- Nektar-users - imperial.ac.uk

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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problem with FieldConvert interpfield
by A.P. 22 Apr '19

22 Apr '19

Hello, I try to convert a Z-homogenious fld file to an another mesh by FieldConvert module 'interpfield' and recieve this error message: Fatal : Level 0 assertion violation Failed to type cast m_exp[0] terminate called after throwing an instance of 'ErrorUtil::NekError' what(): Level 0 assertion violation Failed to type cast m_exp[0] 2D fields are converted OK. What can be done to overcome the error? Alexander.

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Hi all (( problem in prob points in 3D ))
by Moto Light 21 Apr '19

21 Apr '19

Hi All, I am setting prob line on 2.5D for 4D spanwise, for using 32 modes or 64 modes it is ok, but when i am using 48 modes it changes the points location like this: *Reseting History point from z = 2.83333 to z = 2.75* *Reseting History point from z = 2.91667 to z = 2.91667* *Reseting History point from z = 3.08333 to z = 3* *Reseting History point from z = 3.16667 to z = 3.16667* *Reseting History point from z = 3.33333 to z = 3.25* *Reseting History point from z = 3.41667 to z = 3.41667* *Reseting History point from z = 3.58333 to z = 3.5* *Reseting History point from z = 3.66667 to z = 3.66667* *Reseting History point from z = 3.83333 to z = 3.75* *Reseting History point from z = 3.91667 to z = 3.91667* *any suggestions?* *Regards,* *Reda*

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compressible flow solver scalability with fortran subroutines
by Arash Nouri 20 Apr '19

20 Apr '19

Hi all, I've added an equation of state and a chemical reaction to the compressible flow solver via couple of FORTRAN subroutines. In my 2D simulations, everything is cool and I've almost linear scalability up to 2K processors. However, my 3D simulations are surprisingly slow. Do you have any idea about probable reasons? What I basically do for the chemical reaction is: I call a FORTRAN subroutine in DoOdeRhs to get the required forcing terms for energy and species equations. Best, Arash --------------------------------- Arash G. Nouri Research Scientist Computational Modeling & Simulation (http://cmsp.pitt.edu/) 1127 Benedum Hall University of Pittsburgh Pittsburgh, PA 15261, USA E-mail: arn36(a)pitt.edu

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blood flow simulation
by zxiong＠sas.upenn.edu 18 Apr '19

18 Apr '19

Dear all, I am trying to do a cardiovascular simulation by using Nektar++. Here I have two questions about setting boundary conditions. First, how can I set RCR(windkessel model) boundary condition in nektar++? 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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