August 2010 - Nek5000-users - mailman3.cels.anl.gov

problem with closed internal boundaries
by nek5000-users＠lists.mcs.anl.gov 23 Jul '13

23 Jul '13

Hello Neks, I'm trying to model a flow past an obstacle in a channel. As a first step I would like to do a 2D simulation. I'm encountering some problems during the geometry data generation in the nek5000 execution : it looks like the program can only generate NaN values although genmap seems to work well on the .rea file. I can also reopen the rea file with prenek without any problems. Do you have any idea what is going wrong here? Is it problematic to have a closed internal boundary condition? Thanks in advance for any help. Best, Michael B

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Periodic B.C and Genmap Issue
by nek5000-users＠lists.mcs.anl.gov 09 Nov '12

09 Nov '12

Hi Paul, This post is in reference to the previous post by Michael (dated Jun 22). When I try to get a map file for a rea file that has periodic vertices, I get the following error. The rea file was generated the same way as before (Gambit -> Nek through Matlab). I checked on Matlab by plotting the periodic vertices and confirmed for a few faces that they are indeed periodic. Also, as you had earlier suggested (with the new genmap), I tried changing the tolerances fro 0.09 to 0.2 and I get the same periodic mismatch error. Could you provide any leads on where things are going wrong ? Please find below the error message. Thanks. <error> Input (.rea) file name: domain Input mesh tolerance (default 0.2): NOTE: smaller is better, but generous is more forgiving for bad meshes. 0.09 reading .rea file data ... start locglob_lexico: 8 3912 31296 8.99999999999999967E-002 locglob: 1 1 31296 locglob: 2 36 31296 locglob: 3 1224 31296 locglob: 1 4851 31296 locglob: 2 4851 31296 locglob: 3 4851 31296 locglob: 1 4851 31296 locglob: 2 4851 31296 locglob: 3 4851 31296 done locglob_lexico: 4851 4851 31296 10 start periodic vtx: 3912 4851 abort: PERIODIC MISMATCH 2: 1093 1 P ie 0 1 je 4.14470000000000029E-003 0.0000000000000000 bc 8 quit </error> Regards Shriram

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Re: [Nek5000-users] Vanishing Jacobian error description
by nek5000-users＠lists.mcs.anl.gov 10 Mar '11

10 Mar '11

Hi Paul, Here is the rea, usr, & SIZE file I am using. I ran it again without the curved side information and it worked, so I think the problem is somewhere in the curved side section of the rea. The geometry is a square base lofted into a circle in the +z direction. The mesh was generated in gambit. I've developed a matlab code that will take a mesh created in gambit and generate the required REA formatting. I have created some basic shapes to test the matlab portion and the curved side portion, and it worked in most cases (not this one yet). I'm not sure what is going on with the curved side data in this case however. Thanks for looking at this, Michael ----- Original Message ----- From: nek5000-users(a)lists.mcs.anl.gov To: "Nekton User List" <nek5000-users(a)lists.mcs.anl.gov> Sent: Tuesday, April 20, 2010 3:36:44 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Vanishing Jacobian error description Michael, The code is trying to check to ensure that the mesh is valid. Sometimes, however, there are other causes for the problem. Can you send a gzip'd rea/usr file, and I can take a look later tonight. Paul On Tue, 20 Apr 2010, nek5000-users(a)lists.mcs.anl.gov wrote: > Hi, > > I am running into an issue with 'Vanishing Jacobian'. To help understand what the problem > is, could someone explain what is meant in the error? Specifically, what it means by "Xth node" of the element. > Also, I ran into this issue when I was deforming geometries in the usr file, where one of the elements > would overlap another by mistake. However in this case I know there are no overlaps. > > Here is a portion: > > 0 ERROR: Vanishing Jacobian near 91th node of element 69. > 1.40692804605498586E-002 -7.79619559165757245E-003 > 0 xyz: 2.65874E-01 3.54498E-01 2.87050E+00 > 0 xyz: 2.07855E-01 1.77249E-01 2.87050E+00 > > > 0 ERROR: Vanishing Jacobian near 76th node of element 70. > 2.59472856644434001E-002 -2.12442422718029170E-002 > 0 xyz: 2.11655E-01 4.23310E-01 2.62500E+00 > 0 xyz: 3.54498E-01 1.77249E-01 2.87050E+00 > > Thanks for any help deciphering this error! > > - Michael > > > > > > _______________________________________________ Nek5000-users mailing list Nek5000-users(a)lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

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lambda2
by nek5000-users＠lists.mcs.anl.gov 28 Jan '11

28 Jan '11

dear neks, in the source file postpro.f i found the following subroutine: subroutine lambda2(l2) c c Generate Lambda-2 vortex of Jeong & Hussein, JFM '95 c ... but it is not used in the code and i wanted calculate it for some visualizations. may you can explain me how i can use it. because i tried just to call it in the usrchk subroutine but then i get an error message (segmentation fault...). best, fred

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Visit and NEK 3D data
by nek5000-users＠lists.mcs.anl.gov 06 Jan '11

06 Jan '11

Hello all, I am running into a problem with Visit and NEK 3D data files. Visit (version 1.12.2) reads them in, but the mesh is all jumbled up. If anyone could try Visit on this file, I'd be grateful, perhaps there is some setting in Visit that I overlooked. The data file (4MB) is: http://tetra.fluid.tuwien.ac.at/fmuldoo/engineering-marangoni-flows/sim2/si… I use the following meta data file: NEK5000 version: 1.0 filetemplate: c203d.fld%02d firsttimestep: 2 numtimesteps: 1 Cheers, Frank -- Frank Herbert Muldoon, Ph.D. Mechanical Engineering Technische Universität Wien (Technical University of Vienna) Inst. f. Strömungsmechanik und Wärmeübertragung (Institute of Fluid Mechanics and Heat Transfer) Resselgasse 3 1040 Wien Tel: +4315880132232 Fax: +4315880132299 Cell:+436765203470 fmuldoo (skype) http://tetra.fluid.tuwien.ac.at/fmuldoo/public_html/webpage/frank-muldoon.h…

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Re: [Nek5000-users] Compute the derivatives
by nek5000-users＠lists.mcs.anl.gov 26 Nov '10

26 Nov '10

Hi Michael, iostep dump works only for the dump of quantities specified as T in your .rea like ***** OUTPUT FIELD SPECIFICATION ***** 8 SPECIFICATIONS FOLLOW T COORDINATES T VELOCITY T PRESSURE T TEMPERATURE F TEMPERATURE GRADIENT 2 PASSIVE SCALARS F F Since userchk is called every timestep so you'll need something like if (mod(istep,iostep).eq.0) then ... Best, Aleks ----- Original Message ----- From: nek5000-users(a)lists.mcs.anl.gov To: nek5000-users(a)lists.mcs.anl.gov Sent: Thursday, July 1, 2010 7:57:07 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives Hi Paul and Aleks, I have a question regarding this. I have implemented this and it is working nicely, however it is dumping out a .f file every step, rather than every iotime step I have specified in the rea. Do you know how to fix this? - Michael ----- Original Message ----- From: nek5000-users(a)lists.mcs.anl.gov To: nek5000-users(a)lists.mcs.anl.gov Sent: Wednesday, June 2, 2010 10:57:41 AM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Compute the derivatives Hi JC, To dump the computed derivatives into separate field files you can use in userchk ifxyo = .true. ! for cooordinates ifpo = .false. ! turn off pressure output ifto = .false. ! turn off pressure output call outpost(vxx,vxy,vxz,pr,t,'dvx') call outpost(vyx,vyy,vyz,pr,t,'dvy') ... Best, Aleks On Wed, 2 Jun 2010, nek5000-users(a)lists.mcs.anl.gov wrote: > > dudxyz is somewhat dated and slow... > > I recommend somthing like: > > parameter (lt=lx1*ly1*lz1*lelv) > common /mygrad/ vxx(lt),vxy(lt),vxz(lt) > $ , vyx(lt),vyy(lt),vyz(lt) > $ , vzx(lt),vzy(lt),vzz(lt) > > call gradm1(vxx,vxy,vxz,vx) > call gradm1(vyx,vyy,vyz,vy) > call gradm1(vzx,vzy,vzz,vz) > > Note that putting these arrays into a common block, as > shown, is a good idea for several reasons, one of which > is that it guarantees that the data will be byte-aligned with the cache line. > On some machines (e.g., BG/P) this > is crucial for proper functionality - for this reason we > don't mix variable types in a given common block. > > If you subsequently wish to access elements of vxx etc. > on an element-by-element basis you can of course do something > like > > parameter (lt=lx1*ly1*lz1) > common /mygrad/ vxx(lt,lelt),vxy(lt,lelt),vxz(lt,lelt) > : > : > > Paul > > On Wed, 2 Jun 2010, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Hi Nek's, >> >> I have a home-made global stability code, but in order to use it I first >> need to compute the derivatives of my base flow: dUdX, dUdY, dVdX, dVdY. >> How could one compute these derivatives using Nek 5k and drop them along >> with X Y U V in the blah.f**** file (or perhaps another .f**** file) ? I >> assume I have to make use of the subroutine *dudxyz >> (du,u,rm1,sm1,tm1,jm1,imsh,isd)*, but I'm not sure what to put as inputs. >> >> Regards, >> JC >> > _______________________________________________ > 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

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Smooth Restart feature in Nek
by nek5000-users＠lists.mcs.anl.gov 30 Sep '10

30 Sep '10

Hi, I found a function in nek which would let you do a restart from 3 previous fld files. This is how I called the function: % ---- in usrchk: prefix = 'rs6' iosave = iostep iosize = 8 nfld = 3 call restart_save(iosave,iosize,nfld) . %---- in rea file : 3 PRESOLVE/RESTART OPTIONS ***** rs6sqr0.f0004 rs6sqr0.f0005 rs6sqr0.f0006 %----- This dumps out six rs6blah0.f***** and is overwritten once every 2*iostep I believe. When I try to restart using this, I still see that at the restart, the pressure values are off. I am guessing that I am not calling it the right way in the rea file. Is there a separate function for loading multiple restart files that I would have to call in usrchk ? Or is this behavior a by-product of SEM ? Thanks for any help. Regards Shriram

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lelx vs nelx
by nek5000-users＠lists.mcs.anl.gov 27 Aug '10

27 Aug '10

Hi, I am not exactly understanding what is the LELX parameter and how to use it. ( LELX/LELY/LELZ: Maximum number of elements per processor for global fdm solver ) and why sometime in the code there is this check (for example in the turbchannel's userchk or in genbox.f) : if(nelx.gt.lelx .or. nely.gt.lely .or. nelz.gt.lelz) then if(nid.eq.0) write(6,*) 'ABORT: nel_xyz > lel_xyz!' call exitt endif can anyone help me on that ? thank you a lot francesco

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Re: [Nek5000-users] Temperature gradient at a point
by nek5000-users＠lists.mcs.anl.gov 26 Aug '10

26 Aug '10

What's the error message you are getting? It may be the case, I know that I have had issues with settings and conj HT before since they are (mainly because of our group) revisiting CHT and fixing issues that we request. The latest issue, like I mentioned, was the new time stepping scheme and CHT. Did the error show up during compiling, or during the run in the output log? - Mike ----- Original Message ----- From: nek5000-users(a)lists.mcs.anl.gov To: nek5000-users(a)lists.mcs.anl.gov Sent: Thursday, August 26, 2010 2:18:39 PM GMT -06:00 US/Canada Central Subject: Re: [Nek5000-users] Temperature gradient at a point Hi, Is there any reason why a conjucate heat transfer case should not work with IFLOMACH turned on? I did modify the uservp to set utrans = 1./temp. Thanks, Pradeep c----------------------------------------------------------------------- subroutine uservp (ix,iy,iz,ieg) include 'SIZE' include 'TOTAL' include 'NEKUSE' if (ifield.eq.1) then utrans = 1./temp c utrans = param(1) udiff = param(2) else utrans = 1./temp ! thermal properties c utrans = param(7) udiff = param(8) if (ieg .gt. nelgv) then ! properties in the solid udiff = 0.1*param(8) ! conductivity utrans = 1.0 endif endif return end c----------------------------------------------------------------------- On Mon, Aug 23, 2010 at 4:40 PM, Pradeep Rao < stringsofdurga(a)gmail.com > wrote: Thanks Aleks, Will give that a try. On Mon, Aug 23, 2010 at 4:25 PM, < nek5000-users(a)lists.mcs.anl.gov > wrote: Hi Pradeep, Dependence of conductivity on time and space is not a problem once one uses non zero p30 in .rea that activates a call to uservp of .usr file If you also need a dependence of conductivity on temperature you may want to consider either using the values from the previous time step or doing extrapolation in time. Best, Aleks On Mon, 23 Aug 2010, nek5000-users(a)lists.mcs.anl.gov wrote: Hi Paul, Thanks for the detailed reply. The reason I'm not solving it as a conjugate heat transfer problem, is that thermal conductivity is a function of temperature based on some curve fit equations, and I am not sure how to implement that. Thanks, Pradeep On Mon, Aug 23, 2010 at 4:04 PM, < nek5000-users(a)lists.mcs.anl.gov > wrote: Hi Pradeep, Why not just solve the conjugate heat transfer problem directly using fluid + solid elements in nek? Also, nek supports full Robin boundary conditions if you wish to do a Newton law of cooling: k*dT/dn . n_hat = h*(T-Tinf), where Tinf is the external temperature and h is the heat transfer coefficient, both of which can be functions of time and space. Regarding gradm1, you would call it from userchk, and store the output in arrays in a common block, e.g., as below. Paul subroutine userchk : common /mygrad/ tx(lx1,ly1,lz1,lelt) $ , ty(lx1,ly1,lz1,lelt) $ , tz(lx1,ly1,lz1,lelt) call gradm1(tx,ty,tz,t) : : subroutine userbc (ix,iy,iz,iside,eg) include 'SIZE' include 'TOTAL' include 'NEKUSE' common /mygrad/ tx(lx1,ly1,lz1,lelt) $ , ty(lx1,ly1,lz1,lelt) $ , tz(lx1,ly1,lz1,lelt) integer e,eg e = gllel(eg) ! global element number to processor-local el. # gtx=tx(ix,iy,iz,e) gty=ty(ix,iy,iz,e) gtz=tz(ix,iy,iz,e) On Mon, 23 Aug 2010, nek5000-users(a)lists.mcs.anl.gov wrote: Hi Paul, I am basically trying to solve a conjugate heat transfer problem in an iterative manner, for flow over an infinitely long cylinder (2D). I need to use the heat transfer at the boundary, to calculate the new temperature at the boundary for the next time step. The temperature for the next time step is solved for using this heat flux, by a function in the usr file using an FEM algorithm for the solid part (cylinder). The bc type I am using is Temperature - fortran function. Regards, Pradeep On Mon, Aug 23, 2010 at 2:50 PM, < nek5000-users(a)lists.mcs.anl.gov > wrote: Pradeep, if you give me some idea of the nature of your bc, I can perhaps help --- there are a large number of bc types already supported inside nek Paul On Mon, 23 Aug 2010, nek5000-users(a)lists.mcs.anl.gov wrote: Hi, I wanted to know if there was a way to find the temperature gradient at a point. I need that information in the userbc function. I tried using gradm1(), but I am not sure how to get the value at a given point. Thanks, Pradeep _______________________________________________ Nek5000-users mailing list Nek5000-users(a)lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -- Pradeep C. Rao Graduate Research Assistant for FT2L ( http://www1.mengr.tamu.edu/FT2L/ ) Department of Mechanical Engineering Texas A&M University College Station, TX 77843-3123 428 Engineering Physics Building (713) 210-9769 uuuu c----------------------------------------------------------------------- C C USER SPECIFIED ROUTINES: C C - boundary conditions C - initial conditions C - variable properties C - local acceleration for fluid (a) C - forcing function for passive scalar (q) C - general purpose routine for checking errors etc. C c----------------------------------------------------------------------- subroutine uservp (ix,iy,iz,eg) include 'SIZE' include 'TOTAL' include 'NEKUSE' integer e,f,eg c e = gllel(eg) udiff =0. utrans=0. return end c----------------------------------------------------------------------- subroutine userf (ix,iy,iz,eg) include 'SIZE' include 'TOTAL' include 'NEKUSE' integer e,f,eg c e = gllel(eg) c Note: this is an acceleration term, NOT a force! c Thus, ffx will subsequently be multiplied by rho(x,t). ffx = 0.0 ffy = 0.0 ffz = 0.0 return end c----------------------------------------------------------------------- subroutine userq (ix,iy,iz,eg) include 'SIZE' include 'TOTAL' include 'NEKUSE' integer e,f,eg c e = gllel(eg) qvol = 0.0 return end c----------------------------------------------------------------------- subroutine userchk include 'SIZE' include 'TOTAL' return end c----------------------------------------------------------------------- subroutine userbc (ix,iy,iz,iside,ieg) include 'SIZE' include 'TOTAL' include 'NEKUSE' ux=0.0 uy=0.0 uz=0.0 temp=0.0 return end c----------------------------------------------------------------------- subroutine useric (ix,iy,iz,ieg) include 'SIZE' include 'TOTAL' include 'NEKUSE' ux=0.0 uy=0.0 uz=0.0 temp=0 return end c----------------------------------------------------------------------- subroutine usrdat include 'SIZE' include 'TOTAL' c return end c----------------------------------------------------------------------- subroutine usrdat2 include 'SIZE' include 'TOTAL' param(66) = 4. ! These give the std nek binary i/o and are param(67) = 4. ! good default values return end c----------------------------------------------------------------------- subroutine usrdat3 include 'SIZE' include 'TOTAL' c return end c----------------------------------------------------------------------- _______________________________________________ Nek5000-users mailing list Nek5000-users(a)lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -- Pradeep C. Rao Graduate Research Assistant for FT2L ( http://www1.mengr.tamu.edu/FT2L/ ) Department of Mechanical Engineering Texas A&M University College Station, TX 77843-3123 428 Engineering Physics Building (713) 210-9769 _______________________________________________ Nek5000-users mailing list Nek5000-users(a)lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -- Pradeep C. Rao Graduate Research Assistant for FT2L ( http://www1.mengr.tamu.edu/FT2L/ ) Department of Mechanical Engineering Texas A&M University College Station, TX 77843-3123 428 Engineering Physics Building (713) 210-9769 -- Pradeep C. Rao Graduate Research Assistant for FT2L ( http://www1.mengr.tamu.edu/FT2L/ ) Department of Mechanical Engineering Texas A&M University College Station, TX 77843-3123 428 Engineering Physics Building (713) 210-9769 _______________________________________________ Nek5000-users mailing list Nek5000-users(a)lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users

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Temperature gradient at a point
by nek5000-users＠lists.mcs.anl.gov 26 Aug '10

26 Aug '10

Hi, I wanted to know if there was a way to find the temperature gradient at a point. I need that information in the userbc function. I tried using gradm1(), but I am not sure how to get the value at a given point. Thanks, Pradeep

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