On 08/29/2014 10:20 AM, huyanyun@physics.utoronto.ca wrote:

Hi Bruce,

Thank you for your help. Yes, it happens consistently to me, but sometimes I did the same thing and it won't happen. So I was confused.

I'm afraid I don't quite understand your answer. To be clear, if you: * make a fitting model * run one or more fits * re-run feff * save and close artemis the next time you open that project file, it is *guaranteed* to be broken. As I said, this is a shockingly obvious avenue for failure. Until I harden the program against this, the work-around is /never/ to re-run feff after running a fit. In fact, you should /never/ re-run feff after you have started dragging and dropping paths onto the data page. B

Best, Yanyun Quoting Bruce Ravel :

...

On 08/28/2014 07:51 PM, huyanyun@physics.utoronto.ca wrote:

...

I encountered a serious problem with saving an Artermis project on my windows 8 64bit desktop. When I am ready to finish my fitting work, I click to save the log file, and go to main window to choose -File-'save project as...', and then close Artemis. But when I reopen this saved project, the Path Page lost all information for each path, and the 'Include path' button has been surprisingly unchecked for all path. The GDS page have all information there. This happened to me several times, but it seems sometime the PathPage data is saved and sometime is not, although I think I was doing the exact something.

I attached one of my artemis project file and the most recent log file I saved before I close the program. Can anyone have a look and tell me what I did wrong? As my work is proceeding, this would be a very serious problem if I cannot save my 'hardwork'.

Yanyun,

I know what is causing the behavior your are observing, but I do not know how you got to this point. In short, the problem with your project file is that the mechanism that Artemis uses to path pages to paths from the feff caluclation has become completely unhinged. Even though each path is defined in a reasonable way (in the sense of having sensible math expressions for all the path parameters), every path fails to point correctly to the feff calculation.

I was able to reproduce this problem by re-running the Feff calculation then immediately saving the project file. Is this what happened?

This is a rather obvious avenue for failure. It's suprising to me that I've never thought of this before and that no one has ever before complained about that.

I think I may be able to recover your project file -- I'll take a look and let you know. 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://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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

-- 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://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

On 08/29/2014 10:40 AM, huyanyun@physics.utoronto.ca wrote:

Now I understand why it happens --I re-run the feff calculation after running a fit.

Why do you do that? I am not criticizing, I am trying to understand what you are trying to accomplish. As you can tell from my earlier comments, re-running the feff calculation is an action that surprises both me and Artemis, so I'd like to understand what you are aiming to do. 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://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

On 08/29/2014 11:12 AM, huyanyun@physics.utoronto.ca wrote:

I was trying to figure out the absorber's occupancy sites. As I tried one of the possible site I didn't get a good fit or it seems I am in the wrong track, I went back to change the atom's coordination in Feff.inp, assuming a displacement, then re-run feff and do fitting again.

As this would be problem, I will not do this again, instead, I will load more .cif files and run all Feff before I do fitting.

It was my intent that what you want should be done by populating the list of Feff calculations -- a separate Feff window for each time you run Feff. I am sorry for your frustration, it's hard for me to anticipate all the ways that Artemis -- a rather complicated program -- can be used. Attached is a project file containing only the most recent fit from the project file you sent. It loads and will run the fit to completion with a non-ridiculous result. That said, I had to make some assumptions about your intent in the fitting model, so you should examine the fit carefully. Hopefully it will help you recover at least some of your lost hard work. I should also say that producing the attached project file was time-consuming and tedious -- it's not a service that i want to provide. I am about to make a change to Artemis that will make it so you cannot rerun Feff once you begin building a fitting model. Hopefully that will, in the future, obviate the problem you and Matt report. For now, the work-around is to have the discipline not to re-run Feff. 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://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

On Aug 29, 2014 9:32 AM, "Bruce Ravel" wrote:

On 08/29/2014 10:20 AM, huyanyun@physics.utoronto.ca wrote:

...

Hi Bruce,

Thank you for your help. Yes, it happens consistently to me, but sometimes I did the same thing and it won't happen. So I was confused.

I'm afraid I don't quite understand your answer.

To be clear, if you:

* make a fitting model * run one or more fits * re-run feff * save and close artemis

the next time you open that project file, it is *guaranteed* to be broken.

I think this might explain random problems saving fits that I've seen but could never figure out how to reproduce well enough to submit a report. I'm pretty sure this happened to me during a recent "live demo" of Artemis. Great to hear that the problem is identified! --Matt

As I said, this is a shockingly obvious avenue for failure. Until I harden the program against this, the work-around is /never/ to re-run feff after running a fit. In fact, you should /never/ re-run feff after you have started dragging and dropping paths onto the data page.

B

...

Best, Yanyun Quoting Bruce Ravel :

...

On 08/28/2014 07:51 PM, huyanyun@physics.utoronto.ca wrote:

...

I encountered a serious problem with saving an Artermis project on my windows 8 64bit desktop. When I am ready to finish my fitting work, I click to save the log file, and go to main window to choose -File-'save project as...', and then close Artemis. But when I reopen this saved project, the Path Page lost all information for each path, and the 'Include path' button has been surprisingly unchecked for all path. The GDS page have all information there. This happened to me several times, but it seems sometime the PathPage data is saved and sometime is not, although I think I was doing the exact something.

I attached one of my artemis project file and the most recent log file

I

...

saved before I close the program. Can anyone have a look and tell me what I did wrong? As my work is proceeding, this would be a very serious problem if I cannot save my 'hardwork'.

Yanyun,

I know what is causing the behavior your are observing, but I do not know how you got to this point. In short, the problem with your project file is that the mechanism that Artemis uses to path pages to paths from the feff caluclation has become completely unhinged. Even though each path is defined in a reasonable way (in the sense of having sensible math expressions for all the path parameters), every path fails to point correctly to the feff calculation.

I was able to reproduce this problem by re-running the Feff calculation then immediately saving the project file. Is this what happened?

This is a rather obvious avenue for failure. It's suprising to me that I've never thought of this before and that no one has ever before complained about that.

I think I may be able to recover your project file -- I'll take a look and let you know. 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://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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

-- 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://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Dear All, Sorry for resurrecting this old thread but I've been experiencing a bug that produces very similar symptoms and that I guess may be related; but that won't be solved by Bruce's fix. Details are as follows: Software: Demeter 0.9.18.2 and 0.9.20 x64 (possibly earlier releases too) on Windows 8.1 x64 (I've never observed this bug on Windows versions before 8, but I've been using Windows 8 as my main OS for a while now so that may be coincidental) Steps to reproduce: I run a fitting project using quick first shell fits and save it. When I re-open the project around 80% of the time the problem occurs. Symptoms: When I re-open the project around 80-90% of the time one or more of the following occurs: - One of the quick shell paths completely loses all its information (including path information which isn't editable by the user, parameter info etc; see attached screenshot) - Parameter info for one or more paths is reset to the default (i.e. if I've named a path delrauau it's renamed dr_ag_au_1) - In the GDS window starting values for parameters that have a non-zero starting value are set to their previously guessed value, rather than the starting value I set (ie. If I set ss as 0.003 and during the fit it is guessed to be 0.001 when I reopen the project the starting value will be set to 0.001) and "restrain" parameters are changed to "guess". - Phase correct fitting boxes are unticked (sometimes in an "impossible fashion" where the "plot with phase correction" option is set but no paths have the "use path for phase corrected plotting" option set) Attachments: Noinfo.png - screenshot of Artemis when path info is lost Reset.png - screenshot of Artemis when parameter names are reset Dartemis.log - Artemis log file when opening a project that has this problem Artemis.fpj - Artemis project file that displays these symptoms. Please let me know if you need further info/files. Thanks, Ian Ps: OK, things got weird while preparing this bug report: The file in question stopped opening at all - Artemis loaded and went through loading fit x, x+1 etc., once it finished (not exactly sure what stage) it just closed. And then, after several attempts, started working again, as if by magic, before I'd saved a log file.... If I can figure out how to reproduce this I'll send more info... -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel Sent: 29 August 2014 21:59 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] save Artemis project and cannot find Path List information when reopen On 08/29/2014 12:30 PM, Matt Newville wrote:

I think this might explain random problems saving fits that I've seen but could never figure out how to reproduce well enough to submit a report. I'm pretty sure this happened to me during a recent "live demo" of Artemis.

Yikes! That's just swell....

Great to hear that the problem is identified!

I agree. I am grateful to Yanyun for reporting it and for bearing with me, as it took several emails for me to understand the problem. My solution, which I wrote this afternoon and which will be in the next release, was to disable the "Run Atoms" and "Run Feff" buttons the first time you drag and drop a path from the Feff calculation onto a data set. Another solution would be to preserve the results of previous Feff runs from the same Feff window. That is certainly possible, but certainly involves a lot more code than what I did this afternoon! Cheers, 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://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit