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Tutorial Siesta

This document provides instructions for running computational materials science simulations using SIESTA software to study bulk silicon. It describes running SIESTA simulations with different input parameters, analyzing output files to obtain the band structure, density of states, and orbital contributions. It also instructs plotting various results and checking convergence with respect to the mesh cutoff and k-point grid parameters.

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Fardatul Azkiyah
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227 views12 pages

Tutorial Siesta

This document provides instructions for running computational materials science simulations using SIESTA software to study bulk silicon. It describes running SIESTA simulations with different input parameters, analyzing output files to obtain the band structure, density of states, and orbital contributions. It also instructs plotting various results and checking convergence with respect to the mesh cutoff and k-point grid parameters.

Uploaded by

Fardatul Azkiyah
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE

University of Illinois at Urbana-Champaign, June 13-23, 2005

Example 1
Bulk silicon

SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE


University of Illinois at Urbana-Champaign, June 13-23, 2005

Instructions (I)

Have a look at the input file (silicon.fdf)


Run siesta: siesta < silicon.fdf | tee silicon.out

Check output file (silicon.out):

System type
Mesh cutoff
SCF steps
Forces & stress tensor

Find eigen-energies file (silicon.EIG)

SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE


University of Illinois at Urbana-Champaign, June 13-23, 2005

SystemName
silicon
SystemLabel
silicon
NumberOfAtoms
2
NumberOfSpecies 1

%block ChemicalSpeciesLabel
1 14 Si
%endblock ChemicalSpeciesLabel

LatticeConstant

%block LatticeVectors
0.500 0.500 0.000
0.500 0.000 0.500
0.000 0.500 0.500
%endblock LatticeVectors

AtomicCoordinatesFormat ScaledCartesian

%block AtomicCoordinatesAndAtomicSpecies
0.000 0.000 0.000 1 Si
0.250 0.250 0.250 1 Si
%endblock AtomicCoordinatesAndAtomicSpecies

5.430 Ang

silicon.fdf

SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE


University of Illinois at Urbana-Champaign, June 13-23, 2005

Instructions (II)
Check silicon.long.fdf
Run silicon.long.fdf :
siesta < silicon.long.fdf | tee silicon.out

Plot band structure.

Use gnubands gnubands <silicon.bands | tee bands,dat


Plot bands.dat
xmgrace bands.dat &
Select correct range of energies

SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE


University of Illinois at Urbana-Champaign, June 13-23, 2005

SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE


University of Illinois at Urbana-Champaign, June 13-23, 2005

Plot bandstructure

SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE


University of Illinois at Urbana-Champaign, June 13-23, 2005

Instructions (III)
See in the output file, or using silicon.WFS, the
contributions of each orbitals to the bands at :

Open input.wfs

Execute readwf
readwf < input.wfs

The ouput is in silicon.wfs.dat

SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE


University of Illinois at Urbana-Champaign, June 13-23, 2005

Instructions (IV)
Plot the Density Of States (DOS)

Modify the silicon.EIG file


Use the eig2dos utility
eig2dos < silicon.EIG | tee dos,dat

Plot the data


xmgrace dos.dat &
Select the range of energies

SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE


University of Illinois at Urbana-Champaign, June 13-23, 2005

silicon.EIG
Fermi level # k-points
# bands
# Spin
components

K-point, e1, e2, , en

add: eta, ne, emin, emax

SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE


University of Illinois at Urbana-Champaign, June 13-23, 2005

Instructions (IV)
Plot the Density Of States (DOS)

Modify the silicon.EIG file


Use the eig2dos utility
eig2dos < silicon.EIG | tee dos,dat

Plot the data


xmgrace dos.dat &
Select the range of energies

SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE


University of Illinois at Urbana-Champaign, June 13-23, 2005

Instructions (V)
Write down the energy.
Repeat the siesta run with different grids:

Edit the fdf, changing MeshCutoff to 40, 50, 80,


100, 120, 180 and 260 Ry. Write down the total
energies.
Check in the output file the real value of the
MeshCutoff used in each calculation.
Plot the Energy vs. MeshCutoff, to see the
convergence

SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE


University of Illinois at Urbana-Champaign, June 13-23, 2005

Instructions (VI)
Write down the energy.
Repeat the siesta run with different kgrid_cutoff:

Edit the fdf, changing kgrid_cutoff to 5, 10, 15, 20,


25, 30 , 35, 40 and 45 bohr. Write down the total
energies.
Check in the output file the number of k-points used
in each calculation.
Plot the Energy vs. # k-points, to see the convergence

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