Using Avogadro in educational process

Good day!

I was very happy to find such useful and usable program, and now I’m
trying to use it in the educational process in the department of
"Material science and metal physics" of the Ufa State Aviation
Technical University.
Till nowadays a proprietary (and warez) Chem3D was used, but now it’s
a good time to switch it to Avogadro.

Tasks being performed using molecular modeling not include any
scientific jobs - only educational, so the lightweight and easy-to-use
program would be greatly helpful. But now during migration, I’ve got
some issues.

How can I get help with this issues?

Should I create a page in the wiki, or use this mailng list, or any
other mailing list?

Of course, once work will be done, I can publish workbooks, and,
possibly, other working material. Existing workbooks are in Russian,
and based on Chem3D program, so they won’t be such useful to anybody.


With best regards,
Vasiliy Astanin

Moin

I was very happy to find such useful and usable program, and now I’m
trying to use it in the educational process in the department of
“Material science and metal physics” of the Ufa State Aviation
Technical University.

Tasks being performed using molecular modeling not include any
scientific jobs - only educational, so the lightweight and easy-to-use
program would be greatly helpful. But now during migration, I’ve got
some issues.

How can I get help with this issues?

A wiki is a pretty good idea. I am a teacher myself and also using Avogadro (german highschool). I guess I would contribute to that wiki as well.

Do you know chem-file.sf.net? Very good source of information!

Carsten

GMX Kostenlose Spiele: Einfach online spielen und Spaß haben mit Pastry Passion!

2008/10/1 Carsten Niehaus CNiehaus@gmx.de:

Moin

I was very happy to find such useful and usable program, and now I’m
trying to use it in the educational process in the department of
"Material science and metal physics" of the Ufa State Aviation
Technical University.

Tasks being performed using molecular modeling not include any
scientific jobs - only educational, so the lightweight and easy-to-use
program would be greatly helpful. But now during migration, I’ve got
some issues.

How can I get help with this issues?

A wiki is a pretty good idea. I am a teacher myself and also using Avogadro (german highschool). I guess I would contribute to that wiki as well.

Ok, then I should start workiing on it. I’ll use Avogadro wiki, if
noone against this idea.

Do you know chem-file.sf.net? Very good source of information!

Thank you, that’s useful link, but we are much more physics than
chemists, so large organic molecules mostly out of our scope.
“Killer-app” for us will be simplest simulation of metallic bond - I
haven’t seen such feature anywhere. We don’t need precise results, or
"alloy prediction", but simplest simulation of metals (with electron
delocalization) etc. will be great.

Carsten

GMX Kostenlose Spiele: Einfach online spielen und Spaß haben mit Pastry Passion!
http://games.entertainment.gmx.net/de/entertainment/games/free/puzzle/6169196


С наилучшими пожеланиями,
Василий Астанин

On Oct 1, 2008, at 8:42 AM, Василий Астанин wrote:

Ok, then I should start workiing on it. I’ll use Avogadro wiki, if
noone against this idea.

No, in fact, I’ve wanted to start an “Education” section of the
Avogadro wiki for exactly this purpose.

“Killer-app” for us will be simplest simulation of metallic bond - I
haven’t seen such feature anywhere. We don’t need precise results, or
"alloy prediction", but simplest simulation of metals (with electron
delocalization) etc. will be great.

Hmm. That would need some sort of additional extension. I know of
several simple quantum chemistry techniques I’m trying to add, but I
don’t know about band structure.

Do you know of a simple tight-binding quantum code? (Or simulation of
electron gas in a metal?) Certainly we have some support for crystals,
so it would be nice to have solid-state band simulation as well.
Suggestions and/or contributions in this direction would be most
welcome!

Best regards,
-Geoff

2008/10/9 Geoffrey Hutchison geoff@geoffhutchison.net:

On Oct 1, 2008, at 8:42 AM, Василий Астанин wrote:

Ok, then I should start workiing on it. I’ll use Avogadro wiki, if
noone against this idea.

No, in fact, I’ve wanted to start an “Education” section of the Avogadro
wiki for exactly this purpose.

Ok, I’ll use this section

“Killer-app” for us will be simplest simulation of metallic bond - I
haven’t seen such feature anywhere. We don’t need precise results, or
"alloy prediction", but simplest simulation of metals (with electron
delocalization) etc. will be great.

Hmm. That would need some sort of additional extension. I know of several
simple quantum chemistry techniques I’m trying to add, but I don’t know
about band structure.

Do you know of a simple tight-binding quantum code? (Or simulation of
electron gas in a metal?) Certainly we have some support for crystals, so it
would be nice to have solid-state band simulation as well. Suggestions
and/or contributions in this direction would be most welcome!

I don’t know if such code exists, but i’ll try to find out it.

Best regards,
-Geoff


With best regards,
Vasiliy Astanin

It’s night here, and the first issues are met.

I’ve created a page http://avogadro.openmolecules.net/wiki/Hydrogen_molecule,
but I cannot upload any images - there some permission problem.

On Четверг 09 октября 2008 02:19:50 Geoffrey Hutchison wrote:

On Oct 1, 2008, at 8:42 AM, Василий Астанин wrote:

Ok, then I should start workiing on it. I’ll use Avogadro wiki, if
noone against this idea.

No, in fact, I’ve wanted to start an “Education” section of the
Avogadro wiki for exactly this purpose.

“Killer-app” for us will be simplest simulation of metallic bond - I
haven’t seen such feature anywhere. We don’t need precise results, or
"alloy prediction", but simplest simulation of metals (with electron
delocalization) etc. will be great.

Hmm. That would need some sort of additional extension. I know of
several simple quantum chemistry techniques I’m trying to add, but I
don’t know about band structure.

Do you know of a simple tight-binding quantum code? (Or simulation of
electron gas in a metal?) Certainly we have some support for crystals,
so it would be nice to have solid-state band simulation as well.
Suggestions and/or contributions in this direction would be most
welcome!

Best regards,
-Geoff


With best regards,
Vasily Astanin

Good day!

Looks like GAMESS-US has some support for solid-state systems, at
least it has support for Density Functional Theory, but but I’ve
found another package: LAMMPS (http://lammps.sandia.gov/). It’s
GPL-licensed, and under active development. Now I try to build it, and
AFAIU it can be built as a library. Input files are pretty simple, put
I don’t know in which form output files are produced. There are many
promising examples on their homepage, like crack propagation or
tensile deformation of nanowires. Could you take a look on it and give
some decision, if it easy or not to implement support of this package?

“Killer-app” for us will be simplest simulation of metallic bond - I
haven’t seen such feature anywhere. We don’t need precise results, or
"alloy prediction", but simplest simulation of metals (with electron
delocalization) etc. will be great.

Hmm. That would need some sort of additional extension. I know of
several simple quantum chemistry techniques I’m trying to add, but I
don’t know about band structure.

Do you know of a simple tight-binding quantum code? (Or simulation of
electron gas in a metal?) Certainly we have some support for crystals,
so it would be nice to have solid-state band simulation as well.
Suggestions and/or contributions in this direction would be most
welcome!

Best regards,
-Geoff


With best regards,
Vasily Astanin


With best regards,
Vasiliy Astanin

Good morning Vasiliy!

Looks like GAMESS-US has some support for solid-state systems, at
least it has support for Density Functional Theory

Keep in mind there are many applications of DFT in chemistry – for
strictly molecular systems. AFAIK, GAMESS-US has no support for
periodic boundary conditions, so solid-state calculations are out of
the picture.

found another package: LAMMPS (http://lammps.sandia.gov/). It’s
GPL-licensed, and under active development. Now I try to build it, and
AFAIU it can be built as a library.

LAMMPS is a great program and I’d love to see support for it. I
haven’t used it much, but it’s pretty easy to write code to parse
output.

On the other hand, I don’t think LAMMPS really supports metallic bonds
(i.e., band structure). A few other suggestions for you to take a look:
GULP: https://www.ivec.org/GULP/
Amber 10: http://ambermd.org/ (includes DFT-Tight Binding in
periodic cells – probably not surfaces or real electronic metal bonds)
CP2K: http://cp2k.berlios.de/
Ab Init: http://www.abinit.org/
PWscf: http://www.pwscf.org/
DFT++: http://dft.physics.cornell.edu/

Actually, the UFF method in Avogadro can support lattice minimization
– we just don’t (yet) have the code to do calculations with periodic
boundary conditions.

There are also a number of “free for academic use” programs which work
on solid-state and metals too.

Hope that helps,
-Geoff