August 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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postx not working in Ubuntu 16.04
by nek5000-users＠lists.mcs.anl.gov 30 Aug '16

30 Aug '16

Hi All, I built Nek5000 in my Ubuntu 16.04 machine. I ran the eddy_uv case and it finished running successfully. However, when I tried to visualize the results with postx, I got nothing but a black window. Have anyone experienced this before? Thanks in advance !!

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set passive scalar initial conditions after some time t
by nek5000-users＠lists.mcs.anl.gov 26 Aug '16

26 Aug '16

Hello all, I would like to apply some initial conditions for a passive scalar after some time t in the simulation as opposed to at the start of the simulation. In other words, start a simulation, let the flow field evolve, then after some time initialize the passive scalar with some prescribed initial condition, and then continue simulating the flow field and the passive scalar. Is there a simple way to accomplish this in the .usr file? What subroutine would be the best for this situation? If userchk — how do we set the values of the passive scalars in this routine? Side note: we have found that for this case we can not first run the flow field calculation and then restart the calculation with the passive scalar values set as an initial condition. The restart affects the flow field too strongly since we are interested in a very specific state of the flow field. Thanks, Mark Mark Paul Professor of Mechanical Engineering Virginia Tech www.me.vt.edu/mpaul

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Error reading initial condition/drive force data aborting in routine rdicdf. EXIT: rdicdf error
by nek5000-users＠lists.mcs.anl.gov 26 Aug '16

26 Aug '16

Hello all, I have been using the same .rea and .usr files in a different RESTART calculation where the input file is ASCII. But when the file is BINARY, it is showing this error. I have changed the Parameters 66 and 67 but to no avail. Any help is appreciated. Thanks, Saikat. *Saikat Mukherjee,* *Graduate** Student,* *Engineering Science and Mechanics,* *BEAM,* *Virginia Tech.*

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Multiple Restart Files
by nek5000-users＠lists.mcs.anl.gov 23 Aug '16

23 Aug '16

Hi, Sometimes I run into issues when Nek can't load the restart file that is specified in the .rea file. I'm not exactly sure why this is the case, but it's possible that the outputs are corrupted. Is it possible to specify multiple restart files in .rea i.e.: 2 PRESOLVE/RESTART OPTIONS ***** restart0.f00001 restart0.f00002 or do something equivalent so I can specify a backup restart file in case the first one is not readable? It's a non-issue if I'm running it on a system I own, but on queued systems, it's painful to resubmit the job and wait because of this issue. Please let me know if this is possible or there are other ways to read multiple restart files. Sincerely, Kento

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Re: [Nek5000-users] Heat/passive scalar solver - Helmholtz
by nek5000-users＠lists.mcs.anl.gov 22 Aug '16

22 Aug '16

Dear Neks, I am a little confused by the setup in the rea file to run a simulation with a constant cfl. My understanding (from the Nek5000 archives) is that by setting p012 to a positive value in the rea file, it should be sufficient to ensure a constant cfl condition during the run. When I do so, my time step is constant and thus my cfl varies. I tried to set p012 to a positive value in different rea file from the examples directory but none of them yield a constant cfl during the run. If someone has an answer to this problem I would really appreciate the help. Thanks, Marco

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Re: [Nek5000-users] Heat/passive scalar solver - Helmholtz
by nek5000-users＠lists.mcs.anl.gov 22 Aug '16

22 Aug '16

Never mind. I got it. Marco > On Aug 22, 2016, at 2:19 PM, Delchini, Marc-Olivier G. <delchinimg(a)ornl.gov> wrote: > > Dear Neks, > > I am a little confused by the setup in the rea file to run a simulation with a constant cfl. My understanding (from the Nek5000 archives) is that by setting p012 to a positive value in the rea file, it should be sufficient to ensure a constant cfl condition during the run. When I do so, my time step is constant and thus my cfl varies. > > I tried to set p012 to a positive value in different rea file from the examples directory but none of them yield a constant cfl during the run. > > If someone has an answer to this problem I would really appreciate the help. > > Thanks, > Marco

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General functionality of the .usr file
by nek5000-users＠lists.mcs.anl.gov 22 Aug '16

22 Aug '16

Hi! I am a new user of Nek5000. I have read through the User Documentation, and ran some simulations. Now it is time for me to start editing a file that a colleague wrote fo me. I therefore need to know how the .usr file is used. For example: In the User Documentation it is written that uservp() is called "once per processor, and once per discrete point therein". Does this mean that this is called once before the simulation is executed or is it called once per time step or in some other fashion? I would guess that uservp() is called once before the simulation is run, is that correct? Does thi apply to all routines in the .usr file, or are some of them called repeatedly during the simulation? userbc() for instance? I have been looking for a definition of the variables that are accessible in the separate routines. For instance, the input arguments to useric are (ix,iy,iz,ieg). I have gotten to understand that ix, iy and iz relate to a spatial coordinate in some way, and that ieg is some kind of index for the fluid element. Is there a precise definition of these names available? In addition to the input arguments it seems as you have access to more variables than the input arguments in each routine. In useric() you may for instance change ux, uy and uz. Is there a full list of all parameters that are available available? /Johan

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MPI_TAG_UB
by nek5000-users＠lists.mcs.anl.gov 18 Aug '16

18 Aug '16

Hi Neks, I was wondering if someone could tell me the implications of commenting this section of code out in Nekbone: if (nval.lt.(10000+max(lp,lelg))) then if(nid.eq.0) then write(6,*) 'ABORT: MPI_TAG_UB too small!' endif call exitt endif We are testing Nekbone with an experimental MPI library. Regards, Ken The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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vtk into prenek
by nek5000-users＠lists.mcs.anl.gov 14 Aug '16

14 Aug '16

Neks, I am trying to import some mesh information into prenek via a vtk file. Can someone please post an example of one that works into the git repo? Ideally it would be nice to have a 2d and 3d case for vtk files that work in prenek. I have tried using the vtkUnstructuredGridWriter class from the vtk library and prenek does not accept the file. At first I thought it was because the class required 3d points and I am importing a 2d mesh, but after I modified the file to remove the extra coordinate and make it match the style guide ( http://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf) prenek reads the mesh without crashing, but no elements appear. The output to the terminal from prenek is: IMPORT VTK MESH Current number of elements: 0 input name of vtk file 4 0 1 2 3 inside gencen 0 F 4 done gencen 0 The contents of the file I am trying to import are below, so if you see a bug please let me know. # vtk DataFile Version 4.0 vtk output ASCII DATASET UNSTRUCTURED_GRID POINTS 7 float 0 0 2.1 0 1.48492 1.48492 0 2.1 3 0 2.12132 2.12132 0 3 CELLS 3 15 4 0 1 2 3 4 1 4 5 2 4 3 2 5 6 CELL_TYPES 3 9 9 9 Thanks, -- Phil S.

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