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

Re: [Nek5000-users] Using Cartesian grid lookup table in Nekton
by nek5000-users＠lists.mcs.anl.gov 04 Jun '18

04 Jun '18

There is nothing spectral element specific here. You could do e.g. a trilinear interpolation but that's something you have to code yourself. -----Original message----- > From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > Sent: Wednesday 30th May 2018 21:26 > To: nek5000-users <nek5000-users(a)lists.mcs.anl.gov> > Subject: Re: [Nek5000-users] Using Cartesian grid lookup table in Nekton > > The question is how to read in a discrete data set defined in a finite difference grid in ffx or forcing in the .usr file. It seems like there will be some sort of interpolation to the spectral element grid. So yes, that is my question. > > Thank you, > Saikat > Saikat Mukherjee, > PhD Student, > Paul Research Group - http://www.me.vt.edu/mpaul/ <http://www.me.vt.edu/mpaul/> > Engineering Science and Mechanics, > Virginia Tech. > > On Wed, May 30, 2018 at 2:48 PM, <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>> wrote: > What’s your question? How to do the interpolation in your function f? > > On 30 May 2018, at 20:17, "nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>" <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>> wrote: > > Hi, > > Thanks for the reply. My problem is f is given as a discrete data set described in finite difference grid. I want to interpolate this to ffx like you said in my .usr file. Would like to know how to proceed. > > Thanks, > Saikat > Saikat Mukherjee, > PhD Student, > Paul Research Group - http://www.me.vt.edu/mpaul/ <http://www.me.vt.edu/mpaul/> > Engineering Science and Mechanics, > Virginia Tech. > > On Wed, May 30, 2018 at 1:36 PM, <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>> wrote: > Lets consider > > ffx = f(x,y,z) > > here f is an user function (something you have to provide) which get evaluated at x,y,z (your grid points). Interpolation is required if f is given by a discrete data set. > > hth > > > -----Original message----- > > From:[email protected] <mailto:From%[email protected]> <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>> > > Sent: Wednesday 30th May 2018 19:19 > > To: nek5000-users <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>> > > Subject: Re: [Nek5000-users] Using Cartesian grid lookup table in Nekton > > > > Hi, > > > > Thanks for the reply. The look up table is in a finite difference grid. Are you saying I can still feed it to the .usr file and it should be fine? > > > > Thanks, > > Saikat > > Saikat Mukherjee, > > PhD Student, > > Paul Research Group - http://www.me.vt.edu/mpaul/ <http://www.me.vt.edu/mpaul/> <http://www.me.vt.edu/mpaul/ <http://www.me.vt.edu/mpaul/>> > > Engineering Science and Mechanics, > > Virginia Tech. > > > > On Sat, May 26, 2018 at 10:54 PM, <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: > > Hi Saikat, > > > > You can always do the reading from the look up table from .usr file, at once then feed the data to your ffx ffy and ffz through a common block. > > > > On Thu, May 24, 2018 at 10:55 PM, <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: > > Hey all, > > > > Just following up on the query. Would appreciate any input. > > > > Thanks, > > Saikat > > Saikat Mukherjee, > > PhD Student, > > Paul Research Group - http://www.me.vt.edu/mpaul/ <http://www.me.vt.edu/mpaul/> <http://www.me.vt.edu/mpaul/ <http://www.me.vt.edu/mpaul/>> > > Engineering Science and Mechanics, > > Virginia Tech. > > > > On Tue, May 22, 2018 at 4:47 PM, Saikat Mukherjee <msaikat6(a)vt.edu <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: > > Hey Neks, > > > > I have a forcing function which is in the form of a look up table in X-Y cartesian grid. I would like to use this forcing function in the 2-D fluid momentum equation that Nekton solves. Is there a way to do this in the .usr file or elsewhere? > > > > Thanks, > > Saikat > > > > > > Saikat Mukherjee, > > PhD Student, > > Paul Research Group - http://www.me.vt.edu/mpaul/ <http://www.me.vt.edu/mpaul/> <http://www.me.vt.edu/mpaul/ <http://www.me.vt.edu/mpaul/>> > > Engineering Science and Mechanics, > > Virginia Tech. > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>> > > > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>> > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <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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Conversion problem using exo2nek
by nek5000-users＠lists.mcs.anl.gov 31 May '18

31 May '18

Hi, I read the informations regarding the BC from exo2nek folder of NEK5000. There it says the 5th argument of fluid bc array. But when I acces it throught the user file everything is zero it seems. (like this bc(5,j,i,1) ) Could you please tell me if there is any problem with my conversion of exo2nek? Thank you Sijo

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studying materials to understand genmap code
by nek5000-users＠lists.mcs.anl.gov 31 May '18

31 May '18

Hi Neks, I want to have a thorough understand of the genmap code, especially subroutine "periodic_vtx" and "rec_bisect". Do you know if there are some existing documents that can help me quickly understand those code? Thanks, Keke

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How to give NEK5000 boundary conditions to exodus mesh file
by nek5000-users＠lists.mcs.anl.gov 31 May '18

31 May '18

Hi Neks, I did the conversion of a mesh from ICEM to exodus file then to re2 file. But I am bit confused on the boundary conditions. Because from ICEM before I export to exodus I give the B.Cs as side set numbers and after the conversion to re2 I wont be able to put the boundary conditions in NEK format. So could you please tell me how you put the BC in NEK5000 format to a mesh file with exodus format. Thank you

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Issue with visit In-situ
by nek5000-users＠lists.mcs.anl.gov 31 May '18

31 May '18

Dear Neks, I was having issues visualizing pseudocolor plots when using VisIt in-situ processing with Nek5000. I talked to the developer of the Libsim library, Brad Whitlock, and he pointed out that the VISIT_ERROR handles in the "visit.f" should be changed to VISIT_INVALID_HANDLE. After doing this, I was able to visualize the pseudocolor plots. I tested it with Visit 2.10.2 and 2.12.3. I believe this should be changed in the code for correct functioning of in-situ processing. Thank you, Juan Diego

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Re: [Nek5000-users] Using Cartesian grid lookup table in Nekton
by nek5000-users＠lists.mcs.anl.gov 30 May '18

30 May '18

Let's consider ffx = f(x,y,z) here f is an user function (something you have to provide) which get evaluated at x,y,z (your grid points). Interpolation is required if f is given by a discrete data set. hth -----Original message----- > From:[email protected] <nek5000-users(a)lists.mcs.anl.gov> > Sent: Wednesday 30th May 2018 19:19 > To: nek5000-users <nek5000-users(a)lists.mcs.anl.gov> > Subject: Re: [Nek5000-users] Using Cartesian grid lookup table in Nekton > > Hi, > > Thanks for the reply. The look up table is in a finite difference grid. Are you saying I can still feed it to the .usr file and it should be fine? > > Thanks, > Saikat > Saikat Mukherjee, > PhD Student, > Paul Research Group - http://www.me.vt.edu/mpaul/ <http://www.me.vt.edu/mpaul/> > Engineering Science and Mechanics, > Virginia Tech. > > On Sat, May 26, 2018 at 10:54 PM, <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>> wrote: > Hi Saikat, > > You can always do the reading from the look up table from .usr file, at once then feed the data to your ffx ffy and ffz through a common block. > > On Thu, May 24, 2018 at 10:55 PM, <nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]>> wrote: > Hey all, > > Just following up on the query. Would appreciate any input. > > Thanks, > Saikat > Saikat Mukherjee, > PhD Student, > Paul Research Group - http://www.me.vt.edu/mpaul/ <http://www.me.vt.edu/mpaul/> > Engineering Science and Mechanics, > Virginia Tech. > > On Tue, May 22, 2018 at 4:47 PM, Saikat Mukherjee <msaikat6(a)vt.edu <mailto:[email protected]>> wrote: > Hey Neks, > > I have a forcing function which is in the form of a look up table in X-Y cartesian grid. I would like to use this forcing function in the 2-D fluid momentum equation that Nekton solves. Is there a way to do this in the .usr file or elsewhere? > > Thanks, > Saikat > > > Saikat Mukherjee, > PhD Student, > Paul Research Group - http://www.me.vt.edu/mpaul/ <http://www.me.vt.edu/mpaul/> > Engineering Science and Mechanics, > Virginia Tech. > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov <mailto:[email protected]> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <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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Re: [Nek5000-users] Using Cartesian grid lookup table in Nekton
by nek5000-users＠lists.mcs.anl.gov 30 May '18

30 May '18

Hey all, Just following up on the query. Would appreciate any input. Thanks, Saikat Saikat Mukherjee, PhD Student, Paul Research Group - http://www.me.vt.edu/mpaul/ Engineering Science and Mechanics, Virginia Tech. On Tue, May 22, 2018 at 4:47 PM, Saikat Mukherjee <msaikat6(a)vt.edu> wrote: > Hey Neks, > > I have a forcing function which is in the form of a look up table in X-Y > cartesian grid. I would like to use this forcing function in the 2-D fluid > momentum equation that Nekton solves. Is there a way to do this in the .usr > file or elsewhere? > > 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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Mesh conversion from exo to nek using exo2nek
by nek5000-users＠lists.mcs.anl.gov 30 May '18

30 May '18

Hi Neks, I was trying to convert my mesh with exo format to NEK frmat using exo2nek tool from NEK5000. When I run exo2nek I am facing a trouble shown below: Could you please tell me what are the options that I have to solve this: exodus.exo is an EXODUSII file; version 0.00 I/O word size 8 database parameters: title = Created by ICEMCFD - EXODUS II Interface num_dim = 2 num_nodes = 296877 num_elem = 295536 num_elem_blk = 1 num_side_sets = 0 element block id = 1 element type = QUAD num_elem_in_block = 295536 num_nodes_per_elem = 4 ERROR: Only QUAD9 elements are allowed in a 2D mesh! num_nodes_per_elem= 4 Note: The following floating-point exceptions are signalling: IEEE_DENORMAL Thanks Sijo GEORGE

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Re: [Nek5000-users] Nek5000-users Digest, Vol 111, Issue 26
by nek5000-users＠lists.mcs.anl.gov 30 May '18

30 May '18

Re: Converting problem from .msh to NEK5000 format 1. is your fluent mesh in binary format ? I think you should have it ascii format. 2. or, as an alternative, you should try exo2nek utility. if you have access to ICEM, you could import your mesh in ICEM, and export your mesh to exodus format. Then exo2nek will convert it to re2 format. Haomin (Kirk) Yuan ________________________________ From: Nek5000-users <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: Tuesday, May 29, 2018 12:00:13 PM To: nek5000-users(a)lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 111, Issue 26 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. Converting problem from .msh to NEK5000 format (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Tue, 29 May 2018 16:28:32 +0200 (CEST) From: nek5000-users(a)lists.mcs.anl.gov To: nek5000-users <nek5000-users(a)lists.mcs.anl.gov> Subject: [Nek5000-users] Converting problem from .msh to NEK5000 format Message-ID: <mailman.2678.1527604367.86639.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="utf-8" Hello Neks, I have mesh file .msh format and I was trying to convert into NEK5000 format using mshconvert.py but I face some troubles in the function of scan_fluent_mesh. I get this error : IOError: Something went wrong reading fluent mesh. Could you please tell me why? I can send you the mesh file and it may help you understand the problem. Do I have to change anything in the .msh file normally? Thanks Sijo GEORGE

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Converting problem from .msh to NEK5000 format
by nek5000-users＠lists.mcs.anl.gov 30 May '18

30 May '18

Hello Neks, I have mesh file .msh format and I was trying to convert into NEK5000 format using mshconvert.py but I face some troubles in the function of scan_fluent_mesh. I get this error : IOError: Something went wrong reading fluent mesh. Could you please tell me why? I can send you the mesh file and it may help you understand the problem. Do I have to change anything in the .msh file normally? Thanks Sijo GEORGE

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