Avogadro-Discuss Digest, Vol 46, Issue 4

General Discussion
1

I was compiling/installing avogadro-squared with git
According to the page
“If you have Git and CMake installed, you can use the new “Avogadro
Squared” build to fetch and build any needed dependencies.”
But it failed.
Here is my pastebin
http://pastebin.com/baMS0sgA

Is there another easy way to install avogadro 1.1.0 on ubuntu 12.04 ???

On Tue, May 21, 2013 at 8:18 AM,
avogadro-discuss-request@lists.sourceforge.net wrote:

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Today’s Topics:

  1. Re: The defect site changes place after rotation! (David Lonie)
  2. Re: The defect site changes place after rotation! (???)
  3. Re: The defect site changes place after rotation! (David Lonie)
  4. Re: The defect site changes place after rotation! (???)

Message: 1
Date: Tue, 21 May 2013 07:57:32 -0400
From: David Lonie david.lonie@kitware.com
Subject: Re: [Avogadro-Discuss] The defect site changes place after
rotation!
To: avogadro-discuss@lists.sourceforge.net
Message-ID:
CA+=e1osNoSfY+nyjnYY-zXvk2VEhoL6_2vjZgaqeaNWeAJKkLw@mail.gmail.com
Content-Type: text/plain; charset=UTF-8

On Tue, May 21, 2013 at 5:58 AM, ??? limurphy1985@gmail.com wrote:

Dear Avogadro users,

I am visualizing a supercell containing two defect sites, but after
rotating
the
cell, the defect site changes place! It is really terrifying as I
can not
determine
the exact defect site by viewing it. As shown in the attached
files, in
POSCAR.jpg,
the defect at the right-up side is located at the second top atomic
layer,
but after I rotate the
cell, as shown in POSCAR2.jpg, the defect site shifts to the first
top
layer.

Is this problem related to periodic boundary
condition? Does anyone know the reason of this problem and how to
determine
the defect
site by Avogadro?

Thank you very much, and very much looking forward to your help!

It looks like it might be related to periodic boundaries and wrapping
the atoms back into the unit cell. What do you mean by “rotating the
cell”? Are you just moving the camera, or are you modifying the
structure?

Dave

Message: 2
Date: Tue, 21 May 2013 14:05:38 +0200
From: ??? limurphy1985@gmail.com
Subject: Re: [Avogadro-Discuss] The defect site changes place after
rotation!
To: avogadro-discuss@lists.sourceforge.net
Message-ID:
CAJB5uaz=iw6r-0Lw11p4vfLTs_xxGWZDzkbRWqH9iY2w1Zu9Rg@mail.gmail.com
Content-Type: text/plain; charset=“big5”

Dear Dave,

Thank you for your follow-up.

For “rotation”, I mean I drag the cell (pressing the right bottom of
my
mouse),
so it can be rotated around certain axis.

If it is due to PBC, then how could I fix the defect position?

Thank you again!

Sincerely,
Murphy

2013/5/21 David Lonie david.lonie@kitware.com

On Tue, May 21, 2013 at 5:58 AM, ??? limurphy1985@gmail.com wrote:

Dear Avogadro users,

I am visualizing a supercell containing two defect sites, but
after
rotating
the
cell, the defect site changes place! It is really terrifying as I
can not
determine
the exact defect site by viewing it. As shown in the attached
files, in
POSCAR.jpg,
the defect at the right-up side is located at the second top
atomic
layer,
but after I rotate the
cell, as shown in POSCAR2.jpg, the defect site shifts to the
first top
layer.

Is this problem related to periodic boundary
condition? Does anyone know the reason of this problem and how to
determine
the defect
site by Avogadro?

Thank you very much, and very much looking forward to your help!

It looks like it might be related to periodic boundaries and
wrapping
the atoms back into the unit cell. What do you mean by “rotating the
cell”? Are you just moving the camera, or are you modifying the
structure?

Dave

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Message: 3
Date: Tue, 21 May 2013 08:19:17 -0400
From: David Lonie david.lonie@kitware.com
Subject: Re: [Avogadro-Discuss] The defect site changes place after
rotation!
To: avogadro-discuss@lists.sourceforge.net
Message-ID:
CA+=e1otm5rcJsMuiO+QEKTSeHiGG9dPm0VmfwKQFUY6pzan_Dg@mail.gmail.com
Content-Type: text/plain; charset=UTF-8

On Tue, May 21, 2013 at 8:05 AM, ??? limurphy1985@gmail.com wrote:

Dear Dave,

Thank you for your follow-up.

For “rotation”, I mean I drag the cell (pressing the right bottom
of my
mouse),
so it can be rotated around certain axis.

The right mouse button doesn’t perform rotations, it will either
translate the camera (in navigation) or delete an atom (in draw). It
looks like the defect is still in the same corner of the cell, but
there is an atom missing in the top layer of atoms. Is it possible
that an atom was accidentally deleted while manipulating the view?

Can you reproduce this consistently? If so, can you save and send a
copy of the structure with the steps to reproduce the behavior?

Thanks,
Dave

Message: 4
Date: Tue, 21 May 2013 15:18:01 +0200
From: ??? limurphy1985@gmail.com
Subject: Re: [Avogadro-Discuss] The defect site changes place after
rotation!
To: avogadro-discuss@lists.sourceforge.net
Message-ID:
CAJB5uawKkk0GVQH36m9JDGGWRPGvLbL8iN8hsA4hjZVdvgD86g@mail.gmail.com
Content-Type: text/plain; charset=“big5”

My apology, it is the left bottom of the mouse…

Please find attached the POSCAR file.
I do reproduce the problem, but currently I did not find the
way to reproduce it regularly. Basically, what I did was
just keeping pressing the left mouse bottom and rotate the cell
around different axes (Originally I just wanted to investigate
the structure).

It should be worthy to mention, that this problem also occurs
for VESTA!

Hope this helps you to solve the problem!

Sincerely,
Murphy

2013/5/21 David Lonie david.lonie@kitware.com

On Tue, May 21, 2013 at 8:05 AM, ??? limurphy1985@gmail.com wrote:

Dear Dave,

Thank you for your follow-up.

For “rotation”, I mean I drag the cell (pressing the right bottom
of my
mouse),
so it can be rotated around certain axis.

The right mouse button doesn’t perform rotations, it will either
translate the camera (in navigation) or delete an atom (in draw). It
looks like the defect is still in the same corner of the cell, but
there is an atom missing in the top layer of atoms. Is it possible
that an atom was accidentally deleted while manipulating the view?

Can you reproduce this consistently? If so, can you save and send a
copy of the structure with the steps to reproduce the behavior?

Thanks,
Dave

Try New Relic Now & We’ll Send You this Cool Shirt
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service
that delivers powerful full stack analytics. Optimize and monitor
your
browser, app, & servers with just a few lines of code. Try New Relic
and get this awesome Nerd Life shirt!
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Try New Relic Now & We’ll Send You this Cool Shirt
New Relic is the only SaaS-based application performance monitoring
service
that delivers powerful full stack analytics. Optimize and monitor your
browser, app, & servers with just a few lines of code. Try New Relic
and get this awesome Nerd Life shirt!
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End of Avogadro-Discuss Digest, Vol 46, Issue 4