Dear Siesta Users,
Before I calculate B2 structure, I did calculation of H2 and O2, which
both give physical reasonable frequencies. However, when I calculate B2
structure, even use same input .fdf file with little change, I got some
negative frequency.
I did it in this way. I put the B2 molecule in the simple cubic lattice
with a large lattice constant. Using Siesta to calculate the Force
Constant. Then Using Vibra to get the vibration mode. Directly following
the "Vibra Manual". (BeforI try to optimize the structure again and
again using higher "mesh cutoff" (as high as 500Ry) and larger lattice
constant (20 A). The negative frequency never disappear, although it
decreased a little. I really have no idea about this. Could someone
please give me some help? Thank you very much.
Yours,
Zhen Zhu
Below are the input files and the result.
1 vibration frequencies:
eigenvalue # 1 omega= -39.1439738621028
eigenvalue # 2 omega= -8.612283334100170E-006
eigenvalue # 3 omega= 1.092488707080067E-007
eigenvalue # 4 omega= 1.526741848390112E-005
eigenvalue # 5 omega= 17.6737744212619
eigenvalue # 6 omega= 1054.72912084076
2 .fdf input file:
SystemName Boron cluster
SystemLabel B2
NumberOfAtoms 2
NumberOfSpecies 1
%block ChemicalSpeciesLabel
1 5 B # Species index, atomic number, species label
%endblock ChemicalSpeciesLabel
%block LatticeVectors
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
%endblock LatticeVectors
MaxSCFIterations 100
DM.MixingWeight 0.2
# PAO.EnergyShift 0.00735 # 0.00367 , 0.000735
MeshCutoff 200.0 Ry
DM.NumberPulay 3
AtomicCoordinatesFormat ScaledCartesian
LatticeConstant 20 Ang
%block AtomicCoordinatesAndAtomicSpecies
-0.011044238 -0.003227402 -0.001410019 1 10.81
0.070043851 0.003227287 0.001410227 1 10.81
%endblock AtomicCoordinatesAndAtomicSpecies
SuperCell_1 0
SuperCell_2 0
SuperCell_3 0
AtomicDispl 0.02 Bohr
%block BandLines
1 0.000 0.000 0.000 \Gamma
%endblock Bandlines
EigenVectors .true.
3 siesta input .fdf file
SystemName Boron cluster
SystemLabel B2
NumberOfAtoms 2
NumberOfSpecies 1
%block ChemicalSpeciesLabel
1 5 B # Species index, atomic number, species label
%endblock ChemicalSpeciesLabel
%block LatticeVectors
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
%endblock LatticeVectors
MaxSCFIterations 100
DM.MixingWeight 0.2
# PAO.EnergyShift 0.00735 # 0.00367 , 0.000735
MeshCutoff 200.0 Ry
DM.NumberPulay 3
DM.Tolerance 1.0d-5
AtomicCoordinatesFormat ScaledCartesian
LatticeConstant 20 Ang
%block AtomicCoordinatesAndAtomicSpecies
-0.011044238 -0.003227402 -0.001410019 1 10.81
0.070043851 0.003227287 0.001410227 1 10.81
%endblock AtomicCoordinatesAndAtomicSpecies
SuperCell_1 0
SuperCell_2 0
SuperCell_3 0
AtomicDispl 0.01 Bohr
%block BandLines
1 0.000 0.000 0.000 \Gamma
%endblock Bandlines
EigenVectors .true.
%include FC.fdf
4 .fdf used for optimization
SystemName Boron cluster
SystemLabel B2
NumberOfAtoms 2
NumberOfSpecies 1
%block ChemicalSpeciesLabel
1 5 B # Species index, atomic number, species label
%endblock ChemicalSpeciesLabel
%block LatticeVectors
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
%endblock LatticeVectors
MaxSCFIterations 100
DM.MixingWeight 0.2
# PAO.EnergyShift 0.00735 # 0.00367 , 0.000735
MeshCutoff 200.0 Ry
DM.NumberPulay 3
DM.Tolerance 1.0d-5
MD.TypeOfRun cg
MD.NumCGsteps 50
MD.MaxCGDispl 0.01 Ang
MD.MaxForceTol 0.005 eV/Ang
AtomicCoordinatesFormat NotScaledCartesianAng
LatticeConstant 20 Ang
%block AtomicCoordinatesAndAtomicSpecies
-0.223962706 -0.0647897 -0.028318365 1 10.81
1.403979751 0.064791065 0.02831727 1 10.81
%endblock AtomicCoordinatesAndAtomicSpecies
SuperCell_1 0
SuperCell_2 0
SuperCell_3 0
