March 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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Regarding Interpolation on to a Cylindrical Grid
by nek5000-users＠lists.mcs.anl.gov 31 Mar '15

31 Mar '15

Hi Paul, Alex and Nek's, I want to interpolate the data from the Cartesian mesh on to a Cylindrical mesh that I created using python. The Idea is to interpolate the data at each step and to perform post processing on it. 1) I tried to dump data using hpts(), but the problem is that the size of hpts.out gets larger after each time step. 2) Looking into g2gi subroutine, tells that both the *.rea have to be built via nek5000. It would be really helpful for all the users, If some kind of example (stenosis or turbchannel) is added about the solver based data post processing with USERCHK(), (GLL --> Uniform grid) interpolation. Best Regards, KS

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Grid to grid interpolation and 8-byte data format
by nek5000-users＠lists.mcs.anl.gov 31 Mar '15

31 Mar '15

Dear Neks, I noticed that '8-byte fld files are currently not supported' as stated in g2gi subroutine. However, it worked fine when I used 8-byte old field to interpolate to 4-byte new geometry field (8-byte to 8-byte doesn't work). I'm just wondering is there anyway that I can generate 8-byte new field data using g2gi? Anywhere I can change in the interpolation subroutine? Hope anyone can help. Thank you very much in advance. Kind regards, Tony

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lx1 ly1 lz1 not match
by nek5000-users＠lists.mcs.anl.gov 30 Mar '15

30 Mar '15

Hi, I am currently running a case, which gives me this error. Does anyone know which part of .rea it belongs to? read .rea file ERROR: lx1,ly1,lz1: 12 12 1 must be equal for 3D I have checked in SIZE and the parameters match there. I don't know where they are in .rea Thanks, Chu

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Re: [Nek5000-users] Flow Rate Oscillation on 16384 cores
by nek5000-users＠lists.mcs.anl.gov 29 Mar '15

29 Mar '15

Hi Philipp, Yes thanks I solved the problem. It was in fact a slight change I had to do when converting Nek files since changing the number of cores slightly changes the way the Nek dump is written. All is ok now. Thank you, jp

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Re: [Nek5000-users] Flow Rate Oscillation on 16384 cores
by nek5000-users＠lists.mcs.anl.gov 28 Mar '15

28 Mar '15

Dear Philipp, The slight flow rate variations are probably due to quick way we calculate the flow rate.. this is calculated on custom files that contain data which was converted from the original nek dumps.. the mesh spacing is not constant in the y direction and probably causes some oscillations.. what I cannot understand is how changing the number of cores affects this oscillation so much in the region where more cores were used... Regards, JP

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Mesh merging - no curved side data left
by nek5000-users＠lists.mcs.anl.gov 28 Mar '15

28 Mar '15

Dear all, I tried to merge a cylinder with a rectangular hole, with a rectangular box. After merging them, the curved side data in the cylinder is lost. Is there a way to preserve the curvature? Also, I got error with mesh tolerance. Anyone knows what the error means? Performing unique_vertex2 self_chk 24192 2773 2 4 Matrix: SELF!! 1 SELF!! 1189 1377 1189 1377 2 SELF!! 1360 1206 1360 1206 cont: SELF!! 2773 ?? ABORT: SELF-CHK 1 5 2773 0 Try to tighten the mesh tolerance! 3024 8 10 Matrix T: slfchk 3024 0 1 slfchk 2116 2275 2288 2133 2121 2276 2289 2138 2 slfchk 2275 2587 2574 2288 2276 2588 2575 2289 3 slfchk 2587 2821 2769 2574 2588 2822 2770 2575 4 slfchk 2821 2951 2912 2769 2822 2952 2913 2770 5 slfchk 2951 3120 3081 2912 2952 3121 3082 2913 6 slfchk 3120 3237 3224 3081 3121 3238 3225 3082 7 slfchk 3237 3302 3263 3224 3238 3303 3264 3225 8 slfchk 3302 3341 3289 3263 3303 3342 3290 3264 9 slfchk 3341 3354 3328 3289 3342 3355 3329 3290 10 slfchk 2133 2288 2301 2150 2138 2289 2302 2155 3024 this is nel in prexit Thank you very much. Regards, Simon

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NELGT is 0!
by nek5000-users＠lists.mcs.anl.gov 27 Mar '15

27 Mar '15

Hi, I am running this example with 512 elements, however I get an error: read .rea file nelgt/nelgv/lelt: 512 512 512 lx1 /lx2 /lx3 : 6 4 6 mapping elements to processors ABORT: Too many processors ( 1) for to few elements ( 0). ABORTING IN MAPELPR. This is on Cetus@ANL. As can be seen, the .rea file is read successfully and nelgt is set to 512 in connect2.f, however, inside subroutine mapelpr, NELGT gets set to 0. I have no clue why its value is changing. This does not happen on my local machine. The program was compiled on Cetus using mpixlf77 and mpixlc. Any help is greatly appreciated. Thanks, Tania

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