Running FEFF 8 in Artemis

Farideh Jalilehvand

13 Sep 2019 13 Sep '19

4:44 p.m.

Hi everyone, I am trying to do EXAFS data analysis using Artemis and FEFF 8. To do so, I have followed these steps: 1. Changed FEFF executable file path 2. Changed Process from Demeter to FEFF8 FEFF 8.10 runs, but it does not generate paths that I can pick for fitting. The console shows that paths have been found, but does not write it. When I run FEFF outside the Artemis program, it does write the paths as the PRINT card in FEFF.inp file is set at (PRINT 1 1 1 3). So, greatly appreciate if you can help me finding a solution for this problem. Kind regards, Farideh ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Farideh Jalilehvand, Ph.D. Associate Professor, and Associate Head (Undergraduate) Department of Chemistry, University of Calgary 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada Tel: (403) 220-3855 / 220-5353│E-mail: faridehj@ucalgary.ca URL: http://www.chem.ucalgary.ca/research/groups/faridehj/

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Shelly Kelly

13 Sep 13 Sep

8:09 p.m.

Hi Ferideh: Please send us a copy of the FEFF page. The one that looks like this for you. You might try increasing the number on the 4th print card like this: Print 1 0 0 0 change to read Print 1 0 0 4 [image: image.png] On Fri, Sep 13, 2019 at 11:58 AM Farideh Jalilehvand wrote:

...

Hi everyone,

I am trying to do EXAFS data analysis using Artemis and FEFF 8.

To do so, I have followed these steps:

1. Changed FEFF executable file path 2. Changed Process from Demeter to FEFF8

FEFF 8.10 runs, but it does not generate paths that I can pick for fitting.

The console shows that paths have been found, but does not write it.

When I run FEFF outside the Artemis program, it does write the paths as the PRINT card in FEFF.inp file is set at (PRINT 1 1 1 3).

So, greatly appreciate if you can help me finding a solution for this problem.

Kind regards,

Farideh

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Farideh Jalilehvand, Ph.D.

Associate Professor, and Associate Head (Undergraduate)

Department of Chemistry, University of Calgary

2500 University Dr. NW, Calgary, AB T2N 1N4, Canada

Tel: (403) 220-3855 / 220-5353│E-mail: faridehj@ucalgary.ca

URL: http://www.chem.ucalgary.ca/research/groups/faridehj/

_______________________________________________ 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

Matthew Newville

8:26 p.m.

On Fri, Sep 13, 2019, 11:58 AM Farideh Jalilehvand wrote:

...

Hi everyone,

I am trying to do EXAFS data analysis using Artemis and FEFF 8.

To do so, I have followed these steps:

1. Changed FEFF executable file path 2. Changed Process from Demeter to FEFF8

FEFF 8.10 runs, but it does not generate paths that I can pick for fitting.

The console shows that paths have been found, but does not write it.

When I run FEFF outside the Artemis program, it does write the paths as the PRINT card in FEFF.inp file is set at (PRINT 1 1 1 3).

So, greatly appreciate if you can help me finding a solution for this problem.

I believe that feff8 wants 6 numbers in the control and print statements. I think you can just add some zeros there and it will probably work

...

Kind regards,

Farideh

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Farideh Jalilehvand, Ph.D.

Associate Professor, and Associate Head (Undergraduate)

Department of Chemistry, University of Calgary

2500 University Dr. NW, Calgary, AB T2N 1N4, Canada

Tel: (403) 220-3855 / 220-5353│E-mail: faridehj@ucalgary.ca

URL: http://www.chem.ucalgary.ca/research/groups/faridehj/

_______________________________________________ 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

José C. Conesa

14 Sep 14 Sep

6:51 a.m.

Hi, As far as I know, Artemis can only work with the format files produced by feff 6. I tried months ago to urge the Artemis authors to make it work with at least feff 8.5L (which is free for everyone to download), but this does not seem to have been fruitful. Regards, José C. Conesa El 13/09/2019 a las 18:44, Farideh Jalilehvand escribió:

...

Hi everyone,

I am trying to do EXAFS data analysis using Artemis and FEFF 8.

To do so, I have followed these steps:

1. Changed FEFF executable file path 2. Changed Process from Demeter to FEFF8

FEFF 8.10 runs, but it does not generate paths that I can pick for fitting.

The console shows that paths have been found, but does not write it.

When I run FEFF outside the Artemis program, it does write the paths as the PRINT card in FEFF.inp file is set at (PRINT 1 1 1 3).

So, greatly appreciate if you can help me finding a solution for this problem.

Kind regards,

Farideh

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Farideh Jalilehvand, Ph.D.

Associate Professor, and Associate Head (Undergraduate)

Department of Chemistry, University of Calgary

2500 University Dr. NW, Calgary, AB T2N 1N4, Canada

Tel: (403) 220-3855 / 220-5353│E-mail: faridehj@ucalgary.ca

URL: http://www.chem.ucalgary.ca/research/groups/faridehj/

_______________________________________________ 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

-- José C. Conesa Instituto de Catálisis y Petroleoquímica, CSIC Marie Curie 2, Cantoblanco 28049 Madrid, Spain Tel. (+34)915854766

Matt Newville

6:14 p.m.

Hi José, On Sat, Sep 14, 2019 at 1:51 AM José C. Conesa wrote:

...

Hi,

As far as I know, Artemis can only work with the format files produced by feff 6.

Artemis can definitely work with output of Feff8. Lots of people do this.

...

I tried months ago to urge the Artemis authors to make it work with at least feff 8.5L (which is free for everyone to download), but this does not seem to have been fruitful.

Feff85L (Feff8 for EXAFS) is included with Larch and the results can definitely be used with Artemis. What is the problem you were having? --Matt

José C. Conesa

6:53 p.m.

Dear Matt, I exchanged with you on this matter some messages in September 2017, and after that I exchanged also other messages with Bruce Ravel in December 2017 and January 2018. He told me that he was very busy with its new beamline and had no time to adapt Artemis so that it could use feff 8.5L. This was of course long ago. If Artemis can now use the output of feff 8.5L, I'm glad to know and will try it. I presume that it will be enough to tell Artemis the location of this feff code. On the other hand, I do not use normally Larch, although I know about it. Are there advantages in using Larch instead of Artemis? Thanks anyway for the clarification. Best wishes, José Carlos El 14/09/2019 a las 20:14, Matt Newville escribió:

...

Hi José,

On Sat, Sep 14, 2019 at 1:51 AM José C. Conesa mailto:jcconesa@icp.csic.es> wrote:

Hi,

As far as I know, Artemis can only work with the format files produced by feff 6.

Artemis can definitely work with output of Feff8. Lots of people do this.

I tried months ago to urge the Artemis authors to make it work with at least feff 8.5L (which is free for everyone to download), but this does not seem to have been fruitful.

Feff85L (Feff8 for EXAFS) is included with Larch and the results can definitely be used with Artemis.

What is the problem you were having?

--Matt

-- José C. Conesa Instituto de Catálisis y Petroleoquímica, CSIC Marie Curie 2, Cantoblanco 28049 Madrid, Spain Tel. (+34)915854766

Matt Newville

16 Sep 16 Sep

3:59 p.m.

Hi Jose, On Sat, Sep 14, 2019 at 1:53 PM José C. Conesa wrote:

...

Dear Matt,

I exchanged with you on this matter some messages in September 2017, and after that I exchanged also other messages with Bruce Ravel in December 2017 and January 2018. He told me that he was very busy with its new beamline and had no time to adapt Artemis so that it could use feff 8.5L. This was of course long ago. If Artemis can now use the output of feff 8.5L, I'm glad to know and will try it. I presume that it will be enough to tell Artemis the location of this feff code.

Artemis can use the *outputs* of Feff8: the feffnnnn.dat files are the same format as from Feff6. I think that what you were having trouble with was having Artemis run Feff8 for you. I do not believe that has changed, though I'm not entirely sure why that was not working. But you can run Feff8L outside of Artemis and then import the resulting path files.

...

On the other hand, I do not use normally Larch, although I know about it. Are there advantages in using Larch instead of Artemis?

Larch comes with Feff8l, which is sort of what you were asking about. Larch does not (yet?) have a GUI for running Feff or for fitting a sum of Feff paths to a set of EXAFS data. It does have Python functions to do all these steps so that you could write a simple script to perform a fit. Artemis can use Larch as its underlying EXAFS fitting engine. Artemis does not (yet?) do everything that Larch can do (fit in wavelet space, for example), but Larch does not (yet?) provide "fuzzy paths", and you would have to work those out in your own script. Hope that helps, --Matt

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Farideh Jalilehvand
José C. Conesa
Matt Newville
Matthew Newville
Shelly Kelly