January 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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mesh problems (i think)
by nek5000-users＠lists.mcs.anl.gov 02 Feb '14

02 Feb '14

Dear Neks, I am trying to set up a case from scratch. The goal is to create a complex 3d cylindrical mesh, to start I am trying to build a pipe. 1st attempt: I created a simple 2d 'base.rea' file (by hand) and extruded it with n2to3 to create 'base3.rea'. This case works in 3d, the outer edges are curved and the boundary conditions are correct. 2nd attempt: I wrote a piece of code to create a 3d 'pipe.rea'. I tried to reproduce the case that I had done by hand but this time without success. nek runs the case and produces the usual output without giving any errors but... Problems: - the outer edges are not curved - the boundary conditions are not imposed correctly In both cases I used the same .usr and SIZE files. It seemed to me that I had a problem with face numbering, so I tried changing the number of the curved faces in the pipe.rea file. I tried with all 6 numbers but still no curved faces. I have attached both the 'base3.rea' (which works) and the 'pipe.rea' (which doesn't). I also attached a picture of the output generated when running the 'pipe.rea' case and the SIZE and .usr files. All the attached files can be downloaded from my dropbox folder at this link: https://dl.dropboxusercontent.com/u/18689429/attachment.zip Can someone help me understand why 'pipe.rea' does not work? Best regards, Jacopo

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Pipe with expansion
by nek5000-users＠lists.mcs.anl.gov 31 Jan '14

31 Jan '14

Kamal, I've added an example for a step-type expansion in a pipe. New example directory is nek5_svn/examples/expansion, with a README. If you want a standard diffuser, I would use mesh-morphing, as outlined in the nek primer, which can be found on this page: http://nek5000.mcs.anl.gov/index.php/UG#Documentation I've also automated our turbulent outflow bc treatment -- one simply provides an expansion factor (typically ~ 1.5) and two persistent arrays to turb_outflow(), which is now in navier5.f. This can be useful when very strong vortices are leaving the domain, which is possible for certain diffuser flow conditions (and others). 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: Monday, January 13, 2014 3:35 AM To: nek5000-users(a)lists.mcs.anl.gov Subject: [Nek5000-users] Creating a Mesh Hi Can some one please help me in this because I am new to nek 1) How can I create a .rea for a specific geometry say ' A sudden expansion pipe ' or a ' Diverging pipe ' 2) What tool I should use to create that mesh. Thank you kamal _______________________________________________ Nek5000-users mailing list Nek5000-users(a)lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

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Linearised Navier-Stokes time-dependant base flow
by nek5000-users＠lists.mcs.anl.gov 31 Jan '14

31 Jan '14

Hi Nek's, I have a question regarding the linearised Navier-Stokes solver while the underlying base flow is time-dependant. As far as I understand, one should simply have to set param(31) = 1 to achieve this (and p31 = -1 for a steady state base flow). What about the boundary conditions however? For instant, I want to investigate the linear dynamics of perturbations evolving onto a lid-driven cavity flow exhibiting a periodic limit cycle I have computed. How could I impose in userbc: ux = 1 uy = 0 uz = 0 for the periodic base flow time-evolution, and in the meantime: ux = 0 uy = 0 uz = 0 for the perturbation? Cheers, JC -- Jean-Christophe Loiseau Homepage <https://sites.google.com/site/loiseaujc/>

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NEK5000 User Group Metting
by nek5000-users＠lists.mcs.anl.gov 30 Jan '14

30 Jan '14

Hi All, Is there any more info on the possibility of a User Group Meeting this year? Thanks, Murph -- /Confidentiality Notice: I swear and affirm that I will not retransmit, discuss, or disseminate any information in this message to anyone other than the intended recipients.However, at this very second, every entity in the known universe is reading this message.This includes the US Government, Foreign Governments, all telecommunications carriers, all Internet service companies, anyone buying adds from said service companies, most major hardware and software vendors, all hackers and kiddie-scripters older than about 6, and any space aliens within subspace communications range of Earth.Tin Foil Helmets do not work./ ** *Murphy Leo O'Dea, PE"Murph"*<http://www.oakland.edu> PhD Student, Mechanical Engineering /School Of Engineering And Computer Science/ /Oakland University/ mlodea(a)oakland.edu <mailto:[email protected]> http://www.secs.oakland.edu/~mlodea/

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mpi issue
by nek5000-users＠lists.mcs.anl.gov 29 Jan '14

29 Jan '14

Hello, I run into this error with mpi. I am not sure what is about. Has someone an idea? Thank you! Best Tubois ############################################################# # Compilation successful! # ############################################################# text data bss dec hex filename 2405375 3336 196307656 198716367 bd82bcf nek5000 mv: cannot stat `ext_cyl.log.': No such file or directory mv: cannot stat `ext_cyl.sch': No such file or directory -------------------------------------------------------------------------- mpiexec was unable to launch the specified application as it could not find an executable: Executable: -4 Node: boquette while attempting to start process rank 0. --------------------------------------------------------------------------

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Re: [Nek5000-users] Post processing bypass
by nek5000-users＠lists.mcs.anl.gov 28 Jan '14

28 Jan '14

Dear Paul, Thank you. I was basically looking for the space-saving measures you mentioned. Best regards, JP On 28 January 2014 10:39, Jean-Paul Mollicone <jp.mollicone(a)gmail.com>wrote: > Hi All, > > Any follow up please? > > Regards, > JP > > > On 17 January 2014 11:05, Jean-Paul Mollicone <jp.mollicone(a)gmail.com>wrote: > >> Dear All, >> >> A quick question; is there a way to run nek5000 in post-processing mode >> (i.e. with nsteps=0) BUT without re-generating the mesh? >> >> The use would be for example to carry out post-processing from >> large-scale simulation data from a high-performance computer on a less >> powerful computer (that is not able to re-generate the mesh without >> sufficient RAM, etc) >> >> Thank you, >> JP >> > >

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Re: [Nek5000-users] Post processing bypass
by nek5000-users＠lists.mcs.anl.gov 28 Jan '14

28 Jan '14

Hi All, Any follow up please? Regards, JP On 17 January 2014 11:05, Jean-Paul Mollicone <jp.mollicone(a)gmail.com>wrote: > Dear All, > > A quick question; is there a way to run nek5000 in post-processing mode > (i.e. with nsteps=0) BUT without re-generating the mesh? > > The use would be for example to carry out post-processing from large-scale > simulation data from a high-performance computer on a less powerful > computer (that is not able to re-generate the mesh without sufficient RAM, > etc) > > Thank you, > JP >

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Re: [Nek5000-users] Postdoc position available - Please post to the list
by nek5000-users＠lists.mcs.anl.gov 22 Jan '14

22 Jan '14

Prof. Mavriplis and the University of Ottawa are currently looking for a postdoctoral researcher interested in pursuing research in the field of Computational Fluid Dynamics (CFD). The main topic of research will be adaptive discontinuous Galerkin or spectral element methods for direct simulation (incompressible Navier-Stokes equations), and other projects may include control of separated flows, transition, aerodynamics and CFD for blood flow. A PhD degree in CFD or Fluid Dynamics including code development and high performance computing is necessary. The candidate must have already published journal articles. Experience with spectral methods, Nek5000, and VISIT is a plus. The ideal candidate will have excellent computer programming skills, communication skills (written, oral, graphical and with others in the research group), self-motivation and an open mind. The position also requires some training of graduate students. Please send a short email with cv attached by email with 'Nek5000 Postdoc application' in the subject line. Ideally this would be for the immediate timeframe. The position is at University of Ottawa in Ottawa, Canada. Please send a short email with cv attached by email with 'Nek5000 PhD application' in the subject line. Catherine Mavriplis http://www.engineering.uottawa.ca/en/directory/view/mavriplis_catherine -- Prof. Catherine Mavriplis Dept. of Mechanical Engineering / Génie mécanique University of Ottawa / Université d'Ottawa 161 Louis Pasteur Room A331 Ottawa, Ontario CANADA K1N 6N5

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