From nek5000-users at lists.mcs.anl.gov Fri Nov 2 02:50:35 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 02 Nov 2018 10:50:35 +0300 Subject: [Nek5000-users] =?utf-8?q?Double_Precision?= Message-ID: Hi, Neks! Could I set tolerances less than 10^-8 in solvers via .par or .rea file, or 10^-8 is the minimum? In documentation "double precision" means 8 digits, but could Nek5000 write files with 16 digits? Best regards, Mark -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Nov 2 04:05:34 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 2 Nov 2018 10:05:34 +0100 Subject: [Nek5000-users] Double Precision In-Reply-To: References: Message-ID: Hi, double precision for Nek means 8 bytes (64bit) per number, which corresponds to an epsilon of 1e-16; internally everything is run with double precision. So yes, tolerances below 1e-8 are possible, and the typical files are written with 16 digits (which can however be changed with the parameters). Philipp On 2018-11-02 08:50, nek5000-users--- via Nek5000-users wrote: > Hi, Neks! > > Could I set tolerances less than 10^-8 in solvers via .par or .rea file, > or 10^-8 is the minimum? In documentation "double precision" means 8 > digits, but could Nek5000 write files with 16 digits? > > Best regards, > Mark > > > _______________________________________________ > 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 Nov 6 06:07:24 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 6 Nov 2018 13:07:24 +0100 Subject: [Nek5000-users] Nek5000 Gallery Updates Message-ID: Folks, Our simulation gallery (https://nek5000.mcs.anl.gov/category/gallery) was recently updated. Check it out! Do you want to share your work? Just fill out the submission form on the gallery webpage. Cheers, Stefan From nek5000-users at lists.mcs.anl.gov Wed Nov 7 00:39:35 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 07 Nov 2018 09:39:35 +0300 Subject: [Nek5000-users] =?utf-8?q?Interpolation_with_gfldr?= Message-ID: Hi, Neks! I am working with a complex geometry?which was built in gambit.?I have a velocity fields for my grid.?But I want to interpolate these velocity fields to a new grid. The old grid was changed without moving the geometry parameters, I just changed the position of the?computational nodes and reduced their number (see pictures old_grid and new_grid *). I nterpolation ends as usual. The velocity field is interpolated perfectly, but the pressure field is not interpolated correctly?(see pictures pressure_field_before_interpolation and?pressure_field_after_interpolation **). Tell me, what is my mistake? Is it possible to interpolate from a larger number of nodes to a smaller number of nodes? * https://drive.google.com/open?id=1DmsGxc_WR3_aJW0UpLHkcxAVzt5BzABK ? https://drive.google.com/open?id=1RbSsODF49DqGmyHnpz0Bktp-HDjW7j0w ? ** https://drive.google.com/open?id=16Ueepa1lo_aHjya3BnLn8fHI3ek0kvo8 ? ? ? https://drive.google.com/open?id=1CNiN8MdE7tNeu8T4jBtZBtMSX5dlXzNM Best regards, Elizabeth -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 7 01:34:39 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 7 Nov 2018 08:34:39 +0100 Subject: [Nek5000-users] Interpolation with gfldr In-Reply-To: References: Message-ID: What version of Nek5000 are you using? -----Original message----- > From:nek5000-users--- via Nek5000-users > Sent: Wednesday 7th November 2018 7:39 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Interpolation with gfldr > > Hi, Neks!

I am working with a complex geometry?which was built in gambit.?I have a velocity fields for my grid.?But I want to interpolate these velocity fields to a new grid. The old grid was changed without moving the geometry parameters, I just changed the position of the?computational nodes and reduced their number (see pictures old_grid and new_grid *). Interpolation ends as usual. The velocity field is interpolated perfectly, but the pressure field is not interpolated correctly?(see pictures pressure_field_before_interpolation and?pressure_field_after_interpolation **). > Tell me, what is my mistake? Is it possible to interpolate from a larger number of nodes to a smaller number of nodes? > *https://drive.google.com/open?id=1DmsGxc_WR3_aJW0UpLHkcxAVzt5BzABK
?https://drive.google.com/open?id=1RbSsODF49DqGmyHnpz0Bktp-HDjW7j0w ?
**https://drive.google.com/open?id=16Ueepa1lo_aHjya3BnLn8fHI3ek0kvo8 ?
? ?https://drive.google.com/open?id=1CNiN8MdE7tNeu8T4jBtZBtMSX5dlXzNM

Best regards,
Elizabeth > _______________________________________________ > 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 Nov 7 01:53:40 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 07 Nov 2018 10:53:40 +0300 Subject: [Nek5000-users] =?utf-8?q?Interpolation_with_gfldr?= In-Reply-To: References: Message-ID: Version 17.0 ?????????? ?? ????????? ????? Mail.Ru ?????, 7 ?????? 2018 ?., 14:37 +0700 ?? nek5000-users : >What version of Nek5000 are you using? > >-----Original message----- >> From:nek5000-users--- via Nek5000-users < nek5000-users at lists.mcs.anl.gov > >> Sent: Wednesday 7th November 2018 7:39 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: [Nek5000-users] Interpolation with gfldr >> >> Hi, Neks!

I am working with a complex geometry?which was built in gambit.?I have a velocity fields for my grid.?But I want to interpolate these velocity fields to a new grid. The old grid was changed without moving the geometry parameters, I just changed the position of the?computational nodes and reduced their number (see pictures old_grid and new_grid *). Interpolation ends as usual. The velocity field is interpolated perfectly, but the pressure field is not interpolated correctly?(see pictures pressure_field_before_interpolation and?pressure_field_after_interpolation **). >> Tell me, what is my mistake? Is it possible to interpolate from a larger number of nodes to a smaller number of nodes? >> * https://drive.google.com/open?id=1DmsGxc_WR3_aJW0UpLHkcxAVzt5BzABK < https://drive.google.com/open?id=1DmsGxc_WR3_aJW0UpLHkcxAVzt5BzABK >
? https://drive.google.com/open?id=1RbSsODF49DqGmyHnpz0Bktp-HDjW7j0w < https://drive.google.com/open?id=1RbSsODF49DqGmyHnpz0Bktp-HDjW7j0w >?
** https://drive.google.com/open?id=16Ueepa1lo_aHjya3BnLn8fHI3ek0kvo8 < https://drive.google.com/open?id=16Ueepa1lo_aHjya3BnLn8fHI3ek0kvo8 >?
? ? https://drive.google.com/open?id=1CNiN8MdE7tNeu8T4jBtZBtMSX5dlXzNM < https://drive.google.com/open?id=1CNiN8MdE7tNeu8T4jBtZBtMSX5dlXzNM >

Best regards,
Elizabeth >> _______________________________________________ >> 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 Wed Nov 7 03:23:20 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 7 Nov 2018 10:23:20 +0100 Subject: [Nek5000-users] Interpolation with gfldr In-Reply-To: References: Message-ID: How did you generate your .f0000X file which you use for gfldr? Was this created with full_restart_save()? -----Original message----- > From:nek5000-users--- via Nek5000-users > Sent: Wednesday 7th November 2018 8:53 > To: nek5000-users > Subject: Re: [Nek5000-users] Interpolation with gfldr > > Version 17.0 > > > > ?????????? ?? ????????? ????? Mail.Ru > > > ?????, 7 ?????? 2018 ?., 14:37 +0700 ?? nek5000-users : > > What version of Nek5000 are you using? > > -----Original message----- > > From:nek5000-users--- via Nek5000-users > > > Sent: Wednesday 7th November 2018 7:39 > > To: nek5000-users at lists.mcs.anl.gov > > Subject: [Nek5000-users] Interpolation with gfldr > > > > Hi, Neks!

I am working with a complex geometry?which was built in gambit.?I have a velocity fields for my grid.?But I want to interpolate these velocity fields to a new grid. The old grid was changed without moving the geometry parameters, I just changed the position of the?computational nodes and reduced their number (see pictures old_grid and new_grid *). Interpolation ends as usual. The velocity field is interpolated perfectly, but the pressure field is not interpolated correctly?(see pictures pressure_field_before_interpolation and?pressure_field_after_interpolation **). > > Tell me, what is my mistake? Is it possible to interpolate from a larger number of nodes to a smaller number of nodes? > > *https://drive.google.com/open?id=1DmsGxc_WR3_aJW0UpLHkcxAVzt5BzABK >
?https://drive.google.com/open?id=1RbSsODF49DqGmyHnpz0Bktp-HDjW7j0w >?
**https://drive.google.com/open?id=16Ueepa1lo_aHjya3BnLn8fHI3ek0kvo8 >?
? ?https://drive.google.com/open?id=1CNiN8MdE7tNeu8T4jBtZBtMSX5dlXzNM >

Best regards,
Elizabeth > > _______________________________________________ > > 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 Nov 7 10:52:26 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 7 Nov 2018 17:52:26 +0100 Subject: [Nek5000-users] 'COMMON' block issue In-Reply-To: References: Message-ID: To me it looks like the number of elements are to large to fit on just 32 ranks. Increase lpmin! On 7 Nov 2018, at 17:11, nek5000-users--- via Nek5000-users > wrote: When you define your object in the common block, do you define it so that it stays the same size regardless of how many threads you use?? Presumably, it should look something like this: common /mydata/ data(lx1*ly1*lz1*lelt) So that when you double the number of threads, you halve the value of lelt On Mon, Oct 8, 2018 at 8:25 PM > wrote: Dear Nek users, ? Currently, I am working on a simulation with a decent size (11760 * 12 elements) employing ?lpmin = 32?. When I compile, I received an error saying: ?relocation overflows omitted from the output?.? I googled this error and it turned out this error comes from the ?COMMON? block; ?Static data, such as COMMON variables, and all of the code together is still limited to 2GB under any mcmodel.? The suggested solution is to ?move the data out of a COMMON block and into a module and make the data allocatable. The most straightforward way to avoid this would be increase the ?lpmin? (for example if lpmin = 64, then it works), but this does not solve this issue, which is a big constraint. I am wondering has anyone has run into this and got any experience in solving it? ? Thanks a lot in advance _______________________________________________ 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 Wed Nov 7 10:54:19 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 7 Nov 2018 17:54:19 +0100 Subject: [Nek5000-users] Remesh a moving geometry In-Reply-To: References: Message-ID: No, this is currently not implemented.? On 7 Nov 2018, at 17:11, nek5000-users--- via Nek5000-users > wrote: Hi Neks We try to simulate a flow with a moving?geometry. In order to avoid?large geometry distortions, we have to remesh the geometry at regular intervals.? It is possible to remesh the geometry during a simulation without a restart? Best regards, Philipp _______________________________________________ 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 Nov 7 12:01:50 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 07 Nov 2018 21:01:50 +0300 Subject: [Nek5000-users] =?utf-8?q?Genmap_Error=3F?= In-Reply-To: References: Message-ID: Hi! Maybe you should increase MAXNEL parameter in maketools script (Nek5000/tools)? nek5000-users : >Hello, >I created a ".re2" mesh by converting an Exodus (".exo") mesh from Cubit >15.0 using the "exo2nek" script. It's a relatively large mesh (780k >elements) and I need to run it using parallel processing, and so I >wanted to use the "genmap" script. > >However, I keep getting these errors, no matter what input mesh >tolerance value I use, from 0.2 to 0.00001): > >genmap >Input .rea / .re2 name: >RCF_3D_FullSimple >??reading RCF_3D_FullSimple.re2 >Input mesh tolerance (default 0.2): >NOTE: smaller is better, but generous is more forgiving for bad meshes. >0.00001 >??reading mesh data ... >??start locglob_lexico: 8 775728 6205824 >1.0000000000000001E-005 >??locglob: 1 1 6205824 >??locglob: 2 11290 6205824 >??locglob: 3 15413 6205824 >??locglob: 1 632909 6205824 >??locglob: 2 632909 6205824 >??locglob: 3 632909 6205824 >??locglob: 1 632909 6205824 >??locglob: 2 632909 6205824 >??locglob: 3 632909 6205824 > >593741 2 4 Matrix: SELF!! >????????1 SELF!! 313837 313837 313837 313837 >????????2 SELF!! 313837 313837 313837 313837 >??cont: SELF!! 593741 > >??ABORT: SELF-CHK 1 2 593741 0 >??Try to tighten the mesh tolerance! > >????????????0 quit > > >Do you have any idea what this means? Just from the output, it looks >like it's saying there are coincident vertices or elements? Is it a >problem with my mesh or with running the script? > >Thanks, >Matt >_______________________________________________ >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 Nov 7 14:09:07 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 7 Nov 2018 21:09:07 +0100 Subject: [Nek5000-users] Genmap Error? In-Reply-To: References: Message-ID: What you see is not related to MAXNEL otherwise genmap would bail out with an error message.? On 7 Nov 2018, at 19:01, nek5000-users--- via Nek5000-users > wrote: Hi! Maybe you should increase MAXNEL parameter in maketools script (Nek5000/tools)? nek5000-users >: Hello, I created a ".re2" mesh by converting an Exodus (".exo") mesh from Cubit 15.0 using the "exo2nek" script. It's a relatively large mesh (780k elements) and I need to run it using parallel processing, and so I wanted to use the "genmap" script. However, I keep getting these errors, no matter what input mesh tolerance value I use, from 0.2 to 0.00001): genmap Input .rea / .re2 name: RCF_3D_FullSimple ??reading RCF_3D_FullSimple.re2 Input mesh tolerance (default 0.2): NOTE: smaller is better, but generous is more forgiving for bad meshes. 0.00001 ??reading mesh data ... ??start locglob_lexico: 8 775728 6205824 1.0000000000000001E-005 ??locglob: 1 1 6205824 ??locglob: 2 11290 6205824 ??locglob: 3 15413 6205824 ??locglob: 1 632909 6205824 ??locglob: 2 632909 6205824 ??locglob: 3 632909 6205824 ??locglob: 1 632909 6205824 ??locglob: 2 632909 6205824 ??locglob: 3 632909 6205824 593741 2 4 Matrix: SELF!! ????????1 SELF!! 313837 313837 313837 313837 ????????2 SELF!! 313837 313837 313837 313837 ??cont: SELF!! 593741 ??ABORT: SELF-CHK 1 2 593741 0 ??Try to tighten the mesh tolerance! ????????????0 quit Do you have any idea what this means? Just from the output, it looks like it's saying there are coincident vertices or elements? Is it a problem with my mesh or with running the script? Thanks, Matt _______________________________________________ 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 Thu Nov 8 04:05:15 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 8 Nov 2018 11:05:15 +0100 Subject: [Nek5000-users] Genmap Error? Message-ID: The SELF-CHK failed meaning genmap thinks two element vertices of the same element are the same. Please check your mesh for invalid elements. -----Original message----- > From:nek5000-users--- via Nek5000-users > Sent: Wednesday 7th November 2018 21:11 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Genmap Error? > > What you see is not related to MAXNEL otherwise genmap would bail out with an error message.? > > On 7 Nov 2018, at 19:01, nek5000-users--- via Nek5000-users > wrote: > > Hi! > > Maybe you should increase MAXNEL parameter in maketools script (Nek5000/tools)? > > nek5000-users >: > Hello, > I created a ".re2" mesh by converting an Exodus (".exo") mesh from Cubit > 15.0 using the "exo2nek" script. It's a relatively large mesh (780k > elements) and I need to run it using parallel processing, and so I > wanted to use the "genmap" script. > > However, I keep getting these errors, no matter what input mesh > tolerance value I use, from 0.2 to 0.00001): > > genmap > Input .rea / .re2 name: > RCF_3D_FullSimple > ??reading RCF_3D_FullSimple.re2 > Input mesh tolerance (default 0.2): > NOTE: smaller is better, but generous is more forgiving for bad meshes. > 0.00001 > ??reading mesh data ... > ??start locglob_lexico: 8 775728 6205824 > 1.0000000000000001E-005 > ??locglob: 1 1 6205824 > ??locglob: 2 11290 6205824 > ??locglob: 3 15413 6205824 > ??locglob: 1 632909 6205824 > ??locglob: 2 632909 6205824 > ??locglob: 3 632909 6205824 > ??locglob: 1 632909 6205824 > ??locglob: 2 632909 6205824 > ??locglob: 3 632909 6205824 > > 593741 2 4 Matrix: SELF!! > ????????1 SELF!! 313837 313837 313837 313837 > ????????2 SELF!! 313837 313837 313837 313837 > ??cont: SELF!! 593741 > > ??ABORT: SELF-CHK 1 2 593741 0 > ??Try to tighten the mesh tolerance! > > ????????????0 quit > > > Do you have any idea what this means? Just from the output, it looks > like it's saying there are coincident vertices or elements? Is it a > problem with my mesh or with running the script? > > Thanks, > Matt > _______________________________________________ > 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 Nov 8 04:36:22 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 8 Nov 2018 11:36:22 +0100 Subject: [Nek5000-users] Problems in getting eigenvalues using ARNOLDI In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 8 04:44:31 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 8 Nov 2018 11:44:31 +0100 Subject: [Nek5000-users] Problems in getting eigenvalues using ARNOLDI In-Reply-To: References: Message-ID: For me it does not make sense to discuss something on our mailing list which is not part of Nek5000. Cheers, Stefan -----Original message----- > From:nek5000-users--- via Nek5000-users > Sent: Thursday 8th November 2018 11:37 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Problems in getting eigenvalues using ARNOLDI > > Hi Alok, > > First of all I think you should > increase the number of steps per Arnoldi iteration (p109) even > more, for example multiplying it by 4. The columns 2 and 3 ( > re(RITZ) and im(RITZ)) show that the operator seen by ARPACK is > close to identity, all the Ritz values are close to 1. > > I forgot to mention this earlier, but > it might also converge faster if you increase the Krylov space > size p111 to 120 (four times the number of eigenvalues that you > request). > > Regarding the 0 frequency modes, I > often see them related to boundaries. I am not exactly sure where > they come from. It is difficult to say anything without seeing > what the eigenvectors look like. > > Regards, > Guillaume > > On 30/10/2018 06:40, nek5000-users--- > via Nek5000-users wrote: > Hi Guillaume, > > I tried with the help of your valuable suggestions. I am > getting dominant Eigenvalue with time period 8.34 which is > very much close to the literature. However, I require 30 > Eigen values by setting P112=30 and P111=90. Below is the > eigenvalues I am getting after many restarts. > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? re(RITZ); ? > ? ? ? ? ? ? ? ? ? ? im(RITZ) ? > ? ? ? ? ? ? ln|RITZ|; ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? > arg(RITZ) > ? ? ? ? ? ?1 ? 0.991128702238537 > ? ? ? 0.150881402754817 ? ?? 1.272083634754888E-002 > ? ? 0.755360071443281 ? ?? > ? ? ? ? ? ?2 ? 0.991128702238537 > ? ? ?-0.150881402754817 ? ?? 1.272083634754888E-002 > ? ?-0.755360071443281 ? ?? > ? ? ? ? ? ?3 ? 0.991728721496092 > ? ? ? 1.806383192432841E-002 -4.069909517841635E-002 > ? ? 9.106237555496137E-002 > ? ? ? ? ? ?4 ? 0.991728721496092 > ? ? ?-1.806383192432841E-002 -4.069909517841635E-002 > ? ?-9.106237555496137E-002 > ? ? ? ? ? ?5 ? 0.989791831070271 > ? ? ? 3.446186469202143E-002 -4.827437507304033E-002 > ? ? 0.174016133198715 ? ?? > ? ? ? ? ? ?6 ? 0.989791831070271 > ? ? ?-3.446186469202143E-002 -4.827437507304033E-002 > ? ?-0.174016133198715 ? ?? > ? ? ? ? ? ?7 ? 0.987601103156919 > ? ? ? 5.049392478862426E-000 -5.585540570484418E-002 > ? ? 0.255416865677410 ? ?? > ? ? ? ? ? ?8 ? 0.987601103156919 > ? ? ?-5.049392478862426E-002 -5.585540570484418E-002 > ? ?-0.255416865677410 ? ?? > ? ? ? ? ? ?9 ? 0.995627135254111 > ? ? ? 0.000000000000000E+000 -2.191226841613384E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 10 ? 0.995700191328997 > ? ? ? 0.000000000000000E+000 -2.154539716426180E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 11 ? 0.995229254767405 > ? ? ? 0.000000000000000E+000 -2.391080780851450E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 12 ? 0.995434205850176 > ? ? ? 0.000000000000000E+00 -2.288124611941097E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 13 ? 0.994877066906734 > ? ? ? 0.000000000000000E+000 -2.568050152041379E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 14 ? 0.994526533813701 > ? ? ? 0.000000000000000E+000 -2.744250243633435E-002. > ? ?0.000000000000000E+000 > ? ? ? ? ? 15 ? 0.994024234181460 > ? ? ? 0.000000000000000E+000 -2.996846079257938E-002. > ? ?0.000000000000000E+000 > ? ? ? ? ? 16 ? 0.992886352948494 > ? ? ? 0.000000000000000E+000 -3.569534837742794E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 17 ? 0.993531725861019 > ? ? ? 0.000000000000000E+000 -3.244642035911912E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 18 ? 0.992269436061858 > ? ? ? 0.000000000000000E+000 -3.880299821483946E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 19 ? 0.991568951835935 > ? ? ? 0.000000000000000E+000 -4.233395244633451E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 20 ? 0.991491977086931 > ? ? ? 0.000000000000000E+000 -4.272211373739676E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 21 ? 0.991513431383682 > ? ? ? 0.000000000000000E+000 -4.261392292430112E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 22 ? 0.991180149347166 > ? ? ? 0.000000000000000E+00 -4.429487878603097E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 23 ? 0.991284115416627 > ? ? ? 0.000000000000000E+000 -4.377045031887505E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 24 ? 0.990874009258556 > ? ? ? 0.000000000000000E+000 -4.583943845265666E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 25 ? 0.990632850108536 > ? ? ? 0.000000000000000E+000 -4.705648774052894E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 26 ? 0.990852910254318 > ? ? ? 0.000000000000000E+000 -4.594590622089855E-002. > ? ?0.000000000000000E+000 > ? ? ? ? ? 27 ? 0.990206173286647 > ? ? ? 0.000000000000000E+000 -4.921050845320660E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 28 ? 0.990051445648789 > ? ? ? 0.000000000000000E+000 -4.999185950921724E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 29 ? 0.989332783273003 > ? ? ? 0.000000000000000E+000 -5.362259677015029E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 30 ? 0.989848247701740 > ? ? ? 0.000000000000000E+000 -5.101816376314156E-002 > ? ? 0.000000000000000E+000 > ? ? ? ? ? 31 ? 0.989278105749528 > ? ? ? 0.000000000000000E+000 -5.389893975295782E-002 > ? ? 0.000000000000000E+000 > > ? ?I am unable to understand the reason behind getting so > many Eigenvalues with zero imaginary part/rotation. Please > help. > > Regards, > > On Wed, Oct 3, 2018 at 2:54 PM > > wrote: > Hi, > > What > is your time step? I calculated the spectrum of the > cylinder flow a while ago at Re=44 and I got an angular > frequency of 0.7278, which corresponds to a period of > 8.63. > It > is possible that 40 time steps per Arnoldi iteration is > too small; a good start is to integrate for 1/10th of > the period, so dt*p109 = 0.8 approximately. I used 120 > time steps at dt=4.2e-3 but it may be faster with more > steps. > It > depends on which frequencies you want to resolve; if you > integrate for a short time your operator is close to > identity and all eigenvalues are close to 1, but if you > integrate for too long then the frequencies of the > eigenvalues you are interested in will be aliased. > > I > think you could try decreasing p021 and p022 to maybe > 1e-10 or 1e-12 and see if helps, too. > > Best, > Guillaume > > On > 03/10/2018 07:24, nek5000-users at lists.mcs.anl.gov > wrote: > Hi Guillaume, > > Thanks for your?reply. My reply to > your queries is as below:- > > 1) I am getting unstable pair of > Eigen values with growth rate around > 0.02. > 2) Solver tolerance that I used are > ; > ? 7.00000 ? ? ? ? ? ? ?p020 > NORDER > ? 0.100000E-09 ? ?p021 DIVERGENCE > ? 0.100000E-09. ? p022 HELMHOLTZ > ? ?0.00000 ? ? ? ? ? ? p023 > NPSCAL > ? 0.100000E-09 ? ?p024 TOLREL > ? 0.100000E-04 ? ?p025 TOLABS > 1.00000E-05. ? ? ? p113 : ARNOLDI: > arpack tolerance > > > 3) Boundary conditions are : > > I am using sponge strength at inlet > and outlet with following details in > .rea file > ? ?1.00000 ? ? p119 : SPONGE > STRENGTH > ? ?25.0000 ? ? p120 : SPONGE TOTAL > WIDTH > ? ?3.00000 ? ? p121 : SPONGE DROP > WIDTH (INFLOW) > ? ?5.00000 ? ? p122 : SPONGE RISE > WIDTH (OUTFLOW)? > the sponge function and its cal is > detailed in userf subroutine of .usr > file > > Also following is defined in .usr > file > c----------------------------------------------------------------------- > ? ? ? subroutine userbc > (ix,iy,iz,iside,eg) > > ? ? ? include 'SIZE' > ? ? ? include 'NEKUSE' ? ? ? ? ?! > UX, UY, UZ, TEMP, X, Y > ? ? ? include 'PARALLEL' ? ? ? ?! > GLLEL > > > ? ? ? integer e,eg > > c ? ? velocity > c ? ? ?e ?= ?GLLEL(eg) > ? ? ? UX = 0.0 > ? ? ? UY = 0.0 > ? ? ? UZ = 0.0 > > c ? ? t > ? ? ? TEMP=0.0 > > ? ? ? return > ? ? ? end > c----------------------------------------------------------------------- > ? ? ? subroutine useric > (ix,iy,iz,ieg) > > ? ? ? include 'SIZE' > ? ? ? include 'NEKUSE' ? ? ? ? ?! > UX, UY, UZ, TEMP, Z > ? ? ? integer idum > ? ? ? save ? ?idum? > ? ? ? data ? ?idum / 0 / > > ? ? ? real eps > > ? ? ? if (idum.eq.0) idum = 99 + > nid > ? ? ? eps = 0.1 > > c ? ? velocity > c ? ? random distribution > ? ? ? UX = eps*(ran1(idum)-0.50) > ? ? ? UY = eps*(ran1(idum)-0.50) > ? ? ? UZ = eps*(ran1(idum)-0.50) > > c ? ? t > ? ? ? TEMP=0 > > ? ? ? return > ? ? ? end > > > 40.0000 ? ? p109 : ARNOLDI: > frequency of calling arn_solve > ? ?4.00000 ? ? p110 : ARNOLDI: > maximal number of arnoldi cycles > ? 90.0000 ? ? p111 : ARNOLDI: size > of Krylov space > ? ?30.0000 ? ? p112 : ARNOLDI: > number of eigenvectors > > > If I am increasing the Krylov > subspace then will I get Eigen values at > lesser restart ? > > Kindly help please as I am new to > this. Thanks in advance. > > Alok Mishra > Research Scholar? > Computational Propulsion Lab? > Aerospace Department IIT Kanpur > +91-8795844555 > > _______________________________________________ > 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 >
> > -- > Alok Mishra > Research Scholar? > Computational Propulsion Lab? > Aerospace Department IIT Kanpur > +91-8795844555 > > _______________________________________________ > 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 Nov 7 18:59:53 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 8 Nov 2018 00:59:53 +0000 Subject: [Nek5000-users] gradient at every point In-Reply-To: References: Message-ID: Yes, you can use the subroutine 'gradm1(ux,uy,uz,u)'. From: Nek5000-users On Behalf Of nek5000-users--- via Nek5000-users Sent: Tuesday, 16 October 2018 10:10 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] gradient at every point Hi, I am a new user. Want to calculate gradient at every point so as to obtain TKE values. Is there a subroutine for this? Thanks, Samuel -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 14 20:13:06 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 15 Nov 2018 02:13:06 +0000 Subject: [Nek5000-users] Accuracy & errors Message-ID: Dear Nek users, I would like to do a quick test to see the difference in accuracy using two different P-orders, i.e. N = 7, and N = 11. The question I have is about the role of time integration errors. If the code uses 2nd or 3rd order of integration in time. That means that at some point the time-integration error will be larger than the spatial error. I wonder what are conditions under which it happens? Because once you are in that regime you will not see any difference between the various methods. Thanks for the help. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 15 06:48:08 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 15 Nov 2018 13:48:08 +0100 (CET) Subject: [Nek5000-users] Moving wall in userbc Message-ID: Hello Neks, Since my mesh is quiet complex, it is difficult to impose velocities into the moving wall in userbc. Is there any other way to filter(highlight) the moving wall bcs from inlet bcs in userbc other than using the positions? Regards Sijo George From nek5000-users at lists.mcs.anl.gov Thu Nov 15 06:51:19 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 15 Nov 2018 13:51:19 +0100 (CET) Subject: [Nek5000-users] Moving wall in userbc Message-ID: Hello Neks, Since my mesh is quiet complex, it is difficult to impose velocities into the moving wall in userbc. Is there any other way to filter(highlight) the moving wall bcs from inlet bcs in userbc other than using the positions? Regards Sijo George From nek5000-users at lists.mcs.anl.gov Thu Nov 15 07:15:19 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 15 Nov 2018 13:15:19 +0000 Subject: [Nek5000-users] Accuracy & errors In-Reply-To: References: Message-ID: Typically you will see spatial convergence down to a point where temporal errors dominate, then things will level off. See for example Fig. 4 in www.mcs.anl.gov/~fischer/users.pdf for Figs. 4 and 5 in "Recent Developments in Spectral Element Simulations of Moving Domain Problems", Fischer, Schmitt, Tomboulides. The benefits of high order in space, despite relatively low order in time, derive from the fact that the costs are multiplicative (number of spatial dofs X number of timesteps), and from the fact that spatial errors typically dominate most high Reynolds number flow problems because of numerical dispersion and dissipation. Having a high-order method allows you to realize minimal numerical dispersion at a relatively low number of points per wavelength. Paul ________________________________ From: Nek5000-users on behalf of nek5000-users--- via Nek5000-users Sent: Wednesday, November 14, 2018 8:13:06 PM To: NEK5000 Subject: [Nek5000-users] Accuracy & errors Dear Nek users, I would like to do a quick test to see the difference in accuracy using two different P-orders, i.e. N = 7, and N = 11. The question I have is about the role of time integration errors. If the code uses 2nd or 3rd order of integration in time. That means that at some point the time-integration error will be larger than the spatial error. I wonder what are conditions under which it happens? Because once you are in that regime you will not see any difference between the various methods. Thanks for the help. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Nov 18 20:57:50 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 19 Nov 2018 10:57:50 +0800 (CST) Subject: [Nek5000-users] How to achieve the exo format mesh with HEX20 type? Message-ID: Dear Neks, I have seen that the tools exo2nek is proposed for mesh format conversion but I am quite wondering how I can get the .exo format mesh from ICEM. Should I directly output the unstructured mesh with the solver selected as EXODUS-II and put the .exo mesh into use for exo2nek? How can I ensure the .exo format is comprised of HEX20 meshes? Thank you so much for your comments! Haoran -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Nov 19 14:27:34 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 19 Nov 2018 15:27:34 -0500 Subject: [Nek5000-users] Error Loading .re2 Mesh Message-ID: Hello, I've created a mesh using Cubit 15.0 with HEX27 elements. The Jacobian for these elements are all positive and by all appearances it is a conformal mesh (no unmerged vertices, surfaces, or curves and it imports correctly in both Cubit and VisIt). I was able to convert the mesh from Exodus format (.exo) to the .re2 format using the "exo2nek" script and created a map file (.ma2) using the "genmap" script. However, when I try to use this mesh in Nek5000, it gives the following errors (found in the logfile): element load imbalance: 0 612 612 done :: mapping 0.63601 sec ERROR 2 READING MESH DATA NEAR ELEMENT 6 ABORTING IN ROUTINE RDMESH. an error occured: dying ... I cannot tell why it is crashing. My mesh is a 3D mesh with a total of 19584 elements, with all of them being flow elements. I specified in the .rea file the following: **MESH DATA** 19584 3 19584 NELT,NDIM,NELV Is this perhaps the problem? Did I not specify this line correctly? Or is something wrong with the mesh? Thanks, Matt From nek5000-users at lists.mcs.anl.gov Sun Nov 25 13:38:26 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 25 Nov 2018 16:38:26 -0300 Subject: [Nek5000-users] Placing cyllinder near wall Message-ID: Hi all, I'm testing the effects of near wall obstacles, but I'm struggling to decide for a adequate method to build the mesh. The main goals are to have a hyperbolic mesh spacing perpendicularly to the the wall and easiness to place a cylinders inside that mesh close to a wall. So far I've been using makenek to build a series of boxes and replacing one with a cylinder box. The main issue is that grid size is hyperbolic everywhere, except in the boxes that lay in axis of the cylinder, where the mesh becomes uniform in order to fit the cylinder generated with makenek; and that the custom Fortran script that generates the .box files is quite bothersome to modify freely. I was wondering if nekenk could be used to place a cylinder inside a box with user-specified distribution or if you could recommend a meshing software or code that could do the job (hopefully linux-friendly and free). Regards, *Nicol?s* -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Nov 26 00:59:58 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 26 Nov 2018 09:59:58 +0300 Subject: [Nek5000-users] =?utf-8?q?Mesh_with_a_large_number_of_curves?= Message-ID: Hi, Neks! I wonder if there is any instrument to create mesh for Nek5000 with complex geometry with a large number of curves? The problem is in the fact, that typically mesh creators (like GAMBIT or PointWise) create points only for the boundaries of spectral elements, then Nek creates points according with GLL rule so that they either go beyond the boundaries of real geometry or cut it off. I want mesh points to be directly on the surface of my geometry. Best regards, Markus -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 28 10:10:51 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 28 Nov 2018 16:10:51 +0000 Subject: [Nek5000-users] Heat flux boundary condition Message-ID: Hi Neks, i am calculating a laminar pipe flow. The temperature boundary conditions are a fixed fluid temperature at the entrance and a constant wall heat flux over a short section in the middle oft the pipe. The remaining pipe wall is adiabatic. For the velocity field I assume periodic BCs. Because the given heat flux contour over the axial coordinate should be an ideal hat-function, I expected the temperature gradient to have the same contour. But when calculating the temperature gradient at the wall, the resulting temperature gradient contour doesn?t represent an ideal hat-function but a more rounded down contour. Now I am wondering, if Nek can not implement the given heat flux BC correctly. Did anybody have similar experiences? Thank you! Theresa -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Nov 30 07:33:01 2018 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 30 Nov 2018 07:33:01 -0600 Subject: [Nek5000-users] Heat flux boundary condition In-Reply-To: References: Message-ID: You need to have the discontinuous heat flux be prescribed in a discontinuous way. This can be done by having element boundaries at precisely the start and stop points of the top hat region and then using a check to see if the element in question is within that region. Below is a sample userbc routine that should work if the top hat region is on (0,4) and that you have prescribed "f " BCs for temperature along the walls (or a mixture of "f " and "I "). Note that "f " with zero flux behaves the same as "I " (insulated). hth, Paul c----------------------------------------------------------------------- subroutine userbc(i,j,k,f,eg) ! set up boundary conditions c NOTE: This subroutine is not guaranteed to be called by each rank. include 'SIZE' include 'TOTAL' include 'NEKUSE' integer e,f,eg ux = 0.0 uy = 0.0 uz = 1-4*(x*x+y*y) ! Parabolic inflow for radius=0.5 temp = 1.0 ! Temperature at inlet e = gllel(eg) zi = zm1(1,1,2,e) ! Interior z location flux = 0.0 ! Zero flux if (0.lt.zi.and.zi.lt.4) flux=1 ! Flux only on interior region return end c----------------------------------------------------------------------- On Fri, Nov 30, 2018 at 7:04 AM nek5000-users--- via Nek5000-users < nek5000-users at lists.mcs.anl.gov> wrote: > Hi Neks, > > > i am calculating a laminar pipe flow. The temperature boundary conditions > are a fixed fluid temperature at the entrance and a constant wall heat flux > over a short section in the middle oft the pipe. The remaining pipe wall is > adiabatic. For the velocity field I assume periodic BCs. > > Because the given heat flux contour over the axial coordinate should be an > ideal hat-function, I expected the temperature gradient to have the same > contour. > > But when calculating the temperature gradient at the wall, the resulting > temperature gradient contour doesn?t represent an ideal hat-function but a > more rounded down contour. > > Now I am wondering, if Nek can not implement the given heat flux BC > correctly. Did anybody have similar experiences? > > > Thank you! > > Theresa > > > _______________________________________________ > 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: