[MITgcm-support] [EXTERNAL] changing one entry in pickup files
Paola Cessi
pcessi at ucsd.edu
Tue May 12 19:33:14 EDT 2020
Hi Gael,
thanks for the pointers. I will try it out and report on the results.
Cheers,
Paola
----------------------------------------------
Paola Cessi
Scripps Institution of Oceanography
9500 Gilman Drive #0213
La Jolla, CA 92093-0213
USA
Tel: +1 858 534 0622 Fax: +1 858 534 8045
e-mail: pcessi at ucsd.edu Web: http://www-pord.ucsd.edu/~pcessi
Delivery address (Fed-Ex, DHL, UPS, etc.):
Paola Cessi
University of California San Diego
Keck Center - Room 366
8851 Shellback Way
La Jolla, CA 92093-0213
USA
> On May 11, 2020, at 6:44 PM, Gael Forget <gforget at mit.edu> wrote:
>
> Hi Paola
>
> The meta file created by this package indeed does not seem to include the list of variables. However, I think it should be the same list of 9 variables described in https://mitgcm.readthedocs.io/en/latest/outp_pkgs/outp_pkgs.html#input-files <https://mitgcm.readthedocs.io/en/latest/outp_pkgs/outp_pkgs.html#input-files> . Below is an exert from flt_init_varia.F which is consistent with the documented list.
>
> Its important to note that the first record (i.e. 9 element vector) is special. This is stated in the doc but not excessively clear and kind of tricky imho.
>
> In any event, you should be able to read these files in Matlab using rdmds.m as usual (a copy is in https://github.com/MITgcm/gcmfaces <https://github.com/MITgcm/gcmfaces>). Doing it this way may read all tile pickups in one multidimensional array.
>
> Alternatively if you want more granular control on read and write, you can use read2memory and write2file (also in gcmfaces <https://github.com/MITgcm/gcmfaces>; try e.g. `help read2memory`).
>
> In an example where nrecords is 74 (from the meta file), this should be something like this :
>
> >> tmp2=read2memory('pickup_flt.ckptA.001.001.data',[9 74],64)
>
> I copy below the first and 2nd records for reference. All of the others look like #2.
>
> And then writing the modified pickup to a new file would look like this :
>
> >> write2file(‘modified/pickup_flt.ckptA.001.001.data',tmp2,64)
>
> Hope this helps. Sorry this stuff is still not documented well enough. Good luck with your experiment.
>
> Best,
> Gael
>
>
> >> tmp2(:,1)
> 73
> 18001
> 10800600
> 0
> 0
> 300
> 9
> 0
> 0
>
> >> tmp2(:,2)
> 12.0000
> 600.0000
> 13.2794
> 13.2823
> 3.0000
> 0
> 0
> 0
> -1.0000
>
> From flt_init_varia.F :
>
> 152 npart( npart_tile(bi,bj),bi,bj) = tmp(1)
> 153 tstart(npart_tile(bi,bj),bi,bj) = tmp(2)
> 154 ipart( npart_tile(bi,bj),bi,bj) = ix
> 155 jpart( npart_tile(bi,bj),bi,bj) = jy
> 156 kpart( npart_tile(bi,bj),bi,bj) = kz
> 157 kfloat(npart_tile(bi,bj),bi,bj) = tmp(6)
> 158 iup( npart_tile(bi,bj),bi,bj) = tmp(7)
> 159 itop( npart_tile(bi,bj),bi,bj) = tmp(8)
> 160 tend( npart_tile(bi,bj),bi,bj) = tmp(9)
>
>
>
>
>> On May 11, 2020, at 8:18 PM, Paola Cessi <pcessi at ucsd.edu <mailto:pcessi at ucsd.edu>> wrote:
>>
>> Hi Dimitri,
>>
>> I am using matlab. These are pickups files from the flt package, so I am not sure they are the same as the regular MITgcm pickups. They are written and read with the mdsio package.
>>
>> I _think_ that what I need to change is the 9th entry of the “arr" array, i.e. arr(9) written/read by the routines mdsio_wr_rec_rl.F/mdsio_rd_rec_rl.F. That said, I don’t understand how to locate this variable given the .meta file (attached).
>>
>> Many thanks,
>>
>> <pickup_flt.ckptA.001.001.meta>
>>
>>
>> Paola
>>
>> ----------------------------------------------
>> Paola Cessi
>> Scripps Institution of Oceanography
>> 9500 Gilman Drive #0213
>> La Jolla, CA 92093-0213
>> USA
>> Tel: +1 858 534 0622 Fax: +1 858 534 8045
>> e-mail: pcessi at ucsd.edu <mailto:pcessi at ucsd.edu> Web: http://www-pord.ucsd.edu/~pcessi <http://www-pord.ucsd.edu/~pcessi>
>>
>> Delivery address (Fed-Ex, DHL, UPS, etc.):
>> Paola Cessi
>> University of California San Diego
>> Keck Center - Room 366
>> 8851 Shellback Way
>> La Jolla, CA 92093-0213
>> USA
>>
>>
>>
>>
>>> On May 11, 2020, at 4:41 PM, Dimitris Menemenlis <dmenemenlis at gmail.com <mailto:dmenemenlis at gmail.com>> wrote:
>>>
>>> Hi Paola, do you use matlab or python?
>>>
>>> If matlab and if noone answers with a generic answer, please send your pickup*.meta file and let me know which variable you want to replace and I will send you two lines of matlab code (and two small scripts) that will read and write the desired variable from and to the pickup file.
>>>
>>> Cheers, Dimitris
>>>
>>>> On May 11, 2020, at 3:39 PM, Paola Cessi <pcessi at ucsd.edu <mailto:pcessi at ucsd.edu>> wrote:
>>>>
>>>> I need to change one entry in the pick-up files. Is there a simple sample program to read a pickup file change, one entry and write it again with the entry changed?
>>>>
>>>> Thanks,
>>>>
>>>> Paola
>>>>
>>>> ----------------------------------------------
>>>> Paola Cessi
>>>> Scripps Institution of Oceanography
>>>> 9500 Gilman Drive #0213
>>>> La Jolla, CA 92093-0213
>>>> USA
>>>> Tel: +1 858 534 0622 Fax: +1 858 534 8045
>>>> e-mail: pcessi at ucsd.edu <mailto:pcessi at ucsd.edu> Web: http://www-pord.ucsd.edu/~pcessi <http://www-pord.ucsd.edu/~pcessi>
>>>>
>>>> Delivery address (Fed-Ex, DHL, UPS, etc.):
>>>> Paola Cessi
>>>> University of California San Diego
>>>> Keck Center - Room 366
>>>> 8851 Shellback Way
>>>> La Jolla, CA 92093-0213
>>>> USA
>>>>
>>>>
>>>>
>>>>
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