Hi，
I calculate the Au10 cluster by siesta , check the charge density by bader, and get weird result.
The result ACF.dat shows no matter the total charge and atomic charge, they are not correct.
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 10.0307 9.7573 9.5430 1471.6630 0.9123 164092.7937
2 14.4149 7.4044 12.9607 124.0562 1.0730 6258.5757
3 18.4085 6.1856 16.9529 1387.2432 0.5296 151587.8185
4 16.8564 12.3311 12.7011 818.2730 0.4270 85656.6453
5 11.7541 12.0572 13.8600 839.4446 0.6291 83413.1773
6 9.4177 7.2186 14.2902 865.4454 0.9158 100654.7011
7 15.2928 10.4514 17.2985 919.3972 0.7614 83702.3624
8 12.9889 5.5278 17.5879 1267.7044 1.2268 121393.8434
9 15.6194 9.7451 8.4321 1172.4387 1.1152 122398.3813
10 19.5173 7.9331 11.9663 1176.3126 0.3578 124952.3429
--------------------------------------------------------------------------------
NUMBER OF ELECTRONS: 10041.97819
and then I calculated the water molecular and get that result, the total charge is ok, but the atomic charge is still wrong.
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 -0.0963 0.0165 0.0691 0.4447 0.1334 112.8930
2 0.4907 -0.7532 0.0343 3.6161 0.5393 467.6629
3 0.2801 0.6212 -0.5873 3.9464 0.5581 463.5656
--------------------------------------------------------------------------------
NUMBER OF ELECTRONS: 8.00713
I tried several system, they are not right, and it is a little diffcult to find the reason for me. Does there anybody can help me? thanks .
By the way, the steps I did calcultion were:
change *.RHO to *.RHO.cube by denchar(siesta) and then use bader *.RHO.cube to get ACF.dat
I also attacted the siesta inputfile(water molecular) here
SystemLabel h2o # Short name for naming files
NumberOfSpecies 2
NumberOfAtoms 3
%block ChemicalSpeciesLabel
1 8 O
2 1 H
%endblock ChemicalSpeciesLabel
%block AtomicCoordinatesAndAtomicSpecies
-0.069096 -0.097768 0.000000 1
0.898304 -0.048458 0.000000 2
-0.345539 0.830603 0.000000 2
%endblock AtomicCoordinatesAndAtomicSpecies
Denchar.TypeOfRun 3D
Denchar.PlotCharge T
Denchar.PlotWaveFunctions F
Denchar.CoorUnits bohr # Format for coordinate of the points
# Bohr
# Ang
Denchar.DensityUnits Ele/bohr**3 # Units of Charge Density
# Ele/bohr**3
# Ele/Ang**3
# Ele/UnitCell
Denchar.MinX -5.0 bohr # Minimum coordinate of the window in X-dir
Denchar.MaxX 5.0 bohr # Maximum coordinate of the window in X-dir
Denchar.MinY -5.0 bohr # Minimum coordinate of the window in Y-dir
Denchar.MaxY 5.0 bohr # Maximum coordinate of the window in Y-dir
Denchar.MinZ -5.0 bohr # Minimum coordinate of the window in Z-dir
Denchar.MaxZ 5.0 bohr # Maximum coordinate of the window in Z-dir
Denchar.NumberPointsX 70 # Number of points in X-axis
Denchar.NumberPointsY 70 # Number of points in Y-axis
Denchar.NumberPointsZ 70 # Number of points in Z-axis
Denchar.PlaneGeneration ThreePoints # Option to generate the plane
# NormalVector
# TwoLines
# ThreePoints
# ThreeAtomicIndices
%block Denchar.Coor3Points # Coordinates of three points of the plane
0.00000 0.00000 0.00000
2.56530 2.56530 2.56530
0.00000 5.13061 5.13061
%endblock Denchar.Coor3Points
WriteDenchar .true. # Write information for DENCHAR
SaveTotalCharge .true.
weird charge density result was got from siesta
Moderator: moderators
-
JohnnyTsien
- Posts: 1
- Joined: Sun May 09, 2010 5:16 am
Re: weird charge density result was got from siesta
I also got some trouble when I try to calculate the charge density for small clusters. The atomic volume of each metal atom seem to differ a lot.
Look at the atomic volume of your first and second Au atom, they are 164092.7937 and 6258.5757, what caused this huge difference? I got similar results with my metal cluster.
Can you help us, bader masters?
Look at the atomic volume of your first and second Au atom, they are 164092.7937 and 6258.5757, what caused this huge difference? I got similar results with my metal cluster.
Can you help us, bader masters?
Re: weird charge density result was got from siesta
We would like to sort out problems with these charge density files. If you can send them to us, or make them available by posting them, we'll take a look.
Re: weird charge density result was got from siesta
Hi
I put one of the wired result here.
The charge density file ACF.dat, the inputfile and output file. 4d9 5s1 as the valence orbital.Bader only shows about 5 electrons.
Specify SystemLabel (or 'siesta' if none): Pd33-2
Now define the grid cell for your XCrysDen plot.
Note that it can be arbitrarily chosen with respect to the Siesta simulation cell, and it needs not to be orthogonal. We'll define it by the origin point and three spanning vectors. They can be given in Bohr or Ang.
Would you use Bohr (B) or Ang (A) ? A
Enter origin point in Ang : 8.253400 7.898897 17.24630
Enter 1st spanning vector in Ang : 8.253400 0.000000 0.000000
Enter 2nd spanning vector in Ang : -4.126700 6.735200 0.000000
Enter 3rd spanning vector in Ang : 0.000000 0.000000 17.246300
The box contains 18 atoms.
Enter number of grid points along three vectors: 80 80 80
Add grid property (LDOS, RHO, ...; or BYE if none): RHO
Found and opened: Pd33-2.RHO
mesh0 = ( 60 60 150 ), nspin= 2
For is=1: max. grid value = 3.05625E-01 at iix,iiy,iiz= 8 64 13
For is=1: min. grid value =-3.73442E-10 at iix,iiy,iiz= 16 8 31
For is=2: max. grid value = 2.76486E-01 at iix,iiy,iiz= 8 40 13
For is=2: min. grid value =-3.87087E-10 at iix,iiy,iiz= 16 8 31
Add grid property (LDOS, RHO, ...; or BYE if none): BYE
A wild guess! There is no file Pd33-2.BYE; close XSF and quit.
SystemName Pd33-2 # Descriptive name of the system
SystemLabel Pd33-2 # Short name for naming files
NumberOfAtoms 18 # Number of atoms
NumberOfSpecies 1 # Number of species
%block Chemical_Species_Label
1 46 Pd
%endblock Chemical_Species_Label
# Lattice, coordinates, k-sampling
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.000000000 0.000000000 2.246296692 1
1.375570177 0.794185812 0.000000000 1
2.751140354 0.000000000 2.246296692 1
4.126710530 0.794185812 0.000000000 1
5.502280707 0.000000000 2.246296692 1
6.877850884 0.794185812 -0.000000000 1
-1.375570177 2.382557436 2.246296692 1
0.000000000 3.176743247 0.000000000 1
1.375570177 2.382557436 2.246296692 1
2.751140354 3.176743247 -0.000000000 1
4.126710530 2.382557436 2.246296692 1
5.502280707 3.176743247 -0.000000000 1
-2.751140354 4.765114871 2.246296692 1
-1.375570177 5.559300683 0.000000000 1
0.000000000 4.765114871 2.246296692 1
1.375570177 5.559300683 -0.000000000 1
2.751140354 4.765114871 2.246296692 1
4.126710530 5.559300683 -0.000000000 1
%endblock AtomicCoordinatesAndAtomicSpecies
%block GeometryConstraints
position from 1 to 18
%endblock GeometryConstraints
LatticeConstant 1.0 Ang
%block LatticeVectors
8.25340000 0.00000000 0.00000000
-4.12670000 6.735200000 0.00000000
0.00000000 0.00000000 17.24630000
%endblock LatticeVectors
#%block LatticeParameters
# 8.6514 8.6514 17.3546 90.0000 90.0000 120.0000
#%endblock LatticeParameters
#kgrid_cutoff 16. Ang
%block kgrid_Monkhorst_Pack
5 0 0 0.
0 5 0 0.
0 0 1 0.
%endblock kgrid_Monkhorst_Pack
PAO.EnergyShift 50 meV
# Spin
SpinPolarized .true.
FixSpin .false.
#TotalSpin 1.0
# DFT, Grid, SCF
XC.functional GGA # Exchange-correlation functional type
XC.authors PBE # Particular parametrization of xc func
MeshCutoff 200. Ry # Equivalent planewave cutoff for the grid
MaxSCFIterations 200 # Maximum number of SCF iterations per step
DM.MixingWeight 0.05 # New DM amount for next SCF cycle
DM.Tolerance 1.d-4 # Tolerance in maximum difference between input and output DM
DM.NumberPulay 3 # Number of SCF steps between pulay mixing
# Eigenvalue problem: order-N or diagonalization
SolutionMethod diagon # OrderN or Diagon
ElectronicTemperature 5 K # Temp. for Fermi smearing
# Molecular dynamics and relaxations
MD.TypeOfRun CG # Type of dynamics:
MD.NumCGsteps 0
MD.MaxForceTol 0.02 eV/Ang # Tolerance in maximum force (default is 0.04 ev/Ang)
MD.VariableCell .false. # Cell optimization
MD.RelaxCellOnly .false. # cell optimization only (i.e. without internal degrees of freedom)
# Output options
WriteCoorInitial
WriteCoorStep
WriteForces .false.
WriteKpoints .false.
WriteEigenvalues .false.
WriteKbands .false.
WriteBands .false.
WriteMullikenPop 1 # Write Mulliken Population Analysis
WriteCoorXmol .true.
WriteMDCoorXmol .false.
WriteMDhistory .false.
WriteCoorXmol .false.
# Options for saving/reading information
DM.UseSaveDM .false. # Use DM Continuation files
MD.UseSaveXV .false. # Use stored positions and velocities
MD.UseSaveCG .false. # Use stored positions and velocities
SaveRho .true. # Write valence pseudocharge at the mesh
SaveDeltaRho .false. # Write RHOscf-RHOatm at the mesh
SaveElectrostaticPotential .false. # Write the total elect. pot. at the mesh
SaveTotalPotential .false. # Write the total pot. at the mesh
WriteSiestaDim .false. # Write minimum dim to siesta.h and stop
WriteDenchar .false. # Write information for DENCHAR
The ACF.dat
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 15.5967 25.4554 36.8357 5.2374 1.9825 350.3423
2 18.1961 26.9562 32.5908 5.2320 2.0068 347.8278
3 20.7956 25.4554 36.8357 5.2327 1.9803 350.2286
4 23.3950 26.9562 32.5908 5.2331 1.9999 348.5480
5 10.3978 25.4554 36.8357 5.2358 1.9803 349.8242
6 12.9973 26.9562 32.5908 5.2345 1.9653 349.0155
7 20.7956 17.2301 36.8357 5.2172 2.0938 383.9790
8 23.3950 18.7309 32.5908 5.2118 2.1002 377.2441
9 25.9945 17.2301 36.8357 5.2213 2.1534 382.1721
10 28.5939 18.7309 32.5908 5.2232 2.1352 379.7713
11 15.5967 17.2301 36.8357 5.2170 2.1228 381.7045
12 18.1961 18.7309 32.5908 5.2149 2.1705 377.7369
13 18.1961 21.7325 36.8357 5.2253 1.9827 351.8839
14 20.7956 23.2332 32.5908 5.2497 1.9768 347.7140
15 23.3950 21.7325 36.8357 5.2208 2.0111 350.3549
16 25.9945 23.2332 32.5908 5.2379 1.9875 345.1869
17 12.9972 21.7325 36.8357 5.2246 2.0112 350.5697
18 15.5967 23.2332 32.5908 5.2412 2.0232 345.4649
--------------------------------------------------------------------------------
NUMBER OF ELECTRONS: 94.11031
I put one of the wired result here.
The charge density file ACF.dat, the inputfile and output file. 4d9 5s1 as the valence orbital.Bader only shows about 5 electrons.
Specify SystemLabel (or 'siesta' if none): Pd33-2
Now define the grid cell for your XCrysDen plot.
Note that it can be arbitrarily chosen with respect to the Siesta simulation cell, and it needs not to be orthogonal. We'll define it by the origin point and three spanning vectors. They can be given in Bohr or Ang.
Would you use Bohr (B) or Ang (A) ? A
Enter origin point in Ang : 8.253400 7.898897 17.24630
Enter 1st spanning vector in Ang : 8.253400 0.000000 0.000000
Enter 2nd spanning vector in Ang : -4.126700 6.735200 0.000000
Enter 3rd spanning vector in Ang : 0.000000 0.000000 17.246300
The box contains 18 atoms.
Enter number of grid points along three vectors: 80 80 80
Add grid property (LDOS, RHO, ...; or BYE if none): RHO
Found and opened: Pd33-2.RHO
mesh0 = ( 60 60 150 ), nspin= 2
For is=1: max. grid value = 3.05625E-01 at iix,iiy,iiz= 8 64 13
For is=1: min. grid value =-3.73442E-10 at iix,iiy,iiz= 16 8 31
For is=2: max. grid value = 2.76486E-01 at iix,iiy,iiz= 8 40 13
For is=2: min. grid value =-3.87087E-10 at iix,iiy,iiz= 16 8 31
Add grid property (LDOS, RHO, ...; or BYE if none): BYE
A wild guess! There is no file Pd33-2.BYE; close XSF and quit.
SystemName Pd33-2 # Descriptive name of the system
SystemLabel Pd33-2 # Short name for naming files
NumberOfAtoms 18 # Number of atoms
NumberOfSpecies 1 # Number of species
%block Chemical_Species_Label
1 46 Pd
%endblock Chemical_Species_Label
# Lattice, coordinates, k-sampling
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.000000000 0.000000000 2.246296692 1
1.375570177 0.794185812 0.000000000 1
2.751140354 0.000000000 2.246296692 1
4.126710530 0.794185812 0.000000000 1
5.502280707 0.000000000 2.246296692 1
6.877850884 0.794185812 -0.000000000 1
-1.375570177 2.382557436 2.246296692 1
0.000000000 3.176743247 0.000000000 1
1.375570177 2.382557436 2.246296692 1
2.751140354 3.176743247 -0.000000000 1
4.126710530 2.382557436 2.246296692 1
5.502280707 3.176743247 -0.000000000 1
-2.751140354 4.765114871 2.246296692 1
-1.375570177 5.559300683 0.000000000 1
0.000000000 4.765114871 2.246296692 1
1.375570177 5.559300683 -0.000000000 1
2.751140354 4.765114871 2.246296692 1
4.126710530 5.559300683 -0.000000000 1
%endblock AtomicCoordinatesAndAtomicSpecies
%block GeometryConstraints
position from 1 to 18
%endblock GeometryConstraints
LatticeConstant 1.0 Ang
%block LatticeVectors
8.25340000 0.00000000 0.00000000
-4.12670000 6.735200000 0.00000000
0.00000000 0.00000000 17.24630000
%endblock LatticeVectors
#%block LatticeParameters
# 8.6514 8.6514 17.3546 90.0000 90.0000 120.0000
#%endblock LatticeParameters
#kgrid_cutoff 16. Ang
%block kgrid_Monkhorst_Pack
5 0 0 0.
0 5 0 0.
0 0 1 0.
%endblock kgrid_Monkhorst_Pack
PAO.EnergyShift 50 meV
# Spin
SpinPolarized .true.
FixSpin .false.
#TotalSpin 1.0
# DFT, Grid, SCF
XC.functional GGA # Exchange-correlation functional type
XC.authors PBE # Particular parametrization of xc func
MeshCutoff 200. Ry # Equivalent planewave cutoff for the grid
MaxSCFIterations 200 # Maximum number of SCF iterations per step
DM.MixingWeight 0.05 # New DM amount for next SCF cycle
DM.Tolerance 1.d-4 # Tolerance in maximum difference between input and output DM
DM.NumberPulay 3 # Number of SCF steps between pulay mixing
# Eigenvalue problem: order-N or diagonalization
SolutionMethod diagon # OrderN or Diagon
ElectronicTemperature 5 K # Temp. for Fermi smearing
# Molecular dynamics and relaxations
MD.TypeOfRun CG # Type of dynamics:
MD.NumCGsteps 0
MD.MaxForceTol 0.02 eV/Ang # Tolerance in maximum force (default is 0.04 ev/Ang)
MD.VariableCell .false. # Cell optimization
MD.RelaxCellOnly .false. # cell optimization only (i.e. without internal degrees of freedom)
# Output options
WriteCoorInitial
WriteCoorStep
WriteForces .false.
WriteKpoints .false.
WriteEigenvalues .false.
WriteKbands .false.
WriteBands .false.
WriteMullikenPop 1 # Write Mulliken Population Analysis
WriteCoorXmol .true.
WriteMDCoorXmol .false.
WriteMDhistory .false.
WriteCoorXmol .false.
# Options for saving/reading information
DM.UseSaveDM .false. # Use DM Continuation files
MD.UseSaveXV .false. # Use stored positions and velocities
MD.UseSaveCG .false. # Use stored positions and velocities
SaveRho .true. # Write valence pseudocharge at the mesh
SaveDeltaRho .false. # Write RHOscf-RHOatm at the mesh
SaveElectrostaticPotential .false. # Write the total elect. pot. at the mesh
SaveTotalPotential .false. # Write the total pot. at the mesh
WriteSiestaDim .false. # Write minimum dim to siesta.h and stop
WriteDenchar .false. # Write information for DENCHAR
The ACF.dat
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 15.5967 25.4554 36.8357 5.2374 1.9825 350.3423
2 18.1961 26.9562 32.5908 5.2320 2.0068 347.8278
3 20.7956 25.4554 36.8357 5.2327 1.9803 350.2286
4 23.3950 26.9562 32.5908 5.2331 1.9999 348.5480
5 10.3978 25.4554 36.8357 5.2358 1.9803 349.8242
6 12.9973 26.9562 32.5908 5.2345 1.9653 349.0155
7 20.7956 17.2301 36.8357 5.2172 2.0938 383.9790
8 23.3950 18.7309 32.5908 5.2118 2.1002 377.2441
9 25.9945 17.2301 36.8357 5.2213 2.1534 382.1721
10 28.5939 18.7309 32.5908 5.2232 2.1352 379.7713
11 15.5967 17.2301 36.8357 5.2170 2.1228 381.7045
12 18.1961 18.7309 32.5908 5.2149 2.1705 377.7369
13 18.1961 21.7325 36.8357 5.2253 1.9827 351.8839
14 20.7956 23.2332 32.5908 5.2497 1.9768 347.7140
15 23.3950 21.7325 36.8357 5.2208 2.0111 350.3549
16 25.9945 23.2332 32.5908 5.2379 1.9875 345.1869
17 12.9972 21.7325 36.8357 5.2246 2.0112 350.5697
18 15.5967 23.2332 32.5908 5.2412 2.0232 345.4649
--------------------------------------------------------------------------------
NUMBER OF ELECTRONS: 94.11031