Building slab with avogadro

General Discussion
1

Hi,

I was trying to build a 2 layer slab of 101 surface of TiO2 anatase crystal
with avogadro.
First I tried to make a supercell (111) from the unit cell of TiO2 anatase.
Then made the surface 101.
After I make the slab, the cell parameter “C” along Z-direction is
unusually large close to 100 angstrom, even though I give a depth of 12
angstrom.

One someone suggest me to to overcome this problem?

Thanks
Rupa

2

Apologies for the slow reply. The slab method adds space along the Z-direction to facilitate molecular-surface interactions. If you wish to change this:

  • Under Crystallography → Settings → Coordinate Preservation → Preserve Cartesian …
  • Change the “C” parameter as you wish.
  • Done.

Hope that helps,
-Geoff

I was trying to build a 2 layer slab of 101 surface of TiO2 anatase crystal with avogadro.
First I tried to make a supercell (111) from the unit cell of TiO2 anatase. Then made the surface 101.
After I make the slab, the cell parameter “C” along Z-direction is unusually large close to 100 angstrom, even though I give a depth of 12 angstrom.

3

Thanks Geoff.
That really worked. I was wondering, why do I get the slab out of crystal
cell after building the slab?
Is there is way to come around with that?

Best
Rupashree

On Thu, Feb 28, 2013 at 4:38 PM, Geoffrey Hutchison <
geoff.hutchison@gmail.com> wrote:

Apologies for the slow reply. The slab method adds space along the
Z-direction to facilitate molecular-surface interactions. If you wish to
change this:et t

  • Under Crystallography → Settings → Coordinate Preservation → Preserve
    Cartesian …
  • Change the “C” parameter as you wish.
  • Done.

Hope that helps,
-Geoff

I was trying to build a 2 layer slab of 101 surface of TiO2 anatase
crystal with avogadro.
First I tried to make a supercell (111) from the unit cell of TiO2
anatase. Then made the surface 101.
After I make the slab, the cell parameter “C” along Z-direction is
unusually large close to 100 angstrom, even though I give a depth of 12
angstrom.

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4

That really worked. I was wondering, why do I get the slab out of crystal cell after building the slab?
Is there is way to come around with that?

In many cases, people are building a slab, but they wish to do a 2D calculation. Thus, the x/y (or A, B) axes are preserved with a unit cell, but the z-axis is padded.

If you wish to remove the unit cell:

Crystallography → Remove Unit Cell

Hope that helps,
-Geoff

5

Hi,

While building input files for quantum espresso, certain atoms are
duplicated in avogadro.
Can anyone suggest how to deal with the problem within avogadro?
It’s terrible to do a trial and error to remove certain edge atoms to get
the structure correct.

Any suggestions in this regard will be very helpful…

Thanks
Rupa

On Fri, Mar 1, 2013 at 11:01 AM, Geoffrey Hutchison <
geoff.hutchison@gmail.com> wrote:

That really worked. I was wondering, why do I get the slab out of
crystal cell after building the slab?
Is there is way to come around with that?

In many cases, people are building a slab, but they wish to do a 2D
calculation. Thus, the x/y (or A, B) axes are preserved with a unit cell,
but the z-axis is padded.

If you wish to remove the unit cell:

Crystallography → Remove Unit Cell

Hope that helps,
-Geoff

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6

On Thu, Mar 14, 2013 at 5:51 PM, Rupashree Shyama Ray
shyama.tum@gmail.comwrote:

Hi,

While building input files for quantum espresso, certain atoms are
duplicated in avogadro.
Can anyone suggest how to deal with the problem within avogadro?
It’s terrible to do a trial and error to remove certain edge atoms to get
the structure correct.

Can you describe what you mean more clearly? What steps are you taking to
produce the structure? Which atoms are duplicated?

Dave

7

I am trying to build 101 surface of anatase TiO2.
I used 1x1 layer of TiO2. I used the coordinates in quantum espresso input.
The structure looks clumsy.
I realized some edge oxygen atoms are duplicated.
Also learnt from discussions one need to remove deplicate atoms.

On Fri, Mar 15, 2013 at 6:50 AM, David Lonie david.lonie@kitware.comwrote:

On Thu, Mar 14, 2013 at 5:51 PM, Rupashree Shyama Ray <
shyama.tum@gmail.com> wrote:

Hi,

While building input files for quantum espresso, certain atoms are
duplicated in avogadro.
Can anyone suggest how to deal with the problem within avogadro?
It’s terrible to do a trial and error to remove certain edge atoms to get
the structure correct.

Can you describe what you mean more clearly? What steps are you taking to
produce the structure? Which atoms are duplicated?

Dave

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8

I am trying to build 101 surface of anatase TiO2.
I used 1x1 layer of TiO2. I used the coordinates in quantum espresso input. The structure looks clumsy.
I realized some edge oxygen atoms are duplicated.

While I haven’t tested it with the slab builder, there is a Quantum Espresso input builder that should remove duplicated atoms.

Otherwise, what would really help is if you can give us a picture and circle duplicated atoms. I’d appreciate knowing the exact parameters you used in the slab builder.

Thanks very much,
-Geoff

9

I tried to build 101 surface of anatase with cell dimensions x=3 cell
repeats, y=3 cell repeats and z=4 bohr.
The input file of quantum espresso, with coordinates of anatase 101 (as
prepared with above parameters), is displayed weird in xcrysden.
However, chopping few atoms (as high lighted in the picture attached) from
that structure is read well in xcrysden.
The similar phenomena I also observed in super cell building.

On Fri, Mar 15, 2013 at 10:39 AM, Geoffrey Hutchison <
geoff.hutchison@gmail.com> wrote:

I am trying to build 101 surface of anatase TiO2.
I used 1x1 layer of TiO2. I used the coordinates in quantum espresso
input. The structure looks clumsy.
I realized some edge oxygen atoms are duplicated.

While I haven’t tested it with the slab builder, there is a Quantum
Espresso input builder that should remove duplicated atoms.

Otherwise, what would really help is if you can give us a picture and
circle duplicated atoms. I’d appreciate knowing the exact parameters you
used in the slab builder.

Thanks very much,
-Geoff

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