July 2018 - Nek5000-users - mailman3.cels.anl.gov

Pipe Roughness
by nek5000-users＠lists.mcs.anl.gov 31 Jul '18

31 Jul '18

Dear Ketan, Unfortunately, I couldn't modify the neknek script to be run on the Cray machine. Sometimes, it asks me about mpirun for MPMD, and other time the problem comes from the SESSION.NAME. I just got stuck at this point, so could you please help me with that? I.e.Is there something, like nekpbs, handles neknek? Thank you in advance, Ali Embry-Riddle Aeronautical University

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Re: [Nek5000-users] findpts returns ix iy iz iel
by nek5000-users＠lists.mcs.anl.gov 28 Jul '18

28 Jul '18

Hi Nek, What I want is the ix, iy, iz and iel at some points pts. So the findpts would be called with rst returned. But as far as I can see, rst are the coordinates of such element. May I has the grid point in that element, i.e. ix [1,nx1], iy [1,ny1], iz [1,nz1]? Kind regards, Jian

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findpts returns ix iy iz iel
by nek5000-users＠lists.mcs.anl.gov 26 Jul '18

26 Jul '18

Hi nek, I want to use findpts to return ix [1,nx1], iy [1,ny1], iz [1,nz1], and iel [1,nelv] for a set of points as follows, could anyone tell me how which are ix iy and iz? I think elid is the iel. call findpts(ih, rcode, 1, proc, 1, elid, 1, rst, ndim, dist, 1, pts(1), pts(n+1), pts(2*n+1), 1, n) Cheers, Jian

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Re: [Nek5000-users] Planar average in z-direction problem (image updated)
by nek5000-users＠lists.mcs.anl.gov 26 Jul '18

26 Jul '18

DearPaul,Thankyouforyourecommendation.Asyousaid,IalsounderstandthatmycodeisnotMPIfriendly.But,mytopicwasmalfunctionoftheplanar_average_zinmycaseandIjustwantedtoknowwhetherthereareanyproblemsinmygridpoints.Infact,Inoticedthatmycomputationaldomainswith4boxesmadefrom.boxfilehavesomeproblems.(So,Iwroteacodetogeneratemeshgridfor1boxwithclustering.AndImanuallyassignedgridpointsthen,problemwassolved.)Ithinkconnectivitybetweeneachboxwasbadatthetime.Regards,Hyunduk.------------------------------------------------------------------------------------------------------------------------------------------------------Title:Re:Planaraverageinz-directionproblem(imageupdated)DearHyunduk,Iseeseveralissueswiththecodeyouhave.Thefirstpointisthatyourcodewillnotworkproperlyinparallel,soyouneedtobecarefulaboutparalleltreatmentofIOifyouarerunningonmorethanoneMPIrank.Secondly,it'sgenerallynotagoodideatotestforequalitywithrealnumbers--areyoucertainthattheyvaluesofinterestare0.0000000?oraretheypotentially1.e-7(say).Someofthemeshgenerationtoolswillhavenoiseandyourzerovaluesmightnotbeexactlyzero.zgm1isthepositionofthenodalpointsontheinterval[-1,1]inthereferenceelementarea()isthesurfaceareaatthetopandbottomofeachelement.(Here,weassumethat"top"inzmeansalsotopinr-s-tspaceforthecanonicalOmega-hat:=[-1,1]^3.)Thus,aaisali…'inst_field_',insnumOPEN(unit=insuni,file=insnaminsnum=nidinsuni=insnum+1000WRITE(insnam,98)'inst_field_',insnumOpen(unit=insuni,file=insnam)doi=1,nif(ym1(i,1,1,1).eq.0.0)thenWRITE(insuni,5)xm1(i,1,1,1)%,zm1(i,1,1,1)%,vx(i,1,1,1)%,vy(i,1,1,1)%,vz(i,1,1,1)%,phig(i,1,1,1)endifenddoCLOSE(insuni)======================================================Then,Icancollectlotsoffielddatafromeachprocessorandsortdatawithascendingorderusingmatlab.So,Igottheresultas1stimage.ButwhenIuseplannar_average_zIgottheresultasshownin2ndimage.1.Ireallywanttomodifytheproblems,socouldyougivemeyourideaonthisproblem?2.Additionally,couldyouexplain'zgm1'and'area'?Inoticedthat,planar_average_rors...inturbChannelcasehasalso'area'but,thosecaseareusedtocalculateondifferentdirection.Buttheyusedsameinputparameters.WhatIunderstandaboutareais,surfaceareaofelement.ButIthoughtthatdifferentdirectionneedsdifferentindexing=======================================================subroutineplanar_average_z(ua,u,w1,w2)ccComputer-splanaraverageofquantityu()cinclude'SIZE'include'GEOM'include'PARALLEL'include'WZ'include'ZPER'crealua(lz1,nelz),u(lx1*ly1,lz1,nelv),w1(lz1,nelz),w2(lz1,nelz)integere,eg,ezcmelxy=nelx*nelycnz=lz1*nelzcallrzero(ua,nz)callrzero(w1,nz)cdoe=1,neltceg=lglel(e)cez=1+(eg-1)/melxycallget_exyz(ex,ey,ez,eg,nelx,nely,nelz)cdok=1,lz1doi=1,lx1*ly1zz=(1.-zgm1(k,3))/2.!=1fork=1,=0fork=lz1aa=zz*area(i,1,5,e)+(1-zz)*area(i,1,6,e)!wgtdjacobianw1(k,ez)=w1(k,ez)+aaua(k,ez)=ua(k,ez)+aa*u(i,k,e)enddoenddoenddoccallgop(ua,w2,'+',nz)callgop(w1,w2,'+',nz)cdoi=1,nzua(i,1)=ua(i,1)/w1(i,1)!Normalizeenddocreturnend======================================================Regards,Hyunduk.

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Pipe Roughness
by nek5000-users＠lists.mcs.anl.gov 25 Jul '18

25 Jul '18

Yes, that sounds awesome, and thank you for your generous offer. I'll see what is gonna happen and what I can do with NekNek approach. Ali Embry-Riddle Aeronautical University

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Re: [Nek5000-users] Pipe Roughness
by nek5000-users＠lists.mcs.anl.gov 25 Jul '18

25 Jul '18

Hi Ali, Regarding Nek-Nek, this might be helpful: http://nek5000.github.io/NekDoc/tutorials/neknek.html Regarding your question in one of your previous messages: the key aspect in coupling two meshes in a NekNek calculation is the boundary condition of the surfaces that overlap another domain... these surfaces must have ‘int’ boundary condition. At the beginning of the calculation, this serves as the flag for the solver to identify the surface GLL points that overlap with another domain. These surfaces become Dirichlet surfaces from there on, where Dirichlet velocity data is obtained by interpolating solution (velocity and passive scalars) between domains at the end of each time-step and during sub-iterations (number of sub-iterations at each time-step are controlled by the parameter ngeom specified in usrdat). Take a look at this tutorial, and see if it helps make things clear.. You can also look at the article “A spectrally accurate method for overlapping grid solution of incompressible Navier–Stokes equations”. If you still have questions, please let me know. Should you choose to use NekNek for this calculation, I can help you setup the problem/mesh. Ketan

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Pipe Roughness
by nek5000-users＠lists.mcs.anl.gov 25 Jul '18

25 Jul '18

Thank you for your clarification, It seems my assessment was wrong. In my research, adding a roughness is not the main point, but it still should be considered. It doesn't matter which approach I go with as long as it is easy to implement by Nek5000. Anyway, I think I should do more research on these two approaches (NekNek and IBM) or I can build the mesh with a third-party program and convert it to Nek5000, right? Again, thank you for your assistance, Ali Embry-Riddle Aeronautical University

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Pipe Roughness
by nek5000-users＠lists.mcs.anl.gov 25 Jul '18

25 Jul '18

Dear Mr.Philipp, I think I need more help with the first way, changing the location of the mesh. I have used the NekNek script successfully, but I still do n't know how to trigger the main flow by these overlapped elements, near the wall. I.e. I still don't see any sign for a connection between these two meshes. Are there more details you can help me with besides the eddy_nekenk example? I would be very grateful. Thanks, Ali Embry-Riddle Aeronautical University

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Planar average in z-direction problem (image updated)
by nek5000-users＠lists.mcs.anl.gov 24 Jul '18

24 Jul '18

Hi, NeksI wonder why planar_average_z in navier5.f shows wrong result.here I attached 2 images.1, https://drive.google.com/file/d/1Kng9HZfQW-TGTFwmFcXzbrcvhRYrQSdc/view?usp=… image shows the z-directional grids points from zm1(I wrote a code to extract z coordinate at y = 0 as follows:======================================================insnum = nidinsuni = insnum + 1000WRITE(insnam,98) 'inst_field_', insnumOPEN(unit=insuni,file=insnam insnum = nid insuni = insnum + 1000 WRITE(insnam,98) 'inst_field_', insnum Open(unit=insuni,file=insnam) do i = 1,n if (ym1(i,1,1,1).eq.0.0)then WRITE(insuni,5) xm1(i,1,1,1) % , zm1(i,1,1,1) % , vx(i,1,1,1) % , vy(i,1,1,1) % , vz(i,1,1,1) % , phig(i,1,1,1) endif enddo CLOSE(insuni)======================================================Then, I can collect lots of field data from each processor and sort data with ascending order using matlab.So, I got the result as 1st image.But when I use plannar_average_zI got the result as shown in 2nd image.1. I really want to modify the problems, so could you give me your idea on this problem?2. Additionally, could you explain 'zgm1' and 'area'?I noticed that, planar_average_r or s ... in turbChannel case has also 'area' but, those case are used to calculate ondifferent direction.But they used same input parameters.What I understand about area is, surface area of element.But I thought that different direction needs different indexing======================================================= subroutine planar_average_z(ua,u,w1,w2)cc Compute r-s planar average of quantity u()c include 'SIZE' include 'GEOM' include 'PARALLEL' include 'WZ' include 'ZPER'c real ua(lz1,nelz),u(lx1*ly1,lz1,nelv),w1(lz1,nelz),w2(lz1,nelz) integer e,eg,ezc melxy = nelx*nelyc nz = lz1*nelz call rzero(ua,nz) call rzero(w1,nz)c do e=1,neltc eg = lglel(e)c ez = 1 + (eg-1)/melxy call get_exyz(ex,ey,ez,eg,nelx,nely,nelz)c do k=1,lz1 do i=1,lx1*ly1 zz = (1.-zgm1(k,3))/2. ! = 1 for k=1, = 0 for k=lz1 aa = zz*area(i,1,5,e) + (1-zz)*area(i,1,6,e) ! wgtd jacobian w1(k,ez) = w1(k,ez) + aa ua(k,ez) = ua(k,ez) + aa*u(i,k,e) enddo enddo enddoc call gop(ua,w2,'+ ',nz) call gop(w1,w2,'+ ',nz)c do i=1,nz ua(i,1) = ua(i,1) / w1(i,1) ! Normalize enddoc return end======================================================Regards,Hyunduk. ------------------------------<wbr style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 14px; background-color: rgb(255, 255, 255);">------------------------------------------------------------------------------------ HyundukSeo(Mr.) IntegratedPh.D.course,Schoo<wbr style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 14px; background-color: rgb(255, 255, 255);">PusanNationalUniversity ExperimentalThermo-FluidsMec<wbr style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 14px; background-color: rgb(255, 255, 255);">ENsys)Laboratory http://fluid.pusan.ac.kr T.:+82-51-510-1536M.:+82-10<wbr style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 14px; background-color: rgb(255, 255, 255);">-2964-0994

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findpts
by nek5000-users＠lists.mcs.anl.gov 24 Jul '18

24 Jul '18

Hi nek, I am doing the lagrangian particle tracking but got a problem in the findpts. It shows some points are not found after findpts. Can anyone give some suggestions? call intpts call findpts WARNING: point not within mesh xy[z]: ! NaN NaN NaN Kind regards, Jian

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