From nek5000-users at lists.mcs.anl.gov Thu Jul 13 07:20:10 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 13 Jul 2017 13:20:10 +0100 Subject: [Nek5000-users] prenek Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Jul 14 16:04:48 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 14 Jul 2017 16:04:48 -0500 Subject: [Nek5000-users] prenek In-Reply-To: References: Message-ID: Hi Jian, Assuming your mesh is centered around x = 0, y = 0; you can put the following code in the usrdat2 routine in your usr file: do i=1,lx1*ly1*lz1*lelt xm1(i,1,1,1) = 4.*xm1(i,1,1,1) ym1(i,1,1,1) = 4.*ym1(i,1,1,1) enddo When you run your case, the spectral element points in each element gets mapped to a location that is 4x farther away from the origin. Sincerely, Kento > On Jul 13, 2017, at 07:20, nek5000-users at lists.mcs.anl.gov wrote: > > 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 > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Jul 14 04:40:52 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 14 Jul 2017 11:40:52 +0200 Subject: [Nek5000-users] Issue Compiling Prenek and Postnek Message-ID: 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 at edmund-VirtualBox:~/Nek5000/tools$ ---------------------------------------------------------------------------------------------------------- Could you help me please? What I am doing wrong? Thank you for your time and patience. Edmund -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Jul 21 01:12:28 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 20 Jul 2017 23:12:28 -0700 Subject: [Nek5000-users] Issue Compiling Prenek and Postnek In-Reply-To: References: Message-ID: Hi Edmund, try installing the following packages, and see if it works. sudo apt-get install mesa-utils libx11-* libxt-dev xfonts-100dpi xfonts-100dpi-transcoded xfonts-75dpi xfonts-75dpi-transcoded On Fri, Jul 14, 2017 at 2:40 AM, wrote: > 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 at edmund-VirtualBox:~/Nek5000/tools$ > > ------------------------------------------------------------ > ---------------------------------------------- > > Could you help me please? What I am doing wrong? > > Thank you for your time and patience. > > Edmund > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Jul 24 21:06:50 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 25 Jul 2017 10:06:50 +0800 (GMT+08:00) Subject: [Nek5000-users] How to get another element information that in the different processor? In-Reply-To: References: Message-ID: Hi all, I want to get another element information when I handle one element, and the two elements maybe not in the same processor. How to get another element information that in the different processor? Below is some of my code: 1)for element e, get global element number; 2)get the correspond element number at the inlet; 3)call the ym1 value at the inlet element But I don't know how to get ym1(i,j,k,e_ele) in the e_nid processor. do e=1,nelv eg=lglel(e) call get_exyz(ex,ey,ez,eg,nelx,nely,nelz) e_in=(ez-1)*nelx*nely+(ey-1)*nelx+1 e_nid=gllnid(e_in) e_ele=gllel(e_in) c if (nid.eq.e_nid) then do k=1,nz1 do j=1,ny1 do i=1,nx1 temp=-ym1(i,j,k,e)*u_t/vis/A_plus cdyn(i,j,k,e)=cs0*(1-exp(temp)) enddo enddo enddo c endif enddo Best wishes! Hu From nek5000-users at lists.mcs.anl.gov Tue Jul 25 06:54:47 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 25 Jul 2017 11:54:47 +0000 Subject: [Nek5000-users] How to get another element information that in the different processor? In-Reply-To: References: , Message-ID: Dear Hu, What information are you needing from another element. The usual approach, which appears relevant to your situation, is to recognize that communication is generally reciprocal: If element e needs data from element e', then e' also likely needs the same date from e. These operations are most readily handled through the gather-scatter operator, gs_op(), which can exchange data among participating processors. (All processors must participate, but some might not have data to exchange.) Are you trying to effect local averages? or, what? Many such operations can also be effected through existing spectral element operators, etc. hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, July 24, 2017 9:06:50 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] How to get another element information that in the different processor? Hi all, I want to get another element information when I handle one element, and the two elements maybe not in the same processor. How to get another element information that in the different processor? Below is some of my code: 1)for element e, get global element number; 2)get the correspond element number at the inlet; 3)call the ym1 value at the inlet element But I don't know how to get ym1(i,j,k,e_ele) in the e_nid processor. do e=1,nelv eg=lglel(e) call get_exyz(ex,ey,ez,eg,nelx,nely,nelz) e_in=(ez-1)*nelx*nely+(ey-1)*nelx+1 e_nid=gllnid(e_in) e_ele=gllel(e_in) c if (nid.eq.e_nid) then do k=1,nz1 do j=1,ny1 do i=1,nx1 temp=-ym1(i,j,k,e)*u_t/vis/A_plus cdyn(i,j,k,e)=cs0*(1-exp(temp)) enddo enddo enddo c endif enddo Best wishes! Hu _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Jul 25 12:59:00 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 25 Jul 2017 13:59:00 -0400 Subject: [Nek5000-users] simulation termination at istep=0 with NaN Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Jul 26 10:19:35 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 26 Jul 2017 17:19:35 +0200 Subject: [Nek5000-users] Issue Compiling Prenek and Postnek In-Reply-To: References: Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Jul 26 12:38:17 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 26 Jul 2017 19:38:17 +0200 Subject: [Nek5000-users] simulation termination at istep=0 with NaN In-Reply-To: References: Message-ID: I guess something is wrong with your mesh. Can you post a full log file. Please note that mshconvert is a 3rd party tool. > On 26 Jul 2017, at 19:26, "nek5000-users at lists.mcs.anl.gov" wrote: > > 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 > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Wed Jul 26 12:10:24 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 26 Jul 2017 13:10:24 -0400 Subject: [Nek5000-users] simulation termination at istep=0 with NaN Message-ID: 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 ####################### -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Jul 26 16:24:45 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 26 Jul 2017 23:24:45 +0200 Subject: [Nek5000-users] simulation termination at istep=0 with NaN In-Reply-To: References: Message-ID: Any reason why you use the old SVN version? You'll find a new one on GitHub. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Wednesday 26th July 2017 23:12 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] simulation termination at istep=0 with NaN > > 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 > > > ####################### > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Thu Jul 27 02:11:55 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 27 Jul 2017 09:11:55 +0200 Subject: [Nek5000-users] Only neumann and periodic boundary conditions for energy equation Message-ID: 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) = ((z) - T(r,phi,z,t))/T_r with T_r = q_w/(rho c_p U_b) and (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 Kaiserstra?e 10 Building 10.23 76131 Karlsruhe, Germany Phone: +49 721 608-43027 E-mail: steffen.straub at 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. From nek5000-users at lists.mcs.anl.gov Thu Jul 27 15:22:08 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 27 Jul 2017 20:22:08 +0000 Subject: [Nek5000-users] Only neumann and periodic boundary conditions for energy equation In-Reply-To: References: Message-ID: 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 on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, July 27, 2017 2:11 AM To: nek5000-users at 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) = ((z) - T(r,phi,z,t))/T_r with T_r = q_w/(rho c_p U_b) and (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 Kaiserstra?e 10 Building 10.23 76131 Karlsruhe, Germany Phone: +49 721 608-43027 E-mail: steffen.straub at 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. _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: nusselt.tgz Type: application/x-gzip Size: 161930 bytes Desc: nusselt.tgz URL: From nek5000-users at lists.mcs.anl.gov Fri Jul 28 08:07:00 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 28 Jul 2017 15:07:00 +0200 Subject: [Nek5000-users] Only neumann and periodic boundary conditions for energy equation In-Reply-To: References: Message-ID: 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: > > Date: > 07/27/2017 10:22 PM > > To: > "nek5000-users at 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 on > behalf of nek5000-users at lists.mcs.anl.gov > > *Sent:* Thursday, July 27, 2017 2:11 AM > *To:* nek5000-users at 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) = ((z) - T(r,phi,z,t))/T_r > with T_r = q_w/(rho c_p U_b) and (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 > > Kaiserstra?e 10 > Building 10.23 > 76131 Karlsruhe, Germany > > Phone: +49 721 608-43027 > E-mail: steffen.straub at 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: