Hello "saikatp" (please let us know your name).
Are those negative eigenvalues significantly different from
zero and do not correspond to pure translation modes ?.
If so, that generally means the relaxation step is not
good enough, not well converged (assuming your structure is
stable, of course).
Try a lower Max force tolerance, such as 0.01 eV/Ang (instead
of the default 0.04 eV/Ang).
Also watch the energy convergence of the SCF cycles; it should be
pretty smooth and good to the 0.001 eV or so. This might require
using a DM tolerance smaller than the default 0.0001.
Check the manual for the "egg box" effect and the ways to alleviate
it, your MeshCutoff might be too small (I have no experience with
CNTs though).
Regards
Roberto
On Mon, 3 Sep 2012, [email protected] wrote:
Dear siesta user
I am a beginner in siesta and to quantum mechanics simulation.I want to
calculate phonon frequency of (8,0) CNT.In a trial run I followed the
following steps.
a> Structural relaxation with MD.Typeofrun CG with variablecell true.
b> After I used the coordinates output of first step to calculate
MD.typeofrun FC.
my .fdf code is given below.
SystemName Phonon calculation # Descriptive name of the system
SystemLabel 8_0 # Short name for naming files
# Output options
# Species and atoms
%block ChemicalSpeciesLabel
1 6 C
%endblock ChemicalSpeciesLabel
NumberOfSpecies 1
NumberOfAtoms 32
WriteKpoints true
%block kgrid_Monkhorst_Pack
1 0 0 0.5
0 1 0 0.5
0 0 9 0.5
%endblock kgrid_Monkhorst_Pack
LatticeConstant 1 Ang
%block LatticeVectors
99.726332691 -0.002757406 0.000570988
-0.002757317 99.746420222 0.000133496
0.000023914 0.000005308 4.342493175
%endblock LatticeVectors
Messcutoff 200 Ry
xc.functional GGA # Exchange-correlation functional
xc.authors PBE
MaxSCFIterations 500 # Maximum number of SCF iter
MD.TypeOfRun FC # Type of dynamics:
#Atomic coordinates
AtomicCoordinatesFormat Fractional
AtomicCoordinatesAndAtomicSpecies < coord.fdf
After that I have used .FC file in vibrator program to generate
frequency and eigenvector.
input file for vibrator program is--
SystemName Carbon Nanotube 32 atom 8_0
SystemLabel Phonon
NumberOfatoms 32
%block ChemicalSpeciesLabel
1 6 C
%endblock ChemicalSpeciesLabel
%block BandLines
1 0.000000 0.000000 0.0000 \Gamma
5 0.000000 0.000000 1.0000 X
%endblock BandLines
LatticeConstant 1 Ang
%block LatticeVectors
99.726332691 -0.002757406 0.000570988
-0.002757317 99.746420222 0.000133496
0.000023914 0.000005308 4.342493175
%endblock LatticeVectors
Eigenvectors true
AtomicCoordinatesAndAtomicSpecies <coord.fdf
AtomicCoordinatesFormat Fractional
But I am getting negative eigenvalues and even imaginary eigenvectors .
Please help me where I am doing wrong. And suggest me which extra
parameters I should use for the same.
Thanking you.
