July 2017 - Nek5000-users - mailman3.cels.anl.gov

Re: [Nek5000-users] Only neumann and periodic boundary conditions for energy equation
by nek5000-users＠lists.mcs.anl.gov 28 Jul '17

28 Jul '17

Hi Paul, thank you very much for the detailed problem description and the laminar test case. Best Regards, Steffen > Subject: > Re: [Nek5000-users] Only neumann and periodic boundary conditions for > energy equation > From: > <nek5000-users(a)lists.mcs.anl.gov> > Date: > 07/27/2017 10:22 PM > > To: > "nek5000-users(a)lists.mcs.anl.gov" <nek5000-users(a)lists.mcs.anl.gov> > > > > Hi Steffen, > > > The attached file shows how to deal with the case > > you're interested in. > > > Please see the README, the .pdf, and the .usr files. > > > hth, > > > Paul > > > > ------------------------------------------------------------------------ > *From:* Nek5000-users <nek5000-users-bounces(a)lists.mcs.anl.gov> on > behalf of nek5000-users(a)lists.mcs.anl.gov > <nek5000-users(a)lists.mcs.anl.gov> > *Sent:* Thursday, July 27, 2017 2:11 AM > *To:* nek5000-users(a)lists.mcs.anl.gov > *Subject:* [Nek5000-users] Only neumann and periodic boundary > conditions for energy equation > Hi Neks, > > I want to simulate "ideal" isoflux boundary conditions in a pipe. > As the temperature (T) increases in streamwise direction (in my case > z-direction), I define > theta(r,phi,z,t) = (<T_w>(z) - T(r,phi,z,t))/T_r > with T_r = q_w/(rho c_p U_b) and <T_w>(z) denoting the time average of > the wall temperature T_w. > > With that I can recast my energy equation to solve for the temperature > difference theta instead of the temperature T which allows for periodic > boundary conditions as theta does not change in streamwise direction. > This introduces an additional source term 4 u_z. > > I would like to set a constant heat flux boundary condition at the wall > (see e.g. Piller: Direct numerical simulation of turbulent forced > convection in a pipe. 2005), i.e. a Neumann boundary condition (ideal > isoflux), and compare the results to those obtained with the same PDE > but a Dirichlet boundary condition theta_w=0 (mixed-type). This setup of > applying only Neumann boundary conditions is "ill-posed". I believe > because there is no unique solution to this setup, right? > As Piller points out, one can introduce an additional constraint and > enforce the volume averaged temperature to be constant to overcome this > issue. Piller did not face this problem as he was using a finite volume > method. > > I can calculate the volume integral over temperature like this, correct? > nt = nx1*ny1*nz1*nelt > t_vol = glsc2(t, bm1, nt) > > And then I would adjust my source term in each step to keep > t_vol=constant. > However, I do not know this constant in advance. If I set it to an > arbitrary value, e.g. zero, this leads to negative theta at the wall, > which contradicts my definition of theta. > > > I know this is not a specific Nek5000 Problem but maybe someone has > experienced similar issues and found a solution that works in Nek5000? > > Best Regards, > Steffen Straub > > -- > Karlsruhe Institute of Technology (KIT) > Institute of Fluid Mechanics > > M.Sc. Steffen Straub > Doctoral Researcher > > Kaiserstraï¿½e 10 > Building 10.23 > 76131 Karlsruhe, Germany > > Phone: +49 721 608-43027 > E-mail: steffen.straub(a)kit.edu > Web: http://www.istm.kit.edu > > KIT ï¿½ The Research University in the Helmholtz Association > > Since 2010, the KIT has been certified as a family-friendly university.

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Only neumann and periodic boundary conditions for energy equation
by nek5000-users＠lists.mcs.anl.gov 27 Jul '17

27 Jul '17

Hi Neks, I want to simulate "ideal" isoflux boundary conditions in a pipe. As the temperature (T) increases in streamwise direction (in my case z-direction), I define theta(r,phi,z,t) = (<T_w>(z) - T(r,phi,z,t))/T_r with T_r = q_w/(rho c_p U_b) and <T_w>(z) denoting the time average of the wall temperature T_w. With that I can recast my energy equation to solve for the temperature difference theta instead of the temperature T which allows for periodic boundary conditions as theta does not change in streamwise direction. This introduces an additional source term 4 u_z. I would like to set a constant heat flux boundary condition at the wall (see e.g. Piller: Direct numerical simulation of turbulent forced convection in a pipe. 2005), i.e. a Neumann boundary condition (ideal isoflux), and compare the results to those obtained with the same PDE but a Dirichlet boundary condition theta_w=0 (mixed-type). This setup of applying only Neumann boundary conditions is "ill-posed". I believe because there is no unique solution to this setup, right? As Piller points out, one can introduce an additional constraint and enforce the volume averaged temperature to be constant to overcome this issue. Piller did not face this problem as he was using a finite volume method. I can calculate the volume integral over temperature like this, correct? nt = nx1*ny1*nz1*nelt t_vol = glsc2(t, bm1, nt) And then I would adjust my source term in each step to keep t_vol=constant. However, I do not know this constant in advance. If I set it to an arbitrary value, e.g. zero, this leads to negative theta at the wall, which contradicts my definition of theta. I know this is not a specific Nek5000 Problem but maybe someone has experienced similar issues and found a solution that works in Nek5000? Best Regards, Steffen Straub -- Karlsruhe Institute of Technology (KIT) Institute of Fluid Mechanics M.Sc. Steffen Straub Doctoral Researcher Kaiserstraße 10 Building 10.23 76131 Karlsruhe, Germany Phone: +49 721 608-43027 E-mail: steffen.straub(a)kit.edu Web: http://www.istm.kit.edu KIT – The Research University in the Helmholtz Association Since 2010, the KIT has been certified as a family-friendly university.

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Re: [Nek5000-users] simulation termination at istep=0 with NaN
by nek5000-users＠lists.mcs.anl.gov 26 Jul '17

26 Jul '17

Hello, Thanks for your help. Please see below for the log file. Ajay ####################### Number of processors: 8 REAL wdsize : 8 INTEGER wdsize : 4 Timer accuracy : 7.87E-07 Reading /home/ajay/nek5_svn/runs/smallcylinder/simplecylinder.rea mapping elements to processors Reading /home/ajay/nek5_svn/runs/smallercylinder/simpleduct.map 0 2827 2827 22620 22620 NELV 1 2828 2828 22620 22620 NELV 2 2827 2827 22620 22620 NELV 3 2828 2828 22620 22620 NELV 4 2827 2827 22620 22620 NELV 5 2828 2828 22620 22620 NELV 6 2827 2827 22620 22620 NELV 7 2828 2828 22620 22620 NELV RANK 0 IEG 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 . . 19702 19703 19704 19705 19706 19707 19708 19709 19710 19711 19712 19713 19714 19715 19716 19717 19718 19719 19720 element load imbalance: 1 2827 2828 done :: mapping elements to processors 0 objects found 103 Parameters from file: 1 1.00000 p1 DENSITY 2 -500.000 p2 VISCOS 7 1.00000 p7 RHOCP 8 1.00000 p8 CONDUCT 11 10000 p11 NSTEPS 12 0.10000E-05 p12 DT 15 5 p15 IOSTEP 18 -20.00000 p18 GRID 19 -1.00000 p19 INTYPE 20 10.0000 p20 NORDER 26 1.00000 p26 COURANT/NTAU 27 2.00000 p27 TORDER 65 1.00000 p65 #iofiles (eg, 0 or 64); <0 --> sep. dirs 66 4.00000 p66 output : <0=ascii, else binary 67 4.00000 p67 restart: <0=ascii, else binary 93 20.0000 p93 Number of previous pressure solns saved 94 3.00000 p94 start projecting velocity after p94 step 95 5.00000 p95 start projecting pressure after p95 step 99 0. p99 dealiasing: <0--> off/3--> old/4--> new 102 1.00000 p102 Dump out divergence at each time step 103 -1.00000 p103 weight of stabilizing filter (.01) nelgt/nelgv/lelt: 22620 22620 4800 lx1 /lx2 /lx3 : 4 2 4 done :: read .rea file 0.31992 sec Reset the target Courant number to .5 setup mesh topology Right-handed check complete for 22620 elements. OK. setvert3d: 4 442198 623158 442198 442198 call usrsetvert done :: usrsetvert gs_setup: 30559 unique labels shared pairwise times (avg, min, max): 0.000139931 0.000135946 0.000145721 crystal router : 0.000256464 0.000254369 0.000258589 all reduce : 0.00160212 0.00160019 0.00160458 used all_to_all method: pairwise handle bytes (avg, min, max): 1.84397e+06 1811380 1886892 buffer bytes (avg, min, max): 127744 104448 159248 setupds time 2.7611E-01 seconds 0 4 442198 22620 8 max multiplicity done :: setup mesh topology call usrdat done :: usrdat generate geometry data done :: generate geometry data call usrdat2 done :: usrdat2 regenerate geometry data 1 done :: regenerate geometry data 1 verify mesh topology 0.000000000000000E+000 40.0000037000000 Xrange -0.999999929000000 0.999999933000000 Yrange -0.999999934000000 0.999999930000000 Zrange done :: verify mesh topology IFTRAN = T IFFLOW = T IFHEAT = F IFSPLIT = F IFLOMACH = F IFUSERVP = F IFUSERMV = F IFSTRS = F IFCHAR = F IFCYCLIC = F IFAXIS = F IFMVBD = F IFMELT = F IFMODEL = F IFKEPS = F IFMOAB = F IFNEKNEK = F IFSYNC = T IFVCOR = F IFINTQ = F IFCWUZ = F IFSWALL = F IFGEOM = F IFSURT = F IFWCNO = F IFCMT = F IFVISC = F IFFLTR = F IFTMSH for field 1 = F IFADVC for field 1 = T IFNONL for field 1 = F Dealiasing enabled, lxd= 6 Estimated eigenvalues EIGAA = 1.64699045940739 EIGGA = 96667.1875918256 EIGAE = 6.168501609507998E-003 EIGAS = 3.121097622977694E-004 EIGGE = 96667.1875918256 EIGGS = 2.00000000000000 verify mesh topology 0.000000000000000E+000 40.0000037000000 Xrange -0.999999929000000 0.999999933000000 Yrange -0.999999934000000 0.999999930000000 Zrange done :: verify mesh topology E-solver strategy: 1 itr Matrix: 0 aa 4 4 4 0 aa Infinity -4.08542E+02 7.41342E+01 0.00000E+00 0 aa -4.08542E+02 4.65569E+02 -1.31161E+02 0.00000E+00 0 aa 7.41342E+01 -1.31161E+02 7.04788E+01 0.00000E+00 0 aa 0.00000E+00 0.00000E+00 0.00000E+00 1.00000E+00 Matrix: 0 bb 4 4 4 0 bb NaN 0.00000E+00 0.00000E+00 0.00000E+00 0 bb 0.00000E+00 2.66276E-02 -5.47992E-03 0.00000E+00 0 bb 0.00000E+00 -5.47992E-03 2.45184E-02 0.00000E+00 0 bb 0.00000E+00 0.00000E+00 0.00000E+00 1.00000E+00 Error in generalev, info= 3 4 1 Matrix: 0 Aeig 4 4 4 0 Aeig NaN NaN NaN NaN 0 Aeig NaN NaN NaN NaN 0 Aeig NaN NaN NaN NaN 0 Aeig NaN NaN NaN NaN Matrix: 0 Deig 1 4 4 0 Deig NaN NaN NaN NaN Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 call exitt: dying ... backtrace(): obtained 10 stack frames. ./nek5000() [0x6b38f9] ./nek5000() [0x8262fa] ./nek5000() [0x546de7] ./nek5000() [0x68bd34] ./nek5000() [0x66424d] ./nek5000() [0x40a834] ./nek5000() [0x408e17] ./nek5000() [0x408ca6] /lib64/libc.so.6(__libc_start_main+0xf0) [0x7fb5451ef9f0] ./nek5000() [0x408b29] total elapsed time : 2.33935E+00 sec total solver time incl. I/O : 0.00000E+00 sec time/timestep : 0.00000E+00 sec CPU seconds/timestep/gridpt : 0.00000E+00 sec #######################

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simulation termination at istep=0 with NaN
by nek5000-users＠lists.mcs.anl.gov 26 Jul '17

26 Jul '17

Hi NEKs, I just started working on NEK5000 and am having trouble with my first real simulation (tried both PN/PN and PN/PN-2). I first created a .msh file of simple cylindrical geometry, with velocity-inlet (v), Outlet (O) and surrounding walls (W), in ICEM and used "mshconvert" to get a .rea file. In NEK, the simulation is dying before they actually begin. The error message is as follows: ************************************************************************* ************************************************************************* Matrix: 0 aa 4 4 4 0 aa Infinity -4.08542E+02 7.41342E+01 0.00000E+00 0 aa -4.08542E+02 4.65569E+02 -1.31161E+02 0.00000E+00 . . Matrix: 0 Aeig 4 4 4 0 Aeig NaN NaN NaN NaN 0 Aeig NaN NaN NaN NaN 0 Aeig NaN NaN NaN NaN 0 Aeig NaN NaN NaN NaN . . Matrix: 0 Deig 1 4 4 0 Deig NaN NaN NaN NaN Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 Error in generalev, info= 3 4 1 call exitt: dying ... ************************************************************************* ************************************************************************* I saw an older post regarding a similar problem and that was due to improper boundary conditions. I suspect I may be doing something similar but couldn't find anything until now. The .msh file is fine as I was able to import to "fluent" and run the simulation. Please let me know if you can help in some way. I am posting input files below (please pardon the length of this message): ************** FROM .rea FILE********************* 0 objects found 103 Parameters from file: 1 1.00000 p1 DENSITY 2 -500.000 p2 VISCOS 7 1.00000 p7 RHOCP 8 1.00000 p8 CONDUCT 11 10000 p11 NSTEPS 12 0.10000E-05 p12 DT 15 5 p15 IOSTEP 18 -20.00000 p18 GRID 19 -1.00000 p19 INTYPE 20 10.0000 p20 NORDER 26 1.00000 p26 COURANT/NTAU 27 2.00000 p27 TORDER 65 1.00000 p65 #iofiles (eg, 0 or 64); <0 --> sep. dirs 66 4.00000 p66 output : <0=ascii, else binary 67 4.00000 p67 restart: <0=ascii, else binary 93 20.0000 p93 Number of previous pressure solns saved 94 3.00000 p94 start projecting velocity after p94 step 95 5.00000 p95 start projecting pressure after p95 step 99 0. p99 dealiasing: <0--> off/3--> old/4--> new 102 1.00000 p102 Dump out divergence at each time step 103 -1.00000 p103 weight of stabilizing filter (.01) 13 LOGICAL SWITCHES FOLLOW T IFFLOW T IFHEAT T IFTRAN T F F F F F F F F F F IFNAV & IFADVC (convection in P.S. fields) F F T T T T T T T T T T IFTMSH (IF mesh for this field is T mesh) F IFAXIS F IFSTRS F IFSPLIT F IFMGRID F IFMODEL F IFKEPS F IFMVBD F IFCHAR . . **MESH DATA** 22620 3 22620 NEL,NDIM,NELV ELEMENT 1 [ 1 ] GROUP 0 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 -7.07106729e-01 -6.82106736e-01 -5.66056759e-01 -5.87769989e-01 7.07106833e-01 6.82106832e-01 7.76064003e-01 8.08965813e-01 1.02564103e+00 1.02564103e+00 1.02564103e+00 1.02564103e+00 -7.07106715e-01 -6.82106722e-01 -5.65372395e-01 -5.87023410e-01 7.07106818e-01 6.82106817e-01 7.75121255e-01 8.07937362e-01 ELEMENT 2 [ 1 ] GROUP 0 1.02564103e+00 1.02564103e+00 1.02564103e+00 1.02564103e+00 -6.82106722e-01 -5.65372395e-01 -5.43721379e-01 -6.57106729e-01 6.82106817e-01 7.75121255e-01 7.42305149e-01 6.57106816e-01 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 -6.82106736e-01 -5.66056759e-01 -5.44343529e-01 -6.57106742e-01 6.82106832e-01 7.76064003e-01 7.43162193e-01 6.57106831e-01 . . ***** FLUID BOUNDARY CONDITIONS ***** E 1 1 1.4149000e+04 1.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 E 1 2 2.0000000e+00 1.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 E 1 3 1.3000000e+01 1.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 W 1 4 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 v 1 5 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 . O 22620 6 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 ************************************************************** ************** .usr FILE************** c All my user functions are empty except userbc to deal with the "v" condition subroutine userbc (ix,iy,iz,iside,ieg) include 'SIZE' include 'TSTEP' include 'INPUT' include 'NEKUSE' ux=0.005 uy=0.0 uz=0.0 return end **************************************** ***********************FIRST FEW LINES OF .map FILE*********** 22620 24040 14 16384 180960 24040 0 3597 14 4574 4561 4560 4562 4575 5164 5162 3596 4575 5162 4581 5160 4574 4560 4580 4579 3601 4581 5160 4572 5158 4580 4579 4571 4566 3603 4572 5158 4570 5182 4571 4566 4569 5181 3607 4570 5182 4693 5178 4569 5181 4692 5177 3681 4693 5178 4645 5176 4692 5177 4644 5175 3683 4645 5176 4649 5174 4644 5175 4648 5173 3691 4649 5174 5277 5276 4648 5173 5275 5274 3107 5277 5276 4035 4020 5275 5274 4034 4019 3106 4035 4020 4033 4026 4034 4019 4032 4024 3119 4033 4026 4025 4277 4032 4024 4023 4276 3119 4025 4277 4055 4273 4023 4276 4022 4272 3599 5164 4561 5172 5171 5162 4560 5170 5169 ****************************************************************************** Thanks, Ajay

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Re: [Nek5000-users] Issue Compiling Prenek and Postnek
by nek5000-users＠lists.mcs.anl.gov 26 Jul '17

26 Jul '17

Thank you very much! Now everything works perfectly from compilation to execution. For other beginners I think could be useful to know all the libraries I had to download: sudo apt-get update sudo apt-get install gfortran sudo apt-get install libcr-dev mpich mpich-doc sudo apt-get install mesa-utils sudo apt-get install libx11-* (or libx11-dev) sudo apt-get install libxt-dev sudo apt-get install xfonts-100dpi sudo apt-get install xfonts-100dpi-transcoded sudo apt-get install xfonts-75dpi sudo apt-get install xfonts-75dpi-transcoded Thank you again! Edmund

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Re: [Nek5000-users] Full restart with increasing lx ([email protected])
by nek5000-users＠lists.mcs.anl.gov 25 Jul '17

25 Jul '17

Hello, I've been able to use the full restart function increasing lx1, but in my case I had to change the timestep size (DT) in order to satisfy the CFL condition, so the solution that was saved did not work properly with the full restart because it was obtained using a different DT. So this is something for you to consider. Best, Juan Diego

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Issue Compiling Prenek and Postnek
by nek5000-users＠lists.mcs.anl.gov 21 Jul '17

21 Jul '17

Hello, I'm a beginner in both linux and nek5000. Trying to set up Nek5000 I've learned so much about ubuntu but not enough... I've tried several times in two different computers (ubuntu 16.04) to compile postnek and prenek as the documentation recommends but the same error persists for both postnek and prenek. This is what the command window displays after ./maketools all ---------------------- Make postnek... ---------------------- make[1]: Entering directory '/home/edmund/Nek5000/tools/postnek' gfortran -c postnek.f postnek.f:2052:28: call copyi(ig,buf(1 ),1) !1-2 1 Warning: Rank mismatch in argument ‘a’ at (1) (rank-1 and scalar) postnek.f:2053:31: call copy8b(x,buf( 3),4,iel,nelm) !3-10 1 ... Warning: Deleted feature: Assigned GOTO statement at (1) ../../core/3rd_party/blas.f:17283:72: Warning: Deleted feature: ASSIGN statement at (1) ../../core/3rd_party/blas.f:17295:72: Warning: Deleted feature: ASSIGN statement at (1) ../../core/3rd_party/blas.f:17308:72: Warning: Deleted feature: ASSIGN statement at (1) ../../core/3rd_party/blas.f:17319:72: Warning: Deleted feature: ASSIGN statement at (1) gcc -c -O2 -DUNDERSCORE xdriver.c xdriver.c:6:22: fatal error: X11/Xlib.h: No such file or directory compilation terminated. makefile:84: recipe for target 'xdriver.o' failed make[1]: *** [xdriver.o] Error 1 make[1]: Leaving directory '/home/edmund/Nek5000/tools/postnek' makefile:4: recipe for target 'all' failed make: *** [all] Error 1 edmund@edmund-VirtualBox:~/Nek5000/tools$ ---------------------------------------------------------------------------------------------------------- Could you help me please? What I am doing wrong? Thank you for your time and patience. Edmund

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prenek
by nek5000-users＠lists.mcs.anl.gov 14 Jul '17

14 Jul '17

Hi Nek, I got the 2D pipe case with R=0.125. How can I stretch the pipe to R=1 whilst maintaining the other elements in a same scale. Kind regards, Jian

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