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pkg DIC using 3-D calcite-saturation: wish list #678

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jm-c opened this issue Dec 7, 2022 · 2 comments · May be fixed by #718
Open

pkg DIC using 3-D calcite-saturation: wish list #678

jm-c opened this issue Dec 7, 2022 · 2 comments · May be fixed by #718

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@jm-c
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jm-c commented Dec 7, 2022 •
edited

Now that pkg/dic allows to read-in 3-D silicate input file (see PR #620), it would be helpful to get the Calcite-saturation with 3-D pH calculation tested in one verification experiment.
To make this easier, I suggest the following:

  1. Have a pkg/dic run-time parameter to allow to use or not calcite-saturation once the code has been compiled with #define CAR_DISS. Currently this can only be turned on/off at compile time, preventing a single experiment to run both with and without it (with a primary and secondary tests that use the same execuatable).
  2. May be rename "CAR_DISS" using a more explicit name, starting with "DIC_" ?
  3. Put 3-D silica arrays with #ifdef CAR_DISS (or updated new name) so save memory.
  4. Could also speed up compilation by using the same CPP option to empty S/R CALCITE_SATURATION and CAR_FLUX_OMEGA_TOP when it's not defined.
  5. Change the condition around call to 2 S/R above: using a run-time "Freq" type parameter with function DIFFERENT_MULTIPLE and removing the "myIter .lt. (nIter0+5) .or." part which will break the restart.
  6. Test restart ; can restart be improved if we store 3-D pH in pickup file ?
@jm-c jm-c mentioned this issue Dec 7, 2022
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jm-c added a commit to HannahKleppin/MITgcm that referenced this issue Dec 8, 2022
@jm-c
Revert back addition of new run-time param "nCALCITEstep"
a9d405a 
see issue MITgcm#678
jm-c added a commit that referenced this issue Dec 9, 2022
@HannahKleppin @seamanticscience @jm-c
Read in prescribed 3d silicate fields for calculation of pH (#620)
a1d0e45 
* Read in prescribed 3d silicate fields for calculation of pH

* Update data.dic

* Update dic_fields_load.F

* Update dic_readparms.F

* Update data.dic

* Update dic_surfforcing_init.F

* Update DIC_VARS.h

* Update dic_ini_forcing.F

* Update dic_fields_load.F

* introduce SILICAdeep/SILICAsurf arrays to prevent issues when SILICA array changes shape

* move nCALCITEstep from dic_biotic_forcing to runtime parameter in seconds rather than timesteps

* Add diagnostics to output 3d Si, pH, pCO2, carbonate and saturation state fields from S/R calcite_saturation

* Fix segfault in test due to improper use of S/R LEF_ZERO

* Restore original OPTIONS file and "data.dic"

Bring back original pkg/dic OPTIONS file to keep default unchanged.
And for now, keep experiment "tutorial_global_oce_biogeo" unchanged,
might test 3-D silica file in an other set-up.

Also rename new input binary file (suffix "RS" is meaningless, but this
file is not used anymore)

* Update to process 3-D silicate input file

* finish replacing "silica" --> "silicaSurf"

+ minor cleaning in pkg/dic store-dir headers

* Simplify for the adjoint:

when compiling pkg/autodiff, disable the use of 3-D silica for surface silica value

* Restore initialisation as done in master branch

Unconditinal initialisation matters (for TAF adjoint)

* Cleaning: improve indentation

also remove one trailing blank

* Cleaning

- remove trailing blanks
- more consistent upper/lower writing of variable

* adjust new diags parser code + cleaning

* remove duplicate copies (save space)

* Revert back addition of new run-time param "nCALCITEstep"

see issue #678

* improve indentation

* remove un-used 3-D silica file

* document loading 3D silicate input file in pkg/dic

Co-authored-by: Jonathan Lauderdale <jonathan.lauderdale@gmail.com>
Co-authored-by: Jean-Michel Campin <jmc@mit.edu>
Co-authored-by: Jean-Michel Campin <jmc@ocean.mit.edu>
@seamanticscience seamanticscience mentioned this issue Dec 13, 2022
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@jm-c
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jm-c commented Feb 9, 2023

All points listed in this issue have been addressed in PR #683 with the exception of point-6.

@seamanticscience
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seamanticscience commented Aug 10, 2023 •
edited

I made a new PR #759 with the minor bug fixes to carbonate dissolution rates.

@jm-c is rearranging pkg/dic initialization (#757) to enable 3d pH pickups (either in #718 or a new PR?)

@jm-c jm-c linked a pull request Apr 22, 2024 that will close this issue
3D pH pickup for pkg/DIC calcite saturation #718
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3D pH pickup for pkg/DIC calcite saturation seamanticscience/MITgcm
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@jm-c @seamanticscience