February 2018 - Nek5000-users - mailman3.cels.anl.gov

Re: [Nek5000-users] subroutines of gradm1 and interp_v3
by nek5000-users＠lists.mcs.anl.gov 14 Feb '18

14 Feb '18

Hi Jian, gradm1 is a routine in navier5.f that you should be able to use on any mesh to compute the gradient of any field. interp_v is an interpolation routine based on fgslib_findpts. In v17, a wrapper has been made available to use these routines. See intp_usr.f in the repo for these wrappers, and the hemi example in the Nek example repo for its usage. Ketan

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subroutines of gradm1 and interp_v3
by nek5000-users＠lists.mcs.anl.gov 14 Feb '18

14 Feb '18

Hi Nek, May I know whether the following two subroutines can be used for different geometries without changing? 1. gradm1 ( http://www.mcs.anl.gov/research/projects/nek5/docs/html/navier5_8f_source.h… ) 2. interp_v3 ( https://lists.mcs.anl.gov/pipermail/nek5000-users/2011-July/001409.html) Regards, Jian

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v17.0 vs v17.0.0.beta2 regarding Stress Formulation and Pn/Pn-2
by nek5000-users＠lists.mcs.anl.gov 13 Feb '18

13 Feb '18

Dear All, I am using mixed 'W ' and 'SYM' boundary conditions on a boundary that is not aligned with x,y,z axes. (with IFSTRS=T) When using the previous v17.0.0.beta2 version, I could use these mixed boundary conditions with the Pn/Pn pressure formulation, giving a continuous pressure field. After upgrading to v17.0, I get a number of the following runtime errors when using Pn/Pn: --- Mixed B.C. on a side nonaligned with either the X,Y, or Z axis detected for Element 8 side 1 Requires PN/PN-2 STRESS FORMULATION --- Pn/Pn-2 runs, as expected. Granted that I have to use Pn/Pn-2 for mixed BC when not aligned with an axis, the problem is that the pressure is discontinuous, which is stated in the documentation for the Pn/Pn-2 formulation. This is evident when plotting the pressure in Visit. Is there a way to obtain a smooth (correct?) pressure field when using Pn/Pn-2? Or is there a way to use the Pn/Pn formulation with such boundary conditions? Thank you, Jean

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Restart using second order scheme
by nek5000-users＠lists.mcs.anl.gov 13 Feb '18

13 Feb '18

Dear Neks: I am using second order time time integration scheme for the computations. Since the second order scheme uses the flow field at (n) and (n-1) to compute the solution at (n+1) we need two files to do a full restart. If, however, we do not do a full restart and simply load the file using restart feature in .rea file, how is the second order scheme implemented for the first time step? Thank you. Best wishes, NN.

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Re: [Nek5000-users] Nek5000-users Digest, Vol 108, Issue 18
by nek5000-users＠lists.mcs.anl.gov 12 Feb '18

12 Feb '18

Hi Amitvikram, for all practical purposes there shouldn't be any backward compatibility issues between the two versions of Nek5000. It is recommended to use the latest, because there has been some improvements which has been found to reduce the solution time. Also, there is no installation involved with Nek5000, if you have v16 working, you can just download the v17 into your home folder and build/compile exactly the same way you built the previous version. I hope this helps. cheers Som Som Dutta Post Doctoral Research Associate Dept. of Computer Science University of Illinois at Urbana-Champaign On Mon, Feb 12, 2018 at 12:00 PM, <nek5000-users-request(a)lists.mcs.anl.gov> wrote: > Send Nek5000-users mailing list submissions to > nek5000-users(a)lists.mcs.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > or, via email, send a message with subject or body 'help' to > nek5000-users-request(a)lists.mcs.anl.gov > > You can reach the person managing the list at > nek5000-users-owner(a)lists.mcs.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Nek5000-users digest..." > > > Today's Topics: > > 1. Transitioning from v16 to v17 (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: Transitioning from v16 to v17 > (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 11 Feb 2018 22:57:55 +0000 > From: nek5000-users(a)lists.mcs.anl.gov > To: "nek5000-users(a)lists.mcs.anl.gov" > <nek5000-users(a)lists.mcs.anl.gov> > Subject: [Nek5000-users] Transitioning from v16 to v17 > Message-ID: > <mailman.8402.1518389888.19102.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I'm thinking of transitioning from v16 to v17. I do however have a large > number of previous simulations in v16. I'd like to be able to keep using > them in v17. Additionally the cluster I have acess to has only v16 > installed and the process to upgrade the version could take a significant > amount of time. > > What is the back-compatibility level between v16 and v17? What factors must > I keep in mind so that I can run my v16 versions on v17? > > Sincerely, > -- > > *Amitvikram Dutta* > > Graduate Research Assistant > > Fluid Mechanics Research Lab > > Multi-Physics Interaction Lab > > University of Waterloo >

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Re: [Nek5000-users] Transitioning from v16 to v17
by nek5000-users＠lists.mcs.anl.gov 12 Feb '18

12 Feb '18

Note, 16.0 was a development version of the code and not an official release. We do strongly recommend to update to v17.0. There is no installation process. Just untar the tarball and compile the code. In less than 2-3min you are done. The code is fully backward compatbile. For more details please check the release notes. -----Original message----- > From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > Sent: Sunday 11th February 2018 23:58 > To: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] Transitioning from v16 to v17 > > Hi all, > > Im thinking of transitioning from v16 to v17. I do however have a large number of previous simulations in v16. Id like to be able to keep using them in v17. Additionally the cluster I have acess to has only v16 installed and the process to upgrade the version could take a significant amount of time. > > What is the back-compatibility level between v16 and v17? What factors must I keep in mind so that I can run my v16 versions on v17? > > Sincerely, > -- > Amitvikram Dutta > Graduate Research Assistant > Fluid Mechanics Research Lab > Multi-Physics Interaction Lab > University of Waterloo > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

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Transitioning from v16 to v17
by nek5000-users＠lists.mcs.anl.gov 11 Feb '18

11 Feb '18

Hi all, I'm thinking of transitioning from v16 to v17. I do however have a large number of previous simulations in v16. I'd like to be able to keep using them in v17. Additionally the cluster I have acess to has only v16 installed and the process to upgrade the version could take a significant amount of time. What is the back-compatibility level between v16 and v17? What factors must I keep in mind so that I can run my v16 versions on v17? Sincerely, -- *Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab Multi-Physics Interaction Lab University of Waterloo

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turbChannel: Questions about targetCFL and dealiasing
by nek5000-users＠lists.mcs.anl.gov 11 Feb '18

11 Feb '18

Dear Nek users, I have some fundamental questions in terms of CFL and dealiasing in the example of turbChannel. In the .par file, I noticed that the default setting of targetCFL is as high as 3.5, which really makes the code run very fast. But, typically, this CFL value is around 0.5 using implicit fractional time-step approach based on the FV method. Why CFL could be this high here while not compromising the stability? Is it because of the spectral element method? And Could you also please tell me when shall I turn on or off dealiasing? Regards, Emily

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Re: [Nek5000-users] DNS of turbChannel
by nek5000-users＠lists.mcs.anl.gov 10 Feb '18

10 Feb '18

The turbChannel example is using a high pass filter relaxation term as SGS. For a DNS just - set lx1=8 and lxd=12 in SIZE - generate a finer mesh with more elements using genbox (if you change the mesh make sure to delete the old amg files) - set filtering=no in par -----Original message----- > From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > Sent: Friday 9th February 2018 20:32 > To: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] DNS of turbChannel > > Hello Paul, > Thank you a lot for your explanation; it really helps. For now, I am using the most recent turChannel example of NEK5000 V.17. I successfully simulated a turbulent channel with a Retau of 180 using 1536 elements (I am aware of its a lot > of elements). The default settings were applied. I wonder is it in the .par file where you do the modification to convert it into DNS? Or somewhere else as well? > Again, thank you for the help, > Emily > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

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Re: [Nek5000-users] DNS of turbChannel
by nek5000-users＠lists.mcs.anl.gov 09 Feb '18

09 Feb '18

Hello Paul, Thank you a lot for your explanation; it really helps. For now, I am using the most recent turChannel example of NEK5000 V.17. I successfully simulated a turbulent channel with a Retau of 180 using 1536 elements (I am aware of it's a lot of elements). The default settings were applied. I wonder is it in the .par file where you do the modification to convert it into DNS? Or somewhere else as well? Again, thank you for the help, Emily

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