[Nek5000-users] Interpolation between two meshes

Tue Mar 28 02:57:33 CDT 2017

Can you please provide more information about your case (machine, compiler) and include the .usr and log file.
If the case is reasonably small, I can try to run it myself. 

-----Original message-----
> From:nek5000-users at lists.mcs.anl.gov <nek5000-users at lists.mcs.anl.gov>
> Sent: Tuesday 28th March 2017 4:03
> To: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] Interpolation between two meshes
> 
> Hi Stefan,
> 
> Many thanks for your reply. I have tried the new 'gfldr' subroutine in two ways.
> 
> First, I copied the whole 'gfldr.f' into my usr file and ran the interpolation with my legacy nek master code
> (tuned few lines to match the old byte_mpi.f format). The source field was read in successfully and I also confirmed the coordinates from the source field. However, the interpolation halted again at 'findpts' in 'gfldr_intp' subroutine.
> 
> Second, I ran the interpolation directly with the latest master nek code. The same thing happened and the interpolation halted at 'findpts' and never moved on.
> 
> In addition, I also tried reducing polynomial order (lx1) as Mattias suggested, but with no success.
> 
> I really don't know what causes the problem when interpolating between two large meshes. Do you have any workaround?
> 
> Please help me out. Thank you very much.
> 
> Best regards,
> Tony
> 
> 
> -----------
> From: nek5000-users-bounces at lists.mcs.anl.gov <nek5000-users-bounces at lists.mcs.anl.gov> on behalf of nek5000-users-request at lists.mcs.anl.gov <nek5000-users-request at lists.mcs.anl.gov>
> Sent: 27 March 2017 18:00
> To: nek5000-users at lists.mcs.anl.gov
> Subject: Nek5000-users Digest, Vol 97, Issue 29
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> Today's Topics:
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>    1. Re: Interpolation between two meshes
>       (nek5000-users at lists.mcs.anl.gov)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 27 Mar 2017 18:21:52 0200
> From: nek5000-users at lists.mcs.anl.gov
> To: nek5000-users at lists.mcs.anl.gov      <nek5000-users at lists.mcs.anl.gov>
> Subject: Re: [Nek5000-users] Interpolation between two meshes
> Message-ID:
>         <mailman.3273.1490631729.2967.nek5000-users at lists.mcs.anl.gov>
> Content-Type: text/plain; charset=utf-8
> 
> Just give it a whirl.
> It's important for us to see if the latest version fixes your problem. I have some confidence that it will ;)
>  
> -----Original message-----
> > From:nek5000-users at lists.mcs.anl.gov <nek5000-users at lists.mcs.anl.gov>
> > Sent: Monday 27th March 2017 18:19
> > To: nek5000-users at lists.mcs.anl.gov
> > Subject: Re: [Nek5000-users] Interpolation between two meshes
> > 
> > Hi Stefan and Mattias,
> > 
> > Thank you both for your kind advice.
> > 
> > Stefan, I had a look at the new 'gfldr' subroutine. It seems that the spectral interpolation procedure is the same as before, however, the latest subroutine breaks down the number of fields to interpolate in one go. I still don't see why the old g2gi hangs
> >  at 'findpts'. Is it mainly because of memory size? (I have been using my own copy of the legacy nek, so I'm quite keen on making it work with g2gi.)
> > 
> > Mattias, I will give it a go with your suggestion. By reducing the polynomial order, did you mean the order of the old field or the order of the new geometry field, or both?
> > 
> > Thank you again for both your help.
> > 
> > Best regards,
> > Tony
> > 
> > 
> > -----------
> > From: nek5000-users-bounces at lists.mcs.anl.gov <nek5000-users-bounces at lists.mcs.anl.gov> on behalf of nek5000-users-request at lists.mcs.anl.gov <nek5000-users-request at lists.mcs.anl.gov>
> > Sent: 27 March 2017 12:57
> > To: nek5000-users at lists.mcs.anl.gov
> > Subject: Nek5000-users Digest, Vol 97, Issue 27
> > Send Nek5000-users mailing list submissions to
> > ??????? nek5000-users at lists.mcs.anl.gov
> > 
> > To subscribe or unsubscribe via the World Wide Web, visit
> > 
> 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>>
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> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Nek5000-users digest..."
> > 
> > 
> > Today's Topics:
> > 
> > ?? 1. Interpolation between two meshes (nek5000-users at lists.mcs.anl.gov)
> > ?? 2. Re: Interpolation between two meshes
> > ????? (nek5000-users at lists.mcs.anl.gov)
> > ?? 3. Re: Copy velocity slice from one boundary to another
> > ????? (nek5000-users at lists.mcs.anl.gov)
> > ?? 4. Robin Boundary Condition -- Navier's Slip Length
> > ????? (nek5000-users at lists.mcs.anl.gov)
> > ?? 5. Re: Interpolation between two meshes
> > ????? (nek5000-users at lists.mcs.anl.gov)
> > 
> > 
> > ----------------------------------------------------------------------
> > 
> > Message: 1
> > Date: Mon, 27 Mar 2017 04:37:46 0000
> > From: nek5000-users at lists.mcs.anl.gov
> > To: Nek5000 <nek5000-users at lists.mcs.anl.gov>
> > Subject: [Nek5000-users] Interpolation between two meshes
> > Message-ID:
> > ??????? <mailman.3211.1490589471.2967.nek5000-users at lists.mcs.anl.gov>
> > Content-Type: text/plain; charset="iso-8859-1"
> > 
> > Dear Neks,
> > 
> > I have been using 'g2gi' to do interpolation between different meshes. Recently, I have noticed that when I interpolate between two big meshes (say 300000 elements in each mesh), the interpolation hangs at 'call findpts' and never moves on. I tried increasing
> >  number of processors and changing 'lpart', but none of these worked.
> > 
> > I'm wondering what could cause the interpolation to hang at 'findpts'. Has anyone encountered similar issue?
> > 
> > Hope anyone could give me some advice. Thank you very much in advance.
> > 
> > Best regards,
> > Tony
> > -------------- next part --------------
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> > 
> > ------------------------------
> > 
> > Message: 2
> > Date: Mon, 27 Mar 2017 09:47:37 0200
> > From: nek5000-users at lists.mcs.anl.gov
> > To: nek5000-users at lists.mcs.anl.gov????? <nek5000-users at lists.mcs.anl.gov>
> > Subject: Re: [Nek5000-users] Interpolation between two meshes
> > Message-ID:
> > ??????? <mailman.3212.1490600871.2967.nek5000-users at lists.mcs.anl.gov>
> > Content-Type: text/plain; charset=utf-8
> > 
> > Please update to the latest master. Note, g2gi was replaced by gfldr. 
> > 
> > Stefan
> > 
> > -----Original message-----
> > > From:nek5000-users at lists.mcs.anl.gov <nek5000-users at lists.mcs.anl.gov>
> > > Sent: Monday 27th March 2017 6:38
> > > To: Nek5000 <nek5000-users at lists.mcs.anl.gov>
> > > Subject: [Nek5000-users] Interpolation between two meshes
> > > 
> > > Dear Neks,
> > > 
> > > I have been using 'g2gi' to do interpolation between different meshes. Recently, I have?noticed that when I interpolate between two big meshes (say 300000 elements in each mesh), the interpolation hangs at 'call findpts' and never moves on. I tried increasing
> > >? number of processors and changing 'lpart', but none of these worked.
> > > 
> > > I'm wondering what could cause the interpolation to hang at 'findpts'. Has anyone encountered similar issue?
> > > 
> > > Hope anyone could give me some advice. Thank you very much in advance.
> > > 
> > > Best regards,
> > > Tony
> > > _______________________________________________
> > > Nek5000-users mailing list
> > > Nek5000-users at lists.mcs.anl.gov
> > > 
> > 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>>
> > 
> > 
> > ------------------------------
> > 
> > Message: 3
> > Date: Mon, 27 Mar 2017 16:47:00 0700
> > From: nek5000-users at lists.mcs.anl.gov
> > To: nek5000-users at lists.mcs.anl.gov
> > Subject: Re: [Nek5000-users] Copy velocity slice from one boundary to
> > ??????? another
> > Message-ID:
> > ??????? <mailman.3216.1490608022.2967.nek5000-users at lists.mcs.anl.gov>
> > Content-Type: text/plain; charset="utf-8"
> > 
> > Thanks a lot for replying, your answer was very useful.
> > 
> > I look on multimesh.f file.
> > As i understood, i need set subroutine 'set_inflag' to look for 'P? ' bc.
> > After this i need to call 'get_values(field)' subroutine, which interpolate
> > and put the value in valint(ix,iy,iz,ie,ifld) array.
> > And then this array will be available in userbc in .usr file, to set it on
> > inflow boundary.
> > 
> > c-----------------------------------------------------------------------------------------------
> > 
> > Vatslav,
> > you will have to use the neknek script that allows you to exchange data
> > between two Nek5000 sessions that are run simultaneously. You should have a
> > look at the neknek examples to understand how to set up your usr file.
> > Some of the subroutines that will be useful to you are located in the
> > following link: 
> > http://www.mcs.anl.gov/research/projects/nek5/docs/ <http://www.mcs.anl.gov/research/projects/nek5/docs/> <http://www.mcs.anl.gov/research/projects/nek5/docs/ <http://www.mcs.anl.gov/research/projects/nek5/docs/>>
> > html/multimesh_8f_source.html
> > You will have to modify some of them to fit your needs since for example
> > the subroutine ?set_inflag? is written to look for ?in? boundary conditions
> > and replace them with ?v? ?. You will need a subroutine that looks for ?in?
> > and substitute it with either ?v? ? or ?P? ? depending on the which pipe
> > you are at.
> > Marco
> > 
> > Hi, Neks!
> > I have two pipes in my simulation. They are placed near each other on one
> > axis with empty space between.
> > One of them with periodic boundary conditions on z direction, another one -
> > inflow -> outflow.
> > How can I copy velocity slice from one of boundary on first pipe with
> > periodic bc to the inflow boundary on second pipe?
> > Regards, Vatslav
> > 
> > c-----------------------------------------------------------------------------------------------
> > 
> > Regards, Vatslav
> > -------------- next part --------------
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> > 
> > ------------------------------
> > 
> > Message: 4
> > Date: Mon, 27 Mar 2017 11:31:53 0200
> > From: nek5000-users at lists.mcs.anl.gov
> > To: nek5000-users at lists.mcs.anl.gov
> > Subject: [Nek5000-users] Robin Boundary Condition -- Navier's Slip
> > ??????? Length
> > Message-ID:
> > ??????? <mailman.3222.1490614366.2967.nek5000-users at lists.mcs.anl.gov>
> > Content-Type: text/plain; charset="utf-8"
> > 
> > Hi Neks,
> > I wish to simulate a transitional channel flow whose wall respect a
> > "slip-length" boundary condition, such as:
> > 
> > $ [u  \delta \frac{\partial u}{\partial n}]_{wall}=0$
> > 
> > Where \delta is the slip length
> > 
> > ^n
> > |??????? u?????????????? u
> > |????? |-->/???????? |----->/
> > |????? |?? /?????????? |????? /
> > |????? |? /??????????? |???? /
> > |????? | /???????????? |??? /
> > |___|/_______|?? /_____
> > ?????????????????????? | /? ^
> > ?????????????????????? |/?? v \delta
> > 
> > No-slip?????? Slip-length
> > 
> > (a better sketch can be found here:
> > http://www.nature.com/nmat/journal/v2/n4/fig_tab/nmat857_F1.html <http://www.nature.com/nmat/journal/v2/n4/fig_tab/nmat857_F1.html> <http://www.nature.com/nmat/journal/v2/n4/fig_tab/nmat857_F1.html <http://www.nature.com/nmat/journal/v2/n4/fig_tab/nmat857_F1.html>>
>  )
> > 
> >  <http://www.nature.com/nmat/journal/v2/n4/fig_tab/nmat857_F1.html <http://www.nature.com/nmat/journal/v2/n4/fig_tab/nmat857_F1.html>>
> > Figure 1 : Low-friction flows of liquid at nanopatterned ... <http://www.nature.com/nmat/journal/v2/n4/fig_tab/nmat857_F1.html <http://www.nature.com/nmat/journal/v2/n4/fig_tab/nmat857_F1.html>>www.nature.com
> > Nature Materials journal covers a range of topics within materials science, from materials engineering and structural materials (metals, alloys, ceramics, composites ...
> > 
> > 
> > 
> > I would like to know if this Robin boundary condition for velocity field is
> > already implemented in the current code.
> > 
> > Thank you
> > 
> > Ciccio
> > -------------- next part --------------
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> > 
> > ------------------------------
> > 
> > Message: 5
> > Date: Mon, 27 Mar 2017 13:56:02 0200
> > From: nek5000-users at lists.mcs.anl.gov
> > To: nek5000-users at lists.mcs.anl.gov
> > Subject: Re: [Nek5000-users] Interpolation between two meshes
> > Message-ID:
> > ??????? <mailman.3230.1490615875.2967.nek5000-users at lists.mcs.anl.gov>
> > Content-Type: text/plain; charset="windows-1252"; Format="flowed"
> > 
> > Hi Tony,
> > I have encountered the same issue with g2gi when interpolating very 
> > large meshes. I don't know what is causing the issue but a workaround is 
> > to reduce the polynomial order. You obviously loose accuracy by doing 
> > this, but I still find it better than starting from scratch with the new 
> > mesh. Hope this helps.
> > 
> > Best,
> > Mattias
> > 
> > 
> > On 03/27/2017 06:37 AM, nek5000-users at lists.mcs.anl.gov wrote:
> > > Dear Neks,
> > >
> > > I have been using 'g2gi' to do interpolation between different meshes. 
> > > Recently, I have noticed that when I interpolate between two big 
> > > meshes (say 300000 elements in each mesh), the interpolation hangs at 
> > > 'call findpts' and never moves on. I tried increasing number of 
> > > processors and changing 'lpart', but none of these worked.
> > >
> > > I'm wondering what could cause the interpolation to hang at 'findpts'. 
> > > Has anyone encountered similar issue?
> > >
> > > Hope anyone could give me some advice. Thank you very much in advance.
> > >
> > > Best regards,
> > > Tony
> > >
> > >
> > > _______________________________________________
> > > Nek5000-users mailing list
> > > Nek5000-users at lists.mcs.anl.gov
> > > 
> > 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>>
> > 
> > 
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> > 
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> > 
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