Re: [Avogadro-Discuss] building slab with avogadro

2013-03-15 Thread Geoffrey Hutchison
> 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 b

Re: [Avogadro-Discuss] building slab with avogadro

2013-03-15 Thread Rupashree Shyama Ray
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:

Re: [Avogadro-Discuss] building slab with avogadro

2013-03-15 Thread David Lonie
On Thu, Mar 14, 2013 at 5:51 PM, Rupashree Shyama Ray 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 atom

Re: [Avogadro-Discuss] building slab with avogadro

2013-03-14 Thread Rupashree Shyama Ray
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 v

Re: [Avogadro-Discuss] building slab with avogadro

2013-03-01 Thread Geoffrey Hutchison
> 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, bu

Re: [Avogadro-Discuss] building slab with avogadro

2013-02-28 Thread Rupashree Shyama Ray
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.hutchi...@gmail.com> wrote: > Apologies for the slow reply.

Re: [Avogadro-Discuss] building slab with avogadro

2013-02-28 Thread Geoffrey Hutchison
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 tha

[Avogadro-Discuss] building slab with avogadro

2013-02-20 Thread Rupashree Shyama Ray
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 angs