From nek5000-users at lists.mcs.anl.gov Tue Sep 1 07:53:15 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 1 Sep 2015 12:53:15 +0000 Subject: [Nek5000-users] box parameters must kept unchanged when using restart utility? In-Reply-To: References: Message-ID: Hi Allen, Restart requires that you have the same number of elements (more precisely, the same mesh). You can change the polynomial order, however, as you have done when you changed lx1 lxd in SIZE. Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, August 31, 2015 10:58 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] box parameters must kept unchanged when using restart utility? 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 _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Tue Sep 1 16:36:00 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 1 Sep 2015 21:36:00 +0000 Subject: [Nek5000-users] Nek5000-users Digest, Vol 78, Issue 9 In-Reply-To: References: , Message-ID: Hi Allen, It looks like you have an extra line after the file name in the restart section of your .rea file ? Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Saturday, August 29, 2015 2:51 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 78, Issue 9 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 at lists.mcs.anl.gov wrote: > Send Nek5000-users mailing list submissions to > nek5000-users at 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 at lists.mcs.anl.gov > > You can reach the person managing the list at > nek5000-users-owner at 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 at lists.mcs.anl.gov) > 2. Re: restart a case got an error: Error reading initial > condition/drive force data (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 28 Aug 2015 11:22:34 +0800 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] restart a case got an error: Error reading > initial condition/drive force data > Message-ID: > > 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/001560.html_ > > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > Message: 2 > Date: Fri, 28 Aug 2015 10:43:10 +0200 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] restart a case got an error: Error > reading initial condition/drive force data > Message-ID: > > Content-Type: text/plain; charset=windows-1252; format=flowed > > not sure it helps, but we had a similar problem recently when a rea file > went trough Windows and Linux, adding CR and LF as line breaks. As far > as I remember, using dos2unix of the file helped. Also, a tab character > (ASCII 9) somewhere on that line gave some problems. > > Good luck, Philipp > > On 2015-08-28 05:22, nek5000-users at lists.mcs.anl.gov wrote: >> 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/001560.html_ >> >> 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 >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > ------------------------------ > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > End of Nek5000-users Digest, Vol 78, Issue 9 > ******************************************** From nek5000-users at lists.mcs.anl.gov Wed Sep 2 21:14:58 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 2 Sep 2015 22:14:58 -0400 Subject: [Nek5000-users] Display errors in Prenek Message-ID: 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Sep 3 00:35:25 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 3 Sep 2015 05:35:25 +0000 Subject: [Nek5000-users] Display errors in Prenek In-Reply-To: References: Message-ID: Hi David, Out of curiosity, do you have the same issue with postx? Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Wednesday, September 02, 2015 9:14 PM To: Nek Mailing List Subject: [Nek5000-users] Display errors in Prenek 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Sep 4 12:22:30 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 4 Sep 2015 13:22:30 -0400 Subject: [Nek5000-users] Display errors in Prenek In-Reply-To: References: Message-ID: Yes, the same thing happens. I tried both prenek and postx again, and I actually have full mouse functionality now. The only things missing are the option and element labels / numbering. I can successfully make meshes using the label numbering in the terminal window. It seems to be an issue with the installations of Ubuntu 14.04 that I have. On Sep 3, 2015 1:35 AM, wrote: > > Hi David, > > Out of curiosity, do you have the same issue with postx? > > Paul > > ------------------------------ > *From:* nek5000-users-bounces at lists.mcs.anl.gov [ > nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > *Sent:* Wednesday, September 02, 2015 9:14 PM > *To:* Nek Mailing List > *Subject:* [Nek5000-users] Display errors in Prenek > > 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. > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Sep 16 14:14:41 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Sep 2015 15:14:41 -0400 Subject: [Nek5000-users] userchk in turbChannel Message-ID: 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 From nek5000-users at lists.mcs.anl.gov Wed Sep 16 14:53:06 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Sep 2015 19:53:06 +0000 Subject: [Nek5000-users] userchk in turbChannel In-Reply-To: References: Message-ID: Hi David, I think that piece of code applies to a perfectly rectangular geometry where both nelx, nely are clearly defined as provided in e.g. genbox. For pipe it is indeed a tricky if not impossible matter. However the check performed there seems to me not too relevant for your problem. You could in fact just compute nelx*nely*nelz>lelx*lely*lelz Oana ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Wednesday, September 16, 2015 2:14 PM To: Nek Mailing List Subject: [Nek5000-users] userchk in turbChannel 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 _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Sep 18 13:49:08 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 18 Sep 2015 14:49:08 -0400 Subject: [Nek5000-users] userchk in turbChannel In-Reply-To: References: Message-ID: Oana, Okay, I will keep trying to get around it. Can you tell me what exactly this function is doing? Is it checking for mesh or input errors? David On Sep 16, 2015 3:53 PM, wrote: > Hi David, > > I think that piece of code applies to a perfectly rectangular geometry > where both nelx, nely are clearly defined as provided in e.g. genbox. For > pipe it is indeed a tricky if not impossible matter. > > However the check performed there seems to me not too relevant for your > problem. You could in fact just compute > nelx*nely*nelz>lelx*lely*lelz > > Oana > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov [ > nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Wednesday, September 16, 2015 2:14 PM > To: Nek Mailing List > Subject: [Nek5000-users] userchk in turbChannel > > 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 > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Sep 18 13:58:59 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 18 Sep 2015 18:58:59 +0000 Subject: [Nek5000-users] userchk in turbChannel In-Reply-To: References: , Message-ID: Hi David, The routine is doing just some sanity checks on your geometry so you shouldn't be concerned. However if you want to import a lot more from that example file it could be that certain routines/operations are hard wired to a geometry generated by genbox (which is the case here). So keep wary and if something doesn't work you need to adapt that to your case. Oana ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Friday, September 18, 2015 1:49 PM To: Nek Mailing List Subject: Re: [Nek5000-users] userchk in turbChannel Oana, Okay, I will keep trying to get around it. Can you tell me what exactly this function is doing? Is it checking for mesh or input errors? David On Sep 16, 2015 3:53 PM, > wrote: Hi David, I think that piece of code applies to a perfectly rectangular geometry where both nelx, nely are clearly defined as provided in e.g. genbox. For pipe it is indeed a tricky if not impossible matter. However the check performed there seems to me not too relevant for your problem. You could in fact just compute nelx*nely*nelz>lelx*lely*lelz Oana ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Wednesday, September 16, 2015 2:14 PM To: Nek Mailing List Subject: [Nek5000-users] userchk in turbChannel 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 _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Sep 25 13:52:25 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 25 Sep 2015 20:52:25 +0200 Subject: [Nek5000-users] Post-processing with Python Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Sep 28 02:54:17 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 28 Sep 2015 09:54:17 +0200 Subject: [Nek5000-users] Post-processing with Python In-Reply-To: References: Message-ID: Hi, I recently found a script for converting nek files to hdf5 at https://github.com/nbren12/Fld I haven't tried it myself, but I assume it should be a good starting point. Regards, Jan On 09/25/2015 08:52 PM, nek5000-users at lists.mcs.anl.gov wrote: > 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 > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -- ---------------------- Jan Vormann Institut f?r Geophysik Corrensstr. 24 D-48149 M?nster -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Sep 27 07:21:28 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 27 Sep 2015 12:21:28 +0000 Subject: [Nek5000-users] Post-processing with Python Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Sep 29 03:30:50 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 29 Sep 2015 16:30:50 +0800 Subject: [Nek5000-users] Rotating blade Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Sep 29 03:38:43 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 29 Sep 2015 10:38:43 +0200 Subject: [Nek5000-users] Post-processing with Python In-Reply-To: References: Message-ID: Hej, Thanks a lot! I will take a look at your github. I am not an extremely efficient python coder, but I am willing to learn more about this language and its capabilities and use it as often as possible for my post-processing of DNS data. Maybe we could continue this discussion out of the mailing list. Here is my email : loiseau.jc at gmail.com ++ JC On 09/27/2015 02:21 PM, nek5000-users at lists.mcs.anl.gov wrote: > 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 > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Sep 29 10:31:56 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 29 Sep 2015 15:31:56 +0000 Subject: [Nek5000-users] Post-processing with Python In-Reply-To: References: Message-ID: Hi JC, Right now, there are two reasons to consider using nek-analyze: 1) You need to do something complicated and would rather do that in python (due to experience, library support, etc) 2) Your data is big enough that you want to avoid loading it all into memory If neither of those applies, then you're better off userchk post-processing within Nek. If you're interested mostly in (2), I can try to help with the python. If you're interested in (1) but not so much (2), you can probably cannibalize some of my tools (the file reader, for example). Max On Tue, Sep 29, 2015 at 1:39 AM wrote: > Hej, > > Thanks a lot! I will take a look at your github. I am not an extremely > efficient python coder, but I am willing to learn more about this language > and its capabilities and use it as often as possible for my post-processing > of DNS data. Maybe we could continue this discussion out of the mailing > list. Here is my email : loiseau.jc at gmail.com > > ++ > JC > > > On 09/27/2015 02:21 PM, nek5000-users at lists.mcs.anl.gov wrote: > > 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 > > > _______________________________________________ > Nek5000-users mailing listNek5000-users at lists.mcs.anl.govhttps://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Sep 30 22:47:28 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 1 Oct 2015 11:47:28 +0800 Subject: [Nek5000-users] NEK mesh file MATLAB code Message-ID: Hi, i was playing around with the supplied MATLAB code which converts neu files to rea files. I ran the code for the simple.neu example but I am not sure what to do with the numbers and arrays Matlab outputs. Any help on this? Rif -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Sep 29 09:56:31 2015 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 29 Sep 2015 16:56:31 +0200 Subject: [Nek5000-users] nek error Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: curve.usr Type: application/octet-stream Size: 4104 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: curve.map Type: application/octet-stream Size: 109084 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: curve.box Type: application/octet-stream Size: 489 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: curve.rea Type: application/octet-stream Size: 884589 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: SIZE Type: application/octet-stream Size: 3431 bytes Desc: not available URL: