Thanks to Bruce for releasing the new versions. He has been extremely responsive to dealing with
most of my bug reports and suggestions for change. The implementation of reading CIF files
directly into Artemis and Atoms makes going from crystal structures in a database to simulated
EXAFS patterns almost trivial. O.K. enough padding Bruce's ego...now for a question.
Artemis 0.7.010, with FEFF6L on WinXP machine:
What is the best way to deal with a crystalline compound in Artemis/FEFF that has 9 unique
elements? Attached is a CIF file containing a Au cluster that has nine different elements, which is
easily imported in to Artemis using Bruce's new import feature. When imported this compound has
~150 distinct atomic positions in the unit cell. Running FEFF within Artemis with this Atoms.inp
file results in the error message: "Feff 6L.02 Unique potential 8 not allowed. Must be between 0
and 7 8 15 P Fatal Error: at RDINP" It appears that FEFF can only handle 8 unique elements
at a time. No problem, I would like to ignore the H atoms anyway. Any suggestions on how to
handle this within Artemis/FEFF? Otherwise, there is the obvious workaround, I can manually edit
the CIF or Atoms.inp and eliminate the H atoms from one of those files and then run FEFF. It would be
helpful if the Atoms input page would allow the user to sort the atomic positions by element and then
select a range of these atomic positions and delete them all.
Thanks
Dave
ipot Z element
0 79 Au
1 7 N
2 6 C
3 5 B
4 9 F
5 8 O
6 1 H
7 79 Au
8 15 P
<
On Wednesday 01 September 2004 10:45 am, Barton, David (DG) wrote:
Thanks to Bruce for releasing the new versions. He has been extremely responsive to dealing with most of my bug reports and suggestions for change. The implementation of reading CIF files directly into Artemis and Atoms makes going from crystal structures in a database to simulated EXAFS patterns almost trivial. O.K. enough padding Bruce's ego...now for a question.
It's quite all right. You don't need to stop... ;-) I'm glad the CIF thing is making you happy.
Artemis 0.7.010, with FEFF6L on WinXP machine:
What is the best way to deal with a crystalline compound in Artemis/FEFF that has 9 unique elements?
<snip>
ipot Z element 0 79 Au 1 7 N 2 6 C 3 5 B 4 9 F 5 8 O 6 1 H 7 79 Au 8 15 P
My memory is that it is non-trivial to increase the number of unique potentials in Feff, but perhaps that's not the case. Perhaps it would be easy to recompile Feff to allow for more potantials. Removing the hydrogens is a good solution. Another thing that would probably work well would be to treat atoms whose Z numbers differ by one as the same. For instance, if there are only a few B atoms in your material, treat them all as carbon. In Feff6, which does not do the self-consistency loop, this should be a reasonable approximation. (It even may be in Feff8, for all I know.)
It would be helpful if the Atoms input page would allow the user to sort the atomic positions by element and then select a range of these atomic positions and delete them all.
I will be revamping the Atoms page in the development version of Artemis. The new format will make sorting easy. I'll put this suggestion on the list of things to do. Thanks for all your great feedback, Dave. You are making quite a positive impact on my software. B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Bruce, it would be nice to save, in a project file, also the fit that one has performed. Right now the project files I save do not contain the fit. Is this something to improve or is it me who does not use the program correctly? Ciao, Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"
Stefano, what I usually do before saving is to grab & set all values to the ones of the last fit. When you reload the project, pressing "fit" once just returns you the old graphs. But actually, I agree that it would be a nice idea to save the fit as well. Regards, Norbert On Thursday 02 September 2004 12:59, Stefano Ciurli wrote:
Bruce,
it would be nice to save, in a project file, also the fit that one has performed. Right now the project files I save do not contain the fit. Is this something to improve or is it me who does not use the program correctly? Ciao, Stefano
-- Dr. rer. nat. Norbert Weiher (weiher@chem.ethz.ch) Institute for Chemical and Bioengineering - ETH Hönggerberg HCI E 117 - 8093 Zürich - Phone: +41 1 63 3 48 32
On Thursday 02 September 2004 06:59 am, Stefano Ciurli wrote:
Bruce,
it would be nice to save, in a project file, also the fit that one has performed. Right now the project files I save do not contain the fit. Is this something to improve or is it me who does not use the program correctly?
Stefano, That is a splendid idea. In fact it is such a good idea that I have been working hard for the past three weeks on exactly that. Actually, my plan is a bit more ambitious. Artemis will save *every* fit you perform along with its log file and some other information into the project. Each fit will get its own entry in the list of data and paths -- that means that you will be able to plot several fits along with the data in order to see what effect each change has on the quality of fit. And since each log file is saved, you can do things like generate reports on the log files to see how the R-factor, chi-square, and guess parameters have evolved with every change in the fitting model. This is already available in a limited, buggy form in the new development code in the latest source tarball. I am hoping to transition these features into the stable version by the end of the year. Something to look foward to... B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Hello Bruce and Norbert, thanks a lot for your response! I feel less lonely.... :-)
That is a splendid idea. In fact it is such a good idea that I have been working hard for the past three weeks on exactly that.
:-))
Actually, my plan is a bit more ambitious. Artemis will save *every* fit you perform along with its log file and some other information into the project.
This is another question I have planned to ask and never got there: let's say that I want to try different inp files (different models) to fit a single spectrum in artemis. What I currently do is that for every fit I save a project, and after closing it, I reload the spectrum and another input file and redo the feff calculation and the fit and so on. In this way I am producing a project file for each fit tried. Of course I tried to work always in the same project, by loading the spectrum once and then loading several input files and for each running a feff calculation and a fit. However, I find that for each input file the program creates a set of amp, e0, delr and ss and calls these parameters with different names for each feff calculation (for example amp for feff0, amp_1 for feff1 etc). This coule be very nice indeed were it not for the fact that the program also keeps active the previous parameters, and I have all the times to skip them. If they are only four parameters, the time consumed is not an issue, but when I start having a larger number of paramers then it is quite annoying. Wouldn't it be better to set things so that everytime you load a new input file and a new feff calculation within the same project the previous parameters, used for the previously tried fit, were automatically skipped? Just a thought. If I have not been clear let me know I'll try to rephrase things.
Each fit will get its own entry in the list of data and paths -- that means that you will be able to plot several fits along with the data in order to see what effect each change has on the quality of fit.
This would be even greater than it is already (:-)) if the point above is taken into consideration. Unless again I do things in a non correct way, which is possible if not likely.
And since each log file is saved, you can do things like generate reports on the log files to see how the R-factor, chi-square, and guess parameters have evolved with every change in the fitting model.
This is already doable, but I guess things can be improved, as we previously discussed.
This is already available in a limited, buggy form in the new development code in the latest source tarball. I am hoping to transition these features into the stable version by the end of the year. Something to look foward to...
I do look forward to this! :-)) Ciao, Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"
On Friday 03 September 2004 12:36 pm, Stefano Ciurli wrote:
This is another question I have planned to ask and never got there: let's say that I want to try different inp files (different models) to fit a single spectrum in artemis. What I currently do is that for every fit I save a project, and after closing it, I reload the spectrum and another input file and redo the feff calculation and the fit and so on. In this way I am producing a project file for each fit tried. Of course I tried to work always in the same project, by loading the spectrum once and then loading several input files and for each running a feff calculation and a fit. However, I find that for each input file the program creates a set of amp, e0, delr and ss and calls these parameters with different names for each feff calculation (for example amp for feff0, amp_1 for feff1 etc). This coule be very nice indeed were it not for the fact that the program also keeps active the previous parameters, and I have all the times to skip them. If they are only four parameters, the time consumed is not an issue, but when I start having a larger number of paramers then it is quite annoying. Wouldn't it be better to set things so that everytime you load a new input file and a new feff calculation within the same project the previous parameters, used for the previously tried fit, were automatically skipped? Just a thought. If I have not been clear let me know I'll try to rephrase things.
Hi Stefano, I am not 100% sure I followed that, but I think one of my planned features in the current development branch will address this. I plan to be able to restore prior fitting models. This means that you can start a project, do some fits and have the results from those fits saved in the project. Then you can try something very different for a while and have those fitting results saved. Then, if you decide to abandon the second approach, you can click on one of the earlier fits, tell Artemis to restore that fitting model, and carry on from there. That will not completely alleviate the issue with parameter management that you mention, but it will make it possible to try a variety of fitting models within one project. And I have a few other bells and whistles planned... B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Hi Bruce, back from France...
I am not 100% sure I followed that, but I think one of my planned features in the current development branch will address this. I plan to be able to restore prior fitting models.
This means that you can start a project, do some fits and have the results from those fits saved in the project. Then you can try something very different for a while and have those fitting results saved. Then, if you decide to abandon the second approach, you can click on one of the earlier fits, tell Artemis to restore that fitting model, and carry on from there.
That will not completely alleviate the issue with parameter management that you mention, but it will make it possible to try a variety of fitting models within one project.
OK. Thanks! Parameter management could be a significant improvement (in addition to the many things you plan and magically realize!) Ciao, Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"
participants (4)
-
Barton, David (DG) -
Bruce Ravel -
Norbert Weiher -
Stefano Ciurli