April 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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MOAB Cubit problem
by nek5000-users＠lists.mcs.anl.gov 30 Apr '15

30 Apr '15

Thanks

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lxd from old versions of NekBone
by nek5000-users＠lists.mcs.anl.gov 30 Apr '15

30 Apr '15

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Neks, I would like to compare performance results from an earlier version of NekBone wit NekBone 3.1. However I see that lxd is no longer required in the SIZE file. What value should I use in earlier versions to have exactly the same run on the 3.1 version? Thanks, Manos -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.14 (GNU/Linux) iQEcBAEBAgAGBQJVQkN2AAoJEIhcgrtekvd+FfUH/j+k1Wyq0bSPeORrpbR0dR9j 8lpSzsqJQrdxj5GQE5YQOgaHTIx1dVLJSLYaW//jLWeKvcrFJlotiCiAiMoi/4IX dP35Ut/b4KEyUxSr8Lc5IxHBY4usgTu00GFIa5rCPAo/f+Pakp0PNIjJyYxtjfdA p5Gbia34qfSL09JkXYNWSLQKygqOp3UFh2N3++P2Bo3S28ptuwKnvx5bAqIG+GBC 3f3urVFe5X+IzpQ3SOhDLJ8qUc6cZxuJBASP9bY60S+bLNQmdwMpQ3X0yVHpc/GD xYQfWBLo2v0IELHo9PqHrA//KTx22b0JQDGpQm696v7E1giLXNpIHVVMaOizKgs= =MwJe -----END PGP SIGNATURE----- -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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MOAB Cubit problem
by nek5000-users＠lists.mcs.anl.gov 30 Apr '15

30 Apr '15

Hi,I use Trelis (V 15) to generate mesh. However, when I try to use mbconvert to generate h5m file, it says [0]MOAB ERROR: --------------------- Error Message ------------------------------------[0]MOAB ERROR: This doesn't appear to be a .cub file![0]MOAB ERROR: load_file() line 310 in src/io/Tqdcfr.cpp[0]MOAB ERROR: --------------------- Error Message ------------------------------------[0]MOAB ERROR: Failed to load file after trying all possible readers![0]MOAB ERROR: serial_load_file() line 634 in src/Core.cpp[0]MOAB ERROR: load_file() line 523 in src/Core.cppFailed to load "/home/hamid/nek5_svn/moab_conjht/cubit01.cub".Error code: MB_FAILURE (16)Error message: Failed to load file after trying all possible readers I have downloaded other cub files from repository and mbconvert works fine on them. However opening and saving these files with Trelis causes same problem.I think the file format in Trelis is different than Cubit. Is it true? if yes what is the solution? Hamid

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Re: [Nek5000-users] [MOAB-dev] MOAB Cubit problem
by nek5000-users＠lists.mcs.anl.gov 29 Apr '15

29 Apr '15

If the mesh file is not too large, please send us the mesh file that breaks mbconvert. Thanks. Rajeev Jain 630-252-3176 / 630-252-5986 (fax) jain(a)mcs.anl.gov From: Vijay S. Mahadevan <vijay.m(a)gmail.com> To: nek5000-users <nek5000-users(a)lists.mcs.anl.gov>; "moab-dev(a)mcs.anl.gov" <moab-dev(a)mcs.anl.gov> Sent: Wednesday, April 29, 2015 1:23 PM Subject: Re: [MOAB-dev] [Nek5000-users] MOAB Cubit problem Hamid, It is possible that the file formats are quite different between Cubit and Trelis. We have not tested with the Trelis versions so far and do plan to acquire a license to make these conversions possible. Meanwhile, if you want to use Exodus or any other format that MOAB can understand directly, that would simplify your workflow. We will keep you updated about the progress, if you're interested. Vijay On Wed, Apr 29, 2015 at 11:47 AM, <nek5000-users(a)lists.mcs.anl.gov> wrote: > Hi, > I use Trelis (V 15) to generate mesh. However, when I try to use mbconvert > to generate h5m file, it says > > [0]MOAB ERROR: --------------------- Error Message > ------------------------------------ > [0]MOAB ERROR: This doesn't appear to be a .cub file! > [0]MOAB ERROR: load_file() line 310 in src/io/Tqdcfr.cpp > [0]MOAB ERROR: --------------------- Error Message > ------------------------------------ > [0]MOAB ERROR: Failed to load file after trying all possible readers! > [0]MOAB ERROR: serial_load_file() line 634 in src/Core.cpp > [0]MOAB ERROR: load_file() line 523 in src/Core.cpp > Failed to load "/home/hamid/nek5_svn/moab_conjht/cubit01.cub". > Error code: MB_FAILURE (16) > Error message: Failed to load file after trying all possible readers > > I have downloaded other cub files from repository and mbconvert works fine > on them. > However opening and saving these files with Trelis causes same problem. > I think the file format in Trelis is different than Cubit. Is it true? if > yes what is the solution? > > Hamid > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >

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R: Re: distribute a 1d profile to 3d domain
by nek5000-users＠lists.mcs.anl.gov 28 Apr '15

28 Apr '15

Hi Paul and Aleks, Thanks for the quick answer. I am a new Nek5000 user and i'm not yet familiar with all functions and subroutines. However, I have compared the two functions "planar_fill_t (u, ua)" and "fill3d_1d_t (u, ua)", and they seem to do both for me. However I have used "fill3d_1d_t (u, ua)" and it seems to work. I'll keep you aware! -- Mr. Mirko FaranoPh.D. student at Politecnico di BariTel.: +39-0883529289 / +39-0805963462Mob.: +39-3202342719Department of Mechanics Mathematics and Management - Fluid Machinery and Energy SystemsVia Re David, 200 - 70125 BARI (Italy)mirko.farano(a)poliba.itIn joint supervision with theEcole Nationale Supérieure d'Arts et Métiers de Paris - ParistechTel.: +33-144246436Mob.: +33- 789822134Dynfluid Laboratory151 Boulevard de l'Hôpital - 75013 Paris (France) mirko.farano(a)ensam.eu >----Messaggio originale---- >Da: nek5000-users(a)lists.mcs.anl.gov >Data: 28-apr-2015 18.20 >A: <nek5000-users(a)lists.mcs.anl.gov> >Ogg: Re: [Nek5000-users] distribute a 1d profile to 3d domain > > >Dear Mirko, > >It looks like > > call planar_fill_s > >with the appropraite arguments should work... > >Paul > > > >On Mon, 27 Apr 2015, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Dear nek' users >> >> I've a 1d profile u(y) computed with "planar_average_s" subroutine. So now i want to redistribute this profile to the whole domain in order to obtain a 3d field u(x,y,z) How can i do this? >> >> Thanks >> >> -- Mr. Mirko FaranoPh.D. student at Politecnico di BariTel.: +39-0883529289 / +39-0805963462Mob.: +39-3202342719Department of Mechanics Mathematics and Management - Fluid Machinery and Energy SystemsVia Re David, 200 - 70125 BARI (Italy)mirko.farano(a)poliba.itIn joint supervision with theEcole Nationale SupÃ©rieure d'Arts et MÃ©tiers de Paris - ParistechTel.: +33-144246436Mob.: +33- 789822134Dynfluid Laboratory151 Boulevard de l'HÃ´pital - 75013 Paris (France) mirko.farano(a)ensam.eu >>_______________________________________________ >Nek5000-users mailing list >Nek5000-users(a)lists.mcs.anl.gov >https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >

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Open Postdoc Position at KTH Stockholm, Sweden with Nek5000
by nek5000-users＠lists.mcs.anl.gov 28 Apr '15

28 Apr '15

Dear all, Sorry to post it here, but it might be of interest to some of you: There is an open Postdoc position at KTH Stockholm, Sweden, dealing with Nek5000: https://www.kth.se/en/om/work-at-kth/lediga-jobb/what:job/jobID:64250/where… From the announcement: In the recent FET-HPC call under Horizon 2020 a number of exascale computing projects were funded and the successful candidate is expected to join the ExaFLOW project, a collaboration of major European CFD (from Sweden, UK, Germany and Switzerland) and HPC centres (from Sweden, Germany, and UK) that aims at designing, implementing, and testing novel CFD methods with the potential to reach the exascale. The successful candidate is expected to contribute to the efficient implementation of novel algorithms, e.g. in the area of adaptivity, and also to assume a managerial role in the project. The implementations will be based on the NEK5000 code in collaboration with the KTH Mechanics Department. Best regards, Philipp

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distribute a 1d profile to 3d domain
by nek5000-users＠lists.mcs.anl.gov 28 Apr '15

28 Apr '15

Dear nek' users I've a 1d profile u(y) computed with "planar_average_s" subroutine. So now i want to redistribute this profile to the whole domain in order to obtain a 3d field u(x,y,z) How can i do this? Thanks -- Mr. Mirko FaranoPh.D. student at Politecnico di BariTel.: +39-0883529289 / +39-0805963462Mob.: +39-3202342719Department of Mechanics Mathematics and Management - Fluid Machinery and Energy SystemsVia Re David, 200 - 70125 BARI (Italy)mirko.farano(a)poliba.itIn joint supervision with theEcole Nationale Supérieure d'Arts et Métiers de Paris - ParistechTel.: +33-144246436Mob.: +33-789822134Dynfluid Laboratory151 Boulevard de l'Hôpital - 75013 Paris (France)mirko.farano(a)ensam.eu

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Pressure gradient
by nek5000-users＠lists.mcs.anl.gov 20 Apr '15

20 Apr '15

Hi,Is there any problem to specify a fixed pressure gradient rather than fixed flow rate?I want to simulate a channel flow of non-Newtonian fluids, and it is easier to use pressure gradient. Hamid

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