May 2019 - Nektar-users - imperial.ac.uk

Help with adding velocity dependent terms to the incompressible Navier-stokes solver in the conditions file
by Swagat Kumar Nayak 23 May '19

23 May '19

Hi, I am trying to simulate the flow of a precessing cylinder in the cylinder frame of reference. I have got some additional terms in the incompressible Navier-stokes equation which are velocity dependent. (1) How do I add these additional terms to the incompressible Navier-stokes equation? (2) When I create a mesh in Gmsh and try to convert it into the .xml file format, how do I identify the composites corresponding to the global boundaries? I am new to this framework. So, any help will be largely appreciated. Thank you, -- *Swagat Kumar Nayak * *Department of Mechanical Engineering* *IIT Kharagpur*

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post-processing of simulation results
by zxiong＠sas.upenn.edu 16 May '19

16 May '19

Dear all, I use nektar++ to do a simulation and visualize the result in Paraview. The simulation domain is a 3D cylinder and it computes velocity in three directions(x,y,z-axis) and pressure of blood flow. However, I can't use stream tracer filter in Paraview. I read the tutorial of Paraview and can successfully use stream tracer on data inside Paraview. Do I need to compute something else to enable the function stream tracer filter of Paraview? Is there any suggestion？ Many thanks! Best, Zhen

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Improper bounds checking in v_PhysEvaluate among other problems
by Teodoro Collin 12 May '19

12 May '19

Hi all, I've been using Nektar++ to prepare some data for post-processing and in reading the code base, I feel that the conversions between collapsed and cartesian coordinates causes some confusion in the code. For instance, in StdExpansions3d::v_PhysEvaluate <http://doc.nektar.info/latest/class_nektar_1_1_std_regions_1_1_std_expansio…>, the coordinates are only checked to be in the standard hex yet all 3d standard regions use this function, meaning bounds are improperly check for evaluation in all of these cases. This looks like someone meant to check the collapsed coordinates (though there still could be a bug if this was the case). Similarly, various comments throughout the code base sound just a bit confused. For instance, in TetGeom::v_ContainsPoint <http://doc.nektar.info/latest/_tet_geom_8cpp_source.html#l00108>, there is a comment "// Convert to the local (eta) coordinates)" when clearly the conversion is to the local Cartesian coordinates. This bugs me because eta (in all papers and texts that I can find!) is used for Cartesian points. Or the function GetCoord <http://doc.nektar.info/latest/class_nektar_1_1_spatial_domains_1_1_geometry…> says in its doc strings say it takes "local collapsed coordinate Lcoord", but if I follow it to the appropriate implementation <http://doc.nektar.info/latest/class_nektar_1_1_std_regions_1_1_std_expansio…> for say a quad, the argument is converted to collapsed coordinates! This is really confusing for someone trying to determine the mathematical meaning of the code - especially if you are using the suggested texts as references. Beyond fixing things noted here, this leads me to give a suggestion: Why not provide a different type for floats that are in collapsed coordinates vs. cartesian vs. global? This ought to be no cost, and it would make the code base easier to read/prevent these sorts of issues. Thanks for listening, Teo.

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wormersley boundary condition
by zxiong＠sas.upenn.edu 11 May '19

11 May '19

Dear all, I am working on a blood flow simulation. I want to use Womersley boundary condition in the inlet of vessel. However, I found that information on section 10.3.3(page 150) of user-guide-4.4.1.pdf is not clear to me. [image: image.png] First question: On page 150, the second formula define the womersley number which is associated with an 'n'. However, in the third formula defining the scaled Fourier coefficients, the womersley number is not associated with 'n'. So in the third formula, do I still use womersley number defined by the second formula? Second Question: When we set the Fourier coefficients in the input file, do we need to input the original one or the the scaled one? Thank you very much! Best, Zhen

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blood flow simulation
by zxiong＠sas.upenn.edu 10 May '19

10 May '19

Dear all, I am trying to do a cardiovascular simulation by using Incompressible N-S solver in Nektar++. Here I have two questions about setting boundary conditions. First, how can I set RCR(windkessel model) boundary condition if I use Incompressible N-S solver? Is there any similar input file I can find? Second, do I need to make all the variable dimensionless when I set boundary conditions? Thank you very much! Best, Zhen

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Re: [Nektar-users] Nektar read nek5000 binary field
by WEI HE 10 May '19

10 May '19

Hi David, It works, thank you very much! Cheers， Wei > On 10 May 2019, at 11:33, Moxey, David <D.Moxey(a)exeter.ac.uk> wrote: > > Hi Wei, > > The solver restart expects a Nektar++ fld file as input. Prior to the simulation you should run FieldConvert on your Nek5000 file to produce a valid fld file, e.g.: > > FieldConvert cubic0.f00025:fld5000 cubic0.fld > > You should then be able to use this to restart the simulation. > > Cheers, > > Dave > >> On 10 May 2019, at 11:24, WEI HE <mewhe(a)ust.hk> wrote: >> >> Dear nektar users, >> >> I am exploring my 3D dns data computed by nek5000, and hoping it would be used for stability analysis. I found nektar++ could read nek5000 binary field directly in the technical document >> http://doc.nektar.info/latest/class_nektar_1_1_field_utils_1_1_input_nek500… >> >> I run FieldConvert -l, and it gives >> >> Available classes: >> Input: bse: >> Reads stability base-flow file. >> Input: chk: >> Reads checkpoint file. >> Input: dat: >> Reads Tecplot dat file for FE block triangular format. >> Input: fld: >> Reads Fld file. >> Input: fld5000: >> Reads Nek5000 field file. >> ................. >> .................. >> >> I firstly generate a cubic.xml file and then build a new nek5000 dns setup with exactly same coordinates. Then run it in nek5000 to obtain a sequence cubic0.f00001,.... cubic0.f00025 fields. >> >> Next, I defined the binary nek5000 data ( e.g. cubic0.f00025) as the restart file. When I run nektar, it gave an error, as below >> >> IncNavierStokesSolver cubic.xml >> ======================================================================= >> EquationType: UnsteadyNavierStokes >> Session Name: cubic2 >> Spatial Dim.: 3 >> Max SEM Exp. Order: 6 >> Expansion Dim.: 3 >> Projection Type: Continuous Galerkin >> Advection: explicit >> Diffusion: implicit >> Time Step: 0.01 >> No. of Steps: 5 >> Checkpoints (steps): 1 >> Integration Type: IMEXOrder2 >> Splitting Scheme: Velocity correction (strong press. form) >> ======================================================================= >> >> Fatal : Level 0 assertion violation >> Unable to load file: cubic0.f00025 >> Reason: Error document empty. >> Position: Line 0, Column 0 >> >> >> >> Did I miss something? or can someone help me? thanks! >> >> regards, >> Wei >> >> >> >> >> Cheers， >> Wei >> _______________________________________________ >> Nektar-users mailing list >> Nektar-users(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users > > -- > Dr David Moxey, PhD MMath MIMA FHEA > Senior Lecturer in Engineering > d.moxey(a)exeter.ac.uk | tel: 01392 724764 | web: davidmoxey.uk > > Room K1, Innovation Centre, > University of Exeter, > Exeter, EX4 4RN, UK. >

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Nektar read nek5000 binary field
by WEI HE 10 May '19

10 May '19

Dear nektar users, I am exploring my 3D dns data computed by nek5000, and hoping it would be used for stability analysis. I found nektar++ could read nek5000 binary field directly in the technical document http://doc.nektar.info/latest/class_nektar_1_1_field_utils_1_1_input_nek500… I run FieldConvert -l, and it gives Available classes: Input: bse: Reads stability base-flow file. Input: chk: Reads checkpoint file. Input: dat: Reads Tecplot dat file for FE block triangular format. Input: fld: Reads Fld file. Input: fld5000: Reads Nek5000 field file. ................. .................. I firstly generate a cubic.xml file and then build a new nek5000 dns setup with exactly same coordinates. Then run it in nek5000 to obtain a sequence cubic0.f00001,.... cubic0.f00025 fields. Next, I defined the binary nek5000 data ( e.g. cubic0.f00025) as the restart file. When I run nektar, it gave an error, as below IncNavierStokesSolver cubic.xml ======================================================================= EquationType: UnsteadyNavierStokes Session Name: cubic2 Spatial Dim.: 3 Max SEM Exp. Order: 6 Expansion Dim.: 3 Projection Type: Continuous Galerkin Advection: explicit Diffusion: implicit Time Step: 0.01 No. of Steps: 5 Checkpoints (steps): 1 Integration Type: IMEXOrder2 Splitting Scheme: Velocity correction (strong press. form) ======================================================================= Fatal : Level 0 assertion violation Unable to load file: cubic0.f00025 Reason: Error document empty. Position: Line 0, Column 0 Did I miss something? or can someone help me? thanks! regards, Wei Cheers， Wei

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Can Nektar++ support simulation with rotating sliding meshes
by Song Xiang 06 May '19

06 May '19

Dear all, I would like to simulate the flow over the rotating body. To my knowledge, Nektar++ utilizes a conformal Spectral element method. It is difficulty to realize the simulation with rotating sliding meshes. Whether the Nektar++ can realize this kind simulation? If not, Is it realistic to implement sliding mesh method under the existing framework? Has anyone tried a similar job? Thank you very much! Best, Song

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