February 2015 - 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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Linear Advection Equation
by nek5000-users＠lists.mcs.anl.gov 08 Mar '15

08 Mar '15

Dear Users, Is there a way to solve a linear advection equation in nek5k without computing the Navier-Stokes equations? I am simply interested in advecting a profile according to the following: D(phi)/Dt = d (phi) /dt + v*.*grad(phi)= 0 where v*.*grad(phi) = u.d(phi)/dx + v.d(phi)/dy + w.d(phi)/dz and v is a prescribed velocity (for example v = (1,1) in 2D) Best, Saumil

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Solving mesh Laplace equation (Re: Mesh morphing)
by nek5000-users＠lists.mcs.anl.gov 01 Mar '15

01 Mar '15

Dear Neks, What I actually would like to accomplish is to solve the Laplace equation for the mesh (with the boundary deformation as a BC). I saw that this has been done already at least by Paul (a thread 2009) and Matt (for smoothing of a wing mesh, with zero deformation). Could any of you please give me a hint on how to solve the Laplace equation for the mesh like this? Matt? Paul? I would be very grateful. Best regards, Outi Quoting Outi Tammisola <outi(a)mech.kth.se>: > Dear Neks, > > I thought this question might be of interest for someone else as > well, so posting it here: > > I have been looking at the oscillating cylinder example. I would > like to do something similar, but instead of a prescribed boundary > velocity, would like to prescribe a given displacement of one > boundary, and morph my mesh smoothly everywhere to match this > displacement. For example, if one were to describe a deformation of > the cylinder rather than a velocity (but without altering the other > boundaries and without scaling the mesh). This just needs to be done > once, not at every time step. > > Is there an easy way to do this? Can I arrive there somehow by minor > modifications of the elasticity solver? What equation exactly is the > elasticity solver solving at every time step? > (When I outputted the files after every time step for the > oscillating cylinder, the mesh deformation seemed to match the > prescribed one only after 2 time steps. Is there a reason for this, > or did I do something wrong?) > > Best regards, > Outi

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Re: [Nek5000-users] Dump on both regular and SEM grids
by nek5000-users＠lists.mcs.anl.gov 28 Feb '15

28 Feb '15

Hi Aleks (and anyone interested), Just to share an extra solution, I make Nek dump both to uniform and GLL grids simultaneously, when using IOTIME, by adding the following at approximately line 136 of prepost.f : ifreguo = .true. if (ifdoit) call outfld(prefix) ifreguo = .false. Otherwise, when using NSTEPS, the solution you gave me works just fine. Thanks again, JP

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Installation failed - maketools all
by nek5000-users＠lists.mcs.anl.gov 22 Feb '15

22 Feb '15

Dear nek5000 users, Hello everyone, I am a new user. I got stuck when I follow the Quick Start page <https://nek5000.mcs.anl.gov/index.php/Quick_Start>. I follow up till the command - "maketools all" Trouble happens. The error occurs : genbox.f:(.text+0x174cc): undefined reference to `_gfortran_transfer_real_write' And a number of similar errors. Does anyone know how to correct that? Thank you. Regards, Simon

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Re: [Nek5000-users] Error trying to visualize results in VisIt for Eddy_UV example
by nek5000-users＠lists.mcs.anl.gov 19 Feb '15

19 Feb '15

Based on the NEK5000 documentation that I have read so far, I am supposed to find "ifxyo" option in the .rea file, but I don’t see it there. Is it supposed to be a different option or is it in a different file? Ketan

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ALE formulation
by nek5000-users＠lists.mcs.anl.gov 18 Feb '15

18 Feb '15

Hello NEK's I am just getting started to work with ALE formulation and I have a couple of questions regarding it. I try to do the simulation of flow in the channel with the elastic wall. 1. How can I impose the external pressure as boundary conditions for the part on the channel where the wall is elastic? 2. How can I collect the coordinates of the deforming mesh and the ALE velocities of mesh in the each step of time? Thanks a lot. Best regards, Andrew

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Error trying to visualize results in VisIt for Eddy_UV example
by nek5000-users＠lists.mcs.anl.gov 18 Feb '15

18 Feb '15

Hi, I am a new user and I am just getting started with the examples in the Nek guide. I tried using VisIt to visualize results for Eddy_UV example but I get this error: VisIt could not read from the file "/Users/K10/eddy/vis.nek3d". The generated error message was: There was an error opening /Users/K10/eddy/vis.nek3d. It may be an invalid file. VisIt tried using the following file format readers to open the file: Nek5000, Silo The following error(s) may be helpful in identifying the problem: There was an error opening the file: When attempting to use "Nek", the file matched the general format expected by the reader but eventually encountered this error: "The first time step in a Nek file must contain a mesh". Could you please tell me why this might be happening? Ketan Mittal

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