June 2017 - Nek5000-users - mailman3.cels.anl.gov

Re: [Nek5000-users] Full restart with increasing lx ([email protected])
by nek5000-users＠lists.mcs.anl.gov 25 Jul '17

25 Jul '17

Hello, I've been able to use the full restart function increasing lx1, but in my case I had to change the timestep size (DT) in order to satisfy the CFL condition, so the solution that was saved did not work properly with the full restart because it was obtained using a different DT. So this is something for you to consider. Best, Juan Diego

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calculate gradients of fluctuation
by nek5000-users＠lists.mcs.anl.gov 29 Jun '17

29 Jun '17

Hi nek users, For u=U + u’ where U= mean streamwise velocity and u’= fluctuation of streamwise velocity I know how to calculate du/dx , du/dy and du/dz. But how can I calculate gradients of the fluctuation of streamwise veloctity, i.e. du’/dx , du’/dy , du’/dz ? Thank you.

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Re: [Nek5000-users] Nek5000-users Digest, Vol 100, Issue 30
by nek5000-users＠lists.mcs.anl.gov 28 Jun '17

28 Jun '17

Hi Paul, I changed the elements in the straight pipe which is I am doing at the moment. I set the horizontal and vertical axis as 14 spectral elements in the quarter-section for the simulation at Re=5300 based on bulk velocity. And the pipe length is 25R. Do you think it's enough to run the simulation? By the way, I run the simulation for a short time, after which I used visit to check the mesh finding that there are several things inside the pipe which are likely to be walls. And I found the mesh in visit shows that the cross-sectional views are different in the outlet and inlet which is open or closed. I set the axis view in visit to not show the axis. Kind regards, Jian On 27 June 2017 at 18:00, <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. Re: Nek5000-users Digest, Vol 100, Issue 29 > (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: Nek5000-users Digest, Vol 100, Issue 29 > (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 26 Jun 2017 18:06:06 +0100 > From: nek5000-users(a)lists.mcs.anl.gov > To: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 100, Issue 29 > Message-ID: > <mailman.9646.1498496769.2967.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset="utf-8" > > Hi Paul, > > Now the number of total elements is 576000 written in the rea file. By the > way, would you please tell me the reason why only 1/1000 number of elements > are needed indeed with SEM. > > Kind regards, > > Jian > > > > Message: 2 > > Date: Mon, 26 Jun 2017 15:27:28 +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: Re: [Nek5000-users] genmap > > Message-ID: > > <mailman.9625.1498490850.2967.nek5000-users(a)lists.mcs.anl.gov> > > Content-Type: text/plain; charset="us-ascii" > > > > > > Dear Jiang, > > > > > > I think you have too many elements. Keep in mind that with the SEM you > > need about 1/1000th of the number of elements that you would for FEM. > > > > > > What is the largest SEM run you have made so far? > > > > > > Best, Paul > > > > > > ________________________________ > > From: nek5000-users-bounces(a)lists.mcs.anl.gov < > > nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of > > nek5000-users(a)lists.mcs.anl.gov <nek5000-users(a)lists.mcs.anl.gov> > > Sent: Monday, June 26, 2017 8:49:06 AM > > To: nek5000-users(a)lists.mcs.anl.gov > > Subject: [Nek5000-users] genmap > > > > Hi Neks, > > > > Is there anyone know the reason for the following error, in which there > > are hundred millions of grid points in the geometry. > > > > ABORT: NELT>LELM, modify LELM in SIZE and recompile > > > > I changed the LELM to be big enough, even equals to 7000000000000, but it > > doesn't work though. I guess the reasons would be: > > > > 1. genmap cannot regonize large elements mesh; > > 2. I didn't get a recompilation after changing LELM parameter since I > > don't know how to compile and thought genmap commond would be changed > > automatically when the SIZE file in /home/bin/genmap was changed. > > > > Kind regards, > > > > Jian > >

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Re: [Nek5000-users] Nek5000-users Digest, Vol 100, Issue 29
by nek5000-users＠lists.mcs.anl.gov 26 Jun '17

26 Jun '17

Hi Paul, Now the number of total elements is 576000 written in the rea file. By the way, would you please tell me the reason why only 1/1000 number of elements are needed indeed with SEM. Kind regards, Jian > Message: 2 > Date: Mon, 26 Jun 2017 15:27:28 +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: Re: [Nek5000-users] genmap > Message-ID: > <mailman.9625.1498490850.2967.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset="us-ascii" > > > Dear Jiang, > > > I think you have too many elements. Keep in mind that with the SEM you > need about 1/1000th of the number of elements that you would for FEM. > > > What is the largest SEM run you have made so far? > > > Best, Paul > > > ________________________________ > From: nek5000-users-bounces(a)lists.mcs.anl.gov < > nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of > nek5000-users(a)lists.mcs.anl.gov <nek5000-users(a)lists.mcs.anl.gov> > Sent: Monday, June 26, 2017 8:49:06 AM > To: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] genmap > > Hi Neks, > > Is there anyone know the reason for the following error, in which there > are hundred millions of grid points in the geometry. > > ABORT: NELT>LELM, modify LELM in SIZE and recompile > > I changed the LELM to be big enough, even equals to 7000000000000, but it > doesn't work though. I guess the reasons would be: > > 1. genmap cannot regonize large elements mesh; > 2. I didn't get a recompilation after changing LELM parameter since I > don't know how to compile and thought genmap commond would be changed > automatically when the SIZE file in /home/bin/genmap was changed. > > Kind regards, > > Jian >

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genmap
by nek5000-users＠lists.mcs.anl.gov 26 Jun '17

26 Jun '17

Hi Neks, Is there anyone know the reason for the following error, in which there are hundred millions of grid points in the geometry. ABORT: NELT>LELM, modify LELM in SIZE and recompile I changed the LELM to be big enough, even equals to 7000000000000, but it doesn't work though. I guess the reasons would be: 1. genmap cannot regonize large elements mesh; 2. I didn't get a recompilation after changing LELM parameter since I don't know how to compile and thought genmap commond would be changed automatically when the SIZE file in /home/bin/genmap was changed. Kind regards, Jian

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Re: [Nek5000-users] Help: compute dissipation
by nek5000-users＠lists.mcs.anl.gov 24 Jun '17

24 Jun '17

Hi Paul, No, I haven’t tried with Poiseiulle flow. Any reason as to why I should test it on that flow? Thank, Kiran > On 23 Jun 2017, at 16:21, 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. Re: Help: compute dissipation (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 23 Jun 2017 15:17:51 +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: Re: [Nek5000-users] Help: compute dissipation > Message-ID: > <mailman.9487.1498231285.2967.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset="windows-1252" > > > Hi, > > > Have you tested your routine on plane Poiseiulle flow, > > u=1-y^2 ? > > > Paul > > ________________________________ > From: nek5000-users-bounces(a)lists.mcs.anl.gov <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users(a)lists.mcs.anl.gov <nek5000-users(a)lists.mcs.anl.gov> > Sent: Friday, June 23, 2017 8:12:37 AM > To: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] Help: compute dissipation > > Hi NEK users, > > I am trying to calculate dissipation for fully developed turbulent channel flow. I tried the code below, but result I got from this totally disagrees with Vreman?s 2014 paper. x-axis is streamwise, y-axis is wall-normal and z-axis is spanwise. Any errors in the code? Any thoughts? > > real diss_sqr(lx1,ly1,lz1, lelt) > real s11 > real s12 > real s13 > real s22 > real s23 > real s33 > > > common /plane/ uavg_pl(ly1*lely) > $ , vavg_pl(ly1*lely) > $ , wavg_pl(ly1*lely) > $ , urms_pl(ly1*lely) > $ , vrms_pl(ly1*lely) > $ , wrms_pl(ly1*lely) > $ , uvms_pl(ly1*lely) > $ , diss_sqr_pl(ly1*lely) > $ , yy(ly1*lely) > $ , w1(ly1*lely),w2(ly1*lely) > $ , ffx_avg, dragx_avg > > > parameter (lr=lx1*ly1*lz1) > common /scruz/ ur(lr),us(lr),ut(lr) > $ , vr(lr),vs(lr),vt(lr) > $ , wr(lr),ws(lr),wt(lr) > > > common /avg/ uavg(lx1,ly1,lz1,lelv) > & , vavg(lx1,ly1,lz1,lelv) > & , wavg(lx1,ly1,lz1,lelv) > & , urms(lx1,ly1,lz1,lelv) > & , vrms(lx1,ly1,lz1,lelv) > & , wrms(lx1,ly1,lz1,lelv) > & , uvms(lx1,ly1,lz1,lelv) > & , dissavg(lx1,ly1,lz1,lelv) > > > common /scrns/ sij (lx1*ly1*lz1,6,lelv) > > if(icalld.eq.0) then > call rzero(uavg,n) > call rzero(urms,n) > call rzero(vrms,n) > call rzero(wrms,n) > call rzero(uvms,n) > call rzero(dissavg,n) > call rzero(wavg,n) > call rzero(vavg,n) > call rzero(diss_sqr,n) > > > call comp_sij(sij,6,vx,vy,vz,ur,us,ut,vr,vs,vt,wr,ws,wt) > > do e=1,nelt > do i = 1,nx1*ny1*nz1 > s11=sij(i,1,e) > s12=sij(i,4,e) > s22=sij(i,2,e) > s13=sij(i,6,e) > s23=sij(i,5,e) > s33=sij(i,3,e) > > diss_sqr(i,1,1,e) = (s11*s11) + > $ (s22*s22) + > $ (s33*s33) + > $ (s12*s12)*2 + (s23*s23)*2 + > $ (s13*s13)*2 > > enddo > enddo > > call avg1(dissavg,diss_sqr,alpha,beta,n,'diss',ifverbose) > > call planar_average_s(diss_sqr_pl,dissavg,w1,w2) > > do i=1,ny1*nely/2 > uavg_pl(i) = 0.5 * (uavg_pl(i) + uavg_pl(m-i+1)) > vavg_pl(i) = 0.5 * (vavg_pl(i) + vavg_pl(m-i+1)) > wavg_pl(i) = 0.5 * (wavg_pl(i) + wavg_pl(m-i+1)) > diss_sqr_pl(i) = 0.5 * (diss_sqr_pl(i) + diss_sqr_pl(m-i+1)) > urms_pl(i) = 0.5 * (urms_pl(i) + urms_pl(m-i+1)) > vrms_pl(i) = 0.5 * (vrms_pl(i) + vrms_pl(m-i+1)) > wrms_pl(i) = 0.5 * (wrms_pl(i) + wrms_pl(m-i+1)) > > enddo > > > > Many thanks. > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20170623/c4bae…> > > ------------------------------ > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > End of Nek5000-users Digest, Vol 100, Issue 27 > **********************************************

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Help: compute dissipation
by nek5000-users＠lists.mcs.anl.gov 23 Jun '17

23 Jun '17

Hi NEK users, I am trying to calculate dissipation for fully developed turbulent channel flow. I tried the code below, but result I got from this totally disagrees with Vreman’s 2014 paper. x-axis is streamwise, y-axis is wall-normal and z-axis is spanwise. Any errors in the code? Any thoughts? real diss_sqr(lx1,ly1,lz1, lelt) real s11 real s12 real s13 real s22 real s23 real s33 common /plane/ uavg_pl(ly1*lely) $ , vavg_pl(ly1*lely) $ , wavg_pl(ly1*lely) $ , urms_pl(ly1*lely) $ , vrms_pl(ly1*lely) $ , wrms_pl(ly1*lely) $ , uvms_pl(ly1*lely) $ , diss_sqr_pl(ly1*lely) $ , yy(ly1*lely) $ , w1(ly1*lely),w2(ly1*lely) $ , ffx_avg, dragx_avg parameter (lr=lx1*ly1*lz1) common /scruz/ ur(lr),us(lr),ut(lr) $ , vr(lr),vs(lr),vt(lr) $ , wr(lr),ws(lr),wt(lr) common /avg/ uavg(lx1,ly1,lz1,lelv) & , vavg(lx1,ly1,lz1,lelv) & , wavg(lx1,ly1,lz1,lelv) & , urms(lx1,ly1,lz1,lelv) & , vrms(lx1,ly1,lz1,lelv) & , wrms(lx1,ly1,lz1,lelv) & , uvms(lx1,ly1,lz1,lelv) & , dissavg(lx1,ly1,lz1,lelv) common /scrns/ sij (lx1*ly1*lz1,6,lelv) if(icalld.eq.0) then call rzero(uavg,n) call rzero(urms,n) call rzero(vrms,n) call rzero(wrms,n) call rzero(uvms,n) call rzero(dissavg,n) call rzero(wavg,n) call rzero(vavg,n) call rzero(diss_sqr,n) call comp_sij(sij,6,vx,vy,vz,ur,us,ut,vr,vs,vt,wr,ws,wt) do e=1,nelt do i = 1,nx1*ny1*nz1 s11=sij(i,1,e) s12=sij(i,4,e) s22=sij(i,2,e) s13=sij(i,6,e) s23=sij(i,5,e) s33=sij(i,3,e) diss_sqr(i,1,1,e) = (s11*s11) + $ (s22*s22) + $ (s33*s33) + $ (s12*s12)*2 + (s23*s23)*2 + $ (s13*s13)*2 enddo enddo call avg1(dissavg,diss_sqr,alpha,beta,n,'diss',ifverbose) call planar_average_s(diss_sqr_pl,dissavg,w1,w2) do i=1,ny1*nely/2 uavg_pl(i) = 0.5 * (uavg_pl(i) + uavg_pl(m-i+1)) vavg_pl(i) = 0.5 * (vavg_pl(i) + vavg_pl(m-i+1)) wavg_pl(i) = 0.5 * (wavg_pl(i) + wavg_pl(m-i+1)) diss_sqr_pl(i) = 0.5 * (diss_sqr_pl(i) + diss_sqr_pl(m-i+1)) urms_pl(i) = 0.5 * (urms_pl(i) + urms_pl(m-i+1)) vrms_pl(i) = 0.5 * (vrms_pl(i) + vrms_pl(m-i+1)) wrms_pl(i) = 0.5 * (wrms_pl(i) + wrms_pl(m-i+1)) enddo Many thanks.

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Nek5000 documentation details: Pn-Pn pressure solver
by nek5000-users＠lists.mcs.anl.gov 23 Jun '17

23 Jun '17

Dear Neks, reading the documentation I got the impression that Pn-Pn solver (low Mach) first solves the pressure where the convective and viscous (!) terms are taken into account. After that using this p^{n+1} we solve for velocity field. It seems that the algorithm consists of only 2 steps (pressure + velocity). However, reading the paper by Tomboulides, Lee, Orszag (1996) which is referenced inside the code, I see the projection algorithm where first the velocity is updated using the extrapolated convective term, then the Laplacian of pressure is calculated due to convection, after that the velocity is updated using convection and pressure gradient. The last step accounts for viscous term. I am a bit confused, could you please help me out here? Which method is used? PS. Another thing is the coupled Helmholtz solver in Pn-Pn. I see that in case of Pn-Pn-2 each velocity component is treated separately (segregated solver). However, this coupled thing slightly confuses me, why not treating it separately as in Pn-Pn-2? Could you please comment there as well? Thank you. Best regards, Vlad

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Numerical treatment of variable viscosity and diffusivity
by nek5000-users＠lists.mcs.anl.gov 22 Jun '17

22 Jun '17

Hi Neks, I am reporting a turbulent pipe case with temperature dependent viscosity and diffusivity and I would like to have a better understanding of the numerical treatment of the momentum and thermal equations when those properties varies. I would highly appreciate if you could indicate a reference (paper/thesis/document) where you describe how the code works in that situation. Thanks in advance. Antonio -- ANTONIO ANTORANZ PERALES Universidad Carlos III de Madrid

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Restart using a solution computed on different domain
by nek5000-users＠lists.mcs.anl.gov 21 Jun '17

21 Jun '17

Hello, I have carried out a simulation for the flow past a cylinder at Re=100. The extent of the domain in the is [Lx,Ly,Lz] = [30, 10, 10]; x is the streamwise, y transverse and z is the spanwise direction. I have another computational domain with size [50, 10, 10]. The mesh near the cylinder in the two meshes is identical. If I use the fully developed solution obtained using the first domain as a restart file for computation using the second domain, will the first solution be projected on the second mesh automatically by NEK? Thanks. N.

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