May 2015 - Nek5000-users - mailman3.cels.anl.gov

Re: [Nek5000-users] Vorticity
by nek5000-users＠lists.mcs.anl.gov 11 Oct '16

11 Oct '16

Hi, Thanks for your quick reply. Just I wanna know if I can use the interpolated values of velocity at some arbitrary points in the domain (not necessarily the grid points) as the input arguments to theses subroutines. Regards, Alireza Quoting nek5000-users-request(a)lists.mcs.anl.gov: > Send Nek5000-users mailing list submissions to > nek5000-users(a)lists.mcs.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > or, via email, send a message with subject or body 'help' to > nek5000-users-request(a)lists.mcs.anl.gov > > You can reach the person managing the list at > nek5000-users-owner(a)lists.mcs.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Nek5000-users digest..." > > > Today's Topics: > > 1. Vorticity (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: Vorticity (nek5000-users(a)lists.mcs.anl.gov) > 3. Re: Vorticity (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Jul 2011 17:55:35 -0400 > From: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: <20110713175535.1042430oct81vz2v(a)webmail.vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Hi, > > I need to calculate the vorticity vector and the rate of strain tensor > at any arbitrary point in the domain. I wonder if these values are > computed somewhere in the code or if I should interpolate them in the > usr file. I appreciate any kind of help. > > Thanks in advance, > > > Regards, > Alireza Karimi > > > > ------------------------------ > > Message: 2 > Date: Wed, 13 Jul 2011 17:09:48 -0500 (CDT) > From: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: <Pine.LNX.4.64.1107131704140.26989(a)jacobi.mcs.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Alireza, > > For vorticity computation, you can call > > call comp_vort3(vort,work1,work2,vx,vy,vz) > > from userchk with the appropriate definitions of vorticity and work arrays > like > > common /scren/ vort (lx1,ly1,lz1,lelv,3) ! x y z components > $ , work1(lx1,ly1,lz1,lelv) > $ , work2(lx1,ly1,lz1,lelv) > > Let me check what we have for the calculation of strain tensor. > Best, > Aleks > > > On Wed, 13 Jul 2011, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Hi, >> >> I need to calculate the vorticity vector and the rate of strain >> tensor at any >> arbitrary point in the domain. I wonder if these values are computed >> somewhere in the code or if I should interpolate them in the usr file. I >> appreciate any kind of help. >> >> Thanks in advance, >> >> >> Regards, >> Alireza Karimi >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > Message: 3 > Date: Wed, 13 Jul 2011 23:59:08 -0500 (CDT) > From: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: > <600285192.94128.1310619548370.JavaMail.root(a)zimbra.anl.gov> > Content-Type: text/plain; charset=utf-8 > > Hi Alireza, > > > For a strain stress computation you can call subroutine comp_sij > > call comp_sij(sij,nij,vx,vy,vz > $ ,ur,us,ut,vr,vs,vt,wr,ws,wt) > > > (navier5.f:2225) with nij=6 for 3D somewhere from userchk once you > declare the stress component array sij and arrays with local > coordinate r-s-t derivatives of velocity components > > common /csij/ > $ sij(lx1*ly1*lz1,6,lelv) ! 6 components > $ ,ur (lx1*ly1*lz1) > ... > $ ,wt (lx1*ly1*lz1) > > > Best, > Aleks > > > > > > > ----- Original Message ----- > From: nek5000-users(a)lists.mcs.anl.gov > To: nek5000-users(a)lists.mcs.anl.gov > Sent: Wednesday, July 13, 2011 5:09:48 PM > Subject: Re: [Nek5000-users] Vorticity > > Hi Alireza, > > For vorticity computation, you can call > > call comp_vort3(vort,work1,work2,vx,vy,vz) > > from userchk with the appropriate definitions of vorticity and work arrays > like > > common /scren/ vort (lx1,ly1,lz1,lelv,3) ! x y z components > $ , work1(lx1,ly1,lz1,lelv) > $ , work2(lx1,ly1,lz1,lelv) > > Let me check what we have for the calculation of strain tensor. > Best, > Aleks > > > On Wed, 13 Jul 2011, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Hi, >> >> I need to calculate the vorticity vector and the rate of strain >> tensor at any >> arbitrary point in the domain. I wonder if these values are computed >> somewhere in the code or if I should interpolate them in the usr file. I >> appreciate any kind of help. >> >> Thanks in advance, >> >> >> Regards, >> Alireza Karimi >> >> _______________________________________________ >> 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 > > > End of Nek5000-users Digest, Vol 29, Issue 2 > ******************************************** > -- Alireza Karimi PhD Candidate Department of Engineering Science and Mechanics Virginia Polytechnic Institute and State University Blacksburg, VA 24061

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Error when creating own mesh
by nek5000-users＠lists.mcs.anl.gov 01 Mar '16

01 Mar '16

Dear Neks, I am have attempted to use nek5000, firstly by following some of the examples etc. Now I am trying to create my own simulation, which is based upon the ocyl examples. My efforts simply include creating my own grid points in the .rea file to create a slightly different dimension... I believe I have understood how to define the problem however I continually receive errors when creating the genmap it reads as follows.... Input (.rea) file name: ocyl Input mesh tolerance (default 0.2): NOTE: smaller is better, but generous is more forgiving for bad meshes. 0.2 reading .rea file data ... ERROR: error reading 1 11 24 aborting 510 in routine rdbdry. 1 quit All I have done again is change the dimensions of the elements in the .rea file so I do not see why it would now not work? Thank you for any help in advance, Friedrich.

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Using results from a run as boundary condition for another one
by nek5000-users＠lists.mcs.anl.gov 29 May '15

29 May '15

Goodmoring Neks, I'm running some calculation on a laminar channel flow that contains a geometrical disturbance, similar to a "bump". It has been proved experimentally that the flow upwind is not affected by the presence of this impingement. Thus, in order to reduce the computational cost, I would like to *split* the case, say compute the "upwind" laminar channel flow separately, and then use the results as boundary conditions for a successive run, in my case containing the bump itself. My question is: is it possible to extract the computed fields from a given plane, and then use them as an "inflow" boundary condition on a successive run? I think I'll need to use the same mesh topology, in order to avoid any interpolation. Thank you for your attention Sincerely Ciccio

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Detected non-right-handed element
by nek5000-users＠lists.mcs.anl.gov 28 May '15

28 May '15

Dear Nek users, I am simulating a jet-type problem and created my own grid using Prex. I tried using that grid in the turbulent jet example so I could visualize it. However, after a few seconds, the simulation ends and gives me this error: WARNINGb: Detected non-right-handed element. Number 1 V1-8: 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 call exitt: dying ... After perusing the nek users archives, I've found that a similar problem occurred in 2010 but had been fixed in the latest repo at the time. It seemed that it only had that problem for certain compilers (gnu, ifort, etc). The compiler I am using is mpif77. Any input would be appreciated. Regards, Goran Marjanovic

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variable viscosity: perturbative and adjoint
by nek5000-users＠lists.mcs.anl.gov 27 May '15

27 May '15

Hi, Nek's Could I compute the perturbative equations, and so the adjoint one, for a variable viscosity flow? If yes, do I need to do like in the DNS simulation? Thanks. -- Mr. Mirko FaranoPh.D. student at Politecnico di BariTel.: +39-0883529289 / +39-0805963462Mob.: +39-3202342719Department of Mechanics Mathematics and Management - Fluid Machinery and Energy SystemsVia Re David, 200 - 70125 BARI (Italy)mirko.farano(a)poliba.itIn joint supervision with theEcole Nationale Supérieure d'Arts et Métiers de Paris - ParistechTel.: +33-144246436Mob.: +33-789822134Dynfluid Laboratory151 Boulevard de l'Hôpital - 75013 Paris (France)mirko.farano(a)ensam.eu

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R: Re: read temperature
by nek5000-users＠lists.mcs.anl.gov 22 May '15

22 May '15

Hi Aleks, this is the first line: #std 4 8 8 8 7680 7680 0.5487520544140E-02 0 0 1 XUPT so the temperature is written, moreover when i see the BF_Channel0.f00001 in visit, i see the right value of the temperature variable. -- Mr. Mirko FaranoPh.D. student at Politecnico di BariTel.: +39-0883529289 / +39-0805963462Mob.: +39-3202342719Department of Mechanics Mathematics and Management - Fluid Machinery and Energy SystemsVia Re David, 200 - 70125 BARI (Italy)mirko.farano(a)poliba.itIn joint supervision with theEcole Nationale Supérieure d'Arts et Métiers de Paris - ParistechTel.: +33-144246436Mob.: +33-789822134Dynfluid Laboratory151 Boulevard de l'Hôpital - 75013 Paris (France)mirko.farano(a)ensam.eu ----Messaggio originale---- Da: nek5000-users(a)lists.mcs.anl.gov Data: 22-mag-2015 17.11 A: "nek5000-users(a)lists.mcs.anl.gov"<nek5000-users(a)lists.mcs.anl.gov> Ogg: Re: [Nek5000-users] read temperature --> Hi Mirko, Did you check whether you temperature filed is dumped into the field file by checking whether there is a letter 'T' in the header of head BF_Channel0.f00001|strings|head -1 ? If not than you could either turn in the temperature dump by modifying turbChannel.rea's line F TEMPERATURE to T TEMPERATURE or inserting the line in userchk() before your call to outpost() ifto = .true. (which is the output specification) Aleks From: nek5000-users-bounces(a)lists.mcs.anl.gov [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: Friday, May 22, 2015 8:21 AM To: nek5000-users(a)lists.mcs.anl.gov Subject: [Nek5000-users] read temperature Hi Neks I'm trying to save some variables in this way: call outpost(u_bf,v_bf,w_bf,du_bfdy,vis_t,'BF_') after a simulation. then i would to read the aforementioned variables: ifto = .true. b_flow = 'BF_Channel0.f00001' call load_fld(b_flow) but it seems to read in the correct way just the first 4 variables: xyz min 0.0000 -1.0000 0.0000 uvwpt min 0.0000 0.96051E-20 0.96051E-20 -9.6269 0.96051E-20 PS min 0.0000 0.99000E+22 xyz max 12.560 1.0000 6.2800 uvwpt max 0.97894 0.80000E-19 0.80000E-19 9.6744 0.80000E-19 PS max 0.0000 -0.99000E+22 because the tmin e tmax are not zero in BF_Channel0.00001! Could someone help me? Thanks -- Mr. Mirko Farano Ph.D. student at Politecnico di Bari Tel.: +39-0883529289 / +39-0805963462 Mob.: +39-3202342719 Department of Mechanics Mathematics and Management - Fluid Machinery and Energy Systems Via Re David, 200 - 70125 BARI (Italy) mirko.farano(a)poliba.it In joint supervision with the Ecole Nationale Supérieure d'Arts et Métiers de Paris - Paristech Tel.: +33-144246436 Mob.: +33-789822134 Dynfluid Laboratory 151 Boulevard de l'Hôpital - 75013 Paris (France) mirko.farano(a)ensam.eu

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read temperature
by nek5000-users＠lists.mcs.anl.gov 22 May '15

22 May '15

Hi Neks I'm trying to save some variables in this way: call outpost(u_bf,v_bf,w_bf,du_bfdy,vis_t,'BF_') after a simulation. then i would to read the aforementioned variables: ifto = .true. b_flow = 'BF_Channel0.f00001' call load_fld(b_flow) but it seems to read in the correct way just the first 4 variables: xyz min 0.0000 -1.0000 0.0000 uvwpt min 0.0000 0.96051E-20 0.96051E-20 -9.6269 0.96051E-20 PS min 0.0000 0.99000E+22 xyz max 12.560 1.0000 6.2800 uvwpt max 0.97894 0.80000E-19 0.80000E-19 9.6744 0.80000E-19 PS max 0.0000 -0.99000E+22 because the tmin e tmax are not zero in BF_Channel0.00001! Could someone help me? Thanks -- Mr. Mirko FaranoPh.D. student at Politecnico di BariTel.: +39-0883529289 / +39-0805963462Mob.: +39-3202342719Department of Mechanics Mathematics and Management - Fluid Machinery and Energy SystemsVia Re David, 200 - 70125 BARI (Italy)mirko.farano(a)poliba.itIn joint supervision with theEcole Nationale Supérieure d'Arts et Métiers de Paris - ParistechTel.: +33-144246436Mob.: +33-789822134Dynfluid Laboratory151 Boulevard de l'Hôpital - 75013 Paris (France)mirko.farano(a)ensam.eu

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Nek optimal setting
by nek5000-users＠lists.mcs.anl.gov 18 May '15

18 May '15

Hi Nek's I'm going to run Nek5000 on a Bull cluster. In order to submit the process, i have to set the number of nodes, of tasks per node and of threads per core. Setting the threads per core equals to one, how can I adjust the number of nodes and the number of cores per node keeping Nek5000 in an optimal arrangement? In my case, I have 33000 elements with a spectral order equal to 8. Alessandro

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unusual quantities
by nek5000-users＠lists.mcs.anl.gov 17 May '15

17 May '15

Dear Nek5000 Users, I have some unusual quantities I am hoping to compute while solving the 3D Rayleigh-Benard problem. They are described in the attached pdf-file. I am hoping someone has a suggestion how to do this using Nek5000. Thanks, Mike

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Compiling nek5000 with MPI on Mac.
by nek5000-users＠lists.mcs.anl.gov 13 May '15

13 May '15

Hi, I'm trying to use nek5000 with MPI on a Mac. OS is Yosemite. Fortran compiler = gfortran: nikolai:eddy wenhaowu$ gfortran --version GNU Fortran (GCC) 5.1.0 Copyright (C) 2014 Free Software Foundation, Inc. C compiler = mpicc from mpich: nikolai:eddy wenhaowu$ mpicc --version Apple LLVM version 6.1.0 (clang-602.0.49) (based on LLVM 3.6.0svn) Target: x86_64-apple-darwin14.3.0 Thread model: posix And I followed the instruction 'QuickStart': Here is the beginning of my 'makenek': ----------------------------------------------------------------- #!/bin/bash # Nek5000 build config file # (c) 2008,2009,2010 UCHICAGO ARGONNE, LLC # source path SOURCE_ROOT="/Users/wenhaowu/Documents/testcases/nek5/trunk/nek" # Fortran compiler F77="gfortran" # C compiler CC="mpicc" # pre-processor symbol list # (set PPLIST=? to get a list of available symbols) #PPLIST="?" # plug-in list PLUGIN_LIST="" # OPTIONAL SETTINGS # ----------------- # enable MPI (default true) #IFMPI="false" ... ----------------------------------------------------------------- Here is my command: ./makenek eddy_uv Here is an example what goes wrong: ------------------------------------------------------------------------- mpicc -c -O2 -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG -DPRE FIX=jl_ /Users/wenhaowu/Documents/testcases/nek5/trunk/nek/nek_comm.c -o obj/nek _comm.o In file included from /Users/wenhaowu/Documents/testcases/nek5/trunk/nek/nek_com m.c:17: /opt/local/include/mpich-mp/mpi.h:116:56: error: expected identifier static const MPI_Datatype mpich_mpi_char MPICH_ATTR_TYPE_TAG(char) = MPI_CHAR; ^ /opt/local/include/mpich-mp/mpi.h:24:106: note: expanded from macro 'MPICH_ATTR_TYPE_TAG' # define MPICH_ATTR_TYPE_TAG(type) __attribute__((type_tag_for_datatype(MPI,type))) ^ <command line>:2:13: note: expanded from here #define MPI 1 ------------------------------------------------------------------------- The problem is nek5000 has #defined MPI to be 1, but the mpich header file 'mpi.h' uses the symbol 'MPI' (for a completely different reason). How do other people use nek5000 with mpi on a Mac? Thanks. Sincerely, Wenhao Wu

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