The defect site changes place after rotation!

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!

Sincerely,
Murphy

On Tue, May 21, 2013 at 5:58 AM, 李文凡 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

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, 李文凡 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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On Tue, May 21, 2013 at 8:05 AM, 李文凡 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

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, 李文凡 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


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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! http://p.sf.net/sfu/newrelic_d2d_may


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On Tue, May 21, 2013 at 9:18 AM, 李文凡 limurphy1985@gmail.com wrote:

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!

Looking at the structures and the images from the first post again,
this is not a bug. The defect isn’t moving, but it’s remaining in the
plane of atoms with the smallest x coordinate – in the first screen
shot, the X axis is pointing out of the screen, so the defect is on
the back plane of atoms. After rotating the X axis is pointing down,
so now the defect is on the top. The structure is the same in both
cases, nothing is moving – it’s just a matter of perspective :wink:

Dave

Thank you very much Dave!
I think I am getting used to the periodic world! :wink:

Sincerely,
Murphy

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

On Tue, May 21, 2013 at 9:18 AM, 李文凡 limurphy1985@gmail.com wrote:

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!

Looking at the structures and the images from the first post again,
this is not a bug. The defect isn’t moving, but it’s remaining in the
plane of atoms with the smallest x coordinate – in the first screen
shot, the X axis is pointing out of the screen, so the defect is on
the back plane of atoms. After rotating the X axis is pointing down,
so now the defect is on the top. The structure is the same in both
cases, nothing is moving – it’s just a matter of perspective :wink:

Dave


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! http://p.sf.net/sfu/newrelic_d2d_may


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