Dear Teck,

ITFA does transformation factor analysis as well, if you just want to do PCA, the PCA module in Sam Webb's sixpack is quite intuitive to use. https://home.comcast.net/~sam_webb/sixpack.html

cheers Fred

-- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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

Message: 2 Date: Wed, 02 Jul 2014 08:33:25 -0700 From: Matthew Marcus To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES Message-ID: <53B42645.5040005@lbl.gov> Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Athena (IFEFFIT package) does it. So does the ALS Beamline 10.3.2 software package at https://sites.google.com/a/lbl.gov/microxas-lbl-gov/software . If you can't get at it there, I can send the executable and manual. mam

On 7/1/2014 10:59 PM, Teck Kwang Choo wrote:

...

Hi Everyone,

Does anyone know what software I should use to perform a Principal Component Analysis (PCA) on my K-edge XANES spectra (for sulfur)? The reason I need to use this technique is because I have a couple of reference compound spectra but am not sure which of those I should use to fit my unknown sample spectrum.

Any help is appreciated.

Thanks and kind regards.

Teck Kwang Choo PhD Candidate Department of Chemical Engineering Room 225, Building 36 Monash University Mobile No.: 04-11489904

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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

Message: 3 Date: Wed, 2 Jul 2014 21:03:17 +0530 From: Abhijeet Gaur To: ifeffit Subject: Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 4 Message-ID: Content-Type: text/plain; charset="utf-8"

Hi Teck Kwang Choo,

For PCA analysis you can use SixPack data analysis package by Dr. Sam Webb available at https://home.comcast.net/~sam_webb/sixpack.html.

Also you can use Dmeter by Dr Bruce Ravel available at http://bruceravel.github.io/demeter/.

With best wishes

Dr Abhijeet Gaur

On Wed, Jul 2, 2014 at 12:52 PM, < ifeffit-request@millenia.cars.aps.anl.gov> wrote:

...

Send Ifeffit mailing list submissions to ifeffit@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@millenia.cars.aps.anl.gov

You can reach the person managing the list at ifeffit-owner@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. spam on our mailing list (Bruce Ravel) 2. Re: to use scattering path in different model or to construct a new model which is the combination of different simple compound (Bruce Ravel) 3. Principal Component Analysis (PCA) for XANES (Teck Kwang Choo) 4. Re: Principal Component Analysis (PCA) for XANES (Amayri, Dr. Samer)

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

Message: 1 Date: Tue, 01 Jul 2014 13:31:59 -0400 From: Bruce Ravel To: XAFS Analysis using Ifeffit Subject: [Ifeffit] spam on our mailing list Message-ID: <53B2F08F.7000401@bnl.gov> Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi all,

Over the years we've done a pretty good job of keeping spam off this mailing list. As you saw, one slipped through this afternoon. Hopefully it was a one-time event and it will not be necessary to change the friendly nature of security on the list.

B

-- Bruce Ravel ------------------------------------ bravel@bnl.gov

National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973

Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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

Message: 2 Date: Tue, 01 Jul 2014 15:16:20 -0400 From: Bruce Ravel To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] to use scattering path in different model or to construct a new model which is the combination of different simple compound Message-ID: <53B30904.5030207@bnl.gov> Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 07/01/2014 10:43 AM, ZHAN Fei wrote:

...

1 In the example,multiplet scattering path comes from two model respectively,if use path from different model in different shell's fit,there is risk of ignore important multiple path across models.Should construct a cluster ,run feff to ensure?

I don't completely understand the question, but I'll give it a try.

In the example of Shelly's paper, she had a situation where she *couldn't* write a single feff.inp file. Her local environment was the average of all possible ways that the uranyl ion could bond to biomass. The uranyl binding disproportionated into a pH-dependent mixture of carboxyl, phosphoryl, and hydroxyl sites. There was simply no way to write a feff.inp file for that. So her solution was to run Feff more than once, picking and choosing paths that represented her best guess for modeling the average bonding environment.

I think what you are really getting at, though, is whether it was right for Shelly to use parts of Feff calculations on a crystals to model something else. If you were to read up on the theory used in Feff, you would find that the important thing is that the muffin tin radii of the scatterers get calculated reasonably. Unless Shelly had a reason to think that the interatomic distances in her biomass sample were VERY different than in the crystals she used to run Feff, then the scattering amplitudes and phase shifts were almost certainly computed quite well enough.

...

2 I have confusion of the relationship pf N between single path and multiple path,for example I think U-Oe-C U-Oe-Pshould be 1 2 respectively,instead 2 4 in paper.

I think Scott's explanation is correct. In real-space, multiple-scattering theory, both ways around a three-legged path have to be counted.

B

-- Bruce Ravel ------------------------------------ bravel@bnl.gov

National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973

Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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

Message: 3 Date: Wed, 2 Jul 2014 15:59:25 +1000 From: Teck Kwang Choo To: XAFS Analysis using Ifeffit Subject: [Ifeffit] Principal Component Analysis (PCA) for XANES Message-ID: < CAHXRQWDT2LvAsBVBuu7HmAg0oWCC9u8fKBChzDamyw14-uyJ_Q@mail.gmail.com> Content-Type: text/plain; charset="utf-8"

Hi Everyone,

Does anyone know what software I should use to perform a Principal Component Analysis (PCA) on my K-edge XANES spectra (for sulfur)? The reason I need to use this technique is because I have a couple of reference compound spectra but am not sure which of those I should use to fit my unknown sample spectrum.

Any help is appreciated.

Thanks and kind regards.

Teck Kwang Choo PhD Candidate Department of Chemical Engineering Room 225, Building 36 Monash University Mobile No.: 04-11489904