pearseb/1D_OMZ_model

iNitrOMZ

iNitrOMZ is a nitrogen-centric biogeochemical model embeded in a below-mixed layer 1-D advection diffusion model. The model resolves a comprehensive set of processes involved in the remineralization of the sinking organic matter, starting from an imposed export flux at the base of the mixed-layer.

*** This is Pearse Buchanan's version that considers microbes as explicit biomasses ***

Table of Contents

• Updates
• Getting started
• Code structure
• Support
• How to cite

Requires MATLAB 2013 or above.

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Find what you need: Updates

Quick intro

Running iNitrOMZ

Code structure

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Updates

• 12/2019 -- Change the parameter optimization algorithm to the rather new and extremely more efficient CMAES algorithm (https://en.wikipedia.org/wiki/CMA-ES)
• 02/2020 -- Example batch jobs multi-optimization submission scripts added.
• 08/2020 -- Development branch initiated by dbianchi
• 09/2020 -- Re-organized code to store variables in bgc.Types structures, adding a "iMap" to map variables to Types, to be used for example in the "change_input" function etc.

Getting started

Setting the root path

Let's call the path to iNitrOMZ/ -- $NITROMSPATH 
  (1) Open the model initialization function
        `$NITROMSPATH/iNitrOMZ_v6.0/bgc1d_src/bgc1d_initialize.m`
        for editing and set: `bgc.root='$NITROMSPATH'`;
  (2) open the template runscript  `$NITROMSPATH/iNitrOMZv6.0/runscripts/bgc_run.m`
      for editing and set: `bgc1d_root='$NITROMSPATH/'`

Run the model

Run the template script `$NITROMSPATH/iNitrOMZ_v6.0/runscripts/bgc_run.m` in MATLAB

Customizing the run

Change the model defaults by modifying the initialization scripts 
in $NITROMSPATH/bgc1d_src/ (see section on Code structure for a detailing of the 
scripts)

Code structure

iNitrOMZ_v6.0/runscripts/

  Template scripts to run or optimize the model
    - bgc_run.m -- template running script

iNitrOMZ_v6.0/bgc1d_src/

User-customizable initialization functions

    - bgc1d_initialize.m -- main initialization script. The user can modify 
                            general model parameters.
    - bgc1d_initboundary.m -- the user can specify/modify boudary conditions
    - bgc1d_initbgc_params.m -- the user can specify/modify biogeochemical 
                                parameters
    - bgc1d_initIso_params.m -- the user can specify/modify parameters related 
                                to N isotopes

Core model functions

    - bgc1d_initialize_DepParam.m -- calculates dependant model parameters
    - bgc1d_initIso_Dep_params.m -- calculates dependant model parameters 
                                    related to N isotopes
    - bgc1d_initIso_update_r15n.m -- used to update N isotopic fractions
    - bgc1d_advection_diff_opt.m -- this is the model core. This function 
                                    performs the advection and diffusion of 
                                    model tracers, applies sources and sinks,
                                    and applies restoring. Also handles model 
                                    output archiving.
    - bgc1d_sourcesink.m -- calculates sources and sinks of model tracers
    - bgc1d_restoring_initialize.m -- initializes lateral restoring forcing
    - bgc1d_restoring.m -- calculates lateral restoring of model tracers
    - not listed here: small utility functions used during intergration (e.g., n2o_yield.m)

iNitrOMZ_v6.0/processing/

  Processing functions usefull for analysing the solution
    - bgc1d_postprocess.m -- processes the final archived model solution into 
                              a user-friendly structure 
    - more not listed here ...

iNitrOMZ_v6.0/Data/

 Forcing and validation data .

iNitrOMZ_v6.0/restart/

  Where restart files are stored

iNitrOMZ_v6.0/saveOut/

  Where model output is archived.

Support

Contact Simon Yang or Daniele Bianchi at UCLA for support.

How to cite

Please cite this repository

Manuscript reference soon to come.