Magdalena,
Bear in mind that you have a huge supercell! There are a few details that
are in order here and could make a difference in the speed of your
calculation.
1) I suppose you are runnng it in parallel. Are you running it parallelized
over orbitals or k-points? For such a large number of atoms, I guess the
number of orbitals would outweigh the number of k-points and it could be
more advantageous to use Diag.ParallelOverK .false.
2) You use kgridcutoff to determine your k-point mesh. However, you have a
supercell which is enormous along z and thus would render your Brillouin
Zone effectively two-dimensional. I might be wrong, but if you use kgrid
cutoff it will use a k-point grid which has points along the reciprocal z
axis, which is so small that sampling will not make any difference. So you
could save quite a bit on k-points by setting
%block kgrid_Monhkhorst_Pack # (Check the correct spelling...)
Nx 0 0 0.5
0 Ny 0 0.5
0 0 1 0.0
%endblock kgrid_Monkhorst_Pack
thus saving time by not computing unnecessary k-points.
3) Your MaxCGDisplacement could be too high - since the system is very large
and you have quite a few atoms moving (36), try setting it to a much lower
value, like 0.04 Ang.
4) Also, for such a large system, the DM tolerance could be a bit higher for
an initial relaxation. The default value of siesta works quite well. You
could relax it using the default value until you get to, say, 0.06 eV/Ang,
then restart the calculation with a smaller tolerance for the DM and
converge it a bit more on the forces. I would bet the results would not be
different at all.
5) Have you tried using Broyden relaxation? My personal experience is that
Broyden could be much more efficient than CG. You can try starting with the
default value of the initial Hessian for Broyden, but monitor if your system
goes to the correct place. I have done some tests for Broyden and it can
take you to the correct place with as much as 1/3 of the necessary CG steps,
but then I had to tweak the initial value of the Hessian to avoid some
"catastrophes".
6) Coming back to the efficiency of parallel execution, you could also play
with the values of ProcessorY and other parameters that rule the efficiency
of the calculation over four scf steps to see how the execution time
changes. Be sure to rune everything on the same number of processors, of
course.
Finally, be patient. In a system like a surface there are very many degrees
of freedom and with 270 atoms you could end up having a very long
calculation.
Best of luck,
Marcos
On Fri, Jul 23, 2010 at 9:39 AM, Magdalena Birowska <
[email protected]> wrote:
> Dear siesta users;
>
>
> I calculate GaAs slab with one pair of Mn ions on Ga terminated surface.
> I terminated As surface using partially occupied Hydrogen (0.7).
> Should I use diffrent value of partially occupied Hydrogen?
>
> My calcualation has been running for 2 weeks, and it doesn't seem to finish
> at all.
> The atomic forces are as high as at the begginnig of my calcualtions.
> Does anybody know what shoud I change in my input file?
>
> I use parallel mode of siesta.
>
> My input file is following:
>
>
> *l,lSystemName GaAs
> SystemLabel GaAs
> # Output options
> WriteCoorStep
> WriteMullikenPop 1
> WriteCoorXmol true
> # Species and atoms
> NumberOfSpecies 4
> NumberOfAtoms 270
> %block ChemicalSpeciesLabel
> 1 31 Ga
> 2 33 As
> 3 201 H-0.7
> 4 25 Mn
> %endblock ChemicalSpeciesLabel
>
>
> %block PAO.Basis
> Ga 2 0.0
> n=4 0 2
> 0.0 0.0
> n=4 1 2
> 0.0 0.0
> #n=3 2 2
> # 0.0 0.0
> As 2 0.0
> n=4 0 2
> 0.0 0.0
> n=4 1 2
> 0.0 0.0
> H-0.7 2 0.00000
> n=1 0 3 S 0.50 P
> 0.00 0.00 0.00
> 1.00 1.00 1.00
> n=2 0 1
> 8.50
> 1.00
> Mn 3 0.0
> n=4 0 2
> 0.0 0.0
> n=4 1 2
> 0.0 0.0
> n=3 2 3
> 0.0 0.0 0.0
> %endblock PAO.Basis
>
> # Lattice
> LatticeConstant 5.767800944 Ang
> %block LatticeVectors
> 3.00000 0.000000 0.000000
> 0.00000 3.000000 0.000000
> 0.00000 0.000000 10.000000
> %endblock LatticeVectors
> KgridCutoff 12. Ang
> MeshCutOff 600 Ry
> #%block BandLines
> # 1 1.00000 2.000000 0.000000 W
> # 10 1.00000 1.000000 1.000000 L
> # 12 0.00000 0.000000 0.000000 \Gamma
> # 10 0.00000 2.000000 0.000000 X
> # 10 1.00000 2.000000 0.000000 W
> #%endblock BandLines
>
> %block ProjectedDensityOfStates
> -25.00 7.00 0.05 3000 eV
> %endblock ProjectedDensityOfStates
>
> %block LocalDensityOfStates
> -9.10 3.73 eV
> %endblock LocalDensityOfStates
> ProcessorY 4
> BlockSize 8
> Diag.ParallelOverK F
> MeshSubDivisions 4
>
> xc.functional GGA # Exchange-correlation functional
> xc.authors PBE # Exchange-correlation version
> SpinPolarized false # Logical parameters are: yes or no
>
> MD.UseSaveCG true
> MD.UseSaveXV true
> # SCF options
> MaxSCFIterations 1000 # Maximum number of SCF iter
> DM.MixingWeight 0.025 # New DM amount for next SCF cycle
> DM.Tolerance 1.d-5 # Tolerance in maximum difference
> # between input and output DM
> MD.UseSaveCG true
> MD.UseSaveXV true
> DM.UseSaveDM true # to use continuation files
> DM.NumberPulay 12
> SolutionMethod diagon # OrderN or Diagon
> ElectronicTemperature 1300 K # Temp. for Fermi smearing
> #MD options
> #MD.VariableCell true
> SaveTotalPotential .true.
> SaveElectrostaticPotential .true.
> SlabDipoleCorrection .true.
> MD.TypeOfRun cg # Type of dynamics:
> MD.NumCGsteps 1000 # Number of CG steps for
> # coordinate optimization
> MD.MaxCGDispl 0.3 Ang # Maximum atomic displacement
> # in one CG step (Bohr)
> MD.MaxForceTol 0.002 eV/Ang # Tolerance in the maximum
> # atomic force (Ry/Bohr)
> MD.MaxStressTol 0.02 GPa
> WriteWaveFunctions .true.
> #%block GeometryConstraints
> #routine constr
> #%endblock GeometryConstraints
> # Atomic coordinates
> LongOutput .true.
> COOP.Write .true.
> AtomicCoordinatesFormat ScaledCartesian
> AtomCoorFormatOut Ang
> %block SyntheticAtoms
> 3
> 1 2 3 4
> 0.700000 0.000000 0.000000 0.000000
> %endblock SyntheticAtoms
>
> %block GeometryConstraints
> position from 1 to 234 1.0 0.0 0.0
> position from 1 to 234 0.0 1.0 0.0
> position from 1 to 234 0.0 0.0 1.0
> %endblock GeometryConstraints
>
> %block AtomicCoordinatesAndAtomicSpecies
> 0 0 0 3
> 0.5 0.5 0 3
> 0.5 0 0.5 1
> 1.5 1.5 0 3
> 0 0.5 0.5 1
> 1 0 0 3
> 1 1.5 0.5 1
> 1.5 1 0.5 1
> 2 2.5 0.5 1
> 2 1.5 0.5 1
> 1 2.5 0.5 1
> 2 1 0 3
> 1 2 0 3
> 2.5 0.5 0 3
> 0.5 2.5 0 3
> 2.5 1 0.5 1
> 1.5 2 0.5 1
> 1.5 0.5 0 3
> 0.5 1.5 0 3
> 2.5 2 0.5 1
> 2.5 1.5 0 3
> 1.5 2.5 0 3
> 1 0.5 0.5 1
> 0 1.5 0.5 1
> 0 1 0 3
> 2.5 2.5 0 3
> 1 1 0 3
> 2 0 0 3
> 0 2 0 3
> 2 2 0 3
> 1.5 0 0.5 1
> 0.5 1 0.5 1
> 2.5 0 0.5 1
> 0.5 2 0.5 1
> 2.25 0.25 0.25 2
> 0.25 2.25 0.25 2
> 1.25 1.25 0.25 2
> 2.25 1.25 0.25 2
> 1.25 2.25 0.25 2
> 1.75 1.75 0.25 2
> 1.75 1.25 0.75 2
> 2.25 2.25 0.25 2
> 2.75 0.25 0.75 2
> 2.75 2.25 0.75 2
> 0.75 2.25 0.75 2
> 2.25 0.75 0.75 2
> 0.25 2.75 0.75 2
> 1.25 1.75 0.75 2
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> 0.25 1.25 0.25 2
> 1 0 1 1
> 0 1 1 1
> 1 1 1 1
> 0 0 1 1
> 0 0 2 1
> 2 0 2 1
> 0 2 2 1
> 2 2 2 1
> 0 1 2 1
> 0 2 1 1
> 2 0 1 1
> 1 0 2 1
> 1 1 2 1
> 1 2 1 1
> 1 2 2 1
> 2 1 2 1
> 2 1 1 1
> 2 2 1 1
> 0.5 0.5 1 1
> 1.5 0.5 1 1
> 0.5 1.5 1 1
> 1.5 1.5 1 1
> 0.5 0.5 2 1
> 2.5 0.5 2 1
> 0.5 2.5 2 1
> 2.5 2.5 2 1
> 0.5 1.5 2 1
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> 1.5 0.5 2 1
> 1.5 1.5 2 1
> 1.5 2.5 1 1
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> 2.5 1.5 2 1
> 2.5 1.5 1 1
> 2.5 2.5 1 1
> 0.25 2.25 1.25 2
> 0 0.5 1.5 1
> 1 0.5 1.5 1
> 2.5 1 1.5 1
> 2.5 2 1.5 1
> 0 1.5 1.5 1
> 1 1.5 1.5 1
> 2 1.5 1.5 1
> 2 2.5 1.5 1
> 2.25 0.25 1.25 2
> 2.25 1.25 1.25 2
> 2.25 2.25 1.25 2
> 1.25 2.25 1.25 2
> 2.75 1.75 1.25 2
> 2.75 2.75 1.25 2
> 0 2.5 1.5 1
> 2 0.5 1.5 1
> 1.75 2.75 1.25 2
> 1 2.5 1.5 1
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> 1.75 0.75 1.25 2
> 0.75 1.75 1.25 2
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> 2.75 1.25 1.75 2
> 1.75 2.25 1.75 2
> 2.75 2.25 1.75 2
> 0.5 0 1.5 1
> 1.5 0 1.5 1
> 0.5 1 1.5 1
> 1.5 1 1.5 1
> 0.5 2 1.5 1
> 2.5 0 1.5 1
> 1.5 2 1.5 1
> 0.5 0 2.5 1
> 2.5 0 2.5 1
> 0.5 2 2.5 1
> 2.5 2 2.5 1
> 0 0.5 2.5 1
> 2 0.5 2.5 1
> 0 2.5 2.5 1
> 2 2.5 2.5 1
> 0 1.5 2.5 1
> 0 0 3 1
> 0 1 3 1
> 0 2 3 1
> 1 0 3 1
> 1 1 3 1
> 1 2 3 1
> 2 0 3 1
> 2 1 3 1
> 2 2 3 1
> 1 0.5 2.5 1
> 1 1.5 2.5 1
> 1 2.5 2.5 1
> 2 1.5 2.5 1
> 0.5 1 2.5 1
> 1.5 2 2.5 1
> 2.5 1 2.5 1
> 1.5 0 2.5 1
> 1.5 1 2.5 1
> 2.25 0.25 2.25 2
> 0.25 0.25 2.25 2
> 0.25 2.25 2.25 2
> 2.25 2.25 2.25 2
> 0.25 1.25 2.25 2
> 1.25 0.25 2.25 2
> 1.25 1.25 2.25 2
> 1.25 2.25 2.25 2
> 2.25 1.25 2.25 2
> 0.5 0.5 3 1
> 0.5 1.5 3 1
> 0.5 2.5 3 1
> 1.5 0.5 3 1
> 1.5 1.5 3 1
> 1.5 2.5 3 1
> 2.5 0.5 3 1
> 2.5 1.5 3 1
> 2.5 2.5 3 1
> 0.75 0.25 2.75 2
> 2.75 0.25 2.75 2
> 0.75 2.25 2.75 2
> 2.75 2.25 2.75 2
> 0.75 1.25 2.75 2
> 1.25 2.75 2.75 2
> 1.25 0.75 2.75 2
> 1.25 1.75 2.75 2
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> 1.75 2.75 2.25 2
> 2.75 1.75 2.25 2
> 0.5 0 3.5 1
> 0.5 1 3.5 1
> 0.5 2 3.5 1
> 1.5 0 3.5 1
> 1.5 1 3.5 4
> 1.5 2 3.5 1
> 2.5 0 3.5 1
> 2.5 1 3.5 1
> 2.5 2 3.5 1
> 0 0.5 3.5 1
> 0 1.5 3.5 1
> 0 2.5 3.5 1
> 1 0.5 3.5 1
> 1 1.5 3.5 4
> 1 2.5 3.5 1
> 2 0.5 3.5 1
> 2 1.5 3.5 1
> 2 2.5 3.5 1
> 0.75 0.75 3.25 2
> 0.75 1.75 3.25 2
> 0.75 2.75 3.25 2
> 1.75 0.75 3.25 2
> 1.75 1.75 3.25 2
> 1.75 2.75 3.25 2
> 2.75 0.75 3.25 2
> 2.75 1.75 3.25 2
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> 0.25 0.25 3.25 2
> 0.25 1.25 3.25 2
> 0.25 2.25 3.25 2
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> 1.25 2.25 3.25 2
> 2.25 0.25 3.25 2
> 2.25 1.25 3.25 2
> 2.25 2.25 3.25 2
> %endblock AtomicCoordinatesAndAtomicSpecies*
>
> I'm very appreciate for any advice.
>
> Magdalena
>
