[Octopus-users] Any tips for big systems (protein)?
nicola.spallanzani at unimore.it
Mon Jul 14 14:48:54 WEST 2008
only now I notice that you have setted a radius too much large.
I suggest you to find the bigger volume that allow you to run the gs,
then find the smaller volume that go to convergence.
I was able to run the gs with a parallelization both in states and in
domains, and to run the td only with a parall. in domains.
Do you know why for you it is opposite?
Xavier Andrade wrote:
> Actually the input file that Cheng mentions has a lot of input variables
> that you should not normally use, as the default is fine. In particular,
> as Nicola said, do not use parallelization in states (for the moment it
> only works for the time propagation) and leave the default poisson solver
> (isf). With the default parameters I have been able to make test runs
> (non-converged spacing) up to one thousand atoms.
> What could be problematic is the SCF convergency. First of all add some
> few extra states and if still your SCF iteration is not converging you may
> want to put a finite electronic temperature.
> On Mon, 14 Jul 2008, Nicola Spallanzani wrote:
>> Hi Cheng,
>> I was able to do a gs/td calculation of a big molecule of 207 atoms. I
>> can suggest you to use the "isf" PoissonSolver and to make a
>> parallelization only in domains.
>> This was right for me... I hope the same for you!
>> Cheng. W wrote:
>>> Dear all,
>>> I am a new user of octopus, and I am doing a gs/td calculation of a
>>> protein which includes 230 atoms. but the calculation always
>>> automatically stopped at the Hartree part (in output file). The reason
>>> is come from Poission solutions.
>>> This is my input file, would you like to give me any hints on that
>>> calculations for big system? How many atoms can be calculated in Octopus?
>>> # Consult the manual for a brief explanation of the variables.
>>> DebugLevel = 2
>>> CalculationMode = gs
>>> Units = ev_angstrom
>>> UnitsInput = ev_angstrom
>>> UnitsOutput = ev_angstrom
>>> FromScratch = yes
>>> #ParallelizationStrategy = par_domains + par_states
>>> XYZCoordinates = "adjusted.xyz"
>>> BoxShape = minimum
>>> radius = 16
>>> spacing = 0.22
>>> XCFunctional = lda_x + lda_c_pz_mod
>>> MaximumIter = 200
>>> ConvAbsDens = 1e-5
>>> LCAOStart = yes
>>> PoissonSolver = multigrid
>>> EigenSolver = cg_new
>>> EigenSolverInitTolerance = 1e-2
>>> EigenSolverFinalTolerance = 1e-6
>>> EigenSolverFinalToleranceIteration = 6
>>> EigenSolverMaxIter = 25
>>> TypeOfMixing = broyden
>>> siesta PSF format is used for pseudopotential, I know local basis is
>>> faster. Is there any other way to deal with big system?
>>> Thank you in advance
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