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

Laminar pipe flow in Nek5000
by nek5000-users＠lists.mcs.anl.gov 10 Dec '17

10 Dec '17

Hello Neks, I am new to Nek5000 and struggling to understand it. At this moment, I want to simulate laminar flow in a pipe. please advice me, with which example, should I start and what modifications in various file should I be doing. Thanks, Devshi Ziyad

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A meshing generation problem for complex geometric structure
by nek5000-users＠lists.mcs.anl.gov 08 Dec '17

08 Dec '17

Dear experts in Nek5000 : Thank you for reading my email. I am a freshman in using Nek5000 and I am willing to simulate unsteady flow phenomenon in bottom head of PWR with LES method through parallel processes. And Nek5000 is the best solver for resolving my problem and I hope to reach my goal with the outstanding SEM-CFD tools. But it is really a matter for me to generate a mesh file for that structure. So could you please show me a proper way to reach the .rea mesh file for the bottom head for the geometry there is really complex and I am afraid I can not achieve the goal with editing .rea file directly. Thank you for your supporting me and I am waiting for your earlier reply eagerly. Best regards Haoran JU

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Re: [Nek5000-users] avg_all averaging
by nek5000-users＠lists.mcs.anl.gov 07 Dec '17

07 Dec '17

Dear Ketan, Thanks for your attachment. I tried your code 'pp.usr' provided last email but failed in complilation. Can you provide subroutines fgslib_gs_op and fgslib_gs_setup used in subroutines my_z_avg and set_gs_zavg_hndl, respectively. Best wishes, ZJ

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Reproducing rea file in conj_ht example
by nek5000-users＠lists.mcs.anl.gov 07 Dec '17

07 Dec '17

Dear Neks, Looking through the example files of conj_ht, I am unable to reproduce the conj_ht.rea file from the conj_ht.box file by invoking genbox. The appropriate file with parameters, specified in the first line of box file (cht01.rea) is missing. However, if I copy the conj_ht.rea file to cht01.rea and run genbox, the resulting box.rea file is not the same as conj_ht.rea file. The NELV numbers differ, the fluid boundary conditions additionally specify conditions for the solid domain and maybe there are some other differences too that I have not noticed. How was the conj_ht.rea file produced? Was it tweaked manually? In my own cases, I use pretex in combination with the linux utility expect, to automatically merge rea files for fluid and solid domains (generated with genbox). However, pretex needs the display to open the graphical interface. Is there another way to produce a merged file without the need for a display, pretext or user interaction? Thank you in advance. Best regards, Jure Oder

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Re: [Nek5000-users] avg_all averaging
by nek5000-users＠lists.mcs.anl.gov 06 Dec '17

06 Dec '17

Hi ZJ, See the attached tar file for an example of how to use the avg_all files. Read the README file to understand the contents of this example. It has two cases, the first one runs for 5 steps and generates some avg*, rms* and rm2* files. The second one uses these files to calculate the actual rms velocities using the avgp10.f0* and rmsp10.f0* files output by the first case. Hope this helps! Ketan

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Deformed geometry after Post-Processing
by nek5000-users＠lists.mcs.anl.gov 06 Dec '17

06 Dec '17

Hi Neks, Now I am doing post-processing with my results for turbulence flow. I have the mesh with 11264 elements. First of all, I want to find a mean value using the post-processing of NEK5000, but after I get the deformed geometry that i observe witin VisIt (the computational domain is not complete). This kind of job worked well with the mesh with 8960 elements. I run my calculation on one processor. Do you have any idea what is wrong with my case? Thanks, Andrew

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Re: [Nek5000-users] Calculating very small Lewis numbers in Nekton
by nek5000-users＠lists.mcs.anl.gov 05 Dec '17

05 Dec '17

Hello all, Thanks for the replies, I think my log-file was too big even after compression and stuck in moderator approval for the list. But here is the part of the log-file where the problem starts. I have attached a google drive link which has the log file and .rea file, the Lewis Number is set in line 133 of the .rea file after parameter 128 (p128). Link - https://drive.google.com/open?id=1ozsy0IgVKuxDiplGl6CfYDn3GuhDWoWI Solving for fluid F T T 2071 Hmholtz TEMP: 1 1.1353E+00 5.5267E+00 7.0000E+00 2071 Hmholtz PS 1: 13 5.5318E+00 3.8255E+21 7.0000E+00 2071 100 **ERROR**: Failed in HMHOLTZ: PS 2 6.5359E+15 3.8255E+21 7.0000E+00 2071 Hmholtz PS 3: 13 5.5318E+00 3.8255E+21 7.0000E+00 2071 1.3076E+03 2.0528E+00 Heat done 2071 Hmholtz VELX: 38 9.8896E-11 4.9469E+02 1.0000E-10 2071 Hmholtz VELY: 38 9.2808E-11 4.4808E+02 1.0000E-10 2071 Hmholtz VELZ: 38 8.0264E-11 4.6649E+02 1.0000E-10 2071 reorthogo: 0 2071 6 alpha: 9.1687E-01 4.2049E-02 6.7213E-03 2.4412E-03 1.0813E-03 1.7375E-03 2071 6 1.7386E-01 1.3111E-03 1.3260E+02 alph12 2071 U-PRES gmres: 5 7.5724E-09 1.0000E-08 4.0064E-08 7.3007E-02 3.7297E-01 2071 DNORM, DIVEX 5.430060732380546E-007 7.572385434962068E-009 2071 1.3076E+03 2.4498E+00 Fluid done 2071 1 flx 1.307563E+03 5.633556E-02 1.121772E+04 1.174017E+04 5.092129E+02 2071 2 flx 1.307563E+03 5.633556E-02 -1.122518E+04 -1.174681E+04 4.949962E+02 Step 2072, t= 1.3075634E+03, DT= 5.6082644E-05, C= 0.500 6.5792E+03 5.2920E+00 Solving for heat Solving for fluid F T T 2072 Hmholtz TEMP: 1 1.1351E+00 5.5225E+00 7.0000E+00 2072 100 **ERROR**: Failed in HMHOLTZ: PS 1 3.2982E+26 3.0368E+40 7.0000E+00 2072 100 **ERROR**: Failed in HMHOLTZ: PS 2 4.0048E+36 3.0365E+40 7.0000E+00 2072 100 **ERROR**: Failed in HMHOLTZ: PS 3 3.2982E+26 3.0368E+40 7.0000E+00 2072 1.3076E+03 4.8085E+00 Heat done 2072 Hmholtz VELX: 38 9.9602E-11 4.9398E+02 1.0000E-10 2072 Hmholtz VELY: 38 9.3511E-11 4.4755E+02 1.0000E-10 2072 Hmholtz VELZ: 38 8.0881E-11 4.6601E+02 1.0000E-10 2072 reorthogo: 0 2072 7 alpha: 9.1610E-01 4.8479E-02 7.7574E-03 5.1508E-03 1.8164E-03 -4.1065E-04 -4.3921E-04 2072 7 1.7378E-01 1.1572E-03 1.5018E+02 alph12 2072 U-PRES gmres: 4 8.4386E-09 1.0000E-08 3.5390E-08 4.9622E-02 3.2245E-01 2072 DNORM, DIVEX 5.419045247755792E-007 8.438599514879914E-009 2072 1.3076E+03 2.5401E+00 Fluid done Thanks, Saikat Saikat Mukherjee, PhD Student, Paul Research Group - http://www.me.vt.edu/mpaul/ Engineering Science and Mechanics, Virginia Tech. On Tue, Dec 5, 2017 at 1:38 PM, Saikat Mukherjee <msaikat6(a)vt.edu> wrote: > Hello all, > > Thanks for the replies, I think my log-file was too big and stuck in > approval for the list. But here is the part of the log-file where the > problem starts. I have attached the .rea file, the Lewis Number is set in > line 133 of the .rea file after parameter 128 (p128). > > Thanks, > Saikat > > > > > Solving for fluid F T T > 2071 Hmholtz TEMP: 1 1.1353E+00 5.5267E+00 7.0000E+00 > 2071 Hmholtz PS 1: 13 5.5318E+00 3.8255E+21 7.0000E+00 > 2071 100 **ERROR**: Failed in HMHOLTZ: PS 2 6.5359E+15 3.8255E+21 > 7.0000E+00 > 2071 Hmholtz PS 3: 13 5.5318E+00 3.8255E+21 7.0000E+00 > 2071 1.3076E+03 2.0528E+00 Heat done > 2071 Hmholtz VELX: 38 9.8896E-11 4.9469E+02 1.0000E-10 > 2071 Hmholtz VELY: 38 9.2808E-11 4.4808E+02 1.0000E-10 > 2071 Hmholtz VELZ: 38 8.0264E-11 4.6649E+02 1.0000E-10 > 2071 reorthogo: 0 > 2071 6 alpha: 9.1687E-01 4.2049E-02 6.7213E-03 2.4412E-03 > 1.0813E-03 1.7375E-03 > 2071 6 1.7386E-01 1.3111E-03 1.3260E+02 alph12 > 2071 U-PRES gmres: 5 7.5724E-09 1.0000E-08 4.0064E-08 > 7.3007E-02 3.7297E-01 > 2071 DNORM, DIVEX 5.430060732380546E-007 7.572385434962068E-009 > 2071 1.3076E+03 2.4498E+00 Fluid done > 2071 1 flx 1.307563E+03 5.633556E-02 1.121772E+04 1.174017E+04 > 5.092129E+02 > 2071 2 flx 1.307563E+03 5.633556E-02 -1.122518E+04 -1.174681E+04 > 4.949962E+02 > Step 2072, t= 1.3075634E+03, DT= 5.6082644E-05, C= 0.500 6.5792E+03 > 5.2920E+00 > Solving for heat > Solving for fluid F T T > 2072 Hmholtz TEMP: 1 1.1351E+00 5.5225E+00 7.0000E+00 > 2072 100 **ERROR**: Failed in HMHOLTZ: PS 1 3.2982E+26 3.0368E+40 > 7.0000E+00 > 2072 100 **ERROR**: Failed in HMHOLTZ: PS 2 4.0048E+36 3.0365E+40 > 7.0000E+00 > 2072 100 **ERROR**: Failed in HMHOLTZ: PS 3 3.2982E+26 3.0368E+40 > 7.0000E+00 > 2072 1.3076E+03 4.8085E+00 Heat done > 2072 Hmholtz VELX: 38 9.9602E-11 4.9398E+02 1.0000E-10 > 2072 Hmholtz VELY: 38 9.3511E-11 4.4755E+02 1.0000E-10 > 2072 Hmholtz VELZ: 38 8.0881E-11 4.6601E+02 1.0000E-10 > 2072 reorthogo: 0 > 2072 7 alpha: 9.1610E-01 4.8479E-02 7.7574E-03 5.1508E-03 > 1.8164E-03 -4.1065E-04 -4.3921E-04 > 2072 7 1.7378E-01 1.1572E-03 1.5018E+02 alph12 > 2072 U-PRES gmres: 4 8.4386E-09 1.0000E-08 3.5390E-08 > 4.9622E-02 3.2245E-01 > 2072 DNORM, DIVEX 5.419045247755792E-007 8.438599514879914E-009 > 2072 1.3076E+03 2.5401E+00 Fluid done > > > > > > > > > > > > > > > > > > > > > Saikat Mukherjee, > PhD Student, > Paul Research Group - http://www.me.vt.edu/mpaul/ > Engineering Science and Mechanics, > Virginia Tech. > > On Mon, Dec 4, 2017 at 3:52 PM, Saikat Mukherjee <msaikat6(a)vt.edu> wrote: > >> Hey all, >> >> Thanks for the replies. Attached are the log file and the .rea file where >> I set my Lewis Number. The Lewis Number is set after parameter 128 (p128) >> at line 133 of the .rea file. >> >> Saikat >> >> Saikat Mukherjee, >> PhD Student, >> Paul Research Group - http://www.me.vt.edu/mpaul/ >> Engineering Science and Mechanics, >> Virginia Tech. >> >> On Mon, Dec 4, 2017 at 3:15 PM, <nek5000-users(a)lists.mcs.anl.gov> wrote: >> >>> Can you please post your logfile >>> >>> On 4 Dec 2017, at 21:08, "nek5000-users(a)lists.mcs.anl.gov" < >>> nek5000-users(a)lists.mcs.anl.gov> wrote: >>> >>> Hey Marco, >>> >>> The error message is "Failed in HMHOLTZ" for the scalar and NaN value is >>> being returned. >>> >>> Thanks, >>> Saikat >>> >>> Saikat Mukherjee, >>> PhD Student, >>> Paul Research Group - http://www.me.vt.edu/mpaul/ >>> Engineering Science and Mechanics, >>> Virginia Tech. >>> >>> On Mon, Dec 4, 2017 at 2:34 PM, <nek5000-users(a)lists.mcs.anl.gov> wrote: >>> >>>> Salkat, >>>> >>>> could you please be more specific when you write ‘ I have not been >>>> successful’? Do you get an error message? >>>> >>>> Marco >>>> >>>> On Dec 4, 2017, at 2:31 PM, nek5000-users(a)lists.mcs.anl.gov wrote: >>>> >>>> Hello Neks, >>>> >>>> I am solving a Reaction Advection Diffusion equation, where with my >>>> non-dimensionalization, the Lewis Number(Le) is the parameter multiplying >>>> the Laplacian. That is, Le is the non-dimensional Diffusion co-efficient >>>> of the species. Currently I can do Le = 0.1, but to reduce it further down >>>> to 0.01, or 0.001, the spatial resolution has to be increased. I tried >>>> doing that increasing the GLL points in SIZE file by increasing the lx1, >>>> lxd, but till now I have been unsuccessful. >>>> >>>> I am aware there is a special filtering that can be used( Fischer and >>>> Mullen, 2001). My question is how to implement that in my .usr file. Is >>>> there a routine? >>>> >>>> Thanks, >>>> Saikat >>>> >>>> >>>> Saikat Mukherjee, >>>> PhD Student, >>>> Paul Research Group - http://www.me.vt.edu/mpaul/ >>>> Engineering Science and Mechanics, >>>> Virginia Tech. >>>> _______________________________________________ >>>> 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 >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users(a)lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >>> >> >

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hpts for vorticity field
by nek5000-users＠lists.mcs.anl.gov 05 Dec '17

05 Dec '17

Hello Neks, Does anyone knows how to output the vorticity probes using call hpts() When I use the function "call hpts()", it outputs only the probes for native arrays like velocity, prssure (and scalar fields, if they exist). I compute the vorticity using the function comp_vort3(vort,w1,w2,vx,vy,vz). How can I output the values of the vorticity probes in the flow field using hpts? i will be grateful for your answers. Thank you in advance. Cheers, Sandeep

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Calculating very small Lewis numbers in Nekton
by nek5000-users＠lists.mcs.anl.gov 04 Dec '17

04 Dec '17

Hello Neks, I am solving a Reaction Advection Diffusion equation, where with my non-dimensionalization, the Lewis Number(Le) is the parameter multiplying the Laplacian. That is, Le is the non-dimensional Diffusion co-efficient of the species. Currently I can do Le = 0.1, but to reduce it further down to 0.01, or 0.001, the spatial resolution has to be increased. I tried doing that increasing the GLL points in SIZE file by increasing the lx1, lxd, but till now I have been unsuccessful. I am aware there is a special filtering that can be used( Fischer and Mullen, 2001). My question is how to implement that in my .usr file. Is there a routine? Thanks, Saikat Saikat Mukherjee, PhD Student, Paul Research Group - http://www.me.vt.edu/mpaul/ Engineering Science and Mechanics, Virginia Tech.

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Compiling large problem sizes
by nek5000-users＠lists.mcs.anl.gov 04 Dec '17

04 Dec '17

Hi all, I'm trying to compile a 3D mesh with mesh size of 6000 ekements. Unfortunately I keep running into compilation errors. To be clear I can compile problems upto 3000 elements large. But setting lelt value larger than 3000 results in an error. I have realised this might be a memory issue and have tried to compile with increasing amounts of available memory. This does not seem to resolve the issue. To be clear my SIZE looks like this parameter (ldim=3) ! domain dimension (2 or 3) parameter (lx1=6) ! p-order (avoid uneven and values <6) parameter (lxd=10) ! p-order for over-integration (dealiasing) parameter (lx2=lx1-2) ! p-order for pressure (lx1 or lx1-2) parameter (lelg=6000) ! max total number of elements parameter (lpmin=1) ! min MPI ranks parameter (lpmax=1024) ! max MPI ranks parameter (ldimt=1) ! max auxiliary fields (temperature + scalars) Sincerely, -- *Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab University of Waterloo

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