athena 0.8.030, artemis 0.7.008, hephaestus 0.04
Hi folks, A new tarball of the source for Athena, Artemis, and Hephaestus is now available at SourceForge and at my website. Linux, unix, and Mac OSX users can grab it or use the horae_update script at their leisure. Windows users will have to wait just a bit longer. Matt and I have almost settled on the new Windows release. More details should follow later this week. There are only a few new features in the codes this time around. The bulk of the changes are various bug fixes which should address the majority of the problems reported in the last two months. In particular, Artemis should now be a lot more stable. As always, please report any new problems you find with the new versions or any old problems that I did not actually fix! Among the changes to the Artemis: 1. An autosave file is written at certain times so that you can recover work in the event of a crash. 2. Artemis now uses a native menubar. This means that the menus can be driven entirely from the keyboard using (on PC keyboards) the Alt key. 3. There are a couple of small changes in functionality on the GDS page. Now, if you click on a different variable while editing a variable, the first variable will be defined before the new one is displayed. 4. The General->workspace variable is no longer used. I apologize to those who used this feature, but it was the source of too many problems. 5. The writing of trap files has been disabled in this version, but the same information still gets written to the console and should be included by cut-n-paste in bug reports. In Hephaestus there is a new page which shows a chart of the electronic transitions associated with the various single-electron fluorescence lines. Athena just has a bunch of bug fixes. It does not yet use a native menu bar. (Next time for sure!) A final note about Artemis. There is no drag-n-drop functionality anywhere in the program. It is quite easy to trigger a bug when the GDS page is displayed if you click the mouse button and then drag the mouse to another part of the Artemis window. I do not know the cause of this bug, but it is easy to avoid. Regards, 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 and thanks for the tarball, is there any reason why athena opens Aquaterm smoothly while, after a first time in which everything worked, artemis does not open an Aquaterm window even when run in parallel with athena? I am not sure I am being clear. I simply wonder whether this is an easy problem or not. 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 Wednesday 28 July 2004 09:22 am, Stefano Ciurli wrote:
Hi Bruce and thanks for the tarball,
is there any reason why athena opens Aquaterm smoothly while, after a first time in which everything worked, artemis does not open an Aquaterm window even when run in parallel with athena? I am not sure I am being clear. I simply wonder whether this is an easy problem or not.
Not completely. What happens when you run: 1. Athena alone? 2. Artemis alone? 3. Athena first, then Artemis? 4. Artemis first, then Athena? In any case, I think that Paul or Matt will be more helpful on this issue than I will be. 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: the problem is with Artemis and project files. Athena runs smoothly with both data and prj files, while Artemis is smooth with data (Aquaterm opening) but cannot open Aquaterm when I read in project files. Is this a better hint? I think the problem is the old one: Artemis managing zipping and unzipping project files, but I may be wrong. 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 Wednesday 28 July 2004 10:22 am, Stefano Ciurli wrote:
the problem is with Artemis and project files. Athena runs smoothly with both data and prj files, while Artemis is smooth with data (Aquaterm opening) but cannot open Aquaterm when I read in project files.
Is this a better hint? I think the problem is the old one: Artemis managing zipping and unzipping project files, but I may be wrong.
Are there any messages written to the screen (this will require launching the program from the command line rather than from the finder) that give any information? 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,
Are there any messages written to the screen (this will require launching the program from the command line rather than from the finder) that give any information?
No messages in the terminal window (I always open artemis this way), while the echo buffer states the following: Showing new GDS page Using Ifeffit 1.2.5 Copyright (c) 2004 Matt Newville, Univ of Chicago Artemis may be freely redistributed under the terms of its license. Artemis comes with absolutely NO WARRANTY. HINT: Right click on lines in the feff interpretation for a menu of path-related functions. Opening project zipfile /Users/stefano/Documents/In_preparazione/2-UreE-EXAFS:M-binding/EXAFS/modelli_EXAFS/NiH2O3His3fac_feff/Fit#5.apj .... Opening project zipfile Fit#5.apj ... done! Doing intrp for FEFF0 ... Doing intrp for FEFF0 ... done! amp: Opened project file `/Users/stefano/.horae/stash/artemis.project.0/descriptions/artemis'. Plotting in r space ... Plotting in r space .. but nothing happens... 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 Wednesday 28 July 2004 11:08 am, Stefano Ciurli wrote:
Are there any messages written to the screen (this will require launching the program from the command line rather than from the finder) that give any information?
No messages in the terminal window (I always open artemis this way), while the echo buffer states the following:
Hmmm... I'll try to take a look at this later today on my Mac. 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/
Thanks! Stefano
Hmmm... I'll try to take a look at this later today on my Mac.
B
-- ____________________________________________ 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"
Hi Stefano, I don't have a problem plotting from artemis and other Ifeffit applications: they each use a separate Aquaterm plotting window. For better debugging, I'd suggest opening the artemis Ifeffit buffer (Edit->Display Ifeffit buffer) and typing 'testplot' in the command window. This is supposed to generate a simple plot that may help diagnose the problem. It seems that the problem may be project dependent -- perhaps sending the project file would help. --Matt
Hi Matt,
I don't have a problem plotting from artemis and other Ifeffit applications: they each use a separate Aquaterm plotting window. For better debugging, I'd suggest opening the artemis Ifeffit buffer (Edit->Display Ifeffit buffer) and typing 'testplot' in the command window. This is supposed to generate a simple plot that may help diagnose the problem.
the plot is displayed no problem
It seems that the problem may be project dependent -- perhaps sending the project file would help.
It is 195 Mb.... and impossible to compress. How do I send to you Matt and Bruce? 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,
the plot is displayed no problem
OK, then Aquaterm is working fine.
It seems that the problem may be project dependent -- perhaps sending the project file would help.
It is 195 Mb.... and impossible to compress. How do I send to you Matt and Bruce?
Make a simpler project that also fails.
If I run the fit again, I get the following message in the echo buffer:
Error finding data and/or FEFF files:
Artemis could not find the following files: Data: /Users/stefano/.horae/stash/artemis.project.0/chi_data/ni_lyo_athena.chi
so....something happened to the data file while saving the whole project. I have seen this behavior quite a few times. COuld it be related to the zipping process???
I'd guess it's more likely related to being a 195Mb project and filling up and corrupting Ifeffit buffers or machine memory. For future reference, you'll get better help if you are willing to try simple inputs and give more complete information when asking why something appears to not be working right. --Matt
Matt,
Make a simpler project that also fails.
I will
I'd guess it's more likely related to being a 195Mb project and filling up and corrupting Ifeffit buffers or machine memory.
I think so too.
For future reference, you'll get better help if you are willing to try simple inputs and give more complete information when asking why something appears to not be working right.
well, I understand your point. I'll try to. Thanks 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 Wednesday 28 July 2004 12:11 pm, Stefano Ciurli wrote:
It is 195 Mb.... and impossible to compress. How do I send to you Matt and Bruce?
You don't! ;-) Like Matt said, you should try to find a much smaller and simpler project that shows the same behavior. There must be something else wrong here. I just had my computer tell me how big each artemis project on my computer is and none of them are bigger than a Meg. I have trouble imagining how an artemis project could get to be 195 Mb. The project file is, as Paul said, simple a zipfile. Use StuffIt or any other zip tool tool peek inside and find out what is using up so much diskspace. That will probably go a long way towards identifying the source of the problem. It is also possible that the programming tool I use to manage the zip files chokes on something that large -- I don't actually know one way or the other. The only thing I can think of that could cause an artemis project file to grow absurdly large is if you are running HHUUGGEE feff calculations. It is unlikely that you have data with measurable signal much past about 5 or 6 Angstroms. It is therefore unnecessary to have feff compute paths much beyond that. If you are setting RMAX to 10 or 12 or something like that in the feff.inp file, then you are generating a monsterous but unnecessary number of paths. 195 meg's worth seems unlikely, but who knows. B P.S. Actually, I can imagine another way that a prior version of Artemis could get to be that big. It's obscure and not worth explaining here, particularly since the most recent version of Artemis does not have this problem any more. You could install the latest then try rebuilding the project from scratch. -- 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,
You don't! ;-)
I did NOT indeed! :-))
Like Matt said, you should try to find a much smaller and simpler project that shows the same behavior.
I was myself very much astonished by how large the file is.
There must be something else wrong here. I just had my computer tell me how big each artemis project on my computer is and none of them are bigger than a Meg. I have trouble imagining how an artemis project could get to be 195 Mb.
OK. I re-built the project I was meant to send (!) and listen up: the size is 380 kbytes! I checked what was in the large zip file and it contained all sorts of additional fits and feff calculations that I had run within the same artemis session. I guess that I should not do that. In any case, it is not worth any more discussion. I am confident that the problem with Aquaterm was linked to the anomalously large size of the apj file.
The only thing I can think of that could cause an artemis project file to grow absurdly large is if you are running HHUUGGEE feff calculations. It is unlikely that you have data with measurable signal much past about 5 or 6 Angstroms. It is therefore unnecessary to have feff compute paths much beyond that. If you are setting RMAX to 10 or 12 or something like that in the feff.inp file, then you are generating a monsterous but unnecessary number of paths. 195 meg's worth seems unlikely, but who knows.
no, I am NOT running large calculations at all. The total number of atoms is about 20, as I am working on a metal ion site in a protein in solution, so I do not go over 6 Å, and I fit at R less than 5.
P.S. Actually, I can imagine another way that a prior version of Artemis could get to be that big. It's obscure and not worth explaining here, particularly since the most recent version of Artemis does not have this problem any more. You could install the latest then try rebuilding the project from scratch.
that is what I did. The latest release is much much nicer as it solves several little incongruencies present in the old one, especially when opening and closing projects (small ones! :-)) or managing feff.inp files. Thanks a lot, 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"
Matt, I agree that it must be something related to the project file, and in particular to the data file (I have both the data file and the feff calculated paths in the project, as well as the fit): if I ask the program to plot any path, Aquaterm opens... If I run the fit again, I get the following message in the echo buffer: Error finding data and/or FEFF files: Artemis could not find the following files: Data: /Users/stefano/.horae/stash/artemis.project.0/chi_data/ni_lyo_athena.chi so....something happened to the data file while saving the whole project. I have seen this behavior quite a few times. COuld it be related to the zipping process??? 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"
Hi Stefano. Today I am here with Matt at the APS. Have you tried looking in the directory to see if the file is actually there? You can also look inside zip archives with the "zipinfo" command that you can install with fink (I *think* it is installed with the fink base installation -- in my case it is just there -- I didn't install it myself). This will show you a list of file in the archive. You can then look to see if the file the file is there in the original directory and the archive. Paul On Jul 28, 2004, at 11:17 AM, Stefano Ciurli wrote:
Matt, I agree that it must be something related to the project file, and in particular to the data file (I have both the data file and the feff calculated paths in the project, as well as the fit): if I ask the program to plot any path, Aquaterm opens...
If I run the fit again, I get the following message in the echo buffer:
Error finding data and/or FEFF files:
Artemis could not find the following files: Data: /Users/stefano/.horae/stash/artemis.project.0/chi_data/ ni_lyo_athena.chi
so....something happened to the data file while saving the whole project. I have seen this behavior quite a few times. COuld it be related to the zipping process???
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" _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8562 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons@aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８ 茨城県つくば市東１−１−1 つくば中央第４ 近接場光応用工学センター ポール・フォンス主任研究官
Hi Paul,
Hi Stefano. Today I am here with Matt at the APS. Have you tried looking in the directory to see if the file is actually there?
It is. I guess my problem is that I am not realy sure WHAT is saved in an apj file: I thought that also the data were into that. In any case, the data file is in the directory that also contains the apj file (it is not the directory from which I start artemis, should it be???)
You can also look inside zip archives with the "zipinfo" command that you can install with fink (I *think* it is installed with the fink base installation -- in my case it is just there -- I didn't install it myself). This will show you a list of file in the archive. You can then look to see if the file the file is there in the original directory and the archive.
the command works and shows the presence of the data file in the project I am trying to open and display 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)
-
Bruce Ravel -
Matt Newville -
Paul Fons -
Stefano Ciurli