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

Mesh morphing
by nek5000-users＠lists.mcs.anl.gov 17 Feb '15

17 Feb '15

Dear Neks, I thought this question might be of interest for someone else as well, so posting it here: I have been looking at the oscillating cylinder example. I would like to do something similar, but instead of a prescribed boundary velocity, would like to prescribe a given displacement of one boundary, and morph my mesh smoothly everywhere to match this displacement. For example, if one were to describe a deformation of the cylinder rather than a velocity (but without altering the other boundaries and without scaling the mesh). This just needs to be done once, not at every time step. Is there an easy way to do this? Can I arrive there somehow by minor modifications of the elasticity solver? What equation exactly is the elasticity solver solving at every time step? (When I outputted the files after every time step for the oscillating cylinder, the mesh deformation seemed to match the prescribed one only after 2 time steps. Is there a reason for this, or did I do something wrong?) Best regards, Outi

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Spatial average of velocity and pressure
by nek5000-users＠lists.mcs.anl.gov 16 Feb '15

16 Feb '15

Dear Neks, I've been looking at the subroutines for spatial average of variables in nek5000. I'm using PnPn-2 method and my domain is periodic in both X and Z directions. I noticed that the weights for Gauss-Lobatto Legendre points are WXM1, WYM1, WZM1 and the weights for Gauss Legendre points are WXM2, WYM2, WZM2. I'm using the first set of weights for spatial average of my velocity field and the second set of weights for my pressure field, but I'm not sure if that's the correct way to take the spatial average of variables in certain directions?? When I looked at the subroutine planar_average_s in turbChannel example, aa = zz*area(i,k,1,e) + (1-zz)*area(i,k,3,e) (where zz = (1.-zgm1(j,2))/2.) is used for spatial average on r-t plane. I'm wondering which type of weights I should use for spatial average of velocity and pressure in my case. Can I use WXM1 (or WXM2) to average the variables in X direction first and then use WZM1 (or WZM2) to average the variables in Z direction? Hope anyone can help me on this. Thank you very much in advance. Best regards, Tony

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Parallel on several nodes
by nek5000-users＠lists.mcs.anl.gov 12 Feb '15

12 Feb '15

Hi guys, I have a naive questions but I couldn't find my answer in existing posts. Is it possible to run Nek on several nodes, say, on a cluster? If so, which script should be used? A command like /nekmpi eddy_uv 4/ does not help becaue on each node I have 8 CPUs but I'd like to have my 16 nodes (each have 12 CPUs) run together. Any help is appreciated. Saleh

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Dump on both regular and SEM grids
by nek5000-users＠lists.mcs.anl.gov 11 Feb '15

11 Feb '15

Dear All, Is there a possibility to dump result files during run time on both an SEM grid and another regular grid (as done if ifreguo = .true. ). Therefore avoiding the need to run a separate conversion in post-processing (as explained in https://nek5000.mcs.anl.gov/index.php/Data_processing_example ). Thank you, JP

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Re: [Nek5000-users] Dump on both regular and SEM grids
by nek5000-users＠lists.mcs.anl.gov 11 Feb '15

11 Feb '15

Dear Aleks, Sorry to bother you again, a quick question, what if I were to output at a specific time interval, i.e. using IOTIME.. how should I refer to the correct variables / go about it? Thank you, JP

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Re: [Nek5000-users] Dump on both regular and SEM grids
by nek5000-users＠lists.mcs.anl.gov 11 Feb '15

11 Feb '15

Dear Aleks, Thank you. It is exactly what I was looking for. Regards, JP

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question about efficient running nek5000
by nek5000-users＠lists.mcs.anl.gov 10 Feb '15

10 Feb '15

Hi, I ran nek5000 on 1024 CPUs which is divided to 128 nodes and 8 cores per node, and the same problem on 1200 CPUs with 100 nodes and 12 cores per node, however in second case I got lower efficiency, simulation goes slower about 5~8 percent!! I ran both cases on the same cluster!! Does anyone have any idea why I do not get higher efficiency with the higher number of CPUs but less nodes involved!? Could memory be a limitation here or since numbers in first case are power of 2, it is more efficient!? Thanks, Ami

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Postdoc position available
by nek5000-users＠lists.mcs.anl.gov 05 Feb '15

05 Feb '15

Prof. Mavriplis and the University of Ottawa are currently looking for a postdoctoral researcher interested in pursuing research in the field of Computational Fluid Dynamics (CFD). The main topic of research will be adaptive discontinuous Galerkin or spectral element methods for direct simulation (incompressible Navier-Stokes equations), and other projects may include control of separated flows, transition, aerodynamics and CFD for blood flow. A PhD degree in CFD or Fluid Dynamics including code development and high performance computing is necessary. The candidate must have already published journal articles. Experience with spectral methods, Nek5000, and VISIT is a plus. The ideal candidate will have excellent computer programming skills, communication skills (written, oral, graphical and with others in the research group), self-motivation and an open mind. The position also requires some training of graduate students. Ideally this would be for the spring timeframe. The position is at University of Ottawa in Ottawa, Canada. Please send a short email with cv attached by email with 'Nek5000 PhD application' in the subject line. Catherine Mavriplis http://www.engineering.uottawa.ca/en/directory/view/mavriplis_catherine -- Prof. Catherine Mavriplis Dept. of Mechanical Engineering / Génie mécanique University of Ottawa / Université d'Ottawa 161 Louis Pasteur Room A331 Ottawa, Ontario CANADA K1N 6N5 Catherine.Mavriplis(a)uottawa.ca

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Re: [Nek5000-users] Changed mesh coordinates
by nek5000-users＠lists.mcs.anl.gov 04 Feb '15

04 Feb '15

Dear Neks, Sorry for bringing this up again. Just want to know has anyone seen this before? Why are the coordinates for some points at 0.0e0 changed? Thank you very much. Kind regards, Tony ________________________________________ From: nek5000-users-bounces(a)lists.mcs.anl.gov <nek5000-users-bounces(a)lists.mcs.anl.gov> on behalf of nek5000-users-request(a)lists.mcs.anl.gov <nek5000-users-request(a)lists.mcs.anl.gov> Sent: 01 February 2015 18:00 To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 72, Issue 1 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. Changed mesh coordinates (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Sun, 1 Feb 2015 05:05:07 +0000 From: nek5000-users(a)lists.mcs.anl.gov To: "nek5000-users(a)lists.mcs.anl.gov" <nek5000-users(a)lists.mcs.anl.gov> Subject: [Nek5000-users] Changed mesh coordinates Message-ID: <mailman.14423.1422767115.3424.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="iso-8859-1" Dear Neks, I'm doing some data processing for my simulations in nek5000. I found for some elements, however, the coordinates are not exactly as specified. For example, I have an element whose vertices are as follows. ELEMENT 195 [ 1m] GROUP 0 0.000000E+00 -0.130526E+00 -0.129129E+00 0.000000E+00 0.100000E+01 0.991445E+00 0.979179E+00 0.987876E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 -0.130526E+00 -0.129129E+00 0.000000E+00 0.100000E+01 0.991445E+00 0.979179E+00 0.987876E+00 0.263158E+00 0.263158E+00 0.263158E+00 0.263158E+00 When I used the following code to print the coordinates for this element, I got the values below. do e=1,nelv eg = lglel(e) if(eg .eq. 195) then write(*,*) xm1(1,1,1,e),ym1(1,1,1,e),zm1(1,1,1,e) write(*,*) cbc(1:6,e,1) end if end do 7.500381456730263E-017 1.00000000000000 0.000000000000000E+000 0.000000000000000E+000 W E E E P E Is there any reason why the x coordinate for the first element vertex is not exactly 0.0e0? Hope someone can help. Thank you very much. Best regards, Tony

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Compute Pressure from a given velocity field
by nek5000-users＠lists.mcs.anl.gov 02 Feb '15

02 Feb '15

Howdy Nek's, I was wondering if anyone could explain to me how to compute the pressure from a given velocity field? Say I have a blah0.f00001 field containing only vx,vy, and vz. Once I have loaded it in userchk in postprocess mode, is there anyway I can compute the corresponding pressure field? Best regards, JC -- Jean-Christophe Loiseau Homepage <https://sites.google.com/site/loiseaujc/>

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