[MITgcm-support] Barotropic ocean gyre tutorial

Oliver Jahn jahn at mit.edu
Sun Apr 4 09:41:03 EDT 2021


This

[X,Y]=np.meshgrid(x,y,indexing='ij')

should be

[Y,X]=np.meshgrid(y,x,indexing='ij')

(with indexing 'ij' it is y,x, with indexing 'xy' it is x,y)

I am attaching the script from Jeff's pull request where this is all
done correctly.

Oliver


On 2021-04-04 09:00, Jeremy Miller wrote:
> Dear Oliver,
> 
> Thanks for coming back to me. I did just that. I now get a plot for
> "eta" that appears to be two sets of constant values, on the left and
> right of the line x=0.6*1e6 m (see the attached plot in
> fig_bar_gyre_windx_siny.png). I also notice that the output bin file
> (tau_2_1) still shows different values to the original numpy array
> (tau_2). I have attached the latest version of the python script used to
> generate the data (gendata_tut4.1.py <http://gendata_tut4.1.py>) and the
> script used to generate the plots (tut_4.1_plots.py
> <http://tut_4.1_plots.py>).
> 
> Best
> Jeremy
> 
> On Sun, 4 Apr 2021 at 13:48, Oliver Jahn <jahn at mit.edu
> <mailto:jahn at mit.edu>> wrote:
> 
>     Hi Jeremy,
> 
>     this will not work:
> 
>     > if sys.byteorder == 'little': tau_2.byteswap(True)
>     > fid = open('windx_siny.bin', 'wb')
>     > tau_2.astype('float32').tofile(fid)
> 
>     Can you instead try Jeff's suggestion:
> 
>     tau_2.astype('>f4').tofile('windx_siny.bin')
> 
>     and NOT use the byteswap command?  Mixing byteswap and astype is a bad
>     idea as byteswap will create a mismatch between the data in memory and
>     numpy's assumption of the data type.
> 
>     Best,
>     Oliver
> 
> 
>     > as you suggested, the plot still came out blank.
>     > Regarding Jeffrey Scott's comment that the reason I could not read
>     back
>     > the bin file was due to a mismatch between float32 and float64, I
>     > followed his advice and read in the
>     > bin file using the snippet 
>     >
>     > tau_2_1 = np.fromfile('windx_siny.bin',dtype='float32')
>     >
>     > and I got back an array with every entry being 'inf' except the
>     > penultimate column, being all '0'.
>     >
>     > Is it possible that the snippet 
>     >
>     > # X=X.astype('float128')
>     > # Y=Y.astype('float128')
>     >
>     > (which is commented) needs to be included but with 'float128' replaced
>     > with 'float32'?
>     >
>     > Best
>     > Jeremy
>     >
>     >
>     >
>     >
>     >
>     > On Thu, 1 Apr 2021 at 16:47, Jan Klaus Rieck
>     <jan.rieck at mail.mcgill.ca <mailto:jan.rieck at mail.mcgill.ca>
>     > <mailto:jan.rieck at mail.mcgill.ca
>     <mailto:jan.rieck at mail.mcgill.ca>>> wrote:
>     >
>     >     Hello Jeremy Miller,
>     >
>     >     I also use python to to generate input data for the MITgcm. I
>     found
>     >     that, to generate files that can be read by the MITgcm
>     consistently,
>     >     I needed to specify the type explicitly. 
>     >     My way of saving the files would look like this in your case: 
>     >
>     >     if sys.byteorder == 'little': tau_2.byteswap(True)
>     >     fid = open(''windx_siny.bin', 'wb')
>     >     tau_2.astype('float32').tofile(fid)
>     >
>     >     Of course, 'float32' could be replaced by 'float64' if you require
>     >     double precision.
>     >
>     >     I hope this helps,
>     >     Jan Rieck
>     >      
>     >     On Thu, 2021-04-01 at 10:22 +0300, Jeremy Miller wrote:
>     >>     Dear MITGCM forum,
>     >>
>     >>     I am Jeremy Miller, I am new to MITgcm and I've been going
>     through
>     >>     the tutorials. I have a question about the "Barotropic Ocean
>     Gyre"
>     >>     tutorial (section 4.1).
>     >>
>     >>     I managed to compile and run the code, and re-produce the first
>     >>     two plots shown in section 4.1.5 for  wind stress of τ = τ0 cos(
>     >>     πy/Ly), for both the advection and non-advection cases (with the
>     >>     provided input binary files). 
>     >>     I ran into problems when trying to produce the third plot,
>     for the
>     >>     case where τ = τ0 sin( πy/Ly). I am a python user, so I
>     translated
>     >>     gendata.m into python to write the input binary
>     >>     files 'windx_cosy.bin' 'windx_siny.bin' (see the file
>     >>     gendata_tut4.1py attached).  As explained in section 3.9 I've
>     >>     included the snippet 
>     >>
>     >>     if sys.byteorder == 'little': tau_2.byteswap(True)
>     >>
>     >>     where "tau2" is the array to be output. There was no issue in the
>     >>     cosine wind stress, and I managed to reproduce the results that I
>     >>     got with the original 'windx_cosy.bin' provided in the tutorial.
>     >>     However, with the sine wind stress case, the output in
>     >>     'Eta.0000077760.001.001' is all zeros. 
>     >>
>     >>     When I attempt to read  'windx_siny.bin' with python into a new
>     >>     array called tau2_1. I get absurdly big numbers back, which
>     do not
>     >>     match the original array tau2 that I created. If I Remove the
>     >>     snippet " if sys.byteorder == 'little': tau_2.byteswap(True)
>     ", in
>     >>     the python gendata code, tau2_1 and tau2 match. But, then when I
>     >>     run the code again, the file output.txt contains a long list
>     of NaNs.
>     >>
>     >>     I have also included the python code used to generate the
>     plots in
>     >>     the file tut_4.1_plots.py <http://tut_4.1_plots.py>
>     <http://tut_4.1_plots.py/>
>     >>
>     >>     Look forward to hearing from you.
>     >>     Yours sincerely
>     >>     Jeremy Miller
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