Its been awhile since the last time I made a contact, but now, I have the
things more clear.
Finally, I have defined my project, and I can say what I need, and, ask for
help, of course
First, the same as before, draw molecules on a plane surface, all replicas,
and symmetrically spread.
Then run the optimize geometry tool and see what I get.
After that, I will need to ‘see’ from above the result of this. (I tried to
draw a very simple draft, made on some kind of paint).
The final goal will be something like an depth chart, about the molecules’
Now, trying to explain why all this stuff, and what are they about, I can
say that the main point is to simulate one image obtained by the Scanning
Force Microscopy or Atomic Force Microscopy, and initially, compare then
with the original one, for check its precision and later move on simulating
Well guys, beyond asking for help or suggestions, I’m here also to ask for
permission to use Avogadro in my project. I know about the GPL, but its like
using someone’s else stuff: It’s better ask before use it.
I hope it was sufficiently clarifying for you guys understand what I’m
trying to do. If not, please, do not hesitate and ask me.
Tks for all your attention.
On Fri, Jun 27, 2008 at 14:46, Louis Ricard
I tried without success to build a unit cell around a molecule .
I think this would be an elegant solution to this problem since one or two
could be adjusted for molecule spacing and the new "Build Supercell"
would then produce n molecules by adjusting only two of the Miller
Am I wrong ?
Le 27 juin 08 à 18:42, Geoffrey Hutchison a écrit :
On Jun 27, 2008, at 10:18 AM, Leandro Boscariol wrote:
I tried to do this through the draw tool, but it haven’t the precision that
I need to equally spread the molecules on a plane. I thought about some kind
of input file where I could insert the base atom’s position, to fix it, and
the other molecule’s part will come over it.
Here’s my suggestion. Right now, you can use the draw tool (or read in a
file) to create the molecule you want. If you want to make sure the molecule
is in a specific plane (e.g., xy plane, z = 0), use the align tool. Click on
one atom, then a second, pick an axis (e.g., “y”) and click the align
Now what you don’t say is whether you want many copies of the same molecule
in the plane, or many different molecules. Let’s assume you want many of the
What you would want to do is to write an extension which “copies” the
molecule into multiple places on the plane. Take a look at the Copy/Paste
code in avogadro/src/mainwindow.cpp as an example of creating a new copy of
the molecule. That code also makes sure to translate by a small random
amount – you will want your extension to allow translating a large amount.
(I don’t know if it should be random or not – that depends on your
About the geometry optimization, it becomes extremely slow and the program
stop working while I was doing some small tests. I guess that without the
graphical visualization it can be possible, because its a waste showing the
molecule while it is optimized.
You can take a look at the code in the forcefield extension. Right now, it
will make several small steps and then update the graphics. You can either
change the number of steps. Take a look at line 313 in
const int stepsBeforeUpdate = 5; // number of steps before updating the
This is in the SVN trunk – I just added it. But it will allow you to take
more steps before the graphics update.
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Leandro A. Boscariol
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