[Nek5000-users] ?==?utf-8?q? ?==?utf-8?q? ?= Output format of Nek5000 fil

Tue Feb 28 09:04:18 CST 2017

 Thank you very much Adam, this is exactly what I wanted. 

Best regards

On Tuesday, February 28, 2017 10:02 CET, nek5000-users at lists.mcs.anl.gov wrote: 

> Hi,
> About format of ###.f files.f As it was written it is binary format 
> supporting both single- and multi-file output. That is why you have 
> single (or more) digit before the dot in the file number. If you specify 
> multiple file output this first digit numbers files in a single snapshot 
> and the last five digits give snapshot number. When it comes to file 
> interior. First you have 132 character long header that is ascii and can 
> be read directly. It contains:
> - wdsizo -  number of words per real field (to distinguish between 
> single and double precision output
> - nxo,nyo,nzo - number of grid points in the element in each direction
> - nelo -  number of elements in given file (important for multi-file output)
> - nelgt - global number of elements (in all files; the same as nelo for 
> single file output)
> - time - real number for simulation time
> - istep - time step
> - fid0 - current file number (for multi-file output, 0 for single file 
> output)
> - nfileoo -  number of files in the snapshot
> - few characters specifying what fields are saved; e.g. XUP - means 
> coordinates, velocity, pressure. Notice the coordinates do not have to 
> be saved in a file, but they can!!!
> - p0th -  this is only in new format and gives averaged pressure (not 
> all simulations specify this number)
> 
> The header is followed by single real (4 bytes) test pattern to 
> distinguish between  big and little endian. Next come nelo integers with 
> local-to-global element mapping, which assigns every element in the file 
> its global identity that was used by nek5000 during simulation. After 
> that you have fields you've specified for writing
> - X - physical coordinate - vector
> - U - velocity -vector
> - P - pressure - scalar
> - T - temperature - scalar
> - S - passive scalar -scalar; here you can have digits specifying number 
> of passive scalars
> All variables are specified per element, however in the case of scalars 
> you have nelo sections with nxo*nyo*nzo reals, but for vectors you get 
> ndim*nelo sections with nxo*nyo*nzo reals, as vector component are saved 
> per element, to per array. It means you have vx, vy, vz for first 
> element, next vx, vy, vz for second element and so on.
> Concluding. If you want to know exact physical position of your grid 
> points you have to save coordinates in the file. You do it in ###.rea 
> file by specifying at the end of the file:
>             6  SPECIFICATIONS FOLLOW
>   T       COORDINATES
>   T       VELOCITY
>   T       PRESSURE
>   F       TEMPERATURE
>   F       TEMPERATURE GRADIENT
> or in ###.par file be setting
> [MESH]
> writeToFieldFile = yes
> 
> When you have them in the file you can easily read coordinates and use 
> them in any way.
> I hope this was not too long and detailed.
> Regards
> Adam
> 
> On 27/02/17 11:10, nek5000-users at lists.mcs.anl.gov wrote:
> > Hello,
> >
> > Thank you Paul, I tried your method and it worked. But offsetting the slide trouble me, and I would like to really handle the data freely. I got almost all the ingredient I needed, I just need a function that when I feed it the cell information, it give me the coordinates of points. It must be somewhere in the source code, or may be on Internet, is anyone know about it?
> >
> > Thank you very much.
> >
> >
> >
> >
> >
> > On Friday, February 24, 2017 18:33 CET, nek5000-users at lists.mcs.anl.gov wrote:
> >   
> >> Sometimes visit will have dropouts if your slice corresponds precisely to the location of an element
> >> interface.
> >>
> >> Offsetting the slice by, say, .00001, will often correct that issue...
> >>
> >> Paul
> >>
> >> ________________________________________
> >> 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: Friday, February 24, 2017 9:15 AM
> >> To: nek5000-users at lists.mcs.anl.gov
> >> Subject: Re: [Nek5000-users] ?==?utf-8?q?  Output format of Nek5000 file
> >>
> >>   Thank you for your quick response. I just feel more comfortable working interactively with data. The reading tool of data and mesh with Matlab are already there, I just need a way to map the coordinate of those data with the mesh information.
> >>
> >> More specific reason is I read the data with Visit, and when I take slides, it appear a strange white band in my fields, and I don't know the reason so I need an alternative way to visualize my fields.
> >>
> >>
> >>
> >>
> >> On Friday, February 24, 2017 17:45 CET, nek5000-users at lists.mcs.anl.gov wrote:
> >>
> >>> * Yes the .fXXXXX files are the binary fld files. The ASCII and the old binary format ends with .fldXX.
> >>> * Is there any special reason why you want to load the data into MATLAB?
> >>>
> >>>
> >>> -----Original message-----
> >>>> From:nek5000-users at lists.mcs.anl.gov <nek5000-users at lists.mcs.anl.gov>
> >>>> Sent: Friday 24th February 2017 16:46
> >>>> To: nek5000-users at lists.mcs.anl.gov
> >>>> Subject: [Nek5000-users] Output format of Nek5000 file
> >>>>
> >>>> Hello everyone,
> >>>>
> >>>> I have recently started to work with Nek5000, I have few question about the output format:
> >>>>
> >>>> -In all the documents available, they talk about .fld file, but I launched the quickstart tutorial, and I got only .f000... data file. Is this the same?
> >>>>
> >>>> -I found a Matlab script that read binary data into Matlab, and the data I received is a matrix of : nel .  N^3 .  fields
> >>>> So I guess for each spectral element, and for each field, the file store N^3 numbers, corresponding to the values. But I have read somewhere that you can't mix the equally spaced value with GLL points. So in the binary file I got, what type of mapping is using? GLL abscissas or equally spaced?
> >>>>
> >>>> -About GLL points, I got it in 1D, but when it come to 3D, with curved elements, it become a bit complex, do you know where in the program or are there any pre-made tool that map the GLL points coordinates base on coordinate of vertices and curvature?
> >>>>
> >>>>
> >>>> Thank you,
> >>>>
> >>>>
> >>>> _______________________________________________
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> >>>> Nek5000-users at lists.mcs.anl.gov
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> >>>>
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> >>
> >>
> >>
> >>
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