crystal structure

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photon
Posts: 3
Joined: Thu Jul 07, 2011 6:35 pm

crystal structure

Post by photon » Thu Jul 07, 2011 6:48 pm

Hello.

Could somebody please help me to understand.
In input file there is xred defining atoms positions.
But why there is only two positions in tutorial 3 for silicon crystal (code is below) ?
with only translational symmetries there is no way to construct crystal from only these two positions!

And in crystal structure databases like
http://rruff.geo.arizona.edu/AMS/amcsd.php or http://www.crystallography.net/
there is also not enough atoms!
what I do not know?

Code: Select all

# Crystalline silicon : computation of the total energy
#

#Definition of the unit cell
acell 3*10.18          # This is equivalent to   10.18 10.18 10.18
rprim  0.0  0.5  0.5   # In lessons 1 and 2, these primitive vectors
       0.5  0.0  0.5   # (to be scaled by acell) were 1 0 0  0 1 0  0 0 1
       0.5  0.5  0.0   # that is, the default.

#Definition of the atom types
ntypat 1          # There is only one type of atom
znucl 14          # The keyword "znucl" refers to the atomic number of the
                  # possible type(s) of atom. The pseudopotential(s)
                  # mentioned in the "files" file must correspond
                  # to the type(s) of atom. Here, the only type is Silicon.
                         

#Definition of the atoms
natom 2           # There are two atoms
typat 1 1         # They both are of type 1, that is, Silicon.
xred              # This keyword indicate that the location of the atoms
                  # will follow, one triplet of number for each atom
   0.0  0.0  0.0  # Triplet giving the REDUCED coordinate of atom 1.
   1/4  1/4  1/4  # Triplet giving the REDUCED coordinate of atom 2.
                  # Note the use of fractions (remember the limited
                  # interpreter capabilities of ABINIT)

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jzwanzig
Posts: 504
Joined: Mon Aug 17, 2009 9:25 am

Re: crystal structure

Post by jzwanzig » Sat Jul 09, 2011 5:01 pm

A crystal structure is a combination of the lattice and the location of the atoms within the lattice. In the case of silicon it so happens that there is a primitive unit cell that is smaller than the conventional unit cell (which is cubic and contains either 4 or eight atoms, I don't remember which) while the primitive cell contains only two atoms. Some space groups have primitive cells smaller than their conventional cells and some don't. You would benefit from reviewing a basic text on solid state physics and/or crystallography to learn about this aspect of structure, which I agree is confusing at first.
Josef W. Zwanziger
Professor, Department of Chemistry
Canada Research Chair in NMR Studies of Materials
Dalhousie University
Halifax, NS B3H 4J3 Canada
jzwanzig@gmail.com

photon
Posts: 3
Joined: Thu Jul 07, 2011 6:35 pm

Re: crystal structure

Post by photon » Sat Jul 09, 2011 8:15 pm

Thank you for the reply.
I did not know there is a difference between primitive unit cell and conventional unit cell.
I will read about this.
Thank you one more time!

deepak1032
Posts: 12
Joined: Fri May 28, 2010 1:07 pm

Regarding setting supercell

Post by deepak1032 » Wed Aug 03, 2011 2:27 pm

Can any one help me how to set up a supercell for ABINIT calculations.
I tried number of softwares.
Want to setup supercell for graphene.
In particular I am perplexed by the dimensions of the supercell and atomic coordinates.
Certainly they are co-related but how.
How to define the cell dimensions and use what mathematics is bothering.

Any clue will be of great help.

Rgds
Deepak

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