September 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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nek error
by nek5000-users＠lists.mcs.anl.gov 08 Oct '15

08 Oct '15

Hi, i am a new nek5000 user and i am faceing much obstacles to learn how it works. However i read most of your documentation and i am trying to set a 3d sim. I created a simple box 3d, within a simple flow. I run it and i digit: nekmpi name_file 4. The output i receive is: WARNING3 Element mesh mismatch at: I,J,K,IE: 7 1 7 988 Near Z = 9.1046088 5.4000000 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 8 1 7 988 Near Z = 9.1200000 5.4000000 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 1 2 7 988 Near Z = 8.8800000 5.4384780 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 8 2 7 988 Near Z = 9.1200000 5.4384780 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 1 3 7 988 Near Z = 8.8800000 5.5224899 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 8 3 7 988 Near Z = 9.1200000 5.5224899 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 1 4 7 988 Near Z = 8.8800000 5.6372102 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 8 4 7 988 Near Z = 9.1200000 5.6372102 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 1 5 7 988 Near Z = 8.8800000 5.7627898 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 8 5 7 988 Near Z = 9.1200000 5.7627898 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 1 6 7 988 Near Z = 8.8800000 5.8775101 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 8 6 7 988 Near Z = 9.1200000 5.8775101 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 1 7 7 988 Near Z = 8.8800000 5.9615220 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 8 7 7 988 Near Z = 9.1200000 5.9615220 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 1 8 7 988 Near Z = 8.8800000 6.0000000 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 2 8 7 988 Near Z = 8.8953912 6.0000000 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 3 8 7 988 Near Z = 8.9289960 6.0000000 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 4 8 7 988 Near Z = 8.9748841 6.0000000 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 5 8 7 988 Near Z = 9.0251159 6.0000000 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 6 8 7 988 Near Z = 9.0710040 6.0000000 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 7 8 7 988 Near Z = 9.1046088 6.0000000 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 WARNING3 Element mesh mismatch at: I,J,K,IE: 8 8 7 988 Near Z = 9.1200000 6.0000000 0.96793504 , d: 0.0000000 -0.93587007 1.0000000 I attach my .box, .map, .rea, .usr and SIZE files. Can you help me please? Regards

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Post-processing with Python
by nek5000-users＠lists.mcs.anl.gov 29 Sep '15

29 Sep '15

I post-process in python, using a MapReduce-inspired framework called nek-analyze: https://github.com/maxhutch/nek-analyze I haven't used it to write new *.f* files in a while (instead, I visualize directly in python with matplotlib), so that's probably currently broken, but I'd be willing to fix it. Depending on the mesh geometry, there is some built-in functionality for applying operators, but it is not complete. Again, I'd be willing to put some time into supporting new functionality, and VERY happy to accept contributions. GPL, just like Nek. Max

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Rotating blade
by nek5000-users＠lists.mcs.anl.gov 29 Sep '15

29 Sep '15

Hi, I am extremely new to NEK5000 but i will need to have to perform a simulation where I would need to rotate a blade to a certain angle. Any good suggestions on where to start. By the way, what is "eg", "ieg" "gllel(eg)" that i keep seeing in the examples? Many thanks rif

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Post-processing with Python
by nek5000-users＠lists.mcs.anl.gov 28 Sep '15

28 Sep '15

Hej Nek's! I was wondering if any one has a python script that reads Nek 5000 (and would be kind enough to share it)? I would like to read a bunch of blah0.f0???? files, do some post-processing with Python, and output the results as another set of blahbis0.f0????? files to visualize with visit. Regards, JC -- Jean-Christophe Loiseau Homepage <https://sites.google.com/site/loiseaujc/>

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userchk in turbChannel
by nek5000-users＠lists.mcs.anl.gov 18 Sep '15

18 Sep '15

Hi all, I'm trying to use a round pipe mesh with this LES formulation but this section in userchk is tripping me up: nelx = 8 ! Number of elements in x,y, and z directions. nely = 8 ! NOTE, this may vary from one mesh to the next. nelz = 8 ! ntot = nx1*ny1*nz1*nelv ! do some checks if (istep.eq.0) then if(mod(nely,2).ne.0) then if(nid.eq.0) write(6,*) 'ABORT: nely has to be even!' call exitt endif if(nelx.gt.lelx .or. nely.gt.lely .or. nelz.gt.lelz) then if(nid.eq.0) write(6,*) 'ABORT: nel_xyz > lel_xyz!' call exitt endif endif How should I determine nelx and nely for the circular area at the end of the pipe? I have 56 elements in this area (x-y plane) extruded to 10 layers with n2to3 (560 total elements). Thanks, David

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Display errors in Prenek
by nek5000-users＠lists.mcs.anl.gov 04 Sep '15

04 Sep '15

Hi all, I'm trying to use Prenek with Ubuntu 14.04 LTS, and in the Nekton window, I don't see the options "End Elements" and so forth. The boxes and grid graphics are there, but no text. Also, the elements don't display when I use keyboard input. Keyboard input works for using the options on the right side, but not much use to me if I can't see the elements. I'm wondering if I have incompatible graphics libraries. Thanks. David H.

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Re: [Nek5000-users] Nek5000-users Digest, Vol 78, Issue 9
by nek5000-users＠lists.mcs.anl.gov 01 Sep '15

01 Sep '15

Hi, Phillip Thanks for your reply, but the dos2unix actually does not help. And I tried a lot to fix it up, including copy existing command from other examples .rea files to eliminate the error that might have something to do with the "CR and LF" stuff (I know little about these line breaks). I am in Ubuntu, should this this be due to the failue of reading restart parameters?he I have attached the .rea file. It would be greatly that you can have a look and give some advice. Thanks in advance. and have a nice weekend! from Allen On 08/29/2015 01:00 AM, 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://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. restart a case got an error: Error reading initial > condition/drive force data (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: restart a case got an error: Error reading initial > condition/drive force data (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 28 Aug 2015 11:22:34 +0800 > From: nek5000-users(a)lists.mcs.anl.gov > To: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] restart a case got an error: Error reading > initial condition/drive force data > Message-ID: > <mailman.6382.1440732161.24727.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Hi, Nekers: > > I recently want to do some simulation with Nek, so I followed the > tutorial for the eddy_uv case > > I have run the case without problem, but when I want to try the restart > utility with the following modification instructed by the manual > ----------------------------------------------------------------------------- > 1 PRESOLVE/RESTART OPTIONS ***** > eddy_uv0.f00010 > ----------------------------------------------------------------------------- > > affter changing for a new case name and recompile, I started the restart > run, but the logfile gives the following error : > ----------------------------------------------------------------------------- > mapping elements to processors > 2 86 86 256 256 NELV > 0 85 85 256 256 NELV > 1 85 85 256 256 NELV > RANK 0 IEG 133 134 135 136 149 150 151 152 > 161 162 165 166 167 168 177 178 > 179 181 182 183 184 193 194 195 > 196 197 198 199 200 201 202 203 > 204 205 206 207 208 209 210 211 > 212 213 214 215 216 217 218 219 > 220 221 222 223 224 225 226 227 > 228 229 230 231 232 233 234 235 > 236 237 238 239 240 241 242 243 > 244 245 246 247 248 249 250 251 > 252 253 254 255 256 > element load imbalance: 1 85 86 > done :: mapping elements to processors > > Error reading initial condition/drive force data > aborting in routine rdicdf. > EXIT: rdicdf error 1 > > call exitt: dying ... > > backtrace(): obtained 9 stack frames. > ./nek5000(print_stack_+0x18) [0x500ff8] > ./nek5000(exitt_+0x1cc) [0x5be5ec] > ./nek5000(exitti_+0x117) [0x5c1537] > ./nek5000(rdicdf_+0x1e7) [0x442387] > ./nek5000(readat_+0x35f) [0x44951f] > ./nek5000(nek_init_+0x75) [0x41ae25] > ./nek5000(main+0x24) [0x419d84] > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f26a5be276d] > ./nek5000() [0x419dc9] > -------------------------------------------------------------------------------------------------------------------- > > I have searched the post list, but I only found very vague statement of > this > problem:_http://lists.mcs.anl.gov/pipermail/nek5000-users/2011-October/0015… > > Hope some one can give me some hint, I actually do exactly what the > manual does, which makes me confused. > > Thanks, hope it is a minor mistake. > > from Allen >

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box parameters must kept unchanged when using restart utility?
by nek5000-users＠lists.mcs.anl.gov 01 Sep '15

01 Sep '15

Hi, nekers I am running the restart utility. And I found that when I change both the box parameters (nelx,nely,nelz) and the SIZE parameters (lx1, ldx) for the restart run, the computation got stuck and failed at reading the filed result files of U and P, like this: ------------------------------------------------------------------------ set initial conditions Checking restart options: turbChannel0.f00009 nekuic (1) for ifld 1 Reading checkpoint data 0 0 OPEN: turbChannel0.f00009 byte swap: F 6.54321003 -2.93127722E+35 -------------------------------------------------------------------------- Again I follow exactly the tutorial and kept the same set-up in the .box file and just increase the element order (lx1, ldx), and now the restart works fine. so .box parameters must kept unchanged when using restart utility? right? I just want to confirm that. Thanks:-) , from Allen

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