Adding bonds for crystal structure

Hi,

Thank you for the development of a visualizer.
I use the git version of avogadro. From GUI, is it possible to add
bonds of crystal structure after loading a crystal structure.

Thank you,

Togo


Atsushi Togo
http://atztogo.users.sourceforge.net/
atz.togo@gmail.com

On Apr 3, 2011, at 10:23 PM, Atz Togo wrote:

Hi,

Thank you for the development of a visualizer.
I use the git version of avogadro. From GUI, is it possible to add
bonds of crystal structure after loading a crystal structure.

The supercell builder does some of this, and there is a new crystal builder extension that will be merged soon (not sure if that has the simple bonding ported from the supercell builder yet).

Marcus

Hi Marcus,

The supercell builder worked. I’m looking forward to the new crystal
builder extension.

Thank you,

Togo

On Mon, Apr 4, 2011 at 11:47 AM, Marcus D. Hanwell
marcus.hanwell@kitware.com wrote:

On Apr 3, 2011, at 10:23 PM, Atz Togo wrote:

Hi,

Thank you for the development of a visualizer.
I use the git version of avogadro. From GUI, is it possible to add
bonds of crystal structure after loading a crystal structure.

The supercell builder does some of this, and there is a new crystal builder extension that will be merged soon (not sure if that has the simple bonding ported from the supercell builder yet).

Marcus


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Atsushi Togo
http://atztogo.users.sourceforge.net/
atz.togo@gmail.com

On Sun, Apr 3, 2011 at 10:47 PM, Marcus D. Hanwell
marcus.hanwell@kitware.com wrote:

Thank you for the development of a visualizer.
I use the git version of avogadro. From GUI, is it possible to add
bonds of crystal structure after loading a crystal structure.

The supercell builder does some of this, and there is a new crystal builder extension that will be merged soon (not sure if that has the simple bonding ported from the supercell builder yet).

The new extension does not do this yet, but I will add this feature to
my todo list. I would like the ability to automatically construct
bonds based on interatomic distance, so I may work up an interface for
this as well.

Dave

On Mon, Apr 4, 2011 at 10:03 AM, David Lonie loniedavid@gmail.com wrote:

On Sun, Apr 3, 2011 at 10:47 PM, Marcus D. Hanwell
marcus.hanwell@kitware.com wrote:

Thank you for the development of a visualizer.
I use the git version of avogadro. From GUI, is it possible to add
bonds of crystal structure after loading a crystal structure.

The supercell builder does some of this, and there is a new crystal builder extension that will be merged soon (not sure if that has the simple bonding ported from the supercell builder yet).

The new extension does not do this yet, but I will add this feature to
my todo list. I would like the ability to automatically construct
bonds based on interatomic distance, so I may work up an interface for
this as well.

The code to do that bonding can be taken from the supercell builder, I
hardwired the fudge factor (standard number used in inorganic crystals
on top of atomic radii) but it would not be hard to expose that in an
interface. I think it would be a great addition, but we should merge
what you have soon.

I was away at the ACS meeting, and before that another meeting, but am
back now and will be catching up over the next day or so.

Marcus

Marcus D. Hanwell, Ph.D.
R&D Engineer, Kitware Inc.
(518) 881-4937