Faster geometry optimizations

Geoff,

Any chance we can put this in the Mac OSX package? Or have two
packages? I think this is something my colleagues would appreciate in
their Mac packages. Also, any chance of a 2.2 because of this major
change?


Donald

(Mon, Oct 15, 2007 at 01:37:34PM -0400) Geoffrey Hutchison geoff.hutchison@gmail.com:

Over the weekend, I finished up a long-needed change to the SVN trunk,
which just went in.

Previously, the force field code would evaluate geometry optimization
for one atom at a time. This means that for each atom, it would try a
move, evaluate the energy (of the whole molecule), repeat.

The much faster method (used by every other program) is to propose a
step for the entire molecule, then evaluate the energy. This requires
a new LineSearch() method, so it can’t be backported to the 2.1.x
releases.

The benefits are great. For a 63-atom molecule, the previous code
would execute 500 steps in 1 min. 50 sec. on my workstation.

New code: 8 seconds.

The effects are even more significant for larger molecules. OTOH, the
code hasn’t received a full workout. Please let me know if you
encounter problems!

Cheers,
-Geoff

P.S. This fix doesn’t require any user changes – call the
SteepestDescent and ConjugateGradients methods as normal. But it does
mean that Avogadro users may want to try out SVN trunk of Open Babel
soon. :wink:


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Any chance we can put this in the Mac OSX package? Or have two
packages? I think this is something my colleagues would appreciate in
their Mac packages. Also, any chance of a 2.2 because of this major
change?

Certainly my hope is that OB-2.2 will come out relatively soon. I
don’t know what that will mean – I’d like to also get the SMILES ->
3D coordinate generation code and maybe another bit. And I have people
asking me for about 10 new file formats.

That said, it’s easy enough for Windows and/or Mac packages of
Avogadro to ship with custom versions of Open Babel. For example, I
can make an Avogadro.app bundle for Mac which has all the libraries
privately loaded. There wouldn’t need to be an installer – people
could just copy it through the Finder.

Cheers,
-Geoff

It think there is one problem with that and it has something to do with
the plugin search path for QT or something.
If they drag or app to a directory besides /Applications/Avogadro.app/
then we would need a startup script for Avogadro to detect that location
and set the AVOGADRO_* environment variables. I read that on the Qt
site i’m pretty sure. Anyways, I could dig that up if you want.

PS: i’m going out of town this week on Wednesday to NYC and won’t be
back until Sunday but I still think we shoudl do the release. I’ll try
to get the Windows package done by this weekend and use the new trunk
version of OB but that being said I may take out the H2Methyl on windows
cause it was causing crashes and not sure why. Worse case is the
Windows port comes out later.

PPS: We should make a list of tools / extensions / engines we WANT to
include with the release in the distro thing. I know the ribbon engines
doesn’t work. That is my next priority cept i don’t know crap about
what ribbons render.

SO PUMPED ABOUT BETTER OPTIMIZATION>… that was one thing ghemical had
over us. Damn i’m pumped. Thanks so much for diggin’ through it.


Donald

(Mon, Oct 15, 2007 at 02:01:54PM -0400) Geoffrey Hutchison geoff.hutchison@gmail.com:

Any chance we can put this in the Mac OSX package? Or have two
packages? I think this is something my colleagues would appreciate in
their Mac packages. Also, any chance of a 2.2 because of this major
change?

Certainly my hope is that OB-2.2 will come out relatively soon. I
don’t know what that will mean – I’d like to also get the SMILES ->
3D coordinate generation code and maybe another bit. And I have people
asking me for about 10 new file formats.

That said, it’s easy enough for Windows and/or Mac packages of
Avogadro to ship with custom versions of Open Babel. For example, I
can make an Avogadro.app bundle for Mac which has all the libraries
privately loaded. There wouldn’t need to be an installer – people
could just copy it through the Finder.

Cheers,
-Geoff

On Oct 15, 2007, at 2:20 PM, Donald Ephraim Curtis wrote:

PPS: We should make a list of tools / extensions / engines we WANT to
include with the release in the distro thing. I know the ribbon
engines
doesn’t work. That is my next priority cept i don’t know crap about
what ribbons render.

The ribbon engine is currently disabled by the CMakeLists.txt. So if
you’re building a clean release from SVN trunk right now, it won’t
appear.

Cheers,
-Geoff