Example 1 - Materials Computation Center - University of Illinois at ...
Example 1 - Materials Computation Center - University of Illinois at ...
Example 1 - Materials Computation Center - University of Illinois at ...
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SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE<br />
<strong>University</strong> <strong>of</strong> <strong>Illinois</strong> <strong>at</strong> Urbana-Champaign, June 13-23, 2005<br />
<strong>Example</strong> 1<br />
Bulk silicon
SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE<br />
<strong>University</strong> <strong>of</strong> <strong>Illinois</strong> <strong>at</strong> Urbana-Champaign, June 13-23, 2005<br />
Instructions (I)<br />
• Have a look <strong>at</strong> the input file (silicon.fdf)<br />
• Run siesta:<br />
siesta < silicon.fdf | tee silicon.out<br />
• Check output file (silicon.out):<br />
• System type<br />
• Mesh cut<strong>of</strong>f<br />
• SCF steps<br />
• Forces & stress tensor<br />
• Find eigen-energies file (silicon.EIG)
SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE<br />
<strong>University</strong> <strong>of</strong> <strong>Illinois</strong> <strong>at</strong> Urbana-Champaign, June 13-23, 2005<br />
• SystemName silicon<br />
• SystemLabel silicon<br />
• NumberOfAtoms 2<br />
• NumberOfSpecies 1<br />
silicon.fdf<br />
• %block ChemicalSpeciesLabel<br />
• 1 14 Si<br />
• %endblock ChemicalSpeciesLabel<br />
• L<strong>at</strong>ticeConstant 5.430 Ang<br />
• %block L<strong>at</strong>ticeVectors<br />
• 0.500 0.500 0.000<br />
• 0.500 0.000 0.500<br />
• 0.000 0.500 0.500<br />
• %endblock L<strong>at</strong>ticeVectors<br />
• AtomicCoordin<strong>at</strong>esForm<strong>at</strong> ScaledCartesian<br />
• %block AtomicCoordin<strong>at</strong>esAndAtomicSpecies<br />
• 0.000 0.000 0.000 1 Si<br />
• 0.250 0.250 0.250 1 Si<br />
• %endblock AtomicCoordin<strong>at</strong>esAndAtomicSpecies
SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE<br />
<strong>University</strong> <strong>of</strong> <strong>Illinois</strong> <strong>at</strong> Urbana-Champaign, June 13-23, 2005<br />
Instructions (II)<br />
• Check silicon.long.fdf<br />
• Run silicon.long.fdf :<br />
• Plot band structure.<br />
• Use gnubands<br />
• Plot bands.d<strong>at</strong><br />
• xmgrace bands.d<strong>at</strong> &<br />
• Select correct range <strong>of</strong> energies<br />
siesta < silicon.long.fdf | tee silicon.out<br />
gnubands
SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE<br />
<strong>University</strong> <strong>of</strong> <strong>Illinois</strong> <strong>at</strong> Urbana-Champaign, June 13-23, 2005
SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE<br />
<strong>University</strong> <strong>of</strong> <strong>Illinois</strong> <strong>at</strong> Urbana-Champaign, June 13-23, 2005<br />
Plot bandstructure
SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE<br />
<strong>University</strong> <strong>of</strong> <strong>Illinois</strong> <strong>at</strong> Urbana-Champaign, June 13-23, 2005<br />
Instructions (III)<br />
• See in the output file, or using silicon.WFS, the<br />
contributions <strong>of</strong> each orbitals to the bands <strong>at</strong> Γ:<br />
• Open “input.wfs”<br />
• Execute readwf<br />
readwf < input.wfs<br />
• The ouput is in silicon.wfs.d<strong>at</strong>
SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE<br />
<strong>University</strong> <strong>of</strong> <strong>Illinois</strong> <strong>at</strong> Urbana-Champaign, June 13-23, 2005<br />
Instructions (IV)<br />
• Plot the Density Of St<strong>at</strong>es (DOS)<br />
• Modify the silicon.EIG file<br />
• Use the eig2dos utility<br />
• Plot the d<strong>at</strong>a<br />
eig2dos < silicon.EIG | tee dos,d<strong>at</strong><br />
• xmgrace dos.d<strong>at</strong> &<br />
• Select the range <strong>of</strong> energies
SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE<br />
<strong>University</strong> <strong>of</strong> <strong>Illinois</strong> <strong>at</strong> Urbana-Champaign, June 13-23, 2005<br />
silicon.EIG<br />
# bands<br />
Fermi level<br />
# k-points<br />
add: “eta”, “ne”, “emin”, “emax”<br />
# Spin<br />
components<br />
K-point, e 1<br />
, e 2<br />
, …, e n
SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE<br />
<strong>University</strong> <strong>of</strong> <strong>Illinois</strong> <strong>at</strong> Urbana-Champaign, June 13-23, 2005<br />
Instructions (IV)<br />
• Plot the Density Of St<strong>at</strong>es (DOS)<br />
• Modify the silicon.EIG file<br />
• Use the eig2dos utility<br />
• Plot the d<strong>at</strong>a<br />
eig2dos < silicon.EIG | tee dos,d<strong>at</strong><br />
• xmgrace dos.d<strong>at</strong> &<br />
• Select the range <strong>of</strong> energies
SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE<br />
<strong>University</strong> <strong>of</strong> <strong>Illinois</strong> <strong>at</strong> Urbana-Champaign, June 13-23, 2005<br />
Instructions (V)<br />
• Write down the energy.<br />
• Repe<strong>at</strong> the siesta run with different grids:<br />
• Edit the fdf, changing MeshCut<strong>of</strong>f to 40, 50, 80,<br />
100, 120, 180 and 260 Ry. Write down the total<br />
energies.<br />
• Check in the output file the real value <strong>of</strong> the<br />
MeshCut<strong>of</strong>f used in each calcul<strong>at</strong>ion.<br />
• Plot the Energy vs. MeshCut<strong>of</strong>f, to see the<br />
convergence
SUMMER SCHOOL ON COMPUTATIONAL MATERIALS SCIENCE<br />
<strong>University</strong> <strong>of</strong> <strong>Illinois</strong> <strong>at</strong> Urbana-Champaign, June 13-23, 2005<br />
Instructions (VI)<br />
• Write down the energy.<br />
• Repe<strong>at</strong> the siesta run with different kgrid_cut<strong>of</strong>f:<br />
• Edit the fdf, changing kgrid_cut<strong>of</strong>f to 5, 10, 15, 20,<br />
25, 30 , 35, 40 and 45 bohr. Write down the total<br />
energies.<br />
• Check in the output file the number <strong>of</strong> k-points used<br />
in each calcul<strong>at</strong>ion.<br />
• Plot the Energy vs. # k-points, to see the convergence
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