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    Tutorial Siesta

    Uploaded by

    Fardatul Azkiyah
    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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    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd

    Tutorial Siesta

    Uploaded by

    Fardatul Azkiyah
    166 views12 pages
    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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    TUTORIAL SIESTA

    Original Title

    TUTORIAL SIESTA

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    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.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    166 views12 pages

    Tutorial Siesta

    Uploaded by

    Fardatul Azkiyah
    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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    © All Rights Reserved
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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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