Bonds across periodic boundary

Unit cell support in Avogadro is somewhat lacking. Currently, there is
no way to get a good visualization of intercellular bonding in the
public avogadro releases. I have a patch that adds the ability to
render bonds across cells, but it is a bit expensive for large cells,
and still a little rough around the edges, so it hasn’t made it into
Avogadro 1.x (And it likely never will – most of my development
efforts will go into the 2.0 release for now). I’d really like to get
more of this sort of functionality into that release.

Hi Dave,

Thank you for your response, and I apologise for the delay in getting back to
you. Unfortunately I do not feel confident enough with code to try and
implement the patch myself, but I think this is a really great program
and certainly will be looking forward to the next release. If the PBC
features make it in, all the better!

Thanks again,
Livy

I am very new to Avogadro, so pardon any lack of understanding.

I am attempting to use Avogadro to visualize a polymer network
produced by a self-written MD code.
It is a coarse-grained model, so the atom types I have used are
abitrary.
The output consists of bead co-ordinates and connectivity, which I
wrote into a .cml file.

I am having some problems representing bonds which cross the
periodic boundary of my cell.
Must I duplicate the cells in the .cml file to show these bonds,
or is there a way to wrap the bonds around using a unit cell?
Also, is there a way to define the unit cell in a .cml file
instead of going through the GUI?

Very much appreciative of any help.

On Mon, Aug 6, 2012 at 4:58 AM, elleB livybell@hotmail.com wrote:

I am attempting to use Avogadro to visualize a polymer network
produced by a self-written MD code.
It is a coarse-grained model, so the atom types I have used are
abitrary.
The output consists of bead co-ordinates and connectivity, which I
wrote into a .cml file.

I am having some problems representing bonds which cross the
periodic boundary of my cell.
Must I duplicate the cells in the .cml file to show these bonds,
or is there a way to wrap the bonds around using a unit cell?

Unit cell support in Avogadro is somewhat lacking. Currently, there is
no way to get a good visualization of intercellular bonding in the
public avogadro releases. I have a patch that adds the ability to
render bonds across cells, but it is a bit expensive for large cells,
and still a little rough around the edges, so it hasn’t made it into
Avogadro 1.x (And it likely never will – most of my development
efforts will go into the 2.0 release for now). I’d really like to get
more of this sort of functionality into that release.

This mailing list discussion from a few months ago talks about
rendering these bonds:

http://www.mail-archive.com/avogadro-devel@lists.sourceforge.net/msg00435.html

And here’s a link to the patch on github if you’d like to try it:

https://github.com/dlonie/avogadro/commits/ENH_intercell_bonds

Also, is there a way to define the unit cell in a .cml file
instead of going through the GUI?

Sure:

3.000000 3.000000 3.000000 90.000000 90.000000 90.000000 [...]

Hope this helps,

Dave