January 2018 - Nektar-users

how to use HOBC?
by Kurt Sansom 25 Mar '18

25 Mar '18

Hi, I am trying to use the higher order outlet boundary conditions. I know that is formulated for truncated open domains, but am curious if I can use in the following way, where I want to specify the outlet pressure to some value to create back pressure in the system. I realize that for in-compressible flow it doesn't matter that much, but I am interested in implementing a time varying pressure condition at the outlet. I have tried the following boundary condition for a tube and it doesn't appear to apply the VALUE tag? I want to make sure before I file a bug. <REGION REF="2">  <N VAR="u" USERDEFINEDTYPE="HOutflow" VALUE="0" /> <N VAR="v" USERDEFINEDTYPE="HOutflow" VALUE="0" /> <N VAR="w" USERDEFINEDTYPE="HOutflow" VALUE="0" /> <D VAR="p" USERDEFINEDTYPE="HOutflow" VALUE="10665" /></REGION> Regards, ~Kurt -- Kurt Sansom

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Regarding direct stability analysis of Rayleigh Benard Convection
by Abhishek Kumar 01 Feb '18

01 Feb '18

Dear friends, I am trying to do direct stability analysis of Rayleigh Benard Convection (RBC) in Nektar++. I observe positive eigenvalues even for Ra=1000, which is below critical. I have attached my XML file. It would be great if someone would give comment on this issue. With regards Abhishek Kumar --------------------------------------------------------------------------------------- Abhishek Kumar Post Doctoral Researcher Applied Mathematics Research Centre Coventry University, Coventry CV15FB The United Kingdom Email # ac7600(a)coventry.ac.uk, abhishek.kir(a)gmail.com ---------------------------------------------------------------------------------------

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VCSMapping and parallel execution
by Hanbo JIANG 01 Feb '18

01 Feb '18

Dear all, I am a new user. When I tried the VCSMapping with test case (nektar/solvers/IncNavierStokesSolver/Tests/CylFlow_Mov_mapping.xml) it failed to run in parallel with errors: " mpirun -np 8 IncNavierStokesSolver CylFlow_Mov_mapping.xml Fatal : Level 0 assertion violation A parallel solver must be used when run in parallel. " I had to run it in serial to get the final result. However the mesh grid and the position of cylinder remain the same as initial field, even if I have tried different "NumSteps". I just followed the user guide and used "FieldConvert CylFlow_Mov_mapping.xml CylFlow_Mov_mapping.fld cyl.vtu" to get the converted result. I guess maybe because 'CylFlow_Mov_mapping.xml' only contains initial mesh data and CylFlow_Mov_mapping.fld only contains field data, i.e., deformed mesh information is missed by this command. so I think this problem is about post-processing. Could you please help to find out what I've missed and fix this problem? I would appreciate your Help. Kind regards, Hanbo

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Re: [Nektar-users] forces computation in parallel computations
by F Mellibovsky 25 Jan '18

25 Jan '18

Hi, I have tried the preconditioner choices you suggested but they do not seem to work for Quasi-3D simulations (I am using Fourier expansions in 1 direction). I have tried FullLinearSapce instead of LowEnergyBlock, but nektar comes out with the same error message. Is there any preconditioner -other than diagonal- that I can use? By the way, I have the impression (I might be wrong) that the problem with the forces oscillation in parallel computations could be related with the failure to have the data from all nodes upon computation of the pressure forces. Could it be that the mpi communication is missing a "wait" statement and that forces are computed with incomplete data? Cheers On 13/01/18 17:42, Spencer Sherwin wrote: > Hi, > > When running in parallel the code uses an iterative solver where as in > serial we use a direct multi-level static condensation technique. If > nothing else is specified then the default preconditioner on the > iterative solver is a diagonal preconditioner which often is not great > and for a complex mesh it can lead to pressure fluctuation. > > From what has been stated in the thread below what is likely to be > happening is that the introduction of the GlobalSysSolnInfo as > suggested in the user guide will use a more advanced preconditioner > that leads to a more robust pressure solution and then causes the > forces to be less oscillatory. > > Cheers > Spencer > >> On 12 Jan 2018, at 09:18, Feifei Tong <feifei.tong(a)uwa.edu.au >> <mailto:feifei.tong@uwa.edu.au>> wrote: >> >> Hi Mellibovsky, >> >> I am not an expert, but the same issue bothered me for a while. I >> finally managed to solve it by adding the <GLOBALSYSSOLNINFO> into >> the xml file (page 31, User Guide 4.4.0). This does not only smooth >> the force signal, but also appears to speed up the simulation by a >> magnitude. Hopefully some people can give a good explanation on it. >> >> Kind regards, >> Feifei >> >> -----Original Message----- >> From: nektar-users-bounces(a)imperial.ac.uk >> <mailto:nektar-users-bounces@imperial.ac.uk> >> [mailto:nektar-users-bounces@imperial.ac.uk] On Behalf Of F Mellibovsky >> Sent: Friday, 12 January 2018 4:47 PM >> To: nektar-users >> Subject: [Nektar-users] forces computation in parallel computations >> >> Dear all, >> >> When running parallel (72 core) aggregate quantitities such as body >> forces (particularly pressure forces) seem to include a certain >> degree -low amplitude- of randomness in their evolution. The high >> frequency random oscillations seem to be of the order of the sampling >> period. This suggests some kind of issue with the gathering of data >> from all parallel processes for aggregate quantity computation. >> >> Is there some precaution that must be taken upon compilation or in >> defining the cluster parallel environtment to avoid this issue? >> >> I attach one such forces time-series to illustrate this. Viscous >> forces seem to be just fine, while pressure (and total) forces >> oscillate at high frequency. >> >> Cheers >> _______________________________________________ >> Nektar-users mailing list >> Nektar-users(a)imperial.ac.uk <mailto:Nektar-users@imperial.ac.uk> >> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users > > Spencer Sherwin FREng, FRAeS > Head, Aerodynamics, > Professor of Computational Fluid Mechanics, > Department of Aeronautics, > Imperial College London > South Kensington Campus, > London, SW7 2AZ, UK > s.sherwin(a)imperial.ac.uk <mailto:s.sherwin@imperial.ac.uk> > +44 (0)20 7594 5052 > http://www.imperial.ac.uk/people/s.sherwin/ >

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Parallel execution missing files
by Guillermo 24 Jan '18

24 Jan '18

Dear all, I am analyzing some chk folders after a parallel execution and just noticed that some .fld files are missing. However, at the Info.xml the missing files appear as the other files: <Partition FileName="P000000X.fld"> and it is not empty nor corrupted. Has anybody else noticed this problem? The missing files are not the same on each folder, i.e. at ./session_0.chk files P0000002.fld, P0000003.fld and P0000005.fld are missing, but at ./session_2.chk these files are P0000002.fld and P0000003.fld. *Nektar version: 4.3.4 Kind regards, Guillermo

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help for 3D cases
by Moto Light 24 Jan '18

24 Jan '18

i need to run 3D case for square cylinder for Reynolds 600 what do you think is it possible to run the case 2D and start with this case solution as a initial solution for the 3D case, or i can start my case in 3D from beginning. regards, Reda

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Regarding Rayleigh Benard in Nektar++
by Abhishek Kumar 19 Jan '18

19 Jan '18

Dear friends, I am trying to run Rayleigh Benard Convection (RBC) in Nektar++. I am facing problem in applying the buoyancy force (Ra*Pr*T). Is it possible to simulate RBC using Nekar++? I have attached my XML file. It would be great if someone would give comment on this issue. With regards Abhishek Kumar --------------------------------------------------------------------------------------- Abhishek Kumar Post Doctoral Researcher Applied Mathematics Research Centre Coventry University, Coventry CV15FB The United Kingdom Email # ac7600(a)coventry.ac.uk, abhishek.kir(a)gmail.com ---------------------------------------------------------------------------------------

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Localized force
by Daiane Iglesia Dolci 17 Jan '18

17 Jan '18

Dear all, I am working with incompressible flow and I need insert a force localized at a position (x_c, y_c). Anyone know how I can do this? Thanks, Daiane.

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negative jacobians of all prism cells
by Kurt Sansom 16 Jan '18

16 Jan '18

Hi, I wrote a conversion tool (using meshio) to export paraview's vtu format to gmsh so that I could import to .xml format. It seems to be working quite well, except that all of the prisms have negative jacobians and Linearising them has no effect. The commands I used as follows: NekMesh DSI020CALb_vmtk_decimate_trim_ext2_mesh.msh DSI020CALb_nektar.xml NekMesh -m jac:extract DSI020CALb_nektar.xml DSI020CALb_nektar_jac_export.xml FieldConvert DSI020CALb_nektar_jac_export.xml DSI020CALb_nektar_jac_export.vtu NekMesh -m linearise:invalid DSI020CALb_nektar.xml DSI020CALb_nektar_lin.xml There are 3180 prism elements and they all give negative jacobians, and this doesn't change with linearization. Is there a node ordering issue? is there an easy way to fix this? any hints on where to start digging to resolve? Regards, ~Kurt Sansom -- Kurt Sansom Graduate Research Assistant Multiphase & Cardiovascular Flow Lab University of Washington

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Recent merge into master
by David Moxey 13 Jan '18

13 Jan '18

Hi all, Just wanted to let you know that we merged a pretty large branch (feature/hdf5-mesh-4, merge request 900) into master yesterday. This sets the groundwork for a new HDF5-based mesh geometry format to address issues we have with partitioning large meshes at runtime. Although we've taken the usual steps to see if anything major is out of place (regression tests, profiling), a large amount of work was done in SpatialDomains, so it's possible issues might arise in the next few weeks. If you do notice problems then please let me know either on the users list or, preferably, on a gitlab issue! Many thanks, Dave

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