August 2013 - 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 in generalev
by nek5000-users＠lists.mcs.anl.gov 02 Jul '14

02 Jul '14

Hello Neks, I've recently come across an error I haven't seen before. It occurs in the routine "generalev" at the beginning of my run. It looks like the matrix "a" and "b" being fed to the routine have an Infinity or NaN at position (0,0). Are there any ideas of what could cause this type of error? I have attached the logfile to this email. Thanks, -- Josh Camp "All that is necessary for the triumph of evil is that good men do nothing" -- Edmund Burke

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Linearized Nek: Compute only the right-hand side
by nek5000-users＠lists.mcs.anl.gov 21 Jan '14

21 Jan '14

Hi Nek's, Given a random initial vector u and the Jacobian matrix of the linearized Navier-Stokes, I would like to calculate the matrix-vector product J * u. In Nek, that would consists in calculating only the right hand side of the equations, that is: RHS = ( -U.grad(u) - u.grad(U) - grad(p) + 1/Re Lap(u) ; div(u) ) I have a few questions on how to compute those different terms in userchk (Nek is used in post-process mode): - I would tend to use convop() for the convection terms, however I'm not sure whereas it would output the strong or weak form (and I need the strong one obviously)? - Same question regarding grad(p) and div(u) if I use opgradt() and opdiv() to calculate them? Last but not least, for the Laplacian I've read a previous mail where it is said that it can be computed using a sequence of wgradm1() and vec_dssum() so I guess I kown how to compute at the strong form for it. Sincerely, -- Jean-Christophe

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neuman bc for the normal velocity component
by nek5000-users＠lists.mcs.anl.gov 23 Oct '13

23 Oct '13

Dear Nekians, I'm relatively new to nek. I would like to compute the flow of a boundary layer and I would like to impose the following boundary condition on the top (2D) boundary, which is parallel to the wall: u = U_base and dv/dy = - dU_base/dx, where U_base is the known inviscid base flow. The velocity component u is parallel to the boundary, whereas v is normal. I tried to use 'ON ' but this did not give the result I was expecting (Am I doing smth. wrong?). At the boundary nodes u was equal to U_base, but at the very next node u was completly different (and v was of course completly wrong). Thanks for any help Joris

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Compilation Error on BG/Q
by nek5000-users＠lists.mcs.anl.gov 15 Oct '13

15 Oct '13

Hi neks! On the BG/Q in Jï¿½lich we encounter several errors while compiling nek5000 (Revision: 853). Please find attached the compiler output, the makenek script and the makefile. The installed compiler versions are "IBM XL C/C++ for Blue Gene, V12.1" and "IBM XL Fortran for Blue Gene, V14.1". Did you come across similar problems on your BG/Q runs? Do you have any hint how I can fix this? Thanks in advance Fabian

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convert mesh by MOAB
by nek5000-users＠lists.mcs.anl.gov 29 Aug '13

29 Aug '13

Hi All, I am trying to convert cubit mesh to .h5m using MOAB (mbconvert blah.cub blah.h5m), but I get this error Element ids are not contiguous! Failed to load "pipe.cub". Error code: MB_INDEX_OUT_OF_RANGE (1) Error message: No sparse tag CATEGORY value for Vertex 1 I don't know what is the problem, does anybody can help in this problem. FYI, I used Trelis to make a mesh, is there anything wrong with my geometry or mesh? Thanks, Ami

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Body Force And USR Questions
by nek5000-users＠lists.mcs.anl.gov 28 Aug '13

28 Aug '13

Hi All, I hate to ask such lengthy and simple questions, but I'm getting stuck and could use a sharp kick... I read through source code, examples, and the docs, but could still use some help... I have some background with SEM study and my own trivial code, so I have some understanding of the spatial discretization part of it. I have a trivial "template" problem setup and running. My problem is understanding what some of the variables are (in context of their use in the code), and how to use them in the .usr file to do what I want. I'm trying to simulate a horizontal wind turbine wake flow, using the actuator disc method and then the actuator line method. I can get some flow results by specifying constant body forces in .usr. I have also tried a simple use of what I think is the z-velocity in an equation to calculate a body force, and this seems to work also... I'd like to move on to more complex body force calculations, but need to know more about what some of the variables are; how they're calculated, and how they are used/called in .usr. The following is my first pass at a list of questions: 1) Spatially, which variables specify the actual GLL point numbers (not physical coordinates, but point count in each coordinate direction)? Are these ix,iy,iz? I assume they are numbered per element? 2) Are x,y,z the real physical coordinates in space? Are they the actual domain size? Are there non-dimensional coordinates also? What are the xc,yc,zc variables? 3) Are ux, uy, uz the fluid velocities in the coordinate directions? 4) Can the velocities and forces be specified or referred to at any physical location, or only at the GLL points? In other words, is there internal extrapolation going on, or do I need to specify and read my forces at GLL points only? All the subroutines seem to call based on ix,iy,iz; when I run the following, it does calculate some forces: subroutine userf (ix,iy,iz,ieg) include 'SIZE' include 'TOTAL' include 'NEKUSE' c ffx = 0. ffy = 0. ffz = 0. if ((z>70).AND.(z<71.).AND.(x>60.).AND.(x<90.) +.AND.(y>60.).AND.(y<90.)) then ffz = -(.5*1.2*(uz**2.)*(4.*.9*(1.-.9))) c ffz = (-1000.) endif c write (6,*) ffz,ieg return end However, if I change my spatial selection to: if ((z==71.).AND.(x>60.).AND.(x<90.) +.AND.(y>60.).AND.(y<90.)) then I get no force output. If everything is at the GLL locations, are there available subroutines to extrapolate to/from physical locations? 5) I assume that the subroutines in .usr are called at each time step? Is "istep" the number of the time step? Is "time" the actual time integration time, or the wall clock? What is "itime"? Just want to be able to calculate physical location of a line moving on the grid based on time step... Thanks, Murph -- *Murphy Leo O'Dea, PE"Murph"* PhD Student, Mechanical Engineering /School Of Engineering And Computer Science/ /Oakland University/ mlodea(a)oakland.edu <mailto:[email protected]> http://www.secs.oakland.edu/~mlodea/

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error in compilation due to high tensor product grid
by nek5000-users＠lists.mcs.anl.gov 26 Aug '13

26 Aug '13

Hi nek users, When ever I try to compile a case of TurbChannel using very high resolution in x,y,z it would give me error as follows. turbChannel.f:(.text+0x24): relocation truncated to fit: R_X86_64_PC32 against symbol `dimn_' defined in COMMON section in obj/turbChannel.o turbChannel.f:(.text+0x4a): relocation truncated to fit: R_X86_64_PC32 against symbol `dimn_' defined in COMMON section in obj/turbChannel.o turbChannel.f:(.text+0x7c): relocation truncated to fit: R_X86_64_PC32 against symbol `gfdmic_' defined in COMMON section in obj/turbChannel.o turbChannel.f:(.text+0xb0): relocation truncated to fit: R_X86_64_PC32 against symbol `dimn_' defined in COMMON section in obj/turbChannel.o turbChannel.f:(.text+0xdf): relocation truncated to fit: R_X86_64_32S against symbol `hcglb_' defined in COMMON section in obj/turbChannel.o turbChannel.f:(.text+0x163): relocation truncated to fit: R_X86_64_32S against symbol `gfdmic_' defined in COMMON section in obj/turbChannel.o turbChannel.f:(.text+0x177): relocation truncated to fit: R_X86_64_PC32 against symbol `dimn_' defined in COMMON section in obj/turbChannel.o turbChannel.f:(.text+0x18b): relocation truncated to fit: R_X86_64_PC32 against symbol `dimn_' defined in COMMON section in obj/turbChannel.o turbChannel.f:(.text+0x19a): relocation truncated to fit: R_X86_64_PC32 against symbol `dimn_' defined in COMMON section in obj/turbChannel.o turbChannel.f:(.text+0x233): relocation truncated to fit: R_X86_64_32S against symbol `gauss_' defined in COMMON section in obj/turbChannel.o obj/turbChannel.o: In function `set_obj_': turbChannel.f:(.text+0x390): additional relocation overflows omitted from the output collect2: ld returned 1 exit status make: *** [nek5000] Error Can anybody please help me on that. Thanks, Tanmoy

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Div(flux) in weak form
by nek5000-users＠lists.mcs.anl.gov 26 Aug '13

26 Aug '13

Hello Neks, I'm looking for some guidance, or, better, a code snippet. Within userchk, I have calculated a flux vector: flux = (flux_x, flux_y, flux_z). I need to include the divergence of this vector as a forcing term via qvol. I want to incorporate divergence(flux) in weak form (i.e., apply integration by parts). I believe that I need to use wgradm1 to do this, but the exact syntax in not clear. Would one of you kindly point me in the write direction, or give me the code to do that? I understand the term then needs to be multiplied by the inverse mass matrix. Thanks much! Mike

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Solving linearized NS equations in 3D
by nek5000-users＠lists.mcs.anl.gov 19 Aug '13

19 Aug '13

Hi Neks' ! I'm trying to visualize the Crow instability using the linearized equation solver in 3D. However, the resulting vorticity of the perturbation is the same for the calculation in 2D (ie. not the Crow instability). Are there any other parameters to change in the .rea or SIZE files to go from 2D to 3D when using the linearized NS? Any help would be greatly appreciated. Thanks, Holly

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