REMORABiology Namespace Reference

Namespaces
namespace	Fennel

Classes
struct	FennelParameters

Enumerations
enum class	BiologyModel { none , fennel }
enum class	BiologyICType { follow_ic_type , analytic , netcdf }
enum class	PCO2AirType { constant , data , secular }
enum class	CO2SchmidtType { wanninkhof1992 , wanninkhof2014 }
enum class	O2SchmidtType { wanninkhof1992 , wanninkhof2014 , ocmip }

Functions
BiologyModel	parse_biology_model (const std::string &name)
std::string	biology_model_name (BiologyModel model)
BiologyICType	parse_biology_ic_type (const std::string &name)
std::string	biology_ic_type_name (BiologyICType type)
bool	has_biology (BiologyModel model) noexcept
Vector< std::string >	tracer_names (BiologyModel model, FennelParameters const &fennel_parameters)

Enumeration Type Documentation

BiologyICType

enum class REMORABiology::BiologyICType

strong

Source of the biology tracer initial condition, selected independently of remora.ic_type.

The two are decoupled because a NetCDF initial file supplies whichever tracers it happens to contain, and validating an option set the file does not cover (PO4, ODU) would otherwise require regenerating binary input. With analytic, physical fields still come from NetCDF while biology comes from the problem's analytic profile, which is reproducible from source.

Enumerator
follow_ic_type	default: NetCDF when ic_type is netcdf, else analytic
analytic
netcdf

Definition at line 29 of file REMORA_Biology.H.

BiologyModel

enum class REMORABiology::BiologyModel

strong

Enumerator
none
fennel

Definition at line 14 of file REMORA_Biology.H.

CO2SchmidtType

enum class REMORABiology::CO2SchmidtType

strong

Schmidt-number formulation for the air-sea gas transfer velocity.

CO2 offers the Wanninkhof (1992) and (2014) coefficient sets; O2 adds the Keeling et al. (1998) OCMIP set. The choice also selects the leading rate coefficient, 0.31 for 1992 and 0.251 for 2014, so the two must move together and are not independently settable.

Enumerator
wanninkhof1992
wanninkhof2014

Definition at line 55 of file REMORA_Biology.H.

O2SchmidtType

enum class REMORABiology::O2SchmidtType

strong

Enumerator
wanninkhof1992
wanninkhof2014
ocmip

Definition at line 60 of file REMORA_Biology.H.

PCO2AirType

enum class REMORABiology::PCO2AirType

strong

Source of the atmospheric pCO2 used by the surface CO2 gas exchange.

ROMS picks one of these with PCO2AIR_DATA / PCO2AIR_SECULAR or neither. The two time-dependent forms date the model clock with remora_caldate.

Enumerator
constant	remora.fennel.pCO2air, unchanging
data	annual climatology of Laurent et al. (2017)
secular	secular trend plus harmonics, referenced to 1951

Definition at line 41 of file REMORA_Biology.H.

Function Documentation

biology_ic_type_name()

std::string REMORABiology::biology_ic_type_name

(

BiologyICType

type

)

Definition at line 434 of file REMORA_Biology.cpp.

Referenced by REMORA::ReadParameters().

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biology_model_name()

std::string REMORABiology::biology_model_name

(

BiologyModel

model

)

Definition at line 406 of file REMORA_Biology.cpp.

Referenced by REMORA::ReadParameters().

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has_biology()

bool REMORABiology::has_biology ( BiologyModel  model )

noexcept

Definition at line 449 of file REMORA_Biology.cpp.

Referenced by REMORA::advance_biology(), REMORA::init_biology_from_netcdf(), REMORA::init_biology_full_domain_from_netcdf(), REMORA::init_biology_ic(), REMORA::init_biology_ic_full_domain(), REMORA::init_scalar_metadata(), REMORA::ReadParameters(), and REMORA::set3DPlotVariables().

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parse_biology_ic_type()

BiologyICType REMORABiology::parse_biology_ic_type

(

const std::string &

name

)

Definition at line 419 of file REMORA_Biology.cpp.

Referenced by REMORA::ReadParameters().

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parse_biology_model()

BiologyModel REMORABiology::parse_biology_model

(

const std::string &

name

)

Definition at line 392 of file REMORA_Biology.cpp.

Referenced by REMORA::ReadParameters().

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tracer_names()

amrex::Vector< std::string > REMORABiology::tracer_names	(	BiologyModel	model,
		FennelParameters const &	fennel_parameters
	)

Definition at line 455 of file REMORA_Biology.cpp.

Referenced by REMORA::init_scalar_metadata(), and REMORA::ReadParameters().

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