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b4daa24319 Shre*0001 The "BLING" package is adapted from the Biogeochemistry with Light, Iron, Nutrient and Gas model developed at GFDL by Eric Galbraith and collaborators. Several subroutines, such as air-sea exchange and carbonate chemistry, are adapted from the "DIC" package. It is compatible with the MITgcm adjoint.
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0003 N-BLING, with nitrogen cycling, is the default code. It includes 8 tracers: DIC, ALK, O2, NO3, PO4, Fe, DON, DOP (in that order in data.ptracers). Prognostic tracers for silica and phytoplankton biomass are optional.
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0005 The original 6-tracer BLING code (Galbraith et al., 2010) can be compiled by defining the flag USE_BLING_V1. The tracers in data.ptracers must then be specified in the following order: DIC, ALK, O2, PO4, Fe, DOP.
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0009 For more information see:
0010 -------------------------
0011
0012 Galbraith, E.D., Gnanadesikan, A., Dunne, J. and Hiscock, M. 2010. Regional impacts of iron-light colimitation in a global biogeochemical model. Biogeosciences, 7, 1043-1064.
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0014 http://www.gfdl.noaa.gov/simplified-ocean-biogeochemistry-bling
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0016 https://sites.google.com/site/blingmodel/
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0018
0019
0020 Below are the notes from the file generic_BLING.v2.F90:
0021 -------------------------------------------------------
0022
0023 Biogeochemistry with Light, Iron, Nutrient and Gas version two (BLINGv2) includes an implicit ecological model of growth limitation by light, temperature, nitrogen, phosphorus and iron, and simulates organic and O2 pools.
0024
0025 BLINGv2 differs from blingv0 by including a nitrogen cycle (with N2 fixation and denitrification) and flexible N:P stoichiometry. The iron limitation is now treated slightly differently, in order to be consistent with P. In addition, the phytoplankton biomass is now treated as a non-advected tracer (i.e. a diagnostic tracer in GFDL parlance) for the purpose of calculating uptake, which relaxes the strict assumption of balanced growth. There is also a subgridscale sediment parameterization, to capture fine-scale bathymetric features in particle remineralization, and a diel vertical migrator (DVM) parameterization for export and remineralization. In addition, there are numerous small changes and re-tunings.
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0027 Food web processing in the euphotic zone is handled following the empirical relationships discussed by Dunne et al.(2005). O2 equilibria and gas exchange follow OCMIP2 protocols.
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0029 BLING is a biogeochemistry tool, with ecosystem-like behaviour, rather than a full-complexity ecosystem model. It takes certain computational shortcuts in order to represent well-known features of ecosystems, but without having to resolve the ecosystem components explicitly. Most importantly, living and particulate organic matter is not subject to advection and mixing due to ocean circulation. Particular caution should be applied when interpreting small-scale behaviour (scales of advection per week) and the detailed timing of growth in dynamic environments, such as during spring blooms.
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0031 Additional functionality comes from an optional carbon cycle that is non-interactive, i.e. does not change the core bling behaviour, as well as tracers including radiocarbon (14c), d13C (13c), a decomposition of carbon components by gas exchange and remineralization (carbon_pre), a nutrient source tagging module (nut_source) that uses a global pycnocline (pyc_ave), a decomposition of oxygen as preformed and total (o2_pre) as well as photosynthetic, and a decomposition of phosphate and nitrate as preformed and remineralized (nut_pre). All of this - and more! - is found in the module BLING_extras.
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0033 This model is available for public use. The current version is blingv2. The version number refers to the core model behaviour; additional tracers exist in different iterations of the module. There is not yet a publication. blingv0 can be referenced as:
0034 Galbraith, E.D., Gnanadesikan, A., Dunne, J. and Hiscock, M. 2010. Regional impacts of iron-light colimitation in a global biogeochemical model. Biogeosciences, 7, 1043-1064.
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0036 All parameter values are as described in this paper. Note that this reference is only for the core model components, and does not include any of the additional functionalities, which remain undocumented. Please contact Eric Galbraith (eric.galbraith@mcgill.ca) for more information.
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0044 Notes on running BLING in MITgcm:
0045 ---------------------------------
0046
0047 (See the example in MITgcm_contrib/verification_other/global_oce_biogeo_bling)
0048
0049 1) make sure that you have the current BLING code:
0050 in your pkg/bling directory
0051 type:
0052 cvs update
0053
0054 2) in your code folder, add these to packages.conf:
0055 gchem
0056 ptracers
0057 bling
0058
0059 3) in your code folder, copy pkg/bling/BLING_OPTIONS.h
0060 and define / undef options
0061
0062 4) in your run folder, add
0063 data.gchem (useBLING=.TRUE.)
0064 data.ptracers (specify ICS for ptracers)
0065 data.bling (specify atm pCO2, silica field, iron atm deposition field)
0066 You can find examples of these files in MITgcm_contrib/verification_other/global_oce_biogeo_bling/input/
0067
0068 5) in your run folder, update
0069 data.pkg (usePTRACERS=.TRUE., useGCHEM=.TRUE.)
0070 and if you use it
0071 data.obcs or data.rbcs (specify OBCS for ptracers)
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0078 BLING-specific options (to be specified in BLING_OPTIONS.h):
0079 ------------------------------------------------------------
0080
0081 BLING_NO_NEG
0082 When biogeochemical tracer fields become negative (which can happen when advecting fields with low values and high spatial gradients), change negative values to small positive values before nutrient limitations are calculated in bling_production.
0083
0084 ML_MEAN_LIGHT
0085 Assume that phytoplankton in the mixed layer experience the average light over the mixed layer (as in original BLING model)
0086
0087 ML_MEAN_PHYTO
0088 Assume that phytoplankton are homogenized in the mixed layer
0089
0090 ADVECT_PHYTO
0091 Adds a prognostic tracer for total phytoplankton biomass
0092
0093 BLING_ADJOINT_SAFE
0094 Simplify some parts of the code that are problematic when using the adjoint
0095
0096 USE_QSW
0097 Determine PAR from shortwave radiation Qsw (instead of based on location & time)
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0102 Notes on BLING_ADJOINT SAFE:
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0104 - minimum value for Pc_m and Pc_m_diaz
0105 - FreeFe and pfeflux_l are not set to 0 when anoxic
0106 - using fixed wsink0 rather than variable wsink in organic Fe adsorption calculation
0107 - no benthic denitrification
0108 - no DVM
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