I'm very appreciate for your advices.
*
*
*%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*
What do you mean by Nx, Ny? What should be the proper values?
Cheers,
Magdalena
2010/7/23 Marcos Veríssimo Alves <[email protected]>
> 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
>> 2.25 2.75 0.75 2
>> 1.75 0.75 0.25 2
>> 2.75 2.75 0.25 2
>> 0.75 1.75 0.25 2
>> 1.75 0.25 0.75 2
>> 0.75 1.25 0.75 2
>> 2.25 1.75 0.75 2
>> 1.25 2.75 0.75 2
>> 2.75 0.75 0.25 2
>> 2.75 1.75 0.25 2
>> 0.25 0.25 0.25 2
>> 0.75 0.75 0.25 2
>> 0.75 0.25 0.75 2
>> 0.25 0.75 0.75 2
>> 2.75 1.25 0.75 2
>> 1.75 2.25 0.75 2
>> 1.75 2.75 0.25 2
>> 1.25 0.75 0.75 2
>> 0.25 1.75 0.75 2
>> 0.75 2.75 0.25 2
>> 2 0.5 0.5 1
>> 0 2.5 0.5 1
>> 1.25 0.25 0.25 2
>> 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
>> 0.5 2.5 1 1
>> 2.5 0.5 1 1
>> 1.5 0.5 2 1
>> 1.5 1.5 2 1
>> 1.5 2.5 1 1
>> 1.5 2.5 2 1
>> 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
>> 0.25 0.25 1.25 2
>> 1.25 0.25 1.25 2
>> 0.25 1.25 1.25 2
>> 1.25 1.25 1.25 2
>> 0.75 0.25 1.75 2
>> 1.75 0.25 1.75 2
>> 0.75 1.25 1.75 2
>> 1.75 1.25 1.75 2
>> 0.75 2.75 1.25 2
>> 2.75 0.75 1.25 2
>> 0.75 2.25 1.75 2
>> 2.75 0.25 1.75 2
>> 0.75 0.75 1.25 2
>> 1.75 0.75 1.25 2
>> 0.75 1.75 1.25 2
>> 1.75 1.75 1.25 2
>> 0.25 0.75 1.75 2
>> 1.25 0.75 1.75 2
>> 0.25 1.75 1.75 2
>> 1.25 1.75 1.75 2
>> 0.25 2.75 1.75 2
>> 2.25 0.75 1.75 2
>> 1.25 2.75 1.75 2
>> 2.25 1.75 1.75 2
>> 2.25 2.75 1.75 2
>> 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
>> 2.25 0.75 2.75 2
>> 0.25 0.75 2.75 2
>> 0.25 2.75 2.75 2
>> 2.25 2.75 2.75 2
>> 0.25 1.75 2.75 2
>> 2.25 1.75 2.75 2
>> 1.75 0.25 2.75 2
>> 1.75 1.25 2.75 2
>> 1.75 2.25 2.75 2
>> 2.75 1.25 2.75 2
>> 0.75 0.75 2.25 2
>> 2.75 0.75 2.25 2
>> 0.75 2.75 2.25 2
>> 2.75 2.75 2.25 2
>> 0.75 1.75 2.25 2
>> 1.75 0.75 2.25 2
>> 1.75 1.75 2.25 2
>> 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
>> 2.75 2.75 3.25 2
>> 0.25 0.25 3.25 2
>> 0.25 1.25 3.25 2
>> 0.25 2.25 3.25 2
>> 1.25 0.25 3.25 2
>> 1.25 1.25 3.25 2
>> 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
>>
>
>
