[Nek5000-users] extracting data in a smaller computational domain and in a plane

Fri Mar 4 02:44:17 CST 2016

Hi Phil,

thank you very much. I sounds great!
I suppose that I should include PhilFunc.f in trunk/tools and then 
compile it?

Cheers
SL

El 04-03-2016 05:39, nek5000-users at lists.mcs.anl.gov escribió:
> SL,
> 
> I have developed a set of routines for this express purpose which I am
> happy to share. They are modified versions of the hpts routines that
> dump out *fld files of subdomains at arbitrary resolutions.  The
> routines (and a few others) can be found at the following link in the
> file PhilFunc.f:
> 
> https://github.com/psakievich/Nek5000 [3]
> 
> To use you must define your own elements that follow the same format
> as nek (npnts_in_x=npnts_in_y=npnts_in_z) and place them in an ascii
> file named "ps_hpts.in [4]".  Then in nek call ps_hpts("MYF") where
> "MYF" is the three character prefix that will be added to the fld
> files.   
> 
> The format of "ps_hpts.in [4]" is also a little different.  The first
> line should be:
> NPoints, NElm, NPX, NPY, NPZ
> 
> where NElm is the number of elements you are creating, and NPX is the
> points in the x direction for the given element (akin to lx1), etc.
> After that just specify the x,y,z coordinates like the normal hpts.in
> [2] files. 
> 
> A couple of additional points:
> 
> 1) You can crank up the resolution, and use uniform grid spacing to
> get much better iso surfaces inside the subvolume you define. (Very
> nice way to get high quality visualizations that harness the power of
> SEM without interpolating the whole gird onto a finer grid and
> creating huge data sets) 
> 
> 2) You need to ensure enough memory is allocated for the number of
> hpts you are using through the SIZE file like normal.
> 
> 3) You can use a resolution much higher than the lx1 specified in
> nek.  However, if you go too high then it may create a seg fault.  I
> haven't been able to track down the exact buffer sizes, but they are
> dependent on LELT, and LX1 in your size file.  For example, I was to
> dump out elements of with 32 points in each direction when my lx1 was
> set to 10 in the SIZE file (LELT around 1000 I think?). However, when
> I went higher I received a seg fault.  I hope to track this down at
> some point...
> 
> 4)  If you want the elements to meet each other in VisIT you must
> specify redundant boundaries between them (just like in nek) because I
> am using the Nek5000 native output routines.  If the elements don't
> have redundant boundaries then there will be gaps between them. I
> would love to get around this but I haven't had time to write a
> routine for a new output format.
> 
> 5) I have only tested these routines in 3D, and I make no promises
> that they are bug free. Theoretically, they should work for 2D as
> well, but I haven't tried that.
> 
> 6) DO NOT use the normal hpts/intpnts routines while using the ps_hpts
> routines.  They use the same variables and it will create undefined
> behavior.
> 
> Cheers,
> 
> Phil
> 
> On Thu, Mar 3, 2016 at 11:00 AM,
> <nek5000-users-request at lists.mcs.anl.gov> wrote:
> 
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>> Today's Topics:
>> 
>>    1. extracting data in a smaller computational domain and in a
>>       plane (nek5000-users at lists.mcs.anl.gov)
>>    2. Re: extracting data in a smaller computational domain   
>>  and in
>>       a plane (nek5000-users at lists.mcs.anl.gov)
>>    3. Re: extracting data in a smaller computational domain   
>>  and in
>>       a plane (nek5000-users at lists.mcs.anl.gov)
>> 
>> 
> ----------------------------------------------------------------------
>> 
>> Message: 1
>> Date: Thu, 03 Mar 2016 04:29:05 +0100
>> From: nek5000-users at lists.mcs.anl.gov
>> To: Nek5000 Users <nek5000-users at lists.mcs.anl.gov>
>> Subject: [Nek5000-users] extracting data in a smaller computational
>>         domain  and in a plane
>> Message-ID:
>>        
>> <mailman.16887.1456975753.24727.nek5000-users at lists.mcs.anl.gov>
>> Content-Type: text/plain; charset=UTF-8; format=flowed
>> 
>> Hi Neks,
>> 
>> I am trying to do some postprocessing of the Nek5000 results.
>> 
>> I have a 3D domain, however I will be interested in taking a
>> smaller
>> piece of this domain. The idea is to generate a data base of
>> snapshots
>> containing this smaller part of the domain. For example,
>> 
>> if my computational domain is x in (-15, 20), y in (-20, 20), z
>> in(0,2)
>> 
>> I just want to take a data set of snapshots containing the velocity
>> fields in the locations:
>>    x in (-2, 5), y in (-5, 5), z in(0,2)
>> 
>> Is there any way to extract this data?
>> 
>> In addition, is there any way to extract the same data but in a 2d
>> plane? I mean:
>>    x in (-2, 5), y in (-5, 5), z=1
>> 
>> Thank you in advance.
>> Cheers
>> SL
>> 
>> ------------------------------
>> 
>> Message: 2
>> Date: Thu, 3 Mar 2016 03:58:48 +0000
>> 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] extracting data in a smaller
>>         computational domain    and in a plane
>> Message-ID:
>>        
>> <mailman.16888.1456977536.24727.nek5000-users at lists.mcs.anl.gov>
>> Content-Type: text/plain; charset="us-ascii"
>> 
>> Hi SL,
>> 
>> The easiest way for a profile is to do the Lineout in VisIt and
>> choose 'curve' format in 'Set Save Options'.
>> 
>> More accurate way is to setup history/coordinate points in hpts.in
>> [2] file and call hpts routine from userchk which will also work for
>> 2D plane points.
>> 
>> Aleks
>> ________________________________________
>> From: nek5000-users-bounces at lists.mcs.anl.gov
>> [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of
>> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov]
>> Sent: Wednesday, March 02, 2016 9:29 PM
>> To: Nek5000 Users
>> Subject: [Nek5000-users] extracting data in a smaller computational
>> domain      and in a plane
>> 
>> Hi Neks,
>> 
>> I am trying to do some postprocessing of the Nek5000 results.
>> 
>> I have a 3D domain, however I will be interested in taking a
>> smaller
>> piece of this domain. The idea is to generate a data base of
>> snapshots
>> containing this smaller part of the domain. For example,
>> 
>> if my computational domain is x in (-15, 20), y in (-20, 20), z
>> in(0,2)
>> 
>> I just want to take a data set of snapshots containing the velocity
>> fields in the locations:
>>    x in (-2, 5), y in (-5, 5), z in(0,2)
>> 
>> Is there any way to extract this data?
>> 
>> In addition, is there any way to extract the same data but in a 2d
>> plane? I mean:
>>    x in (-2, 5), y in (-5, 5), z=1
>> 
>> Thank you in advance.
>> Cheers
>> SL
>> _______________________________________________
>> Nek5000-users mailing list
>> Nek5000-users at lists.mcs.anl.gov
>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1]
>> 
>> ------------------------------
>> 
>> Message: 3
>> Date: Thu, 03 Mar 2016 05:26:16 +0100
>> From: nek5000-users at lists.mcs.anl.gov
>> To: nek5000-users at lists.mcs.anl.gov
>> Subject: Re: [Nek5000-users] extracting data in a smaller
>>         computational domain    and in a plane
>> Message-ID:
>>        
>> <mailman.16889.1456979182.24727.nek5000-users at lists.mcs.anl.gov>
>> Content-Type: text/plain; charset=UTF-8; format=flowed
>> 
>> Thank you Aleks,
>> 
>> that is also very useful. However, it would be nice if I could
>> extract a
>> smaller 3d domain from my big computational domain. The idea is to
>> work
>> with the entire 3d small computational domain...
>> 
>> I need to do the same for several time steps (velocity snapshots,
>> changing in time), so if it would be any way to do it directly from
>> Nek5000 it would make the things much easier...
>> 
>> Thanks again.
>> SL
>> 
>> El 03-03-2016 04:58, nek5000-users at lists.mcs.anl.gov escribi?:
>>> Hi SL,
>>> 
>>> The easiest way for a profile is to do the Lineout in VisIt and
>> choose
>>> 'curve' format in 'Set Save Options'.
>>> 
>>> More accurate way is to setup history/coordinate points in
>> hpts.in [2]
>>> file and call hpts routine from userchk which will also work for
>> 2D
>>> plane points.
>>> 
>>> Aleks
>>> ________________________________________
>>> From: nek5000-users-bounces at lists.mcs.anl.gov
>>> [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of
>>> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov]
>>> Sent: Wednesday, March 02, 2016 9:29 PM
>>> To: Nek5000 Users
>>> Subject: [Nek5000-users] extracting data in a smaller
>> computational
>>> domain      and in a plane
>>> 
>>> Hi Neks,
>>> 
>>> I am trying to do some postprocessing of the Nek5000 results.
>>> 
>>> I have a 3D domain, however I will be interested in taking a
>> smaller
>>> piece of this domain. The idea is to generate a data base of
>> snapshots
>>> containing this smaller part of the domain. For example,
>>> 
>>> if my computational domain is x in (-15, 20), y in (-20, 20), z
>> in(0,2)
>>> 
>>> I just want to take a data set of snapshots containing the
>> velocity
>>> fields in the locations:
>>>     x in (-2, 5), y in (-5, 5), z in(0,2)
>>> 
>>> Is there any way to extract this data?
>>> 
>>> In addition, is there any way to extract the same data but in a
>> 2d
>>> plane? I mean:
>>>     x in (-2, 5), y in (-5, 5), z=1
>>> 
>>> Thank you in advance.
>>> Cheers
>>> SL
>>> _______________________________________________
>>> Nek5000-users mailing list
>>> Nek5000-users at lists.mcs.anl.gov
>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1]
>>> _______________________________________________
>>> Nek5000-users mailing list
>>> Nek5000-users at lists.mcs.anl.gov
>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users [1]
>> 
>> ------------------------------
>> 
>> _______________________________________________
>> Nek5000-users mailing list
>> Nek5000-users at lists.mcs.anl.gov
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>> 
>> End of Nek5000-users Digest, Vol 85, Issue 5
>> ********************************************
> 
> --
> 
> Phil Sakievich
> 
> PhD Candidate - Mechanical Engineering
> Arizona State University - Ira A. Fulton School for Engineering of
> Matter Transport and Energy
> Tempe, Arizona
> 
> Links:
> ------
> [1] https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> [2] http://hpts.in
> [3] https://github.com/psakievich/Nek5000
> [4] http://ps_hpts.in
> 
> _______________________________________________
> Nek5000-users mailing list
> Nek5000-users at lists.mcs.anl.gov
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users