repro_default_README: instructions to reproduce this model experiment
mjuerchott@geomar.de, 28.03.2025



Instructions to reproduce runs related to the data repository:

Title:
"Direct cooling effect of artificial upwelling dominates over its marine carbon dioxide removal potential."

Authors:
Jürchott, M.(1), Oschlies, A.(1,2), Mengis, N.(1), Frenger, I.(1), Koeve, W.(1)

(1) GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
(2) University of Kiel, Germany

Currently this data set is shared only for the purpose of the review process.
See the LICENCE file for details.



Step by step instructions:
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- download UVic 2.9 from the official UVic web site
- configure UVic 2.9 to run on your local machine in the default mode
   (see UVic web site for details)
- make sure you can compile and run UVic in the default mode; follow the instructions
  provided by the official UVic web site (you may need to make run/mk.ver compliant with your system)

For each of the runs to be reproduced

- mkdir a respective run folder (e.g. 'REF_26_WL') 
- mkdir a subfolder called 'updates' within the run folder
- copy all files code/*.f, code/*.h from the respective repro repository folder to that updates folder
- cd to the updates folder
- rename all .f files to .F files, e.g. by means of the perl script rename (rename .f .F *.f )
- cd back to your run folder
- update the Version_Directory entry in mk.in to your local path.
- compile the code given your system's needs and the mk script provided.
  You may also need to copy netcdf.inc from the UVic original source/netcdf to the updates folder. 
- check that the first line in each .f and .h file which you find after 
  compilation in the code folder, points to the subfolder updates as the source of the code
- mkdir a subfolder 'data' inside the run folder
- copy forcing files and restart files (both can be found in the 
  data folder of the repro repository) to that data folder
- copy control* files from the repository to your run folder
- copy .slr file from repository to your run folder
- adopt command sequence from .slr runscript to your run environment; 
  in particular make sure to use correct restart.nc and control.in files, 
  as indicated in that .slr runs script
- carry out the respective run

You should have an overall structure like this:

YourVersionDirectory
  |- source   (with the original UVic 2.9 files)
  |- updates  
  |- run      
  |- data.100.100.19
  |- 2024_run1_repro (or whatever you name it; one folder per run!)
         |- updates  (with code from the repository, .f converted to .F)
         |- code     (where your precompiled code will be found after you compile)
         |- data     (forcing data from repository)
         mk.in
         control*.in
         *.slr
         ... your output files (tsi, tavg, restart and log files) after the run has completed

Note: The folder 'run' which comes with the original UVic 2.9 code contains the file mk.ver. You may need to configure
this file given your local paths; eventually ask your admin for help, if needed.  
For compiling the code from this paper, make sure to link netcdf libs etc suitable for your system and compiled with 
your compiler. Folder data.100.100.19 which comes with orig UVic contains forcing data. By default, you will overwrite
this generic forcing dataset by specific forcing files provided here and stored in the run's local data subfolder.