June 2015 - Nek5000-users - mailman3.cels.anl.gov

Re: [Nek5000-users] Vorticity
by nek5000-users＠lists.mcs.anl.gov 11 Oct '16

11 Oct '16

Hi, Thanks for your quick reply. Just I wanna know if I can use the interpolated values of velocity at some arbitrary points in the domain (not necessarily the grid points) as the input arguments to theses subroutines. Regards, Alireza Quoting nek5000-users-request(a)lists.mcs.anl.gov: > 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. Vorticity (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: Vorticity (nek5000-users(a)lists.mcs.anl.gov) > 3. Re: Vorticity (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Jul 2011 17:55:35 -0400 > From: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: <20110713175535.1042430oct81vz2v(a)webmail.vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Hi, > > I need to calculate the vorticity vector and the rate of strain tensor > at any arbitrary point in the domain. I wonder if these values are > computed somewhere in the code or if I should interpolate them in the > usr file. I appreciate any kind of help. > > Thanks in advance, > > > Regards, > Alireza Karimi > > > > ------------------------------ > > Message: 2 > Date: Wed, 13 Jul 2011 17:09:48 -0500 (CDT) > From: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: <Pine.LNX.4.64.1107131704140.26989(a)jacobi.mcs.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Alireza, > > For vorticity computation, you can call > > call comp_vort3(vort,work1,work2,vx,vy,vz) > > from userchk with the appropriate definitions of vorticity and work arrays > like > > common /scren/ vort (lx1,ly1,lz1,lelv,3) ! x y z components > $ , work1(lx1,ly1,lz1,lelv) > $ , work2(lx1,ly1,lz1,lelv) > > Let me check what we have for the calculation of strain tensor. > Best, > Aleks > > > On Wed, 13 Jul 2011, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Hi, >> >> I need to calculate the vorticity vector and the rate of strain >> tensor at any >> arbitrary point in the domain. I wonder if these values are computed >> somewhere in the code or if I should interpolate them in the usr file. I >> appreciate any kind of help. >> >> Thanks in advance, >> >> >> Regards, >> Alireza Karimi >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > Message: 3 > Date: Wed, 13 Jul 2011 23:59:08 -0500 (CDT) > From: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: > <600285192.94128.1310619548370.JavaMail.root(a)zimbra.anl.gov> > Content-Type: text/plain; charset=utf-8 > > Hi Alireza, > > > For a strain stress computation you can call subroutine comp_sij > > call comp_sij(sij,nij,vx,vy,vz > $ ,ur,us,ut,vr,vs,vt,wr,ws,wt) > > > (navier5.f:2225) with nij=6 for 3D somewhere from userchk once you > declare the stress component array sij and arrays with local > coordinate r-s-t derivatives of velocity components > > common /csij/ > $ sij(lx1*ly1*lz1,6,lelv) ! 6 components > $ ,ur (lx1*ly1*lz1) > ... > $ ,wt (lx1*ly1*lz1) > > > Best, > Aleks > > > > > > > ----- Original Message ----- > From: nek5000-users(a)lists.mcs.anl.gov > To: nek5000-users(a)lists.mcs.anl.gov > Sent: Wednesday, July 13, 2011 5:09:48 PM > Subject: Re: [Nek5000-users] Vorticity > > Hi Alireza, > > For vorticity computation, you can call > > call comp_vort3(vort,work1,work2,vx,vy,vz) > > from userchk with the appropriate definitions of vorticity and work arrays > like > > common /scren/ vort (lx1,ly1,lz1,lelv,3) ! x y z components > $ , work1(lx1,ly1,lz1,lelv) > $ , work2(lx1,ly1,lz1,lelv) > > Let me check what we have for the calculation of strain tensor. > Best, > Aleks > > > On Wed, 13 Jul 2011, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Hi, >> >> I need to calculate the vorticity vector and the rate of strain >> tensor at any >> arbitrary point in the domain. I wonder if these values are computed >> somewhere in the code or if I should interpolate them in the usr file. I >> appreciate any kind of help. >> >> Thanks in advance, >> >> >> Regards, >> Alireza Karimi >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > _______________________________________________ > 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 29, Issue 2 > ******************************************** > -- Alireza Karimi PhD Candidate Department of Engineering Science and Mechanics Virginia Polytechnic Institute and State University Blacksburg, VA 24061

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Error when creating own mesh
by nek5000-users＠lists.mcs.anl.gov 01 Mar '16

01 Mar '16

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.

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Spectral interpolation of velocity gradients
by nek5000-users＠lists.mcs.anl.gov 01 Jul '15

01 Jul '15

Hi Neks, I study particles in a turbulent flow and need to know velocity gradients dvi_dxj at particle positions x_p. In order to do this, I modified the subroutine interp_v(uvw,xyz,n) from the particle tracking example ''hemi''. First, I calculate the velocity gradients with the subroutine gradm1(): call gradm1(vxx,vxy,vxz,vx) call gradm1(vyx,vzy,vzz,vy) call gradm1(vzx,vzy,vzz,vz) Second, I interpolate the velocity gradients to the particle positions with the subroutine intpts(): call opcopy(wrk(1,1),wrk(1,2),wrk(1,3),vxx,vyx,vzx) call intpts(wrk,ndm,pts,npart,outint,ifjac,ifpts,ihandle) I have a few questions regarding this approach: 1. Is intpts() capable of interpolating derived fields like the velocity gradient field? 2. Do you have a good explanatory reference where the mathematical principles behind intpts() are explained? 3. As far as I understand, the fields vx, vy, vz and consequently the derived fields vxx, vxy, vxz, ... are local and defined on the local coordinate fields xm1, ym1, zm1. What is happens if an interpolation point is on a different processor and outside the coordinates stored in xm1, ym1, zm1? Best regards, Philipp Weiss

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Regarding Post-Processing
by nek5000-users＠lists.mcs.anl.gov 30 Jun '15

30 Jun '15

Hi Neks, I would like to post process the 0.f00* files. I set my Nsteps = 0 to run in post processing mode. and used the below code. Can someone tell me how to create the 'file.list' file ? I tried creating a file.list, something like this: ca0.f00001 ca0.f00002 ca0.f00003 . . . . . . but still I get error "Bad integer for item 1 in list input " subroutine userchk include 'SIZE' include 'TOTAL' include 'RESTART' logical if_drag_out,if_torq_out character*80 filename(9999) parameter (lt=lx1*ly1*lz1*lelt) real l2(lx1,ly1,lz1,nelt) integer nfiles ntot = nx1*ny1*nz1*nelv ifreguo = .true. 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)) call lambda2(L2) ifto = .true. call outpost(vx,vy,vz,pr,l2,'his') enddo call exitt Thanks, Kamal

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Newton
by nek5000-users＠lists.mcs.anl.gov 10 Jun '15

10 Jun '15

Hi Nek's I'm trying to code in Nek5000 the Newton algorithm. In order to do so, I'm referring to the Tuckerman's paper "Bifurcation analysis for timesteppers" of 2000. I would like to take advantage from the semi-implicit temporal scheme in order to precondition the Bi-CGStab algorithm to solve the linear problem that carry out the Newton step. As explained in the Tuckerman's paper, in order to get a good preconditioning, I should have a time step with a dt which is about 100 to 1000 times greater than that which ensures the CFL condition. I'm not able to increase the dt has the Helmholtz fails in the projection methods. So, I tried to preconditioning the Bi-CGStab routine with a one step of Stoke problem always with a large dt because if L is the linear operator: U(n+1) = (I-dt*L^-1)U(n) ~ (-dt*L^-1)U(n) but the Helmholtz Helmholtz fails too. I would like to know if I can do somethings like: r0 = K^(-1)*r0 where r0 = is the residue vector in the Bi-CGStab routine and K^(-1) is the inverse of the stiffness matrix. In the stokes problem, using a large DT, H (Helmholtz) tends to the limit K so i could do a matrix-vector problem H^(-1)*r0 if there is a way to call a routine the do this yet for the pressure preconditioning. Can someone please help me? thanks Alessandro PhD student at Dynfluid Laboratory Ecole Nationale Supérieure d'Arts et Métiers de Paris - Paristech

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Problem in TurbChannel example
by nek5000-users＠lists.mcs.anl.gov 08 Jun '15

08 Jun '15

Hi Neks, I am trying to use standard Smagorinsky model to simulate the flow for my case. For that, we have used comp_gije, comp_sije, mag_tensor_e, cmult, set_grid_spacing subroutines from the turbChannel example to calculate turbulent or eddy viscosity. (I have attached the subroutine here). subroutine eddy_visc(ediff,e) c c Compute eddy viscosity using dynamic smagorinsky model c include 'SIZE' include 'TOTAL' include 'ZPER' real ediff(nx1*ny1*nz1,nelv),cs integer e common /dynsmg/ sij (lx1*ly1*lz1,ldim,ldim) $ , dg2 (lx1*ly1*lz1,lelv) $ , snrm(lx1*ly1*lz1,lelv) real sij,dg2,snrm parameter(lxyz=lx1*ly1*lz1) ntot = nx1*ny1*nz1 call comp_gije(sij,vx(1,1,1,e),vy(1,1,1,e),vz(1,1,1,e),e) call comp_sije(sij) call mag_tensor_e(snrm(1,e),sij) call cmult(snrm(1,e),2.0,ntot) call set_grid_spacing(dg2) if (e.eq.nelv) then ! planar avg and define nu_tau cs = 0.10 ntot = nx1*ny1*nz1*nelv do i=1,ntot cstat = (cs**2.0)*dg2(i,1) ediff(i,1) = param(2) + cstat*snrm(i,1) enddo endif return end However, we faced some difficulties running our case. We found that when the element distribution is not uniform between the processors (mod (lelg,lp).ne.0) the code freezes in the set_grid_spacing subroutine when Dsavg is called. In order to debug this case we did some tests on TurbChannel example with dynamic Smagorinsky model and we found that this problem also exists there. Thus, it seems that we will be having this problem except from the cases that (mod (lelg,lp).eq.0) and we do not understand the reason for that. Therefore, could you please guide me so that I can deal with this problem? Thanks, Mahzad *PhD** Mechanical Engineering* *Arizona State University* *School for engineering of matter, transport and energy (SEMTE)* Mahzad Khoshlessan *PhD** Mechanical Engineering* *Arizona State University* *School for engineering of matter, transport and energy (SEMTE)*

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