From nek5000-users at lists.mcs.anl.gov Tue Mar 1 02:24:22 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 1 Mar 2016 09:24:22 +0100 Subject: [Nek5000-users] Error when creating own mesh In-Reply-To: References: Message-ID: Try a lower order mesh in Gmsh. Wei 2016-03-01 4:34 GMT+01:00 : > Hello, > > finally, did you solve this problem? I am having the same problem. > > First I generate a 2D mesh using gmsh, and after that I am using gmsh2nek > to create the .rea file. This file seems to be ok. However, when I run > genmap, I find the following error: > > genmap > Input (.rea) file name: > Cylinder > 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 1 782 > aborting 510 in routine rdbdry. > > 1 quit > > > What is the problem? Could you help me, please? > > Thanks > SL > > > El 09-07-2014 23:29, nek5000-users at lists.mcs.anl.gov escribi?: > >> Dear Friedrich, >> >> I recommend running "diff" on the example file and your file. >> Assuming that the example file works you should then be close >> to understanding the source of difficulty. >> >> 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, July 09, 2014 5:57 AM >> TO: nek5000-users at lists.mcs.anl.gov >> SUBJECT: [Nek5000-users] Error when creating own mesh >> >> 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. >> >> _______________________________________________ >> 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 > -- Wei HE ?? School of Aeronautics Universidad Polit?cnica de Madrid http://www.cfm.upm.es/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Mar 1 16:50:38 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 1 Mar 2016 23:50:38 +0100 Subject: [Nek5000-users] Post processing mode Message-ID: Hi neks, can someone tell me step by step how can i set Nek5000 in post-processing mode? I read something about it into the mailing list archive, but nothing that explain step by step what i have to do. I have done the following step: -create a file, named file.list where in the first row i have to write the total number analyzed. In the following rows i have to write the file's output name, since the first to the last, - now, i read i have to set in .rea file the parameter related to Nstep equal 0 (param p011), i have to fix P010,P14 and P15 equal 0 too? I find out this post in your mailing list archive and i added it in my usercheck subroutine, but everytime i have errors in compilation! SUBROUTINE USERCHK INCLUDE 'SIZE' INCLUDE 'TOTAL' INCLUDE 'RESTART' character*80 filename(9999) ntot = nx1*ny1*nz1*nelv ifreguo = .true. ! dump on regular (uniform) grid instead of GLL nrg = 16 ! dimension of regular grid (nrg**ndim) ! read file-list if (nid.eq.0) then open(unit=199,file='file.list',form='formatted',status='old') read(199,*) nfiles read(199,'(A80)') (filename(i),i=1,nfiles) close(199) endif call bcast(nfiles,isize) call bcast(filename,nfiles*80) do i = 1,nfiles call load_fld(filename(i)) ! do something ! note: make sure you save the result into arrays which are ! dumped by prepost() e.g. T(nx1,ny1,nz1,nelt,ldimt) ... ! dump results into file call prepost(.true.,'his') enddo ! we're done call exitt Ifreguo is a logical switch to have a grid without elemnts?Only knots? Thanks to everyone. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Mar 1 16:57:18 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 1 Mar 2016 16:57:18 -0600 Subject: [Nek5000-users] VISIT and NEKTON Message-ID: Can anyone help me in visualizing the data on VISIT and or NEKTON, my problem is that I am not able to visualize the data using any of these. For instance in VISIT I am able to generate .nek5000 file and was able to load it in VISIT but whenever I try to plot something it crashes. Similarly in NEKTON (POSTX), I was able to see the mesh grid , however whenever I click on the plot it makes the whole grid go blue and time remains at "0", I tried to change the time to some other value but I failed. Please guide me what is causing this issue and what I am doing wrong. I am using linux mint to run the nek5000. Thanks, Abhinav -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Mar 1 21:57:13 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 02 Mar 2016 14:57:13 +1100 Subject: [Nek5000-users] Error when creating own mesh In-Reply-To: References: Message-ID: Hi, thank you! On the one hand, if I use a high order mesh in Gmsh, then I find an error using gmsh2nek, however the error is different to the one that I posted before. On the other hand, the error that I was asking for is solved: 1) using a low order mesh, 2) using a higher number of nodes to create my computational domain in Gmsh. Cheers SL El 01-03-2016 19:24, nek5000-users at lists.mcs.anl.gov escribi?: > Try a lower order mesh in Gmsh. > > Wei > > 2016-03-01 4:34 GMT+01:00 : > >> Hello, >> >> finally, did you solve this problem? I am having the same problem. >> >> First I generate a 2D mesh using gmsh, and after that I am using >> gmsh2nek to create the .rea file. This file seems to be ok. However, >> when I run genmap, I find the following error: >> >> genmap >> Input (.rea) file name: >> Cylinder >> 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? ? ? ? ? ?1? ? ? ? ?782 >> ? aborting 510 in routine rdbdry. >> >> ? ? ? ? ? ?1? quit >> >> What is the problem? Could you help me, please? >> >> Thanks >> SL >> >> El 09-07-2014 23:29, nek5000-users at lists.mcs.anl.gov escribi?: >> >>> Dear Friedrich, >>> >>> I recommend running "diff" on the example file and your file. >>> Assuming that the example file works you should then be close >>> to understanding the source of difficulty. >>> >>> 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, July 09, 2014 5:57 AM >>> ?TO: nek5000-users at lists.mcs.anl.gov >>> ?SUBJECT: [Nek5000-users] Error when creating own mesh >>> >>> 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. >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] > > -- > > Wei HE ?? > > School of Aeronautics > Universidad Polit?cnica de Madridhttp://www.cfm.upm.es/ [2] > > > Links: > ------ > [1] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > [2] http://www.cfm.upm.es/ > > _______________________________________________ > 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 Mar 1 22:07:08 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 2 Mar 2016 04:07:08 +0000 Subject: [Nek5000-users] VISIT and NEKTON In-Reply-To: References: Message-ID: It is very likely your mesh has a double precision output, see parameter 63 http://nek5000.github.io/NekDoc/Nek_usersch7.html#x9-690007.1 Older versions of visit do not support field files in double precision, so you should have that parameter set to anything but 8. If this doesn't work please make sure your computation did not blow up prior to writing to file. 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: Tuesday, March 01, 2016 4:57 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] VISIT and NEKTON Can anyone help me in visualizing the data on VISIT and or NEKTON, my problem is that I am not able to visualize the data using any of these. For instance in VISIT I am able to generate .nek5000 file and was able to load it in VISIT but whenever I try to plot something it crashes. Similarly in NEKTON (POSTX), I was able to see the mesh grid , however whenever I click on the plot it makes the whole grid go blue and time remains at "0", I tried to change the time to some other value but I failed. Please guide me what is causing this issue and what I am doing wrong. I am using linux mint to run the nek5000. Thanks, Abhinav From nek5000-users at lists.mcs.anl.gov Tue Mar 1 22:09:50 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 1 Mar 2016 22:09:50 -0600 Subject: [Nek5000-users] VISIT and NEKTON In-Reply-To: References: Message-ID: Visit is working now, there was a problem because of the version of the visit I was using, easy solution, well thanks for your advice. On Mar 1, 2016 10:07 PM, wrote: > It is very likely your mesh has a double precision output, see parameter 63 > http://nek5000.github.io/NekDoc/Nek_usersch7.html#x9-690007.1 > Older versions of visit do not support field files in double precision, so > you should have that parameter set to anything but 8. > > If this doesn't work please make sure your computation did not blow up > prior to writing to file. > > 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: Tuesday, March 01, 2016 4:57 PM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] VISIT and NEKTON > > Can anyone help me in visualizing the data on VISIT and or NEKTON, my > problem is that I am not able to visualize the data using any of these. For > instance in VISIT I am able to generate .nek5000 file and was able to load > it in VISIT but whenever I try to plot something it crashes. Similarly in > NEKTON (POSTX), I was able to see the mesh grid , however whenever I click > on the plot it makes the whole grid go blue and time remains at "0", I > tried to change the time to some other value but I failed. > > Please guide me what is causing this issue and what I am doing wrong. I am > using linux mint to run the nek5000. > > Thanks, > Abhinav > _______________________________________________ > 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 Mar 1 22:11:20 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 2 Mar 2016 04:11:20 +0000 Subject: [Nek5000-users] Post processing mode In-Reply-To: References: Message-ID: We should indeed add this more explicitly in our documentation. The main aspect is to have an output file which is written at which iostep value is written in the .rea file, see parameter 15 http://nek5000.github.io/NekDoc/Nek_usersch7.html#x9-690007.1 This file can be later visualized in Visit, for which you will need to run the visnek script. (visnek is in the tools/scripts folder) 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: Tuesday, March 01, 2016 4:50 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Post processing mode Hi neks, can someone tell me step by step how can i set Nek5000 in post-processing mode? I read something about it into the mailing list archive, but nothing that explain step by step what i have to do. I have done the following step: -create a file, named file.list where in the first row i have to write the total number analyzed. In the following rows i have to write the file's output name, since the first to the last, - now, i read i have to set in .rea file the parameter related to Nstep equal 0 (param p011), i have to fix P010,P14 and P15 equal 0 too? I find out this post in your mailing list archive and i added it in my usercheck subroutine, but everytime i have errors in compilation! SUBROUTINE USERCHK INCLUDE 'SIZE' INCLUDE 'TOTAL' INCLUDE 'RESTART' character*80 filename(9999) ntot = nx1*ny1*nz1*nelv ifreguo = .true. ! dump on regular (uniform) grid instead of GLL nrg = 16 ! dimension of regular grid (nrg**ndim) ! read file-list if (nid.eq.0) then open(unit=199,file='file.list',form='formatted',status='old') read(199,*) nfiles read(199,'(A80)') (filename(i),i=1,nfiles) close(199) endif call bcast(nfiles,isize) call bcast(filename,nfiles*80) do i = 1,nfiles call load_fld(filename(i)) ! do something ! note: make sure you save the result into arrays which are ! dumped by prepost() e.g. T(nx1,ny1,nz1,nelt,ldimt) ... ! dump results into file call prepost(.true.,'his') enddo ! we're done call exitt Ifreguo is a logical switch to have a grid without elemnts?Only knots? Thanks to everyone. From nek5000-users at lists.mcs.anl.gov Wed Mar 2 06:46:52 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 2 Mar 2016 12:46:52 +0000 Subject: [Nek5000-users] Post processing mode In-Reply-To: References: Message-ID: NSTEPS=FINTIME=0 in .rea is enough to trigger post-processing mode -- i.e. call of userchk and exit after initialization. Aleks ________________________________ 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: Tuesday, March 01, 2016 4:50 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Post processing mode Hi neks, can someone tell me step by step how can i set Nek5000 in post-processing mode? I read something about it into the mailing list archive, but nothing that explain step by step what i have to do. I have done the following step: -create a file, named file.list where in the first row i have to write the total number analyzed. In the following rows i have to write the file's output name, since the first to the last, - now, i read i have to set in .rea file the parameter related to Nstep equal 0 (param p011), i have to fix P010,P14 and P15 equal 0 too? I find out this post in your mailing list archive and i added it in my usercheck subroutine, but everytime i have errors in compilation! SUBROUTINE USERCHK INCLUDE 'SIZE' INCLUDE 'TOTAL' INCLUDE 'RESTART' character*80 filename(9999) ntot = nx1*ny1*nz1*nelv ifreguo = .true. ! dump on regular (uniform) grid instead of GLL nrg = 16 ! dimension of regular grid (nrg**ndim) ! read file-list if (nid.eq.0) then open(unit=199,file='file.list',form='formatted',status='old') read(199,*) nfiles read(199,'(A80)') (filename(i),i=1,nfiles) close(199) endif call bcast(nfiles,isize) call bcast(filename,nfiles*80) do i = 1,nfiles call load_fld(filename(i)) ! do something ! note: make sure you save the result into arrays which are ! dumped by prepost() e.g. T(nx1,ny1,nz1,nelt,ldimt) ... ! dump results into file call prepost(.true.,'his') enddo ! we're done call exitt Ifreguo is a logical switch to have a grid without elemnts?Only knots? Thanks to everyone. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 2 06:16:17 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 2 Mar 2016 17:46:17 +0530 Subject: [Nek5000-users] error in genmap Message-ID: Dear Sir I am trying to run an oscillating airfoil case. For this purpose I am trying to make use of "neknek". I created two separate geometry files , one for the airfoil and other for the outside surrounding. I have created the geometry and mesh using GMSH. I have attached the .geo and .msh files for your perusal. Now, I am able to successfully create the "naca0012.map" but I am getting an error when I try to genmap the outside.rea file. The error is shown below: ratnavk at vamana:~/NEK/test_neknek$ ../trunk/bin/genmap Input (.rea) file name: outside Input mesh tolerance (default 0.2): NOTE: smaller is better, but generous is more forgiving for bad meshes. 0.01 reading .rea file data ... ERROR: error reading 1 1 406 aborting 510 in routine rdbdry. 1 quit Looking forward to your positive reply. T/R Prashanth Mohanasundaram -------------- next part -------------- A non-text attachment was scrubbed... Name: naca0012.geo Type: application/octet-stream Size: 15609 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: naca0012.msh Type: model/mesh Size: 1492849 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: naca0012.py Type: text/x-python Size: 184 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: naca0012.rea Type: application/octet-stream Size: 6225898 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mshconvert.py Type: text/x-python Size: 57834 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: outside.geo Type: application/octet-stream Size: 381 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: outside.msh Type: model/mesh Size: 77365 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: outside.py Type: text/x-python Size: 186 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 2 09:31:18 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 2 Mar 2016 21:01:18 +0530 Subject: [Nek5000-users] got the sol. for error in genmap Message-ID: Dear Sir Got the answer to resolve the error. Had to go through the rd_bc subroutine in the genmap.f code. By increasing the no. of elements in the outer.msh ( >10000) this issue was resolved. T/R Prashanth Mohanasundaram -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 2 10:31:37 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 2 Mar 2016 16:31:37 +0000 Subject: [Nek5000-users] Restart option failed Message-ID: Kamal I am not sure if you have solved your problem. I met the same problem, but I found a better way to get around this problem. Instead of modifying 'byte.c' you could put full path to your restart file in .rea file. Such as 1 PRESOLVE/RESTART OPTIONS ***** /your/path/to/case/*0.f00001 Haomin (Kirk) Yuan Post Doctoral, Building 208/C145, Nuclear Engineering Division, Argonne National Laboratory -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 2 21:29:05 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 03 Mar 2016 04:29:05 +0100 Subject: [Nek5000-users] extracting data in a smaller computational domain and in a plane Message-ID: Hi Neks, I am trying to do some postprocessing of the Nek5000 results. I have a 3D domain, however I will be interested in taking a smaller piece of this domain. The idea is to generate a data base of snapshots containing this smaller part of the domain. For example, if my computational domain is x in (-15, 20), y in (-20, 20), z in(0,2) I just want to take a data set of snapshots containing the velocity fields in the locations: x in (-2, 5), y in (-5, 5), z in(0,2) Is there any way to extract this data? In addition, is there any way to extract the same data but in a 2d plane? I mean: x in (-2, 5), y in (-5, 5), z=1 Thank you in advance. Cheers SL From nek5000-users at lists.mcs.anl.gov Wed Mar 2 21:58:48 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 3 Mar 2016 03:58:48 +0000 Subject: [Nek5000-users] extracting data in a smaller computational domain and in a plane In-Reply-To: References: Message-ID: Hi SL, The easiest way for a profile is to do the Lineout in VisIt and choose 'curve' format in 'Set Save Options'. More accurate way is to setup history/coordinate points in hpts.in file and call hpts routine from userchk which will also work for 2D plane points. Aleks ________________________________________ 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, March 02, 2016 9:29 PM To: Nek5000 Users Subject: [Nek5000-users] extracting data in a smaller computational domain and in a plane Hi Neks, I am trying to do some postprocessing of the Nek5000 results. I have a 3D domain, however I will be interested in taking a smaller piece of this domain. The idea is to generate a data base of snapshots containing this smaller part of the domain. For example, if my computational domain is x in (-15, 20), y in (-20, 20), z in(0,2) I just want to take a data set of snapshots containing the velocity fields in the locations: x in (-2, 5), y in (-5, 5), z in(0,2) Is there any way to extract this data? In addition, is there any way to extract the same data but in a 2d plane? I mean: x in (-2, 5), y in (-5, 5), z=1 Thank you in advance. Cheers SL _______________________________________________ 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 Wed Mar 2 22:26:16 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 03 Mar 2016 05:26:16 +0100 Subject: [Nek5000-users] extracting data in a smaller computational domain and in a plane In-Reply-To: References: Message-ID: Thank you Aleks, that is also very useful. However, it would be nice if I could extract a smaller 3d domain from my big computational domain. The idea is to work with the entire 3d small computational domain... I need to do the same for several time steps (velocity snapshots, changing in time), so if it would be any way to do it directly from Nek5000 it would make the things much easier... Thanks again. SL El 03-03-2016 04:58, nek5000-users at lists.mcs.anl.gov escribi?: > Hi SL, > > The easiest way for a profile is to do the Lineout in VisIt and choose > 'curve' format in 'Set Save Options'. > > More accurate way is to setup history/coordinate points in hpts.in > file and call hpts routine from userchk which will also work for 2D > plane points. > > Aleks > ________________________________________ > 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, March 02, 2016 9:29 PM > To: Nek5000 Users > Subject: [Nek5000-users] extracting data in a smaller computational > domain and in a plane > > Hi Neks, > > I am trying to do some postprocessing of the Nek5000 results. > > I have a 3D domain, however I will be interested in taking a smaller > piece of this domain. The idea is to generate a data base of snapshots > containing this smaller part of the domain. For example, > > if my computational domain is x in (-15, 20), y in (-20, 20), z in(0,2) > > I just want to take a data set of snapshots containing the velocity > fields in the locations: > x in (-2, 5), y in (-5, 5), z in(0,2) > > Is there any way to extract this data? > > In addition, is there any way to extract the same data but in a 2d > plane? I mean: > x in (-2, 5), y in (-5, 5), z=1 > > Thank you in advance. > Cheers > SL > _______________________________________________ > 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 From nek5000-users at lists.mcs.anl.gov Thu Mar 3 12:39:00 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 3 Mar 2016 11:39:00 -0700 Subject: [Nek5000-users] extracting data in a smaller computational domain and in a plane Message-ID: SL, I have developed a set of routines for this express purpose which I am happy to share. They are modified versions of the hpts routines that dump out *fld files of subdomains at arbitrary resolutions. The routines (and a few others) can be found at the following link in the file PhilFunc.f: https://github.com/psakievich/Nek5000 To use you must define your own elements that follow the same format as nek (npnts_in_x=npnts_in_y=npnts_in_z) and place them in an ascii file named " ps_hpts.in". Then in nek call ps_hpts("MYF") where "MYF" is the three character prefix that will be added to the fld files. The format of "ps_hpts.in" is also a little different. The first line should be: NPoints, NElm, NPX, NPY, NPZ where NElm is the number of elements you are creating, and NPX is the points in the x direction for the given element (akin to lx1), etc. After that just specify the x,y,z coordinates like the normal hpts.in files. A couple of additional points: 1) You can crank up the resolution, and use uniform grid spacing to get much better iso surfaces inside the subvolume you define. (Very nice way to get high quality visualizations that harness the power of SEM without interpolating the whole gird onto a finer grid and creating huge data sets) 2) You need to ensure enough memory is allocated for the number of hpts you are using through the SIZE file like normal. 3) You can use a resolution much higher than the lx1 specified in nek. However, if you go too high then it may create a seg fault. I haven't been able to track down the exact buffer sizes, but they are dependent on LELT, and LX1 in your size file. For example, I was to dump out elements of with 32 points in each direction when my lx1 was set to 10 in the SIZE file (LELT around 1000 I think?). However, when I went higher I received a seg fault. I hope to track this down at some point... 4) If you want the elements to meet each other in VisIT you must specify redundant boundaries between them (just like in nek) because I am using the Nek5000 native output routines. If the elements don't have redundant boundaries then there will be gaps between them. I would love to get around this but I haven't had time to write a routine for a new output format. 5) I have only tested these routines in 3D, and I make no promises that they are bug free. Theoretically, they should work for 2D as well, but I haven't tried that. 6) DO NOT use the normal hpts/intpnts routines while using the ps_hpts routines. They use the same variables and it will create undefined behavior. Cheers, Phil On Thu, Mar 3, 2016 at 11:00 AM, 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. extracting data in a smaller computational domain and in a > plane (nek5000-users at lists.mcs.anl.gov) > 2. Re: extracting data in a smaller computational domain and in > a plane (nek5000-users at lists.mcs.anl.gov) > 3. Re: extracting data in a smaller computational domain and in > a plane (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 03 Mar 2016 04:29:05 +0100 > From: nek5000-users at lists.mcs.anl.gov > To: Nek5000 Users > Subject: [Nek5000-users] extracting data in a smaller computational > domain and in a plane > Message-ID: > > Content-Type: text/plain; charset=UTF-8; format=flowed > > Hi Neks, > > I am trying to do some postprocessing of the Nek5000 results. > > I have a 3D domain, however I will be interested in taking a smaller > piece of this domain. The idea is to generate a data base of snapshots > containing this smaller part of the domain. For example, > > if my computational domain is x in (-15, 20), y in (-20, 20), z in(0,2) > > I just want to take a data set of snapshots containing the velocity > fields in the locations: > x in (-2, 5), y in (-5, 5), z in(0,2) > > Is there any way to extract this data? > > In addition, is there any way to extract the same data but in a 2d > plane? I mean: > x in (-2, 5), y in (-5, 5), z=1 > > Thank you in advance. > Cheers > SL > > > ------------------------------ > > Message: 2 > Date: Thu, 3 Mar 2016 03:58:48 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] extracting data in a smaller > computational domain and in a plane > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > Hi SL, > > The easiest way for a profile is to do the Lineout in VisIt and choose > 'curve' format in 'Set Save Options'. > > More accurate way is to setup history/coordinate points in hpts.in file > and call hpts routine from userchk which will also work for 2D plane points. > > Aleks > ________________________________________ > 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, March 02, 2016 9:29 PM > To: Nek5000 Users > Subject: [Nek5000-users] extracting data in a smaller computational > domain and in a plane > > Hi Neks, > > I am trying to do some postprocessing of the Nek5000 results. > > I have a 3D domain, however I will be interested in taking a smaller > piece of this domain. The idea is to generate a data base of snapshots > containing this smaller part of the domain. For example, > > if my computational domain is x in (-15, 20), y in (-20, 20), z in(0,2) > > I just want to take a data set of snapshots containing the velocity > fields in the locations: > x in (-2, 5), y in (-5, 5), z in(0,2) > > Is there any way to extract this data? > > In addition, is there any way to extract the same data but in a 2d > plane? I mean: > x in (-2, 5), y in (-5, 5), z=1 > > Thank you in advance. > Cheers > SL > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > Message: 3 > Date: Thu, 03 Mar 2016 05:26:16 +0100 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] extracting data in a smaller > computational domain and in a plane > Message-ID: > > Content-Type: text/plain; charset=UTF-8; format=flowed > > Thank you Aleks, > > that is also very useful. However, it would be nice if I could extract a > smaller 3d domain from my big computational domain. The idea is to work > with the entire 3d small computational domain... > > I need to do the same for several time steps (velocity snapshots, > changing in time), so if it would be any way to do it directly from > Nek5000 it would make the things much easier... > > Thanks again. > SL > > El 03-03-2016 04:58, nek5000-users at lists.mcs.anl.gov escribi?: > > Hi SL, > > > > The easiest way for a profile is to do the Lineout in VisIt and choose > > 'curve' format in 'Set Save Options'. > > > > More accurate way is to setup history/coordinate points in hpts.in > > file and call hpts routine from userchk which will also work for 2D > > plane points. > > > > Aleks > > ________________________________________ > > 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, March 02, 2016 9:29 PM > > To: Nek5000 Users > > Subject: [Nek5000-users] extracting data in a smaller computational > > domain and in a plane > > > > Hi Neks, > > > > I am trying to do some postprocessing of the Nek5000 results. > > > > I have a 3D domain, however I will be interested in taking a smaller > > piece of this domain. The idea is to generate a data base of snapshots > > containing this smaller part of the domain. For example, > > > > if my computational domain is x in (-15, 20), y in (-20, 20), z in(0,2) > > > > I just want to take a data set of snapshots containing the velocity > > fields in the locations: > > x in (-2, 5), y in (-5, 5), z in(0,2) > > > > Is there any way to extract this data? > > > > In addition, is there any way to extract the same data but in a 2d > > plane? I mean: > > x in (-2, 5), y in (-5, 5), z=1 > > > > Thank you in advance. > > Cheers > > SL > > _______________________________________________ > > 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 > > > > > ------------------------------ > > _______________________________________________ > 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 85, Issue 5 > ******************************************** > -- Phil Sakievich PhD Candidate - Mechanical Engineering Arizona State University - Ira A. Fulton School for Engineering of Matter Transport and Energy Tempe, Arizona -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 3 13:47:03 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 3 Mar 2016 19:47:03 +0000 Subject: [Nek5000-users] Point votices at inlet In-Reply-To: References: Message-ID: Hi Rif, Let's talk offline on that -- my email obabko at mcs.anl.gov Aleks ________________________________ 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, February 01, 2016 11:00 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Point votices at inlet Hi neks, I still cannot for the life of me figure out how to apply this vortex method at the inlet to generate turbulence. Let's say i specify a point at the inlet plane say for example at the coordinate (x1, y1). I need to apply the Biot-Savart law at this point which has a term like (x_i - x) (Note these are vectors) where x_i is the point i specify and x is all the nodes on that plane. How do i call on the nodes to do this vector subtraction? Can anybody help? rif -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 3 13:52:18 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 3 Mar 2016 19:52:18 +0000 Subject: [Nek5000-users] Find out which cell a meshpoint belongs to In-Reply-To: References: , , Message-ID: Hi Lee, Take a look at nr, ns, nt, nel return arguments of findpts_setup() in nek/jl/findpts.c An example of usage of this routine is in intpts_setup() and intpts() of nek/postpro.f Aleks ________________________________ 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: Tuesday, February 02, 2016 4:31 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Find out which cell a meshpoint belongs to Hi neks, I'm just wondering if there's currently a function which acts on a meshpoint and returns the cell it is closest to. I have also tried doing this manually but I need to know the corners of each cell, if that is stored somewhere? Otherwise, is there a way of generating a list of every gridpoint so I can calculate the corners using brute force. Thanks, Lee On Tue, Feb 2, 2016 at 12:10 AM -0800, "nek5000-users at lists.mcs.anl.gov" > wrote: Hi The adjoint implementation in nek assumes change of the direction of time evolution. The goal is to use the standard nek solver with minimal modifications (only advection terms have to be changed). You get these equations from you standard one by changing the time and pressure sign (t -> -t; p-> -p). This of course changes your time integration limits, but it shouldn't be a problem. So when you have your linear direct simulation, to turn it into dual one it is enough to include in your userchk include files ADJOINT and TSTEP, and for ISTEP.eq.0 set IFADJOINT to true. Something like: subroutine userchk include 'SIZE' include 'TSTEP' ! ISTEP include 'ADJOINT' ! IFADJ if(ISTEP.eq.0) ADJOINT=.TRUE. There is no need to modify ###.rea or ###.map files. The only problem are boundary conditions for open flows, as they would require non-homogeneous bc. In this case to avoid problems we usually use sufficiently large domain together with zero Dirichlet bc. The last issue is sufficient resolution for both direct and adjoin runs. I hope this gives you some idea about nek implementation. Regards Adam On 2016-02-01 22:17, nek5000-users at lists.mcs.anl.gov wrote: > Hi Neks, > > To my knowledge, Nek5000 is able to solve adjoint equations of the form: > $\partial u_a/\partial t + V.\nabla u_a - u_a.(\nabla V)^T + \nabla > \p_a + 1/Re \nabla^2 u_a=0$ and $\nabla.u_a=0$ > where u_a and p_a are adjoint velocity and pressure. (Slightly > different formulation may be seen in literature). > > Let's assume the forward problem is already solved so that $V$, i.e. > velocity, (and possibly $p$ as the pressure) is (are) already know. > Thus, the initial and boundary conditions for adjoint NS are also > known. How can we now solve the dual/adjoint NS problem with Nek5000? > Is there any example on how to modify .rea files? Specailly, the > "convection term of $V.\nabla u_a - u_a.(\nabla V)^T$ needs to be > modified compared to forward NS but am not sure how. > My search of mailing list entails some modifications in "perturb.f" > subroutine, but a little bit more clarification on that would be > really appreciated. > > Yours, > Saleh > _______________________________________________ > 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 Mar 4 02:44:17 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 04 Mar 2016 19:44:17 +1100 Subject: [Nek5000-users] extracting data in a smaller computational domain and in a plane In-Reply-To: References: Message-ID: Hi Phil, thank you very much. I sounds great! I suppose that I should include PhilFunc.f in trunk/tools and then compile it? Cheers SL El 04-03-2016 05:39, nek5000-users at lists.mcs.anl.gov escribi?: > SL, > > I have developed a set of routines for this express purpose which I am > happy to share. They are modified versions of the hpts routines that > dump out *fld files of subdomains at arbitrary resolutions.? The > routines (and a few others) can be found at the following link in the > file PhilFunc.f: > > https://github.com/psakievich/Nek5000 [3] > > To use you must define your own elements that follow the same format > as nek (npnts_in_x=npnts_in_y=npnts_in_z) and place them in an ascii > file named "ps_hpts.in [4]".? Then in nek call ps_hpts("MYF") where > "MYF" is the three character prefix that will be added to the fld > files. ?? > > The format of "ps_hpts.in [4]" is also a little different.? The first > line should be: > NPoints, NElm, NPX, NPY, NPZ > > where NElm is the number of elements you are creating, and NPX is the > points in the x direction for the given element (akin to lx1), etc. > After that just specify the x,y,z coordinates like the normal hpts.in > [2] files.? > > A couple of additional points: > > 1) You can crank up the resolution, and use uniform grid spacing to > get much better iso surfaces inside the subvolume you define. (Very > nice way to get high quality visualizations that harness the power of > SEM without interpolating the whole gird onto a finer grid and > creating huge data sets)? > > 2) You need to ensure enough memory is allocated for the number of > hpts you are using through the SIZE file like normal. > > 3) You can use a resolution much higher than the lx1 specified in > nek.? However, if you go too high then it may create a seg fault.? I > haven't been able to track down the exact buffer sizes, but they are > dependent on LELT, and LX1 in your size file.? For example, I was to > dump out elements of with 32 points in each direction when my lx1 was > set to 10 in the SIZE file (LELT around 1000 I think?). However, when > I went higher I received a seg fault.? I hope to track this down at > some point... > > 4) ?If you want the elements to meet each other in VisIT you must > specify redundant boundaries between them (just like in nek) because I > am using the Nek5000 native output routines.? If the elements don't > have redundant boundaries then there will be gaps between them. I > would love to get around this but I haven't had time to write a > routine for a new output format. > > 5) I have only tested these routines in 3D, and I make no promises > that they are bug free. Theoretically, they should work for 2D as > well, but I haven't tried that. > > 6) DO NOT use the normal hpts/intpnts routines while using the ps_hpts > routines.? They use the same variables and it will create undefined > behavior. > > Cheers, > > Phil > > On Thu, Mar 3, 2016 at 11:00 AM, > 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 [1] >> 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. extracting data in a smaller computational domain and in a >> ? ? ? plane (nek5000-users at lists.mcs.anl.gov) >> ? ?2. Re: extracting data in a smaller computational domain? ? >> ?and in >> ? ? ? a plane (nek5000-users at lists.mcs.anl.gov) >> ? ?3. Re: extracting data in a smaller computational domain? ? >> ?and in >> ? ? ? a plane (nek5000-users at lists.mcs.anl.gov) >> >> > ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Thu, 03 Mar 2016 04:29:05 +0100 >> From: nek5000-users at lists.mcs.anl.gov >> To: Nek5000 Users >> Subject: [Nek5000-users] extracting data in a smaller computational >> ? ? ? ? domain? and in a plane >> Message-ID: >> ? ? ? ? >> >> Content-Type: text/plain; charset=UTF-8; format=flowed >> >> Hi Neks, >> >> I am trying to do some postprocessing of the Nek5000 results. >> >> I have a 3D domain, however I will be interested in taking a >> smaller >> piece of this domain. The idea is to generate a data base of >> snapshots >> containing this smaller part of the domain. For example, >> >> if my computational domain is x in (-15, 20), y in (-20, 20), z >> in(0,2) >> >> I just want to take a data set of snapshots containing the velocity >> fields in the locations: >> ? ?x in (-2, 5), y in (-5, 5), z in(0,2) >> >> Is there any way to extract this data? >> >> In addition, is there any way to extract the same data but in a 2d >> plane? I mean: >> ? ?x in (-2, 5), y in (-5, 5), z=1 >> >> Thank you in advance. >> Cheers >> SL >> >> ------------------------------ >> >> Message: 2 >> Date: Thu, 3 Mar 2016 03:58:48 +0000 >> From: nek5000-users at lists.mcs.anl.gov >> To: "nek5000-users at lists.mcs.anl.gov" >> ? ? ? ? >> Subject: Re: [Nek5000-users] extracting data in a smaller >> ? ? ? ? computational domain? ? and in a plane >> Message-ID: >> ? ? ? ? >> >> Content-Type: text/plain; charset="us-ascii" >> >> Hi SL, >> >> The easiest way for a profile is to do the Lineout in VisIt and >> choose 'curve' format in 'Set Save Options'. >> >> More accurate way is to setup history/coordinate points in hpts.in >> [2] file and call hpts routine from userchk which will also work for >> 2D plane points. >> >> Aleks >> ________________________________________ >> 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, March 02, 2016 9:29 PM >> To: Nek5000 Users >> Subject: [Nek5000-users] extracting data in a smaller computational >> domain? ? ? and in a plane >> >> Hi Neks, >> >> I am trying to do some postprocessing of the Nek5000 results. >> >> I have a 3D domain, however I will be interested in taking a >> smaller >> piece of this domain. The idea is to generate a data base of >> snapshots >> containing this smaller part of the domain. For example, >> >> if my computational domain is x in (-15, 20), y in (-20, 20), z >> in(0,2) >> >> I just want to take a data set of snapshots containing the velocity >> fields in the locations: >> ? ?x in (-2, 5), y in (-5, 5), z in(0,2) >> >> Is there any way to extract this data? >> >> In addition, is there any way to extract the same data but in a 2d >> plane? I mean: >> ? ?x in (-2, 5), y in (-5, 5), z=1 >> >> Thank you in advance. >> Cheers >> SL >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] >> >> ------------------------------ >> >> Message: 3 >> Date: Thu, 03 Mar 2016 05:26:16 +0100 >> From: nek5000-users at lists.mcs.anl.gov >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] extracting data in a smaller >> ? ? ? ? computational domain? ? and in a plane >> Message-ID: >> ? ? ? ? >> >> Content-Type: text/plain; charset=UTF-8; format=flowed >> >> Thank you Aleks, >> >> that is also very useful. However, it would be nice if I could >> extract a >> smaller 3d domain from my big computational domain. The idea is to >> work >> with the entire 3d small computational domain... >> >> I need to do the same for several time steps (velocity snapshots, >> changing in time), so if it would be any way to do it directly from >> Nek5000 it would make the things much easier... >> >> Thanks again. >> SL >> >> El 03-03-2016 04:58, nek5000-users at lists.mcs.anl.gov escribi?: >>> Hi SL, >>> >>> The easiest way for a profile is to do the Lineout in VisIt and >> choose >>> 'curve' format in 'Set Save Options'. >>> >>> More accurate way is to setup history/coordinate points in >> hpts.in [2] >>> file and call hpts routine from userchk which will also work for >> 2D >>> plane points. >>> >>> Aleks >>> ________________________________________ >>> 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, March 02, 2016 9:29 PM >>> To: Nek5000 Users >>> Subject: [Nek5000-users] extracting data in a smaller >> computational >>> domain? ? ? and in a plane >>> >>> Hi Neks, >>> >>> I am trying to do some postprocessing of the Nek5000 results. >>> >>> I have a 3D domain, however I will be interested in taking a >> smaller >>> piece of this domain. The idea is to generate a data base of >> snapshots >>> containing this smaller part of the domain. For example, >>> >>> if my computational domain is x in (-15, 20), y in (-20, 20), z >> in(0,2) >>> >>> I just want to take a data set of snapshots containing the >> velocity >>> fields in the locations: >>> ? ? x in (-2, 5), y in (-5, 5), z in(0,2) >>> >>> Is there any way to extract this data? >>> >>> In addition, is there any way to extract the same data but in a >> 2d >>> plane? I mean: >>> ? ? x in (-2, 5), y in (-5, 5), z=1 >>> >>> Thank you in advance. >>> Cheers >>> SL >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] >> >> ------------------------------ >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] >> >> End of Nek5000-users Digest, Vol 85, Issue 5 >> ******************************************** > > -- > > Phil Sakievich > > PhD Candidate - Mechanical Engineering > Arizona State University - Ira A. Fulton School for Engineering of > Matter Transport and Energy > Tempe, Arizona > > Links: > ------ > [1] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > [2] http://hpts.in > [3] https://github.com/psakievich/Nek5000 > [4] http://ps_hpts.in > > _______________________________________________ > 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 Mar 4 02:52:36 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 04 Mar 2016 09:52:36 +0100 Subject: [Nek5000-users] extracting data in a smaller computational domain and in a plane In-Reply-To: References: Message-ID: The build-in function g2gi() does something similar and works with big data sets. Cheers, Stefan Am 3/4/16, 9:44 AM schrieb "nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users at lists.mcs.anl.gov" unter : >Hi Phil, > >thank you very much. I sounds great! >I suppose that I should include PhilFunc.f in trunk/tools and then >compile it? > >Cheers >SL > >El 04-03-2016 05:39, nek5000-users at lists.mcs.anl.gov escribi?: >> SL, >> >> I have developed a set of routines for this express purpose which I am >> happy to share. They are modified versions of the hpts routines that >> dump out *fld files of subdomains at arbitrary resolutions. The >> routines (and a few others) can be found at the following link in the >> file PhilFunc.f: >> >> https://github.com/psakievich/Nek5000 [3] >> >> To use you must define your own elements that follow the same format >> as nek (npnts_in_x=npnts_in_y=npnts_in_z) and place them in an ascii >> file named "ps_hpts.in [4]". Then in nek call ps_hpts("MYF") where >> "MYF" is the three character prefix that will be added to the fld >> files. >> >> The format of "ps_hpts.in [4]" is also a little different. The first >> line should be: >> NPoints, NElm, NPX, NPY, NPZ >> >> where NElm is the number of elements you are creating, and NPX is the >> points in the x direction for the given element (akin to lx1), etc. >> After that just specify the x,y,z coordinates like the normal hpts.in >> [2] files. >> >> A couple of additional points: >> >> 1) You can crank up the resolution, and use uniform grid spacing to >> get much better iso surfaces inside the subvolume you define. (Very >> nice way to get high quality visualizations that harness the power of >> SEM without interpolating the whole gird onto a finer grid and >> creating huge data sets) >> >> 2) You need to ensure enough memory is allocated for the number of >> hpts you are using through the SIZE file like normal. >> >> 3) You can use a resolution much higher than the lx1 specified in >> nek. However, if you go too high then it may create a seg fault. I >> haven't been able to track down the exact buffer sizes, but they are >> dependent on LELT, and LX1 in your size file. For example, I was to >> dump out elements of with 32 points in each direction when my lx1 was >> set to 10 in the SIZE file (LELT around 1000 I think?). However, when >> I went higher I received a seg fault. I hope to track this down at >> some point... >> >> 4) If you want the elements to meet each other in VisIT you must >> specify redundant boundaries between them (just like in nek) because I >> am using the Nek5000 native output routines. If the elements don't >> have redundant boundaries then there will be gaps between them. I >> would love to get around this but I haven't had time to write a >> routine for a new output format. >> >> 5) I have only tested these routines in 3D, and I make no promises >> that they are bug free. Theoretically, they should work for 2D as >> well, but I haven't tried that. >> >> 6) DO NOT use the normal hpts/intpnts routines while using the ps_hpts >> routines. They use the same variables and it will create undefined >> behavior. >> >> Cheers, >> >> Phil >> >> On Thu, Mar 3, 2016 at 11:00 AM, >> 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 [1] >>> 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. extracting data in a smaller computational domain and in a >>> plane (nek5000-users at lists.mcs.anl.gov) >>> 2. Re: extracting data in a smaller computational domain >>> and in >>> a plane (nek5000-users at lists.mcs.anl.gov) >>> 3. Re: extracting data in a smaller computational domain >>> and in >>> a plane (nek5000-users at lists.mcs.anl.gov) >>> >>> >> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Thu, 03 Mar 2016 04:29:05 +0100 >>> From: nek5000-users at lists.mcs.anl.gov >>> To: Nek5000 Users >>> Subject: [Nek5000-users] extracting data in a smaller computational >>> domain and in a plane >>> Message-ID: >>> >>> >>> Content-Type: text/plain; charset=UTF-8; format=flowed >>> >>> Hi Neks, >>> >>> I am trying to do some postprocessing of the Nek5000 results. >>> >>> I have a 3D domain, however I will be interested in taking a >>> smaller >>> piece of this domain. The idea is to generate a data base of >>> snapshots >>> containing this smaller part of the domain. For example, >>> >>> if my computational domain is x in (-15, 20), y in (-20, 20), z >>> in(0,2) >>> >>> I just want to take a data set of snapshots containing the velocity >>> fields in the locations: >>> x in (-2, 5), y in (-5, 5), z in(0,2) >>> >>> Is there any way to extract this data? >>> >>> In addition, is there any way to extract the same data but in a 2d >>> plane? I mean: >>> x in (-2, 5), y in (-5, 5), z=1 >>> >>> Thank you in advance. >>> Cheers >>> SL >>> >>> ------------------------------ >>> >>> Message: 2 >>> Date: Thu, 3 Mar 2016 03:58:48 +0000 >>> From: nek5000-users at lists.mcs.anl.gov >>> To: "nek5000-users at lists.mcs.anl.gov" >>> >>> Subject: Re: [Nek5000-users] extracting data in a smaller >>> computational domain and in a plane >>> Message-ID: >>> >>> >>> Content-Type: text/plain; charset="us-ascii" >>> >>> Hi SL, >>> >>> The easiest way for a profile is to do the Lineout in VisIt and >>> choose 'curve' format in 'Set Save Options'. >>> >>> More accurate way is to setup history/coordinate points in hpts.in >>> [2] file and call hpts routine from userchk which will also work for >>> 2D plane points. >>> >>> Aleks >>> ________________________________________ >>> 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, March 02, 2016 9:29 PM >>> To: Nek5000 Users >>> Subject: [Nek5000-users] extracting data in a smaller computational >>> domain and in a plane >>> >>> Hi Neks, >>> >>> I am trying to do some postprocessing of the Nek5000 results. >>> >>> I have a 3D domain, however I will be interested in taking a >>> smaller >>> piece of this domain. The idea is to generate a data base of >>> snapshots >>> containing this smaller part of the domain. For example, >>> >>> if my computational domain is x in (-15, 20), y in (-20, 20), z >>> in(0,2) >>> >>> I just want to take a data set of snapshots containing the velocity >>> fields in the locations: >>> x in (-2, 5), y in (-5, 5), z in(0,2) >>> >>> Is there any way to extract this data? >>> >>> In addition, is there any way to extract the same data but in a 2d >>> plane? I mean: >>> x in (-2, 5), y in (-5, 5), z=1 >>> >>> Thank you in advance. >>> Cheers >>> SL >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] >>> >>> ------------------------------ >>> >>> Message: 3 >>> Date: Thu, 03 Mar 2016 05:26:16 +0100 >>> From: nek5000-users at lists.mcs.anl.gov >>> To: nek5000-users at lists.mcs.anl.gov >>> Subject: Re: [Nek5000-users] extracting data in a smaller >>> computational domain and in a plane >>> Message-ID: >>> >>> >>> Content-Type: text/plain; charset=UTF-8; format=flowed >>> >>> Thank you Aleks, >>> >>> that is also very useful. However, it would be nice if I could >>> extract a >>> smaller 3d domain from my big computational domain. The idea is to >>> work >>> with the entire 3d small computational domain... >>> >>> I need to do the same for several time steps (velocity snapshots, >>> changing in time), so if it would be any way to do it directly from >>> Nek5000 it would make the things much easier... >>> >>> Thanks again. >>> SL >>> >>> El 03-03-2016 04:58, nek5000-users at lists.mcs.anl.gov escribi?: >>>> Hi SL, >>>> >>>> The easiest way for a profile is to do the Lineout in VisIt and >>> choose >>>> 'curve' format in 'Set Save Options'. >>>> >>>> More accurate way is to setup history/coordinate points in >>> hpts.in [2] >>>> file and call hpts routine from userchk which will also work for >>> 2D >>>> plane points. >>>> >>>> Aleks >>>> ________________________________________ >>>> 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, March 02, 2016 9:29 PM >>>> To: Nek5000 Users >>>> Subject: [Nek5000-users] extracting data in a smaller >>> computational >>>> domain and in a plane >>>> >>>> Hi Neks, >>>> >>>> I am trying to do some postprocessing of the Nek5000 results. >>>> >>>> I have a 3D domain, however I will be interested in taking a >>> smaller >>>> piece of this domain. The idea is to generate a data base of >>> snapshots >>>> containing this smaller part of the domain. For example, >>>> >>>> if my computational domain is x in (-15, 20), y in (-20, 20), z >>> in(0,2) >>>> >>>> I just want to take a data set of snapshots containing the >>> velocity >>>> fields in the locations: >>>> x in (-2, 5), y in (-5, 5), z in(0,2) >>>> >>>> Is there any way to extract this data? >>>> >>>> In addition, is there any way to extract the same data but in a >>> 2d >>>> plane? I mean: >>>> x in (-2, 5), y in (-5, 5), z=1 >>>> >>>> Thank you in advance. >>>> Cheers >>>> SL >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] >>> >>> End of Nek5000-users Digest, Vol 85, Issue 5 >>> ******************************************** >> >> -- >> >> Phil Sakievich >> >> PhD Candidate - Mechanical Engineering >> Arizona State University - Ira A. Fulton School for Engineering of >> Matter Transport and Energy >> Tempe, Arizona >> >> Links: >> ------ >> [1] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> [2] http://hpts.in >> [3] https://github.com/psakievich/Nek5000 >> [4] http://ps_hpts.in >> >> _______________________________________________ >> 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 From nek5000-users at lists.mcs.anl.gov Fri Mar 4 12:17:19 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 04 Mar 2016 18:17:19 +0000 Subject: [Nek5000-users] foamToNek Message-ID: Hi All, I'm trying to compare results from traditional FVM solvers to that of the SEM methods using Nek5000. From the Nek500 page on meshes I found that a python utility, foamToNek has been developed which converts native OpenFOAM meshes into a nek5000 format. I was wondering where that script might be available. I have been unable to contact Haomin Yuan, it's author. If someone could provide me with his email-id, that would be great as well. Sincerely, -- *Amitvikram Dutta* *MASc Candidate* *Graduate Research Assistant * *Okanagan CFD Laboratory* *University of British Columbia | Okanagan Campus* -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 4 16:28:09 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 4 Mar 2016 15:28:09 -0700 Subject: [Nek5000-users] extracting data in a smaller computational domain and in a plane Message-ID: SL, Yes that will work, but you will need to modify "makefile.template" in the [..]/trunk/nek. There is a copy of the one I use in my github repo as well. You can use it as a starting point, or just copy it (provided it references all the files in the version of Nek you are using). My reference template file is based on having a directory [..]/trunk/nek/ps/ where PhilFunc.f is located (at least that's the way I do it). If you update your makefile.template correctly then it will be included as a file that is compiled and copied to your obj directory for each run. Hope that helps, Phil On Fri, Mar 4, 2016 at 1:52 AM, 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. Re: Find out which cell a meshpoint belongs to > (nek5000-users at lists.mcs.anl.gov) > 2. Re: extracting data in a smaller computational domain and in > a plane (nek5000-users at lists.mcs.anl.gov) > 3. Re: extracting data in a smaller computational domain and in > a plane (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 3 Mar 2016 19:52:18 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] Find out which cell a meshpoint belongs > to > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Lee, > > Take a look at nr, ns, nt, nel return arguments of findpts_setup() in > nek/jl/findpts.c > > An example of usage of this routine is in intpts_setup() and intpts() of > nek/postpro.f > > Aleks > ________________________________ > 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: Tuesday, February 02, 2016 4:31 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Find out which cell a meshpoint belongs to > > Hi neks, > > I'm just wondering if there's currently a function which acts on a > meshpoint and returns the cell it is closest to. > > I have also tried doing this manually but I need to know the corners of > each cell, if that is stored somewhere? > > Otherwise, is there a way of generating a list of every gridpoint so I can > calculate the corners using brute force. > > Thanks, > > Lee > > > > > On Tue, Feb 2, 2016 at 12:10 AM -0800, "nek5000-users at lists.mcs.anl.gov" < > nek5000-users at lists.mcs.anl.gov> > wrote: > > Hi > > The adjoint implementation in nek assumes change of the direction of > time evolution. The goal is to use the standard nek solver with minimal > modifications (only advection terms have to be changed). You get these > equations from you standard one by changing the time and pressure sign > (t -> -t; p-> -p). This of course changes your time integration limits, > but it shouldn't be a problem. So when you have your linear direct > simulation, to turn it into dual one it is enough to include in your > userchk include files ADJOINT and TSTEP, and for ISTEP.eq.0 set > IFADJOINT to true. Something like: > subroutine userchk > > include 'SIZE' > include 'TSTEP' ! ISTEP > include 'ADJOINT' ! IFADJ > > if(ISTEP.eq.0) ADJOINT=.TRUE. > > There is no need to modify ###.rea or ###.map files. The only problem > are boundary conditions for open flows, as they would require > non-homogeneous bc. In this case to avoid problems we usually use > sufficiently large domain together with zero Dirichlet bc. The last > issue is sufficient resolution for both direct and adjoin runs. I hope > this gives you some idea about nek implementation. > Regards > Adam > > On 2016-02-01 22:17, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Neks, > > > > To my knowledge, Nek5000 is able to solve adjoint equations of the form: > > $\partial u_a/\partial t + V.\nabla u_a - u_a.(\nabla V)^T + \nabla > > \p_a + 1/Re \nabla^2 u_a=0$ and $\nabla.u_a=0$ > > where u_a and p_a are adjoint velocity and pressure. (Slightly > > different formulation may be seen in literature). > > > > Let's assume the forward problem is already solved so that $V$, i.e. > > velocity, (and possibly $p$ as the pressure) is (are) already know. > > Thus, the initial and boundary conditions for adjoint NS are also > > known. How can we now solve the dual/adjoint NS problem with Nek5000? > > Is there any example on how to modify .rea files? Specailly, the > > "convection term of $V.\nabla u_a - u_a.(\nabla V)^T$ needs to be > > modified compared to forward NS but am not sure how. > > My search of mailing list entails some modifications in "perturb.f" > > subroutine, but a little bit more clarification on that would be > > really appreciated. > > > > Yours, > > Saleh > > _______________________________________________ > > 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: < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160303/67eefdce/attachment-0001.html > > > > ------------------------------ > > Message: 2 > Date: Fri, 04 Mar 2016 19:44:17 +1100 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] extracting data in a smaller > computational domain and in a plane > Message-ID: > > Content-Type: text/plain; charset=UTF-8; format=flowed > > Hi Phil, > > thank you very much. I sounds great! > I suppose that I should include PhilFunc.f in trunk/tools and then > compile it? > > Cheers > SL > > El 04-03-2016 05:39, nek5000-users at lists.mcs.anl.gov escribi?: > > SL, > > > > I have developed a set of routines for this express purpose which I am > > happy to share. They are modified versions of the hpts routines that > > dump out *fld files of subdomains at arbitrary resolutions.? The > > routines (and a few others) can be found at the following link in the > > file PhilFunc.f: > > > > https://github.com/psakievich/Nek5000 [3] > > > > To use you must define your own elements that follow the same format > > as nek (npnts_in_x=npnts_in_y=npnts_in_z) and place them in an ascii > > file named "ps_hpts.in [4]".? Then in nek call ps_hpts("MYF") where > > "MYF" is the three character prefix that will be added to the fld > > files. ?? > > > > The format of "ps_hpts.in [4]" is also a little different.? The first > > line should be: > > NPoints, NElm, NPX, NPY, NPZ > > > > where NElm is the number of elements you are creating, and NPX is the > > points in the x direction for the given element (akin to lx1), etc. > > After that just specify the x,y,z coordinates like the normal hpts.in > > [2] files.? > > > > A couple of additional points: > > > > 1) You can crank up the resolution, and use uniform grid spacing to > > get much better iso surfaces inside the subvolume you define. (Very > > nice way to get high quality visualizations that harness the power of > > SEM without interpolating the whole gird onto a finer grid and > > creating huge data sets)? > > > > 2) You need to ensure enough memory is allocated for the number of > > hpts you are using through the SIZE file like normal. > > > > 3) You can use a resolution much higher than the lx1 specified in > > nek.? However, if you go too high then it may create a seg fault.? I > > haven't been able to track down the exact buffer sizes, but they are > > dependent on LELT, and LX1 in your size file.? For example, I was to > > dump out elements of with 32 points in each direction when my lx1 was > > set to 10 in the SIZE file (LELT around 1000 I think?). However, when > > I went higher I received a seg fault.? I hope to track this down at > > some point... > > > > 4) ?If you want the elements to meet each other in VisIT you must > > specify redundant boundaries between them (just like in nek) because I > > am using the Nek5000 native output routines.? If the elements don't > > have redundant boundaries then there will be gaps between them. I > > would love to get around this but I haven't had time to write a > > routine for a new output format. > > > > 5) I have only tested these routines in 3D, and I make no promises > > that they are bug free. Theoretically, they should work for 2D as > > well, but I haven't tried that. > > > > 6) DO NOT use the normal hpts/intpnts routines while using the ps_hpts > > routines.? They use the same variables and it will create undefined > > behavior. > > > > Cheers, > > > > Phil > > > > On Thu, Mar 3, 2016 at 11:00 AM, > > 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 [1] > >> 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. extracting data in a smaller computational domain and in a > >> ? ? ? plane (nek5000-users at lists.mcs.anl.gov) > >> ? ?2. Re: extracting data in a smaller computational domain? ? > >> ?and in > >> ? ? ? a plane (nek5000-users at lists.mcs.anl.gov) > >> ? ?3. Re: extracting data in a smaller computational domain? ? > >> ?and in > >> ? ? ? a plane (nek5000-users at lists.mcs.anl.gov) > >> > >> > > ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Thu, 03 Mar 2016 04:29:05 +0100 > >> From: nek5000-users at lists.mcs.anl.gov > >> To: Nek5000 Users > >> Subject: [Nek5000-users] extracting data in a smaller computational > >> ? ? ? ? domain? and in a plane > >> Message-ID: > >> ? ? ? ? > >> > >> Content-Type: text/plain; charset=UTF-8; format=flowed > >> > >> Hi Neks, > >> > >> I am trying to do some postprocessing of the Nek5000 results. > >> > >> I have a 3D domain, however I will be interested in taking a > >> smaller > >> piece of this domain. The idea is to generate a data base of > >> snapshots > >> containing this smaller part of the domain. For example, > >> > >> if my computational domain is x in (-15, 20), y in (-20, 20), z > >> in(0,2) > >> > >> I just want to take a data set of snapshots containing the velocity > >> fields in the locations: > >> ? ?x in (-2, 5), y in (-5, 5), z in(0,2) > >> > >> Is there any way to extract this data? > >> > >> In addition, is there any way to extract the same data but in a 2d > >> plane? I mean: > >> ? ?x in (-2, 5), y in (-5, 5), z=1 > >> > >> Thank you in advance. > >> Cheers > >> SL > >> > >> ------------------------------ > >> > >> Message: 2 > >> Date: Thu, 3 Mar 2016 03:58:48 +0000 > >> From: nek5000-users at lists.mcs.anl.gov > >> To: "nek5000-users at lists.mcs.anl.gov" > >> ? ? ? ? > >> Subject: Re: [Nek5000-users] extracting data in a smaller > >> ? ? ? ? computational domain? ? and in a plane > >> Message-ID: > >> ? ? ? ? > >> > >> Content-Type: text/plain; charset="us-ascii" > >> > >> Hi SL, > >> > >> The easiest way for a profile is to do the Lineout in VisIt and > >> choose 'curve' format in 'Set Save Options'. > >> > >> More accurate way is to setup history/coordinate points in hpts.in > >> [2] file and call hpts routine from userchk which will also work for > >> 2D plane points. > >> > >> Aleks > >> ________________________________________ > >> 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, March 02, 2016 9:29 PM > >> To: Nek5000 Users > >> Subject: [Nek5000-users] extracting data in a smaller computational > >> domain? ? ? and in a plane > >> > >> Hi Neks, > >> > >> I am trying to do some postprocessing of the Nek5000 results. > >> > >> I have a 3D domain, however I will be interested in taking a > >> smaller > >> piece of this domain. The idea is to generate a data base of > >> snapshots > >> containing this smaller part of the domain. For example, > >> > >> if my computational domain is x in (-15, 20), y in (-20, 20), z > >> in(0,2) > >> > >> I just want to take a data set of snapshots containing the velocity > >> fields in the locations: > >> ? ?x in (-2, 5), y in (-5, 5), z in(0,2) > >> > >> Is there any way to extract this data? > >> > >> In addition, is there any way to extract the same data but in a 2d > >> plane? I mean: > >> ? ?x in (-2, 5), y in (-5, 5), z=1 > >> > >> Thank you in advance. > >> Cheers > >> SL > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users at lists.mcs.anl.gov > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] > >> > >> ------------------------------ > >> > >> Message: 3 > >> Date: Thu, 03 Mar 2016 05:26:16 +0100 > >> From: nek5000-users at lists.mcs.anl.gov > >> To: nek5000-users at lists.mcs.anl.gov > >> Subject: Re: [Nek5000-users] extracting data in a smaller > >> ? ? ? ? computational domain? ? and in a plane > >> Message-ID: > >> ? ? ? ? > >> > >> Content-Type: text/plain; charset=UTF-8; format=flowed > >> > >> Thank you Aleks, > >> > >> that is also very useful. However, it would be nice if I could > >> extract a > >> smaller 3d domain from my big computational domain. The idea is to > >> work > >> with the entire 3d small computational domain... > >> > >> I need to do the same for several time steps (velocity snapshots, > >> changing in time), so if it would be any way to do it directly from > >> Nek5000 it would make the things much easier... > >> > >> Thanks again. > >> SL > >> > >> El 03-03-2016 04:58, nek5000-users at lists.mcs.anl.gov escribi?: > >>> Hi SL, > >>> > >>> The easiest way for a profile is to do the Lineout in VisIt and > >> choose > >>> 'curve' format in 'Set Save Options'. > >>> > >>> More accurate way is to setup history/coordinate points in > >> hpts.in [2] > >>> file and call hpts routine from userchk which will also work for > >> 2D > >>> plane points. > >>> > >>> Aleks > >>> ________________________________________ > >>> 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, March 02, 2016 9:29 PM > >>> To: Nek5000 Users > >>> Subject: [Nek5000-users] extracting data in a smaller > >> computational > >>> domain? ? ? and in a plane > >>> > >>> Hi Neks, > >>> > >>> I am trying to do some postprocessing of the Nek5000 results. > >>> > >>> I have a 3D domain, however I will be interested in taking a > >> smaller > >>> piece of this domain. The idea is to generate a data base of > >> snapshots > >>> containing this smaller part of the domain. For example, > >>> > >>> if my computational domain is x in (-15, 20), y in (-20, 20), z > >> in(0,2) > >>> > >>> I just want to take a data set of snapshots containing the > >> velocity > >>> fields in the locations: > >>> ? ? x in (-2, 5), y in (-5, 5), z in(0,2) > >>> > >>> Is there any way to extract this data? > >>> > >>> In addition, is there any way to extract the same data but in a > >> 2d > >>> plane? I mean: > >>> ? ? x in (-2, 5), y in (-5, 5), z=1 > >>> > >>> Thank you in advance. > >>> Cheers > >>> SL > >>> _______________________________________________ > >>> Nek5000-users mailing list > >>> Nek5000-users at lists.mcs.anl.gov > >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] > >>> _______________________________________________ > >>> Nek5000-users mailing list > >>> Nek5000-users at lists.mcs.anl.gov > >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] > >> > >> ------------------------------ > >> > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users at lists.mcs.anl.gov > >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] > >> > >> End of Nek5000-users Digest, Vol 85, Issue 5 > >> ******************************************** > > > > -- > > > > Phil Sakievich > > > > PhD Candidate - Mechanical Engineering > > Arizona State University - Ira A. Fulton School for Engineering of > > Matter Transport and Energy > > Tempe, Arizona > > > > Links: > > ------ > > [1] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > [2] http://hpts.in > > [3] https://github.com/psakievich/Nek5000 > > [4] http://ps_hpts.in > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > ------------------------------ > > Message: 3 > Date: Fri, 04 Mar 2016 09:52:36 +0100 > From: nek5000-users at lists.mcs.anl.gov > To: > Subject: Re: [Nek5000-users] extracting data in a smaller > computational domain and in a plane > Message-ID: > > Content-Type: text/plain; charset="ISO-8859-1" > > The build-in function g2gi() does something similar and works with big > data sets. > > Cheers, > Stefan > > > Am 3/4/16, 9:44 AM schrieb "nek5000-users-bounces at lists.mcs.anl.gov on > behalf of nek5000-users at lists.mcs.anl.gov" unter > nek5000-users at lists.mcs.anl.gov>: > > >Hi Phil, > > > >thank you very much. I sounds great! > >I suppose that I should include PhilFunc.f in trunk/tools and then > >compile it? > > > >Cheers > >SL > > > >El 04-03-2016 05:39, nek5000-users at lists.mcs.anl.gov escribi?: > >> SL, > >> > >> I have developed a set of routines for this express purpose which I am > >> happy to share. They are modified versions of the hpts routines that > >> dump out *fld files of subdomains at arbitrary resolutions. The > >> routines (and a few others) can be found at the following link in the > >> file PhilFunc.f: > >> > >> https://github.com/psakievich/Nek5000 [3] > >> > >> To use you must define your own elements that follow the same format > >> as nek (npnts_in_x=npnts_in_y=npnts_in_z) and place them in an ascii > >> file named "ps_hpts.in [4]". Then in nek call ps_hpts("MYF") where > >> "MYF" is the three character prefix that will be added to the fld > >> files. > >> > >> The format of "ps_hpts.in [4]" is also a little different. The first > >> line should be: > >> NPoints, NElm, NPX, NPY, NPZ > >> > >> where NElm is the number of elements you are creating, and NPX is the > >> points in the x direction for the given element (akin to lx1), etc. > >> After that just specify the x,y,z coordinates like the normal hpts.in > >> [2] files. > >> > >> A couple of additional points: > >> > >> 1) You can crank up the resolution, and use uniform grid spacing to > >> get much better iso surfaces inside the subvolume you define. (Very > >> nice way to get high quality visualizations that harness the power of > >> SEM without interpolating the whole gird onto a finer grid and > >> creating huge data sets) > >> > >> 2) You need to ensure enough memory is allocated for the number of > >> hpts you are using through the SIZE file like normal. > >> > >> 3) You can use a resolution much higher than the lx1 specified in > >> nek. However, if you go too high then it may create a seg fault. I > >> haven't been able to track down the exact buffer sizes, but they are > >> dependent on LELT, and LX1 in your size file. For example, I was to > >> dump out elements of with 32 points in each direction when my lx1 was > >> set to 10 in the SIZE file (LELT around 1000 I think?). However, when > >> I went higher I received a seg fault. I hope to track this down at > >> some point... > >> > >> 4) If you want the elements to meet each other in VisIT you must > >> specify redundant boundaries between them (just like in nek) because I > >> am using the Nek5000 native output routines. If the elements don't > >> have redundant boundaries then there will be gaps between them. I > >> would love to get around this but I haven't had time to write a > >> routine for a new output format. > >> > >> 5) I have only tested these routines in 3D, and I make no promises > >> that they are bug free. Theoretically, they should work for 2D as > >> well, but I haven't tried that. > >> > >> 6) DO NOT use the normal hpts/intpnts routines while using the ps_hpts > >> routines. They use the same variables and it will create undefined > >> behavior. > >> > >> Cheers, > >> > >> Phil > >> > >> On Thu, Mar 3, 2016 at 11:00 AM, > >> 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 [1] > >>> 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. extracting data in a smaller computational domain and in a > >>> plane (nek5000-users at lists.mcs.anl.gov) > >>> 2. Re: extracting data in a smaller computational domain > >>> and in > >>> a plane (nek5000-users at lists.mcs.anl.gov) > >>> 3. Re: extracting data in a smaller computational domain > >>> and in > >>> a plane (nek5000-users at lists.mcs.anl.gov) > >>> > >>> > >> ---------------------------------------------------------------------- > >>> > >>> Message: 1 > >>> Date: Thu, 03 Mar 2016 04:29:05 +0100 > >>> From: nek5000-users at lists.mcs.anl.gov > >>> To: Nek5000 Users > >>> Subject: [Nek5000-users] extracting data in a smaller computational > >>> domain and in a plane > >>> Message-ID: > >>> > >>> > >>> Content-Type: text/plain; charset=UTF-8; format=flowed > >>> > >>> Hi Neks, > >>> > >>> I am trying to do some postprocessing of the Nek5000 results. > >>> > >>> I have a 3D domain, however I will be interested in taking a > >>> smaller > >>> piece of this domain. The idea is to generate a data base of > >>> snapshots > >>> containing this smaller part of the domain. For example, > >>> > >>> if my computational domain is x in (-15, 20), y in (-20, 20), z > >>> in(0,2) > >>> > >>> I just want to take a data set of snapshots containing the velocity > >>> fields in the locations: > >>> x in (-2, 5), y in (-5, 5), z in(0,2) > >>> > >>> Is there any way to extract this data? > >>> > >>> In addition, is there any way to extract the same data but in a 2d > >>> plane? I mean: > >>> x in (-2, 5), y in (-5, 5), z=1 > >>> > >>> Thank you in advance. > >>> Cheers > >>> SL > >>> > >>> ------------------------------ > >>> > >>> Message: 2 > >>> Date: Thu, 3 Mar 2016 03:58:48 +0000 > >>> From: nek5000-users at lists.mcs.anl.gov > >>> To: "nek5000-users at lists.mcs.anl.gov" > >>> > >>> Subject: Re: [Nek5000-users] extracting data in a smaller > >>> computational domain and in a plane > >>> Message-ID: > >>> > >>> > >>> Content-Type: text/plain; charset="us-ascii" > >>> > >>> Hi SL, > >>> > >>> The easiest way for a profile is to do the Lineout in VisIt and > >>> choose 'curve' format in 'Set Save Options'. > >>> > >>> More accurate way is to setup history/coordinate points in hpts.in > >>> [2] file and call hpts routine from userchk which will also work for > >>> 2D plane points. > >>> > >>> Aleks > >>> ________________________________________ > >>> 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, March 02, 2016 9:29 PM > >>> To: Nek5000 Users > >>> Subject: [Nek5000-users] extracting data in a smaller computational > >>> domain and in a plane > >>> > >>> Hi Neks, > >>> > >>> I am trying to do some postprocessing of the Nek5000 results. > >>> > >>> I have a 3D domain, however I will be interested in taking a > >>> smaller > >>> piece of this domain. The idea is to generate a data base of > >>> snapshots > >>> containing this smaller part of the domain. For example, > >>> > >>> if my computational domain is x in (-15, 20), y in (-20, 20), z > >>> in(0,2) > >>> > >>> I just want to take a data set of snapshots containing the velocity > >>> fields in the locations: > >>> x in (-2, 5), y in (-5, 5), z in(0,2) > >>> > >>> Is there any way to extract this data? > >>> > >>> In addition, is there any way to extract the same data but in a 2d > >>> plane? I mean: > >>> x in (-2, 5), y in (-5, 5), z=1 > >>> > >>> Thank you in advance. > >>> Cheers > >>> SL > >>> _______________________________________________ > >>> Nek5000-users mailing list > >>> Nek5000-users at lists.mcs.anl.gov > >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] > >>> > >>> ------------------------------ > >>> > >>> Message: 3 > >>> Date: Thu, 03 Mar 2016 05:26:16 +0100 > >>> From: nek5000-users at lists.mcs.anl.gov > >>> To: nek5000-users at lists.mcs.anl.gov > >>> Subject: Re: [Nek5000-users] extracting data in a smaller > >>> computational domain and in a plane > >>> Message-ID: > >>> > >>> > >>> Content-Type: text/plain; charset=UTF-8; format=flowed > >>> > >>> Thank you Aleks, > >>> > >>> that is also very useful. However, it would be nice if I could > >>> extract a > >>> smaller 3d domain from my big computational domain. The idea is to > >>> work > >>> with the entire 3d small computational domain... > >>> > >>> I need to do the same for several time steps (velocity snapshots, > >>> changing in time), so if it would be any way to do it directly from > >>> Nek5000 it would make the things much easier... > >>> > >>> Thanks again. > >>> SL > >>> > >>> El 03-03-2016 04:58, nek5000-users at lists.mcs.anl.gov escribi?: > >>>> Hi SL, > >>>> > >>>> The easiest way for a profile is to do the Lineout in VisIt and > >>> choose > >>>> 'curve' format in 'Set Save Options'. > >>>> > >>>> More accurate way is to setup history/coordinate points in > >>> hpts.in [2] > >>>> file and call hpts routine from userchk which will also work for > >>> 2D > >>>> plane points. > >>>> > >>>> Aleks > >>>> ________________________________________ > >>>> 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, March 02, 2016 9:29 PM > >>>> To: Nek5000 Users > >>>> Subject: [Nek5000-users] extracting data in a smaller > >>> computational > >>>> domain and in a plane > >>>> > >>>> Hi Neks, > >>>> > >>>> I am trying to do some postprocessing of the Nek5000 results. > >>>> > >>>> I have a 3D domain, however I will be interested in taking a > >>> smaller > >>>> piece of this domain. The idea is to generate a data base of > >>> snapshots > >>>> containing this smaller part of the domain. For example, > >>>> > >>>> if my computational domain is x in (-15, 20), y in (-20, 20), z > >>> in(0,2) > >>>> > >>>> I just want to take a data set of snapshots containing the > >>> velocity > >>>> fields in the locations: > >>>> x in (-2, 5), y in (-5, 5), z in(0,2) > >>>> > >>>> Is there any way to extract this data? > >>>> > >>>> In addition, is there any way to extract the same data but in a > >>> 2d > >>>> plane? I mean: > >>>> x in (-2, 5), y in (-5, 5), z=1 > >>>> > >>>> Thank you in advance. > >>>> Cheers > >>>> SL > >>>> _______________________________________________ > >>>> Nek5000-users mailing list > >>>> Nek5000-users at lists.mcs.anl.gov > >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] > >>>> _______________________________________________ > >>>> Nek5000-users mailing list > >>>> Nek5000-users at lists.mcs.anl.gov > >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] > >>> > >>> ------------------------------ > >>> > >>> _______________________________________________ > >>> Nek5000-users mailing list > >>> Nek5000-users at lists.mcs.anl.gov > >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1] > >>> > >>> End of Nek5000-users Digest, Vol 85, Issue 5 > >>> ******************************************** > >> > >> -- > >> > >> Phil Sakievich > >> > >> PhD Candidate - Mechanical Engineering > >> Arizona State University - Ira A. Fulton School for Engineering of > >> Matter Transport and Energy > >> Tempe, Arizona > >> > >> Links: > >> ------ > >> [1] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> [2] http://hpts.in > >> [3] https://github.com/psakievich/Nek5000 > >> [4] http://ps_hpts.in > >> > >> _______________________________________________ > >> 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 > > > > > ------------------------------ > > _______________________________________________ > 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 85, Issue 7 > ******************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 4 16:44:05 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 4 Mar 2016 22:44:05 +0000 Subject: [Nek5000-users] foamToNek Message-ID: Hi, Amitvikram You could find this utility here: https://github.com/yhaomin2007/foamToNek However, you could only convert hex8 from OpenFOAM to nek, which means there is not curvature information in both openFoam cell and nek element. I have tested a pipe and a box case. You could also find them in this link. Haomin (Kirk) Yuan Post Doctoral, Building 208/C145, Nuclear Engineering Division, Argonne National Laboratory -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 4 17:52:01 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 04 Mar 2016 23:52:01 +0000 Subject: [Nek5000-users] foamToNek In-Reply-To: References: Message-ID: Thanks Hao! On Fri, Mar 4, 2016 at 2:44 PM wrote: > Hi, Amitvikram > > > > You could find this utility here: > > > > https://github.com/yhaomin2007/foamToNek > > > > However, you could only convert hex8 from OpenFOAM to nek, which means > there is not curvature information in both openFoam cell and nek element. > > I have tested a pipe and a box case. You could also find them in this link. > > > > > > Haomin (Kirk) Yuan > > Post Doctoral, Building 208/C145, > > Nuclear Engineering Division, > > Argonne National Laboratory > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -- *Amitvikram Dutta* *MASc Candidate* *Graduate Research Assistant * *Okanagan CFD Laboratory* *University of British Columbia | Okanagan Campus* -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Mar 8 22:08:03 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 09 Mar 2016 05:08:03 +0100 Subject: [Nek5000-users] convective boundary conditions Message-ID: Hi Neks, is there any non-reflective or convective boundary condition implemented in Nek5000? I need to use that boundary condition at the outlet surface. I have tried using ON, but it is not working... Thanks SL From nek5000-users at lists.mcs.anl.gov Wed Mar 9 02:34:43 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 9 Mar 2016 16:34:43 +0800 (GMT+08:00) Subject: [Nek5000-users] output the postprocessing data to a file Message-ID: Hi,neks I have learned from some previous posts to output postprocessing data with outpost function. However,that function only provides .fld file that can be viewed in visIt. I need the exact value of posrprocessing data. As for my case, I need the temperature gradient on the bottom side of a square domain,so I used function gram1(tx,ty,tz,t) and had the value of ty(for example) on every grid point of the whole domain, then I met the problem that what I should do to get value of ty only on the bottom side, in other words that how to export the ty of the bottom side to a dat file. My case ran on 8 processors, I wonder whether the parallel settings also matter.Thanks for help. Regards B.L.Xu -- Xu Bolun, University of Science and Techonology of China, Hefei,Anhui,China -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Mar 7 14:16:38 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 7 Mar 2016 21:16:38 +0100 Subject: [Nek5000-users] Lagrangian Particle Tracking Message-ID: Hi , I am currently working on my master thesis concerning a lid driven cavity. I am trying to implement Lagrangian Particle Tracking and saw that you implemented such a tool in January. Currently I am searching for an example of such implementation. Could you help me by telling me how to do so or providing me an example code? Thanks in advance, Best regards and greetings from Austria, Michael Riedl -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Mar 8 08:01:07 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 8 Mar 2016 19:31:07 +0530 Subject: [Nek5000-users] Unable to read the coefficient of lift and drag Message-ID: Dear Sir I am trying to run a simulation involving a plunging airfoil. For this purpose I have created two geometry files, one consisting of the airfoil & the other consisting of the outer mesh. My aim is to find the coefficient of lift ( Cl )and drag ( Cd ) & for this purpose i introduced a code in the subroutine function usrchk(). Upon compilation, I get the following error: In function `userchk_': naca0012.f:(.text+0x42b): undefined reference to `set_ob_' collect2: ld returned 1 exit status make: *** [nek5000] Error 1 I am attaching herewith the files for your perusal. Looking forward to your positive reply. T/R Prashanth Mohanasundaram -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: naca0012.f Type: text/x-fortran Size: 9852 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: naca0012.usr Type: application/octet-stream Size: 8971 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Name: outside.rea Type: application/octet-stream Size: 3857009 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 9 12:57:24 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 9 Mar 2016 18:57:24 +0000 Subject: [Nek5000-users] Lagrangian Particle Tracking In-Reply-To: References: Message-ID: Hi Michael, Take a look at http://nek5000.github.io/NekDoc/Nek_usersch6.html#x8-670006.7 Aleks ________________________________ 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, March 07, 2016 2:16 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Lagrangian Particle Tracking Hi , I am currently working on my master thesis concerning a lid driven cavity. I am trying to implement Lagrangian Particle Tracking and saw that you implemented such a tool in January. Currently I am searching for an example of such implementation. Could you help me by telling me how to do so or providing me an example code? Thanks in advance, Best regards and greetings from Austria, Michael Riedl -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 9 13:06:01 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 09 Mar 2016 20:06:01 +0100 Subject: [Nek5000-users] Lagrangian Particle Tracking In-Reply-To: References: Message-ID: Dear Michael, we have written an implementation of particles with (nonlinear) Stokes drag, essentially based on spectral interpolation. The tricky bit is to make sure that the boundary conditions are done correctly. There is one paper already published (see http://arxiv.org/abs/1501.04483), and one more is in the thesis by Azad Noorani. What type of particles are you interested in, inertial ones, or just fluid tracers? Best regards, Philipp Quoting nek5000-users at lists.mcs.anl.gov: > Hi Michael, > > Take a look at > > http://nek5000.github.io/NekDoc/Nek_usersch6.html#x8-670006.7 > > Aleks > > ________________________________ > 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, March 07, 2016 2:16 PM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Lagrangian Particle Tracking > > Hi , > > I am currently working on my master thesis concerning a lid driven cavity. > > I am trying to implement Lagrangian Particle Tracking and saw that > you implemented such a tool in January. Currently I am searching for > an example of such implementation. Could you help me by telling me > how to do so or providing me an example code? > > Thanks in advance, > Best regards and greetings from Austria, > > Michael Riedl From nek5000-users at lists.mcs.anl.gov Wed Mar 9 20:58:28 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 10 Mar 2016 03:58:28 +0100 Subject: [Nek5000-users] convective boundary conditions In-Reply-To: <844db190096319ee1e617b2620d45de1@upm.es> References: <844db190096319ee1e617b2620d45de1@upm.es> Message-ID: Hi Neks, regarding my question about convective boundary conditions: In the problem that I am solving, there are vortex traveling across the boundary. Using O boundary conditions, the solution blows up (due to the negative flux of the vortex). On the contrary, if I use ON, the simulation continues running, but I get very strong reflections. In addition, although my flow is laminar, if I use turb_outflow subroutine (with O boundary conditions) with rq=2, the simulation works better, but at a certain moment, it also crashes. I am wondering if I should increase rq to, let say 3, or maybe I should use a different boundary condition, i.e. non reflective. I would like to ask, if I am using turb_outflow subroutine I am imposing grad U>0 in the boundary (please correct me if I am wrong). The question is, is it physical? What I am doing is -pn+(1/Re)(n*grad(U))>0 ? What does it mean? Finally, I have seen that in 2015 you implemented some non-reflective boundary conditions and they were working very well. Please, could you help me with this issue? (i.e.: a piece of advise or some procedure to follow...) Thank you very much in advance. SL From nek5000-users at lists.mcs.anl.gov Wed Mar 9 21:27:42 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 10 Mar 2016 03:27:42 +0000 Subject: [Nek5000-users] convective boundary conditions In-Reply-To: References: <844db190096319ee1e617b2620d45de1@upm.es>, Message-ID: SL, I had the same problem before. I've had to set rq = 200. If your flow is very turbulent, just turn up that value a lot. No, it's not physical because you're imposing a divergence on the last layer of elements. You can just exclude that part of your solution in your post processing. Regards, Goran > On Mar 9, 2016, at 21:58, "nek5000-users at lists.mcs.anl.gov" wrote: > > Hi Neks, > > regarding my question about convective boundary conditions: > > In the problem that I am solving, there are vortex traveling across the boundary. Using O boundary conditions, the solution blows up (due to the negative flux of the vortex). On the contrary, if I use ON, the simulation continues running, but I get very strong reflections. > > In addition, although my flow is laminar, if I use turb_outflow subroutine (with O boundary conditions) with rq=2, the simulation works better, but at a certain moment, it also crashes. I am wondering if I should increase rq to, let say 3, or maybe I should use a different boundary condition, i.e. non reflective. > > I would like to ask, if I am using turb_outflow subroutine I am imposing grad U>0 in the boundary (please correct me if I am wrong). The question is, is it physical? What I am doing is > -pn+(1/Re)(n*grad(U))>0 ? What does it mean? > > Finally, I have seen that in 2015 you implemented some non-reflective boundary conditions and they were working very well. Please, could you help me with this issue? (i.e.: a piece of advise or some procedure to follow...) > > Thank you very much in advance. > SL > _______________________________________________ > 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 Thu Mar 10 00:14:39 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 10 Mar 2016 07:14:39 +0100 Subject: [Nek5000-users] convective boundary conditions In-Reply-To: References: <844db190096319ee1e617b2620d45de1@upm.es>, Message-ID: Hi Goran, thank you for your answer. However I still not understand very well what happens in your simulation if you are using unphysical boundary conditions... Activating turb_outflow subroutine, are you emulating a suction (from the boundary to the inner domain)? In this case, is it not affecting your physical results from your numerical simulation? Please, correct me if I am wrong... One more question, the effect that you are producing with the turb_outflow subroutine, is it similar to applying convective boundary condition? Thanks again. SL El 10-03-2016 04:27, nek5000-users at lists.mcs.anl.gov escribi?: > SL, > > I had the same problem before. I've had to set rq = 200. If your flow > is very turbulent, just turn up that value a lot. > > No, it's not physical because you're imposing a divergence on the last > layer of elements. You can just exclude that part of your solution in > your post processing. > > Regards, > > Goran > > >> On Mar 9, 2016, at 21:58, "nek5000-users at lists.mcs.anl.gov" >> wrote: >> >> Hi Neks, >> >> regarding my question about convective boundary conditions: >> >> In the problem that I am solving, there are vortex traveling across >> the boundary. Using O boundary conditions, the solution blows up (due >> to the negative flux of the vortex). On the contrary, if I use ON, the >> simulation continues running, but I get very strong reflections. >> >> In addition, although my flow is laminar, if I use turb_outflow >> subroutine (with O boundary conditions) with rq=2, the simulation >> works better, but at a certain moment, it also crashes. I am wondering >> if I should increase rq to, let say 3, or maybe I should use a >> different boundary condition, i.e. non reflective. >> >> I would like to ask, if I am using turb_outflow subroutine I am >> imposing grad U>0 in the boundary (please correct me if I am wrong). >> The question is, is it physical? What I am doing is >> -pn+(1/Re)(n*grad(U))>0 ? What does it mean? >> >> Finally, I have seen that in 2015 you implemented some non-reflective >> boundary conditions and they were working very well. Please, could you >> help me with this issue? (i.e.: a piece of advise or some procedure to >> follow...) >> >> Thank you very much in advance. >> SL >> _______________________________________________ >> 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 From nek5000-users at lists.mcs.anl.gov Thu Mar 10 00:21:10 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 10 Mar 2016 06:21:10 +0000 Subject: [Nek5000-users] convective boundary conditions In-Reply-To: References: <844db190096319ee1e617b2620d45de1@upm.es>, , Message-ID: Because you impose a divergence in the last layer of elements, it emulates an acceleration (or suction) only in that last layer of elements without affecting the rest of your domain. The effect the two produce is similar in the sense that it ensure that turbulent vortices don't recirculate back into your domain through the outflow boundary. Regards Goran ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, March 10, 2016 1:14 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] convective boundary conditions Hi Goran, thank you for your answer. However I still not understand very well what happens in your simulation if you are using unphysical boundary conditions... Activating turb_outflow subroutine, are you emulating a suction (from the boundary to the inner domain)? In this case, is it not affecting your physical results from your numerical simulation? Please, correct me if I am wrong... One more question, the effect that you are producing with the turb_outflow subroutine, is it similar to applying convective boundary condition? Thanks again. SL El 10-03-2016 04:27, nek5000-users at lists.mcs.anl.gov escribi?: > SL, > > I had the same problem before. I've had to set rq = 200. If your flow > is very turbulent, just turn up that value a lot. > > No, it's not physical because you're imposing a divergence on the last > layer of elements. You can just exclude that part of your solution in > your post processing. > > Regards, > > Goran > > >> On Mar 9, 2016, at 21:58, "nek5000-users at lists.mcs.anl.gov" >> wrote: >> >> Hi Neks, >> >> regarding my question about convective boundary conditions: >> >> In the problem that I am solving, there are vortex traveling across >> the boundary. Using O boundary conditions, the solution blows up (due >> to the negative flux of the vortex). On the contrary, if I use ON, the >> simulation continues running, but I get very strong reflections. >> >> In addition, although my flow is laminar, if I use turb_outflow >> subroutine (with O boundary conditions) with rq=2, the simulation >> works better, but at a certain moment, it also crashes. I am wondering >> if I should increase rq to, let say 3, or maybe I should use a >> different boundary condition, i.e. non reflective. >> >> I would like to ask, if I am using turb_outflow subroutine I am >> imposing grad U>0 in the boundary (please correct me if I am wrong). >> The question is, is it physical? What I am doing is >> -pn+(1/Re)(n*grad(U))>0 ? What does it mean? >> >> Finally, I have seen that in 2015 you implemented some non-reflective >> boundary conditions and they were working very well. Please, could you >> help me with this issue? (i.e.: a piece of advise or some procedure to >> follow...) >> >> Thank you very much in advance. >> SL >> _______________________________________________ >> 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 _______________________________________________ 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 Thu Mar 10 06:16:06 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 10 Mar 2016 13:16:06 +0100 Subject: [Nek5000-users] convective boundary conditions In-Reply-To: References: <844db190096319ee1e617b2620d45de1@upm.es> Message-ID: Dear all, indeed we studied different way to have "better" outflow conditions for Nek. In particular we were interested in open (or semi-open) flows in which the nozzle condition does not properly work (at least to our experience, as the free-stream was disturbed). We have thus studied two different alternatives: the convective condition and the stabilized stress-free condition. The former follows essentially standard text books, whereas the latter was presented in a paper by Dong et al. in JCP (2014). If you are interested in any of these, please let me know a little bit better what case you are studying, such that we could prepare a code that suits your situation. Best, Philipp KTH Mechanics On 2016-03-10 07:21, nek5000-users at lists.mcs.anl.gov wrote: > Because you impose a divergence in the last layer of elements, it > emulates an acceleration (or suction) only in that last layer of > elements without affecting the rest of your domain. > > The effect the two produce is similar in the sense that it ensure > that turbulent vortices don't recirculate back into your domain > through the outflow boundary. > > Regards > > Goran > > ________________________________________ From: > nek5000-users-bounces at lists.mcs.anl.gov > on behalf of > nek5000-users at lists.mcs.anl.gov > Sent: Thursday, March 10, 2016 1:14 AM To: > nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] > convective boundary conditions > > Hi Goran, > > thank you for your answer. However I still not understand very well > what happens in your simulation if you are using unphysical boundary > conditions... Activating turb_outflow subroutine, are you emulating > a suction (from the boundary to the inner domain)? In this case, is > it not affecting your physical results from your numerical > simulation? Please, correct me if I am wrong... > > One more question, the effect that you are producing with the > turb_outflow subroutine, is it similar to applying convective > boundary condition? > > Thanks again. SL > > > > El 10-03-2016 04:27, nek5000-users at lists.mcs.anl.gov escribi?: >> SL, >> >> I had the same problem before. I've had to set rq = 200. If your >> flow is very turbulent, just turn up that value a lot. >> >> No, it's not physical because you're imposing a divergence on the >> last layer of elements. You can just exclude that part of your >> solution in your post processing. >> >> Regards, >> >> Goran >> >> >>> On Mar 9, 2016, at 21:58, "nek5000-users at lists.mcs.anl.gov" >>> wrote: >>> >>> Hi Neks, >>> >>> regarding my question about convective boundary conditions: >>> >>> In the problem that I am solving, there are vortex traveling >>> across the boundary. Using O boundary conditions, the solution >>> blows up (due to the negative flux of the vortex). On the >>> contrary, if I use ON, the simulation continues running, but I >>> get very strong reflections. >>> >>> In addition, although my flow is laminar, if I use turb_outflow >>> subroutine (with O boundary conditions) with rq=2, the >>> simulation works better, but at a certain moment, it also >>> crashes. I am wondering if I should increase rq to, let say 3, or >>> maybe I should use a different boundary condition, i.e. non >>> reflective. >>> >>> I would like to ask, if I am using turb_outflow subroutine I am >>> imposing grad U>0 in the boundary (please correct me if I am >>> wrong). The question is, is it physical? What I am doing is >>> -pn+(1/Re)(n*grad(U))>0 ? What does it mean? >>> >>> Finally, I have seen that in 2015 you implemented some >>> non-reflective boundary conditions and they were working very >>> well. Please, could you help me with this issue? (i.e.: a piece >>> of advise or some procedure to follow...) >>> >>> Thank you very much in advance. SL >>> _______________________________________________ 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 > > > _______________________________________________ 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 > From nek5000-users at lists.mcs.anl.gov Thu Mar 10 06:35:15 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 10 Mar 2016 23:35:15 +1100 Subject: [Nek5000-users] convective boundary conditions In-Reply-To: References: <844db190096319ee1e617b2620d45de1@upm.es> Message-ID: Dear Philipp, thank you very much. I am running a 3D numerical simulation of a jet with time dependent velocity conditions at the inlet surface (periodically ux=uy=uz=0). Since it is an open flow, I am having some troubles with the boundary conditions. Specially at the outlet surface, where I have a couple of vortex traveling across the boundary. The flow is laminar, however I have used ON boundary conditions and I have some reflections. I have also tried with turb_outflow subroutine, rq=2 (the simulation crash) and rq=100 (it is affecting the flow and it also has some reflections). I think that the solution to solve this problem could be using convective boundary conditions at the outlet... Regards, SL El 10-03-2016 23:16, nek5000-users at lists.mcs.anl.gov escribi?: > Dear all, > indeed we studied different way to have "better" outflow conditions > for Nek. In particular we were interested in open (or semi-open) flows > in which the nozzle condition does not properly work (at least to our > experience, as the free-stream was disturbed). We have thus studied > two different alternatives: the convective condition and the > stabilized stress-free condition. The former follows essentially > standard text books, whereas the latter was presented in a paper by > Dong et al. in JCP (2014). If you are interested in any of these, > please let me know a little bit better what case you are studying, > such that we could prepare a code that suits your situation. > > Best, > Philipp > KTH Mechanics > > On 2016-03-10 07:21, nek5000-users at lists.mcs.anl.gov wrote: >> Because you impose a divergence in the last layer of elements, it >> emulates an acceleration (or suction) only in that last layer of >> elements without affecting the rest of your domain. >> >> The effect the two produce is similar in the sense that it ensure >> that turbulent vortices don't recirculate back into your domain >> through the outflow boundary. >> >> Regards >> >> Goran >> >> ________________________________________ From: >> nek5000-users-bounces at lists.mcs.anl.gov >> on behalf of >> nek5000-users at lists.mcs.anl.gov >> Sent: Thursday, March 10, 2016 1:14 AM To: >> nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] >> convective boundary conditions >> >> Hi Goran, >> >> thank you for your answer. However I still not understand very well >> what happens in your simulation if you are using unphysical boundary >> conditions... Activating turb_outflow subroutine, are you emulating >> a suction (from the boundary to the inner domain)? In this case, is >> it not affecting your physical results from your numerical >> simulation? Please, correct me if I am wrong... >> >> One more question, the effect that you are producing with the >> turb_outflow subroutine, is it similar to applying convective >> boundary condition? >> >> Thanks again. SL >> >> >> >> El 10-03-2016 04:27, nek5000-users at lists.mcs.anl.gov escribi?: >>> SL, >>> >>> I had the same problem before. I've had to set rq = 200. If your >>> flow is very turbulent, just turn up that value a lot. >>> >>> No, it's not physical because you're imposing a divergence on the >>> last layer of elements. You can just exclude that part of your >>> solution in your post processing. >>> >>> Regards, >>> >>> Goran >>> >>> >>>> On Mar 9, 2016, at 21:58, "nek5000-users at lists.mcs.anl.gov" >>>> wrote: >>>> >>>> Hi Neks, >>>> >>>> regarding my question about convective boundary conditions: >>>> >>>> In the problem that I am solving, there are vortex traveling >>>> across the boundary. Using O boundary conditions, the solution >>>> blows up (due to the negative flux of the vortex). On the >>>> contrary, if I use ON, the simulation continues running, but I >>>> get very strong reflections. >>>> >>>> In addition, although my flow is laminar, if I use turb_outflow >>>> subroutine (with O boundary conditions) with rq=2, the >>>> simulation works better, but at a certain moment, it also >>>> crashes. I am wondering if I should increase rq to, let say 3, or >>>> maybe I should use a different boundary condition, i.e. non >>>> reflective. >>>> >>>> I would like to ask, if I am using turb_outflow subroutine I am >>>> imposing grad U>0 in the boundary (please correct me if I am >>>> wrong). The question is, is it physical? What I am doing is >>>> -pn+(1/Re)(n*grad(U))>0 ? What does it mean? >>>> >>>> Finally, I have seen that in 2015 you implemented some >>>> non-reflective boundary conditions and they were working very >>>> well. Please, could you help me with this issue? (i.e.: a piece >>>> of advise or some procedure to follow...) >>>> >>>> Thank you very much in advance. SL >>>> _______________________________________________ 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 >> >> >> _______________________________________________ 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 >> > _______________________________________________ > 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 Thu Mar 10 08:46:43 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 10 Mar 2016 15:46:43 +0100 Subject: [Nek5000-users] Periodic B.C and Genmap Issue Message-ID: Hi Paul, It is looks like that the n2to3 not generate the 3D mesh with periodic boundary conditions correctly by rotating. First I tried to generate a 3D mesh, then after applied genmap it appears the similar error. Following the discussions some years ago, it seems I need to update the genmap.f, Have you update the new version, or Would you like to post the genmap.f again? thanks! Wei n2to3 This is the code that establishes proper element connectivities, as of Oct., 2006. Input old (source) file name: box Input new (output) file name: boxss For ASCII output only: 0; For .rea/.re2: 1 0 input number of levels: (1, 2, 3,...; < 0 for circular sweep.): -20 input z min: 0 input z max: 90 input gain (0=custom,1=uniform,other=geometric spacing): 1 This is for CEM: yes or no: no Enter Z(5) FLUID boundary condition (P,v,O,ect): P this is FLUID cbz: P P <--- F F 0 1 ifheat,ifmhd 360 elements written to boxss.rea genmap Input (.rea) file name: boxss Input mesh tolerance (default 0.2): NOTE: smaller is better, but generous is more forgiving for bad meshes. 0.1 reading .rea file data ... start locglob_lexico: 8 360 2880 0.10000000000000001 locglob: 1 1 2880 locglob: 2 59 2880 locglob: 3 84 2880 locglob: 1 588 2880 locglob: 2 588 2880 locglob: 3 588 2880 locglob: 1 588 2880 locglob: 2 588 2880 locglob: 3 588 2880 done locglob_lexico: 588 588 2880 8 start periodic vtx: 360 588 1 4 4 Matrix: x0 1 x0 1.2084E-06 1.2084E-06 1.6729E-06 1.6729E-06 2 x0 -1.2362E-03 -1.2362E-03 1.2363E-03 1.2363E-03 3 x0 -0.0000E+00 -0.0000E+00 -0.0000E+00 -0.0000E+00 4 x0 -2.6465E-03 2.6465E-03 2.6465E-03 -2.6465E-03 343 4 4 Matrix: x1 1 x1 1.2084E-06 1.6729E-06 1.6729E-06 1.2084E-06 2 x1 5.4038E-11 -5.4038E-11 -5.4038E-11 5.4038E-11 3 x1 1.2362E-03 -1.2363E-03 -1.2363E-03 1.2362E-03 4 x1 -2.6465E-03 -2.6465E-03 2.6465E-03 2.6465E-03 1 4 4 Matrix: z0 1 z0 1.2084E-06 1.2084E-06 1.6729E-06 1.6729E-06 2 z0 1.4000E-02 1.4000E-02 1.6473E-02 1.6473E-02 3 z0 -0.0000E+00 -0.0000E+00 -0.0000E+00 -0.0000E+00 4 z0 -1.1000E-01 -1.0471E-01 -1.0471E-01 -1.1000E-01 343 4 4 Matrix: z1 1 z1 1.2084E-06 1.6729E-06 1.6729E-06 1.2084E-06 2 z1 -6.1196E-10 -7.2004E-10 -7.2004E-10 -6.1196E-10 3 z1 -1.4000E-02 -1.6473E-02 -1.6473E-02 -1.4000E-02 4 z1 -1.1000E-01 -1.1000E-01 -1.0471E-01 -1.0471E-01 1 5 3 1.00000000E-03 1.10000000E-01 abort: FACE MATCH FAIL 343 6 5 1.10000000E-04 3.49664311E-03 abort: FACE MATCH FAIL 0 quit ==================================================== Hi, Yes, got it now. I don't know why it wasn't working either. I use the same thing to compress files, either way it's good now. Thanks Paul. - Michael ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Tuesday, June 22, 2010 10:40:57 AM GMT -06:00 Guadalajara / Mexico City / Monterrey Subject: Re: [Nek5000-users] Periodic BC & Genmap issue Hi Michael, not sure why gunzip didn't work - it worked here... but I've put the unzipped version in: www.mcs.anl.gov/~fischer/genmap.f Let me know if that works for you. Cheers, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 10 09:58:59 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 10 Mar 2016 15:58:59 +0000 Subject: [Nek5000-users] Monitoring solutions during runtime Message-ID: Hi all, I seem to have forgotten the command to monitor the solution results during runtime. I vaguly recall that it was something along the lines of grep -___ logfile tail Could someone help fill in the blanks? Thanks in advance, Sincerely, -- *Amitvikram Dutta* *MASc Candidate* *Graduate Research Assistant * *Okanagan CFD Laboratory* *University of British Columbia | Okanagan Campus* -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 10 12:11:31 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 10 Mar 2016 19:11:31 +0100 Subject: [Nek5000-users] Nek5000-users Digest, Vol 85, Issue 13 In-Reply-To: References: Message-ID: Try: grep Step logfile | tail Ciao Francesco 2016-03-10 19:00 GMT+01:00 : > 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. Monitoring solutions during runtime > (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 10 Mar 2016 15:58:59 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: [Nek5000-users] Monitoring solutions during runtime > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I seem to have forgotten the command to monitor the solution results during > runtime. I vaguly recall that it was something along the lines of > > grep -___ logfile tail > > Could someone help fill in the blanks? > > > Thanks in advance, > Sincerely, > -- > > *Amitvikram Dutta* > > *MASc Candidate* > > *Graduate Research Assistant * > > *Okanagan CFD Laboratory* > > *University of British Columbia | Okanagan Campus* > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160310/cadffdcb/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > 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 85, Issue 13 > ********************************************* > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 10 12:16:46 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 10 Mar 2016 19:16:46 +0100 Subject: [Nek5000-users] Nek5000-users Digest, Vol 85, Issue 13 In-Reply-To: References: Message-ID: in any case, you'll find everything on the Quick Start guide http://www.mcs.anl.gov/~oanam/old_page/index.php/Quick_Start F 2016-03-10 19:11 GMT+01:00 Francesco Picella : > Try: > grep Step logfile | tail > > Ciao > Francesco > > 2016-03-10 19:00 GMT+01:00 : > >> 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. Monitoring solutions during runtime >> (nek5000-users at lists.mcs.anl.gov) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Thu, 10 Mar 2016 15:58:59 +0000 >> From: nek5000-users at lists.mcs.anl.gov >> To: "nek5000-users at lists.mcs.anl.gov" >> >> Subject: [Nek5000-users] Monitoring solutions during runtime >> Message-ID: >> >> Content-Type: text/plain; charset="utf-8" >> >> Hi all, >> >> I seem to have forgotten the command to monitor the solution results >> during >> runtime. I vaguly recall that it was something along the lines of >> >> grep -___ logfile tail >> >> Could someone help fill in the blanks? >> >> >> Thanks in advance, >> Sincerely, >> -- >> >> *Amitvikram Dutta* >> >> *MASc Candidate* >> >> *Graduate Research Assistant * >> >> *Okanagan CFD Laboratory* >> >> *University of British Columbia | Okanagan Campus* >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160310/cadffdcb/attachment-0001.html >> > >> >> ------------------------------ >> >> _______________________________________________ >> 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 85, Issue 13 >> ********************************************* >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 11 05:54:57 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 11 Mar 2016 12:54:57 +0100 Subject: [Nek5000-users] Nek5000-users Digest, Vol 85, Issue 13 In-Reply-To: References: Message-ID: or my favorite expression: tail -f logfile | grep Step Philipp On 2016-03-10 19:11, nek5000-users at lists.mcs.anl.gov wrote: > Try: > grep Step logfile | tail > > Ciao > Francesco > > 2016-03-10 19:00 GMT+01:00 >: > > 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. Monitoring solutions during runtime > (nek5000-users at lists.mcs.anl.gov > ) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 10 Mar 2016 15:58:59 +0000 > From: nek5000-users at lists.mcs.anl.gov > > To: "nek5000-users at lists.mcs.anl.gov > " > > > Subject: [Nek5000-users] Monitoring solutions during runtime > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I seem to have forgotten the command to monitor the solution results > during > runtime. I vaguly recall that it was something along the lines of > > grep -___ logfile tail > > Could someone help fill in the blanks? > > > Thanks in advance, > Sincerely, > -- > > *Amitvikram Dutta* > > *MASc Candidate* > > *Graduate Research Assistant * > > *Okanagan CFD Laboratory* > > *University of British Columbia | Okanagan Campus* > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > _______________________________________________ > 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 85, Issue 13 > ********************************************* > > > > > _______________________________________________ > 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 Mar 11 09:26:28 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 11 Mar 2016 16:26:28 +0100 Subject: [Nek5000-users] convective boundary conditions In-Reply-To: References: <844db190096319ee1e617b2620d45de1@upm.es> Message-ID: Hi SL, I recommend as a first step the stabilized O condition, just to try. That is very easy to test. Please contact me directly via email so that we can discuss that (pschlatt at mech.kth.se). Best regards, Philipp On 2016-03-10 13:35, nek5000-users at lists.mcs.anl.gov wrote: > Dear Philipp, > > thank you very much. I am running a 3D numerical simulation of a jet > with time dependent velocity conditions at the inlet surface > (periodically ux=uy=uz=0). Since it is an open flow, I am having some > troubles with the boundary conditions. Specially at the outlet surface, > where I have a couple of vortex traveling across the boundary. The flow > is laminar, however I have used ON boundary conditions and I have some > reflections. I have also tried with turb_outflow subroutine, rq=2 (the > simulation crash) and rq=100 (it is affecting the flow and it also has > some reflections). I think that the solution to solve this problem could > be using convective boundary conditions at the outlet... > > Regards, > SL > > El 10-03-2016 23:16, nek5000-users at lists.mcs.anl.gov escribi?: >> Dear all, >> indeed we studied different way to have "better" outflow conditions >> for Nek. In particular we were interested in open (or semi-open) flows >> in which the nozzle condition does not properly work (at least to our >> experience, as the free-stream was disturbed). We have thus studied >> two different alternatives: the convective condition and the >> stabilized stress-free condition. The former follows essentially >> standard text books, whereas the latter was presented in a paper by >> Dong et al. in JCP (2014). If you are interested in any of these, >> please let me know a little bit better what case you are studying, >> such that we could prepare a code that suits your situation. >> >> Best, >> Philipp >> KTH Mechanics >> >> On 2016-03-10 07:21, nek5000-users at lists.mcs.anl.gov wrote: >>> Because you impose a divergence in the last layer of elements, it >>> emulates an acceleration (or suction) only in that last layer of >>> elements without affecting the rest of your domain. >>> >>> The effect the two produce is similar in the sense that it ensure >>> that turbulent vortices don't recirculate back into your domain >>> through the outflow boundary. >>> >>> Regards >>> >>> Goran >>> >>> ________________________________________ From: >>> nek5000-users-bounces at lists.mcs.anl.gov >>> on behalf of >>> nek5000-users at lists.mcs.anl.gov >>> Sent: Thursday, March 10, 2016 1:14 AM To: >>> nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] >>> convective boundary conditions >>> >>> Hi Goran, >>> >>> thank you for your answer. However I still not understand very well >>> what happens in your simulation if you are using unphysical boundary >>> conditions... Activating turb_outflow subroutine, are you emulating >>> a suction (from the boundary to the inner domain)? In this case, is >>> it not affecting your physical results from your numerical >>> simulation? Please, correct me if I am wrong... >>> >>> One more question, the effect that you are producing with the >>> turb_outflow subroutine, is it similar to applying convective >>> boundary condition? >>> >>> Thanks again. SL >>> >>> >>> >>> El 10-03-2016 04:27, nek5000-users at lists.mcs.anl.gov escribi?: >>>> SL, >>>> >>>> I had the same problem before. I've had to set rq = 200. If your >>>> flow is very turbulent, just turn up that value a lot. >>>> >>>> No, it's not physical because you're imposing a divergence on the >>>> last layer of elements. You can just exclude that part of your >>>> solution in your post processing. >>>> >>>> Regards, >>>> >>>> Goran >>>> >>>> >>>>> On Mar 9, 2016, at 21:58, "nek5000-users at lists.mcs.anl.gov" >>>>> wrote: >>>>> >>>>> Hi Neks, >>>>> >>>>> regarding my question about convective boundary conditions: >>>>> >>>>> In the problem that I am solving, there are vortex traveling >>>>> across the boundary. Using O boundary conditions, the solution >>>>> blows up (due to the negative flux of the vortex). On the >>>>> contrary, if I use ON, the simulation continues running, but I >>>>> get very strong reflections. >>>>> >>>>> In addition, although my flow is laminar, if I use turb_outflow >>>>> subroutine (with O boundary conditions) with rq=2, the >>>>> simulation works better, but at a certain moment, it also >>>>> crashes. I am wondering if I should increase rq to, let say 3, or >>>>> maybe I should use a different boundary condition, i.e. non >>>>> reflective. >>>>> >>>>> I would like to ask, if I am using turb_outflow subroutine I am >>>>> imposing grad U>0 in the boundary (please correct me if I am >>>>> wrong). The question is, is it physical? What I am doing is >>>>> -pn+(1/Re)(n*grad(U))>0 ? What does it mean? >>>>> >>>>> Finally, I have seen that in 2015 you implemented some >>>>> non-reflective boundary conditions and they were working very >>>>> well. Please, could you help me with this issue? (i.e.: a piece >>>>> of advise or some procedure to follow...) >>>>> >>>>> Thank you very much in advance. SL >>>>> _______________________________________________ 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 >>> >>> >>> _______________________________________________ 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 >>> >> _______________________________________________ >> 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 From nek5000-users at lists.mcs.anl.gov Tue Mar 15 01:35:39 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 15 Mar 2016 09:35:39 +0300 Subject: [Nek5000-users] =?utf-8?q?LES_and_heat_transfer_model?= Message-ID: Hi Neks,? we are students of second year and we a trying to learn nek5000 for different simulations. We have already studied DNS and LES, dynamic Smagorinsky model and noticed that LES and DNS results for velocity were very closed. Then we added a heat transfer with a constant wall-temp and saw that temperature's profiles from LES and DNS are very different (also theta-theta rms). We decided to write a model for temperature, like Smagorinsky model for viscosity, but don't have enough information about it and how to add model in the code. Could you help us? Thank you very much, VV -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Mar 15 02:49:02 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 15 Mar 2016 18:49:02 +1100 Subject: [Nek5000-users] linear stability tool Message-ID: Hi Neks, I'm trying to use the linear stability tool of Nek5000. To start with, I am trying to run the ext_cyl example. However, I have found the following problem: ERROR: arnoldi assumes constant base flow. I have found on the README tutorial that the base flow has to be specified on the .rea file. I have included a file in the PRESOLVE/RESTART option, however I still have the same error. What should I modify? Finally, I have also used a subroutine defined in the .usr file that reads the file containing the base flow. However, the error persist... Could you help me, please? Cheers SL From nek5000-users at lists.mcs.anl.gov Tue Mar 15 03:06:51 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 15 Mar 2016 09:06:51 +0100 Subject: [Nek5000-users] linear stability tool In-Reply-To: References: Message-ID: Hi To force base flow to be constant you have to set negative param(31) in your ###.rea file. Something like -1.00000 p031 NPERT: #perturbation modes Of course you need the base flow as well. It could be analytical one set in useric, or just a field read during initialisation. Regards Adam On 2016-03-15 08:49, nek5000-users at lists.mcs.anl.gov wrote: > Hi Neks, > > I'm trying to use the linear stability tool of Nek5000. > > To start with, I am trying to run the ext_cyl example. However, I have > found the following problem: > > ERROR: arnoldi assumes constant base flow. > > I have found on the README tutorial that the base flow has to be > specified on the .rea file. I have included a file in the > PRESOLVE/RESTART option, however I still have the same error. > > What should I modify? > > Finally, I have also used a subroutine defined in the .usr file that > reads the file containing the base flow. However, the error persist... > > Could you help me, please? > > Cheers > SL > _______________________________________________ > 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 Mar 15 07:18:33 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 15 Mar 2016 23:18:33 +1100 Subject: [Nek5000-users] linear stability tool In-Reply-To: References: Message-ID: Hi Adam, thank you, it works now. However I still have a question about this tool. My base flow is time dependent, so I did in usrchk call opcopy (u,v,w,vx,vy,vz) u=u*function(time) v=v*function(time) w=w*function(time) call gop(u,work,'+ ',n) call gop(v,work,'+ ',n) call gop(w,work,'+ ',n) do e=1,nelv eg = lglel(e) call copy(vx(1,1,1,e),u(1,1,1,eg),nxyz) call copy(vy(1,1,1,e),v(1,1,1,eg),nxyz) call copy(vz(1,1,1,e),w(1,1,1,eg),nxyz) enddo However, I am not sure how to specify this velocity filed as the base flow each time step... Thank you in advance. SL El 15-03-2016 19:06, nek5000-users at lists.mcs.anl.gov escribi?: > Hi > > To force base flow to be constant you have to set negative param(31) > in your ###.rea file. Something like > -1.00000 p031 NPERT: #perturbation modes > Of course you need the base flow as well. It could be analytical one > set in useric, or just a field read during initialisation. > Regards > Adam > > > On 2016-03-15 08:49, nek5000-users at lists.mcs.anl.gov wrote: >> Hi Neks, >> >> I'm trying to use the linear stability tool of Nek5000. >> >> To start with, I am trying to run the ext_cyl example. However, I have >> found the following problem: >> >> ERROR: arnoldi assumes constant base flow. >> >> I have found on the README tutorial that the base flow has to be >> specified on the .rea file. I have included a file in the >> PRESOLVE/RESTART option, however I still have the same error. >> >> What should I modify? >> >> Finally, I have also used a subroutine defined in the .usr file that >> reads the file containing the base flow. However, the error persist... >> >> Could you help me, please? >> >> Cheers >> SL >> _______________________________________________ >> 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 From nek5000-users at lists.mcs.anl.gov Tue Mar 15 09:58:45 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 15 Mar 2016 15:58:45 +0100 Subject: [Nek5000-users] Courant number Message-ID: Hi to all, from theory i know that courant number must be always less than 1. Now, in many examples, i saw that Courant number is fixed and sometimes the value is less than 1 and sometime greater than 1, for example in turbchannel, it is fixed to 2. So my question is, why? With a Courant number greater than 1, i should have instability?! How nek5000 estimate the Courant number? Nek in fuction of change the value? Thanks From nek5000-users at lists.mcs.anl.gov Tue Mar 15 10:25:24 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 15 Mar 2016 16:25:24 +0100 (CET) Subject: [Nek5000-users] dns mode vs perturbative one Message-ID: Hi neks, I'm trying to perform two simulations with Nek5000. The first one is a DNS of turbulent plane Poiseuille flow with the classical dns code (npert = 0), and the second one is the same but in nonlinear perturbative form (npert = -1), using the classical parabolic profile as a base flow. I'm using the same spatial discretisation. The only difference is the time order integration: 3 in the first case and 2 in the second. I'm using the same parameter in the .rea file in the turbChannel example. My questions are: 1) Why in the first formulation (npert=0) i'm able to use a cfl greater than 1, and for the second (npert=-1) I get an error in the gmres solver (it does not converge) for cfl greater than 0.4 after few time steps. 2) Even when I use a cfl lower than 0.4 for the perturbative form, the gmres solver fails again when the flow reaches a fully turbulent state and I don't understand why. I hope to have been clear, Thank. -- 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 at poliba.itIn joint supervision with theEcole Nationale Sup?rieure d'Arts et M?tiers de Paris - ParistechTel.: +33-144246436Mob.: +33-789822134Dynfluid Laboratory151 Boulevard de l'H?pital - 75013 Paris (France)mirko.farano at ensam.eu -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Mar 15 14:14:43 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 15 Mar 2016 20:14:43 +0100 Subject: [Nek5000-users] Problem when running with variable fluid properties Message-ID: Hi, After successfully running some DNS cases of a turbulent pipe with heat transfer in NEK ( http://www.sciencedirect.com/science/article/pii/S0142727X15000533), I am now struggling to run a similar case but with variable fluid properties (Re and Pe being functions of temperature). I am currently using Pn-Pn2 (lx2=lx1-2 in SIZE) method and stress formulation (IFSTRS=true), together with IFUSERVP=true (p030=1.0 in REA file) to be able to define the viscosity and conductivity functions. Initial flow conditions are taken from a previous constant fluid properties turbulent pipe case. My problem is that, when setting IFUSERVP=true, the flow velocities go to zero in very few time steps, even though I was setting constant fluid properties in USERVP subroutine for trial purposes. I have checked that the forcing in the momentum equation (subroutine USERF) is correctly set. Could you please give me some indications as to what I can be doing wrong? Thanks in advance. Regards Antonio -- ANTONIO ANTORANZ PERALES Universidad Carlos III de Madrid -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Mar 15 14:26:47 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 15 Mar 2016 19:26:47 +0000 Subject: [Nek5000-users] Nek5000 simulations of High Re flows ~ 10^5 Message-ID: Hello all, I was wondering if anyone on the mailing list has experience with simulating high Re flows of the order 10^5. I'm studying flow instabilities over airfoils and have been struggling to obtain a stable simulation for these high Re flows. Its worthwhile to note that I have simulated low Re flows using identical geometries. Making the mesh finer or increasing the order of the method does not seem to be doing the trick. The simulations usually diverge after something like 5 seconds of flow time. If there are any specific conditions/settings that I should be looking at, I'd really appreciate the information. Thanks, -- *Amitvikram Dutta* *MASc Candidate* *Graduate Research Assistant * *Okanagan CFD Laboratory* *University of British Columbia | Okanagan Campus* -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 16 02:05:15 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Mar 2016 18:05:15 +1100 Subject: [Nek5000-users] param 31 Message-ID: Hi Neks, I would like to use Nek5000 to perform the stability analysis based on a time periodic base flow. To do this, I need to introduce my base flow that changes with time, thus I need to update the base flow each flow iteration. I have seen that if param(31)=-1, nek5000 considers constant base flow, however if param(31)=1 it considers time variable base flow. Could you explain me the difference? I suppose that if param(31)=-1 I introduce the base flow in the first time step, however, what should I do if param(31)=1? I did the following tests. Assuming that u,v,w are the vectors containing the base flow, I have tried two different things: 1) considering param(31) = -1 call opcopy(vx,vy,vz,u,v,w) ! update the base flow each time iteration 2) considering param(31) = 1 call opcopy(vx,vy,vz,u,v,w) ! update the base flow each time iteration I obtain different results, and I would like to know the difference and what would be the correct option to solve my problem. Even if I don't update the base flow, the results that I obtain are different using param(31)= +1, -1. Finally, I have found that vxp, vyp, vzp are the perturbed variables u', v', w' (please, correct me if I am wrong). Is there any way to plot only these variables? Thank you in advance. Cheers SL From nek5000-users at lists.mcs.anl.gov Wed Mar 16 04:02:51 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Mar 2016 10:02:51 +0100 Subject: [Nek5000-users] linear stability tool In-Reply-To: References: Message-ID: Hi I didn't work with time dependent base flow, so I'm not sure if there are some serious problem in implementation or not. First of all, the base flow is stored in the arrays for non linear solution (vx, vy, vz) and the perturbation in (vxp,vyp,vzp) (both in SOLN). Negative value of param(31) sets the logical ifbase to .false. excluding call to fluid in nek_advance. In this case only fluidp is executed. To get time dependent base flow you could set positive param(31) and comment ifbase check in arnoldi initialisation routine. This would activate fluid and evolve both perturbation and base flow. In this case you would need to resent vx,vy,vz to your initial conditions for base flow at the end of every arnoldi cycle (where pressure is set to zero). Other solution would be keeping ifbase=.false. and recalculating vx, vy,vz at every step within arnoldi cycle. That what you wrote in your mail, but this should be mostly local operation. I do not see any reason to use gop routines. If you have analytical solution for base flow you simply replace vx,vy,vz with new values base on the position of the gll point (xm1,ym1,zm1 arrays in GEOM) and the time within the given cycle. If you are not 100% sure the function is continuous at the element faces, edges and vertices, you can add averaging step: ! face averaging call opdssum(VX,VY,VZ) call opcolv (VX,VY,VZ,VMULT) vmult is inverse of grid point multiplicity and is stored in SOLN. No more global operations is required. However, I'm not sure if this method would work, as ifbase shows up in navier5.f as well, and one would need to check the code to see what variables are really used. I would guess it should work, but I cannot guarantee it. You can try. You have to be sure the base flow evolution is exactly the same in each arnoldi cycle, to mimic the matrix operation properly. Regards Adam On 2016-03-15 13:18, nek5000-users at lists.mcs.anl.gov wrote: > Hi Adam, > > thank you, it works now. > > However I still have a question about this tool. My base flow is time > dependent, so I did in usrchk > > call opcopy (u,v,w,vx,vy,vz) > u=u*function(time) > v=v*function(time) > w=w*function(time) > > call gop(u,work,'+ ',n) > call gop(v,work,'+ ',n) > call gop(w,work,'+ ',n) > > do e=1,nelv > eg = lglel(e) > call copy(vx(1,1,1,e),u(1,1,1,eg),nxyz) > call copy(vy(1,1,1,e),v(1,1,1,eg),nxyz) > call copy(vz(1,1,1,e),w(1,1,1,eg),nxyz) > enddo > > However, I am not sure how to specify this velocity filed as the base > flow each time step... > > Thank you in advance. > SL > > El 15-03-2016 19:06, nek5000-users at lists.mcs.anl.gov escribi?: >> Hi >> >> To force base flow to be constant you have to set negative param(31) >> in your ###.rea file. Something like >> -1.00000 p031 NPERT: #perturbation modes >> Of course you need the base flow as well. It could be analytical one >> set in useric, or just a field read during initialisation. >> Regards >> Adam >> >> >> On 2016-03-15 08:49, nek5000-users at lists.mcs.anl.gov wrote: >>> Hi Neks, >>> >>> I'm trying to use the linear stability tool of Nek5000. >>> >>> To start with, I am trying to run the ext_cyl example. However, I >>> have found the following problem: >>> >>> ERROR: arnoldi assumes constant base flow. >>> >>> I have found on the README tutorial that the base flow has to be >>> specified on the .rea file. I have included a file in the >>> PRESOLVE/RESTART option, however I still have the same error. >>> >>> What should I modify? >>> >>> Finally, I have also used a subroutine defined in the .usr file that >>> reads the file containing the base flow. However, the error persist... >>> >>> Could you help me, please? >>> >>> Cheers >>> SL >>> _______________________________________________ >>> 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 > > > _______________________________________________ > 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 Wed Mar 16 09:47:21 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Mar 2016 15:47:21 +0100 Subject: [Nek5000-users] Nek5000 simulations of High Re flows ~ 10^5 In-Reply-To: References: Message-ID: Hi, what type of problems do you have? Are you looking at a 3D geometry? Do you get wiggles, which then lead to a blow up? Best, Philipp On 2016-03-15 20:26, nek5000-users at lists.mcs.anl.gov wrote: > Hello all, > > I was wondering if anyone on the mailing list has experience with > simulating high Re flows of the order 10^5. I'm studying flow > instabilities over airfoils and have been struggling to obtain a stable > simulation for these high Re flows. > > Its worthwhile to note that I have simulated low Re flows using > identical geometries. Making the mesh finer or increasing the order of > the method does not seem to be doing the trick. The simulations usually > diverge after something like 5 seconds of flow time. > > If there are any specific conditions/settings that I should be looking > at, I'd really appreciate the information. > > Thanks, > -- > > *Amitvikram Dutta* > > *MASc Candidate** > * > > *Graduate Research Assistant * > > *Okanagan CFD Laboratory* > > *University of British Columbia | Okanagan Campus*** > > > > _______________________________________________ > 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 Wed Mar 16 10:04:39 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Mar 2016 15:04:39 +0000 Subject: [Nek5000-users] Nek5000 simulations of High Re flows ~ 10^5 In-Reply-To: References: Message-ID: Hi Philipp, My Geometry is a 2D C Grid of a NACA airfoil. And yes, wiggles leading to a blow up are exactly how I would describe my problems. Sincerely, On Wed, Mar 16, 2016, 7:47 AM wrote: > Hi, > what type of problems do you have? Are you looking at a 3D geometry? Do > you get wiggles, which then lead to a blow up? > > Best, > Philipp > > On 2016-03-15 20:26, nek5000-users at lists.mcs.anl.gov wrote: > > Hello all, > > > > I was wondering if anyone on the mailing list has experience with > > simulating high Re flows of the order 10^5. I'm studying flow > > instabilities over airfoils and have been struggling to obtain a stable > > simulation for these high Re flows. > > > > Its worthwhile to note that I have simulated low Re flows using > > identical geometries. Making the mesh finer or increasing the order of > > the method does not seem to be doing the trick. The simulations usually > > diverge after something like 5 seconds of flow time. > > > > If there are any specific conditions/settings that I should be looking > > at, I'd really appreciate the information. > > > > Thanks, > > -- > > > > *Amitvikram Dutta* > > > > *MASc Candidate** > > * > > > > *Graduate Research Assistant * > > > > *Okanagan CFD Laboratory* > > > > *University of British Columbia | Okanagan Campus*** > > > > > > > > _______________________________________________ > > 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 > -- *Amitvikram Dutta* *MASc Candidate* *Graduate Research Assistant * *Okanagan CFD Laboratory* *University of British Columbia | Okanagan Campus* -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 16 10:09:04 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Mar 2016 16:09:04 +0100 Subject: [Nek5000-users] Nek5000 simulations of High Re flows ~ 10^5 In-Reply-To: References: Message-ID: can you send me a picture of that, perhaps off-list? (pschlatt at mech.kth.se). Thanks, Philipp On 2016-03-16 16:04, nek5000-users at lists.mcs.anl.gov wrote: > Hi Philipp, > > My Geometry is a 2D C Grid of a NACA airfoil. And yes, wiggles leading > to a blow up are exactly how I would describe my problems. > > Sincerely, > > > On Wed, Mar 16, 2016, 7:47 AM > wrote: > > Hi, > what type of problems do you have? Are you looking at a 3D geometry? Do > you get wiggles, which then lead to a blow up? > > Best, > Philipp > > On 2016-03-15 20:26, nek5000-users at lists.mcs.anl.gov > wrote: > > Hello all, > > > > I was wondering if anyone on the mailing list has experience with > > simulating high Re flows of the order 10^5. I'm studying flow > > instabilities over airfoils and have been struggling to obtain a > stable > > simulation for these high Re flows. > > > > Its worthwhile to note that I have simulated low Re flows using > > identical geometries. Making the mesh finer or increasing the > order of > > the method does not seem to be doing the trick. The simulations > usually > > diverge after something like 5 seconds of flow time. > > > > If there are any specific conditions/settings that I should be > looking > > at, I'd really appreciate the information. > > > > Thanks, > > -- > > > > *Amitvikram Dutta* > > > > *MASc Candidate** > > * > > > > *Graduate Research Assistant * > > > > *Okanagan CFD Laboratory* > > > > *University of British Columbia | Okanagan Campus*** > > > > > > > > _______________________________________________ > > 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 > > -- > > *Amitvikram Dutta* > > *MASc Candidate** > * > > *Graduate Research Assistant * > > *Okanagan CFD Laboratory* > > *University of British Columbia | Okanagan Campus*** > > > > _______________________________________________ > 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 Wed Mar 16 16:54:01 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Mar 2016 17:54:01 -0400 Subject: [Nek5000-users] Nek5000 simulations of High Re flows ~ 10^5 In-Reply-To: References: Message-ID: Amitvikram, Hi... I'm doing very high Re on some wind turbine wake flows, and yes, I have resolution problems also. I had to drastically reduce my time step/CFL to prevent blowup. Then, my results showed much more "clutter" (poor resolution), and "exposed" the grid element outlines in isosurface plots; I assume from gradients near the element boundaries... Increasing DOF and reducing grid spacing did help resolve the problem; vortices and other flow structures became much more defined. However, the "exposed grid" is still there, and I have not reduced the grid spacing enough yet to see these artifacts completely removed... See Ya, Murph O'Dea On 3/16/2016 1:00 PM, nek5000-users-request at lists.mcs.anl.gov wrote: > can you send me a picture of that, perhaps off-list? (pschlatt at mech.kth.se). > > Thanks, > > Philipp > > > > On 2016-03-16 16:04,nek5000-users at lists.mcs.anl.gov wrote: > > Hi Philipp, > > > > My Geometry is a 2D C Grid of a NACA airfoil. And yes, wiggles leading > > to a blow up are exactly how I would describe my problems. > > > > Sincerely, > > > > > > On Wed, Mar 16, 2016, 7:47 AM > > wrote: > > > > Hi, > > what type of problems do you have? Are you looking at a 3D geometry? Do > > you get wiggles, which then lead to a blow up? > > > > Best, > > Philipp > > > > On 2016-03-15 20:26,nek5000-users at lists.mcs.anl.gov > > wrote: > > > Hello all, > > > > > > I was wondering if anyone on the mailing list has experience with > > > simulating high Re flows of the order 10^5. I'm studying flow > > > instabilities over airfoils and have been struggling to obtain a > > stable > > > simulation for these high Re flows. > > > > > > Its worthwhile to note that I have simulated low Re flows using > > > identical geometries. Making the mesh finer or increasing the > > order of > > > the method does not seem to be doing the trick. The simulations > > usually > > > diverge after something like 5 seconds of flow time. > > > > > > If there are any specific conditions/settings that I should be > > looking > > > at, I'd really appreciate the information. > > > > > > Thanks, > > > -- > > > > > >*Amitvikram Dutta* > > > > > > *MASc Candidate** > > > * > > > > > > *Graduate Research Assistant * > > > > > >*Okanagan CFD Laboratory* > > > > > > *University of British Columbia | Okanagan Campus*** > > > > > > > > > > > > _______________________________________________ > > > 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 > > > > -- > > > > *Amitvikram Dutta* > > > > *MASc Candidate** > > * > > > > *Graduate Research Assistant * > > > > *Okanagan CFD Laboratory* > > > > *University of British Columbia | Okanagan Campus*** > > > > > > > Re: Nek5000 simulations of High Re flows ~ 10^5 -- Murphy Leo O'Dea PhD Student Oakland University mlodea at oakland.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 16 17:02:15 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 16 Mar 2016 22:02:15 +0000 Subject: [Nek5000-users] Nek5000 simulations of High Re flows ~ 10^5 In-Reply-To: References: Message-ID: Hi Murph, Whats your domain size, and how far did you have to reduce grid spacing? I have an airfoil study with a standard C Grid, and that didn't work with a 30000 element mesh and n = 9 polynomial. My timestep had to go down to 10e-6, and still I got blow-up. What about you? Sincerely, On Wed, Mar 16, 2016 at 2:54 PM wrote: > Amitvikram, > > Hi... I'm doing very high Re on some wind turbine wake flows, and yes, I have resolution problems also. I had to drastically reduce my time step/CFL to prevent blowup. Then, my results showed much more "clutter" (poor resolution), and "exposed" the grid element outlines in isosurface plots; I assume from gradients near the element boundaries... > > Increasing DOF and reducing grid spacing did help resolve the problem; vortices and other flow structures became much more defined. However, the "exposed grid" is still there, and I have not reduced the grid spacing enough yet to see these artifacts completely removed... > > See Ya, > Murph O'Dea > > > > On 3/16/2016 1:00 PM, nek5000-users-request at lists.mcs.anl.gov wrote: > > can you send me a picture of that, perhaps off-list? (pschlatt at mech.kth.se). > > Thanks, > > Philipp > > > > On 2016-03-16 16:04, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Philipp, > > > > My Geometry is a 2D C Grid of a NACA airfoil. And yes, wiggles leading > > to a blow up are exactly how I would describe my problems. > > > > Sincerely, > > > > > > On Wed, Mar 16, 2016, 7:47 AM > wrote: > > > > Hi, > > what type of problems do you have? Are you looking at a 3D geometry? Do > > you get wiggles, which then lead to a blow up? > > > > Best, > > Philipp > > > > On 2016-03-15 20:26, nek5000-users at lists.mcs.anl.gov > > wrote: > > > Hello all, > > > > > > I was wondering if anyone on the mailing list has experience with > > > simulating high Re flows of the order 10^5. I'm studying flow > > > instabilities over airfoils and have been struggling to obtain a > > stable > > > simulation for these high Re flows. > > > > > > Its worthwhile to note that I have simulated low Re flows using > > > identical geometries. Making the mesh finer or increasing the > > order of > > > the method does not seem to be doing the trick. The simulations > > usually > > > diverge after something like 5 seconds of flow time. > > > > > > If there are any specific conditions/settings that I should be > > looking > > > at, I'd really appreciate the information. > > > > > > Thanks, > > > -- > > > > > > **Amitvikram Dutta** > > > > > > *MASc Candidate** > > > * > > > > > > *Graduate Research Assistant * > > > > > > **Okanagan CFD Laboratory** > > > > > > *University of British Columbia | Okanagan Campus*** > > > > > > > > > > > > _______________________________________________ > > > 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 > > > > -- > > > **Amitvikram Dutta** > > > > *MASc Candidate** > > * > > > > *Graduate Research Assistant * > > > **Okanagan CFD Laboratory** > > > > > > *University of British Columbia | Okanagan Campus*** > > > > > > > Re: Nek5000 simulations of High Re flows ~ 10^5 > > > -- > Murphy Leo O'Dea > PhD Student > Oakland Universitymlodea at oakland.edu > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -- *Amitvikram Dutta* *MASc Candidate* *Graduate Research Assistant * *Okanagan CFD Laboratory* *University of British Columbia | Okanagan Campus* -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 17 00:07:29 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 17 Mar 2016 06:07:29 +0100 Subject: [Nek5000-users] linear stability tool In-Reply-To: References: Message-ID: Thank you Adam, to start with the implementation, I am re-defining the base flow (as function of t) each time step. The base flow is time dependent, however, I cannot see any evolution of the perturbation variables. I have set param31=-1. At the beginning of the simulation I am adding some random noise to the perturbed variables in the following way: common /scrns/ uf(lx1,ly1,lz1,lelg),vf(lx1,ly1,lz1,lelg), + wf(lx1,ly1,lz1,lelg) n = nelgv*nx1*ny1*nz1 if (istep.eq.0) then call rzero(uf,n) ! zero-out u on all processors call rzero(vf,n) call rzero(wf,n) eps = 0.1 call add_noise(uf,vf,wf,n,eps) ! Subroutine that calculates random noise variables call gop(uf,work,'+ ',n) call gop(vf,work,'+ ',n) call gop(wf,work,'+ ',n) call opcopy(vxp(1,jp),vyp(1,jp),vzp(1,jp),uf,vf,wf) ! COPY TO PERTURBATION VARIABLES end if In SIZE: lpert=1 However the perturbed variables don't seem to change and they don't seem to have any effect on the flow. If I plot my results, I can only see the base flow varying with time (following its definition), but nothing else. In addition, vz is always maintained to 0 (or to any initial condition). Should I initialize (or define) the perturbation variables in a different way? Best regards, SL El 16-03-2016 10:02, nek5000-users at lists.mcs.anl.gov escribi?: > Hi > > I didn't work with time dependent base flow, so I'm not sure if there > are some serious problem in implementation or not. First of all, the > base flow is stored in the arrays for non linear solution (vx, vy, vz) > and the perturbation in (vxp,vyp,vzp) (both in SOLN). Negative value > of param(31) sets the logical ifbase to .false. excluding call to > fluid in nek_advance. In this case only fluidp is executed. To get > time dependent base flow you could set positive param(31) and comment > ifbase check in arnoldi initialisation routine. This would activate > fluid and evolve both perturbation and base flow. In this case you > would need to resent vx,vy,vz to your initial conditions for base flow > at the end of every arnoldi cycle (where pressure is set to zero). > Other solution would be keeping ifbase=.false. and recalculating vx, > vy,vz at every step within arnoldi cycle. That what you wrote in your > mail, but this should be mostly local operation. I do not see any > reason to use gop routines. If you have analytical solution for base > flow you simply replace vx,vy,vz with new values base on the position > of the gll point (xm1,ym1,zm1 arrays in GEOM) and the time within the > given cycle. If you are not 100% sure the function is continuous at > the element faces, edges and vertices, you can add averaging step: > ! face averaging > call opdssum(VX,VY,VZ) > call opcolv (VX,VY,VZ,VMULT) > vmult is inverse of grid point multiplicity and is stored in SOLN. No > more global operations is required. However, I'm not sure if this > method would work, as ifbase shows up in navier5.f as well, and one > would need to check the code to see what variables are really used. I > would guess it should work, but I cannot guarantee it. You can try. > You have to be sure the base flow evolution is exactly the same in > each arnoldi cycle, to mimic the matrix operation properly. > Regards > Adam > > On 2016-03-15 13:18, nek5000-users at lists.mcs.anl.gov wrote: >> Hi Adam, >> >> thank you, it works now. >> >> However I still have a question about this tool. My base flow is time >> dependent, so I did in usrchk >> >> call opcopy (u,v,w,vx,vy,vz) >> u=u*function(time) >> v=v*function(time) >> w=w*function(time) >> >> call gop(u,work,'+ ',n) >> call gop(v,work,'+ ',n) >> call gop(w,work,'+ ',n) >> >> do e=1,nelv >> eg = lglel(e) >> call copy(vx(1,1,1,e),u(1,1,1,eg),nxyz) >> call copy(vy(1,1,1,e),v(1,1,1,eg),nxyz) >> call copy(vz(1,1,1,e),w(1,1,1,eg),nxyz) >> enddo >> >> However, I am not sure how to specify this velocity filed as the base >> flow each time step... >> >> Thank you in advance. >> SL >> >> El 15-03-2016 19:06, nek5000-users at lists.mcs.anl.gov escribi?: >>> Hi >>> >>> To force base flow to be constant you have to set negative param(31) >>> in your ###.rea file. Something like >>> -1.00000 p031 NPERT: #perturbation modes >>> Of course you need the base flow as well. It could be analytical one >>> set in useric, or just a field read during initialisation. >>> Regards >>> Adam >>> >>> >>> On 2016-03-15 08:49, nek5000-users at lists.mcs.anl.gov wrote: >>>> Hi Neks, >>>> >>>> I'm trying to use the linear stability tool of Nek5000. >>>> >>>> To start with, I am trying to run the ext_cyl example. However, I >>>> have found the following problem: >>>> >>>> ERROR: arnoldi assumes constant base flow. >>>> >>>> I have found on the README tutorial that the base flow has to be >>>> specified on the .rea file. I have included a file in the >>>> PRESOLVE/RESTART option, however I still have the same error. >>>> >>>> What should I modify? >>>> >>>> Finally, I have also used a subroutine defined in the .usr file that >>>> reads the file containing the base flow. However, the error >>>> persist... >>>> >>>> Could you help me, please? >>>> >>>> Cheers >>>> SL >>>> _______________________________________________ >>>> 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 >> >> >> _______________________________________________ >> 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 From nek5000-users at lists.mcs.anl.gov Fri Mar 18 04:02:05 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 18 Mar 2016 10:02:05 +0100 Subject: [Nek5000-users] Problem running on more than 4 proc Message-ID: Hi neks, I'm trying to run some little DNS of a temporal mixing layer using the low-mach formulation in nek5000. I have used the lowMach_test example as a template for my run directory, but I'm really struggling to understand why it seems to work fine only on 4 (or less) proc. while on 5 (or more) it accumulates errors in the velocity field until the blow-up. I tried both openmpi and mpich, but I got the same results on two different linux version (ubuntu 12. and OpenSuse 13). Could you please give me some indications? Thanks in advance. Regards Pasquale Pasquale Eduardo Lapenna PhD student 'La Sapienza' University of Rome Department of Aerospace and Mechanical Engineering -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Mar 18 23:45:05 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 19 Mar 2016 10:15:05 +0530 Subject: [Nek5000-users] NEKNEK Message-ID: Dear Sir Can we apply neknek when one has an unstructured grid. T/R Prashanth Mohanasundaram -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Mar 20 12:33:06 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 20 Mar 2016 17:33:06 +0000 Subject: [Nek5000-users] Heat/passive scalar solver - Helmholtz Message-ID: Hi Neks, We simulated the turbulent mixing of passive scalars with the Helmholtz solver. Parameter p22 in the .rea file is set to 10E-09. Our scalar fields show numerical errors, e.g. the scalar volumetric means are not constant but oscillate in time. Is there a way to reduce the numerical errors / increase the accuracy of the Helmholtz solver? Best, Philipp Weiss From nek5000-users at lists.mcs.anl.gov Sun Mar 20 12:39:24 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 20 Mar 2016 17:39:24 +0000 Subject: [Nek5000-users] Heat/passive scalar solver - CVODE Message-ID: Hi Neks, Could you briefly explain how to solve the heat/passive scalar equation with CVODE? We set parameter p16 in the .rea file to 2 and define the path to the static and shared CVODE libraries in the makenek file. However, when we run the compiled code, the error message 'ABORT: not compiled with CVODE support!' shows up. Best, Philipp Weiss From nek5000-users at lists.mcs.anl.gov Sun Mar 20 17:01:40 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 20 Mar 2016 22:01:40 +0000 Subject: [Nek5000-users] Heat/passive scalar solver - Helmholtz In-Reply-To: References: Message-ID: Dear Philipp, The usual way to cure the problem is to increase the spatial resolution. This can be done by changing lx1 in the SIZE file (and, typically, reducing dt). What is your Peclet or Reynolds number? What is your grid resolution? What is your grid Peclet number? Best, 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: Sunday, March 20, 2016 12:33 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Heat/passive scalar solver - Helmholtz Hi Neks, We simulated the turbulent mixing of passive scalars with the Helmholtz solver. Parameter p22 in the .rea file is set to 10E-09. Our scalar fields show numerical errors, e.g. the scalar volumetric means are not constant but oscillate in time. Is there a way to reduce the numerical errors / increase the accuracy of the Helmholtz solver? Best, Philipp Weiss _______________________________________________ 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 Mon Mar 21 04:24:45 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 21 Mar 2016 10:24:45 +0100 Subject: [Nek5000-users] linear stability tool In-Reply-To: References: Message-ID: Hi Sorry for late reply (I was busy with other stuff). First of all, when you write you do not see evolution of the perturbation do you mean lack of output files or something else? By default nek outputs only the non-linear fields not the perturbation, so if you would like to see the evolution of the perturbation itself you need to add in the userchk something like this include 'SIZE' ! NX1, NY1, NZ1, NELV, NIO include 'TSTEP' ! ISTEP, IOSTEP include 'SOLN' ! V[XYZ]P, TP ! write perturbation field if (mod(ISTEP,IOSTEP).eq.0) then call outpost2(VXP,VYP,VZP,PRP,TP,0,'prt') endif Other stuff is initialisation of the perturbation. You do it in useric only. To distinguish between base-flow (non-linear solution) and perturbation you use jp integer from SOLN. So the code should look in the following way: subroutine useric (ix,iy,iz,ieg) include 'SIZE' include 'NEKUSE' ! U[XYZ], X, Y include 'SOLN' ! JP real amp, ran if (JP.eq.0) then c place for base flow else c velocity for perturbation c random distribution amp = 1.0 ran = 3.e4*(ieg+X*sin(Y)) - 1.5e3*ix*iy + .5e5*ix ran = 1.e3*sin(ran) ran = 1.e3*sin(ran) ran = cos(ran) UX = ran*amp ran = 2.3e4*(ieg+X*sin(Y)) + 2.3e3*ix*iy - 2.e5*ix ran = 1.e3*sin(ran) ran = 1.e3*sin(ran) ran = cos(ran) UY = ran*amp UZ = 0.0 endif c no temperature this time return end This would set initial values for base flow and perturbation, but it is called only once (as should be). There is not need to average element faces after this routine as code does it by itself. Next question. Why do you use global element number lelg in you arrays with combination of gop? It SHOUDLN'T be used this way unless you have no other way. This prevents any scaling, as you force the code to store the whole global mesh on every processor. You can do it with small toy problem, but not with the real case running on 10k processors. Nek is the distributed memory software, and avoids storing non-local data unless it is really need it (e.g. global-to-local element numbering). You should work with local grid only (lelt, nelt; lelv, nelv) and perform global face averaging with dssum. Under ftp://ftp.mech.kth.se/pub/adam/Nek5000/Creta/ you can find some linear example for lid driven cavity. It you can start to play with it and later introduce time dependent base flow. The easiest solution would be changing sing of param31. Regards Adam On 2016-03-17 06:07, nek5000-users at lists.mcs.anl.gov wrote: > Thank you Adam, > > to start with the implementation, I am re-defining the base flow (as > function of t) each time step. The base flow is time dependent, > however, I cannot see any evolution of the perturbation variables. I > have set param31=-1. At the beginning of the simulation I am adding > some random noise to the perturbed variables in the following way: > > common /scrns/ uf(lx1,ly1,lz1,lelg),vf(lx1,ly1,lz1,lelg), > + wf(lx1,ly1,lz1,lelg) > > n = nelgv*nx1*ny1*nz1 > > if (istep.eq.0) then > call rzero(uf,n) ! zero-out u on all processors > call rzero(vf,n) > call rzero(wf,n) > > eps = 0.1 > call add_noise(uf,vf,wf,n,eps) ! Subroutine that calculates > random noise variables > > call gop(uf,work,'+ ',n) > call gop(vf,work,'+ ',n) > call gop(wf,work,'+ ',n) > > call opcopy(vxp(1,jp),vyp(1,jp),vzp(1,jp),uf,vf,wf) ! COPY TO > PERTURBATION VARIABLES > > end if > > In SIZE: lpert=1 > > > However the perturbed variables don't seem to change and they don't > seem to have any effect on the flow. If I plot my results, I can only > see the base flow varying with time (following its definition), but > nothing else. In addition, vz is always maintained to 0 (or to any > initial condition). > > Should I initialize (or define) the perturbation variables in a > different way? > > Best regards, > SL > > > El 16-03-2016 10:02, nek5000-users at lists.mcs.anl.gov escribi?: >> Hi >> >> I didn't work with time dependent base flow, so I'm not sure if there >> are some serious problem in implementation or not. First of all, the >> base flow is stored in the arrays for non linear solution (vx, vy, vz) >> and the perturbation in (vxp,vyp,vzp) (both in SOLN). Negative value >> of param(31) sets the logical ifbase to .false. excluding call to >> fluid in nek_advance. In this case only fluidp is executed. To get >> time dependent base flow you could set positive param(31) and comment >> ifbase check in arnoldi initialisation routine. This would activate >> fluid and evolve both perturbation and base flow. In this case you >> would need to resent vx,vy,vz to your initial conditions for base flow >> at the end of every arnoldi cycle (where pressure is set to zero). >> Other solution would be keeping ifbase=.false. and recalculating vx, >> vy,vz at every step within arnoldi cycle. That what you wrote in your >> mail, but this should be mostly local operation. I do not see any >> reason to use gop routines. If you have analytical solution for base >> flow you simply replace vx,vy,vz with new values base on the position >> of the gll point (xm1,ym1,zm1 arrays in GEOM) and the time within the >> given cycle. If you are not 100% sure the function is continuous at >> the element faces, edges and vertices, you can add averaging step: >> ! face averaging >> call opdssum(VX,VY,VZ) >> call opcolv (VX,VY,VZ,VMULT) >> vmult is inverse of grid point multiplicity and is stored in SOLN. No >> more global operations is required. However, I'm not sure if this >> method would work, as ifbase shows up in navier5.f as well, and one >> would need to check the code to see what variables are really used. I >> would guess it should work, but I cannot guarantee it. You can try. >> You have to be sure the base flow evolution is exactly the same in >> each arnoldi cycle, to mimic the matrix operation properly. >> Regards >> Adam >> >> On 2016-03-15 13:18, nek5000-users at lists.mcs.anl.gov wrote: >>> Hi Adam, >>> >>> thank you, it works now. >>> >>> However I still have a question about this tool. My base flow is >>> time dependent, so I did in usrchk >>> >>> call opcopy (u,v,w,vx,vy,vz) >>> u=u*function(time) >>> v=v*function(time) >>> w=w*function(time) >>> >>> call gop(u,work,'+ ',n) >>> call gop(v,work,'+ ',n) >>> call gop(w,work,'+ ',n) >>> >>> do e=1,nelv >>> eg = lglel(e) >>> call copy(vx(1,1,1,e),u(1,1,1,eg),nxyz) >>> call copy(vy(1,1,1,e),v(1,1,1,eg),nxyz) >>> call copy(vz(1,1,1,e),w(1,1,1,eg),nxyz) >>> enddo >>> >>> However, I am not sure how to specify this velocity filed as the >>> base flow each time step... >>> >>> Thank you in advance. >>> SL >>> >>> El 15-03-2016 19:06, nek5000-users at lists.mcs.anl.gov escribi?: >>>> Hi >>>> >>>> To force base flow to be constant you have to set negative param(31) >>>> in your ###.rea file. Something like >>>> -1.00000 p031 NPERT: #perturbation modes >>>> Of course you need the base flow as well. It could be analytical one >>>> set in useric, or just a field read during initialisation. >>>> Regards >>>> Adam >>>> >>>> >>>> On 2016-03-15 08:49, nek5000-users at lists.mcs.anl.gov wrote: >>>>> Hi Neks, >>>>> >>>>> I'm trying to use the linear stability tool of Nek5000. >>>>> >>>>> To start with, I am trying to run the ext_cyl example. However, I >>>>> have found the following problem: >>>>> >>>>> ERROR: arnoldi assumes constant base flow. >>>>> >>>>> I have found on the README tutorial that the base flow has to be >>>>> specified on the .rea file. I have included a file in the >>>>> PRESOLVE/RESTART option, however I still have the same error. >>>>> >>>>> What should I modify? >>>>> >>>>> Finally, I have also used a subroutine defined in the .usr file >>>>> that reads the file containing the base flow. However, the error >>>>> persist... >>>>> >>>>> Could you help me, please? >>>>> >>>>> Cheers >>>>> SL >>>>> _______________________________________________ >>>>> 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 >>> >>> >>> _______________________________________________ >>> 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 > > > _______________________________________________ > 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 Mon Mar 21 13:22:09 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 21 Mar 2016 18:22:09 +0000 Subject: [Nek5000-users] Heat/passive scalar solver - Helmholtz In-Reply-To: References: , Message-ID: Dear Paul, The Peclet and Reynolds number based on the Taylor-microscale and rms velocity are Pe = 33.9 and Re = 48.5. The periodic box of edge legnth 2*pi is discretized with 20^3 spectral elements of polynomial order 7. The grid Peclet number based on the mean grid spacing 2*pi/(20*7) and the rms velocity is Pe_grid = 6.69. We increased the polynomial order from 7 to 11 and 17 and reduced dt accordingly (CFL < 0.4). However, the volumetric scalar means are still not constant. Is there a stability criterion for the solution of the passive scalar equations in Nek? Are there other possible reasons for our numerical errors? Best, Philipp ________________________________________ Von: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov]" im Auftrag von "nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Gesendet: Sonntag, 20. M?rz 2016 23:01 An: nek5000-users at lists.mcs.anl.gov Betreff: Re: [Nek5000-users] Heat/passive scalar solver - Helmholtz Dear Philipp, The usual way to cure the problem is to increase the spatial resolution. This can be done by changing lx1 in the SIZE file (and, typically, reducing dt). What is your Peclet or Reynolds number? What is your grid resolution? What is your grid Peclet number? Best, 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: Sunday, March 20, 2016 12:33 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Heat/passive scalar solver - Helmholtz Hi Neks, We simulated the turbulent mixing of passive scalars with the Helmholtz solver. Parameter p22 in the .rea file is set to 10E-09. Our scalar fields show numerical errors, e.g. the scalar volumetric means are not constant but oscillate in time. Is there a way to reduce the numerical errors / increase the accuracy of the Helmholtz solver? Best, Philipp Weiss _______________________________________________ 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 From nek5000-users at lists.mcs.anl.gov Mon Mar 21 13:33:35 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 21 Mar 2016 18:33:35 +0000 Subject: [Nek5000-users] Heat/passive scalar solver - Helmholtz In-Reply-To: References: , , Message-ID: Dear Philipp, These seem like reasonable numbers. What is the magnitude of the error? Do you see a decrease when you increase resolution? If you'd like to contact me off list I can take a look at your log and usr files and see if anything appears to be wrong. Best, 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, March 21, 2016 1:22 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Heat/passive scalar solver - Helmholtz Dear Paul, The Peclet and Reynolds number based on the Taylor-microscale and rms velocity are Pe = 33.9 and Re = 48.5. The periodic box of edge legnth 2*pi is discretized with 20^3 spectral elements of polynomial order 7. The grid Peclet number based on the mean grid spacing 2*pi/(20*7) and the rms velocity is Pe_grid = 6.69. We increased the polynomial order from 7 to 11 and 17 and reduced dt accordingly (CFL < 0.4). However, the volumetric scalar means are still not constant. Is there a stability criterion for the solution of the passive scalar equations in Nek? Are there other possible reasons for our numerical errors? Best, Philipp ________________________________________ Von: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov]" im Auftrag von "nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Gesendet: Sonntag, 20. M?rz 2016 23:01 An: nek5000-users at lists.mcs.anl.gov Betreff: Re: [Nek5000-users] Heat/passive scalar solver - Helmholtz Dear Philipp, The usual way to cure the problem is to increase the spatial resolution. This can be done by changing lx1 in the SIZE file (and, typically, reducing dt). What is your Peclet or Reynolds number? What is your grid resolution? What is your grid Peclet number? Best, 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: Sunday, March 20, 2016 12:33 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Heat/passive scalar solver - Helmholtz Hi Neks, We simulated the turbulent mixing of passive scalars with the Helmholtz solver. Parameter p22 in the .rea file is set to 10E-09. Our scalar fields show numerical errors, e.g. the scalar volumetric means are not constant but oscillate in time. Is there a way to reduce the numerical errors / increase the accuracy of the Helmholtz solver? Best, Philipp Weiss _______________________________________________ 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 _______________________________________________ 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 Mon Mar 21 13:53:02 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 21 Mar 2016 11:53:02 -0700 Subject: [Nek5000-users] NEKNEK In-Reply-To: References: Message-ID: Dear Prashanth, Neknek should be able to handle the same type of grids as the stand-alone Nek5000 does. What grids are you thinking about? Thanks, Yulia On Mar 18, 2016, at 9:45 PM, nek5000-users at lists.mcs.anl.gov wrote: > Dear Sir > > Can we apply neknek when one has an unstructured grid. > > T/R > Prashanth Mohanasundaram > _______________________________________________ > 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 Mar 23 17:55:47 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 23 Mar 2016 22:55:47 +0000 Subject: [Nek5000-users] Apply boundary conditions form a restart file Message-ID: Dear Nek users, I am modeling a laminar boundary layer over a flat plate which will be used as inlet condition for a larger problem afterwards. I got accurate results by letting the boundary layer develop from a uniform velocity boundary condition. Right now I want to truncate the domain, such that the boundary layer is modeled from a point downstream of the flat plate's leading edge. So far I've managed to interpolate the solution from the complete domain to the truncated domain using grid-to-grid interpolation (subroutine g2gi). I saved the interpolated solution a file called 'new0.f00001'. When I start my new simulation (on the truncated domain), I load 'new0.f00001' on the first timestep (istep = 0) using load_fld() in userchk(). Finally, I copy the initial field to a common variables such that I can access them at every timestep in userbc(), where I impose the appropriate values. I outpost the initial field (in istep=0) and everything looks fine when plotted on VisIT or examined using hpts(). I've also examined 'ux' and 'uv' from userbc() by writing the values to an external file and again everything looks correct. However, when it's time to solve the Helmholtz system I get this: " Starting time loop ... DT/DTCFL/DTFS/DTINIT 0.450E-01 0.000E+00 0.694-309 0.450E-01 Step 1, t= 1.7500450E+03, DT= 4.5000000E-02, C= 0.242 0.0000E+00 0.0000E+00 Solving for fluid F T T 1.0000000000000000E-008 p22 1 1 1 1 Helmholtz VELX F: NaN 1.0000E-08 2.5238E-04 2.2222E+01 1 2 Helmholtz VELX F: NaN 1.0000E-08 2.5238E-04 2.2222E+01 1 3 Helmholtz VELX F: NaN 1.0000E-08 2.5238E-04 2.2222E+01 ... " Could anyone suggest a reason why this is happening? The field values seem to be loading just fine, and I think the boundary conditions are being applied correctly, so I don't understand why I would get NaN. Thank you. Juan Diego -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Mar 24 17:45:44 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 24 Mar 2016 22:45:44 +0000 Subject: [Nek5000-users] Apply boundary conditions form a restart file Message-ID: I guess I will answer my own question. It turns out that by loading the file the way I was doing it (calling load_fld() in userchk()), the program tries to calculate the convection terms using previous timesteps, which were not specified in my case. This produces the NaN during the calculation of the RHS. I solved my problem by setting my *.rea file to: 1 PRESOLVE/RESTART OPTIONS ***** new0.f00001 Then in userchk() I copy the initial field to auxiliary common arrays (ub and vb, similar to those used in the "blasius" example) during istep=0 which remain unchanged throughout the simulation and are used to set the appropriate boundary conditions. Juan Diego -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 23 00:33:36 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 23 Mar 2016 11:03:36 +0530 Subject: [Nek5000-users] NEKNEK Message-ID: Dear Mam (Ms. Yulia) Thanks for your reply. I am attaching herewith the geo and mesh files of both the aerofoil and the outside region for your perusal. My doubt is whether I can use unstructured grid for the outside regime as well as the regime surrounding the aerofoil. ( I have made use of GMSH. ) T/R Prashanth Mohanasundaram -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2016-03-23 11:06:50.png Type: image/png Size: 114329 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2016-03-23 11:07:13.png Type: image/png Size: 109880 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2016-03-23 11:08:35.png Type: image/png Size: 102547 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: naca.geo Type: application/octet-stream Size: 16784 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: naca.msh Type: model/mesh Size: 3448632 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: outside.geo Type: application/octet-stream Size: 2403 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: outside.msh Type: model/mesh Size: 1295756 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Sat Mar 26 21:45:06 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 26 Mar 2016 22:45:06 -0400 Subject: [Nek5000-users] linear stability tool In-Reply-To: References: Message-ID: Hi Adam, I am guessing I am using your code for stability tools in NEK. I have downloaded the code from https://nek5000.mcs.anl.gov/toolboxes/. I am trying to reproduce the ext_cyl example, as is, to get some familiarity. I have been able to compile the code (after some modifications to compile on the platform I intent to run my analysis). I have the base flow file "ext_cyl0.f00005" in the simulation folder. When I run the ext_cyl, I get the following error: ****************************************************************************************************************** call userchk ARNOLDI: Reading checkpoint 0 0 OPEN: ARPext_cyl0.f00005 ARPext_cyl0.f00005 byte_read() :: fopen failure2! ERROR: mfi_arnp, wrong header; abort. call exitt: dying ... ****************************************************************************************************************** I have also pasted below the parameters printed in the log file for your reference. ****************************************************************************************************************** 122 Parameters from file:/global/u2/r/rtumkur/eig_Setup/ARNOLDI/ext_cyl.rea 1 1.00000 p001 DENSITY 2 -50.0000 p002 VISCOS 7 1.00000 p007 RHOCP 8 1.00000 p008 CONDUCT 11 50003.0 p011 NSTEPS 12 -5.000000E-03 p012 DT 15 2500.00 p015 IOSTEP 17 1.00000 p017 18 0.500000E-01 p018 GRID < 0 --> # cells on screen 19 -1.00000 p019 INTYPE 20 7.00000 p020 NORDER 21 0.100000E-09 p021 DIVERGENCE 22 0.100000E-09 p022 HELMHOLTZ 24 0.100000E-09 p024 TOLREL 25 0.100000E-04 p025 TOLABS 26 1.00000 p026 COURANT/NTAU 27 3.00000 p027 TORDER 28 0.00000 p028 TORDER: mesh velocity (0: p28=p27) 31 -1.00000 p031 NPERT: #perturbation modes 59 0.00000 p059 !=0 --> full Jac. eval. for each el. 65 1.00000 p065 #iofiles (eg, 0 or 64); <0 --> sep. dirs 66 4.00000 p066 output : <0=ascii, else binary 67 4.00000 p067 restart: <0=ascii, else binary 69 1.00000 p069 : PROPER RESTART: 0 - do not use my_full_restart; 1- use it 71 5.00000 p071 : ARNOLDI: checkpoint file number for restart (reading) 72 6.00000 p072 : ARNOLDI: checkpoint file number for saving data 99 3.00000 p099 dealiasing: <0--> off/3--> old/4--> new 102 1.00000 p102 Dump out divergence at each time step 108 1.00000 p108 : ARNOLDI: 0 if no arnoldi 109 40.0000 p109 : ARNOLDI: frequency of calling arn_solve 110 4.00000 p110 : ARNOLDI: maximal number of arnoldi cycles 111 90.0000 p111 : ARNOLDI: size of Krylov space 112 30.0000 p112 : ARNOLDI: number of eigenvectors 113 1.00000E-06 p113 : ARNOLDI: arpack tolerance 119 1.00000 p119 : SPONGE STRENGTH 120 25.0000 p120 : SPONGE TOTAL WIDTH 121 3.00000 p121 : SPONGE DROP WIDTH (INFLOW) 122 5.00000 p122 : SPONGE RISE WIDTH (OUTFLOW) ****************************************************************************************************************** I'd appreciate if you can let me what am I missing in the set up which might be leading to this issue? Please let me know if you need any other information to understand this issue. Regards, Ravi On Tue, Mar 15, 2016 at 4:06 AM, wrote: > Hi > > To force base flow to be constant you have to set negative param(31) in > your ###.rea file. Something like > -1.00000 p031 NPERT: #perturbation modes > Of course you need the base flow as well. It could be analytical one set > in useric, or just a field read during initialisation. > Regards > Adam > > > > On 2016-03-15 08:49, nek5000-users at lists.mcs.anl.gov wrote: > >> Hi Neks, >> >> I'm trying to use the linear stability tool of Nek5000. >> >> To start with, I am trying to run the ext_cyl example. However, I have >> found the following problem: >> >> ERROR: arnoldi assumes constant base flow. >> >> I have found on the README tutorial that the base flow has to be >> specified on the .rea file. I have included a file in the PRESOLVE/RESTART >> option, however I still have the same error. >> >> What should I modify? >> >> Finally, I have also used a subroutine defined in the .usr file that >> reads the file containing the base flow. However, the error persist... >> >> Could you help me, please? >> >> Cheers >> SL >> _______________________________________________ >> 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 > -- Ravi Kumar R. Tumkur, PhD. Phone: 217 778 7538 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 30 05:52:28 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 30 Mar 2016 12:52:28 +0200 Subject: [Nek5000-users] linear stability tool In-Reply-To: References: Message-ID: Hi Ravi The first error means you have no restart files, which is obvious for the first run. Restart files are (ARP### and ARV###) are generated at the end of the run if the tolerance is not reached. You control it by parameter 69 in ###.rea. Simply set it to 0 for the first run. In addition parameters 71 and 72 set the checkpoint number for reading and writing (to avoid overwriting). Number of files depends on the other parameters and preprocessing flags used. Regards Adam On 2016-03-27 04:45, nek5000-users at lists.mcs.anl.gov wrote: > Hi Adam, > > I am guessing I am using your code for stability tools in NEK. I have > downloaded the code from https://nek5000.mcs.anl.gov/toolboxes/. > > I am trying to reproduce the ext_cyl example, as is, to get some > familiarity. > > I have been able to compile the code (after some modifications to > compile on the platform I intent to run my analysis). I have the base > flow file "ext_cyl0.f00005" in the simulation folder. When I run the > ext_cyl, I get the following error: > > > ****************************************************************************************************************** > call userchk > ARNOLDI: > Reading checkpoint > 0 0 OPEN: ARPext_cyl0.f00005 > ARPext_cyl0.f00005 > byte_read() :: fopen failure2! > ERROR: mfi_arnp, wrong header; abort. > > call exitt: dying ... > ****************************************************************************************************************** > > > I have also pasted below the parameters printed in the log file for > your reference. > > ****************************************************************************************************************** > 122 Parameters from > file:/global/u2/r/rtumkur/eig_Setup/ARNOLDI/ext_cyl.rea > 1 1.00000 p001 DENSITY > 2 -50.0000 p002 VISCOS > 7 1.00000 p007 RHOCP > 8 1.00000 p008 CONDUCT > 11 50003.0 p011 NSTEPS > 12 -5.000000E-03 p012 DT > 15 2500.00 p015 IOSTEP > 17 1.00000 p017 > 18 0.500000E-01 p018 GRID < 0 --> # cells on screen > 19 -1.00000 p019 INTYPE > 20 7.00000 p020 NORDER > 21 0.100000E-09 p021 DIVERGENCE > 22 0.100000E-09 p022 HELMHOLTZ > 24 0.100000E-09 p024 TOLREL > 25 0.100000E-04 p025 TOLABS > 26 1.00000 p026 COURANT/NTAU > 27 3.00000 p027 TORDER > 28 0.00000 p028 TORDER: mesh velocity (0: p28=p27) > 31 -1.00000 p031 NPERT: #perturbation modes > 59 0.00000 p059 !=0 --> full Jac. eval. for each el. > 65 1.00000 p065 #iofiles (eg, 0 or 64); <0 --> sep. dirs > 66 4.00000 p066 output : <0=ascii, else binary > 67 4.00000 p067 restart: <0=ascii, else binary > 69 1.00000 p069 : PROPER RESTART: 0 - do not use > my_full_restart; 1- use it > 71 5.00000 p071 : ARNOLDI: checkpoint file number for > restart (reading) > 72 6.00000 p072 : ARNOLDI: checkpoint file number for > saving data > 99 3.00000 p099 dealiasing: <0--> off/3--> old/4--> new > 102 1.00000 p102 Dump out divergence at each time step > 108 1.00000 p108 : ARNOLDI: 0 if no arnoldi > 109 40.0000 p109 : ARNOLDI: frequency of calling arn_solve > 110 4.00000 p110 : ARNOLDI: maximal number of arnoldi cycles > 111 90.0000 p111 : ARNOLDI: size of Krylov space > 112 30.0000 p112 : ARNOLDI: number of eigenvectors > 113 1.00000E-06 p113 : ARNOLDI: arpack tolerance > 119 1.00000 p119 : SPONGE STRENGTH > 120 25.0000 p120 : SPONGE TOTAL WIDTH > 121 3.00000 p121 : SPONGE DROP WIDTH (INFLOW) > 122 5.00000 p122 : SPONGE RISE WIDTH (OUTFLOW) > ****************************************************************************************************************** > > I'd appreciate if you can let me what am I missing in the set up which > might be leading to this issue? Please let me know if you need any > other information to understand this issue. > > > Regards, > Ravi > > > > On Tue, Mar 15, 2016 at 4:06 AM, > wrote: > > Hi > > To force base flow to be constant you have to set negative > param(31) in your ###.rea file. Something like > -1.00000 p031 NPERT: #perturbation modes > Of course you need the base flow as well. It could be analytical > one set in useric, or just a field read during initialisation. > Regards > Adam > > > > On 2016-03-15 08:49, nek5000-users at lists.mcs.anl.gov > wrote: > > Hi Neks, > > I'm trying to use the linear stability tool of Nek5000. > > To start with, I am trying to run the ext_cyl example. > However, I have found the following problem: > > ERROR: arnoldi assumes constant base flow. > > I have found on the README tutorial that the base flow has to > be specified on the .rea file. I have included a file in the > PRESOLVE/RESTART option, however I still have the same error. > > What should I modify? > > Finally, I have also used a subroutine defined in the .usr > file that reads the file containing the base flow. However, > the error persist... > > Could you help me, please? > > Cheers > SL > _______________________________________________ > 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 > > > > > -- > Ravi Kumar R. Tumkur,**PhD. > Phone: 217 778 7538 > > > _______________________________________________ > 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 Mar 30 07:25:26 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 30 Mar 2016 08:25:26 -0400 Subject: [Nek5000-users] linear stability tool In-Reply-To: References: Message-ID: Hi Adam, Thanks for your response. Here is what I understand the steps I should follow to run the 'ext_cyl' example, from https://nek5000.mcs.anl.gov/toolboxes/: Base flow run: Compile with the following parameter setting: p031 = 0 p069 = 0 and I think I should also set p108 = 0 (without setting p108 = 0, I get an error saying "ERROR: arnoldi has to be run in perturbation mode") Hence, I do a base flow run with p031=0, p069=0 and p108 = 0. Am I correct here? If I do the base flow run with p031=0, p069=0 and p108 = 0, I see lot of error in ext_cyl.log file as: Step 1826, t= 9.1300000E+00, DT= 5.0000000E-03, C= 0.000 3.5844E+02 1.9493E-01 Solving for fluid F T T 1826 100 **ERROR**: Failed in HMHOLTZ: VELX NaN NaN 1.0000E-10 1826 100 **ERROR**: Failed in HMHOLTZ: VELY NaN NaN 1.0000E-10 Nevertheless, I do see a file 'ext_cyl0.f00001' written after some simulation time, however, I do not see the restart files, 'ARVext_cy0.f00001' and 'ARPext_cy0.f00001', written at the same time. I will continue to run the base flow simulation for longer duration, in the meantime, I wanted to confirm if I am on the right path so far? Regards, Ravi On Wed, Mar 30, 2016 at 6:52 AM, wrote: > Hi Ravi > > The first error means you have no restart files, which is obvious for the > first run. Restart files are (ARP### and ARV###) are generated at the end > of the run if the tolerance is not reached. You control it by parameter 69 > in ###.rea. Simply set it to 0 for the first run. In addition parameters 71 > and 72 set the checkpoint number for reading and writing (to avoid > overwriting). Number of files depends on the other parameters and > preprocessing flags used. > Regards > Adam > > > On 2016-03-27 04:45, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Adam, > > I am guessing I am using your code for stability tools in NEK. I have > downloaded the code from > https://nek5000.mcs.anl.gov/toolboxes/. > > I am trying to reproduce the ext_cyl example, as is, to get some > familiarity. > > I have been able to compile the code (after some modifications to compile > on the platform I intent to run my analysis). I have the base flow file > "ext_cyl0.f00005" in the simulation folder. When I run the ext_cyl, I get > the following error: > > > > ****************************************************************************************************************** > call userchk > ARNOLDI: > Reading checkpoint > 0 0 OPEN: ARPext_cyl0.f00005 > ARPext_cyl0.f00005 > byte_read() :: fopen failure2! > ERROR: mfi_arnp, wrong header; abort. > > call exitt: dying ... > > ****************************************************************************************************************** > > > I have also pasted below the parameters printed in the log file for your > reference. > > > ****************************************************************************************************************** > 122 Parameters from > file:/global/u2/r/rtumkur/eig_Setup/ARNOLDI/ext_cyl.rea > 1 1.00000 p001 DENSITY > 2 -50.0000 p002 VISCOS > 7 1.00000 p007 RHOCP > 8 1.00000 p008 CONDUCT > 11 50003.0 p011 NSTEPS > 12 -5.000000E-03 p012 DT > 15 2500.00 p015 IOSTEP > 17 1.00000 p017 > 18 0.500000E-01 p018 GRID < 0 --> # cells on screen > 19 -1.00000 p019 INTYPE > 20 7.00000 p020 NORDER > 21 0.100000E-09 p021 DIVERGENCE > 22 0.100000E-09 p022 HELMHOLTZ > 24 0.100000E-09 p024 TOLREL > 25 0.100000E-04 p025 TOLABS > 26 1.00000 p026 COURANT/NTAU > 27 3.00000 p027 TORDER > 28 0.00000 p028 TORDER: mesh velocity (0: p28=p27) > 31 -1.00000 p031 NPERT: #perturbation modes > 59 0.00000 p059 !=0 --> full Jac. eval. for each el. > 65 1.00000 p065 #iofiles (eg, 0 or 64); <0 --> sep. dirs > 66 4.00000 p066 output : <0=ascii, else binary > 67 4.00000 p067 restart: <0=ascii, else binary > 69 1.00000 p069 : PROPER RESTART: 0 - do not use > my_full_restart; 1- use it > 71 5.00000 p071 : ARNOLDI: checkpoint file number for restart > (reading) > 72 6.00000 p072 : ARNOLDI: checkpoint file number for saving > data > 99 3.00000 p099 dealiasing: <0--> off/3--> old/4--> new > 102 1.00000 p102 Dump out divergence at each time step > 108 1.00000 p108 : ARNOLDI: 0 if no arnoldi > 109 40.0000 p109 : ARNOLDI: frequency of calling arn_solve > 110 4.00000 p110 : ARNOLDI: maximal number of arnoldi cycles > 111 90.0000 p111 : ARNOLDI: size of Krylov space > 112 30.0000 p112 : ARNOLDI: number of eigenvectors > 113 1.00000E-06 p113 : ARNOLDI: arpack tolerance > 119 1.00000 p119 : SPONGE STRENGTH > 120 25.0000 p120 : SPONGE TOTAL WIDTH > 121 3.00000 p121 : SPONGE DROP WIDTH (INFLOW) > 122 5.00000 p122 : SPONGE RISE WIDTH (OUTFLOW) > > ****************************************************************************************************************** > > I'd appreciate if you can let me what am I missing in the set up which > might be leading to this issue? Please let me know if you need any other > information to understand this issue. > > > Regards, > Ravi > > > > On Tue, Mar 15, 2016 at 4:06 AM, wrote: > >> Hi >> >> To force base flow to be constant you have to set negative param(31) in >> your ###.rea file. Something like >> -1.00000 p031 NPERT: #perturbation modes >> Of course you need the base flow as well. It could be analytical one set >> in useric, or just a field read during initialisation. >> Regards >> Adam >> >> >> >> On 2016-03-15 08:49, nek5000-users at lists.mcs.anl.gov wrote: >> >>> Hi Neks, >>> >>> I'm trying to use the linear stability tool of Nek5000. >>> >>> To start with, I am trying to run the ext_cyl example. However, I have >>> found the following problem: >>> >>> ERROR: arnoldi assumes constant base flow. >>> >>> I have found on the README tutorial that the base flow has to be >>> specified on the .rea file. I have included a file in the PRESOLVE/RESTART >>> option, however I still have the same error. >>> >>> What should I modify? >>> >>> Finally, I have also used a subroutine defined in the .usr file that >>> reads the file containing the base flow. However, the error persist... >>> >>> Could you help me, please? >>> >>> Cheers >>> SL >>> _______________________________________________ >>> 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 >> > > > > -- > Ravi Kumar R. Tumkur, PhD. > Phone: 217 778 7538 > > > _______________________________________________ > 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 > > -- Ravi Kumar R. Tumkur, PhD. Phone: 217 778 7538 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 30 09:24:16 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 30 Mar 2016 16:24:16 +0200 Subject: [Nek5000-users] linear stability tool In-Reply-To: References: Message-ID: Hi No, not this way. First of all you have to setup linear simulation. For this you need to modify SIZE to let all the perturbation variables to be used. You should have following section setting correct array sizes: parameter (lpelv=lelv,lpelt=lelt,lpert=1) ! perturbation parameter (lpx1=lx1,lpy1=ly1,lpz1=lz1) ! array sizes parameter (lpx2=lx2,lpy2=ly2,lpz2=lz2) Next you have to set p031 = -1 to have evolution of the single perturbation with constant base flow. Base flow has to be specified in and ###.rea file as a restart option; e.g. 1 PRESOLVE/RESTART OPTIONS ***** baseflow.bsf 7 INITIAL CONDITIONS ***** Setting p108 = 0 you simply turn off Arnoldi, so only dns is performed. Regards Adam On 2016-03-30 14:25, nek5000-users at lists.mcs.anl.gov wrote: > Hi Adam, > > Thanks for your response. Here is what I understand the steps I should > follow to run the 'ext_cyl' example, from > https://nek5000.mcs.anl.gov/toolboxes/: > > Base flow run: Compile with the following parameter setting: > > p031 = 0 > p069 = 0 > > and I think I should also set p108 = 0 (without setting p108 = 0, I > get an error saying "ERROR: arnoldi has to be run in perturbation mode") > > Hence, I do a base flow run with p031=0, p069=0 and p108 = 0. Am I > correct here? > > If I do the base flow run with p031=0, p069=0 and p108 = 0, I see lot > of error in ext_cyl.log file as: > > Step 1826, t= 9.1300000E+00, DT= 5.0000000E-03, C= 0.000 3.5844E+02 > 1.9493E-01 > Solving for fluid F T T > 1826 100 **ERROR**: Failed in HMHOLTZ: VELX NaN NaN > 1.0000E-10 > 1826 100 **ERROR**: Failed in HMHOLTZ: VELY NaN NaN > 1.0000E-10 > > Nevertheless, I do see a file 'ext_cyl0.f00001' written after some > simulation time, however, I do not see the restart files, > 'ARVext_cy0.f00001' and 'ARPext_cy0.f00001', written at the same time. > I will continue to run the base flow simulation for longer duration, > in the meantime, I wanted to confirm if I am on the right path so far? > > Regards, > Ravi > > > > > On Wed, Mar 30, 2016 at 6:52 AM, > wrote: > > Hi Ravi > > The first error means you have no restart files, which is obvious > for the first run. Restart files are (ARP### and ARV###) are > generated at the end of the run if the tolerance is not reached. > You control it by parameter 69 in ###.rea. Simply set it to 0 for > the first run. In addition parameters 71 and 72 set the checkpoint > number for reading and writing (to avoid overwriting). Number of > files depends on the other parameters and preprocessing flags used. > Regards > Adam > > > On 2016-03-27 04:45, nek5000-users at lists.mcs.anl.gov > wrote: >> Hi Adam, >> >> I am guessing I am using your code for stability tools in NEK. I >> have downloaded the code from https://nek5000.mcs.anl.gov/toolboxes/. >> >> I am trying to reproduce the ext_cyl example, as is, to get some >> familiarity. >> >> I have been able to compile the code (after some modifications to >> compile on the platform I intent to run my analysis). I have the >> base flow file "ext_cyl0.f00005" in the simulation folder. When I >> run the ext_cyl, I get the following error: >> >> >> ****************************************************************************************************************** >> call userchk >> ARNOLDI: >> Reading checkpoint >> 0 0 OPEN: ARPext_cyl0.f00005 >> ARPext_cyl0.f00005 >> byte_read() :: fopen failure2! >> ERROR: mfi_arnp, wrong header; abort. >> >> call exitt: dying ... >> ****************************************************************************************************************** >> >> >> I have also pasted below the parameters printed in the log file >> for your reference. >> >> ****************************************************************************************************************** >> 122 Parameters from >> file:/global/u2/r/rtumkur/eig_Setup/ARNOLDI/ext_cyl.rea >> 1 1.00000 p001 DENSITY >> 2 -50.0000 p002 VISCOS >> 7 1.00000 p007 RHOCP >> 8 1.00000 p008 CONDUCT >> 11 50003.0 p011 NSTEPS >> 12 -5.000000E-03 p012 DT >> 15 2500.00 p015 IOSTEP >> 17 1.00000 p017 >> 18 0.500000E-01 p018 GRID < 0 --> # cells on screen >> 19 -1.00000 p019 INTYPE >> 20 7.00000 p020 NORDER >> 21 0.100000E-09 p021 DIVERGENCE >> 22 0.100000E-09 p022 HELMHOLTZ >> 24 0.100000E-09 p024 TOLREL >> 25 0.100000E-04 p025 TOLABS >> 26 1.00000 p026 COURANT/NTAU >> 27 3.00000 p027 TORDER >> 28 0.00000 p028 TORDER: mesh velocity (0: p28=p27) >> 31 -1.00000 p031 NPERT: #perturbation modes >> 59 0.00000 p059 !=0 --> full Jac. eval. for each el. >> 65 1.00000 p065 #iofiles (eg, 0 or 64); <0 --> sep. dirs >> 66 4.00000 p066 output : <0=ascii, else binary >> 67 4.00000 p067 restart: <0=ascii, else binary >> 69 1.00000 p069 : PROPER RESTART: 0 - do not use >> my_full_restart; 1- use it >> 71 5.00000 p071 : ARNOLDI: checkpoint file number for >> restart (reading) >> 72 6.00000 p072 : ARNOLDI: checkpoint file number for >> saving data >> 99 3.00000 p099 dealiasing: <0--> off/3--> old/4--> new >> 102 1.00000 p102 Dump out divergence at each time step >> 108 1.00000 p108 : ARNOLDI: 0 if no arnoldi >> 109 40.0000 p109 : ARNOLDI: frequency of calling arn_solve >> 110 4.00000 p110 : ARNOLDI: maximal number of arnoldi >> cycles >> 111 90.0000 p111 : ARNOLDI: size of Krylov space >> 112 30.0000 p112 : ARNOLDI: number of eigenvectors >> 113 1.00000E-06 p113 : ARNOLDI: arpack tolerance >> 119 1.00000 p119 : SPONGE STRENGTH >> 120 25.0000 p120 : SPONGE TOTAL WIDTH >> 121 3.00000 p121 : SPONGE DROP WIDTH (INFLOW) >> 122 5.00000 p122 : SPONGE RISE WIDTH (OUTFLOW) >> ****************************************************************************************************************** >> >> I'd appreciate if you can let me what am I missing in the set up >> which might be leading to this issue? Please let me know if you >> need any other information to understand this issue. >> >> >> Regards, >> Ravi >> >> >> >> On Tue, Mar 15, 2016 at 4:06 AM, > > wrote: >> >> Hi >> >> To force base flow to be constant you have to set negative >> param(31) in your ###.rea file. Something like >> -1.00000 p031 NPERT: #perturbation modes >> Of course you need the base flow as well. It could be >> analytical one set in useric, or just a field read during >> initialisation. >> Regards >> Adam >> >> >> >> On 2016-03-15 08:49, nek5000-users at lists.mcs.anl.gov >> wrote: >> >> Hi Neks, >> >> I'm trying to use the linear stability tool of Nek5000. >> >> To start with, I am trying to run the ext_cyl example. >> However, I have found the following problem: >> >> ERROR: arnoldi assumes constant base flow. >> >> I have found on the README tutorial that the base flow >> has to be specified on the .rea file. I have included a >> file in the PRESOLVE/RESTART option, however I still have >> the same error. >> >> What should I modify? >> >> Finally, I have also used a subroutine defined in the >> .usr file that reads the file containing the base flow. >> However, the error persist... >> >> Could you help me, please? >> >> Cheers >> SL >> _______________________________________________ >> 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 >> >> >> >> >> -- >> Ravi Kumar R. Tumkur,**PhD. >> Phone: 217 778 7538 >> >> >> _______________________________________________ >> 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 > > > > > -- > Ravi Kumar R. Tumkur,**PhD. > Phone: 217 778 7538 > > > _______________________________________________ > 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 Mar 30 12:33:45 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 30 Mar 2016 19:33:45 +0200 Subject: [Nek5000-users] Problem when running with variable fluid properties In-Reply-To: References: Message-ID: Equation Momentum Eq.1.1 Energy Eq.1.4 Passive scalar Eq.1.6 udiff ? ?c p (?c p ) i utrans ? k k i ifield 1 2 i-1 2016-03-15 20:14 GMT+01:00 ANTONIO ANTORANZ PERALES : > Hi, > > After successfully running some DNS cases of a turbulent pipe with heat > transfer in NEK ( > http://www.sciencedirect.com/science/article/pii/S0142727X15000533), I am > now struggling to run a similar case but with variable fluid properties (Re > and Pe being functions of temperature). > > I am currently using Pn-Pn2 (lx2=lx1-2 in SIZE) method and stress > formulation (IFSTRS=true), together with IFUSERVP=true (p030=1.0 in REA > file) to be able to define the viscosity and conductivity functions. > Initial flow conditions are taken from a previous constant fluid properties > turbulent pipe case. > > My problem is that, when setting IFUSERVP=true, the flow velocities go to > zero in very few time steps, even though I was setting constant fluid > properties in USERVP subroutine for trial purposes. > > I have checked that the forcing in the momentum equation (subroutine > USERF) is correctly set. > > Could you please give me some indications as to what I can be doing wrong? > Thanks in advance. > > Regards > Antonio > > > > -- > ANTONIO ANTORANZ PERALES > Universidad Carlos III de Madrid > -- ANTONIO ANTORANZ PERALES Universidad Carlos III de Madrid -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 30 12:43:58 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 30 Mar 2016 19:43:58 +0200 Subject: [Nek5000-users] Problem when running with variable fluid properties In-Reply-To: References: Message-ID: Hi again, NEK users. I think I have found the problem. Following the table on page 17 of http://nek5000.github.io/NekDoc/Nek_users.pdf, I was mistakenly setting density in udiff and viscosity in utrans (field=1). Please correct this typo in the manual. NEK examples are however correct. Regards Antonio 2016-03-15 20:14 GMT+01:00 ANTONIO ANTORANZ PERALES : > Hi, > > After successfully running some DNS cases of a turbulent pipe with heat > transfer in NEK ( > http://www.sciencedirect.com/science/article/pii/S0142727X15000533), I am > now struggling to run a similar case but with variable fluid properties (Re > and Pe being functions of temperature). > > I am currently using Pn-Pn2 (lx2=lx1-2 in SIZE) method and stress > formulation (IFSTRS=true), together with IFUSERVP=true (p030=1.0 in REA > file) to be able to define the viscosity and conductivity functions. > Initial flow conditions are taken from a previous constant fluid properties > turbulent pipe case. > > My problem is that, when setting IFUSERVP=true, the flow velocities go to > zero in very few time steps, even though I was setting constant fluid > properties in USERVP subroutine for trial purposes. > > I have checked that the forcing in the momentum equation (subroutine > USERF) is correctly set. > > Could you please give me some indications as to what I can be doing wrong? > Thanks in advance. > > Regards > Antonio > > > > -- > ANTONIO ANTORANZ PERALES > Universidad Carlos III de Madrid > -- ANTONIO ANTORANZ PERALES Universidad Carlos III de Madrid -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Mar 30 14:15:51 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 30 Mar 2016 19:15:51 +0000 Subject: [Nek5000-users] Problem when running with variable fluid properties In-Reply-To: References: , Message-ID: Thanks a lot Antonio, Indeed you are right the name even suggests udiff for diffusion term. I'll fix it asap. 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, March 30, 2016 12:43 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Problem when running with variable fluid properties Hi again, NEK users. I think I have found the problem. Following the table on page 17 of http://nek5000.github.io/NekDoc/Nek_users.pdf, I was mistakenly setting density in udiff and viscosity in utrans (field=1). Please correct this typo in the manual. NEK examples are however correct. Regards Antonio 2016-03-15 20:14 GMT+01:00 ANTONIO ANTORANZ PERALES >: Hi, After successfully running some DNS cases of a turbulent pipe with heat transfer in NEK (http://www.sciencedirect.com/science/article/pii/S0142727X15000533), I am now struggling to run a similar case but with variable fluid properties (Re and Pe being functions of temperature). I am currently using Pn-Pn2 (lx2=lx1-2 in SIZE) method and stress formulation (IFSTRS=true), together with IFUSERVP=true (p030=1.0 in REA file) to be able to define the viscosity and conductivity functions. Initial flow conditions are taken from a previous constant fluid properties turbulent pipe case. My problem is that, when setting IFUSERVP=true, the flow velocities go to zero in very few time steps, even though I was setting constant fluid properties in USERVP subroutine for trial purposes. I have checked that the forcing in the momentum equation (subroutine USERF) is correctly set. Could you please give me some indications as to what I can be doing wrong? Thanks in advance. Regards Antonio -- ANTONIO ANTORANZ PERALES Universidad Carlos III de Madrid -- ANTONIO ANTORANZ PERALES Universidad Carlos III de Madrid