October 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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website of NEK5000
by nek5000-users＠lists.mcs.anl.gov 05 Nov '15

05 Nov '15

Dear neks, The old version of the site had some pages which are absent in the new version, f.e. genbox description, boundary definitions, and especially description of useful functions. Is it possible to give a link to the old version of the site, since the new information does not contain all the information? Thank you, Ilias

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new to nek5000
by nek5000-users＠lists.mcs.anl.gov 03 Nov '15

03 Nov '15

hey I am extremely new to nek5000 I am trying to solve the examples that are already present. If I just want to compile the already existing files, what are the steps? This may seem lame but cant help it..sry AVR

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energy dissipation over a subdomain
by nek5000-users＠lists.mcs.anl.gov 02 Nov '15

02 Nov '15

Dear neks! I would like to compute kinetic energy dissipation over different subdomains. It involves the calculation of the dissipation itself in GLL points, and integration over some domain. I understand now that it is more accurate to involve whole number of elements for integration, and that for computation of the integral over a subdomain one can use a mask (of 1s and 0es) over the whole domain, and after that to use global scalar product like glsc3. Are there the implementations of these ideas? first of all, the creation of a mask, based on geometrical constructions like IF (Y.gt.something) THEN ... and also if somebody has already a procedure of kinetic energy dissipation, though here it is more strait: calculation of of velocity gradient and contraction of its multiplication with itself, Thank you, Ilias

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Elsasser subroutines in the MHD solver
by nek5000-users＠lists.mcs.anl.gov 30 Oct '15

30 Oct '15

Hi all, I have a question regarding the implementation of the MHD solver. The manual and the comment in the subroutine elsasserh (in induct.f) says that Nek uses the Elsasser formulation to solve for u and B simultanously. A quick 'grep -i'elsasser' *' in the source directory tells me that there are subroutines to convert between u and B and the Elsasser variables. However, it seems to me that only one of these is ever called (in the cfl_check routine). Shouldn't there be many more calls, e.g. for converting the starting field, boundary conditions, writing output...? I have no experience so far with the Elsasser formulation, so I am a bit lost concerning what is happening in the code. Best regards, Jan

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Time step independence
by nek5000-users＠lists.mcs.anl.gov 29 Oct '15

29 Oct '15

Good morning all, I'm relatively inexperienced with DNS simulations, so I'd appreciate your help with the following: Are there any tests specific to Nek that can be run to determine whether the solution is independent of the time step length? I've attempted a couple of approaches, including: i.) Running for extended periods of time with different fixed time step lengths before using avg_all to calculate velocities and other statistical parameters and then comparing for the different time step lengths. ii.) Calculate the spectra from the velocity magnitude and check whether it is resolving past the -5/3 inertial range. This seems to be the case, as beyond a certain frequency the slope becomes more negative as is the general expectation in the dissipation scale range. iii.) I'm using a subroutine I wrote to calculate the minimum Kolmogorov time and length scales in the domain and comparing those values with my time step length and maximum grid spacing, so as to ensure that those parameter maxima are still smaller than the minimum Kolmogorov scales. Would any of these approaches suffice when making an explicit statement of time step independence? I am at the beginnings a draft manuscript for a publication relating to the work, and I understand that to claim DNS we have to be rigorous in terms of conforming to all the requirements, so I want to get it right from the start. Thanks in advance for your help! Lambert

1 0

MOAB partitioning
by nek5000-users＠lists.mcs.anl.gov 27 Oct '15

27 Oct '15

Dear Nek/Moab users, I built Moab, but in the bin folder the 'mbpart' code is missing and I need it to partition an .h5m mesh file for Nek. Any suggestions? Thanks, -emilian

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output through .rea and through usrchk
by nek5000-users＠lists.mcs.anl.gov 27 Oct '15

27 Oct '15

Dear neks, Strange thing happend to a simulation where I made "standart" output through .rea file, i.e. -0.010000E-01 p012 DT 0.00000 p013 IOCOMM 0.50000 p014 IOTIME and at the same time I need scalar gradients, so I've put to usrchk: il_hptsout=-0.5/param(12) if ((istep.gt.0).and.(mod(istep,il_hptsout).eq.0)) then call gradm1(dtdx,dtdy,dtdz,t) call outpost(dtdx,dtdy,dtdz,pr,t,'gdt') endif The strange thing that gdt* (from usrchk) files are saved as should should be, but "standart" CASE0.f* were saved onli partially, below is 'ls -rt' of the case directory. Why whould that happen? may it be cluster issue? (file sizes are not small ~530mb) -rw-rw-r-- 1 35K Oct 15 02:52 compiler.out -rw-rw-r-- 1 99 Oct 15 02:55 SESSION.NAME -rw-rw-r-- 1 52 Oct 15 02:55 lognekbmpi.txt -rw-rw-r-- 1 353M Oct 15 03:54 gdtI0.f00001 -rw-rw-r-- 1 353M Oct 15 04:51 gdtI0.f00002 -rw-rw-r-- 1 353M Oct 15 05:29 gdtI0.f00003 -rw-rw-r-- 1 529M Oct 15 05:29 I0.f00001 -rw-rw-r-- 1 353M Oct 15 06:07 gdtI0.f00004 -rw-rw-r-- 1 529M Oct 15 06:07 I0.f00002 -rw-rw-r-- 1 353M Oct 15 06:39 gdtI0.f00005 -rw-rw-r-- 1 529M Oct 15 06:39 I0.f00003 -rw-rw-r-- 1 353M Oct 15 08:23 gdtI0.f00006 -rw-rw-r-- 1 529M Oct 15 08:23 I0.f00004 -rw-rw-r-- 1 353M Oct 15 09:29 gdtI0.f00007 -rw-rw-r-- 1 529M Oct 15 09:29 I0.f00005 -rw-rw-r-- 1 353M Oct 15 10:11 gdtI0.f00008 -rw-rw-r-- 1 529M Oct 15 10:12 I0.f00006 -rw-rw-r-- 1 353M Oct 15 10:57 gdtI0.f00009 -rw-rw-r-- 1 529M Oct 15 10:58 I0.f00007 -rw-rw-r-- 1 353M Oct 15 11:49 gdtI0.f00010 -rw-rw-r-- 1 353M Oct 15 12:41 gdtI0.f00011 -rw-rw-r-- 1 353M Oct 15 13:12 gdtI0.f00012 -rw-rw-r-- 1 353M Oct 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Limits on Buffer for Writing Binary Data
by nek5000-users＠lists.mcs.anl.gov 23 Oct '15

23 Oct '15

Neks, I have been working on routines to dump out interpolated data from Nek to binary files that can be read in VisIt. The data I'm outputting is designed to cover any subdomain inside the simulation and at any resolution (typically much higher than Nelm*lx1^3). I have found that when I try to dump too much data at once through a modified version of out_buff() and byte_write() it can cause an error and kill my program. I am assuming there must be some sort of buffer limit on how much data can be written at once, but I haven't been able to determine what it is specifically. It seems to be a function of lx1 and lelt though. Anyone know what the limit is/what is causing this error? Thanks, -- Phil S.

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