January 2016 - Nek5000-users - mailman3.cels.anl.gov

Re: [Nek5000-users] Vorticity
by nek5000-users＠lists.mcs.anl.gov 11 Oct '16

11 Oct '16

Hi, Thanks for your quick reply. Just I wanna know if I can use the interpolated values of velocity at some arbitrary points in the domain (not necessarily the grid points) as the input arguments to theses subroutines. Regards, Alireza Quoting nek5000-users-request(a)lists.mcs.anl.gov: > Send Nek5000-users mailing list submissions to > nek5000-users(a)lists.mcs.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > or, via email, send a message with subject or body 'help' to > nek5000-users-request(a)lists.mcs.anl.gov > > You can reach the person managing the list at > nek5000-users-owner(a)lists.mcs.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Nek5000-users digest..." > > > Today's Topics: > > 1. Vorticity (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: Vorticity (nek5000-users(a)lists.mcs.anl.gov) > 3. Re: Vorticity (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Jul 2011 17:55:35 -0400 > From: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: <20110713175535.1042430oct81vz2v(a)webmail.vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Hi, > > I need to calculate the vorticity vector and the rate of strain tensor > at any arbitrary point in the domain. I wonder if these values are > computed somewhere in the code or if I should interpolate them in the > usr file. I appreciate any kind of help. > > Thanks in advance, > > > Regards, > Alireza Karimi > > > > ------------------------------ > > Message: 2 > Date: Wed, 13 Jul 2011 17:09:48 -0500 (CDT) > From: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: <Pine.LNX.4.64.1107131704140.26989(a)jacobi.mcs.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Alireza, > > For vorticity computation, you can call > > call comp_vort3(vort,work1,work2,vx,vy,vz) > > from userchk with the appropriate definitions of vorticity and work arrays > like > > common /scren/ vort (lx1,ly1,lz1,lelv,3) ! x y z components > $ , work1(lx1,ly1,lz1,lelv) > $ , work2(lx1,ly1,lz1,lelv) > > Let me check what we have for the calculation of strain tensor. > Best, > Aleks > > > On Wed, 13 Jul 2011, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Hi, >> >> I need to calculate the vorticity vector and the rate of strain >> tensor at any >> arbitrary point in the domain. I wonder if these values are computed >> somewhere in the code or if I should interpolate them in the usr file. I >> appreciate any kind of help. >> >> Thanks in advance, >> >> >> Regards, >> Alireza Karimi >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > Message: 3 > Date: Wed, 13 Jul 2011 23:59:08 -0500 (CDT) > From: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: > <600285192.94128.1310619548370.JavaMail.root(a)zimbra.anl.gov> > Content-Type: text/plain; charset=utf-8 > > Hi Alireza, > > > For a strain stress computation you can call subroutine comp_sij > > call comp_sij(sij,nij,vx,vy,vz > $ ,ur,us,ut,vr,vs,vt,wr,ws,wt) > > > (navier5.f:2225) with nij=6 for 3D somewhere from userchk once you > declare the stress component array sij and arrays with local > coordinate r-s-t derivatives of velocity components > > common /csij/ > $ sij(lx1*ly1*lz1,6,lelv) ! 6 components > $ ,ur (lx1*ly1*lz1) > ... > $ ,wt (lx1*ly1*lz1) > > > Best, > Aleks > > > > > > > ----- Original Message ----- > From: nek5000-users(a)lists.mcs.anl.gov > To: nek5000-users(a)lists.mcs.anl.gov > Sent: Wednesday, July 13, 2011 5:09:48 PM > Subject: Re: [Nek5000-users] Vorticity > > Hi Alireza, > > For vorticity computation, you can call > > call comp_vort3(vort,work1,work2,vx,vy,vz) > > from userchk with the appropriate definitions of vorticity and work arrays > like > > common /scren/ vort (lx1,ly1,lz1,lelv,3) ! x y z components > $ , work1(lx1,ly1,lz1,lelv) > $ , work2(lx1,ly1,lz1,lelv) > > Let me check what we have for the calculation of strain tensor. > Best, > Aleks > > > On Wed, 13 Jul 2011, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Hi, >> >> I need to calculate the vorticity vector and the rate of strain >> tensor at any >> arbitrary point in the domain. I wonder if these values are computed >> somewhere in the code or if I should interpolate them in the usr file. I >> appreciate any kind of help. >> >> Thanks in advance, >> >> >> Regards, >> Alireza Karimi >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > End of Nek5000-users Digest, Vol 29, Issue 2 > ******************************************** > -- Alireza Karimi PhD Candidate Department of Engineering Science and Mechanics Virginia Polytechnic Institute and State University Blacksburg, VA 24061

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Error when creating own mesh
by nek5000-users＠lists.mcs.anl.gov 01 Mar '16

01 Mar '16

Dear Neks, I am have attempted to use nek5000, firstly by following some of the examples etc. Now I am trying to create my own simulation, which is based upon the ocyl examples. My efforts simply include creating my own grid points in the .rea file to create a slightly different dimension... I believe I have understood how to define the problem however I continually receive errors when creating the genmap it reads as follows.... Input (.rea) file name: ocyl Input mesh tolerance (default 0.2): NOTE: smaller is better, but generous is more forgiving for bad meshes. 0.2 reading .rea file data ... ERROR: error reading 1 11 24 aborting 510 in routine rdbdry. 1 quit All I have done again is change the dimensions of the elements in the .rea file so I do not see why it would now not work? Thank you for any help in advance, Friedrich.

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Does Nek5000 use any kind of parallelism inside one element?
by nek5000-users＠lists.mcs.anl.gov 01 Feb '16

01 Feb '16

Dear Nek5000 developpers and users, my name is Lars Haupt and I'am writing my phd-thesis at the moment, which has something to do with scalable p-multigrid based approaches. Therefore i have to understand the state of the art multigrid solver Nek5000 and thats why i'am trying to get some insides into Nek5000 parallelism. I read the article about the scalability of the Nek5000 Code which was achieved on the Juelich Supercomputer in 2010. I thought that the impressive strong scaling speedup was a result of an optimised hybrid parallelization strategy (MPI and OpenMP). But the general info on the Nek5000 website says that only MPI does the parallel job. Which means, domain decomposition is the only kind of parallelism? What happens with the huge amount of nodes inside one element? The FAQ tells something about high efficient matrix-matrix multiplications. Which are implemented using MKL-BLAS 3 dgemm routines, i guess? If that is the case, does Nek5000 use any OpenMP based parallelism inside MKL or why not? Many thanks in advance Lars Haupt Dipl.-Math. Lars Haupt Wissenschaftlicher Mitarbeiter Technische Universität Dresden Fakultät Maschinenwesen Institut für Energietechnik Professur für Gebäudeenergietechnik und Wärmeversorgung 01062 Dresden Tel.: +49(351) 463-37619 Fax.: +49(351) 463-37076 E-Mail: lars.haupt(a)tu-dresden.de

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Need for clarification on boundary condition (inlet velocity)
by nek5000-users＠lists.mcs.anl.gov 30 Jan '16

30 Jan '16

Dear Sir I am basically trying to simulate a plunging airfoil using NEK5000. What I thought was, keeping the NACA profile stationary while making the flow to oscillate. I wish to give the inlet velocity boundary condition as oscillating ( some sine or cos function dependent on time). How shall I incorporate this in my subroutine userbc()? Thanks/Regards Prashanth Mohanasundaram

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Low-Mach equations with source term for mass
by nek5000-users＠lists.mcs.anl.gov 29 Jan '16

29 Jan '16

Hi Neks, We want to solve the Low-Mach equations with a source term S in the continuity equation, i.e. d(rho)/dt + div(rho*u) = S. Is there a way to define S via the Fortan77 interface? Best, Philipp Weiss

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Point votices at inlet
by nek5000-users＠lists.mcs.anl.gov 29 Jan '16

29 Jan '16

Hi neks, Is there a way to prescribe point vortices at the inlet? I am trying to apply the vortex method (see attached link for description) at the inlet to generate turbulence. In that formulation, we have | x_i - x |. I am not sure how to incorporate this part to the usr file. Has anybody done this before? http://aerojet.engr.ucdavis.edu/fluenthelp/html/ug/node509.htm Many thanks Rif

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Local Refinement
by nek5000-users＠lists.mcs.anl.gov 26 Jan '16

26 Jan '16

Hi All, I have simulated an eccentric stenosis problem at Re=1000 to verify against Varghese et al., JFM 2007 but my RMS and TKE plots are relatively damped compared to their study. The mesh used in their study appears to show local refinement near the jet breakdown region, which would indicated non-conforming elements. On the other hand, I have no local refinement where the jet breakdown occurs, which probably explains the discrepancy. Without local refinement, my mesh size would be on the order of ~20M grid points, compared to 5M grid points used by Varghese et al. to achieve DNS. I have searched the documentations but couldn’t find a clear answer on this. I have two questions and I would greatly appreciate if someone could answer them, or point me in the correct direction: 1) Is local refinement already implemented in the current version of NEK5000? If yes, is there any documentation available to which I can refer? 2) If local refinement is implemented, what is the best method to refine my mesh? Can I somehow loop over the elements and tag the ones I want to refine in .usr file? Or is there a graphical interface to do so? Thank you very much in advance and any help is greatly appreciated :) Regards, Owais Khan

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BC type
by nek5000-users＠lists.mcs.anl.gov 25 Jan '16

25 Jan '16

Hi,Nek I want to set Neumann boundary conditions of temperature on the right and left sides of a cavity. I wonder how to set it in .box file.Thank you for your help. Kind regards Xu Bolun -- 徐博伦

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Re: [Nek5000-users] WARNING: DIV(V)-QTL too large
by nek5000-users＠lists.mcs.anl.gov 25 Jan '16

25 Jan '16

dear neks, nobody is replying me??? Thanks > On 12 Jan 2016, at 13:43, Desanga Fernando <desanga(a)gmail.com> wrote: > > > dear developers , > > I'm doing a rotator-stator type of simulation using Pn-Pn method (lx1=8 lxd=12 ). Annular mesh has been created using genbox (box file is attached). Inner radius is considered as the hub and outer radius is the case (or the sidewalls of the disk ). I use following settings in rea file > > 3 p27 TORDER > 20.00000 p93 Number of prev pressure solns saved > 5.000000 p94 start projecting vel. after p94 step > 5.000000 p95 start projecting pr after p95 step > 4.000000 p99 dealiasing:if <0 disable > 1.000000 p101 No. of additional filter modes > 5.000000E-02 p103 weight of stabilizing filter (.01) > > Hub and rotor (z=0) rotating in a constant angular velocity. Stator (z=0.2) and side walls are stationary. singularities among rotor and stationary components are resolved using a method which is very similar to vortex example (using an exponential ramp instead of a polynomial ramp) . After 3000-4000 iterations , CFL number reached around 0.48 and I got following warning > > > L1/L2 DIV(V) : -1.6903E-16 1.0198E-01 > L1/L2 QTL : 0.0000E+00 0.0000E+00 > L1/L2 DIV(V)-QTL: -1.6903E-16 1.0198E-01 > WARNING: DIV(V)-QTL too large! > > I'm not using any inlets or outlets in my simulation. I'm not sure the reason for this warning. can anybody give me a little advice regarding this situation. I can provide more details on request. > > > Desanga > > <3da.box>

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Need for clarification on the SOURCE TERM
by nek5000-users＠lists.mcs.anl.gov 22 Jan '16

22 Jan '16

Dear Sir, How to find out whether the source term which I wish to incorporate in the Navier Stokes equation, will be added to the momentum or energy equation. Thanks & Regards Prashanth Mohanasundaram

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