<div dir="ltr">SL,<div><br></div><div>Yes that will work, but you will need to modify "makefile.template" in the [..]/trunk/nek. There is a copy of the one I use in my github repo as well. You can use it as a starting point, or just copy it (provided it references all the files in the version of Nek you are using). My reference template file is based on having a directory [..]/trunk/nek/ps/ where PhilFunc.f is located (at least that's the way I do it). If you update your makefile.template correctly then it will be included as a file that is compiled and copied to your obj directory for each run. </div><div><br></div><div>Hope that helps,</div><div><br></div><div>Phil<br><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Mar 4, 2016 at 1:52 AM, <span dir="ltr"><<a href="mailto:nek5000-users-request@lists.mcs.anl.gov" target="_blank">nek5000-users-request@lists.mcs.anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Nek5000-users mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Re: Find out which cell a meshpoint belongs to<br>
(<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>)<br>
2. Re: extracting data in a smaller computational domain and in<br>
a plane (<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>)<br>
3. Re: extracting data in a smaller computational domain and in<br>
a plane (<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 3 Mar 2016 19:52:18 +0000<br>
From: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
To: "<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>"<br>
<<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>><br>
Subject: Re: [Nek5000-users] Find out which cell a meshpoint belongs<br>
to<br>
Message-ID:<br>
<<a href="mailto:mailman.16965.1457034739.24727.nek5000-users@lists.mcs.anl.gov">mailman.16965.1457034739.24727.nek5000-users@lists.mcs.anl.gov</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi Lee,<br>
<br>
Take a look at nr, ns, nt, nel return arguments of findpts_setup() in nek/jl/findpts.c<br>
<br>
An example of usage of this routine is in intpts_setup() and intpts() of nek/postpro.f<br>
<br>
Aleks<br>
________________________________<br>
From: <a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov">nek5000-users-bounces@lists.mcs.anl.gov</a> [<a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov">nek5000-users-bounces@lists.mcs.anl.gov</a>] on behalf of <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a> [<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>]<br>
Sent: Tuesday, February 02, 2016 4:31 AM<br>
To: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
Subject: [Nek5000-users] Find out which cell a meshpoint belongs to<br>
<br>
Hi neks,<br>
<br>
I'm just wondering if there's currently a function which acts on a meshpoint and returns the cell it is closest to.<br>
<br>
I have also tried doing this manually but I need to know the corners of each cell, if that is stored somewhere?<br>
<br>
Otherwise, is there a way of generating a list of every gridpoint so I can calculate the corners using brute force.<br>
<br>
Thanks,<br>
<br>
Lee<br>
<br>
<br>
<br>
<br>
On Tue, Feb 2, 2016 at 12:10 AM -0800, "<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>" <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><mailto:<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>>> wrote:<br>
<br>
Hi<br>
<br>
The adjoint implementation in nek assumes change of the direction of<br>
time evolution. The goal is to use the standard nek solver with minimal<br>
modifications (only advection terms have to be changed). You get these<br>
equations from you standard one by changing the time and pressure sign<br>
(t -> -t; p-> -p). This of course changes your time integration limits,<br>
but it shouldn't be a problem. So when you have your linear direct<br>
simulation, to turn it into dual one it is enough to include in your<br>
userchk include files ADJOINT and TSTEP, and for ISTEP.eq.0 set<br>
IFADJOINT to true. Something like:<br>
subroutine userchk<br>
<br>
include 'SIZE'<br>
include 'TSTEP' ! ISTEP<br>
include 'ADJOINT' ! IFADJ<br>
<br>
if(ISTEP.eq.0) ADJOINT=.TRUE.<br>
<br>
There is no need to modify ###.rea or ###.map files. The only problem<br>
are boundary conditions for open flows, as they would require<br>
non-homogeneous bc. In this case to avoid problems we usually use<br>
sufficiently large domain together with zero Dirichlet bc. The last<br>
issue is sufficient resolution for both direct and adjoin runs. I hope<br>
this gives you some idea about nek implementation.<br>
Regards<br>
Adam<br>
<br>
On 2016-02-01 22:17, <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a> wrote:<br>
> Hi Neks,<br>
><br>
> To my knowledge, Nek5000 is able to solve adjoint equations of the form:<br>
> $\partial u_a/\partial t + V.\nabla u_a - u_a.(\nabla V)^T + \nabla<br>
> \p_a + 1/Re \nabla^2 u_a=0$ and $\nabla.u_a=0$<br>
> where u_a and p_a are adjoint velocity and pressure. (Slightly<br>
> different formulation may be seen in literature).<br>
><br>
> Let's assume the forward problem is already solved so that $V$, i.e.<br>
> velocity, (and possibly $p$ as the pressure) is (are) already know.<br>
> Thus, the initial and boundary conditions for adjoint NS are also<br>
> known. How can we now solve the dual/adjoint NS problem with Nek5000?<br>
> Is there any example on how to modify .rea files? Specailly, the<br>
> "convection term of $V.\nabla u_a - u_a.(\nabla V)^T$ needs to be<br>
> modified compared to forward NS but am not sure how.<br>
> My search of mailing list entails some modifications in "perturb.f"<br>
> subroutine, but a little bit more clarification on that would be<br>
> really appreciated.<br>
><br>
> Yours,<br>
> Saleh<br>
> _______________________________________________<br>
> Nek5000-users mailing list<br>
> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" rel="noreferrer" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
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<br>
Message: 2<br>
Date: Fri, 04 Mar 2016 19:44:17 +1100<br>
From: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
To: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
Subject: Re: [Nek5000-users] extracting data in a smaller<br>
computational domain and in a plane<br>
Message-ID:<br>
<<a href="mailto:mailman.16998.1457081065.24727.nek5000-users@lists.mcs.anl.gov">mailman.16998.1457081065.24727.nek5000-users@lists.mcs.anl.gov</a>><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br>
<br>
Hi Phil,<br>
<br>
thank you very much. I sounds great!<br>
I suppose that I should include PhilFunc.f in trunk/tools and then<br>
compile it?<br>
<br>
Cheers<br>
SL<br>
<br>
El 04-03-2016 05:39, <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a> escribi?:<br>
> SL,<br>
><br>
> I have developed a set of routines for this express purpose which I am<br>
> happy to share. They are modified versions of the hpts routines that<br>
> dump out *fld files of subdomains at arbitrary resolutions.? The<br>
> routines (and a few others) can be found at the following link in the<br>
> file PhilFunc.f:<br>
><br>
> <a href="https://github.com/psakievich/Nek5000" rel="noreferrer" target="_blank">https://github.com/psakievich/Nek5000</a> [3]<br>
><br>
> To use you must define your own elements that follow the same format<br>
> as nek (npnts_in_x=npnts_in_y=npnts_in_z) and place them in an ascii<br>
> file named "<a href="http://ps_hpts.in" rel="noreferrer" target="_blank">ps_hpts.in</a> [4]".? Then in nek call ps_hpts("MYF") where<br>
> "MYF" is the three character prefix that will be added to the fld<br>
> files. ??<br>
><br>
> The format of "<a href="http://ps_hpts.in" rel="noreferrer" target="_blank">ps_hpts.in</a> [4]" is also a little different.? The first<br>
> line should be:<br>
> NPoints, NElm, NPX, NPY, NPZ<br>
><br>
> where NElm is the number of elements you are creating, and NPX is the<br>
> points in the x direction for the given element (akin to lx1), etc.<br>
> After that just specify the x,y,z coordinates like the normal <a href="http://hpts.in" rel="noreferrer" target="_blank">hpts.in</a><br>
> [2] files.?<br>
><br>
> A couple of additional points:<br>
><br>
> 1) You can crank up the resolution, and use uniform grid spacing to<br>
> get much better iso surfaces inside the subvolume you define. (Very<br>
> nice way to get high quality visualizations that harness the power of<br>
> SEM without interpolating the whole gird onto a finer grid and<br>
> creating huge data sets)?<br>
><br>
> 2) You need to ensure enough memory is allocated for the number of<br>
> hpts you are using through the SIZE file like normal.<br>
><br>
> 3) You can use a resolution much higher than the lx1 specified in<br>
> nek.? However, if you go too high then it may create a seg fault.? I<br>
> haven't been able to track down the exact buffer sizes, but they are<br>
> dependent on LELT, and LX1 in your size file.? For example, I was to<br>
> dump out elements of with 32 points in each direction when my lx1 was<br>
> set to 10 in the SIZE file (LELT around 1000 I think?). However, when<br>
> I went higher I received a seg fault.? I hope to track this down at<br>
> some point...<br>
><br>
> 4) ?If you want the elements to meet each other in VisIT you must<br>
> specify redundant boundaries between them (just like in nek) because I<br>
> am using the Nek5000 native output routines.? If the elements don't<br>
> have redundant boundaries then there will be gaps between them. I<br>
> would love to get around this but I haven't had time to write a<br>
> routine for a new output format.<br>
><br>
> 5) I have only tested these routines in 3D, and I make no promises<br>
> that they are bug free. Theoretically, they should work for 2D as<br>
> well, but I haven't tried that.<br>
><br>
> 6) DO NOT use the normal hpts/intpnts routines while using the ps_hpts<br>
> routines.? They use the same variables and it will create undefined<br>
> behavior.<br>
><br>
> Cheers,<br>
><br>
> Phil<br>
><br>
> On Thu, Mar 3, 2016 at 11:00 AM,<br>
> <<a href="mailto:nek5000-users-request@lists.mcs.anl.gov">nek5000-users-request@lists.mcs.anl.gov</a>> wrote:<br>
><br>
>> Send Nek5000-users mailing list submissions to<br>
>> ? ? ? ? <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
>><br>
>> To subscribe or unsubscribe via the World Wide Web, visit<br>
>> ? ? ? ?<br>
>> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" rel="noreferrer" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a> [1]<br>
>> or, via email, send a message with subject or body 'help' to<br>
>> ? ? ? ? <a href="mailto:nek5000-users-request@lists.mcs.anl.gov">nek5000-users-request@lists.mcs.anl.gov</a><br>
>><br>
>> You can reach the person managing the list at<br>
>> ? ? ? ? <a href="mailto:nek5000-users-owner@lists.mcs.anl.gov">nek5000-users-owner@lists.mcs.anl.gov</a><br>
>><br>
>> When replying, please edit your Subject line so it is more specific<br>
>> than "Re: Contents of Nek5000-users digest..."<br>
>><br>
>> Today's Topics:<br>
>><br>
>> ? ?1. extracting data in a smaller computational domain and in a<br>
>> ? ? ? plane (<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>)<br>
>> ? ?2. Re: extracting data in a smaller computational domain? ?<br>
>> ?and in<br>
>> ? ? ? a plane (<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>)<br>
>> ? ?3. Re: extracting data in a smaller computational domain? ?<br>
>> ?and in<br>
>> ? ? ? a plane (<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>)<br>
>><br>
>><br>
> ----------------------------------------------------------------------<br>
>><br>
>> Message: 1<br>
>> Date: Thu, 03 Mar 2016 04:29:05 +0100<br>
>> From: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
>> To: Nek5000 Users <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>><br>
>> Subject: [Nek5000-users] extracting data in a smaller computational<br>
>> ? ? ? ? domain? and in a plane<br>
>> Message-ID:<br>
>> ? ? ? ?<br>
>> <<a href="mailto:mailman.16887.1456975753.24727.nek5000-users@lists.mcs.anl.gov">mailman.16887.1456975753.24727.nek5000-users@lists.mcs.anl.gov</a>><br>
>> Content-Type: text/plain; charset=UTF-8; format=flowed<br>
>><br>
>> Hi Neks,<br>
>><br>
>> I am trying to do some postprocessing of the Nek5000 results.<br>
>><br>
>> I have a 3D domain, however I will be interested in taking a<br>
>> smaller<br>
>> piece of this domain. The idea is to generate a data base of<br>
>> snapshots<br>
>> containing this smaller part of the domain. For example,<br>
>><br>
>> if my computational domain is x in (-15, 20), y in (-20, 20), z<br>
>> in(0,2)<br>
>><br>
>> I just want to take a data set of snapshots containing the velocity<br>
>> fields in the locations:<br>
>> ? ?x in (-2, 5), y in (-5, 5), z in(0,2)<br>
>><br>
>> Is there any way to extract this data?<br>
>><br>
>> In addition, is there any way to extract the same data but in a 2d<br>
>> plane? I mean:<br>
>> ? ?x in (-2, 5), y in (-5, 5), z=1<br>
>><br>
>> Thank you in advance.<br>
>> Cheers<br>
>> SL<br>
>><br>
>> ------------------------------<br>
>><br>
>> Message: 2<br>
>> Date: Thu, 3 Mar 2016 03:58:48 +0000<br>
>> From: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
>> To: "<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>"<br>
>> ? ? ? ? <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>><br>
>> Subject: Re: [Nek5000-users] extracting data in a smaller<br>
>> ? ? ? ? computational domain? ? and in a plane<br>
>> Message-ID:<br>
>> ? ? ? ?<br>
>> <<a href="mailto:mailman.16888.1456977536.24727.nek5000-users@lists.mcs.anl.gov">mailman.16888.1456977536.24727.nek5000-users@lists.mcs.anl.gov</a>><br>
>> Content-Type: text/plain; charset="us-ascii"<br>
>><br>
>> Hi SL,<br>
>><br>
>> The easiest way for a profile is to do the Lineout in VisIt and<br>
>> choose 'curve' format in 'Set Save Options'.<br>
>><br>
>> More accurate way is to setup history/coordinate points in <a href="http://hpts.in" rel="noreferrer" target="_blank">hpts.in</a><br>
>> [2] file and call hpts routine from userchk which will also work for<br>
>> 2D plane points.<br>
>><br>
>> Aleks<br>
>> ________________________________________<br>
>> From: <a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov">nek5000-users-bounces@lists.mcs.anl.gov</a><br>
>> [<a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov">nek5000-users-bounces@lists.mcs.anl.gov</a>] on behalf of<br>
>> <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a> [<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>]<br>
>> Sent: Wednesday, March 02, 2016 9:29 PM<br>
>> To: Nek5000 Users<br>
>> Subject: [Nek5000-users] extracting data in a smaller computational<br>
>> domain? ? ? and in a plane<br>
>><br>
>> Hi Neks,<br>
>><br>
>> I am trying to do some postprocessing of the Nek5000 results.<br>
>><br>
>> I have a 3D domain, however I will be interested in taking a<br>
>> smaller<br>
>> piece of this domain. The idea is to generate a data base of<br>
>> snapshots<br>
>> containing this smaller part of the domain. For example,<br>
>><br>
>> if my computational domain is x in (-15, 20), y in (-20, 20), z<br>
>> in(0,2)<br>
>><br>
>> I just want to take a data set of snapshots containing the velocity<br>
>> fields in the locations:<br>
>> ? ?x in (-2, 5), y in (-5, 5), z in(0,2)<br>
>><br>
>> Is there any way to extract this data?<br>
>><br>
>> In addition, is there any way to extract the same data but in a 2d<br>
>> plane? I mean:<br>
>> ? ?x in (-2, 5), y in (-5, 5), z=1<br>
>><br>
>> Thank you in advance.<br>
>> Cheers<br>
>> SL<br>
>> _______________________________________________<br>
>> Nek5000-users mailing list<br>
>> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
>> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" rel="noreferrer" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a> [1]<br>
>><br>
>> ------------------------------<br>
>><br>
>> Message: 3<br>
>> Date: Thu, 03 Mar 2016 05:26:16 +0100<br>
>> From: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
>> To: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
>> Subject: Re: [Nek5000-users] extracting data in a smaller<br>
>> ? ? ? ? computational domain? ? and in a plane<br>
>> Message-ID:<br>
>> ? ? ? ?<br>
>> <<a href="mailto:mailman.16889.1456979182.24727.nek5000-users@lists.mcs.anl.gov">mailman.16889.1456979182.24727.nek5000-users@lists.mcs.anl.gov</a>><br>
>> Content-Type: text/plain; charset=UTF-8; format=flowed<br>
>><br>
>> Thank you Aleks,<br>
>><br>
>> that is also very useful. However, it would be nice if I could<br>
>> extract a<br>
>> smaller 3d domain from my big computational domain. The idea is to<br>
>> work<br>
>> with the entire 3d small computational domain...<br>
>><br>
>> I need to do the same for several time steps (velocity snapshots,<br>
>> changing in time), so if it would be any way to do it directly from<br>
>> Nek5000 it would make the things much easier...<br>
>><br>
>> Thanks again.<br>
>> SL<br>
>><br>
>> El 03-03-2016 04:58, <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a> escribi?:<br>
>>> Hi SL,<br>
>>><br>
>>> The easiest way for a profile is to do the Lineout in VisIt and<br>
>> choose<br>
>>> 'curve' format in 'Set Save Options'.<br>
>>><br>
>>> More accurate way is to setup history/coordinate points in<br>
>> <a href="http://hpts.in" rel="noreferrer" target="_blank">hpts.in</a> [2]<br>
>>> file and call hpts routine from userchk which will also work for<br>
>> 2D<br>
>>> plane points.<br>
>>><br>
>>> Aleks<br>
>>> ________________________________________<br>
>>> From: <a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov">nek5000-users-bounces@lists.mcs.anl.gov</a><br>
>>> [<a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov">nek5000-users-bounces@lists.mcs.anl.gov</a>] on behalf of<br>
>>> <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a> [<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>]<br>
>>> Sent: Wednesday, March 02, 2016 9:29 PM<br>
>>> To: Nek5000 Users<br>
>>> Subject: [Nek5000-users] extracting data in a smaller<br>
>> computational<br>
>>> domain? ? ? and in a plane<br>
>>><br>
>>> Hi Neks,<br>
>>><br>
>>> I am trying to do some postprocessing of the Nek5000 results.<br>
>>><br>
>>> I have a 3D domain, however I will be interested in taking a<br>
>> smaller<br>
>>> piece of this domain. The idea is to generate a data base of<br>
>> snapshots<br>
>>> containing this smaller part of the domain. For example,<br>
>>><br>
>>> if my computational domain is x in (-15, 20), y in (-20, 20), z<br>
>> in(0,2)<br>
>>><br>
>>> I just want to take a data set of snapshots containing the<br>
>> velocity<br>
>>> fields in the locations:<br>
>>> ? ? x in (-2, 5), y in (-5, 5), z in(0,2)<br>
>>><br>
>>> Is there any way to extract this data?<br>
>>><br>
>>> In addition, is there any way to extract the same data but in a<br>
>> 2d<br>
>>> plane? I mean:<br>
>>> ? ? x in (-2, 5), y in (-5, 5), z=1<br>
>>><br>
>>> Thank you in advance.<br>
>>> Cheers<br>
>>> SL<br>
>>> _______________________________________________<br>
>>> Nek5000-users mailing list<br>
>>> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
>>> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" rel="noreferrer" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a> [1]<br>
>>> _______________________________________________<br>
>>> Nek5000-users mailing list<br>
>>> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
>>> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" rel="noreferrer" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a> [1]<br>
>><br>
>> ------------------------------<br>
>><br>
>> _______________________________________________<br>
>> Nek5000-users mailing list<br>
>> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
>> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" rel="noreferrer" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a> [1]<br>
>><br>
>> End of Nek5000-users Digest, Vol 85, Issue 5<br>
>> ********************************************<br>
><br>
> --<br>
><br>
> Phil Sakievich<br>
><br>
> PhD Candidate - Mechanical Engineering<br>
> Arizona State University - Ira A. Fulton School for Engineering of<br>
> Matter Transport and Energy<br>
> Tempe, Arizona<br>
><br>
> Links:<br>
> ------<br>
> [1] <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" rel="noreferrer" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
> [2] <a href="http://hpts.in" rel="noreferrer" target="_blank">http://hpts.in</a><br>
> [3] <a href="https://github.com/psakievich/Nek5000" rel="noreferrer" target="_blank">https://github.com/psakievich/Nek5000</a><br>
> [4] <a href="http://ps_hpts.in" rel="noreferrer" target="_blank">http://ps_hpts.in</a><br>
><br>
> _______________________________________________<br>
> Nek5000-users mailing list<br>
> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" rel="noreferrer" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Fri, 04 Mar 2016 09:52:36 +0100<br>
From: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
To: <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>><br>
Subject: Re: [Nek5000-users] extracting data in a smaller<br>
computational domain and in a plane<br>
Message-ID:<br>
<<a href="mailto:mailman.16999.1457081578.24727.nek5000-users@lists.mcs.anl.gov">mailman.16999.1457081578.24727.nek5000-users@lists.mcs.anl.gov</a>><br>
Content-Type: text/plain; charset="ISO-8859-1"<br>
<br>
The build-in function g2gi() does something similar and works with big<br>
data sets.<br>
<br>
Cheers,<br>
Stefan<br>
<br>
<br>
Am 3/4/16, 9:44 AM schrieb "<a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov">nek5000-users-bounces@lists.mcs.anl.gov</a> on<br>
behalf of <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>" unter<br>
<<a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov">nek5000-users-bounces@lists.mcs.anl.gov</a> on behalf of<br>
<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>>:<br>
<br>
>Hi Phil,<br>
><br>
>thank you very much. I sounds great!<br>
>I suppose that I should include PhilFunc.f in trunk/tools and then<br>
>compile it?<br>
><br>
>Cheers<br>
>SL<br>
><br>
>El 04-03-2016 05:39, <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a> escribi?:<br>
>> SL,<br>
>><br>
>> I have developed a set of routines for this express purpose which I am<br>
>> happy to share. They are modified versions of the hpts routines that<br>
>> dump out *fld files of subdomains at arbitrary resolutions. The<br>
>> routines (and a few others) can be found at the following link in the<br>
>> file PhilFunc.f:<br>
>><br>
>> <a href="https://github.com/psakievich/Nek5000" rel="noreferrer" target="_blank">https://github.com/psakievich/Nek5000</a> [3]<br>
>><br>
>> To use you must define your own elements that follow the same format<br>
>> as nek (npnts_in_x=npnts_in_y=npnts_in_z) and place them in an ascii<br>
>> file named "<a href="http://ps_hpts.in" rel="noreferrer" target="_blank">ps_hpts.in</a> [4]". Then in nek call ps_hpts("MYF") where<br>
>> "MYF" is the three character prefix that will be added to the fld<br>
>> files.<br>
>><br>
>> The format of "<a href="http://ps_hpts.in" rel="noreferrer" target="_blank">ps_hpts.in</a> [4]" is also a little different. The first<br>
>> line should be:<br>
>> NPoints, NElm, NPX, NPY, NPZ<br>
>><br>
>> where NElm is the number of elements you are creating, and NPX is the<br>
>> points in the x direction for the given element (akin to lx1), etc.<br>
>> After that just specify the x,y,z coordinates like the normal <a href="http://hpts.in" rel="noreferrer" target="_blank">hpts.in</a><br>
>> [2] files.<br>
>><br>
>> A couple of additional points:<br>
>><br>
>> 1) You can crank up the resolution, and use uniform grid spacing to<br>
>> get much better iso surfaces inside the subvolume you define. (Very<br>
>> nice way to get high quality visualizations that harness the power of<br>
>> SEM without interpolating the whole gird onto a finer grid and<br>
>> creating huge data sets)<br>
>><br>
>> 2) You need to ensure enough memory is allocated for the number of<br>
>> hpts you are using through the SIZE file like normal.<br>
>><br>
>> 3) You can use a resolution much higher than the lx1 specified in<br>
>> nek. However, if you go too high then it may create a seg fault. I<br>
>> haven't been able to track down the exact buffer sizes, but they are<br>
>> dependent on LELT, and LX1 in your size file. For example, I was to<br>
>> dump out elements of with 32 points in each direction when my lx1 was<br>
>> set to 10 in the SIZE file (LELT around 1000 I think?). However, when<br>
>> I went higher I received a seg fault. I hope to track this down at<br>
>> some point...<br>
>><br>
>> 4) If you want the elements to meet each other in VisIT you must<br>
>> specify redundant boundaries between them (just like in nek) because I<br>
>> am using the Nek5000 native output routines. If the elements don't<br>
>> have redundant boundaries then there will be gaps between them. I<br>
>> would love to get around this but I haven't had time to write a<br>
>> routine for a new output format.<br>
>><br>
>> 5) I have only tested these routines in 3D, and I make no promises<br>
>> that they are bug free. Theoretically, they should work for 2D as<br>
>> well, but I haven't tried that.<br>
>><br>
>> 6) DO NOT use the normal hpts/intpnts routines while using the ps_hpts<br>
>> routines. They use the same variables and it will create undefined<br>
>> behavior.<br>
>><br>
>> Cheers,<br>
>><br>
>> Phil<br>
>><br>
>> On Thu, Mar 3, 2016 at 11:00 AM,<br>
>> <<a href="mailto:nek5000-users-request@lists.mcs.anl.gov">nek5000-users-request@lists.mcs.anl.gov</a>> wrote:<br>
>><br>
>>> Send Nek5000-users mailing list submissions to<br>
>>> <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
>>><br>
>>> To subscribe or unsubscribe via the World Wide Web, visit<br>
>>><br>
>>> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" rel="noreferrer" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a> [1]<br>
>>> or, via email, send a message with subject or body 'help' to<br>
>>> <a href="mailto:nek5000-users-request@lists.mcs.anl.gov">nek5000-users-request@lists.mcs.anl.gov</a><br>
>>><br>
>>> You can reach the person managing the list at<br>
>>> <a href="mailto:nek5000-users-owner@lists.mcs.anl.gov">nek5000-users-owner@lists.mcs.anl.gov</a><br>
>>><br>
>>> When replying, please edit your Subject line so it is more specific<br>
>>> than "Re: Contents of Nek5000-users digest..."<br>
>>><br>
>>> Today's Topics:<br>
>>><br>
>>> 1. extracting data in a smaller computational domain and in a<br>
>>> plane (<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>)<br>
>>> 2. Re: extracting data in a smaller computational domain<br>
>>> and in<br>
>>> a plane (<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>)<br>
>>> 3. Re: extracting data in a smaller computational domain<br>
>>> and in<br>
>>> a plane (<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>)<br>
>>><br>
>>><br>
>> ----------------------------------------------------------------------<br>
>>><br>
>>> Message: 1<br>
>>> Date: Thu, 03 Mar 2016 04:29:05 +0100<br>
>>> From: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
>>> To: Nek5000 Users <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>><br>
>>> Subject: [Nek5000-users] extracting data in a smaller computational<br>
>>> domain and in a plane<br>
>>> Message-ID:<br>
>>><br>
>>> <<a href="mailto:mailman.16887.1456975753.24727.nek5000-users@lists.mcs.anl.gov">mailman.16887.1456975753.24727.nek5000-users@lists.mcs.anl.gov</a>><br>
>>> Content-Type: text/plain; charset=UTF-8; format=flowed<br>
>>><br>
>>> Hi Neks,<br>
>>><br>
>>> I am trying to do some postprocessing of the Nek5000 results.<br>
>>><br>
>>> I have a 3D domain, however I will be interested in taking a<br>
>>> smaller<br>
>>> piece of this domain. The idea is to generate a data base of<br>
>>> snapshots<br>
>>> containing this smaller part of the domain. For example,<br>
>>><br>
>>> if my computational domain is x in (-15, 20), y in (-20, 20), z<br>
>>> in(0,2)<br>
>>><br>
>>> I just want to take a data set of snapshots containing the velocity<br>
>>> fields in the locations:<br>
>>> x in (-2, 5), y in (-5, 5), z in(0,2)<br>
>>><br>
>>> Is there any way to extract this data?<br>
>>><br>
>>> In addition, is there any way to extract the same data but in a 2d<br>
>>> plane? I mean:<br>
>>> x in (-2, 5), y in (-5, 5), z=1<br>
>>><br>
>>> Thank you in advance.<br>
>>> Cheers<br>
>>> SL<br>
>>><br>
>>> ------------------------------<br>
>>><br>
>>> Message: 2<br>
>>> Date: Thu, 3 Mar 2016 03:58:48 +0000<br>
>>> From: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
>>> To: "<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>"<br>
>>> <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>><br>
>>> Subject: Re: [Nek5000-users] extracting data in a smaller<br>
>>> computational domain and in a plane<br>
>>> Message-ID:<br>
>>><br>
>>> <<a href="mailto:mailman.16888.1456977536.24727.nek5000-users@lists.mcs.anl.gov">mailman.16888.1456977536.24727.nek5000-users@lists.mcs.anl.gov</a>><br>
>>> Content-Type: text/plain; charset="us-ascii"<br>
>>><br>
>>> Hi SL,<br>
>>><br>
>>> The easiest way for a profile is to do the Lineout in VisIt and<br>
>>> choose 'curve' format in 'Set Save Options'.<br>
>>><br>
>>> More accurate way is to setup history/coordinate points in <a href="http://hpts.in" rel="noreferrer" target="_blank">hpts.in</a><br>
>>> [2] file and call hpts routine from userchk which will also work for<br>
>>> 2D plane points.<br>
>>><br>
>>> Aleks<br>
>>> ________________________________________<br>
>>> From: <a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov">nek5000-users-bounces@lists.mcs.anl.gov</a><br>
>>> [<a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov">nek5000-users-bounces@lists.mcs.anl.gov</a>] on behalf of<br>
>>> <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a> [<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>]<br>
>>> Sent: Wednesday, March 02, 2016 9:29 PM<br>
>>> To: Nek5000 Users<br>
>>> Subject: [Nek5000-users] extracting data in a smaller computational<br>
>>> domain and in a plane<br>
>>><br>
>>> Hi Neks,<br>
>>><br>
>>> I am trying to do some postprocessing of the Nek5000 results.<br>
>>><br>
>>> I have a 3D domain, however I will be interested in taking a<br>
>>> smaller<br>
>>> piece of this domain. The idea is to generate a data base of<br>
>>> snapshots<br>
>>> containing this smaller part of the domain. For example,<br>
>>><br>
>>> if my computational domain is x in (-15, 20), y in (-20, 20), z<br>
>>> in(0,2)<br>
>>><br>
>>> I just want to take a data set of snapshots containing the velocity<br>
>>> fields in the locations:<br>
>>> x in (-2, 5), y in (-5, 5), z in(0,2)<br>
>>><br>
>>> Is there any way to extract this data?<br>
>>><br>
>>> In addition, is there any way to extract the same data but in a 2d<br>
>>> plane? I mean:<br>
>>> x in (-2, 5), y in (-5, 5), z=1<br>
>>><br>
>>> Thank you in advance.<br>
>>> Cheers<br>
>>> SL<br>
>>> _______________________________________________<br>
>>> Nek5000-users mailing list<br>
>>> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
>>> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" rel="noreferrer" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a> [1]<br>
>>><br>
>>> ------------------------------<br>
>>><br>
>>> Message: 3<br>
>>> Date: Thu, 03 Mar 2016 05:26:16 +0100<br>
>>> From: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
>>> To: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
>>> Subject: Re: [Nek5000-users] extracting data in a smaller<br>
>>> computational domain and in a plane<br>
>>> Message-ID:<br>
>>><br>
>>> <<a href="mailto:mailman.16889.1456979182.24727.nek5000-users@lists.mcs.anl.gov">mailman.16889.1456979182.24727.nek5000-users@lists.mcs.anl.gov</a>><br>
>>> Content-Type: text/plain; charset=UTF-8; format=flowed<br>
>>><br>
>>> Thank you Aleks,<br>
>>><br>
>>> that is also very useful. However, it would be nice if I could<br>
>>> extract a<br>
>>> smaller 3d domain from my big computational domain. The idea is to<br>
>>> work<br>
>>> with the entire 3d small computational domain...<br>
>>><br>
>>> I need to do the same for several time steps (velocity snapshots,<br>
>>> changing in time), so if it would be any way to do it directly from<br>
>>> Nek5000 it would make the things much easier...<br>
>>><br>
>>> Thanks again.<br>
>>> SL<br>
>>><br>
>>> El 03-03-2016 04:58, <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a> escribi?:<br>
>>>> Hi SL,<br>
>>>><br>
>>>> The easiest way for a profile is to do the Lineout in VisIt and<br>
>>> choose<br>
>>>> 'curve' format in 'Set Save Options'.<br>
>>>><br>
>>>> More accurate way is to setup history/coordinate points in<br>
>>> <a href="http://hpts.in" rel="noreferrer" target="_blank">hpts.in</a> [2]<br>
>>>> file and call hpts routine from userchk which will also work for<br>
>>> 2D<br>
>>>> plane points.<br>
>>>><br>
>>>> Aleks<br>
>>>> ________________________________________<br>
>>>> From: <a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov">nek5000-users-bounces@lists.mcs.anl.gov</a><br>
>>>> [<a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov">nek5000-users-bounces@lists.mcs.anl.gov</a>] on behalf of<br>
>>>> <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a> [<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>]<br>
>>>> Sent: Wednesday, March 02, 2016 9:29 PM<br>
>>>> To: Nek5000 Users<br>
>>>> Subject: [Nek5000-users] extracting data in a smaller<br>
>>> computational<br>
>>>> domain and in a plane<br>
>>>><br>
>>>> Hi Neks,<br>
>>>><br>
>>>> I am trying to do some postprocessing of the Nek5000 results.<br>
>>>><br>
>>>> I have a 3D domain, however I will be interested in taking a<br>
>>> smaller<br>
>>>> piece of this domain. The idea is to generate a data base of<br>
>>> snapshots<br>
>>>> containing this smaller part of the domain. For example,<br>
>>>><br>
>>>> if my computational domain is x in (-15, 20), y in (-20, 20), z<br>
>>> in(0,2)<br>
>>>><br>
>>>> I just want to take a data set of snapshots containing the<br>
>>> velocity<br>
>>>> fields in the locations:<br>
>>>> x in (-2, 5), y in (-5, 5), z in(0,2)<br>
>>>><br>
>>>> Is there any way to extract this data?<br>
>>>><br>
>>>> In addition, is there any way to extract the same data but in a<br>
>>> 2d<br>
>>>> plane? I mean:<br>
>>>> x in (-2, 5), y in (-5, 5), z=1<br>
>>>><br>
>>>> Thank you in advance.<br>
>>>> Cheers<br>
>>>> SL<br>
>>>> _______________________________________________<br>
>>>> Nek5000-users mailing list<br>
>>>> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
>>>> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" rel="noreferrer" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a> [1]<br>
>>>> _______________________________________________<br>
>>>> Nek5000-users mailing list<br>
>>>> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
>>>> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" rel="noreferrer" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a> [1]<br>
>>><br>
>>> ------------------------------<br>
>>><br>
>>> _______________________________________________<br>
>>> Nek5000-users mailing list<br>
>>> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
>>> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" rel="noreferrer" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a> [1]<br>
>>><br>
>>> End of Nek5000-users Digest, Vol 85, Issue 5<br>
>>> ********************************************<br>
>><br>
>> --<br>
>><br>
>> Phil Sakievich<br>
>><br>
>> PhD Candidate - Mechanical Engineering<br>
>> Arizona State University - Ira A. Fulton School for Engineering of<br>
>> Matter Transport and Energy<br>
>> Tempe, Arizona<br>
>><br>
>> Links:<br>
>> ------<br>
>> [1] <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" rel="noreferrer" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
>> [2] <a href="http://hpts.in" rel="noreferrer" target="_blank">http://hpts.in</a><br>
>> [3] <a href="https://github.com/psakievich/Nek5000" rel="noreferrer" target="_blank">https://github.com/psakievich/Nek5000</a><br>
>> [4] <a href="http://ps_hpts.in" rel="noreferrer" target="_blank">http://ps_hpts.in</a><br>
>><br>
>> _______________________________________________<br>
>> Nek5000-users mailing list<br>
>> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
>> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" rel="noreferrer" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
><br>
><br>
>_______________________________________________<br>
>Nek5000-users mailing list<br>
><a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
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End of Nek5000-users Digest, Vol 85, Issue 7<br>
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