Running Feff -- In Artemis
Hi Feff guys, I'm sure you've answered this question before, but I was wondering about the error message "There are no FeffNNNN.dat files! Something has gone wrong with your feff calculation." I entered all the information into Atoms correctly and Atoms ran fine, but when I run Feff I get this message. Is there a directory that I have to place my Feff.INP file in to make this work? I can't figure it out. Thanks, Dan Carter
Hi Dan, I'll save Bruce the trouble and copy a recent response of his: At 6:49 PM -0400 8/3/04, Bruce Ravel wrote:
I don't understand this at all. As I have said many times before: it is unrealistic to expect me to be able to address any problem if you do not give me enough information to reproduce it on my own computer.
To refresh everyone's memory: http://leonardo.phys.washington.edu/~ravel/software/exafs/bugs.html
B
Artemis does not usually produce the error you describe, although I have seen it before. There are a multitude of possible causes. We have to have more information before we can narrow down what might be causing it. --Scott Calvin Sarah Lawrence College
Hi Feff guys,
I'm sure you've answered this question before, but I was wondering about the error message "There are no FeffNNNN.dat files! Something has gone wrong with your feff calculation." I entered all the information into Atoms correctly and Atoms ran fine, but when I run Feff I get this message. Is there a directory that I have to place my Feff.INP file in to make this work? I can't figure it out.
Thanks, Dan Carter
On Monday 09 August 2004 03:31 pm, dmc@pdx.edu wrote:
Hi Feff guys,
I'm sure you've answered this question before, but I was wondering about the error message "There are no FeffNNNN.dat files! Something has gone wrong with your feff calculation." I entered all the information into Atoms correctly and Atoms ran fine, but when I run Feff I get this message.
I often start a response to a posting like this by referring everyone to my bug report page. This time I will try another approach. Here is a link to a wonderful article entitled "How to Report Bugs Effectively" http://www.chiark.greenend.org.uk/~sgtatham/bugs.html In particular, note the first paragraph after the header "It doesn't work", the entire section under the heading "Show me how to show myself", and the list right before the summary. The whole point of having Atoms built into Artemis is so that you do not need to worry about the feff.inp file or, indeed, any of the other files from Feff. Artemis manages those files for you in a (hopefully) transparent manner. I would not have released artemis if I did not believe it would behave as I describe. There are many reasons why the problem you report may have happened. Sadly, I don't know which one it is since you have not yet been forthcoming with the information. 1. What version of Artemis are you using? Did you update to the new release when it was announced two weeks ago? 2. The run time messages from Feff are written in a window that is displayed during while feff is running. Is anything written in there that might indicate a problem? 3. Does this happen every time you try? If you try importing, say, the atoms.inp file for copper metal, does the same thing happen? If not, then perhaps there is some problem with the atoms information you entered. 4. Are you trying to use some version of feff other than the one that comes with Ifeffit? If so, does feff *ever* run correctly on your computer (either within artemis or outside)?
Is there a directory that I have to place my Feff.INP file in to make this work? I can't figure it out.
A statement like this would actually be useful to me if you referred to the passage in the artemis document (http://leonardo.phys.washington.edu/~ravel/software/exafs/doc/artemis.pdf) that is confusing to you and explained why that passage mislead you. 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 Dan,
I'm sure you've answered this question before, but I was wondering about the error message "There are no FeffNNNN.dat files! Something has gone wrong with your feff calculation." I entered all the information into Atoms correctly and Atoms ran fine, but when I run Feff I get this message. Is there a directory that I have to place my Feff.INP file in to make this work? I can't figure it out.
I don't read this as a bug report, or see why this question deserves a response about how to submit a bug report. The way I read this, you aren't claiming that "it doesn't work" but are asking for help figuring out what is supposed to happen. I also believe the question you're asking is actually not answered in the Artemis docs, but I could be wrong. Anyway, there is a directory where Artemis puts feff.inp and then tries to run it from, but you do _not_ have to put it there yourself. Artemis should put feff.inp in Artemis's "stash", the exact location depends on what computer system you're using. On windows, look in C:\Program Files\Ifeffit\horae\stash. On Unix, look in ~/.horae/stash. From there, look under 'artemis.project.N' (N=0,1,2, ...), and then in the folder 'dataJ.feffL' (J,L=0,1,2, ...). If you clear out old projects it might be easier to find, but sort-by-date will help too. As for why you're getting these messages: Artemis tries to run feff, then looks for feffNNNN.dat files in that folder. If it can't find any feffNNNN.dat files, it gives your "Something has gone wrong" message. Likely scenarios are: a) feff didn't run. There should have been progress messages from Feff written to an output screen. Did this happen? If so, what do the messages say? b) you don't have permissions to run feff, or to write in the directory. Does the stash directory get created, and is there a feff.inp file there? If so, you could try running feff6l on this file -- that could answer a lot of questions. c) feff ran and either died somewhere in the middle or never wrote any feffNNNN.dat files. That might have to do with strange input in feff.inp. Hope that's a start. Please let us know when you figure it out... --Matt
Hi, I apologize for being so peevish yesterday. Matt is correct that Dan asked a legitimate question and I offered a very snarky response. Someone just starting out with XAFS doesn't deserve that kind of attitude and should not be discouraged from posting to the mailing list. Dan, I apologize for the 'tude. Please don't let one day in which I was in a bad mood keep you from participating in the community on the mailing list. That said, this line: I entered all the information into Atoms correctly and Atoms ran fine, but when I run Feff I get this message. was the part that triggered my peevish response. Instead of being peevish, though, I should have explained how to better ask the question. Now, I still don't know what the problem was, so I'll use as an example another problem that exists in the current version of Artemis and about which there has been some discussion recently here on the list. There are situations where the potentials list contains atoms that are not in the atoms list and so Feff does not run to completion. One such material that readily triggers this problem is YBa2Cu3O7, the superconductor. Suppose a posting to the mailing list said "I entered the data for YBa2Cu3O7 correctly and atoms ran but then Feff did not run." It is very hard for me to know how to address that because I have run Atoms and Feff within Artemis hundreds of times without any problem. Without more information, I cannot offer good advice. Now consider a posting that says this: I entered the following data for YBa2Cu3O7 into the atoms page in Artemis 0.7.008 on my linux machine: title = YBCO: Y Ba2 Cu3 O7 space = P M M M a = 3.8230 b = 3.8860 c = 11.6810 core = cu1 rmax = 5.20 atoms ! elem x y z tag Y 0.50000 0.50000 0.50000 Ba 0.50000 0.50000 0.18400 Cu 0.00000 0.00000 0.00000 cu1 Cu 0.00000 0.00000 0.35600 cu2 O 0.00000 0.50000 0.00000 o1 O 0.00000 0.00000 0.15800 o2 O 0.00000 0.50000 0.37900 o3 O 0.50000 0.00000 0.37700 o4 Atoms ran to completion, and the feff.inp file looked ok, but when I ran Feff, I saw this written in the window where feff's runtime messages are written: Feff 6L.02 No atoms or overlap cards for unique pot 1 Cannot calculate potentials, etc. Fatal Error: at RDINP What is the meaning of this error and how can I fix it? Do you see how that is a much better explanation of the problem? Rather than asserting that the atoms data was correct, the atoms data used was cut and pasted into the email. That way, I can enter the exact same data into my running copy of Artemis and observe the problem myself. Then, the messages from Feff were transcribed into the email. While I admit that what Feff says is cryptic, I actually understand that message and would have recognized the problem for what it was. Also note that the improved explanation started by stating the version number of Artemis and the computer platform used. (The answer to the example problem: there is a bug in Atoms. The work-around is to increase Rmax in Atoms, then rerun Atoms and Feff.) There are some other places to look for useful clues as to the problem. You will notice that the window that displays the feff runtime messages also contains several other spaces arranged as note tabs. The one marked "Echo" shows every message that has been written to the echo area at the bottom of the main window. Sometimes a useful message gets written to the echo area but then something else comes along. Looking at the history of echo messages sometimes helps. The other space that is very useful is the one labeled "Ifeffit". That space records the most recent 2000 lines of communication between Artemis and Ifeffit. If Ifeffit has ever become confused by something Artemis asks it to do, it's response will be printed in blue text. By examining this text, you can actually uncover lots of clues about the inner workings of Artemis. Another useful bit of information, and one that speaks directly to Dan's original question, can be found in the "Theory" menu. Selecting "Identify this feff calculation" will write something like This Feff: data0.feff0 This project: /home/bruce/.horae/stash/artemis.project.2/ in the echo area. This identifies the space on your hard drive where artemis stores all the data and information from feff that it is using in the current project. It also identifies the current feff calculation with an identifier that is used both internally in the program and as the name of the folder in the project space containing the results of the atoms and feff runs. Thus the feff.inp file generated by atoms in this example would be found at: /home/bruce/.horae/stash/artemis.project.2/data0.feff0/feff.inp I could write up a thorough explanation of the project file format and the contents of its files if anyone is interested. HTH, 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/
participants (4)
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Bruce Ravel -
dmc＠pdx.edu -
Matt Newville -
Scott Calvin