Dear Siesta users,
I have a question about how exactly periodicity works in Siesta and how
the size of an auxiliary supercell is decided.
Why I ask: I want to run calculations with Siesta being driven by an
external code (i-PI). I have two options how to treat periodicity:
a) I can wrap atoms to the unit cell inside the master code. This causes
troubles with reusing the DM from a previous geometry if there were
jumps of atoms to the opposite side of the cell. I'll write another
email for this problem.
b) I can pass the coordinates as they are, which implies possibility
that some molecules will diffuse far away from the origin.
In this email, I ask about (b) only.
I do a simple test and put one atom far away from the box
##############################
%block kgridMonkhorstPack
2 0 0 0.0
0 2 0 0.0
0 0 1 0.0
%endblock kgridMonkhorstPack
LatticeConstant 1. Bohr
%block LatticeVectors
10. 0. 0.
0. 10. 0.
0. 0. 10.
%endblock LatticeVectors
AtomicCoordinatesFormat Bohr
%block AtomicCoordinatesAndAtomicSpecies
1.2 1.6 1. 2 O
2.6 2.8 1. 1 H
2.0 -0.9 1. 1 H
105. 105. 105. 1 H
%endblock AtomicCoordinatesAndAtomicSpecies
##############################
Doing this, I get crazy auxiliary supercell:
**************************************************************************
superc: Internal auxiliary supercell: 23 x 23 x 23 = 12167
superc: Number of atoms, orbitals, and projectors: 48668 340676 523181
**************************************************************************
It's unclear how Siesta treats atoms outside the unit cell, the manual
just states "/Notice that the atomic positions (shifted or not) need not
be within the cell formed by LatticeVectors, since periodic boundary
conditions are always assumed/". Could you please explain this and maybe
point to literature or to the relevant pieces of the code?
Many thanks,
Karen Fidanyan
PhD student
Max Planck Institute for the Structure and Dynamics of Matter
Hamburg, Germany
--
SIESTA is supported by the Spanish Research Agency (AEI) and by the European
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
