How to use Artemis with feff85L
Hi, I should like to use feff85L within Artemis (from Demeter 0.9.25), just to check in my system whether selfconsistency has a role in unifying E0 values (with feff 6, allowing different E0 for each scatterer leads to E0 differences >10 eV, which seems too much to me). I find that after loading the EXAFS data (from Athena) and a model (a .cif file containing Cu, Ce and O atoms), if I click Run Atoms and then Run Feff with feff6 as executable I get the usual set of paths that allow me doing a fit of the data, but if I try to use the feff85L.exe that comes with the Demeter software (by changing the feff executable in the File/Edit preferences menu), after clicking the Run Feff button (without including the SCF card) a bit of computation happens and after finishing it the path list is empty. ¿Any idea of the possible reason why I get no path list? Thanks in advance -- José C. Conesa Instituto de Catálisis y Petroleoquímica, CSIC Marie Curie 2, Madrid, Spain www.icp.csic.es Tel. (+34)915854766
Hi Jose,
On Tue, Sep 12, 2017 at 11:54 AM, José Carlos Conesa
Hi,
I should like to use feff85L within Artemis (from Demeter 0.9.25), just to check in my system whether selfconsistency has a role in unifying E0 values (with feff 6, allowing different E0 for each scatterer leads to E0 differences >10 eV, which seems too much to me). I find that after loading the EXAFS data (from Athena) and a model (a .cif file containing Cu, Ce and O atoms), if I click Run Atoms and then Run Feff with feff6 as executable I get the usual set of paths that allow me doing a fit of the data, but if I try to use the feff85L.exe that comes with the Demeter software (by changing the feff executable in the File/Edit preferences menu), after clicking the Run Feff button (without including the SCF card) a bit of computation happens and after finishing it the path list is empty.
Does demeter come with a Feff85L executable? I think it may not. In fact, I just today added a standalone "feff8l" program to Larch and on a development branch of the feff85exafs code (wherein I am tring to improve the Python interface for "calculated an XAFS path on the fly"). But none of that is released yet. And it may have bugs, especially on Windows. So, it's great that you're interested in trying to run Feff8L. But I suspect that you may have to build it yourself, especially if you're hoping to run it on Windows. Then again, maybe Demeter does come with a working feff8l, and I just wasn't aware of it. --Matt
On 09/13/2017 09:35 PM, Matt Newville wrote:
Then again, maybe Demeter does come with a working feff8l, and I just wasn't aware of it.
Not yet. :( B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
Hi, Well, the information on this was somewhat confusing. Thus: 1-In the main Artemis window, after importing a .cif file to do a Feff calculation, the Atoms tab includes in the Export button the possibility of generating a .inp file with feff8 format; this is mentioned as well in the corresponding part of the Help documentation. Since no warning appears at that point about the impossibility of using that .inp file in Demeter, one would believe that such thing is indeed possible. For this reason, although indeed no feff8 executable comes with Demeter (my excuses for having assumed otherwise), I managed to obtain a feff85L.exe file and put it some time ago in the same Demeter directory as feff6.exe. Then I forgot that feff85L.exe did not come with Demeter. And when choosing the feff executable with the Edit preferences menu item, I thought that the mention there that feff8 was not yet supported was outdated. 2-In that same Help documentation, section 4.2 The Feff tab gives a link to the documentation of FEFF9. This gives the impression that the documentation is not very consistent. All this said, one can now only wish that a Demeter version allowing the use of feff8 is released some day. Thanks anyway for the clarifications. José Carlos El 14/09/2017 a las 5:08, Bruce Ravel escribió:
On 09/13/2017 09:35 PM, Matt Newville wrote:
Then again, maybe Demeter does come with a working feff8l, and I just wasn't aware of it.
Not yet. :( B
-- José C. Conesa Instituto de Catálisis y Petroleoquímica, CSIC Marie Curie 2, Cantoblanco 28049 Madrid, Spain Tel. (+34)915854766
Hi Jose,
On Thu, Sep 14, 2017 at 2:32 AM, José C. Conesa
Hi,
Well, the information on this was somewhat confusing. Thus:
1-In the main Artemis window, after importing a .cif file to do a Feff calculation, the Atoms tab includes in the Export button the possibility of generating a .inp file with feff8 format; this is mentioned as well in the corresponding part of the Help documentation. Since no warning appears at that point about the impossibility of using that .inp file in Demeter, one would believe that such thing is indeed possible.
It's long been the case that Artemis / Atoms can generate an input file for Feff8, even though Feff8 is not distrubuted with Demeter. There have been several discussions on this list over the past several years about how to use a version of Feff other than feff6l included in the distribution.
For this reason, although indeed no feff8 executable comes with Demeter (my excuses for having assumed otherwise), I managed to obtain a feff85L.exe file and put it some time ago in the same Demeter directory as feff6.exe.
If you have a working Feff8 executable, Artemis should be able to use it. But, I am not aware of a distribution of feff85L.exe for Windows. Bruce and I have been working on Feff85L for EXAFS, but there is not a single Windows executable in that work. Maybe someone else has produced such a thing.
Then I forgot that feff85L.exe did not come with Demeter. And when choosing the feff executable with the Edit preferences menu item, I thought that the mention there that feff8 was not yet supported was outdated.
Artemis has been able to use various versions of Feff8 for a very long time. It does not come with a version of Feff8, at least not yet. 2-In that same Help documentation, section 4.2 The Feff tab gives a link to
the documentation of FEFF9. This gives the impression that the documentation is not very consistent.
Feff9 is the latest version of Feff. Isn't it awesome that the Feff tab gives you a link to the Feff documention?
All this said, one can now only wish that a Demeter version allowing the use of feff8 is released some day.
Well, it's not exactly true that one can now only wish that Demeter allow use of Feff8. One can also work on it. These are open source projects, desparate for help, including things as simple as encouragement, testing, and giving complete and actionable error reports. If you expect someone else to give you a free, pre-packaged solution that works for you without effort, you might be waiting a very long time. --Matt
Hi Matt, Some comments (hopefully final): 1-A Windows version of feff85L (called FEFF8-Lite) is freely available, with some other codes, at http://leonardo.phys.washington.edu/feff/Bin-Source-feff8Lite/Bin-Source.htm... One can also find the feff85L.f source code in other places. 2-Being able to generate automatically with Artemis an input file for feff8 is of course convenient, even if one would have to enterby hand some keywords (e.g. SCF) to get the full functionality. I did this, added into Artemis the so modified feff.inp file and tried to run feff8 with that file. I found a message saying "You are running Feff8 with self-consistent potentials.It WILL be time consuming and all interaction with Artemis will be blocked until the Feff calculation is done. Currently Artemis does not provide real-time feedback, so you will have to be very patient." I would say that gives the impression that Feff8 can indeed be used within Artemis. Indeed you say "Artemis has been able to use various versions of Feff8 for a very long time". Is it still possible? 3-I do have (properly licensed) feff 9, and indeed have its documentation independently of Demeter. On the other hand, unless one has an illegal copy of feff 9 I do not see the usefulness of having that documentation without having a license. 4-Unfortunately I am not competent enough as programmer. I would not be able to contribute to make Artemis able to use feff8 calculations. If you have not time to devote to it, I fully understand it. Already what has been done in Demeter is a great work. All the best, José Carlos El 14/09/2017 a las 15:08, Matt Newville escribió:
Hi Jose,
On Thu, Sep 14, 2017 at 2:32 AM, José C. Conesa
mailto:jcconesa@icp.csic.es> wrote: Hi,
Well, the information on this was somewhat confusing. Thus:
1-In the main Artemis window, after importing a .cif file to do a Feff calculation, the Atoms tab includes in the Export button the possibility of generating a .inp file with feff8 format; this is mentioned as well in the corresponding part of the Help documentation. Since no warning appears at that point about the impossibility of using that .inp file in Demeter, one would believe that such thing is indeed possible.
It's long been the case that Artemis / Atoms can generate an input file for Feff8, even though Feff8 is not distrubuted with Demeter. There have been several discussions on this list over the past several years about how to use a version of Feff other than feff6l included in the distribution.
For this reason, although indeed no feff8 executable comes with Demeter (my excuses for having assumed otherwise), I managed to obtain a feff85L.exe file and put it some time ago in the same Demeter directory as feff6.exe.
If you have a working Feff8 executable, Artemis should be able to use it. But, I am not aware of a distribution of feff85L.exe for Windows. Bruce and I have been working on Feff85L for EXAFS, but there is not a single Windows executable in that work. Maybe someone else has produced such a thing.
Then I forgot that feff85L.exe did not come with Demeter. And when choosing the feff executable with the Edit preferences menu item, I thought that the mention there that feff8 was not yet supported was outdated.
Artemis has been able to use various versions of Feff8 for a very long time. It does not come with a version of Feff8, at least not yet.
2-In that same Help documentation, section 4.2 The Feff tab gives a link to the documentation of FEFF9. This gives the impression that the documentation is not very consistent.
Feff9 is the latest version of Feff. Isn't it awesome that the Feff tab gives you a link to the Feff documention?
All this said, one can now only wish that a Demeter version allowing the use of feff8 is released some day.
Well, it's not exactly true that one can now only wish that Demeter allow use of Feff8. One can also work on it. These are open source projects, desparate for help, including things as simple as encouragement, testing, and giving complete and actionable error reports. If you expect someone else to give you a free, pre-packaged solution that works for you without effort, you might be waiting a very long time.
--Matt
-- José C. Conesa Instituto de Catálisis y Petroleoquímica, CSIC Marie Curie 2, Cantoblanco 28049 Madrid, Spain Tel. (+34)915854766
Hi Jose,
On Thu, Sep 14, 2017 at 3:54 PM, José C. Conesa
Hi Matt,
Some comments (hopefully final):
1-A Windows version of feff85L (called FEFF8-Lite) is freely available, with some other codes, at
http://leonardo.phys.washington.edu/feff/Bin-Source- feff8Lite/Bin-Source.html
OK, thanks for the link. I was not aware that binaries were being distributed there. I would guess that they work, though I have not tried these myself.
One can also find the feff85L.f source code in other places.
2-Being able to generate automatically with Artemis an input file for feff8 is of course convenient, even if one would have to enter by hand some keywords (e.g. SCF) to get the full functionality. I did this, added into Artemis the so modified feff.inp file and tried to run feff8 with that file. I found a message saying "You are running Feff8 with self-consistent potentials.It WILL be time consuming and all interaction with Artemis will be blocked until the Feff calculation is done. Currently Artemis does not provide real-time feedback, so you will have to be very patient." I would say that gives the impression that Feff8 can indeed be used within Artemis. Indeed you say "Artemis has been able to use various versions of Feff8 for a very long time". Is it still possible?
Yes. Or, it should be. Perhaps this Feff85L.exe did run for you, but just not do everything you wanted?
3-I do have (properly licensed) feff 9, and indeed have its documentation independently of Demeter. On the other hand, unless one has an illegal copy of feff 9 I do not see the usefulness of having that documentation without having a license.
I don't know of anyone with an illegal copy of Feff9. I've only seen it run in classes, and do not have a copy myself. The fact that Artemis points to the on-line Feff documentation is very convenient. That this is for Feff9 and not Feff8 or other versions is not really in our control. Artemis comes with the latest version of Feff that it can.
4-Unfortunately I am not competent enough as programmer. I would not be able to contribute to make Artemis able to use feff8 calculations. If you have not time to devote to it, I fully understand it. Already what has been done in Demeter is a great work.
A great many people say the same thing. If that "many" becomes "everyone" you will not have to worry which version of Feff can be run by Artemis. --Matt
participants (4)
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Bruce Ravel
-
José C. Conesa
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José Carlos Conesa
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Matt Newville