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

Re: [Nek5000-users] Mesh-morphing for bend pipe
by nek5000-users＠lists.mcs.anl.gov 23 Jan '15

23 Jan '15

Hi Paul, I see. Many thanks for your help. It all works fine now. Best regards, Tony ________________________________________ From: nek5000-users-bounces(a)lists.mcs.anl.gov <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Sent: 23 January 2015 18:00 To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 71, Issue 12 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. Re: Nek5000-users Digest, Vol 71, Issue 11 (nek5000-users(a)lists.mcs.anl.gov) 2. Re: Nek5000-users Digest, Vol 71, Issue 11 (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Fri, 23 Jan 2015 02:37:53 +0000 From: nek5000-users(a)lists.mcs.anl.gov To: "nek5000-users(a)lists.mcs.anl.gov" <nek5000-users(a)lists.mcs.anl.gov> Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 71, Issue 11 Message-ID: <mailman.13977.1421980699.3424.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="iso-8859-1" Dear Paul, Thank you very much for your help. Yes, the problem was the jump in y direction. I wasn't aware of the shift in y direction after bending the pipe. The code works fine now. Just a quick question, if I want to do a U-bend pipe simulation, should I just change my geometry in usrdat2 subroutine or are there any other ways you would suggest? Thanks again. Cheers, Tony ________________________________________ From: nek5000-users-bounces(a)lists.mcs.anl.gov <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Sent: 22 January 2015 18:00 To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 71, Issue 11 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. Mesh-morphing for bend pipe (nek5000-users(a)lists.mcs.anl.gov) 2. Re: Mesh-morphing for bend pipe (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Wed, 21 Jan 2015 21:53:36 +0000 From: nek5000-users(a)lists.mcs.anl.gov To: "nek5000-users(a)lists.mcs.anl.gov" <nek5000-users(a)lists.mcs.anl.gov> Subject: [Nek5000-users] Mesh-morphing for bend pipe Message-ID: <mailman.13846.1421877222.3424.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="iso-8859-1" Dear Neks, I have been looking at the mesh-morphing for a bend pipe recently. I found the thread https://lists.mcs.anl.gov/mailman/htdig/nek5000-users/2011-June/001398.html on how to bend a straight pipe. The code worked perfectly for bending a straight pipe into a 90 degree bend shape. The problem is I need to bend my pipe at certain section, say I have a pipe with total length of 10 and I want to bend it in the second half, i.e. from 5-10. However, when I tried to do it in this way, the error of 'Vanishing Jacobian near Xth node of element XX' appeared and the simulation couldn't start. I can't see why it doesn't work. Below is the code I'm using to bend the pipe (from 5-10) into a 90 degree bend. Hope someone could help me on this. Any suggestion would be appreciated. Thank you very much in advance. Kind regards, Tony c----------------------------------------------------------------------- subroutine usrdat2() ! This routine to modify mesh coordinates include 'SIZE' include 'TOTAL' n = nx1*ny1*nz1*nelv c First, rotate x into axial position do i=1,n x_original = xm1(i,1,1,1) y_original = ym1(i,1,1,1) z_original = zm1(i,1,1,1) xm1(i,1,1,1) = z_original ym1(i,1,1,1) = y_original zm1(i,1,1,1) = -x_original enddo c Second, bend pipe into 90 degree bend xmin = glmin(xm1,n) xmax = glmax(xm1,n) ymin = glmin(ym1,n) ymax = glmax(ym1,n) if (nid==0) print *,xmin,xmax,ymin,ymax !which are 0, 10, -1, 1 rad0 = 0.5*(ymax-ymin) ! Radius of initial pipe rad1 = 1.0 ! Radius of new pipe radm = 2.0 ! Major radius of torus do i=1,n x = xm1(i,1,1,1) y = ym1(i,1,1,1) if (x .gt. 5.0e0) then theta = 0.5*pi*(x-5.0e0)/(xmax-5.0e0) rad = radm + 2.0e0*rad1*(y-ymin)/(ymax-ymin) ym1(i,1,1,1) = rad*cos(theta) xm1(i,1,1,1) = rad*sin(theta)+5.0e0 end if end do return end

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Re: [Nek5000-users] Nek5000-users Digest, Vol 71, Issue 11
by nek5000-users＠lists.mcs.anl.gov 23 Jan '15

23 Jan '15

Dear Paul, Thank you very much for your help. Yes, the problem was the jump in y direction. I wasn't aware of the shift in y direction after bending the pipe. The code works fine now. Just a quick question, if I want to do a U-bend pipe simulation, should I just change my geometry in usrdat2 subroutine or are there any other ways you would suggest? Thanks again. Cheers, Tony ________________________________________ From: nek5000-users-bounces(a)lists.mcs.anl.gov <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Sent: 22 January 2015 18:00 To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 71, Issue 11 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. Mesh-morphing for bend pipe (nek5000-users(a)lists.mcs.anl.gov) 2. Re: Mesh-morphing for bend pipe (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Wed, 21 Jan 2015 21:53:36 +0000 From: nek5000-users(a)lists.mcs.anl.gov To: "nek5000-users(a)lists.mcs.anl.gov" <nek5000-users(a)lists.mcs.anl.gov> Subject: [Nek5000-users] Mesh-morphing for bend pipe Message-ID: <mailman.13846.1421877222.3424.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="iso-8859-1" Dear Neks, I have been looking at the mesh-morphing for a bend pipe recently. I found the thread https://lists.mcs.anl.gov/mailman/htdig/nek5000-users/2011-June/001398.html on how to bend a straight pipe. The code worked perfectly for bending a straight pipe into a 90 degree bend shape. The problem is I need to bend my pipe at certain section, say I have a pipe with total length of 10 and I want to bend it in the second half, i.e. from 5-10. However, when I tried to do it in this way, the error of 'Vanishing Jacobian near Xth node of element XX' appeared and the simulation couldn't start. I can't see why it doesn't work. Below is the code I'm using to bend the pipe (from 5-10) into a 90 degree bend. Hope someone could help me on this. Any suggestion would be appreciated. Thank you very much in advance. Kind regards, Tony c----------------------------------------------------------------------- subroutine usrdat2() ! This routine to modify mesh coordinates include 'SIZE' include 'TOTAL' n = nx1*ny1*nz1*nelv c First, rotate x into axial position do i=1,n x_original = xm1(i,1,1,1) y_original = ym1(i,1,1,1) z_original = zm1(i,1,1,1) xm1(i,1,1,1) = z_original ym1(i,1,1,1) = y_original zm1(i,1,1,1) = -x_original enddo c Second, bend pipe into 90 degree bend xmin = glmin(xm1,n) xmax = glmax(xm1,n) ymin = glmin(ym1,n) ymax = glmax(ym1,n) if (nid==0) print *,xmin,xmax,ymin,ymax !which are 0, 10, -1, 1 rad0 = 0.5*(ymax-ymin) ! Radius of initial pipe rad1 = 1.0 ! Radius of new pipe radm = 2.0 ! Major radius of torus do i=1,n x = xm1(i,1,1,1) y = ym1(i,1,1,1) if (x .gt. 5.0e0) then theta = 0.5*pi*(x-5.0e0)/(xmax-5.0e0) rad = radm + 2.0e0*rad1*(y-ymin)/(ymax-ymin) ym1(i,1,1,1) = rad*cos(theta) xm1(i,1,1,1) = rad*sin(theta)+5.0e0 end if end do return end

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Mesh-morphing for bend pipe
by nek5000-users＠lists.mcs.anl.gov 21 Jan '15

21 Jan '15

Dear Neks, I have been looking at the mesh-morphing for a bend pipe recently. I found the thread https://lists.mcs.anl.gov/mailman/htdig/nek5000-users/2011-June/001398.html on how to bend a straight pipe. The code worked perfectly for bending a straight pipe into a 90 degree bend shape. The problem is I need to bend my pipe at certain section, say I have a pipe with total length of 10 and I want to bend it in the second half, i.e. from 5-10. However, when I tried to do it in this way, the error of 'Vanishing Jacobian near Xth node of element XX' appeared and the simulation couldn't start. I can't see why it doesn't work. Below is the code I'm using to bend the pipe (from 5-10) into a 90 degree bend. Hope someone could help me on this. Any suggestion would be appreciated. Thank you very much in advance. Kind regards, Tony c----------------------------------------------------------------------- subroutine usrdat2() ! This routine to modify mesh coordinates include 'SIZE' include 'TOTAL' n = nx1*ny1*nz1*nelv c First, rotate x into axial position do i=1,n x_original = xm1(i,1,1,1) y_original = ym1(i,1,1,1) z_original = zm1(i,1,1,1) xm1(i,1,1,1) = z_original ym1(i,1,1,1) = y_original zm1(i,1,1,1) = -x_original enddo c Second, bend pipe into 90 degree bend xmin = glmin(xm1,n) xmax = glmax(xm1,n) ymin = glmin(ym1,n) ymax = glmax(ym1,n) if (nid==0) print *,xmin,xmax,ymin,ymax !which are 0, 10, -1, 1 rad0 = 0.5*(ymax-ymin) ! Radius of initial pipe rad1 = 1.0 ! Radius of new pipe radm = 2.0 ! Major radius of torus do i=1,n x = xm1(i,1,1,1) y = ym1(i,1,1,1) if (x .gt. 5.0e0) then theta = 0.5*pi*(x-5.0e0)/(xmax-5.0e0) rad = radm + 2.0e0*rad1*(y-ymin)/(ymax-ymin) ym1(i,1,1,1) = rad*cos(theta) xm1(i,1,1,1) = rad*sin(theta)+5.0e0 end if end do return end

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bc for a jet in stratified fluid
by nek5000-users＠lists.mcs.anl.gov 21 Jan '15

21 Jan '15

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Re: [Nek5000-users] Compilation of nek5000 in ubuntu
by nek5000-users＠lists.mcs.anl.gov 15 Jan '15

15 Jan '15

Hi, Simon I met the similar problem as you before. What I did is : 1) check which and where mpif77 have been installed sth@sth:~$ which mpif77 /usr/.../mpif77 2) change this path to the makenek F77="/usr/.../mpif77" also you can include this path to you profile then you don't need to change makenek every time. hope it helps Qiong

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Compilation of nek5000 in ubuntu
by nek5000-users＠lists.mcs.anl.gov 14 Jan '15

14 Jan '15

Hi there, I am compiling the eddy example in my ubuntu OS, but the system returns error with "*Error: Can't open included file 'mpif.h'*". The fortran compiler in makenek file was changed to gfortran since mpif77 gives error: *--------------------------------------------------------------------------** **Unfortunately, this installation of Open MPI was not compiled with** **Fortran 77 support. As such, the mpif77 compiler is non-functional.** **--------------------------------------------------------------------------** **FATAL ERROR: Basic compiler test for mpif77 failed!* Is there anyone experience the same problem when compiling in ubuntu? You assistance will be greatly appreciated. Sincerely, Simon

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Nek MPI subroutine
by nek5000-users＠lists.mcs.anl.gov 08 Jan '15

08 Jan '15

Hello, I don't understand the following subroutine in the Nek mpi_dummy.f file: --------------------------------------------------------------------------------------------------------- subroutine mpi_comm_rank ( comm, me, ierror ) implicit none integer comm integer ierror integer me integer MPI_FAILURE parameter ( MPI_FAILURE = 1 ) integer MPI_SUCCESS parameter ( MPI_SUCCESS = 0 ) ierror = MPI_SUCCESS me = 0 return end --------------------------------------------------------------------------------------------------------- This will always return one. How does this give the rank of the process then? Can someone please explain the reason for this function? Thanks, Pradeep

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turbchannel-dsavg
by nek5000-users＠lists.mcs.anl.gov 06 Jan '15

06 Jan '15

Hello all, I am working on the Dynamic SGS model used in turbChannel example. There are two geometries in this example, one with 512 elements and the other one with 36 elements. I modified the routine "set_grid_spacing(dg2)" in .usr file to have a non-trivial filter width, rather than a constant one. When using the 36-element case, the code comes to a halt at routine "dofcnt" after calling "userchk", in which the unique gridpoints are counted. I realized that this happens when varaible "dg2" is being averaged on the elements boundaries via "dsavg()" in subroutine "set_grid_spacing(dg2)". However, I couldn't figure out the reason for that. This issue, however, does not happen for 512-element case. So I wondered if anyone has noticed similar issue with this example. I also wanted to echo my previous post (in the following link) on whether or not the SGS model in turbChannel example can be used in other geometries (e.g. for flow over a cylinder). I couldn't find anything that prevents one from using this model in other configurations except the spatial averaging routines, which are used to create a homogeneity in turbulent characteristics over the homogenous planes of channel example. https://lists.mcs.anl.gov/mailman/htdig/nek5000-users/2015-January/003159.h… Regards, Mohsen

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Melting front
by nek5000-users＠lists.mcs.anl.gov 06 Jan '15

06 Jan '15

Dear Neks, I'm interested in the possibility of solving melting front problems with Nek5000 (with Navier-Stokes in the fluid and heat transfer in both fluid and solid). However, I could only find relatively outdated documentation about this topic (User's guide Nekton v2.85 or http://www.mcs.anl.gov/~fischer/Nek5000/nekmanual.pdf for example). Is this option still available in more recent releases of Nek, and should I follow the old documentation to setup my problem or is there a more recent version? Many thanks, Benjamin.

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LES-wall
by nek5000-users＠lists.mcs.anl.gov 01 Jan '15

01 Jan '15

Hello all, I have a question regarding LES capability of Nek. I know that the explicit filtering introduced in Nek can be effective for velocity field to provide sort of eddy viscosity modeling. Nevertheless, there should be some form of modeling for the near wall regions, since it is almost infeasible to have DNS like resolution in such regions for problems with relatively high Reynolds number and large scale geometries. I have seen SFR assemblies example on the Nek web in which LES used, however, I am not sure if that was an LES with near-wall resolution or with near-wall modeling. So I was wondering if anyone has any experience of using Nek LES with near wall models, or kind of hybrid RANS-LES approaches. Thanks, Mohsen

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