June 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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symmetry boundary conditions and genmap
by nek5000-users＠lists.mcs.anl.gov 01 Jul '16

01 Jul '16

Hello, I have two rea files that are exactly identical but for the boundary conditions: one has ‘W’ and the other one has ‘SYM’. If I am not mistaken, the ‘SYM’ boundary type is supported by Nek5000 but is causing problem when I try to generate a map file with genmap. It returns the following error message: reading .rea file data ... ERROR: error reading 1 79200 299357 aborting 530 in routine rdbdry. 1 quit The rea file with ‘W’ boundary type successfully goes through the genmap script. Is there anything I should be aware when setting SYM bc type in the rea file? I could not find any related post in the archive of the mailing list. Thanks, Marco

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Refining Mesh for turbChannel
by nek5000-users＠lists.mcs.anl.gov 28 Jun '16

28 Jun '16

Modifying just the .box file is sufficient? I know the .rea file also contains geometry information. Do I leave that alone? Thanks, Virgilio A. Gomez -----Original Message----- From: nek5000-users-bounces(a)lists.mcs.anl.gov [mailto:[email protected]] On Behalf Of nek5000-users-request(a)lists.mcs.anl.gov Sent: Saturday, June 25, 2016 12:00 PM To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 88, Issue 21 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. Refining Mesh for turbChannel (nek5000-users(a)lists.mcs.anl.gov) 2. Re: Refining Mesh for turbChannel (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Fri, 24 Jun 2016 21:45:00 +0000 From: nek5000-users(a)lists.mcs.anl.gov To: "nek5000-users(a)lists.mcs.anl.gov" <nek5000-users(a)lists.mcs.anl.gov> Subject: [Nek5000-users] Refining Mesh for turbChannel Message-ID: <mailman.24686.1466804704.24727.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="iso-8859-1" Hello, I want to refine the mesh for the example turbChannel to resolve the Kolmogrov scale by modifying the given example files. How can I do that? Thank you.

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Projection technique's parameters
by nek5000-users＠lists.mcs.anl.gov 27 Jun '16

27 Jun '16

Hi Neks, My question is about the parameters which manage the projection method in the NEK5000: p93, p94 and p95. How can the correct values be selected for these parameters to obtain the better performance depending on the nature of simulation: laminar / turbulent, convection / diffusion, time step? Thank you for any suggestion, Andrew

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Refining Mesh for turbChannel
by nek5000-users＠lists.mcs.anl.gov 25 Jun '16

25 Jun '16

Hello, I want to refine the mesh for the example turbChannel to resolve the Kolmogrov scale by modifying the given example files. How can I do that? Thank you.

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Pretex and Prex
by nek5000-users＠lists.mcs.anl.gov 24 Jun '16

24 Jun '16

Hello, My question is related to the use of Pretex and Prex: according to the user’s manual, Pretex is the command line version of Prex. When I open Pretex, however, the GUI opens as well, causing Pretex to crash when running on the cluster. I need to call Pretex through a script that is ‘qsub' to perform a sensitivity analysis. Because Pretex looks for an interface to open the GUI, my script fails to run. Has anybody else experienced such a behavior when using Pretex? If someone has, is there a work around this problem? Thanks, Marco

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Pretex script
by nek5000-users＠lists.mcs.anl.gov 22 Jun '16

22 Jun '16

Hello, I have a script that uses Pretex to generate a circle that is then extruded in a pipe. I think the script has some option that do not match my current version of Pretex. Here is the script (only the part for generating and meshing the circle): pretex << EOF inlet2d 1 READ PREVIOUS PARAMETERS one2d 1 BUILD FROM FILE one2d 5 DELETE ELEMENT 4 CURVE SIDES 5 Autosphere 4 3 Enter number of elements in core and shell: .65 Enter ratio in outer shell: 8 Convert Midside to Circle 2. Input maxium radius: 1 BUILD MENU 3 GLOBAL REFINE 13 Clean up vertices 7 REPLICATE/ROTATE 3 Rep. (1), Rot. (2), Rep/Rot (3) Template (4)? (0=abort) 90 Input rotation angle (deg): 1 Input number of reps (e.g., 1 --> double mesh size) 13 Clean up vertices 1 END GLOBAL REFINE 1 END ELEMENTS 1 ACCEPT MATL,QVOL 1 ACCEPT B.C.'s 1 ACCEPT B.C.'s 1 EXIT EOF The line that is causing the error message is '8 Convert Midside to Circle’. In my pretex version I have ‘8 RENUMBER ELEMENTS’. Could you please let me know what I can do to fix the script? Thanks, marco

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Re: [Nek5000-users] Re : CYCLIC BC for bend pipe
by nek5000-users＠lists.mcs.anl.gov 22 Jun '16

22 Jun '16

Hello, I have a script that uses Pretex to generate a circle that is then extruded in a pipe. I think the script has some option that do not match my current version of Pretex. Here is the script (only the part for generating and meshing the circle): pretex << EOF inlet2d 1 READ PREVIOUS PARAMETERS one2d 1 BUILD FROM FILE one2d 5 DELETE ELEMENT 4 CURVE SIDES 5 Autosphere 4 3 Enter number of elements in core and shell: .65 Enter ratio in outer shell: 8 Convert Midside to Circle 2. Input maxium radius: 1 BUILD MENU 3 GLOBAL REFINE 13 Clean up vertices 7 REPLICATE/ROTATE 3 Rep. (1), Rot. (2), Rep/Rot (3) Template (4)? (0=abort) 90 Input rotation angle (deg): 1 Input number of reps (e.g., 1 --> double mesh size) 13 Clean up vertices 1 END GLOBAL REFINE 1 END ELEMENTS 1 ACCEPT MATL,QVOL 1 ACCEPT B.C.'s 1 ACCEPT B.C.'s 1 EXIT EOF The line that is causing the error message is '8 Convert Midside to Circle’. In my pretex version I have ‘8 RENUMBER ELEMENTS’. Could you please let me know what I can do to fix the script? Thanks, marco

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Re: [Nek5000-users] Configure a stress at boundary
by nek5000-users＠lists.mcs.anl.gov 17 Jun '16

17 Jun '16

Thank you Aleks! It works. Peng > On Jun 17, 2016, at 1:00 PM, nek5000-users-request(a)lists.mcs.anl.gov wrote: > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__lists.mcs.anl.gov_mail… > 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. Configure a stress at boundary (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: Configure a stress at boundary > (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 17 Jun 2016 14:33:22 +0000 > From: nek5000-users(a)lists.mcs.anl.gov > To: "nek5000-users(a)lists.mcs.anl.gov" > <nek5000-users(a)lists.mcs.anl.gov> > Subject: [Nek5000-users] Configure a stress at boundary > Message-ID: > <mailman.23977.1466174696.24727.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset="utf-8" > > Dear Neks, > > I am simulating a water flow in the 3dbox example. > In order to simulate the wind blowing over the water, I hope to add a wind stress at the top boundary. > The wind stress (tau) formulation is given as > tau = rho*C_d*U*U > where tau is the wind stress, rho is the air density, C_d is the drag coefficient, and U is the wind speed. > I guess the wind stress should be configured in ?userbc?, but how to do it? Can anyone help? > > Thank you! > Peng > > > > ************************* > Peng Wang, Ph.D. > > Postdoctoral Associate > Department of Ocean Sciences > Rosenstiel School of Marine and Atmospheric Science > University of Miami > 4600 Rickenbacker Causeway > Miami, Florida 33149-1098, USA > > > > ------------------------------ > > Message: 2 > Date: Fri, 17 Jun 2016 16:31:38 +0000 > From: nek5000-users(a)lists.mcs.anl.gov > To: "nek5000-users(a)lists.mcs.anl.gov" > <nek5000-users(a)lists.mcs.anl.gov> > Subject: Re: [Nek5000-users] Configure a stress at boundary > Message-ID: > <mailman.23994.1466181101.24727.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset="Windows-1252" > > Hi Peng, > > We have looked a bit into this type of boundary condition of Nek5000 stress-formulation -- you need to set boundary condition character in .box file (or choose prenek' option) to > > 'shl' > > (which probably stands for stress-horizontal-local) and set NEKUSE's the horizontal stress components to tr1 and tr2 in userbc. > > Aleks > > ________________________________________ > 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: Friday, June 17, 2016 9:33 AM > To: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] Configure a stress at boundary > > Dear Neks, > > I am simulating a water flow in the 3dbox example. > In order to simulate the wind blowing over the water, I hope to add a wind stress at the top boundary. > The wind stress (tau) formulation is given as > tau = rho*C_d*U*U > where tau is the wind stress, rho is the air density, C_d is the drag coefficient, and U is the wind speed. > I guess the wind stress should be configured in ?userbc?, but how to do it? Can anyone help? > > Thank you! > Peng > > > > ************************* > Peng Wang, Ph.D. > > Postdoctoral Associate > Department of Ocean Sciences > Rosenstiel School of Marine and Atmospheric Science > University of Miami > 4600 Rickenbacker Causeway > Miami, Florida 33149-1098, USA > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.mcs.anl.gov_mail… > > > ------------------------------ > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.mcs.anl.gov_mail… > > > End of Nek5000-users Digest, Vol 88, Issue 17 > *********************************************

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Configure a stress at boundary
by nek5000-users＠lists.mcs.anl.gov 17 Jun '16

17 Jun '16

Dear Neks, I am simulating a water flow in the 3dbox example. In order to simulate the wind blowing over the water, I hope to add a wind stress at the top boundary. The wind stress (tau) formulation is given as tau = rho*C_d*U*U where tau is the wind stress, rho is the air density, C_d is the drag coefficient, and U is the wind speed. I guess the wind stress should be configured in ‘userbc’, but how to do it? Can anyone help? Thank you! Peng ************************* Peng Wang, Ph.D. Postdoctoral Associate Department of Ocean Sciences Rosenstiel School of Marine and Atmospheric Science University of Miami 4600 Rickenbacker Causeway Miami, Florida 33149-1098, USA

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