2011-2 qt siesta tutorial-1
TRANSCRIPT
SIESTA Tutorial #1
Yong-Hoon Kim & Han Seul KimGraduate School of EEWS
Korea Advanced Institute of Science & Technology
EEW522 Quantum Transport (Fall 2011)
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011 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
EEW522Fall 2011
EEW522Fall 2011 Algorithm of LCAO KS‐DFT
Yes
No
μ
μiμi χcφ )()( rr kkk i
ki
ki
ki
k ccfD *
k
H
Itot RF,Ε
converged?
kkkkkiii cScH
kkkkkiii cScH
LCAO:
Notation:
ki
kki
ki
k cScH
rnnE
r|rr|
rnrdr xc
xcH
;
rrDkdV
rn kkk
V~
*1
Postprocessing: Bandstructure, (P)DOS, population analysis, etc.
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011 Overview for SIESTA
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
EEW522Fall 2011
EEW522Fall 2011 Exercise 1. Basic SIESTA execution
• Contents: CH3 and CH4 Basics (Basis sets, SCF, structural optimization, spin polarization, etc.)
• e.g. CH4
ch4.fdfC.psfH.psf
3Dplot/CH3/CH4/cubic/Exercise-1.pdfGGA/relax/
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011 Exercise 1. Basic SIESTA execution
Basic single point energy calculation: File ch4.fdf
#General system specificationsSystemName CH4 moleculeSystemLabel ch4NumberOfAtoms 5NumberOfSpecies 2
%block ChemicalSpeciesLabel1 6 C # Species index, atomic number, label2 1 H # Species index, atomic number, label%endblock ChemicalSpeciesLabel
#Unit cell for the calculationLatticeConstant 40 Ang%block LatticeVectors1.000 0.000 0.0000.000 1.000 0.0000.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinatesAtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies0.000 0.000 0.000 11.219 -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 definitionPAO.EnergyShift 250 meVPAO.SplitNorm 0.15PAO.BasisSize SZ
#Density functionalXC.functional GGAXC.authors PBE
#Real space grid MeshCutoff 125.0 Ry
# Convergence of SCF MaxSCFIterations 50DM.MixingWeight 0.9DM.NumberPulay 2
# Type of solution (diagon is the default for less than 100 atoms)SolutionMethod diagon
“Modeling” “Simulation”
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011
Basic single point energy calculation: File ch4.fdf
#General system specificationsSystemName CH4 moleculeSystemLabel ch4NumberOfAtoms 5NumberOfSpecies 2
%block ChemicalSpeciesLabel1 6 C # Species index, atomic number, label2 1 H # Species index, atomic number, label%endblock ChemicalSpeciesLabel
#Unit cell for the calculationLatticeConstant 40 Ang%block LatticeVectors1.000 0.000 0.0000.000 1.000 0.0000.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinatesAtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies0.000 0.000 0.000 11.219 -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 definitionPAO.EnergyShift 250 meVPAO.SplitNorm 0.15PAO.BasisSize SZ
#Density functionalXC.functional GGAXC.authors PBE
#Real space grid MeshCutoff 125.0 Ry
# Convergence of SCF MaxSCFIterations 50DM.MixingWeight 0.9DM.NumberPulay 2
# Type of solution (diagon is the default for less than 100 atoms)SolutionMethod diagon
Exercise 1. Basic SIESTA execution
Atomic species info.
Should match pseudopotential file name
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011
Basic single point energy calculation: File ch4.fdf
#General system specificationsSystemName CH4 moleculeSystemLabel ch4NumberOfAtoms 5NumberOfSpecies 2
%block ChemicalSpeciesLabel1 6 C # Species index, atomic number, label2 1 H # Species index, atomic number, label%endblock ChemicalSpeciesLabel
#Unit cell for the calculationLatticeConstant 40 Ang%block LatticeVectors1.000 0.000 0.0000.000 1.000 0.0000.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinatesAtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies0.000 0.000 0.000 11.219 -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 definitionPAO.EnergyShift 250 meVPAO.SplitNorm 0.15PAO.BasisSize SZ
#Density functionalXC.functional GGAXC.authors PBE
#Real space grid MeshCutoff 125.0 Ry
# Convergence of SCF MaxSCFIterations 50DM.MixingWeight 0.9DM.NumberPulay 2
# Type of solution (diagon is the default for less than 100 atoms)SolutionMethod diagon
Exercise 1. Basic SIESTA execution
Atomic coord. Info.
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011
Basic single point energy calculation: File ch4.fdf
#General system specificationsSystemName CH4 moleculeSystemLabel ch4NumberOfAtoms 5NumberOfSpecies 2
%block ChemicalSpeciesLabel1 6 C # Species index, atomic number, label2 1 H # Species index, atomic number, label%endblock ChemicalSpeciesLabel
#Unit cell for the calculationLatticeConstant 40 Ang%block LatticeVectors1.000 0.000 0.0000.000 1.000 0.0000.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinatesAtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies0.000 0.000 0.000 11.219 -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 definitionPAO.EnergyShift 250 meVPAO.SplitNorm 0.15PAO.BasisSize SZ
#Density functionalXC.functional GGAXC.authors PBE
#Real space grid MeshCutoff 125.0 Ry
# Convergence of SCF MaxSCFIterations 50DM.MixingWeight 0.9DM.NumberPulay 2
# Type of solution (diagon is the default for less than 100 atoms)SolutionMethod diagon
Exercise 1. Basic SIESTA execution
Basis sets (automatic)
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011
Basic single point energy calculation: File ch4.fdf
#General system specificationsSystemName CH4 moleculeSystemLabel ch4NumberOfAtoms 5NumberOfSpecies 2
%block ChemicalSpeciesLabel1 6 C # Species index, atomic number, label2 1 H # Species index, atomic number, label%endblock ChemicalSpeciesLabel
#Unit cell for the calculationLatticeConstant 40 Ang%block LatticeVectors1.000 0.000 0.0000.000 1.000 0.0000.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinatesAtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies0.000 0.000 0.000 11.219 -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 definitionPAO.EnergyShift 250 meVPAO.SplitNorm 0.15PAO.BasisSize SZ
#Density functionalXC.functional GGAXC.authors PBE
#Real space grid MeshCutoff 125.0 Ry
# Convergence of SCF MaxSCFIterations 50DM.MixingWeight 0.9DM.NumberPulay 2
# Type of solution (diagon is the default for less than 100 atoms)SolutionMethod diagon
Exercise 1. Basic SIESTA execution
Basis sets (automatic)
Number of orbitals per atom
SZ : cheap calculation* SIESTA default : DZP
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011
Basic single point energy calculation: File ch4.fdf
#General system specificationsSystemName CH4 moleculeSystemLabel ch4NumberOfAtoms 5NumberOfSpecies 2
%block ChemicalSpeciesLabel1 6 C # Species index, atomic number, label2 1 H # Species index, atomic number, label%endblock ChemicalSpeciesLabel
#Unit cell for the calculationLatticeConstant 40 Ang%block LatticeVectors1.000 0.000 0.0000.000 1.000 0.0000.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinatesAtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies0.000 0.000 0.000 11.219 -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 definitionPAO.EnergyShift 250 meVPAO.SplitNorm 0.15PAO.BasisSize SZ
#Density functionalXC.functional GGAXC.authors PBE
#Real space grid MeshCutoff 125.0 Ry
# Convergence of SCF MaxSCFIterations 50DM.MixingWeight 0.9DM.NumberPulay 2
# Type of solution (diagon is the default for less than 100 atoms)SolutionMethod diagon
Exercise 1. Basic SIESTA execution
DFT
If you are using GGA with a pseudopotential generated using LDA, the code will give an ERROR.
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011
Basic single point energy calculation: File ch4.fdf
#General system specificationsSystemName CH4 moleculeSystemLabel ch4NumberOfAtoms 5NumberOfSpecies 2
%block ChemicalSpeciesLabel1 6 C # Species index, atomic number, label2 1 H # Species index, atomic number, label%endblock ChemicalSpeciesLabel
#Unit cell for the calculationLatticeConstant 40 Ang%block LatticeVectors1.000 0.000 0.0000.000 1.000 0.0000.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinatesAtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies0.000 0.000 0.000 11.219 -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 definitionPAO.EnergyShift 250 meVPAO.SplitNorm 0.15PAO.BasisSize SZ
#Density functionalXC.functional GGAXC.authors PBE
#Real space grid MeshCutoff 125.0 Ry
# Convergence of SCF MaxSCFIterations 50DM.MixingWeight 0.9DM.NumberPulay 2
# Type of solution (diagon is the default for less than 100 atoms)SolutionMethod diagon
Exercise 1. Basic SIESTA execution
Grid optionFineness of the real-space grid for Hartree & XC potential & energy (100~200 Ry)
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011
Basic single point energy calculation: File ch4.fdf
#General system specificationsSystemName CH4 moleculeSystemLabel ch4NumberOfAtoms 5NumberOfSpecies 2
%block ChemicalSpeciesLabel1 6 C # Species index, atomic number, label2 1 H # Species index, atomic number, label%endblock ChemicalSpeciesLabel
#Unit cell for the calculationLatticeConstant 40 Ang%block LatticeVectors1.000 0.000 0.0000.000 1.000 0.0000.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinatesAtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies0.000 0.000 0.000 11.219 -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 definitionPAO.EnergyShift 250 meVPAO.SplitNorm 0.15PAO.BasisSize SZ
#Density functionalXC.functional GGAXC.authors PBE
#Real space grid MeshCutoff 125.0 Ry
# Convergence of SCF MaxSCFIterations 50DM.MixingWeight 0.9DM.NumberPulay 2
# Type of solution (diagon is the default for less than 100 atoms)SolutionMethod diagon
Exercise 1. Basic SIESTA execution
SCF
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011
Basic single point energy calculation: File ch4.fdf
#General system specificationsSystemName CH4 moleculeSystemLabel ch4NumberOfAtoms 5NumberOfSpecies 2
%block ChemicalSpeciesLabel1 6 C # Species index, atomic number, label2 1 H # Species index, atomic number, label%endblock ChemicalSpeciesLabel
#Unit cell for the calculationLatticeConstant 40 Ang%block LatticeVectors1.000 0.000 0.0000.000 1.000 0.0000.000 0.000 1.000
%endblock LatticeVectors
#Atomic coordinatesAtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies0.000 0.000 0.000 11.219 -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 definitionPAO.EnergyShift 250 meVPAO.SplitNorm 0.15PAO.BasisSize SZ
#Density functionalXC.functional GGAXC.authors PBE
#Real space grid MeshCutoff 125.0 Ry
# Convergence of SCF MaxSCFIterations 50DM.MixingWeight 0.9DM.NumberPulay 2
# Type of solution (diagon is the default for less than 100 atoms)SolutionMethod diagon
Exercise 1. Basic SIESTA execution
Type of solution
For now, “diagon” or “ordern”. Later, + “transiesta”
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011 Exercise 1. Basic SIESTA execution
Run the program:
siesta < ch4.fdf > ch4.out
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011
Structural optimization: File ch4_relax.fdf under /relax
Add the following:
#Geometrical optimizationMD.TypeOfRun CGMD.NumCGsteps 50MD.MaxCGDispl 0.1 BohrMD.MaxForceTol 0.04d0 eV/Ang
Exercise 1. Basic SIESTA execution
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011
Plotting densities: File ch3_3Dplot.fdf
#General system specificationsSystemName CH3 moleculeSystemLabel ch3NumberOfAtoms 4NumberOfSpecies 2
%block ChemicalSpeciesLabel1 6 C # Species index, atomic number, label2 1 H # Species index, atomic number, label%endblock ChemicalSpeciesLabel
# Basis set definitionPAO.EnergyShift 200 meVPAO.SplitNorm 0.15PAO.BasisSize DZP
#Atomic coordinatesAtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies0.02088760 0.02088714 -0.29121489 1 C1.08698535 -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 50DM.MixingWeight 0.4DM.NumberPulay 2
# Type of solution (diagon is the default for less than 100 atoms)SolutionMethod diagon
#Spin polarizationSpinPolarized .true.
#3DPlotsSaveRho .true.%block LocalDensityOfStates-6.00 -3.00 eV%endblock LocalDensityOfStates
Exercise 1. Basic SIESTA execution
Spin polarization
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011
Plotting densities: File ch3_3Dplot.fdf
#General system specificationsSystemName CH3 moleculeSystemLabel ch3NumberOfAtoms 4NumberOfSpecies 2
%block ChemicalSpeciesLabel1 6 C # Species index, atomic number, label2 1 H # Species index, atomic number, label%endblock ChemicalSpeciesLabel
# Basis set definitionPAO.EnergyShift 200 meVPAO.SplitNorm 0.15PAO.BasisSize DZP
#Atomic coordinatesAtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies0.02088760 0.02088714 -0.29121489 1 C1.08698535 -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 50DM.MixingWeight 0.4DM.NumberPulay 2
# Type of solution (diagon is the default for less than 100 atoms)SolutionMethod diagon
#Spin polarizationSpinPolarized .true.
#3DPlotsSaveRho .true.%block LocalDensityOfStates-6.00 -3.00 eV%endblock LocalDensityOfStates
Exercise 1. Basic SIESTA execution
Charge density, DOS option
Set to get HOMO here.
Post-SCF
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011
Plotting densities: File ch3_3Dplot.fdf
Exercise 1. Basic SIESTA execution
ch3.RHOCh3.LDOS
After running siesta output:
ch3 #system labelrho #Type of file to read5.0 5.0 5.0 #Shift of the origin of coordinates (bohr)1unformatted
To visualize,
grid2cube.x < grid2cube.dat
grid2cube.dat
ch3.RHO.UP.cubech3.RHO.DN.cube
Generated:
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011
Plotting densities: visualization with Molekel
Exercise 1. Basic SIESTA execution
ch3.RHO.UP.cube ch3.RHO.DN.cube
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011
Plotting densities: visualization with Molekel
Exercise 1. Basic SIESTA execution
ch3.LDOS.UP.cube ch3.LDOS.DN.cube
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011 Exercise 2. Bulk crystals: Band structures and DOS
Crystalline material, FCC Al : Al_bulk.fdf
SystemName FCC AlSystemLabel AlNumberOfAtoms 1NumberOfSpecies 1
%block ChemicalSpeciesLabel1 13 Al%endblock ChemicalSpeciesLabel
#Experimental lattice parameter 4.05 AngLatticeConstant 4.05 Ang
%block LatticeVectors0.000000 0.500000 0.50000000.500000 0.000000 0.50000000.500000 0.500000 0.0000000%endblock LatticeVectors
PAO.EnergyShift 200 meVPAO.SplitNorm 0.15PAO.BasisSize SZ
AtomicCoordinatesFormat scaledcartesian
%block AtomicCoordinatesAndAtomicSpecies0.000000 0.000000 0.000000 1
%endblock AtomicCoordinatesAndAtomicSpecies
MeshCutoff 125.0 Ry
%block kgrid_Monkhorst_Pack4 0 0 0.50 4 0 0.50 0 4 0.5
%endblock kgrid_Monkhorst_Pack
MaxSCFIterations 50DM.MixingWeight 0.5DM.NumberPulay 3ElectronicTemperature 300 KSolutionMethod diagon
BandLinesScale pi/a
%block BandLines1 1.0000 1.0000 1.0000 L # Begin L20 0.0000 0.0000 0.0000 \Gamma # 20 points L ~ gamma25 2.0000 0.0000 0.0000 X # 25 points gamma ~ X30 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
EEW522Fall 2011
EEW522Fall 2011 Exercise 2. Bulk crystals: Band structures and DOS
Crystalline material, FCC Al : Al_bulk.fdf
SystemName FCC AlSystemLabel AlNumberOfAtoms 1NumberOfSpecies 1
%block ChemicalSpeciesLabel1 13 Al%endblock ChemicalSpeciesLabel
#Experimental lattice parameter 4.05 AngLatticeConstant 4.05 Ang
%block LatticeVectors0.000000 0.500000 0.50000000.500000 0.000000 0.50000000.500000 0.500000 0.0000000%endblock LatticeVectors
PAO.EnergyShift 200 meVPAO.SplitNorm 0.15PAO.BasisSize SZ
AtomicCoordinatesFormat scaledcartesian
%block AtomicCoordinatesAndAtomicSpecies0.000000 0.000000 0.000000 1
%endblock AtomicCoordinatesAndAtomicSpecies
MeshCutoff 125.0 Ry
%block kgrid_Monkhorst_Pack4 0 0 0.50 4 0 0.50 0 4 0.5
%endblock kgrid_Monkhorst_Pack
MaxSCFIterations 50DM.MixingWeight 0.5DM.NumberPulay 3ElectronicTemperature 300 KSolutionMethod diagon
BandLinesScale pi/a
%block BandLines1 1.0000 1.0000 1.0000 L # Begin L20 0.0000 0.0000 0.0000 \Gamma # 20 points L ~ gamma25 2.0000 0.0000 0.0000 X # 25 points gamma ~ X30 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
EEW522Fall 2011
EEW522Fall 2011 Exercise 2. Bulk crystals: Band structures and DOS
Crystalline material, FCC Al : Al_bulk.fdf
SystemName FCC AlSystemLabel AlNumberOfAtoms 1NumberOfSpecies 1
%block ChemicalSpeciesLabel1 13 Al%endblock ChemicalSpeciesLabel
#Experimental lattice parameter 4.05 AngLatticeConstant 4.05 Ang
%block LatticeVectors0.000000 0.500000 0.50000000.500000 0.000000 0.50000000.500000 0.500000 0.0000000%endblock LatticeVectors
PAO.EnergyShift 200 meVPAO.SplitNorm 0.15PAO.BasisSize SZ
AtomicCoordinatesFormat scaledcartesian
%block AtomicCoordinatesAndAtomicSpecies0.000000 0.000000 0.000000 1
%endblock AtomicCoordinatesAndAtomicSpecies
MeshCutoff 125.0 Ry
%block kgrid_Monkhorst_Pack4 0 0 0.50 4 0 0.50 0 4 0.5
%endblock kgrid_Monkhorst_Pack
MaxSCFIterations 50DM.MixingWeight 0.5DM.NumberPulay 3ElectronicTemperature 300 KSolutionMethod diagon
BandLinesScale pi/a
%block BandLines1 1.0000 1.0000 1.0000 L # Begin L20 0.0000 0.0000 0.0000 \Gamma # 20 points L ~ gamma25 2.0000 0.0000 0.0000 X # 25 points gamma ~ X30 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
EEW522Fall 2011
EEW522Fall 2011 Exercise 2. Bulk crystals: Band structures and DOS
Crystalline material, FCC Al : Al_bulk.fdf
SystemName FCC AlSystemLabel AlNumberOfAtoms 1NumberOfSpecies 1
%block ChemicalSpeciesLabel1 13 Al%endblock ChemicalSpeciesLabel
#Experimental lattice parameter 4.05 AngLatticeConstant 4.05 Ang
%block LatticeVectors0.000000 0.500000 0.50000000.500000 0.000000 0.50000000.500000 0.500000 0.0000000%endblock LatticeVectors
PAO.EnergyShift 200 meVPAO.SplitNorm 0.15PAO.BasisSize SZ
AtomicCoordinatesFormat scaledcartesian
%block AtomicCoordinatesAndAtomicSpecies0.000000 0.000000 0.000000 1
%endblock AtomicCoordinatesAndAtomicSpecies
MeshCutoff 125.0 Ry
%block kgrid_Monkhorst_Pack4 0 0 0.50 4 0 0.50 0 4 0.5
%endblock kgrid_Monkhorst_Pack
MaxSCFIterations 50DM.MixingWeight 0.5DM.NumberPulay 3ElectronicTemperature 300 KSolutionMethod diagon
BandLinesScale pi/a
%block BandLines1 1.0000 1.0000 1.0000 L # Begin L20 0.0000 0.0000 0.0000 \Gamma # 20 points L ~ gamma25 2.0000 0.0000 0.0000 X # 25 points gamma ~ X30 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
EEW522Fall 2011
EEW522Fall 2011 Exercise 2. Bulk crystals: Band structures and DOS
Crystalline material, FCC Al : Al_bulk.fdf
SystemName FCC AlSystemLabel AlNumberOfAtoms 1NumberOfSpecies 1
%block ChemicalSpeciesLabel1 13 Al%endblock ChemicalSpeciesLabel
#Experimental lattice parameter 4.05 AngLatticeConstant 4.05 Ang
%block LatticeVectors0.000000 0.500000 0.50000000.500000 0.000000 0.50000000.500000 0.500000 0.0000000%endblock LatticeVectors
PAO.EnergyShift 200 meVPAO.SplitNorm 0.15PAO.BasisSize SZ
AtomicCoordinatesFormat scaledcartesian
%block AtomicCoordinatesAndAtomicSpecies0.000000 0.000000 0.000000 1
%endblock AtomicCoordinatesAndAtomicSpecies
MeshCutoff 125.0 Ry
%block kgrid_Monkhorst_Pack4 0 0 0.50 4 0 0.50 0 4 0.5
%endblock kgrid_Monkhorst_Pack
MaxSCFIterations 50DM.MixingWeight 0.5DM.NumberPulay 3ElectronicTemperature 300 KSolutionMethod diagon
BandLinesScale pi/a
%block BandLines1 1.0000 1.0000 1.0000 L # Begin L20 0.0000 0.0000 0.0000 \Gamma # 20 points L ~ gamma25 2.0000 0.0000 0.0000 X # 25 points gamma ~ X30 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
EEW522Fall 2011
EEW522Fall 2011
gnubands.x < Al.bands > bands.out
Band structure:
Plotting with gnuplot
Exercise 2. Bulk crystals: Band structures and DOS
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011
DOS plot:
Exercise 2. Bulk crystals: Band structures and DOS
python dos.py Al.DOS
K-point sampling 4x4x4 K-point sampling 18x18x18
Y.-H. Kim@ KAIST EEWS
EEW522Fall 2011
EEW522Fall 2011 Summary
• Background: DFT
• Calculation parameters
• Specific examples
1. Molecules: CH4, CH3, visualization, etc.
2. Solids: Al, band structure, etc.