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 ***
Requires MATLAB 2013 or above.
Find what you need: 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.
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='$NITROMSPATH/'`
Run the template script `$NITROMSPATH/iNitrOMZ_v6.0/runscripts/bgc_run.m` in MATLAB
Change the model defaults by modifying the initialization scripts
in $NITROMSPATH/bgc1d_src/ (see section on Code structure for a detailing of the
scripts)
Template scripts to run or optimize the model
- bgc_run.m -- template running script
- 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
- 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)
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 ...
Forcing and validation data .
Where restart files are stored
Where model output is archived.
Contact Simon Yang or Daniele Bianchi at UCLA for support.
Manuscript reference soon to come.