Dear Marcos,
Thank you very much for your help.
Best regards,
Piotrek
On 15.09.2011 20:05, Marcos Veríssimo Alves wrote:
Piotr,
One possible reason is that your convergence parameters are not
sufficiently strict. DM convergences of 10^-3 will give you very poor
results. Ideally, the DM convergence should be as strict as possible,
and you can easily get down to 10^-5 or even 10^-6 with systems as
easy to handle as graphene.
However, perhaps the most important thing is to check that Harris and
Kohn-Sham energies are equal. Check Eq. 61 of the Siesta paper (the
one with the description of the code,
http://es.arxiv.org/abs/cond-mat/0111138). Thus, set the DM tolerance
low enough so that the Harris and KS energies are equal at the end of
your SCF cycle, which will improve the numerical accuracy of the
forces and stresses on the system. Your SCF cycles will be longer, but
it could be that you get to your target stress tensor in less CG steps.
Also, one thing that might help you is to set the off-diagonal and zz
stress-tensor components to zero at the end of each step, since they
should be just numerical noise due to a finite grid fineness. You can
check the manual for the use of subroutine constr and the setting of
stress tensor elements there. Only after you get reliable forces and
stresses for a given mesh cutoff (with good scf convergence) should
you worry about how it increases with a change in the mesh cutoff.
Cheers,
Marcos
On Thu, Sep 15, 2011 at 12:31 AM, Piotr Tempczyk <piotrtempc...@wp.pl
<mailto:piotrtempc...@wp.pl>> wrote:
Dear siesta users,
I have a problem with obtaining a graphene 2x2 cell (8 atoms) with
Stress-Tensor-Voigt elements less than 0.01 kBar.
The best I have managed to get is:
Stress-tensor-Voigt (kbar): 0.02 0.01
0.00 0.01 0.00 0.00
with fdf attached at the end of this email.
I was trying to obtain it with parameters
MD.VariableCell T
MD.MaxStressTol 0.001 GPa
but siesta made 1000 CG steps and did not manage to achieve a goal.
I have also discovered, that when I incerase MeshCutoff from 300
to 400 Ry the stress
tensor elements become ten times bigger. Why is that happening?
In my future work I want to replace one or more carbon atoms in my
2x2 cell with
other atoms, so I need to optimize that heterogenous cell and I am
afraid, that
it will be much more complicated problem that this with pure
graphene, so I will
appreciate any hints how to optimize pure graphene and that with
other atoms.
I will be grateful for any help and hints about my problem,
Best regards,
Peter Tempczyk
University of Warsaw
ul. Hoza 69
Pl-00-681 WARSZAWA, POLAND
SystemLabel graf
NumberOfAtoms 8
NumberOfSpecies 1
%block ChemicalSpeciesLabel
1 6 C
%endblock ChemicalSpeciesLabel
PAO.BasisSize DZP
PAO.BasisType split
kgrid_cutoff 10 Ang
MeshCutoff 300. Ry
SolutionMethod diagon # diagonalizacion. order-N. TD-DFT
MaxSCFIterations 1000 # Max. number of iterations in
SCF.
DM.MixingWeight 0.1 # weight of mixing in the DM for
convergence
DM.Tolerance 1.d-3 # Tolerance in differences of DM
DM.NumberPulay 4 # Number of previous steps of
DM for mixing
ElectronicTemperature 300 K
MD.TypeOfRun CG #molecular dynamics conjugate
gradients
MD.NumCGsteps 1000 # number of steps
MD.MaxForceTol 0.00001 eV/Ang
MD.MaxCGDispl 0.01 Bohr
DM.Energy.Tolerance 1.d-3 eV # Tolerance in energy
DM.Require.Harris.Convergence T
DM.Harris.Tolerance 1.d-3 eV
DM.Require.Energy.Convergence T # energia musi zejsc ponizej
zadanego poziomu!!!
WriteCoorInitial T
WriteCoorStep T # must be set true to write coords
at each relax step to .ANI file
WriteForces T
WriteKpoints F
WriteEigenvalues F # use with eig2dos to plot density
of states
WriteKbands F
WriteBands F
WriteCoorXmol T
WriteCoorCerius T # writes final coordinats for Cerius
WriteMDCoorXmol T
WriteDM T # true is default - allows for a
restart using DM from previous run
WriteMDhistory T
WriteCoorXmol T
# Options for saving/reading information
DM.UseSaveDM T # Use DM Continuation files (use
for restarting jobs)
MD.UseSaveXV T # Use stored positions and
velocities (use for restart jobs)
UseSaveData T # useful if a restart is needed
MD.UseSaveCG T # Use stored positions and velocities
SaveRho F # Write valence pseudocharge at
the mesh
SaveDeltaRho F # Write RHOscf-RHOatm at the mesh
SaveElectrostaticPotential F # Write the total elect. pot. at
the mesh
SaveTotalPotential F # Write the total pot. at the mesh
WriteSiestaDim F # Write minimum dim to siesta.h and
stop
WriteDenchar F # Write information for DENCHAR
NetCharge 0.00
#SlabDipoleCorrection T
#SimulateDoping T
SpinPolarized F # spin polarization
xc.functional GGA # flavour of functional (LDA/GGA)
xc.authors PBE # Parametrization fos xc
WriteMullikenPop 0
WriteEigenvalues .true.
WriteWaveFunctions .true.
#inny sposob podawania parametrow
LatticeConstant 2.481807 Ang
%block LatticeParameters
2.000000 2.000000 60.0 90. 90. 60.
%endblock LatticeParameters
AtomicCoordinatesFormat NotScaledCartesianAng
%block AtomicCoordinatesAndAtomicSpecies
1.24192412 0.71702548 0.00000 1
2.48283025 1.43346309 0.00000 1
2.48282797 2.86633383 0.00000 1
3.72373434 3.58277111 0.00000 1
3.72373167 0.71702567 0.00000 1
4.96463747 1.43346348 0.00000 1
4.96463527 2.86633370 0.00000 1
6.20554162 3.58277150 0.00000 1
%endblock AtomicCoordinatesAndAtomicSpecies
AtomCoorFormatOut Ang
