December 2014 - 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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VisIt error: The first time step in a Nek file must contain a mesh
by nek5000-users＠lists.mcs.anl.gov 01 Apr '15

01 Apr '15

Hi all, I get error of mesh need to contain the first time step in Nek file everytime I run .nek5000 file from results of some example (turbchannel, blasius and expansion). However for the 3dbox example, I got no error to open it. I've checked the first line in the first time step file (.f00001) and have the geometry (X) in them. I also changed the logic for coordinate output to (T COORDINATES) and different param66, but still getting the same error. Perhaps even if I put the mesh output for each timestep not just in first timestep, I still getting the same error. Note that I've already set the right plugin and type file during open the .Nek5000 file. In addition, I've checked the same parameters for 3dbox example which is same with the other example rea file, plus 3dbox still gives me no error even if i not switch the coordinate output to true (F COORDINATES) I really hope that anyone who has encountered the same problem and has solved it to assist me. That would be really helpful. Regards, -- Muhsin Mohd Amin Graduate Student Department of Mechanical Engineering The University of Sheffield

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LES-wall
by nek5000-users＠lists.mcs.anl.gov 01 Jan '15

01 Jan '15

Hello all, I have a question regarding LES capability of Nek. I know that the explicit filtering introduced in Nek can be effective for velocity field to provide sort of eddy viscosity modeling. Nevertheless, there should be some form of modeling for the near wall regions, since it is almost infeasible to have DNS like resolution in such regions for problems with relatively high Reynolds number and large scale geometries. I have seen SFR assemblies example on the Nek web in which LES used, however, I am not sure if that was an LES with near-wall resolution or with near-wall modeling. So I was wondering if anyone has any experience of using Nek LES with near wall models, or kind of hybrid RANS-LES approaches. Thanks, Mohsen

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Conjugate Heat Transfer: Flow past a Heated Cylinder
by nek5000-users＠lists.mcs.anl.gov 27 Dec '14

27 Dec '14

Hello, I am currently using nek5000 to simulate flow past a heated cylinder (with volumetric energy generation) and I am interested in gathering local Nusselt number (i.e. dT/dn) information at all locations on the surface of the cylinder (with Boundary ID 'W '). "n" is the normal pointing outward from the cylinder. Since I am using mulltiple processors, I am a little stumped on how to proceed. Can anyone recommend an algorithm to output this information in an ascii file (.txt or .dat)? Thank you for your help, Saumil

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surface integral as function of z
by nek5000-users＠lists.mcs.anl.gov 19 Dec '14

19 Dec '14

Dear Nek's I am planning to calculate the surface integral at a given ' z ' position . ( z is my flow direction) I know there is a sub routine surface_int(U,A,v,e,f) to calculate the surface integral, where the elements are identified using the boundary condition. What should I do calculate the surface integral as function of z position. / i.e E= | omega^2 dx dy / s I tried to dump the data using the function interp_v(uvw,xyz,n) at a particular cross section but it is not helping much, since I need thousands of cross section data to have E as a function of z . Thanks in advance Best Regards, Kamal

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Forcing term in weak form
by nek5000-users＠lists.mcs.anl.gov 17 Dec '14

17 Dec '14

Hi NEK's I need to add a forcing term f to the linearized momentum equation which is proportional to the divergence of the viscous stress div(grad(Ub)+grad(Ub)^T), where Ub is the base-flow. Thus, if grad(Ub)+grad(Ub)^T=c I would like to use the weak form formulation where *-c grad w* is used, instead of *div(c)*w* (w being the test functions). Is it possible? Andrea

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USERVP
by nek5000-users＠lists.mcs.anl.gov 11 Dec '14

11 Dec '14

Hi all, I am quite new in Nek5000 and I still trying to develop the understanding to use this program. May i know what are udiff and utrans stands for in uservp subroutine in .usr file? I aware that both will be using to control the variable properties. But which parameter are those control in the equation? Thanks Muhsin

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Re: [Nek5000-users] Unrealistic values at element edges
by nek5000-users＠lists.mcs.anl.gov 10 Dec '14

10 Dec '14

Hi Paul, Thank you very much for your reply. I'm doing DNS of turbulent pipe flow and the plots were from a pipe flow with Re_D=5300 (Re_tau=180). Basically, I used the same grid resolution as specified in the paper "Direct numerical simulation of turbulent pipe flow at moderately high Reynolds numbers" which I think should be reasonably good for the given low Reynolds number. And I'm also using PnPn-2, the same as used in the papers which use nek5000. In this case, shall I use even better grid resolution for this Reynolds number in order to get rid of the wiggles? For Lambda2, I'll have a look at the filtering subroutines you suggested. Best regards, Tony ________________________________________ From: nek5000-users-bounces(a)lists.mcs.anl.gov <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Sent: 10 December 2014 18:00 To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 70, Issue 6 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. Re: Unrealistic values at element edges (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Wed, 10 Dec 2014 17:34:21 +0000 From: nek5000-users(a)lists.mcs.anl.gov To: "nek5000-users(a)lists.mcs.anl.gov" <nek5000-users(a)lists.mcs.anl.gov> Subject: Re: [Nek5000-users] Unrealistic values at element edges Message-ID: <mailman.11825.1418232863.3424.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="us-ascii" Tony, The wiggles in the quantities your plotting are generally indicative of marginal resolution for the given Reynolds number. They will go away with increased resolution. Lambda2 is not continuous a priori, but converges to a continuous function with increased resolution (exponentially fast). Are you using PnPn or PnPn-2 ? Pressure will generally look better with PnPn (and be better, in the marginally resolved, i.e., LES, case). For lambda2 it might be possible to do some filtering to get a smoother plot...(same for other quantities). I would suggest going that route --- there are several filtering strategies but I'm not certain which would be best for your particular case. You might start with the g_filter() routine in navier5.f with a diagonal scaling of the wavenumbers like: ( 1 1 1 1 1 ... 1 .99 .95 .90 ) say... which reduces the energy in the top 3 modes. There is also filter_d2() that you can experiment with. Paul ________________________________________ From: nek5000-users-bounces(a)lists.mcs.anl.gov [nek5000-users-bounces(a)lists.mcs.anl.gov] on behalf of nek5000-users(a)lists.mcs.anl.gov [nek5000-users(a)lists.mcs.anl.gov] Sent: Wednesday, December 10, 2014 10:28 AM To: nek5000-users(a)lists.mcs.anl.gov Subject: Re: [Nek5000-users] Unrealistic values at element edges Dear Neks, Sorry that the image wasn't shown. I've attached it here. Hope someone can help. Thanks and regards, Tony ________________________________________ From: nek5000-users-bounces(a)lists.mcs.anl.gov <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Sent: 10 December 2014 16:23 To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 70, Issue 4 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. Unrealistic values at element edges (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Wed, 10 Dec 2014 16:23:02 +0000 From: nek5000-users(a)lists.mcs.anl.gov To: "nek5000-users(a)lists.mcs.anl.gov" <nek5000-users(a)lists.mcs.anl.gov> Subject: [Nek5000-users] Unrealistic values at element edges Message-ID: <mailman.11813.1418228589.3424.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="iso-8859-1" Dear Neks, I've been running turbulent channel and pipe flows using nek5000 for a while. However, recently when I created movies of lambda2 structures and pressure iso-surfaces in channel and pipe flows I observed some "strange" values at the edge between elements. [cid:cec5092f-41be-4ae9-a468-a5fa9ab9f7ff] This is lambda2 structures in turbulent pipe flow. It is clearly visible from the picture that at some slices in streamwise direction, the values don't seem to be realistic and it feels like the flow is passing through some filters. Interestingly, when I plotted the mesh together with the variables, the vertical noise lines happened to be at the edge between adjacent elements, which is particularly clear in lambda2 plot. Same behaviour was also found in 2D pressure plots and in turbulent channel flow cases. Has anyone observed similar things before in visualisation? I used both Paraview and VisIt for visualisation and the same thing was observed, so it shouldn't be a problem of software. In this case, I'm just wondering why the result is like this or is it because I set something wrong in my simulations? Any comments will be appreciated and thank you very much in advance. Best regards, Tony

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Re: [Nek5000-users] Unrealistic values at element edges
by nek5000-users＠lists.mcs.anl.gov 10 Dec '14

10 Dec '14

Dear Neks, Sorry that the image wasn't shown. I've attached it here. Hope someone can help. Thanks and regards, Tony ________________________________________ From: nek5000-users-bounces(a)lists.mcs.anl.gov <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Sent: 10 December 2014 16:23 To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 70, Issue 4 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. Unrealistic values at element edges (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Wed, 10 Dec 2014 16:23:02 +0000 From: nek5000-users(a)lists.mcs.anl.gov To: "nek5000-users(a)lists.mcs.anl.gov" <nek5000-users(a)lists.mcs.anl.gov> Subject: [Nek5000-users] Unrealistic values at element edges Message-ID: <mailman.11813.1418228589.3424.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="iso-8859-1" Dear Neks, I've been running turbulent channel and pipe flows using nek5000 for a while. However, recently when I created movies of lambda2 structures and pressure iso-surfaces in channel and pipe flows I observed some "strange" values at the edge between elements. [cid:cec5092f-41be-4ae9-a468-a5fa9ab9f7ff] This is lambda2 structures in turbulent pipe flow. It is clearly visible from the picture that at some slices in streamwise direction, the values don't seem to be realistic and it feels like the flow is passing through some filters. Interestingly, when I plotted the mesh together with the variables, the vertical noise lines happened to be at the edge between adjacent elements, which is particularly clear in lambda2 plot. Same behaviour was also found in 2D pressure plots and in turbulent channel flow cases. Has anyone observed similar things before in visualisation? I used both Paraview and VisIt for visualisation and the same thing was observed, so it shouldn't be a problem of software. In this case, I'm just wondering why the result is like this or is it because I set something wrong in my simulations? Any comments will be appreciated and thank you very much in advance. Best regards, Tony

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