Ola Shelton.
Verify if my examplo with CeO2 as correct. Follow CeO2.fdf appended.
Luiz Adolfo de Mello
Em 21/04/2010 15:03, Shelton Jr, William Allison < [email protected] > escreveu:
Thank you Marcos. I will search for "ghost atom" in the manual rather then "vacancy" to see what keywords I need.
Cheers
Bill
On 4/21/10 1:56 PM, "Marcos Veríssimo Alves" wrote:
I'd say you'd only need ghost atoms (the basis functions you talk about) if you need to calculate the formation energy of the vacancy - the so-called BSSE correction.
Marcos
On Wed, Apr 21, 2010 at 7:49 PM, Shelton Jr, William Allison wrote:
I might be mistaken but doesn't siesta use atom-centered basis ? If so, don't you need to put some basis functions on the vacant site ?
Cheers
Bill
On 4/21/10 1:39 PM, "Marcos Veríssimo Alves" wrote:
Just as a vacancy in real life, a vacancy in a DFT calculation is not an addition, but a removal... :)
All you need to do is to remove the undesirable atom(s) from the atom coordinates list in your supercell. Of course, don't forget to update the number of atoms.
Marcos
On Wed, Apr 21, 2010 at 7:30 PM, Shelton Jr, William Allison wrote:
Can siesta treat vacancies ? If so, how can it be added to the input file ?
Cheers
Bill
#General system specifications SystemName CeO2 molecule SystemLabel CeO2 NumberOfAtoms 37 NumberOfSpecies 3
%block ChemicalSpeciesLabel
1 58 Ce # Species index, atomic number, species label
2 8 O # segunda especie
3 -8 O_ghost # ghost atom do O
%endblock ChemicalSpeciesLabel
#Experimental lattice parameter 5.4113 Ang
LatticeConstant 5.4113 Ang
%block LatticeVectors
3.00000000 0.00000000 0.00000000
0.00000000 3.00000000 0.00000000
0.00000000 0.00000000 3.00000000
%endblock LatticeVectors
# Basis set definition
PAO.EnergyShift 200 meV
PAO.SplitNorm 0.15
AO.BasisSize DZP
#%block AtomicMass
# 3 1d30
#%endblock AtomicMass
#Atomic coordinates
AtomicCoordinatesFormat ScaledCartesian
#cluster com 60 atomos
%block AtomicCoordinatesAndAtomicSpecies
0.000000 0.000000 0.000000 1 # 1 0.00000
0.250000 0.250000 0.250000 3 # 2 0.86600
0.750000 0.750000 0.750000 3 # 3 1.50000
0.500000 0.500000 0.000000 1 # 4 0.50000
0.500000 0.000000 0.500000 1 # 5 0.50000
0.000000 0.500000 0.500000 1 # 6 0.50000
0.750000 0.250000 0.250000 2 # 7 0.68750
0.250000 0.750000 0.250000 2 # 8 0.68750
0.250000 0.250000 0.750000 3 # 9 0.68750
1.000000 0.000000 0.000000 1 # 10 1.00000
0.000000 1.000000 0.000000 1 # 11 1.00000
0.000000 0.000000 1.000000 1 # 12 1.00000
0.750000 0.750000 0.250000 2 # 13 1.18750
0.750000 0.250000 0.750000 3 # 14 1.18750
0.250000 0.750000 0.750000 2 # 15 1.18750
1.000000 0.500000 0.500000 1 # 16 1.50000
0.500000 1.000000 0.500000 1 # 17 1.50000
0.500000 0.500000 1.000000 1 # 18 1.50000
1.000000 1.000000 0.000000 1 # 19 2.00000
1.000000 0.000000 1.000000 1 # 20 2.00000
0.000000 1.000000 1.000000 1 # 21 2.00000
1.250000 0.750000 0.250000 2 # 22 2.18750
1.250000 0.250000 0.750000 2 # 23 2.18750
0.750000 1.250000 0.250000 3 # 24 2.18750
0.750000 0.250000 1.250000 2 # 25 2.18750
0.250000 1.250000 0.750000 3 # 26 2.18750
0.250000 0.750000 1.250000 2 # 27 2.18750
1.500000 0.500000 0.000000 1 # 28 2.50000
0.500000 1.500000 0.000000 1 # 29 2.50000
1.500000 0.000000 0.500000 1 # 30 2.50000
0.000000 1.500000 0.500000 1 # 31 2.50000
0.500000 0.000000 1.500000 1 # 32 2.50000
0.000000 0.500000 1.500000 1 # 33 2.50000
1.250000 0.750000 0.750000 2 # 34 2.68750
0.750000 1.250000 0.750000 2 # 35 2.68750
0.750000 0.750000 1.250000 2 # 36 2.68750
1.000000 1.000000 1.000000 1 # 37 3.00000
1.500000 1.000000 0.500000 1 # 38 3.50000
1.000000 1.500000 0.500000 1 # 39 3.50000
1.500000 0.500000 1.000000 1 # 40 3.50000
0.500000 1.500000 1.000000 1 # 41 3.50000
1.000000 0.500000 1.500000 1 # 42 3.50000
0.500000 1.000000 1.500000 1 # 43 3.50000
1.250000 1.250000 0.750000 2 # 44 3.68750
1.250000 0.750000 1.250000 2 # 45 3.68750
0.750000 1.250000 1.250000 2 # 46 3.68750
1.500000 1.500000 0.000000 1 # 47 4.50000
2.000000 0.500000 0.500000 1 # 48 4.50000
0.500000 2.000000 0.500000 1 # 49 4.50000
1.500000 0.000000 1.500000 1 # 50 4.50000
0.000000 1.500000 1.500000 1 # 51 4.50000
0.500000 0.500000 2.000000 1 # 52 4.50000
1.250000 1.250000 1.250000 2 # 54 4.68750
2.000000 1.000000 0.000000 1 # 55 5.00000
1.000000 2.000000 0.000000 1 # 56 5.00000
2.000000 0.000000 1.000000 1 # 57 5.00000
0.000000 2.000000 1.000000 1 # 58 5.00000
1.000000 0.000000 2.000000 1 # 59 5.00000
0.000000 1.000000 2.000000 1 # 60 5.00000
%endblock AtomicCoordinatesAndAtomicSpecies
#%block SuperCell
# 3 0 0
# 0 3 0
# 0 0 3
#%endblock Supercell
#Real space grid
MeshCutoff 50.0 Ry
# K-sampling (alternative specification using kgrid_cutoff)
%block kgrid_Monkhorst_Pack
4 0 0 0.5
0 4 0 0.5
0 0 4 0.5
%endblock kgrid_Monkhorst_Pack
# Convergence of SCF
MaxSCFIterations 1
DM.MixingWeight 0.5
DM.NumberPulay 3
ElectronicTemperature 500 K
SpinPolarized yes
MD.TypeOfRun cg
MD.NumCGsteps 10
MD.MaxCGDispl 0.1 Ang
MD.MaxForceTol 0.04 eV/Ang
# Type of solver
SolutionMethod diagon
# Output (Band structure calculation)
BandLinesScale pi/a
#%block BandLines
#1 1.0000 1.0000 1.0000 L # Begin at L
#20 0.0000 0.0000 0.0000 \Gamma # 20 points from L to gamma
#25 2.0000 0.0000 0.0000 X # 25 points from gamma to X
#30 2.0000 2.0000 2.0000 \Gamma # 30 points from X to gamma
#%endblock BandLines
%block LocalDensityOfStates
-3.50 0.00 eV
%endblock LocalDensityOfStates
%block ProjectedDensityOfStates
-10.00 0.00 0.40 2000 eV
%endblock ProjectedDensityOfStates
#MD.UseStructFile .true.
WriteCoorXmol .true.
#use save data ---- recupera dados anteriores
UseSaveData .true.
#DM.UseSaveDM .true.
