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

Fri Mar 4 02:52:36 CST 2016

The build-in function g2gi() does something similar and works with big
data sets.

Cheers,
Stefan

Am 3/4/16, 9:44 AM schrieb "nek5000-users-bounces at lists.mcs.anl.gov on
behalf of nek5000-users at lists.mcs.anl.gov" unter
<nek5000-users-bounces at lists.mcs.anl.gov on behalf of
nek5000-users at lists.mcs.anl.gov>:

>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
>
>
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