Plot geometry optimization, excitation data

Development
1

Couldn’t help but notice a flurry of formats and data read by OB nowadays, including data types. I was wondering, if that means that Avogadro now can “see” electronic excitations and plot them as spectra? CD spectra, UV spectra?.. How about energetics of geometry optimization and visualizing those?

Jonas

2

Couldn’t help but notice a flurry of formats and data read by OB nowadays, including data types. I was wondering, if that means that Avogadro now can “see” electronic excitations and plot them as spectra? CD spectra, UV spectra?

The latest Avogadro source (using the latest OB source) can do these for some QM formats. David could probably come up with a list, but it’s not implemented in every QM format in babel, that’s for sure.

… How about energetics of geometry optimization and visualizing those?

There was a discussion on the list about this. Some preliminary support for getting the energies and geometries of optimization are supported in Gaussian and GAMESS-US. There’s no visualization in Avogadro yet.

So if this is something that interests you, we can definitely point you at some easy, quick projects.

Cheers,
-Geoff

3

They all are. However, the course I am taking is C# and C++ is needed in OB and Avogadro, I am not sure if I can pull it off

— On Fri, 3/12/10, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

From: Geoffrey Hutchison geoff.hutchison@gmail.com
Subject: Re: [Avogadro-devel] plot geometry optimization, excitation data
To: “Jonas Baltrusaitis” jasius_1@yahoo.com
Cc: “Avogadro-devel Devel” avogadro-devel@lists.sourceforge.net
Date: Friday, March 12, 2010, 9:52 AM

Couldn’t help but notice a
flurry of formats and data read by OB nowadays, including
data types. I was wondering, if that means that Avogadro now
can “see” electronic excitations and plot them as spectra?
CD spectra, UV spectra?

The latest Avogadro source (using the latest OB source) can
do these for some QM formats. David could probably come up
with a list, but it’s not implemented in every QM format in
babel, that’s for sure.

… How about energetics of geometry optimization and
visualizing those?

There was a discussion on the list about this. Some
preliminary support for getting the energies and geometries
of optimization are supported in Gaussian and GAMESS-US.
There’s no visualization in Avogadro yet.

So if this is something that interests you, we can
definitely point you at some easy, quick projects.

Cheers,
-Geoff

4

On the other hand, please give me some easy project to do so I can familiarize myself with C++ this way

— On Fri, 3/12/10, Jonas Baltrusaitis jasius_1@yahoo.com wrote:

From: Jonas Baltrusaitis jasius_1@yahoo.com
Subject: Re: [Avogadro-devel] plot geometry optimization, excitation data
To: “Geoffrey Hutchison” geoff.hutchison@gmail.com
Cc: “Avogadro-devel Devel” avogadro-devel@lists.sourceforge.net
Date: Friday, March 12, 2010, 1:56 PM
They all are. However, the course I
am taking is C# and C++ is needed in OB and Avogadro, I am
not sure if I can pull it off

— On Fri, 3/12/10, Geoffrey Hutchison geoff@geoffhutchison.net
wrote:

From: Geoffrey Hutchison geoff@geoffhutchison.net
Subject: Re: [Avogadro-devel] plot geometry
optimization, excitation data
To: “Jonas Baltrusaitis” jasius_1@yahoo.com
Cc: “Avogadro-devel Devel” avogadro-devel@lists.sourceforge.net
Date: Friday, March 12, 2010, 9:52 AM

Couldn’t help but notice a
flurry of formats and data read by OB nowadays,
including
data types. I was wondering, if that means that
Avogadro now
can “see” electronic excitations and plot them as
spectra?
CD spectra, UV spectra?

The latest Avogadro source (using the latest OB
source) can
do these for some QM formats. David could probably
come up
with a list, but it’s not implemented in every QM
format in
babel, that’s for sure.

… How about energetics of geometry optimization
and
visualizing those?

There was a discussion on the list about this. Some
preliminary support for getting the energies and
geometries
of optimization are supported in Gaussian and
GAMESS-US.
There’s no visualization in Avogadro yet.

So if this is something that interests you, we can
definitely point you at some easy, quick projects.

Cheers,
-Geoff

5

They all are. However, the course I am taking is C# and C++ is needed in OB and Avogadro, I am not sure if I can pull it off

I’d recommended you a book written by J. Liberty “Teach Yourself C++ in 21 Days”. I’ve learned C++ with it having absolutely no knowledge of C or C#
For Avogadro, you’ll need to use Qt. It has thorough on-line documentation. Qt programming is a bit simplier than “pure C++”

— On Fri, 3/12/10, Geoffrey Hutchison wrote:

From: Geoffrey Hutchison
Subject: Re: [Avogadro-devel] plot geometry optimization, excitation data
To: “Jonas Baltrusaitis”
Cc: “Avogadro-devel Devel”
Date: Friday, March 12, 2010, 9:52 AM

Couldn’t help but notice a
flurry of formats and data read by OB nowadays, including
data types. I was wondering, if that means that Avogadro now
can “see” electronic excitations and plot them as spectra?
CD spectra, UV spectra?

The latest Avogadro source (using the latest OB source) can
do these for some QM formats. David could probably come up
with a list, but it’s not implemented in every QM format in
babel, that’s for sure.

… How about energetics of geometry optimization and
visualizing those?

There was a discussion on the list about this. Some
preliminary support for getting the energies and geometries
of optimization are supported in Gaussian and GAMESS-US.
There’s no visualization in Avogadro yet.

So if this is something that interests you, we can
definitely point you at some easy, quick projects.

Cheers,
-Geoff

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Regards,
Konstantin

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