-----Original Message-----
From: Eric Brown [mailto:eric.c.brown@mac.com]
Sent: Thu 11/11/2010 19:55
To: Thomas, Jens (STFC,DL,CSE)
Cc: mhanwell@gmail.com; loniedavid@gmail.com; louis.ricard@polytechnique.edu; avogadro-devel@lists.sourceforge.net
Subject: Re: [Avogadro-devel] Announcement about testing builds?
On Nov 11, 2010, at 1:46 PM, jens.thomas@stfc.ac.uk wrote:
This is probably on someone’s radar - and is maybe what Marcus meant, but I just wanted to say that I was looking at the QTAIM stuff earlier and it looks like the data that it needs is already parsed for the orbital rendering code.
If you’re refactoring some of the code around this, it’s make sense to make it possible to instantiate a QTAIM wavefunction from the stuff parsed for the orbital code. That way Avogadro would instantly support AIM for all the codes it can render orbitals, which would be a pretty impressive feature for not much work.
Unfortunately I’m away for the rest of the week, but I might be able to help out with this next week if people think it’s a good idea.
Best wishes,
Jens
Hi Jens,
Absolutely, this is what I am working on now this instant. I got bogged down grading midterms, but now I'm back. Now I am following Geoff's advice and stuff the required the Molden, Gaussian, GAMESS etc. wavefunction information into properties of the Molecule class so that they can be read by the QTAIM code.
Thanks for your encouragement!!!
That’s great - really looking forward to giving it a go when you’re done!
Best wishes,
Jens
Scanned by iCritical.
Hi all,
Currently we have fresh binary builds for all major platforms (Windows x86, Mac x86+x86_64,
Linux x86, Linux x86_64).
Maybe it’s worth to make a public announcement about it? I also mean news on front page
with download links. Maybe some attribute like ‘Beta’ could be applied (of course, tag is needed
in this case)?
–
Regards,
Konstantin
Hi all.
I started testing the Windows installer shortly after David’s message.
I was puzzled by absence of forcefield entries in the extension menu,
so I tried compiling Avo trunk in Linux against OB-2.3.0. The program
complains that it cannot load or use any forcefield. This is with
CenOS5.5 or Fedora14.
Strangely, there are lots of warnings regarding OB plugin.h: the 2.3
version is very different than the 2.2.9 one, so I recompiled with
this version and now have a complete extensions menu.
I think the molecular mechanics extension is crucial in Avo and,
consequently, it should be part of any preview of the coming
Avo-1.1.
Best regards,
Louis
Le 3 nov. 2010 à 11:40, Konstantin Tokarev a écrit :
Hi all,
Currently we have fresh binary builds for all major platforms (Windows x86, Mac x86+x86_64,
Linux x86, Linux x86_64).
Maybe it’s worth to make a public announcement about it? I also mean news on front page
with download links. Maybe some attribute like ‘Beta’ could be applied (of course, tag is needed
in this case)?
–
Regards,
Konstantin
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04.11.2010, 20:52, “Louis Ricard” louis.ricard@polytechnique.edu:
Hi all.
I started testing the Windows installer shortly after David’s message.
I was puzzled by absence of forcefield entries in the extension menu,
so I tried compiling Avo trunk in Linux against OB-2.3.0. The program
complains that it cannot load or use any forcefield. This is with
CenOS5.5 or Fedora14.
Strangely, there are lots of warnings regarding OB plugin.h: the 2.3
version is very different than the 2.2.9 one, so I recompiled with
this version and now have a complete extensions menu.
Maybe OB is not compiled properly.
Have you tried binary build for Linux?
–
Regards,
Konstantin
Strangely, there are lots of warnings regarding OB plugin.h
Could you post them here?
–
Regards,
Konstantin
Downloaded OB-2.3.0 from official OB site.
It compiles with absolutely no warnings.
Then, compile Avo: on launching,
“Loading plugins: “/usr/local/bin/…/lib/avogadro/1_1”
Searching for plugins in “/usr/local/bin/…/lib/avogadro/1_1/colors”
Searching for plugins in “/usr/local/bin/…/lib/avogadro/1_1/engines”
Searching for plugins in “/usr/local/bin/…/lib/avogadro/1_1/extensions”
Searching for plugins in “/usr/local/bin/…/lib/avogadro/1_1/tools”
Searching for plugins in “/usr/local/bin/…/lib/avogadro/1_1/contrib”
Loading plugins: “/home/ricard/.avogadro/1_1/plugins”
Searching for plugins in “/home/ricard/.avogadro/1_1/plugins/colors”
Searching for plugins in “/home/ricard/.avogadro/1_1/plugins/engines”
Searching for plugins in “/home/ricard/.avogadro/1_1/plugins/extensions”
Searching for plugins in “/home/ricard/.avogadro/1_1/plugins/tools”
Searching for plugins in “/home/ricard/.avogadro/1_1/plugins/contrib”
Unable to set up and use any force fields.
QStackedLayout::setCurrentWidget: Widget 0x7d53900 not contained in stack
Finished queue.”
No force field menus.
And in make.log :
“/usr/local/include/openbabel-2.0/openbabel/plugin.h:331: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:332: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:333: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:334: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:335: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:336: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:337: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:338: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:339: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:340: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:341: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:342: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:343: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:344: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:345: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:346: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:347: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:348: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:349: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:350: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:351: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:352: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:353: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:354: attention :
extra ‘;’
/usr/local/include/openbabel-2.0/openbabel/plugin.h:355: attention :
extra ‘;’”
and more (3700 times).
In fact, the new OB plugin.h totally differs from the one I have
from late october OB trunk 2.2.99 (diff attached).
To answer your second question: no I did not test precompiled linux
versions.
Louis
On 04.11.2010 21:14, Konstantin Tokarev wrote:
04.11.2010, 20:52, "Louis Ricard"louis.ricard@polytechnique.edu:
Hi all.
I started testing the Windows installer shortly after David’s message.
I was puzzled by absence of forcefield entries in the extension menu,
so I tried compiling Avo trunk in Linux against OB-2.3.0. The program
complains that it cannot load or use any forcefield. This is with
CenOS5.5 or Fedora14.
Strangely, there are lots of warnings regarding OB plugin.h: the 2.3
version is very different than the 2.2.9 one, so I recompiled with
this version and now have a complete extensions menu.
Maybe OB is not compiled properly.
Have you tried binary build for Linux?
On Thu, Nov 4, 2010 at 1:52 PM, Louis Ricard
louis.ricard@polytechnique.edu wrote:
Hi all.
I started testing the Windows installer shortly after David’s message.
I was puzzled by absence of forcefield entries in the extension menu,
I’d noticed this on linux, too. I’ll take a look at it and try to get
a new windows installer out on Monday.
Dave
so I tried compiling Avo trunk in Linux against OB-2.3.0. The program
complains that it cannot load or use any forcefield. This is with
CenOS5.5 or Fedora14.
Strangely, there are lots of warnings regarding OB plugin.h: the 2.3
version is very different than the 2.2.9 one, so I recompiled with
this version and now have a complete extensions menu.
I think the molecular mechanics extension is crucial in Avo and,
consequently, it should be part of any preview of the coming
Avo-1.1.
Best regards,
Louis
Le 3 nov. 2010 à 11:40, Konstantin Tokarev a écrit :
Hi all,
Currently we have fresh binary builds for all major platforms (Windows x86, Mac x86+x86_64,
Linux x86, Linux x86_64).
Maybe it’s worth to make a public announcement about it? I also mean news on front page
with download links. Maybe some attribute like ‘Beta’ could be applied (of course, tag is needed
in this case)?
–
Regards,
Konstantin
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I ran a few more tests this morning and a fully functional Avo seems
to depend both on OB version and the compiler one.
Compiling Avo trunk version f02263d with OB-2.3.0 on Mac OS X 10.6,
CentOS-5.5 or Fedora-14 always result in absence of molecular mechanics
entries in the extension menu.
With OB-2.2.99, however, I had to use g+±4.2 on the Mac and g++44
in CentOS. Fedora has g++ 4.5. And Avo is fully functional.
Running diff between the two OB versions reveals an astonishingly
large number of differences, notably in plugin.cpp and plugin.h;
could this be the reason for failing to compile with 2.3.0?
Louis
Le 5 nov. 2010 à 17:09, David Lonie a écrit :
On Thu, Nov 4, 2010 at 1:52 PM, Louis Ricard
louis.ricard@polytechnique.edu wrote:
Hi all.
I started testing the Windows installer shortly after David’s message.
I was puzzled by absence of forcefield entries in the extension menu,
I’d noticed this on linux, too. I’ll take a look at it and try to get
a new windows installer out on Monday.
Dave
Running diff between the two OB versions reveals an astonishingly
large number of differences, notably in plugin.cpp and plugin.h;
could this be the reason for failing to compile with 2.3.0?
Probably you are right, and it is OB issue
–
Regards,
Konstantin
Hi Louis,
I’ve uploaded a new windows installer that should fix the FF problems.
Please let us know if you find any other bugs!
http://avogadro.openmolecules.net/nightly/win/unstable/
Thanks,
Dave
Hi David,
Thanks a lot!
I gave the new version a very quick look in a VM and have to check
more carefully on a real Windows box tomorrow. At first sight, it seems
O.K.
But for the fact that translations are not included, it should give Windows
users a good idea of the great additions that Avo-1.1 is bringing.
Cheers,
Louis
Le 9 nov. 2010 à 17:52, David Lonie a écrit :
Hi Louis,
I’ve uploaded a new windows installer that should fix the FF problems.
Please let us know if you find any other bugs!
Index of /nightly/win/unstable
Thanks,
Dave
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09.11.2010, 20:39, “Louis Ricard” louis.ricard@polytechnique.edu:
Hi David,
Thanks a lot!
I gave the new version a very quick look in a VM and have to check
more carefully on a real Windows box tomorrow. At first sight, it seems
O.K.
But for the fact that translations are not included, it should give Windows
users a good idea of the great additions that Avo-1.1 is bringing.
There’s no problem with translations - I guess David just forgotten to copy
them from Linux build 
–
Regards,
Konstantin
There’s no problem with translations - I guess David just forgotten to copy
them from Linux build
I’m about to patch the Mac unstable build to work with David’s forcefield patch. Konstantin, is the Linux build patched too?
I’d like to have a recent, working build of Avogadro available for download by Sunday, since I’m giving a workshop (with David) at Cornell. There will be lots of devs there, including ABINIT, OCTOPUS, …
Thanks,
-Geoff
10.11.2010, 19:06, “Geoffrey Hutchison” geoff.hutchison@gmail.com:
There’s no problem with translations - I guess David just forgotten to copy
them from Linux build
I’m about to patch the Mac unstable build to work with David’s forcefield patch. Konstantin, is the Linux build patched too?
Current build is not very fresh, but forcefields worked in it.
I will update builds this week, using Qt-4.7.1. Maybe I’ll get Python working
–
Regards,
Konstantin
On Wed, Nov 10, 2010 at 11:06 AM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:
There’s no problem with translations - I guess David just forgotten to copy
them from Linux build
I’m about to patch the Mac unstable build to work with David’s forcefield patch. Konstantin, is the Linux build patched too?
Since gerrit is down, the patch is available on my github fork in the
fix_OBFF branch:
https://github.com/dlonie/avogadro/tree/fix_OBFF
Dave
10.11.2010, 19:34, “David Lonie” loniedavid@gmail.com:
On Wed, Nov 10, 2010 at 11:06 AM, Geoffrey Hutchison
geoff.hutchison@gmail.com; wrote:
There’s no problem with translations - I guess David just forgotten to copy
them from Linux build
I’m about to patch the Mac unstable build to work with David’s forcefield patch. Konstantin, is the Linux build patched too?
Since gerrit is down, the patch is available on my github fork in the
fix_OBFF branch:
https://github.com/dlonie/avogadro/tree/fix_OBFF
Dave
It seemed like OpenBabel bug, why Avogadro needs patching?
–
Regards,
Konstantin
2010/11/10 Konstantin Tokarev annulen@yandex.ru:
10.11.2010, 19:34, “David Lonie” loniedavid@gmail.com:
On Wed, Nov 10, 2010 at 11:06 AM, Geoffrey Hutchison
geoff.hutchison@gmail.com; wrote:
There’s no problem with translations - I guess David just forgotten to copy
them from Linux build
I’m about to patch the Mac unstable build to work with David’s forcefield patch. Konstantin, is the Linux build patched too?
Since gerrit is down, the patch is available on my github fork in the
fix_OBFF branch:
https://github.com/dlonie/avogadro/tree/fix_OBFF
It seemed like OpenBabel bug, why Avogadro needs patching?
See the email from yesterday that Noel answered.
Hi David.
I think you should make an official post of this installer on the Avogadro
official site. I feel certain that others gave it a try and I am aware that
anyone may have biases in testing (preferred options …), but overall
my biases worked, not meaning that I made extensive tests. This can
only come from a larger community, being aware that “bugs” are often
missusages.
It might be a good idea to develop a test suite for Avo. Not so simple
to implement.
Best wishes to Geoff and you for your nearing meeting,
Cheers,
Louis
Le 9 nov. 2010 à 17:52, David Lonie a écrit :
Hi Louis,
I’ve uploaded a new windows installer that should fix the FF problems.
Please let us know if you find any other bugs!
Index of /nightly/win/unstable
Thanks,
Dave
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10.11.2010, 23:03, “Louis Ricard” louis.ricard@polytechnique.edu:
Hi David.
I think you should make an official post of this installer on the Avogadro
official site.
I think we should create a tag (e.g., 1.1.beta) and make build for all platforms
from this tag
–
Regards,
Konstantin
On Nov 10, 2010, at 4:34 PM, Konstantin Tokarev wrote:
I think we should create a tag (e.g., 1.1.beta) and make build for all platforms
from this tag
I vote to just call it 1.1.0, tag this tomorrow perhaps? We can add big “WARNING, not STABLE” signs, but that was always true of 0.9 and previous releases too.
-Geoff