April 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 in generalev
by nek5000-users＠lists.mcs.anl.gov 02 Jul '14

02 Jul '14

Hello Neks, I've recently come across an error I haven't seen before. It occurs in the routine "generalev" at the beginning of my run. It looks like the matrix "a" and "b" being fed to the routine have an Infinity or NaN at position (0,0). Are there any ideas of what could cause this type of error? I have attached the logfile to this email. Thanks, -- Josh Camp "All that is necessary for the triumph of evil is that good men do nothing" -- Edmund Burke

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Rules of thumb for element aspect ratio limits
by nek5000-users＠lists.mcs.anl.gov 07 May '14

07 May '14

Hello, I am looking to do simulations of flow past a wing in 3D using nek5000 and I have been thinking more about potential issues with high aspect ratio elements. In general we have very fine resolution near the wing and then as we get further away the wall normal and wall parallel spacing increases. As a first try we will extend the domain in the cross stream direction which will result in small dz values. I know that in general the best performance is obtained with elements having dx=dy=dz and that as the aspect ratio increases the performance will degrade. I'm wondering if there are general rules of thumb for the performance degradation with increased aspect ratio. For example, is an aspect ratio of 10 ok but an aspect ratio of 100 unacceptable? Is this even something we can estimate in general or does it vary so much problem to problem that no general estimate is possible? I saw an earlier post that referred to the paper "An Overlapping Schwarz Method for Spectral Element Solution of the Incompressible Navier-Stokes Equations", P. Fischer JCP 1997. From the paper I see two general strategies. 1. limit the maximum aspect ratio to a critical value 2. design a grid for our case, run it for a short time and then iteratively add more grid points to decrease the aspect ratio until optimal performance is achieved. Does anyone have a general or specific suggestion regarding how we should handle the grid generation in terms of selecting the largest aspect ratio possible with low computational cost? Thanks, Matt

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curved side in a block
by nek5000-users＠lists.mcs.anl.gov 30 Apr '14

30 Apr '14

Dear Users, I'm trying to construct a 3D mesh which consist on a small portion of a sphere. First, I've constructed a single element. Now I'm trying to curve the edges using the "midpoint" routine, but nothing happens. What is the problem? This is my mesh: 1500.00 500.000 0.00000 0.00000 XFAC,YFAC,XZERO,YZERO **MESH DATA** 6 lines are X,Y,Z;X,Y,Z. Columns corners 1-4;5-8 1 3 1 NEL,NDIM,NELV ELEMENT 1 [ 1A] GROUP 0 144.3500 7.217500 8.838700 176.7750 -144.3500 -7.217500 0.000000 0.000000 -144.3500 -7.217500 -8.838700 -176.7750 0.000000 0.000000 0.000000 0.000000 -176.7750 -8.838700 0.000000 0.000000 -176.7750 -8.838700 -12.50000 -250.0000 ***** CURVED SIDE DATA ***** 8 Curved sides follow IEDGE,IEL,CURVE(I),I=1,5, CCURVE 2 1 8.829300 -3.6572E+00 -8.057200E+00 0.000000E+00 0.000000E+00 m 4 1 176.5864 -63.1445E+00 -1.611432E+02 0.000000E+00 0.000000E+00 m 6 1 0.000000 -1.1335E+01 5.269500E+00 0.000000E+00 0.000000E+00 m 8 1 0.000000 -2.2670E+02 1.053902E+02 0.000000E+00 0.000000E+00 m 9 1 73.14450 -1.7658E+02 -1.611443E+02 0.000000E+00 0.000000E+00 m 10 1 3.657200 -8.8293E+00 -8.057200E+00 0.000000E+00 0.000000E+00 m 11 1 11.33500 0.00000E+00 5.269500E+00 0.000000E+00 0.000000E+00 m 12 1 226.7000 0.00000E+00 1.053902E+02 0.000000E+00 0.000000E+00 m In 'CURVED SIDE DATA': Edge Element x y z dummy dummy m (x,y,z represent the coordinates of the mid point of the edge) Thank you in advance.

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Prex problem
by nek5000-users＠lists.mcs.anl.gov 25 Apr '14

25 Apr '14

Dear All, I am trying nek5000 under ubuntu. Now I adapted mkmesh from case expansion for my own case, which is a flat plane boundary layer with a slot. I build one box for the jet slot and 23 boxes for the plane wall around it (mbox in SIZE of genbox.f was changed for it). Now when I use pretex to merge both 2d mesh together, pretex show no picture for the mesh (but just an empty menubar and a black window, no errors shown) then I cannot assign properly B.C. for the boundaries. Could anyone give any hints? Thank you very much in advance. If you need, I can send the setup files to you. Zhenyu Zhang

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Question on drawing streamlines for Nek5000 data
by nek5000-users＠lists.mcs.anl.gov 24 Apr '14

24 Apr '14

Dear All, I am sorry to launch this question about VisIt here. I submitted it in visit-user.org. But it seems nobody there uses Nek5000. So may I ask any help from you. I tried to use Visit 2.7.2 to draw streamlines for a flow field through a backward step from Nek5000. Parameters in Visit: step length: 0.1 (size of my mesh between 0.05 and 0.2) max steps: 10000 source type: line (1 -0.99 1.5) to (1 0.99 1.5) (this line is well inside the flow field down stream of the step (at x=0)) 50 sample along line uniformly integration: forward scheme: Forward Euler (default Dromand-Prince diverged ) Now the questions is: 1. Only part of the line is positioned with seeds. part of the line is blank with No streamlines at all. 2. According to Visit user manual, step length should agree with average size of mesh, in my case even I reduce the step to 0.01. The integration is broken . 3. To my knowledge, RK4 is good for its stability. But in this case it cannot even give a good result . However, the 1st -order forward Euler can be used. don't know why yet. 4. Generally before visualizing spectral element results, interpolation is necessary a priori. Sorry I did not do this work here just for simplicity, so the accuracy of streamline may not be quite good. But I don't think this broke the streamline generation. 5. There is a laminar separation vortex just downstream (about x=2) of the seeding line (x=1), if I want to plot the stream lines across the whole flow field, could you please leave me any hints to do that? In fact, what ever the max steps is set, my streamline seems never extend up to x=1.3 6. Is it possible to introduce adaptive local time step for streamline production? this tech. is quite well known for steady CFD problems. If you need , I can upload a picture later to show above questions. I'll appreciate any hints from you. Zhenyu Zhang

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Setting viscosity in usr file
by nek5000-users＠lists.mcs.anl.gov 24 Apr '14

24 Apr '14

Hello Praveen, Try to set parameter 'udiff' for field 1 ('ifield.eq.1', i.e. velocity field) in subroutine uservp. Param(30) in .rea file has to be equal to 1.. Regards, Donato From: nek5000-users-bounces(a)lists.mcs.anl.gov [mailto:[email protected]] On Behalf Of nek5000-users(a)lists.mcs.anl.gov Sent: 24 April 2014 06:31 To: nek5000 Subject: [Nek5000-users] Setting viscosity in usr file Hello neks Which is the place to set viscosity (param(2)) in the usr file ? In example fs_2, it is done in usrdat2, but the param seems to be read after usrdat2 is called. Thanks praveen

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Multiple velocity inlets
by nek5000-users＠lists.mcs.anl.gov 24 Apr '14

24 Apr '14

Hi, Does nek5000 now support boundary conditions for multiple velocity inlets? I am really interested in esp. two or more inlets with unsteady velocities. Cheers, Zhenyu

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Setting viscosity in usr file
by nek5000-users＠lists.mcs.anl.gov 23 Apr '14

23 Apr '14

Hello neks Which is the place to set viscosity (param(2)) in the usr file ? In example fs_2, it is done in usrdat2, but the param seems to be read after usrdat2 is called. Thanks praveen

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Internal boundary condition
by nek5000-users＠lists.mcs.anl.gov 22 Apr '14

22 Apr '14

Dear all, I have a question regarding the internal boundary condition in the code. My problem consists of a fan-shaped nozzle, which parts of its walls are located within the flow domain (a cylindrical tank with inflow/ outflow boundary conditions). The question is how to set the boundary conditions for such internal zero-thickness walls? I thought the walls could be defined as internal faces by creating a side-set (in the Cubit) and setting the velocity and the temperature fields of these faces to 'W ' and 'E ', respectively, similar to the solid-fluid interface in the conjugate heat transfer example. Nevertheless, there is a fluid at both sides of the interface in this case. Below is part of the boundary conditions in .rea file. ..... ..... 1 0 ! 1 fluid set, 0 other/solid sets 10 ! fluid set is 10 1 ! block 10 is material 1 10 ! no. bc sets (side-sets); bc set id, 100 1 W , (external walls) 100 2 I , (external walls) 120 1 W , (internal walls corresponding to the nozzle) 120 2 E , (internal walls corresponding to the nozzle) 200 1 v , (inflow) 200 2 t , (inflow) 300 1 O , (outflow) 300 2 O , (outflow) 400 1 SYM, 400 2 SYM, ..... ..... When I run this case, warning messages appear during assigning the sidesets to the element faces, saying that: "face shared by 2 Hexes (say) 2331 5227". It seems that this warning is only because I defined some faces as "internal", however, no "other solid/fluids" has been defined in the input file. Nevertheless, the issue with such definition is that, although, the velocity field is zero at the internal walls, there seems to be a pressure gradient across the wall, which is not physically consistent with internal walls, and drives a flow through the walls. It would be appreciated if anyone could help me on this problem. Thanks, Mohsen

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