September 2014 - 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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Parallel issue: Inflow conditions from external files
by nek5000-users＠lists.mcs.anl.gov 30 Sep '14

30 Sep '14

Hi all, I have a question on how to read in information from external files as an inflow boundary condition when running in parallel. Similar problem to this: http://lists.mcs.anl.gov/pipermail/nek5000-users/2010-December/001151.html My geometry is a simple 3D rectangle prism with the inlet on the Y-Z plane @ x=0. I have developed some code that reads in a 2D plane of velocity data from another simulation (in this case fluent) as the boundary condition in userbc(). I am happy to share the process and the code (Fortran input/output from NEK, and MATLAB to do interpolation) however here I am primarily focused on getting it working in parallel. The process works fine in serial - it reads in 3 files (01.dat, 02.dat, 03.dat) that hold the x,y,z velocity (respectively) for each node on the inlet. However it does not work correctly when running in parallel - looking at the results after a few iterations shows that the velocities are being mapped to nodes that are not all on the inlet. It does compile and run though. I'd sincerely appreciate any the help in making it work. Warm regards, Tom I have included my .usr file below. C----------------------------- ------------------------------------------ C nek5000 user-file template C C user specified routines: C - userbc : boundary conditions C - useric : initial conditions C - uservp : variable properties C - userf : local acceleration term for fluid C - userq : local source term for scalars C - userchk: general purpose routine for checking errors etc. C C----------------------------------------------------------------------- subroutine uservp(ix,iy,iz,eg) ! set variable properties include 'SIZE' include 'TOTAL' include 'NEKUSE' integer e,f,eg c e = gllel(eg) udiff = 0.0 utrans = 0.0 return end c----------------------------------------------------------------------- subroutine userf(ix,iy,iz,eg) ! set acceleration term c c Note: this is an acceleration term, NOT a force! c Thus, ffx will subsequently be multiplied by rho(x,t). c include 'SIZE' include 'TOTAL' include 'NEKUSE' integer e,f,eg ffx=0 ffy=0 ffz=0 return end c----------------------------------------------------------------------- subroutine userq(ix,iy,iz,eg) ! set source term include 'SIZE' include 'TOTAL' include 'NEKUSE' integer e,f,eg c e = gllel(eg) qvol = 0.0 source = 0.0 return end c----------------------------------------------------------------------- subroutine userbc(ix,iy,iz,iside,eg) ! set up boundary conditions c NOTE: This routine may or may not be called by every processor include 'SIZE' include 'TOTAL' include 'NEKUSE' integer e,eg,ix,iy,iz,NELY,NELZ,egs common /myinlet/ Arrangedu(ly1,lz1,lelt), > Arrangedv(ly1,lz1,lelt), > Arrangedw(ly1,lz1,lelt) e = gllel(eg) ux = Arrangedu(iy,iz,eg) uy = Arrangedv(iy,iz,eg) uz = Arrangedw(iy,iz,eg) temp = 0.0 return end c----------------------------------------------------------------------- subroutine useric(ix,iy,iz,eg) ! set up initial conditions include 'SIZE' include 'TOTAL' include 'NEKUSE' integer e,eg ux = 7.235 uy = 0.0 uz = 0.0 temp = 0.0 return end c----------------------------------------------------------------------- subroutine userchk() include 'SIZE' include 'TOTAL' return end c----------------------------------------------------------------------- subroutine usrdat() ! This routine to modify element vertices include 'SIZE' include 'TOTAL' return end c----------------------------------------------------------------------- subroutine usrdat2() ! This routine to modify mesh coordinates include 'SIZE' include 'TOTAL' common /myinlet/ Arrangedu(ly1,lz1,lelt), > Arrangedv(ly1,lz1,lelt), > Arrangedw(ly1,lz1,lelt) call read_inlet(Arrangedu,Arrangedv,Arrangedw) ! Read in inlet data for BCs return end c----------------------------------------------------------------------- subroutine usrdat3() include 'SIZE' include 'TOTAL' return end C------------------------------------------------------------------------------- subroutine read_inlet(Arrangedu,Arrangedv,Arrangedw) ! Read in the inlet data include 'SIZE' include 'TOTAL' Integer Max_Nodes, Lun_Dat Parameter( Max_Nodes = 200000, Lun_Dat = 3) real Var_1( Max_Nodes,lx1), Var_2( Max_Nodes), Var_3( Max_Nodes) real Var_4( Max_Nodes), Var_5( Max_Nodes), Var_6( Max_Nodes) real Arrangedu(ly1,lz1,lelt) real Arrangedv(ly1,lz1,lelt) real Arrangedw(ly1,lz1,lelt) integer i_row( Max_Nodes), i_eg( Max_Nodes), i_y( Max_Nodes) real junk integer i, j, k, l, m, n, imin, imax, N_Nodes,ze, iyz, egs,egz integer fcount Character Line* 72 Character Directory* 57 Parameter( Directory= > '/home/tom/NEK/meshControl/MultiBox/MultiBox_10/NewInlet4/') c 1234567890123456789012345678901234567890123456789012345678 Character Filename* 4 Parameter( Filename= '.dat') c 12345 character(2) fc C +-----------+ C | Execution | C +-----------+ 1 format( 1x, a) do fcount=1,3 !for each file 01=u;02=v;03=w. 37 format (I2.2) write (fc,37) fcount ! converting integer to string print *,'Readining file #: ',fc open( unit = Lun_Dat, status = 'old', form='formatted', err = 2, > file = Directory//trim(fc)//Filename) go to 3 2 write( 6, 1) 'Error Opening file - EXIT' 3 read( Lun_Dat, 1) Line N_Nodes = 0 do i = 1, Max_Nodes read( Lun_Dat, 11, end=5) i_row(i), i_eg(i), i_y(i), > Var_1(i,1), Var_1(i,2), Var_1(i,3), > Var_1(i,4), Var_1(i,5), Var_1(i,6), > Var_1(i,7), Var_1(i,8), Var_1(i,9) 11 format( i6, 1x, i5, 1x, i4, 9( 1x, 1P E16.9)) N_Nodes = N_Nodes + 1 if( fcount .EQ. 1) THEN iyz=i_y(i) egz=i_eg(i) do ze=1,lx1 Arrangedu(iyz,ze,egz)= Var_1(i,ze) end do else if( fcount .EQ. 2) THEN iyz=i_y(i) egz=i_eg(i) do ze=1,lx1 Arrangedv(iyz,ze,egz)= Var_1(i,ze) end do else if( fcount .EQ. 3) THEN iyz=i_y(i) egz=i_eg(i) do ze=1,lx1 Arrangedw(iyz,ze,egz)= Var_1(i,ze) end do end if end do write( 6, 1) ' ' write( 6, 1) ' WARNING - Max nodes exceeeded' write( 6, 1) ' ' 5 write( 6, 6) N_Nodes 6 format( ' Number of nodes read = ', I8) end do end C-------------------------------------------------------------------------------

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Re: [Nek5000-users] Nek5000+MOAB
by nek5000-users＠lists.mcs.anl.gov 26 Sep '14

26 Sep '14

Hi Aleks, thanks a lot. It works perfectly. Andrea >Hi Adrea, >Thanks for your note on the work-around with Exodus. >Yes, you are right that perturbation mode is not yet available in Pn-Pn but you could dump the .rea file from Pn-Pn Nek-MOAB setup (say with lx1=3) by > call gen_rea(2) >or > call gen_re2(2) > and then proceed with Pn-2 - Pn-2 with Nek only. >Let me know if you have any questions. >Aleks

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Saving perturbation solution
by nek5000-users＠lists.mcs.anl.gov 25 Sep '14

25 Sep '14

Hello neks I am running the perturbation code by modifying the os7000 example. The code runs. But if I try to save the perturbation solution like this ifxyo = .false. if(istep.eq.0)then ifxyo = .true. call out_pert() else if(mod(istep,iostep).eq.0)then call out_pert() endif then I get the crash 1 U-PRES gmres: 25 3.8311E-12 5.0000E-12 1.6258E-08 3.7787E-03 1.1255E-02 filt amp 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0500 filt trn 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 0.9500 2.000000E-03 1 1.78124472E-03 1.78124472E-03 1.00000713E+00 1.00000686E+00 2.63413513E-07 3.83894325E-02 egn Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation. Backtrace for this error: #0 0x10fa6770d #1 0x10fa67c1b #2 0x7fff872745a9 #3 0x1042ad8fe #4 0x1042aeafb #5 0x1044e705c Thanks praveen

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interpolation of results to uniform grid
by nek5000-users＠lists.mcs.anl.gov 25 Sep '14

25 Sep '14

In a 2D flow simulation I would like to make manually some spectral analysis on spacial fields of temperature, velocity etc. Spacial field must be on a regular uniform rectangular mesh. Schematically I need a procedure like T=getfield('foo0.f00009'), where T is in the matrix form, f.e. for 3 point in one dimension and 2 in the other: T11 T12 T13 T21 T22 T23 In tools there is an interpolation tool int_tp that could solve the problem. But to get it work you have to supply .box files. The problem is complicated with the fact that though the geometry is quadrilateral, it is not rectangular and nonuniform. I have created it in prex. There you have "Multi-SPLIT" in menu which refines the opposite sides of quadrilateral the same way, just what I needed (first I divided the whole domain to four parts by quadsplit and after I refine each part nonuniformly to make it more dense towards the boundary). Finally I have trapezuim domain in which mesh is refined towards each of the four boundaries. You can see the picture following the link. https://www.dropbox.com/s/7sb2njt6ju2qo1b/mesh24x24.png?dl=0 I would be happy to interpolate this mesh to "uniform" (the sides are meshed uniformly) and get it in matrix form. But in terms of .box files I don't know how to set the quadrilateral geometry. So is there a way to create this type of geometry scriptwize? I saw in mailing list that there a utility sem2lex. But I could not find it. As a temporary solution I think about hpts.in. Though there will be 10^4 points in hpts.out for each time. Thank you, Ilias

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Re: [Nek5000-users] Nek5000+MOAB
by nek5000-users＠lists.mcs.anl.gov 25 Sep '14

25 Sep '14

>Andrea, thanks for reporting the issue about the cub file version >incompatibility. Can you give details on the version of Trelis and cub >file format (13.x, 14.x ?) used here ? Trelis version is 15.03 ( I just downloaded the trial version a couple of days ago). I don't know the version of the cubit file format, how I can inquire? >Just a note for the future: it would be good to email moab-dev about >any issues like these since most of the MOAB devs aren't subscribed to >NEK mailing lists. Ok, I will keep in mind for the future. Initially I was not sure that it was a problem of MOAB. Indeed mbconvert was working without any warnings. It is just that inside the mesh all the information linked to geometrical entities are lost. For instance, if I define a sideset with a surface is lost, if it is defined with the mesh elements it was keeped. >Vijay On Thu, Sep 25, 2014 at 4:56 AM, <nek5000-users at lists.mcs.anl.gov <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>> wrote: >* Just an update. *>>* The problem was related to MOAB which is not able to read the latest .cub of *>* Trelis. I exported the mesh in Exodus II format and then I convert it with *>* MOAB and everything is working now. *>>>* Here comes another issue. I noticed that I can use only the PnPn *>* formulation, but I would like to use the perturbation mode. At first glance *>* (looking at drive1.f) it seems that the perturbation mode is available only *>* on PnPn-2 formulation. Am I wrong? *>>* Thanks, *>>* Andrea *>>* _____*

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error reading .fld ascii file
by nek5000-users＠lists.mcs.anl.gov 25 Sep '14

25 Sep '14

Hi Neks, I'm trying to restar an ascii *.fld02 file, but I get the following error message: set initial conditions Checking restart options: start.fl02 nekuic (1) for ifld 1 Reading checkpoint data 0 0 OPEN: start.fl02 byte swap: T 1.35684711E-19 6.40740794E-10 17872 5 5 5 1.530191500E-03 2 X Y Z U NELT,NX,NY,N 0.000 0.000 0.000 0.0 NONSTD HDR, parse_hdr, abort. ERROR: Error reading restart header in mfi_prepare ierr= 1 I set param(67)=0. in the .rea file and also in userchk subroutine. What is wrong? I saved the file using param(66)=0. and I didn't change anything... Thank you in advance SL

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Re: [Nek5000-users] Nek5000+MOAB
by nek5000-users＠lists.mcs.anl.gov 25 Sep '14

25 Sep '14

Just an update. The problem was related to MOAB which is not able to read the latest .cub of Trelis. I exported the mesh in Exodus II format and then I convert it with MOAB and everything is working now. Here comes another issue. I noticed that I can use only the PnPn formulation, but I would like to use the perturbation mode. At first glance (looking at drive1.f) it seems that the perturbation mode is available only on PnPn-2 formulation. Am I wrong? Thanks, Andrea

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2D to 3D
by nek5000-users＠lists.mcs.anl.gov 24 Sep '14

24 Sep '14

Hi Nek's Following this post: http://lists.mcs.anl.gov/pipermail/nek5000-users/2013-October/002333.html I'm trying to extrude a 2D file to a 3D file. First, I've run a 2D case. Then I've used n2to3 to generate the new 3D .rea file, called: new3d.rea. I've launch a new simulation with new3d.rea and everything works fine. However, when I include the information about the 3D extrusion in the usrdat2 subroutine, I get the following error message if I try to run the code. It seems something related to the z_average_transpose subroutine. What is wrong? Thanks call usrdat done :: usrdat generate geometry data vol_t,vol_v: 1749.7930352474154 1749.7930352474154 done :: generate geometry data call usrdat2 ===================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 8 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES ===================================================================================== APPLICATION TERMINATED WITH THE EXIT STRING: Floating point exception (signal 8) SL

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