SIESTATutorial#1

Yong-Hoon Kim & Han Seul Kim

GraduateSchoolofEEWS
KoreaAdvancedInstituteofScience&Technology
y.h.kim@kaist.ac.kr
EEW522QuantumTransport(Fall2011)
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011 Outline&References
Plan for this tutorial
Lecture 1: SIESTA Based on SIESTA school @ Barcelona 2007
Lecture 2: TranSIESTA Based on SIESTA school @ Barcelona 2009
References
SIESTA homepage (http://www.icmab.es/siesta/) Documentation
Tutorials
TranSIESTA school 2009 (http://wiki.tstutorial.dreamhosters.com)
Exercises available at ..
quest.kaist.ac.kr
ID : class
Pw : siesta
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011 AlgorithmofLCAOKSDFT
Yes
No

i i
c ) ( ) ( r r
k k k

=
i
k
i
k
i
k
i
k
c c f D
*

v v
k

H
( )
I tot
R F ,

converged?

=

k
c
k k k k k
i i i
c S c H
k k k k k
i i i
c S c H c =
LCAO:
Notation:

=

k
c
k
i
k k
i
k
i
k
c S c H

( )
( )
( )
| |
( ) r n
n E
r
| r r |
r n
r d r
xc
xc H

o
o
u u =
'
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' =
}
;
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}
=
v
v v
_ _ r r D k d
V
r n
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~

*
1
Postprocessing: Bandstructure, (P)DOS, population analysis, etc.
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011 OverviewforSIESTA
input
*.psf
*.vps
*.fdf Including structure, SCF options, etc.
Pseudopotential for each atomic species.
output
Post-processing
*.bands
*.PDOS
*.LDOS
*.EIG

Visualization / plotting of
Band structure,
PDOS
LDOS
MD movie
Phonon vibration mode
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011 Exercise1.BasicSIESTAexecution
Contents: CH
3
and CH
4
Basics (Basis sets, SCF, structural optimization,
spin polarization, etc.)
e.g. CH4
ch4.fdf
C.psf
H.psf
3Dplot/
CH3/
CH4/
cubic/
Exercise-1.pdf
GGA/
relax/
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011 Exercise1.BasicSIESTAexecution
Basic single point energy calculation: File ch4.fdf
#General system specifications
SystemName CH4 molecule
SystemLabel ch4
NumberOfAtoms 5
NumberOfSpecies 2
%block ChemicalSpeciesLabel
1 6 C # Species index, atomic number, label
2 1 H # Species index, atomic number, label
%endblock ChemicalSpeciesLabel
#Unit cell for the calculation
LatticeConstant 40 Ang
%block LatticeVectors
1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinates
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.000 0.000 0.000 1
1.219 -0.284 -0.377 2
-0.284 1.219 -0.377 2
-0.140 -0.140 1.219 2
-0.833 -0.833 -0.503 2
%endblock AtomicCoordinatesAndAtomicSpecies
# Basis set definition
PAO.EnergyShift 250 meV
PAO.SplitNorm 0.15
PAO.BasisSize SZ
#Density functional
XC.functional GGA
XC.authors PBE
#Real space grid
MeshCutoff 125.0 Ry
# Convergence of SCF
MaxSCFIterations 50
DM.MixingWeight 0.9
DM.NumberPulay 2
# Type of solution (diagon is the default for less than
100 atoms)
SolutionMethod diagon
Modeling Simulation
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011
Basic single point energy calculation: File ch4.fdf
#General system specifications
SystemName CH4 molecule
SystemLabel ch4
NumberOfAtoms 5
NumberOfSpecies 2
%block ChemicalSpeciesLabel
1 6 C # Species index, atomic number, label
2 1 H # Species index, atomic number, label
%endblock ChemicalSpeciesLabel
#Unit cell for the calculation
LatticeConstant 40 Ang
%block LatticeVectors
1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinates
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.000 0.000 0.000 1
1.219 -0.284 -0.377 2
-0.284 1.219 -0.377 2
-0.140 -0.140 1.219 2
-0.833 -0.833 -0.503 2
%endblock AtomicCoordinatesAndAtomicSpecies
# Basis set definition
PAO.EnergyShift 250 meV
PAO.SplitNorm 0.15
PAO.BasisSize SZ
#Density functional
XC.functional GGA
XC.authors PBE
#Real space grid
MeshCutoff 125.0 Ry
# Convergence of SCF
MaxSCFIterations 50
DM.MixingWeight 0.9
DM.NumberPulay 2
# Type of solution (diagon is the default for less than
100 atoms)
SolutionMethod diagon
Exercise1.BasicSIESTAexecution
Atomic species info.
Should match pseudopotential file name
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011
Basic single point energy calculation: File ch4.fdf
#General system specifications
SystemName CH4 molecule
SystemLabel ch4
NumberOfAtoms 5
NumberOfSpecies 2
%block ChemicalSpeciesLabel
1 6 C # Species index, atomic number, label
2 1 H # Species index, atomic number, label
%endblock ChemicalSpeciesLabel
#Unit cell for the calculation
LatticeConstant 40 Ang
%block LatticeVectors
1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinates
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.000 0.000 0.000 1
1.219 -0.284 -0.377 2
-0.284 1.219 -0.377 2
-0.140 -0.140 1.219 2
-0.833 -0.833 -0.503 2
%endblock AtomicCoordinatesAndAtomicSpecies
# Basis set definition
PAO.EnergyShift 250 meV
PAO.SplitNorm 0.15
PAO.BasisSize SZ
#Density functional
XC.functional GGA
XC.authors PBE
#Real space grid
MeshCutoff 125.0 Ry
# Convergence of SCF
MaxSCFIterations 50
DM.MixingWeight 0.9
DM.NumberPulay 2
# Type of solution (diagon is the default for less than
100 atoms)
SolutionMethod diagon
Exercise1.BasicSIESTAexecution
Atomic coord. Info.
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011
Basic single point energy calculation: File ch4.fdf
#General system specifications
SystemName CH4 molecule
SystemLabel ch4
NumberOfAtoms 5
NumberOfSpecies 2
%block ChemicalSpeciesLabel
1 6 C # Species index, atomic number, label
2 1 H # Species index, atomic number, label
%endblock ChemicalSpeciesLabel
#Unit cell for the calculation
LatticeConstant 40 Ang
%block LatticeVectors
1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinates
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.000 0.000 0.000 1
1.219 -0.284 -0.377 2
-0.284 1.219 -0.377 2
-0.140 -0.140 1.219 2
-0.833 -0.833 -0.503 2
%endblock AtomicCoordinatesAndAtomicSpecies
# Basis set definition
PAO.EnergyShift 250 meV
PAO.SplitNorm 0.15
PAO.BasisSize SZ
#Density functional
XC.functional GGA
XC.authors PBE
#Real space grid
MeshCutoff 125.0 Ry
# Convergence of SCF
MaxSCFIterations 50
DM.MixingWeight 0.9
DM.NumberPulay 2
# Type of solution (diagon is the default for less than
100 atoms)
SolutionMethod diagon
Exercise1.BasicSIESTAexecution
Basis sets (automatic)
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011
Basic single point energy calculation: File ch4.fdf
#General system specifications
SystemName CH4 molecule
SystemLabel ch4
NumberOfAtoms 5
NumberOfSpecies 2
%block ChemicalSpeciesLabel
1 6 C # Species index, atomic number, label
2 1 H # Species index, atomic number, label
%endblock ChemicalSpeciesLabel
#Unit cell for the calculation
LatticeConstant 40 Ang
%block LatticeVectors
1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinates
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.000 0.000 0.000 1
1.219 -0.284 -0.377 2
-0.284 1.219 -0.377 2
-0.140 -0.140 1.219 2
-0.833 -0.833 -0.503 2
%endblock AtomicCoordinatesAndAtomicSpecies
# Basis set definition
PAO.EnergyShift 250 meV
PAO.SplitNorm 0.15
PAO.BasisSize SZ
#Density functional
XC.functional GGA
XC.authors PBE
#Real space grid
MeshCutoff 125.0 Ry
# Convergence of SCF
MaxSCFIterations 50
DM.MixingWeight 0.9
DM.NumberPulay 2
# Type of solution (diagon is the default for less than
100 atoms)
SolutionMethod diagon
Exercise1.BasicSIESTAexecution
Basis sets (automatic)
Number of orbitals per atom
SZ : cheap calculation
* SIESTA default : DZP
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011
Basic single point energy calculation: File ch4.fdf
#General system specifications
SystemName CH4 molecule
SystemLabel ch4
NumberOfAtoms 5
NumberOfSpecies 2
%block ChemicalSpeciesLabel
1 6 C # Species index, atomic number, label
2 1 H # Species index, atomic number, label
%endblock ChemicalSpeciesLabel
#Unit cell for the calculation
LatticeConstant 40 Ang
%block LatticeVectors
1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinates
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.000 0.000 0.000 1
1.219 -0.284 -0.377 2
-0.284 1.219 -0.377 2
-0.140 -0.140 1.219 2
-0.833 -0.833 -0.503 2
%endblock AtomicCoordinatesAndAtomicSpecies
# Basis set definition
PAO.EnergyShift 250 meV
PAO.SplitNorm 0.15
PAO.BasisSize SZ
#Density functional
XC.functional GGA
XC.authors PBE
#Real space grid
MeshCutoff 125.0 Ry
# Convergence of SCF
MaxSCFIterations 50
DM.MixingWeight 0.9
DM.NumberPulay 2
# Type of solution (diagon is the default for less than
100 atoms)
SolutionMethod diagon
Exercise1.BasicSIESTAexecution
DFT
If you are using
GGA with a pseudopotential generated
using LDA, the code will give an ERROR.
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011
Basic single point energy calculation: File ch4.fdf
#General system specifications
SystemName CH4 molecule
SystemLabel ch4
NumberOfAtoms 5
NumberOfSpecies 2
%block ChemicalSpeciesLabel
1 6 C # Species index, atomic number, label
2 1 H # Species index, atomic number, label
%endblock ChemicalSpeciesLabel
#Unit cell for the calculation
LatticeConstant 40 Ang
%block LatticeVectors
1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinates
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.000 0.000 0.000 1
1.219 -0.284 -0.377 2
-0.284 1.219 -0.377 2
-0.140 -0.140 1.219 2
-0.833 -0.833 -0.503 2
%endblock AtomicCoordinatesAndAtomicSpecies
# Basis set definition
PAO.EnergyShift 250 meV
PAO.SplitNorm 0.15
PAO.BasisSize SZ
#Density functional
XC.functional GGA
XC.authors PBE
#Real space grid
MeshCutoff 125.0 Ry
# Convergence of SCF
MaxSCFIterations 50
DM.MixingWeight 0.9
DM.NumberPulay 2
# Type of solution (diagon is the default for less than
100 atoms)
SolutionMethod diagon
Exercise1.BasicSIESTAexecution
Grid option
Fineness of the real-space grid
for Hartree & XC potential &
energy (100~200 Ry)
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011
Basic single point energy calculation: File ch4.fdf
#General system specifications
SystemName CH4 molecule
SystemLabel ch4
NumberOfAtoms 5
NumberOfSpecies 2
%block ChemicalSpeciesLabel
1 6 C # Species index, atomic number, label
2 1 H # Species index, atomic number, label
%endblock ChemicalSpeciesLabel
#Unit cell for the calculation
LatticeConstant 40 Ang
%block LatticeVectors
1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinates
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.000 0.000 0.000 1
1.219 -0.284 -0.377 2
-0.284 1.219 -0.377 2
-0.140 -0.140 1.219 2
-0.833 -0.833 -0.503 2
%endblock AtomicCoordinatesAndAtomicSpecies
# Basis set definition
PAO.EnergyShift 250 meV
PAO.SplitNorm 0.15
PAO.BasisSize SZ
#Density functional
XC.functional GGA
XC.authors PBE
#Real space grid
MeshCutoff 125.0 Ry
# Convergence of SCF
MaxSCFIterations 50
DM.MixingWeight 0.9
DM.NumberPulay 2
# Type of solution (diagon is the default for less than
100 atoms)
SolutionMethod diagon
Exercise1.BasicSIESTAexecution
SCF
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011
Basic single point energy calculation: File ch4.fdf
#General system specifications
SystemName CH4 molecule
SystemLabel ch4
NumberOfAtoms 5
NumberOfSpecies 2
%block ChemicalSpeciesLabel
1 6 C # Species index, atomic number, label
2 1 H # Species index, atomic number, label
%endblock ChemicalSpeciesLabel
#Unit cell for the calculation
LatticeConstant 40 Ang
%block LatticeVectors
1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinates
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.000 0.000 0.000 1
1.219 -0.284 -0.377 2
-0.284 1.219 -0.377 2
-0.140 -0.140 1.219 2
-0.833 -0.833 -0.503 2
%endblock AtomicCoordinatesAndAtomicSpecies
# Basis set definition
PAO.EnergyShift 250 meV
PAO.SplitNorm 0.15
PAO.BasisSize SZ
#Density functional
XC.functional GGA
XC.authors PBE
#Real space grid
MeshCutoff 125.0 Ry
# Convergence of SCF
MaxSCFIterations 50
DM.MixingWeight 0.9
DM.NumberPulay 2
# Type of solution (diagon is the default for less than
100 atoms)
SolutionMethod diagon
Exercise1.BasicSIESTAexecution
Type of solution
For now, diagon or ordern.
Later, + transiesta
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011 Exercise1.BasicSIESTAexecution
Run the program:
siesta < ch4.fdf > ch4.out
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@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011
Structural optimization: File ch4_relax.fdf under /relax
Add the following:
#Geometrical optimization
MD.TypeOfRun CG
MD.NumCGsteps 50
MD.MaxCGDispl 0.1 Bohr
MD.MaxForceTol 0.04d0 eV/Ang
Exercise1.BasicSIESTAexecution
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011
Plotting densities: File ch3_3Dplot.fdf
#General system specifications
SystemName CH3 molecule
SystemLabel ch3
NumberOfAtoms 4
NumberOfSpecies 2
%block ChemicalSpeciesLabel
1 6 C # Species index, atomic number, label
2 1 H # Species index, atomic number, label
%endblock ChemicalSpeciesLabel
# Basis set definition
PAO.EnergyShift 200 meV
PAO.SplitNorm 0.15
PAO.BasisSize DZP
#Atomic coordinates
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.02088760 0.02088714 -0.29121489 1 C
1.08698535 -0.26624925 -0.24725790 2 H
-0.26624937 1.08698563 -0.24725791 2 H
-0.75546282 -0.75546274 -0.40463117 2 H
%endblock AtomicCoordinatesAndAtomicSpecies
#Real space grid
MeshCutoff 125.0 Ry
# Convergence of SCF
MaxSCFIterations 50
DM.MixingWeight 0.4
DM.NumberPulay 2
# Type of solution (diagon is the default for less than
100 atoms)
SolutionMethod diagon
#Spin polarization
SpinPolarized .true.
#3DPlots
SaveRho .true.
%block LocalDensityOfStates
-6.00 -3.00 eV
%endblock LocalDensityOfStates
Exercise1.BasicSIESTAexecution
Spin polarization
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011
Plotting densities: File ch3_3Dplot.fdf
#General system specifications
SystemName CH3 molecule
SystemLabel ch3
NumberOfAtoms 4
NumberOfSpecies 2
%block ChemicalSpeciesLabel
1 6 C # Species index, atomic number, label
2 1 H # Species index, atomic number, label
%endblock ChemicalSpeciesLabel
# Basis set definition
PAO.EnergyShift 200 meV
PAO.SplitNorm 0.15
PAO.BasisSize DZP
#Atomic coordinates
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.02088760 0.02088714 -0.29121489 1 C
1.08698535 -0.26624925 -0.24725790 2 H
-0.26624937 1.08698563 -0.24725791 2 H
-0.75546282 -0.75546274 -0.40463117 2 H
%endblock AtomicCoordinatesAndAtomicSpecies
#Real space grid
MeshCutoff 125.0 Ry
# Convergence of SCF
MaxSCFIterations 50
DM.MixingWeight 0.4
DM.NumberPulay 2
# Type of solution (diagon is the default for less than
100 atoms)
SolutionMethod diagon
#Spin polarization
SpinPolarized .true.
#3DPlots
SaveRho .true.
%block LocalDensityOfStates
-6.00 -3.00 eV
%endblock LocalDensityOfStates
Exercise1.BasicSIESTAexecution
Charge density, DOS option
Set to get HOMO here.
Post-SCF
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011
Plotting densities: File ch3_3Dplot.fdf
Exercise1.BasicSIESTAexecution
ch3.RHO
Ch3.LDOS
After running siesta output:
ch3 #system label
rho #Type of file to read
5.0 5.0 5.0 #Shift of the origin of coordinates (bohr)
1
unformatted
To visualize,
grid2cube.x < grid2cube.dat
grid2cube.dat
ch3.RHO.UP.cube
ch3.RHO.DN.cube
Generated:
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011
Plotting densities: visualization with Molekel
Exercise1.BasicSIESTAexecution
ch3.RHO.UP.cube ch3.RHO.DN.cube
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011
Plotting densities: visualization with Molekel
Exercise1.BasicSIESTAexecution
ch3.LDOS.UP.cube ch3.LDOS.DN.cube
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011 Exercise2.Bulkcrystals:BandstructuresandDOS
Crystalline material, FCC Al : Al_bulk.fdf
SystemName FCC Al
SystemLabel Al
NumberOfAtoms 1
NumberOfSpecies 1
%block ChemicalSpeciesLabel
1 13 Al
%endblock ChemicalSpeciesLabel
#Experimental lattice parameter 4.05 Ang
LatticeConstant 4.05 Ang
%block LatticeVectors
0.000000 0.500000 0.5000000
0.500000 0.000000 0.5000000
0.500000 0.500000 0.0000000
%endblock LatticeVectors
PAO.EnergyShift 200 meV
PAO.SplitNorm 0.15
PAO.BasisSize SZ
AtomicCoordinatesFormat scaledcartesian
%block AtomicCoordinatesAndAtomicSpecies
0.000000 0.000000 0.000000 1
%endblock AtomicCoordinatesAndAtomicSpecies
MeshCutoff 125.0 Ry
%block kgrid_Monkhorst_Pack
4 0 0 0.5
0 4 0 0.5
0 0 4 0.5
%endblock kgrid_Monkhorst_Pack
MaxSCFIterations 50
DM.MixingWeight 0.5
DM.NumberPulay 3
ElectronicTemperature 300 K
SolutionMethod diagon
BandLinesScale pi/a
%block BandLines
1 1.0000 1.0000 1.0000 L # Begin L
20 0.0000 0.0000 0.0000 \Gamma # 20 points L ~ gamma
25 2.0000 0.0000 0.0000 X # 25 points gamma ~ X
30 2.0000 2.0000 2.0000 \Gamma # 30 points X ~ gamma
%endblock BandLines
%block ProjetedDensityOfStates
-15.0 10.0 0.1 2501 eV
%endblock ProjetedDensityOfStates
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011 Exercise2.Bulkcrystals:BandstructuresandDOS
Crystalline material, FCC Al : Al_bulk.fdf
SystemName FCC Al
SystemLabel Al
NumberOfAtoms 1
NumberOfSpecies 1
%block ChemicalSpeciesLabel
1 13 Al
%endblock ChemicalSpeciesLabel
#Experimental lattice parameter 4.05 Ang
LatticeConstant 4.05 Ang
%block LatticeVectors
0.000000 0.500000 0.5000000
0.500000 0.000000 0.5000000
0.500000 0.500000 0.0000000
%endblock LatticeVectors
PAO.EnergyShift 200 meV
PAO.SplitNorm 0.15
PAO.BasisSize SZ
AtomicCoordinatesFormat scaledcartesian
%block AtomicCoordinatesAndAtomicSpecies
0.000000 0.000000 0.000000 1
%endblock AtomicCoordinatesAndAtomicSpecies
MeshCutoff 125.0 Ry
%block kgrid_Monkhorst_Pack
4 0 0 0.5
0 4 0 0.5
0 0 4 0.5
%endblock kgrid_Monkhorst_Pack
MaxSCFIterations 50
DM.MixingWeight 0.5
DM.NumberPulay 3
ElectronicTemperature 300 K
SolutionMethod diagon
BandLinesScale pi/a
%block BandLines
1 1.0000 1.0000 1.0000 L # Begin L
20 0.0000 0.0000 0.0000 \Gamma # 20 points L ~ gamma
25 2.0000 0.0000 0.0000 X # 25 points gamma ~ X
30 2.0000 2.0000 2.0000 \Gamma # 30 points X ~ gamma
%endblock BandLines
%block ProjetedDensityOfStates
-15.0 10.0 0.1 2501 eV
%endblock ProjetedDensityOfStates
Solid = Lattice + Basis (cf. Kittel Ch.1)
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011 Exercise2.Bulkcrystals:BandstructuresandDOS
Crystalline material, FCC Al : Al_bulk.fdf
SystemName FCC Al
SystemLabel Al
NumberOfAtoms 1
NumberOfSpecies 1
%block ChemicalSpeciesLabel
1 13 Al
%endblock ChemicalSpeciesLabel
#Experimental lattice parameter 4.05 Ang
LatticeConstant 4.05 Ang
%block LatticeVectors
0.000000 0.500000 0.5000000
0.500000 0.000000 0.5000000
0.500000 0.500000 0.0000000
%endblock LatticeVectors
PAO.EnergyShift 200 meV
PAO.SplitNorm 0.15
PAO.BasisSize SZ
AtomicCoordinatesFormat scaledcartesian
%block AtomicCoordinatesAndAtomicSpecies
0.000000 0.000000 0.000000 1
%endblock AtomicCoordinatesAndAtomicSpecies
MeshCutoff 125.0 Ry
%block kgrid_Monkhorst_Pack
4 0 0 0.5
0 4 0 0.5
0 0 4 0.5
%endblock kgrid_Monkhorst_Pack
MaxSCFIterations 50
DM.MixingWeight 0.5
DM.NumberPulay 3
ElectronicTemperature 300 K
SolutionMethod diagon
BandLinesScale pi/a
%block BandLines
1 1.0000 1.0000 1.0000 L # Begin L
20 0.0000 0.0000 0.0000 \Gamma # 20 points L ~ gamma
25 2.0000 0.0000 0.0000 X # 25 points gamma ~ X
30 2.0000 2.0000 2.0000 \Gamma # 30 points X ~ gamma
%endblock BandLines
%block ProjetedDensityOfStates
-15.0 10.0 0.1 2501 eV
%endblock ProjetedDensityOfStates
K-point sampling
Convergence test should be done!
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011 Exercise2.Bulkcrystals:BandstructuresandDOS
Crystalline material, FCC Al : Al_bulk.fdf
SystemName FCC Al
SystemLabel Al
NumberOfAtoms 1
NumberOfSpecies 1
%block ChemicalSpeciesLabel
1 13 Al
%endblock ChemicalSpeciesLabel
#Experimental lattice parameter 4.05 Ang
LatticeConstant 4.05 Ang
%block LatticeVectors
0.000000 0.500000 0.5000000
0.500000 0.000000 0.5000000
0.500000 0.500000 0.0000000
%endblock LatticeVectors
PAO.EnergyShift 200 meV
PAO.SplitNorm 0.15
PAO.BasisSize SZ
AtomicCoordinatesFormat scaledcartesian
%block AtomicCoordinatesAndAtomicSpecies
0.000000 0.000000 0.000000 1
%endblock AtomicCoordinatesAndAtomicSpecies
MeshCutoff 125.0 Ry
%block kgrid_Monkhorst_Pack
4 0 0 0.5
0 4 0 0.5
0 0 4 0.5
%endblock kgrid_Monkhorst_Pack
MaxSCFIterations 50
DM.MixingWeight 0.5
DM.NumberPulay 3
ElectronicTemperature 300 K
SolutionMethod diagon
BandLinesScale pi/a
%block BandLines
1 1.0000 1.0000 1.0000 L # Begin L
20 0.0000 0.0000 0.0000 \Gamma # 20 points L ~ gamma
25 2.0000 0.0000 0.0000 X # 25 points gamma ~ X
30 2.0000 2.0000 2.0000 \Gamma # 30 points X ~ gamma
%endblock BandLines
%block ProjetedDensityOfStates
-15.0 10.0 0.1 2501 eV
%endblock ProjetedDensityOfStates
Band calculation option
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011 Exercise2.Bulkcrystals:BandstructuresandDOS
Crystalline material, FCC Al : Al_bulk.fdf
SystemName FCC Al
SystemLabel Al
NumberOfAtoms 1
NumberOfSpecies 1
%block ChemicalSpeciesLabel
1 13 Al
%endblock ChemicalSpeciesLabel
#Experimental lattice parameter 4.05 Ang
LatticeConstant 4.05 Ang
%block LatticeVectors
0.000000 0.500000 0.5000000
0.500000 0.000000 0.5000000
0.500000 0.500000 0.0000000
%endblock LatticeVectors
PAO.EnergyShift 200 meV
PAO.SplitNorm 0.15
PAO.BasisSize SZ
AtomicCoordinatesFormat scaledcartesian
%block AtomicCoordinatesAndAtomicSpecies
0.000000 0.000000 0.000000 1
%endblock AtomicCoordinatesAndAtomicSpecies
MeshCutoff 125.0 Ry
%block kgrid_Monkhorst_Pack
4 0 0 0.5
0 4 0 0.5
0 0 4 0.5
%endblock kgrid_Monkhorst_Pack
MaxSCFIterations 50
DM.MixingWeight 0.5
DM.NumberPulay 3
ElectronicTemperature 300 K
SolutionMethod diagon
BandLinesScale pi/a
%block BandLines
1 1.0000 1.0000 1.0000 L # Begin L
20 0.0000 0.0000 0.0000 \Gamma # 20 points L ~ gamma
25 2.0000 0.0000 0.0000 X # 25 points gamma ~ X
30 2.0000 2.0000 2.0000 \Gamma # 30 points X ~ gamma
%endblock BandLines
%block ProjetedDensityOfStates
-15.0 10.0 0.1 2501 eV
%endblock ProjetedDensityOfStates
PDOS option
energy range (min / max), broadening, number of points, unit
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011
gnubands.x < Al.bands > bands.out
Band structure:
Plotting with gnuplot
Exercise2.Bulkcrystals:BandstructuresandDOS
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011
DOS plot:
Exercise2.Bulkcrystals:BandstructuresandDOS
python dos.py Al.DOS
K-point sampling 4x4x4 K-point sampling 18x18x18
Y.-H. Kim
@ KAIST EEWS
EEW522
Fall2011
EEW522
Fall2011 Summary
Background: DFT
Calculation parameters
Specific examples
1. Molecules: CH
4
, CH
3
, visualization, etc.
2. Solids: Al, band structure, etc.