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

Сollocation of i,j,k in each spectral element
by nek5000-users＠lists.mcs.anl.gov 11 Jan '18

11 Jan '18

Hi, Neks! I am working with a complex geometry witch was built in gambit. And I want to change positions of some points in spectral elements. I've read in documentation that i,j,k,e in xm1(i,j,k,e), for example, are changed from 1 to nx1,ny1,nz1 and nelv respectively. But during my tests it's seemed that in different elements x,y,z axis not always correspond to the global coordinate system. Am I right? And how could I find out the principle of collocation of i,j,k in each spectral element? Best regards, Elizabeth

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Question about iside value
by nek5000-users＠lists.mcs.anl.gov 11 Jan '18

11 Jan '18

Hi, Neks! I am working with a complex geometry witch was built in gambit. I want to know a parameter "iside" for each of faces ( outflow, inflow and all walls) on zero step. If I ask in userbc ( in *.usr file) write "iside", I receive only iside=1, that matches inflow. It means that faces with type "wall" don't have "iside" value,am i right? And how each surface is assigned value "iside"? Best regards, Elizabeth

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Outputting to 2d VTK using Postnek
by nek5000-users＠lists.mcs.anl.gov 05 Jan '18

05 Jan '18

Hi, all: I have run into problems using postnek/postex to convert simulation output to VTK format for 2d simulations (3d simulations work fine). I have tested this using the eddy_uv example from the NekExamples directory. When using postex, I use the option "DUMP vtk ALL", which produces the attached VTK output. It seems that the grid point position information is incorrect. Also, I have looked through the postnek functions in trap.f and it seems that VTK cell information (CELLS, CELL_TYPES) is omitted for 2d cases. Is there a way to output this information for 2d results? Perhaps there is something I am overlooking? Any help is greatly appreciated. Thanks, Taiyo

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Different velocity values in different 'v' inlets
by nek5000-users＠lists.mcs.anl.gov 02 Jan '18

02 Jan '18

Hi all, I'm trying to simulate a shear-layer which involves two different jets emerging at different velocities. The simulation is 2D for now. The width of the first jet extends from y=0.0 to y=1.0 and the second extends from y=1.0 to y=3.0 I generated a mesh using genbox with 'v' BCs for both inlets. In the .usr file I have the following form for usrbc subroutine userbc (ix,iy,iz,iside,ieg) c NOTE ::: This subroutine MAY NOT be called by every process include 'SIZE' include 'TOTAL' include 'NEKUSE' if (ym1(i,j,k,e).lt.1) then ux=10.0 elseif (ym1(i,j,k,e).gt.1) then ux=1.0 endif ux=1.0 uy=0.0 uz=0.0 temp=0.0 return end As you can see I try assigning ux = 10.0 and 1.0 to the different zones. However the results show a uniform value of 1.0 across both the inlets. What am I missing here? Sincerely, -- *Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab Multi-Physics Interaction Lab University of Waterloo

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avg_all post processing
by nek5000-users＠lists.mcs.anl.gov 28 Dec '17

28 Dec '17

Hi Nek, I am struggling with a problem in post-processing the files generated by calling avg_all (see https://lists.mcs.anl.gov/mailman/htdig/nek5000-users/2017-December/004832.…) I used the attached usr files to get the time averaged velocity profile and vms. But until then, it worked with wrong results. The usr file generated only one visit file and the number scale of averaged streamwise velocity is not correct. Questions: 1. May I how I can have a velocity profile dat file and rms file by using the avg*0.f000.. rms*0.f000...and rm2*0.f000, rather than a visit file. 2. Would you please help me check the attached usr file whether correct. Kind regards, ZJ

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Re: [Nek5000-users] Set gradient and/or pressure at outlet
by nek5000-users＠lists.mcs.anl.gov 27 Dec '17

27 Dec '17

Thanks Paul for the answer. Yes, I'm using Boussinesq approximation, but using incompresible equations, there are no stratification in the density, like the equations you mention. But, anyway, I'm more interested in setting the spatial gradient equal to cero in the boundary. ¿How can I achieve that? dUy/dy=0 dTEMP/dy=0 Thanks a lot, Juan Pablo.

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Set gradient and/or pressure at outlet
by nek5000-users＠lists.mcs.anl.gov 26 Dec '17

26 Dec '17

Dear Nek users, I've been struggling to program an adecuate outlet BC. I simulate a vertical isothermal surface in an open domain, forming a free convection boundary layer. When there are vortex leaving the domain, the code diverges. I've tried turb_outflow subroutine, stabilized outflow BC (Dong 2014), convective BC (sommerfield radiation condition, thanks to Phillip and Eric, from this comunity), etc. But I can't achieve to make the code run propperly, and I can't go on with my research while I have this problem. There is a paper, from Desrayaud (2013), "Benchmark solutions for natural convection flows in vertical channels submitted to different open boundary conditions". I want to try these BC, which can be stated as: (x: horizontal and y:vertical.) At the top face (outlet) Ux=0 dUy/dy=0 If Uy > 0 (fluid going out) dTEMP/dy=0 pressure=0 If Uy < 0 (fluid going in because there is backflow) TEMP=0 pressure= -0.5Uy^2 or 0 (these are two options in the paper) As far as I know, in Pn-Pn-2 formulation there are not pressure BC, but it is possible to set it using Pn-Pn. Am I right? If so, how can I set BC for pressure in Pn-Pn? And for the velocity gradient and temperature gradient equal cero at the top face, how can it be done? Would it be enough to set dirichlet BC and replicate the last row of values to the last one? Any help is welcomed, thanks in advance, Juan Pablo.

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Re: [Nek5000-users] MAXNEL
by nek5000-users＠lists.mcs.anl.gov 22 Dec '17

22 Dec '17

Hi Thilina, I set maketools file as followed. Then, I did './maketools genmap' even './maketools all' after which all files were updated, but they all didnt work. Do you have any idea? #!/bin/bash # maximum number of elements MAXNEL=350000 # binary path #bin_nek_tools=`cd ../bin && pwd` # Fortran compiler #FC="gfortran" #FFLAGS="" # C compiler #CC="gcc" #CFLAGS="" # linking flags #LDFLAGS="-L$HOME/lib -lm" Best wishes, Z

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Re: [Nek5000-users] DIV(V)-QTL too large!
by nek5000-users＠lists.mcs.anl.gov 22 Dec '17

22 Dec '17

Hi, After 500 and 3000, it shows, Step 517, t= 1.1788322E+00, DT= 2.3973162E-03, C= 0.500 3.9951E+03 6.9817E+00 Solving for fluid T T T 517 PRES alph1n 8.7302E-02 6.4306E-03 1.3576E+01 11 517 PRES halpha 11 1.1966E-03 3.4135E-04 3.5797E-04 3.1090E-04 3.1099E-04 2.3543E-04 1.9043E-04 2.0750E-04 1.7930E-04 1.2367E-04 517 PRES gmres: 4 8.3071E-07 1.0000E-06 4.9308E-06 8.4564E-01 1.1845E+00 F 517 1 1.7008E-01 1.7008E-01 1.0000E+00 0 alph1x 517 halpha 0 517 Hmholtz VELX: 5 6.7578E-09 1.7008E-01 1.0000E-07 517 2 1.1899E-01 1.1899E-01 1.0000E+00 0 alph1x 517 halpha 0 517 Hmholtz VELY: 5 6.5549E-09 1.1899E-01 1.0000E-07 517 3 2.4613E-01 2.4613E-01 1.0000E+00 0 alph1x 517 halpha 0 517 Hmholtz VELZ: 5 2.1073E-08 2.4613E-01 1.0000E-07 L1/L2 DIV(V) : 6.3228E-18 1.6443E-03 L1/L2 QTL : 0.0000E+00 0.0000E+00 L1/L2 DIV(V)-QTL: 6.3228E-18 1.6443E-03 517 PRES gmres: 1 2.6792E-16 1.0000E-06 7.4460E-16 2.1149E-01 3.5070E-01 F 517 Hmholtz VELX: 1 3.4482E-17 1.9046E-15 1.0000E-07 517 Hmholtz VELY: 1 3.4750E-17 1.9137E-15 1.0000E-07 517 Hmholtz VELZ: 5 6.4296E-08 9.9916E-01 1.0000E-07 517 1.02488E-03 1.25000E+01 1.00000E+00 basflow Z 517 0.1178832E+01 6.94484E-03 7.11765E-06 7.85392E-01 7.85399E-01 volflow Z 517 1.1788E+00 6.5287E+00 Fluid done Step 3003, t= 7.0457310E+00, DT= 2.3271524E-03, C= 0.500 2.1994E+04 7.7898E+00 Solving for fluid T T T 3003 PRES alph1n 2.2485E-01 1.2721E-02 1.7676E+01 17 3003 PRES halpha 17 -7.5402E-04 -1.9963E-04 6.1782E-04 7.0527E-04 3.4415E-04 7.8125E-05 6.1111E-04 1.2665E-03 9.2238E-04 1.1935E-03 3003 PRES gmres: 5 8.4347E-07 1.0000E-06 9.5886E-06 1.0585E+00 1.4770E+00 F 3003 1 2.4280E-01 2.4280E-01 1.0000E+00 0 alph1x 3003 halpha 0 3003 Hmholtz VELX: 4 6.7528E-08 2.4280E-01 1.0000E-07 3003 2 9.1891E-02 9.1891E-02 1.0000E+00 0 alph1x 3003 halpha 0 3003 Hmholtz VELY: 4 5.1734E-08 9.1891E-02 1.0000E-07 3003 3 1.9637E-01 1.9637E-01 1.0000E+00 0 alph1x 3003 halpha 0 3003 Hmholtz VELZ: 5 9.5563E-09 1.9637E-01 1.0000E-07 L1/L2 DIV(V) : -2.5507E-17 1.8315E-03 L1/L2 QTL : 0.0000E+00 0.0000E+00 L1/L2 DIV(V)-QTL: -2.5507E-17 1.8315E-03 3003 PRES gmres: 1 2.6792E-16 1.0000E-06 7.4460E-16 2.1105E-01 3.5033E-01 F 3003 Hmholtz VELX: 1 3.3517E-17 1.9046E-15 1.0000E-07 3003 Hmholtz VELY: 1 3.3777E-17 1.9137E-15 1.0000E-07 3003 Hmholtz VELZ: 5 5.6177E-08 9.9916E-01 1.0000E-07 3003 9.95014E-04 1.25000E+01 1.00000E+00 basflow Z 3003 0.7045731E+01 5.43569E-03 5.40859E-06 7.85394E-01 7.85399E-01 volflow Z 3003 7.0457E+00 7.3717E+00 Fluid done Compute statistics ...

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Mortar_spectral_element_method
by nek5000-users＠lists.mcs.anl.gov 22 Dec '17

22 Dec '17

Hi Can on help me to write a matlab code for mortar legendre spectral finite element method in two domains to solve poisson equation. I m tired to imposed the non-matching conditions Thank you Radouen

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