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SIESTA
Spanish Initiative for Electronic
Simulations with Thousands of Atoms

The SIESTA code is freely available for the academic community.

(http://www.uam.es/siesta)

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We are going to do our calculation on
an infinite structure

simulation

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 Structure simulation

Smallest piece of a infinite structure

+
repeat

=
infinite structure
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 simulation
We need to figure
1- a cell which repeat in space and make the infinite structure
2- how many atoms are in this cell
3- three vectors which this cell will repeat with them in space

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 What do we need?
Access to the executable file: siesta
An input file
Flexible Data Format (FDF) (A. Garca & J.M.
Soler).

A psedopotential file for each kind of

element in the input file.
Unformatted binary (vps)
Formatted ASCII (.psf): more transportable
and readable
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 Siesta package: (under
license)
Src: Sources of the Siesta code
Docs: Documentation and user
conditions
Users Guide (siesta.tex)
Pseudo: ATOM program to generate
and test pseudopotentials
Examples: fdf and pseudopotentials
input files for simple systems
Utils: Programs or scripts to analyze 8
FDF

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 FDF characteristics(I)

Data can be given in any order

Data can be omitted in favour of default

values.

Text following # are comments

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 FDF characteristics (II)
Syntax: data label followed by its value
Character string: SystemLabel h2o
Integer: NumberOfAtoms 3
Real: PAO.SplitNorm 0.15
Logical: SpinPolarized .false.
Physical magnitudes LatticeConstant 5.43 Ang

Physical magnitudes: followed by their units.

Many units are valid for the same magnitude (m, cm,
nm, Ang, Bohr).

Character strings, NOT in apostrophes

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 FDF characteristics (III)
Logical values: T / .true. / true / yes
F / .false. / false / no

Complex data structures: blocks

%block label

%endblock label

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 General System description
SystemName: descriptive name of the system
SystemName C surface, .
SystemLabel: nickname to label output files
SystemLabel graphene
After a succesful run, you should have files like
graphene.XV : Final positions and velocities
graphene.EIG : Eigen-energies
...
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 Geometrical and structural
variables
NumberOfAtoms: number of atoms in the
simulation
NumberOfAtoms 2

NumberOfSpecies: number of different

NumberOfSpecies 1
atomic species

ChemicalSpeciesLabel: specify the

different chemical species. ALL THESE
%block ChemicalSpeciesLabel
1 6 C VARIABLES ARE
%endblock ChemicalSpeciesLabel MANDATORY!!14
 Lattice Vectors
LatticeConstant: length to define the scale of the lattice
vectors LatticeConstant 2.47 Ang
LatticeParameters: Crystallograhic way
%block LatticeParameters
1.0 1.0 1.0 60.0 60.0 90.0
%endblock LatticeParameters

LatticeVectors: read as a matrix, each vector being a

line
%block LatticeVectors
0.866 0.5 0.0
-0.866 0.5 0.0
0.0 0.0 10
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%endblock LatticeVectors
 XC-functional DFT

XC.Functional LDA GGA

CA PW92 PBE
XC.authors
PZ CA Ceperley-Alder
PZ Perdew-Zunger
PW92 Perdew-Wang-92
PBE Perdew-Burke-
Ernzerhof 16
 K-point sampling
Spetial set of k-points: Accurate results for a
small # k-points:
Baldereschi, Chadi-Cohen, Monkhorst-Pack
kgrid_cutoff:

Kgrid_cutoff 10.0 Ang

kgrid_Monkhorst_Pack:
%block kgrid_Monkhorst_Pack
40 0 0 0.5
0 40 0 0.5
0 0 40 0.5
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%endblock kgrid_Monkhorst_Pack
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 Analyzing the electronic
structure (I)
Band structure along the high symetry lines
of the BZ
BandLineScale: scale of the k vectors in
BandLines
BandLinesScale pi/a

BandLines: lines along with band energies are

calculated. %block BandLines
1 0.577 1.000 0.000 M
20 0.000 0.000 0.000 \Gamma
25 0.000 2.309 0.000 K
30 0.577 1.000 0.000 M
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%endblock BandLines
 Analyzing the electronic structure
(II)
Density Of States: total and projected on the
atomic orbitals

ProjectedDensityOfStates:

%block ProjectedDensityOfStates
-20.00 10.00 0.200 500 eV
%endblock ProjectedDensityOfStates
Lower energy Higher energy width # points 20
 Run Siesta

esta < systemname.fdf | tee outputname.out

esta < systemname.fdf > outputname.out

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 Output files

Self-
consistenc
y

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 Output files

Total energy

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Symbolname.XV

xv2xsf

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 Symbolname.EIG
Fermi level add: eta, ne, emin, ema
Number of bands Spin components number of k-points
K-point, e1, e2, , en

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eig2dos < silicon.EIG | tee dos.out

eig2dos < silicon.EIG > dos.out

xmgrace dos.out

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Symbolname. DOS

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symbolname.PDOS

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Symbolname.bands
Fermi level
Kmin Kmax
Emin Emax
Number of bands number of spin (1 or 2) number of kpoints

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gnuband < graphene.bands | tee band.out

gnuband < graphene.bands > band.out

Xmgrace band.out
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Band structure

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 Lattice constant optimization

Edit the fdf, changing lattice constant in

a small range around the number which is
experimental.
Run SIESTA.
Write down the total energies after any
run.
Plot the Energy vs. Lattic constant , to
see the
convergence 32
optimization

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 MeshCutoff optimization

Edit the fdf, changing MeshCutoff in a rang

that you want.
Run SIESTA.
Write down the total energies after any run.

Plot the Energy vs. MeshCutoff, to see the

convergence

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Meshcutoff optimization

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Thanks
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