July 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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Conjugate Heat Transfer Example: **ERROR** Failed in HMHOLTZ: TEMP
by nek5000-users＠lists.mcs.anl.gov 30 Jul '15

30 Jul '15

Hello Nek5K Users, I am having trouble running the "conj_ht" example. Attached is a copy of the output. Without making any changes (other than number of timesteps) to the .rea file I seem to be getting errors when I seek to compute the Temperature field. As the subject states - it looks like there is an error in the HMHOLTZ step when performing the "cggo" subroutine. Any help you can provide would be much appreciated. Best, Saumil

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Dynamo set up with weird results
by nek5000-users＠lists.mcs.anl.gov 28 Jul '15

28 Jul '15

Hello everyone, I am currently looking into using Nek5000 for a (kinematic) dynamo problem in a spheroid. I started by combining the mhd example from the examples with a working case which only solved for the velocity the following way: - lbelv=lelv, lbx1=lx1 etc. in SIZE - adding (dummy) bc's for Temperature to the rea file and setting ifheat=.false. in usrchk - adding bc's for the magnetic field to the rea file as Passive Scalar 1, after the temperature. The string is 'E ' inside the Volume and 'v ' at the boundary - ux,uy,uz=0.0 in userbc for both (ifield .eq. 1) and (ifield .eq. ifldmhd) - ux,uy,uz=0.0 in useric for both (ifield .eq. 1) and (ifield .eq. ifldmhd) - param(29) is set to the magn. viscosity My actual problem is of course more complicated in regards to init. and boundary conditions, but this simple example produces weird output. The magnetic field should stay zero, but grows with the same rate as the velocityfield (computed via glsc3(bm1,bx,bx,n)+glsc3(bm1,by,by,n)+glsc3(bm1,bz,bz,n) and (glsc3(bm1,vx,vx,n)+glsc3(bm1,vy,vy,n)+glsc3(bm1,vz,vz,n))). I then removed the custom forcing to the velocity in userf, which caused the simulation to produce NaNs after 4 timesteps (everything is zero before, as expected). Without the additions for the magnetic field, the case runs fine with the same resolution and timestep length (but has a slightly lower growthrate for the velocity). Has anyone seen similar behaviour? I think that I am missing something obvious in the the mhd setup. Cheers, Jan

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userf Questions
by nek5000-users＠lists.mcs.anl.gov 26 Jul '15

26 Jul '15

Hi All, Hate to be so long winded, but I'm seeing problems with my code and was wondering if anyone could help... I'm modeling a wind turbine using a modified actuator line method, where I describe the blades (3) as a set of rotating rectangular outlines, advanced in space at each time step. I'm selecting GLL points which fall within my outlines, reading in the velocities, calculating the body forces, then assigning them back to ffx,ffy,ffz. This generates a downstream flowfield and wake in NEK... Looking at rough results, they compare (velocity and vorticity plots and isosurfaces) favorably with other work. However, during some recent debugging to add some features to my code, I noticed that when I repeatedly ran short runs and printed results at the same time step, my point selections for the 3 blades varied with each run, even though I made no other changes to the code or any runtime parameters. A chunk of my point selection for a given area of blade passage looks like: ---------------------F77 Code In userf----------------------------------------------------------------------------------- C Test for location in Quadrant... C if (thetacalc .GE. (pi/2.0 - epsim2)) then C C Close to Vertical Axis... C C Sin+ ... C xlo = centerx + (rhubm*SIN(thetacalc)) xhi = centerx + (bladeradius*SIN(thetacalc)) ymax=centery+(1./SIN(thetacalc))*(chordbig/2.0) ymin=centery-(1./SIN(thetacalc))*(chordbig/2.0) if (((x.GE.xlo).AND.(x.LE.xhi)).AND. & ((y.GE.ymin).AND.(y.LE.ymax))) then C C Calculate forces... C radm = SQRT((x-centerx)**2.0 + (y-centery)**2.0) vthetam = SQRT(ux**2.0 + uy**2.0) psim = ATAN(uz/(avelm*radm + vthetam)) .... .......... .......... -----------------------F77 Code Continues------------------------------------------------------ The xlo,xhi,ymax,ymin values are calculated based on the rotational location of the blade, which changes at each time step, and defines an outline of the blade. Then the IF statements test the x,y point (z-axis location has already been tested) to be within this blade outline, and when a point "HITS" any one of these outlines for the 3 blades, it calculates the forces, prints a diagnostic line, etc... A typical print clip, which only runs at one time step I define and prints for the "Hit" point, is: ---------------------F77 Code In userf----------------------------------------------------------------------------------- C Print output C if(istep.eq.pstepm)then WRITE(4,1000)'Q1V',x,y,z,ux,uy,uz,psim,ffx,ffy,ffz endif ........ ........ -----------------------F77 Code Continues------------------------------------------------------ This tells me the quadrant and general area of the point; because of geometric issues, I have separate selection (and associated print) routines for each Cartesian quadrant which are all tested in turn... So... My problem is if I run this code over and over, and print at say istep=10, the code shows a different number of points selected for each of the 3 blades, on each run! Oddly, there are repeated patterns, and the total is always the same; for this particular setup at this istep, it was 204 points for all 3 blades. An example of the differences is: Blade 1 Blade 2 Blade 3 ----------------------------------------------------------------------------- Run 1 76 125 3 Run 2 32 110 62 Run 3 78 79 47 I've tried a bunch of things to fix it, including going back to a previous version which had no SAVE statements in it (had more manual parameter input); compiling between each run, etc... All my code is within userf. I'm running this in MPI mode on a large SMP server/workstation; compiled with gfortran. I've run this out to 10000 cycles with repeated runs and have always gotten qualitatively identical results. I ran into this problem when I was debugging a new version which added a bunch of automated features I've been working on. But, when going back to previous versions and performing repeated short runs, I discovered that it did it there too... Am I missing something here with MPI and my selection code not working correctly because of the way userf is called? My understanding of the code is that at each time step, all the GLL points and elements are cycled through with a call to userf for each point; the forces are brought back in as ffx,ffy,ffz. If I look qualitatively at a typical run through time, you can see each blade rotating step-by-step, and see the physical outline and edges of the blades. It makes me think that my selection code (which I've debugged and checked out a lot in the past) is basically correct; just don't know why it would select different points with those IF statements on repeated runs. Now, I can see some roundoff-resolution issues where it might vary one or two points between runs, but here the differences are huge. Thanks for listening ;-) Murph Murphy Leo O'Dea PhD Student Mechanical Engineering Oakland University mlodea(a)oakland.edu

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simplify viscosity terms
by nek5000-users＠lists.mcs.anl.gov 26 Jul '15

26 Jul '15

Hi,I want to reduce navier stokes to something like boundary layer equations.I want to keep all the term (3D), just reduce viscosity term to something line mu*d2u/dy2 (omitting other derivatives). Would you help me where to start? Hamid

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gradm1 vs opdiv for computing velocity divergence
by nek5000-users＠lists.mcs.anl.gov 09 Jul '15

09 Jul '15

Dear all, I am new to Nek5000 and am trying to output the velocity divergence of my 2D, unsteady N-S solution for a flat plate with elliptic leading edge using PN-PN-2 formulation. I compute divergence using gradm1() and opdiv() and the values I get from the two don't seem to match the DIVERGENCE and HELMHOLTZ (p021 and p022) residuals in the .rea file (which are 1e-9 and 1e-11). I get div ~ 1 using gradm1() and div~1e-2 using opdiv() and the divergence is close to the elliptic leading edge. Am I missing something(scaling factor maybe?) in the computation of divergence here? subroutine userchk include 'SIZE' include 'TOTAL' common /scren/ vort (lx1,ly1,lz1,lelv,3) ! x y z components $ , work1(lx1,ly1,lz1,lelv) $ , work2(lx1,ly1,lz1,lelv) $ , dudx(lx1,ly1,lz1,lelv) $ , dvdy(lx1,ly1,lz1,lelv) $ , div1(lx1,ly1,lz1,lelv) $ , div2(lx2,ly2,lz2,lelv) $ , div3(lx1,ly1,lz1,lelv) n = nx1*ny1*nz1*nelt ntot2 = nx2*ny2*nz2*nelt c Compute divergence using gradm1() call gradm1(dudx,work1,work2,vx) call gradm1(work1,dvdy,work2,vy) div1 = dudx + dvdy c Compute divergence using opdiv() call opdiv(div2,vx,vy,vz) c opdiv returns bm2*div call col2(div2,bm2inv,ntot2) call mappr(div3,div2,work1,work2) if(nid .eq.0)write(6,*)'Done mapping div2 to xm1' call outpost(div1,div3,vx,pr,vort(:,:,:,:,1), & 'divvort') return end This is from the output file showing the DNORM, DIVEX Step 2, t= 4.0340639E+00, DT= 1.0892282E-04, C= 0.500 2.1168E+01 2.1168E+01 Solving for fluid F T T 9.999999999999999E-012 p22 2 1 2 Hmholtz VELX: 42 6.4400E-12 8.2479E-02 1.0000E-11 9.999999999999999E-012 p22 2 1 2 Hmholtz VELY: 40 6.3878E-12 9.2957E-02 1.0000E-11 2 U-PRES gmres: 120 6.0275E-08 1.0000E-09 6.4717E-04 5.7658E+00 1.6938E+01 2 DNORM, DIVEX 6.027476742433520E-008 6.027476742402435E-008 2 4.0341E+00 2.0912E+01 Fluid done Thanks Prahladh Iyer Postdoctoral Researcher National Institute of Aerospace, Hampton, Virginia Resident: NASA Langley Research Center Email : prahladh.s.iyer(a)nasa.gov

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Large simulations
by nek5000-users＠lists.mcs.anl.gov 07 Jul '15

07 Jul '15

Dear All, Is it normal for a nek simulation (220 000 elements with lx1=12) to have long initial setup times (basically gs_setup) such as 5 hours when running on 32768 cores, even when restarting? As expected, more elements and/or more cores used results in longer setup times. My problem is that I wish to carry out simulations with a higher number of elements but I am limited to 24 hour runs and must carry out restarts. Is there a way to carry out faster restarts? Thank you, jp

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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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how to use nek only with fem
by nek5000-users＠lists.mcs.anl.gov 01 Jul '15

01 Jul '15

Hi Nek's I wanted to know if there is a way to use nek only with finite elements, without spectral. If yes, which is the best way to do it? -- 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(a)poliba.itIn joint supervision with theEcole Nationale Supérieure d'Arts et Métiers de Paris - ParistechTel.: +33-144246436Mob.: +33-789822134Dynfluid Laboratory151 Boulevard de l'Hôpital - 75013 Paris (France)mirko.farano(a)ensam.eu

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