NML

aed_nml

AEDNML

Bases: NML

NML subclass for the aed .NML file.

Attributes:

Name	Type	Description
blocks	Dict[str, NMLBlock]	Dictionary of NMLBlock objects.
strict	bool	Switch to turn on or off block and parameter validation.

__init__(aed_models=ModelsBlock(), aed_tracer=TracerBlock(), aed_noncohesive=NonCohesiveBlock(), aed_oxygen=OxygenBlock(), aed_carbon=CarbonBlock(), aed_sedflux=SedFluxBlock(), aed_sed_const2d=SedConst2DBlock(), aed_silica=SilicaBlock(), aed_nitrogen=NitrogenBlock(), aed_phosphorus=PhosphorusBlock(), aed_organic_matter=OrganicMatterBlock(), aed_phytoplankton=PhytoplanktonBlock(), aed_zooplankton=ZooplanktonBlock(), aed_macrophyte=MacrophyteBlock(), aed_bivalve=BivalveBlock(), aed_totals=TotalsBlock())

Parameters:

Name	Type	Description	Default
aed_models	ModelsBlock		ModelsBlock()
aed_tracer	TracerBlock		TracerBlock()
aed_noncohesive	NonCohesiveBlock		NonCohesiveBlock()
aed_oxygen	OxygenBlock		OxygenBlock()
aed_carbon	CarbonBlock		CarbonBlock()
aed_sedflux	SedFluxBlock		SedFluxBlock()
aed_sed_const2d	SedConst2DBlock		SedConst2DBlock()
aed_silica	SilicaBlock		SilicaBlock()
aed_nitrogen	NitrogenBlock		NitrogenBlock()
aed_phosphorus	PhosphorusBlock		PhosphorusBlock()
aed_organic_matter	OrganicMatterBlock		OrganicMatterBlock()
aed_phytoplankton	PhytoplanktonBlock		PhytoplanktonBlock()
aed_zooplankton	ZooplanktonBlock		ZooplanktonBlock()
aed_macrophyte	MacrophyteBlock		MacrophyteBlock()
aed_bivalve	BivalveBlock		BivalveBlock()
aed_totals	TotalsBlock		TotalsBlock()

from_dict(nml_dict) classmethod

Initialise class instance from a dictionary.

Returns an instance of the class that has been initialised with a nested dictionary of NML parameters.

Parameters:

Name	Type	Description	Default
nml_dict	dict	A dictionary where the keys are the block names and the values are dictionaries of parameter names (keys) and parameter values (values).	required

from_file(nml_path) classmethod

Initialise class instance from a NML file.

Returns an instance of the class that has been initialised with parameters from a NML file.

Parameters:

Name	Type	Description	Default
nml_path	dict	Path to the NML file.	required

get_block(block_name)

Get a NML Block.

Returns an instance of a NMLBlock subclass from the NML.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required

get_block_names()

List the block names.

Returns a list of the name attribute for all NMLBlock subclass instances.

get_param_names(block_name)

List the parameter names in a block.

Returns a list of the name attribute for all NMLParam instances.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required

get_param_units(block_name, param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required
param_name	str	The name of the parameter to return the value for.	required

get_param_value(block_name, param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required
param_name	str	The name of the parameter to return the value for.	required

init_blocks(*args)

Populate the blocks dictionary with instances of NMLBlock subclasses.

is_none_nml()

Test if all NML parameter values are None.

Returns True if is_none_block() is True for all subclassed NMLBlock instances in the blocks dictionary.

iter_blocks()

Iterate over all NMLBlock objects.

iter_params()

Iterate over all NMLParam objects.

set_block(block_name, block)

Set a NML Block.

Overrides, or adds a new block, to a NML.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required
block	NMLBlock	The block to set.	required

set_param_value(block_name, param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_blocks=True, none_params=True)

Nested dictionary of parameters.

Returns a nested dictionary where the keys are the block names and the values a dictionary of parameter values.

Parameters:

Name	Type	Description	Default
none_blocks	bool	Whether to include blocks where all parameter values are None.	True
none_params	bool	Whether to include parameter values that are None.	True

to_nml(nml_path='glm3.nml')

Write a NML file.

Parameters with values of None are omitted.

Parameters:

Name	Type	Description	Default
nml_path	str	Path to the NML file	'glm3.nml'

BivalveBlock

Bases: NMLBlock

NMLBlock subclass for the aed_bivalve block.

A model of one or more groups of benthic filter feeders, able to assimilate C, N and P and recycle filter material back to the water column and sediment.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(num_biv=None, the_biv=None, dbase=None, x_c=None, n_zones=None, active_zones=None, initfromdensity=None, simbivtracer=None, simbivfeedback=None, simstaticbiomass=None, bt_renewal=None, dn_target_variable=None, pn_target_variable=None, dp_target_variable=None, pp_target_variable=None, dc_target_variable=None, pc_target_variable=None, do_uptake_variable=None, ss_uptake_variable=None, simfixedenv=None, fixed_temp=None, fixed_oxy=None, fixed_food=None, extra_diag=None, diag_level=None)

Parameters:

Name	Type	Description	Default
num_biv	Union[int, None]	Number of zooplankton groups.	None
the_biv	Union[List[int], int, None]	List of IDs of groups in aed_bivalve_pars dbase (length equals num_biv).	None
dbase	Union[str, None]	aed_bivalve_pars path.	None
x_c	Union[float, None]	Undocumented parameter.	None
n_zones	Union[int, None]	Number of sediment zones where bivalves will be active.	None
active_zones	Union[List[int], int, None]	The vector of sediment zones to include.	None
initfromdensity	Union[bool, None]	Undocumented parameter,	None
simbivtracer	Union[bool, None]	Opton to include water column tracer tracking filtration amount.	None
simbivfeedback	Union[bool, None]	Switch to enable/disable feedbacks between bivalve metabolism and water column variable concentration.	None
simstaticbiomass	Union[bool, None]	Undocumented parameter.	None
bt_renewal	Union[float, None]	Undocumented parameter.	None
dn_target_variable	Union[str, None]	Water column variable to receive DON excretion.	None
pn_target_variable	Union[str, None]	Water column variable to receive PON egestion/mortality.	None
dp_target_variable	Union[str, None]	Water column variable to receive DOP excretion.	None
pp_target_variable	Union[str, None]	Water column variable to receive POP egestion/mortality.	None
dc_target_variable	Union[str, None]	Water column variable to receive DOC excretion.	None
pc_target_variable	Union[str, None]	Water column variable to receive POC egestion/mortality.	None
do_uptake_variable	Union[str, None]	Water column variable providing DO concentration.	None
ss_uptake_variable	Union[str, None]	Water column variable providing SS concentration.	None
simfixedenv	Union[bool, None]	Switch to enable/disable environmental variables to be fixed (for testing).	None
fixed_temp	Union[float, None]	Fixed temperature.	None
fixed_oxy	Union[float, None]	Fixed oxygen concentration.	None
fixed_food	Union[float, None]	Fixed food concentration.	None
extra_diag	Union[bool, None]	Switch to enable/disable extra diagnostics to be output.	None
diag_level	Union[int, None]	Undocumented parameter.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

CarbonBlock

Bases: NMLBlock

NMLBlock subclass for the aed_carbon block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(dic_initial=None, ph_initial=None, ch4_initial=None, co2_model=None, alk_mode=None, ionic=None, atm_co2=None, atm_ch4=None, co2_piston_model=None, ch4_piston_model=None, rch4ox=None, kch4ox=None, vtch4ox=None, methane_reactant_variable=None, fsed_dic=None, ksed_dic=None, theta_sed_dic=None, fsed_dic_variable=None, fsed_ch4=None, ksed_ch4=None, theta_sed_ch4=None, fsed_ch4_variable=None, ebb_model=None, fsed_ebb_variable=None, fsed_ch4_ebb=None, ch4_bub_all=None, ch4_bub_cll=None, ch4_bub_kll=None, ch4_bub_disf1=None, ch4_bub_disf2=None, ch4_bub_disdp=None)

Parameters:

Name	Type	Description	Default
dic_initial	Union[float, None]	Initial DIC cooncentrations.	None
ph_initial	Union[float, None]	Initial pH values.	None
ch4_initial	Union[float, None]	Initial CH4 values.	None
co2_model	Union[int, None]	Selection of pCO2 model algorithms. 0 for aed_geochem, 1 for CO2SYS, and 2 for Butler.	None
alk_mode	Union[int, None]	Selection of total alkalinity model algorithms.	None
ionic	Union[float, None]	Average ionic strength of the water column.	None
atm_co2	Union[float, None]	Atmospheric CO2 concentration.	None
atm_ch4	Union[float, None]	Atmospheric CH4 concentration.	None
co2_piston_model	Union[int, None]	Selection of air-water Co2 flux velocity method.	None
ch4_piston_model	Union[int, None]	Selection of air-water CH4 flux velocity method.	None
rch4ox	Union[float, None]	Maximum reaction rate of CH4 oxidation at 20C.	None
kch4ox	Union[float, None]	Half-saturation oxygen concentration for CH4 oxidation.	None
vtch4ox	Union[float, None]	Arrhenius temperature multiplier for CH4 oxidation.	None
methane_reactant_variable	Union[str, None]	State variable to be consumed during CH4 oxidation.	None
fsed_dic	Union[float, None]	Sediment CO2 flux.	None
ksed_dic	Union[float, None]	Half-saturation oxygen concentration controlling CO2 flux.	None
theta_sed_dic	Union[float, None]	Arrhenius temperature multiplier for sediment CO2 flux.	None
fsed_dic_variable	Union[str, None]	Variable name to link to for spatially resolved sediment zones.	None
fsed_ch4	Union[float, None]	Sediment CH4 flux.	None
ksed_ch4	Union[float, None]	Half-saturation oxygen concentration controlling CH4 flux.	None
theta_sed_ch4	Union[float, None]	Arrhenius temperature multiplier for sediment CH4 flux.	None
fsed_ch4_variable	Union[str, None]	Variable name to link to for spatially resolved sediment zone.	None
ebb_model	Union[int, None]	Option to activate CH4 ebullition. 0 for no ebullition, 1 for simple release model.	None
fsed_ebb_variable	Union[str, None]	Variable name to link to for spatially resolved sediment zones.	None
fsed_ch4_ebb	Union[float, None]	Undocumented parameter.	None
ch4_bub_all	Union[float, None]	Mean water depth.	None
ch4_bub_cll	Union[float, None]	Normalising constant.	None
ch4_bub_kll	Union[float, None]	Exponential factor from the depth-ebullition regression relation.	None
ch4_bub_disf1	Union[float, None]	Bubble dissolution fraction (surface).	None
ch4_bub_disf1	Union[float, None]	Bubble dissolution fraction (deep).	None
ch4_bub_disdp	Union[float, None]	Bubble dissolution fraction depth interface.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

MacrophyteBlock

Bases: NMLBlock

aed_macrophyte block.

Simulates benthic habitat and/or growth of macrophytes such as seagrasses in specified sediment zones.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(num_mphy=None, the_mphy=None, n_zones=None, active_zones=None, simstaticbiomass=None, simmacfeedback=None, dbase=None)

Parameters:

Name	Type	Description	Default
num_mphy	Union[int, None]	Undocumented parameter.	None
the_mphy	Union[List[int], None]	Undocumented parameter.	None
n_zones	Union[int, None]	Undocumented parameter.	None
active_zones	Union[List[int], None]	Undocumented parameter.	None
simstaticbiomass	Union[bool, None]	Undocumented parameter.	None
simmacfeedback	Union[bool, None]	Undocumented parameter.	None
dbase	Union[str, None]	Undocumented parameter.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

ModelsBlock

Bases: NMLBlock

NMLBlock subclass for the aed_models block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(models=None)

Parameters:

Name	Type	Description	Default
models	Union[List[str], None]	The AED modules to use.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

NitrogenBlock

Bases: NMLBlock

NMLBlock subclass for the aed_nitrogen block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(amm_initial=None, nit_initial=None, n2o_initial=None, no2_initial=None, rnitrif=None, knitrif=None, theta_nitrif=None, nitrif_reactant_variable=None, nitrif_ph_variable=None, simnitrfph=None, rnh4o2=None, rno2o2=None, simn2o=None, rn2o=None, kpart_ammox=None, kin_deamm=None, atm_n2o=None, n2o_piston_model=None, rnh4no2=None, kanammox=None, kanmx_nit=None, kanmx_amm=None, rdenit=None, kdenit=None, theta_denit=None, rdnra=None, kdnra_oxy=None, simdrydeposition=None, atm_din_dd=None, simwetdeposition=None, atm_din_conc=None, ksed_amm=None, ksed_nit=None, fsed_n2o=None, ksed_n2o=None, theta_sed_amm=None, theta_sed_nit=None, fsed_amm=None, fsed_nit=None, fsed_amm_variable=None, fsed_nit_variable=None)

Parameters:

Name	Type	Description	Default
amm_initial	Union[float, None]	Initial CH4 concentrations.	None
nit_initial	Union[float, None]	Initial NO3 concentrations.	None
n2o_initial	Union[float, None]	Initial N2O concentrations.	None
no2_initial	Union[float, None]	Initial NO2 concentrations.	None
rnitrif	Union[float, None]	Maximum reaction rate of nitrification at 20C.	None
knitrif	Union[float, None]	Half-saturation oxygen concentration for nitrification.	None
theta_nitrif	Union[float, None]	Undocumented parameter.	None
nitrif_reactant_variable	Union[str, None]	State variable to be consumed during nitrifition.	None
nitrif_ph_variable	Union[str, None]	Undocumented parameter.	None
simnitrfph	Union[bool, None]	Undocumented parameter.	None
rnh4o2	Union[float, None]	Kinetic rate constant for nitratation.	None
rno2o2	Union[float, None]	Kinetic rate constant for nitratation.	None
simn2o	Union[int, None]	Switch to use simple or advanced N reactions.	None
rn2o	Union[float, None]	Kinetic rate constant for N2O consumption	None
kpart_ammox	Union[float, None]	Partitioning parameter for the products of ammonium oxidation, based on O2 concentration.	None
kin_deamm	Union[float, None]	O2 concentration for inhibition of deammonification.	None
atm_n2o	Union[float, None]	Atmospheric N2O concentration.	None
n2o_piston_model	Union[int, None]	Undocumented parameter.	None
rnh4no2	Union[float, None]	Kinetic rate constant for deammonification.	None
kanammox	Union[float, None]	Undocumented parameter.	None
kanmx_nit	Union[float, None]	Undocumented parameter.	None
kanmx_amm	Union[float, None]	Undocumented parameter.	None
rdenit	Union[float, None]	Maximum reaction rate of denitrification at 20C.	None
kdenit	Union[float, None]	Half-saturation oxygen concentration for denitrification.	None
theta_denit	Union[float, None]	Undocumented parameter.	None
rdnra	Union[float, None]	Undocumented parameter.	None
kdnra_oxy	Union[float, None]	Undocumented parameter.	None
simdrydeposition	Union[bool, None]	Undocumented parameter.	None
atm_din_dd	Union[float, None]	Undocumented parameter.	None
simwetdeposition	Union[bool, None]	Undocumented parameter.	None
atm_din_conc	Union[float, None]	Undocumented parameter.	None
ksed_amm	Union[float, None]	Undocumented parameter.	None
ksed_nit	Union[float, None]	Undocumented parameter.	None
fsed_n2o	Union[float, None]	Maximum N2O sediment flux rate.	None
ksed_n2o	Union[float, None]	O2 inhibition concentration parameter.	None
theta_sed_amm	Union[float, None]	Undocumented parameter.	None
theta_sed_nit	Union[float, None]	Undocumented parameter.	None
fsed_amm	Union[float, None]	Sediment NH4 flux.	None
fsed_nit	Union[float, None]	Undocumented parameter.	None
fsed_amm_variable	Union[str, None]	Undocumented parameter.	None
fsed_nit_variable	Union[str, None]		None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

NonCohesiveBlock

Bases: NMLBlock

NMLBlock subclass for the aed_noncohesive block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(num_ss=None, ss_initial=None, ke_ss=None, settling=None, w_ss=None, d_ss=None, rho_ss=None, resuspension=None, epsilon=None, tau_0=None, tau_r=None, ktau_0=None, macrophyte_link_var=None, simsedimentmass=None, fs=None, sed_porosity=None)

Parameters:

Name	Type	Description	Default
num_ss	Union[int, None]	Undocumented parameter.	None
ss_initial	Union[List[int], None]	Undocumented parameter.	None
ke_ss	Union[List[float], None]	Undocumented parameter.	None
settling	Union[int, None]	Undocumented parameter.	None
w_ss	Union[List[float], None]	Undocumented parameter.	None
d_ss	Union[List[float], None]	Undocumented parameter.	None
rho_ss	Union[List[float], None]	Undocumented parameter.	None
resuspension	Union[int, None]	Undocumented parameter.	None
epsilon	Union[float, None]	Undocumented parameter.	None
tau_0	Union[List[float], None]	Undocumented parameter.	None
tau_r	Union[float, None]	Undocumented parameter.	None
ktau_0	Union[float, None]	Undocumented parameter.	None
macrophyte_link_var	Union[str, None]	Undocumented parameter.	None
simsedimentmass	Union[bool, None]	Undocumented parameter.	None
fs	Union[List[float], None]	Undocumented parameter.	None
sed_porosity	Union[float, None]	Undocumented parameter.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

OrganicMatterBlock

Bases: NMLBlock

NMLBlock subclass for the aed_organic_matter block.

Organic matter variables cover the C, N & P stored in the dissolved and particulate organic matter pools. This module optionally also supports depiction of “labile” vs “refractory” fractions of organic matter, including the breakdown and hydrolysis process, photo-degradation and mineralisation.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(poc_initial=None, doc_initial=None, pon_initial=None, don_initial=None, pop_initial=None, dop_initial=None, docr_initial=None, donr_initial=None, dopr_initial=None, cpom_initial=None, rdom_minerl=None, rdoc_minerl=None, rdon_minerl=None, rdop_minerl=None, rpoc_hydrol=None, rpon_hydrol=None, rpop_hydrol=None, theta_hydrol=None, theta_minerl=None, kpom_hydrol=None, kdom_minerl=None, simdenitrification=None, dom_miner_oxy_reactant_var=None, dom_miner_nit_reactant_var=None, dom_miner_no2_reactant_var=None, dom_miner_n2o_reactant_var=None, dom_miner_fe3_reactant_var=None, dom_miner_so4_reactant_var=None, dom_miner_ch4_reactant_var=None, doc_miner_product_variable=None, don_miner_product_variable=None, dop_miner_product_variable=None, f_an=None, k_nit=None, simrpools=None, rdomr_minerl=None, rcpom_bdown=None, x_cpom_n=None, x_cpom_p=None, kedom=None, kepom=None, kedomr=None, kecpom=None, simphotolysis=None, photo_c=None, settling=None, w_pom=None, d_pom=None, rho_pom=None, w_cpom=None, d_cpom=None, rho_cpom=None, resuspension=None, resus_link=None, sedimentomfrac=None, xsc=None, xsn=None, xsp=None, fsed_doc=None, fsed_don=None, fsed_dop=None, ksed_dom=None, theta_sed_dom=None, fsed_doc_variable=None, fsed_don_variable=None, fsed_dop_variable=None, diag_level=None, extra_diag=None)

Parameters:

Name	Type	Description	Default
poc_initial	Union[float, None]	Initial POC concentration.	None
doc_initial	Union[float, None]	Initial DOC concentration.	None
pon_initial	Union[float, None]	Initial PON concentration.	None
don_initial	Union[float, None]	Initial DON concentration.	None
pop_initial	Union[float, None]	Initial POP concentration.	None
dop_initial	Union[float, None]	Initial DOP concentration.	None
docr_initial	Union[float, None]	Initial DOCR concentration. Required if simrpools is True.	None
donr_initial	Union[float, None]	Initial DONR concentration. Required if simrpools is True.	None
dopr_initial	Union[float, None]	Initial DOPR concentration. Required if simrpools is True.	None
cpom_initial	Union[float, None]	Initial CPOM concentration. Required if simrpools is True.	None
rdom_minerl	Union[float, None]	Reference DOM mineralisation rate at 20C.	None
rdoc_minerl	Union[float, None]	Reference DOC mineralisation rate at 20C.	None
rdon_minerl	Union[float, None]	Reference DON mineralisation rate at 20C.	None
rdop_minerl	Union[float, None]	Reference DOP mineralisation rate at 20C.	None
rpoc_hydrol	Union[float, None]	Reference POC hydrolysis/breakdown rate at 20C.	None
rpon_hydrol	Union[float, None]	Reference PON hydrolysis/breakdown rate at 20C.	None
rpop_hydrol	Union[float, None]	Reference POP hydrolysis/breakdown rate at 20C.	None
theta_hydrol	Union[float, None]	Arrhenius temperature scaling coefficient for POC hydrolysis.	None
theta_minerl	Union[float, None]	Arrhenius temperature scaling coefficient for DOM mineralisation.	None
kpom_hydrol	Union[float, None]	Half-saturation O2 concentration for POM hydrolysis.	None
kdom_minerl	Union[float, None]	Half-saturation O2 concentration for DOM hydrolysis.	None
simdenitrification	Union[int, None]	Option to select denitrification sub-model.	None
dom_miner_oxy_reactant_var	Union[str, None]	State variable used to control aerobic mineralisation.	None
dom_miner_nit_reactant_var	Union[str, None]	State variable used to control nitrate reduction.	None
dom_miner_no2_reactant_var	Union[str, None]	State variable used to control nitrite reduction.	None
dom_miner_n2o_reactant_var	Union[str, None]	State variable used to control N2O reduction.	None
dom_miner_fe3_reactant_var	Union[str, None]	State variable used to control iron reduction.	None
dom_miner_so4_reactant_var	Union[str, None]	State variable used to control sulfate reduction.	None
dom_miner_ch4_reactant_var	Union[str, None]	State variable to receive methan.	None
doc_miner_product_variable	Union[str, None]	State variable to receive DIC.	None
don_miner_product_variable	Union[str, None]	State variable to receive NH4.	None
dop_miner_product_variable	Union[str, None]	State variable to receive PO4.	None
f_an	Union[float, None]	Undocumented parameter.	None
k_nit	Union[float, None]	Undocumented parameter.	None
simrpools	Union[bool, None]	Option to include refractory OM pools, including DOM_{R} and CPOM.	None
rdomr_minerl	Union[float, None]	Reference DOM_{R} mineralisation rate at 20C.	None
rcpom_bdown	Union[float, None]	Reference CPOM hydrolysis/breakdown rate at 20C.	None
x_cpom_n	Union[float, None]	CPOM nitrogen stoichiometry.	None
x_cpom_p	Union[float, None]	CPOM phosphorus stoichiometry.	None
kedom	Union[float, None]	Specific light attenuation coefficient for DOM.	None
kepom	Union[float, None]	Specific light attenuation coefficient for POM.	None
kedomr	Union[float, None]	Specific light attenuation coefficient for DOM_{R}.	None
kecpom	Union[float, None]	Specific light attenuation coefficient for CPOM.	None
simphotolysis	Union[bool, None]	Option to include photo-mineralisation of DOM_{R}.	None
photo_c	Union[float, None]	Photolysis constant.	None
settling	Union[int, None]	Option to set the method of settling for POM and CPOM.	None
w_pom	Union[float, None]	Sedimentation velocity of POM detrital particles. Used if settling is 1 or 2.	None
d_pom	Union[float, None]	Diameter of POM detrital particles. Used if settling is 3.	None
rho_pom	Union[float, None]	Density of POM detrital particles. Used if settling is 3.	None
w_cpom	Union[float, None]	Sedimentation velocity of CPOM particles. Used if settling is 1 or 2.	None
d_cpom	Union[float, None]	Diameter of CPOM particles. Used if settling is 3.	None
rho_cpom	Union[float, None]	Density of CPOM detrital particles. Used if settling is 3.	None
resuspension	Union[int, None]	Option to set the method of resuspension for POM and CPOM.	None
resus_link	Union[str, None]	Diagnostic variable to link to for resuspension rate.	None
sedimentomfrac	Union[float, None]	Fraction by weight of surficial sediment organic matter.	None
xsc	Union[float, None]	Stoichiometry of sedment particulate carbon.	None
xsn	Union[float, None]	Stoichiometry of sedment particulate nitrogen.	None
xsp	Union[float, None]	Stoichiometry of sedment particulate phosphorus.	None
fsed_doc	Union[float, None]	Reference sediment DOC flux at 20C.	None
fsed_don	Union[float, None]	Reference sediment DON flux at 20C.	None
fsed_dop	Union[float, None]	Reference sediment DOP flux at 20C.	None
ksed_dom	Union[float, None]	Half-saturation oxygen concentraion controlling DOM sediment flux.	None
theta_sed_dom	Union[float, None]	Arrhenius temperature multiplier for sediment DOM flux.	None
fsed_doc_variable	Union[str, None]	Variable name to link to for spatially resolved sediment zones.	None
fsed_don_variable	Union[str, None]	Variable name to link to for spatially resolved sediment zones.	None
fsed_dop_variable	Union[str, None]	Variable name to link to for spatially resolved sediment zones.	None
diag_level	Union[int, None]	Undocumented parameter.	None
extra_diag	Union[bool, None]	Undocumented parameter.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

OxygenBlock

Bases: NMLBlock

NMLBlock subclass for the aed_oxygen block.

Dissolved oxygen (DO) dynamics are able to be simulated, accounting for atmospheric exchange and sediment oxygen demand, and through links to other modules will account for microbial use during organic matter mineralisation and nitrification, photosynthetic oxygen production and respiratory oxygen consumption, and respiration by other optional biotic components

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(oxy_initial=None, oxy_min=None, oxy_max=None, fsed_oxy=None, ksed_oxy=None, theta_sed_oxy=None, fsed_oxy_variable=None, oxy_piston_model=None, altitude=None)

Parameters:

Name	Type	Description	Default
oxy_initial	Union[float, None]	Initial O2 concentration.	None
oxy_min	Union[float, None]	Minimum O2 concentration.	None
oxy_max	Union[float, None]	Maximum O2 concentration.	None
fsed_oxy	Union[float, None]	Sediment O2 flux at 20C.	None
ksed_oxy	Union[float, None]	Arrhenius temperature multiplier for sediment O2 flux.	None
fsed_oxy_variable	Union[str, None]	Variable name to link to for spatially resolved sediment zones.	None
oxy_piston_model	Union[int, None]	Selection of air/water O2 flux velocity method.	None
altitude	Union[float, None]	Altitude of site above sea level.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

PhosphorusBlock

Bases: NMLBlock

NMLBlock subclass for the aed_phosphorus block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(frp_initial=None, frp_min=None, frp_max=None, fsed_frp=None, ksed_frp=None, theta_sed_frp=None, phosphorus_reactant_variable=None, fsed_frp_variable=None, simpo4adsorption=None, ads_use_external_tss=None, po4sorption_target_variable=None, po4adsorptionmodel=None, kpo4p=None, kadsratio=None, qmax=None, w_po4ads=None, ads_use_ph=None, ph_variable=None, simdrydeposition=None, atm_pip_dd=None, simwetdeposition=None, atm_frp_conc=None)

Parameters:

Name	Type	Description	Default
frp_initial	Union[float, None]	Initial PO4 concentration.	None
frp_min	Union[float, None]	Minimum PO4 concentration.	None
frp_max	Union[float, None]	Maximum PO4 concentration.	None
fsed_frp	Union[float, None]	Sediment PO4 flux at 20C.	None
ksed_frp	Union[float, None]	Half-saturation oxygen concentration controlling O2 flux.	None
theta_sed_frp	Union[float, None]	Arrhenius temperature multiplier for sediment O2 flux.	None
phosphorus_reactant_variable	Union[str, None]	State variable used to control PO4 sediment release.	None
fsed_frp_variable	Union[str, None]	Variable name to link to for spatially resolved sediment zones.	None
simpo4adsorption	Union[bool, None]	Option to allow include absorption.	None
ads_use_external_tss	Union[bool, None]	Option to use externally simulated TSS concentration as sorbent.	None
po4sorption_target_variable	Union[str, None]	Variable name to link to for PO4 sorbent.	None
po4adsorptionmodel	Union[int, None]	Selection of PO4 sorption method. 1 for Ji (2008), 2 for Choa et al (2010).	None
kpo4p	Union[float, None]	Sorption partitioning coefficient.	None
kadsratio	Union[float, None]	Ratio of adsorption and desorp-tion rate coefficients (for po4adsorptionmodel equals 2).	None
qmax	Union[float, None]	Maximum adsorption capacity (for po4adsorptionmodel equals 2).	None
w_po4ads	Union[float, None]	Sedimentation velocity of PO_{4}^{ads}.	None
ads_use_ph	Union[bool, None]	Option to include pH control on sorption coefficient. Function based on pH sorption control on Fe minerals.	None
ph_variable	Union[str, None]	Variable name to link to for pH to influence sorption.	None
simdrydeposition	Union[bool, None]	Option to include dry (particulate) deposition of P.	None
atm_pip_dd	Union[float, None]	PO_{4}^{ads} deposition rate.	None
simwetdeposition	Union[bool, None]	Option to include wet deposition of P through rainfall.	None
atm_frp_conc	Union[float, None]	PO4 concentration in rainfall.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

PhytoplanktonBlock

Bases: NMLBlock

NMLBlock subclass for the aed_phytoplankton block.

Highly customisable phytoplankton module for simulating change in algae, cyano-bacteria and chl-a, including phytoplankton production/respiration, nutrient uptake, excretion, vertical movement (eg buoyancy control), and grazing effects. Benthic phytoplankton may also be optionally configured.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(num_phytos=None, the_phytos=None, settling=None, do_mpb=None, r_mpbg=None, r_mpbr=None, i_kmpb=None, mpb_max=None, resuspension=None, n_zones=None, active_zones=None, resus_link=None, p_excretion_target_variable=None, n_excretion_target_variable=None, c_excretion_target_variable=None, si_excretion_target_variable=None, p_mortality_target_variable=None, n_mortality_target_variable=None, c_mortality_target_variable=None, si_mortality_target_variable=None, p1_uptake_target_variable=None, n1_uptake_target_variable=None, n2_uptake_target_variable=None, si_uptake_target_variable=None, do_uptake_target_variable=None, c_uptake_target_variable=None, dbase=None, min_rho=None, max_rho=None, diag_level=None, extra_diag=None)

Parameters:

Name	Type	Description	Default
num_phytos	Union[int, None]	Number of phytoplankton groups/species.	None
the_phytos	Union[List[int], int, None]	Set of chosen group IDs within the database file.	None
settling	Union[List[int], int, None]	Option to set the method of settling for PHY group alpha.	None
do_mpb	Union[int, None]	Option to include MPB as a simulated benthic variable.	None
r_mpbg	Union[float, None]	Maximum growth rate of MPB.	None
r_mpbr	Union[float, None]	Dark respiration rate of MPB.	None
i_kmpb	Union[float, None]	Half saturation constant for light limitation of growth.	None
mpb_max	Union[float, None]	Maximum biomass density of MPB.	None
resuspension	Union[float, None]	Fraction to set the amount of resuspension for PHY group alpha.	None
n_zones	Union[int, None]	Number of benthic zones where MPB is active.	None
active_zones	Union[int, None]	Set of benthic zones with MPB active.	None
resus_link	Union[str, None]	Undocumented parameter.	None
p_excretion_target_variable	Union[str, None]	State variable to add DOP excretion.	None
n_excretion_target_variable	Union[str, None]	State variable to add DON excretion.	None
c_excretion_target_variable	Union[str, None]	State variable to add DOC excretion.	None
si_excretion_target_variable	Union[str, None]	State variable to add Si excretion.	None
p_mortality_target_variable	Union[str, None]	State variable to add POP mortality	None
n_mortality_target_variable	Union[str, None]	State variable to add PON mortality.	None
c_mortality_target_variable	Union[str, None]	State variable to add POC mortality.	None
si_mortality_target_variable	Union[str, None]	State variable to add Si mortality.	None
p1_uptake_target_variable	Union[str, None]	State variable to provide FRP for growth.	None
n1_uptake_target_variable	Union[str, None]	State variable to provide NO3 for growth.	None
n2_uptake_target_variable	Union[str, None]	State variable to provide NH4 for growth.	None
si_uptake_target_variable	Union[str, None]	State variable to provide Si for growth.	None
do_uptake_target_variable	Union[str, None]	State variable to incremen during growth.	None
c_uptake_target_variable	Union[str, None]	State variable to provide DIC during growth.	None
dbase	Union[str, None]	Phytoplankton parameter database file.	None
min_rho	Union[float, None]	Minimum cellular density. Used if settling is 3.	None
max_rho	Union[float, None]	Maximum cellular density. Used if settling is 3.	None
diag_level	Union[int, None]	Extent of diagnostic output.	None
extra_diag	Union[bool, None]	Undocumented parameter.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

SedConst2DBlock

Bases: NMLBlock

NMLBlock subclass for the aed_sed_const2d block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(n_zones=None, active_zones=None, fsed_oxy=None, fsed_rsi=None, fsed_amm=None, fsed_nit=None, fsed_frp=None, fsed_pon=None, fsed_don=None, fsed_pop=None, fsed_dop=None, fsed_poc=None, fsed_doc=None, fsed_dic=None, fsed_ch4=None, fsed_feii=None)

Parameters:

Name	Type	Description	Default
n_zones	Union[int, None]	Number of zones.	None
active_zones	Union[int, None].	The zones to activate.	None
fsed_oxy	Union[List[float], None]	Sedimentation flux for oxygen.	None
fsed_rsi	Union[List[float], float, None]	Sedimentation flux for silica.	None
fsed_amm	Union[List[float], None]	Sedimentation flux for ammonia.	None
fsed_nit	Union[List[float], None]	Sedimentation flux for nitrogen.	None
fsed_frp	Union[List[float], None]	Sedimentation flux for phosphorus.	None
fsed_pon	Union[List[float], float, None]	Sedimentation flux for particulate organic nitrogen.	None
fsed_don	Union[List[float], float, None]	Sedimentation flux for dissolved organic nitrogen.	None
fsed_pop	Union[List[float], float, None]	Sedimentation flux for particulate organic phosphorus.	None
fsed_dop	Union[List[float], float, None]	Sedimentation flux for dissolved organic phosphorus.	None
fsed_poc	Union[List[float], float, None]	Sedimentation flux for particulate organic carbon.	None
fsed_doc	Union[List[float], float, None]	Sedimentation flux for dissolved organic carbon.	None
fsed_dic	Union[List[float], float, None]	Sedimentation flux for dissolved inorganic carbon.	None
fsed_ch4	Union[List[float], None]	Sedimentation flux for methane.	None
fsed_feii	Union[List[float], float, None]	Sedimentation flux for iron.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

SedFluxBlock

Bases: NMLBlock

NMLBlock subclass for the aed_sedflux block.

An interface module designed to provide spatially variable sediment flux settings to key modules (e.g., OXY, OGM, NUT), and/or link these variables to the dynamic sediment biogeochemistry model (SDG).

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(sedflux_model=None)

Parameters:

Name	Type	Description	Default
sedflux_model	Union[str, None]	Controls the setup of zones and whether the flux is taken from a constant value or from CANDI-AED.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

SilicaBlock

Bases: NMLBlock

NMLBlock subclass for the aed_silica block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(rsi_initial=None, rsi_min=None, rsi_max=None, fsed_rsi=None, ksed_rsi=None, theta_sed_rsi=None, fsed_rsi_variable=None, silica_reactant_variable=None)

Parameters:

Name	Type	Description	Default
rsi_initial	Union[float, None]	Initial RSi concentration.	None
rsi_min	Union[float, None]	Minimum RSi concentration.	None
rsi_max	Union[float, None]	Maximum RSi concentration.	None
fsed_rsi	Union[float, None]	Reference sediment RSi flux at 20C.	None
ksed_rsi	Union[float, None]	Half-saturation oxygen concentration controlling Si flux.	None
theta_sed_rsi	Union[float, None]	Arrhenius temperature multiplier for sediment Si flux.	None
fsed_rsi_variable	Union[str, None]	Variable name to link to for spatially resolved sediment zones.	None
silica_reactant_variable	Union[str, None]	State variable used to control Si sediment release.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

TotalsBlock

Bases: NMLBlock

NMLBlock subclass for the aed_totals block.

aed_totals is a summary module, allowing users to “sum-up” component variables from other modules into a total, for example, to compute TN, TP or TSS.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(outputlight=None, tn_vars=None, tn_varscale=None, tp_vars=None, tp_varscale=None, toc_vars=None, toc_varscale=None, tss_vars=None, tss_varscale=None)

Parameters:

Name	Type	Description	Default
outputlight	Union[bool, None]	Undocumented parameter.	None
tn_vars	Union[List[str], str, None]	Undocumented parameter.	None
tn_varscale	Union[List[float], float, None]	Undocumented parameter.	None
tp_vars	Union[List[str], str, None]	Undocumented parameter.	None
tp_varscale	Union[List[float], float, None]	Undocumented parameter.	None
toc_vars	Union[List[str], str, None]	Undocumented parameter.	None
toc_varscale	Union[List[float], float, None]	Undocumented parameter.	None
tss_vars	Union[List[str], str, None]	Undocumented parameter.	None
tss_varscale	Union[List[float], float, None]	Undocumented parameter.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

TracerBlock

Bases: NMLBlock

NMLBlock subclass for the aed_tracer block.

Modellers can use the aed_tracer to simulate a dissolved or particulate tracer (subject to transport processes only), or this can be optionally configured to account for decay, sedimentation and/or resuspension. This module also include an option to simulate water “retention time” where the water age increments once enters into the waterbody.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(retention_time=None, num_tracers=None, decay=None, fsed=None, ke_ss=None, settling=None, w_ss=None, d_ss=None, rho_ss=None, resuspension=None, fs=None, epsilon=None, tau_0=None, tau_r=None, ktau_0=None, macrophyte_link_var=None)

Parameters:

Name	Type	Description	Default
retention_time	Union[bool, None]	Activates the retention time variable.	None
num_tracers	Union[int, None]	Number of tracers to model.	None
decay	Union[List[float], float, None]	Vector of decay rates for each simulated tracer group.	None
fsed	Union[List[float], None]	Vector of sediment flux rates for each simulated tracer group.	None
ke_ss	Union[List[float], float, None]	Vector of specific light attenuation constants for each simulated tracer group.	None
settling	Union[int, None]	Settling sub-model. 0 for none, 1 for constant, 2 for constant (temp. adjusted), 3 for Stokes.	None
w_ss	Union[List[float], float, None]	Vector of sedimentation velocity. Used if settling is 1 or 2.	None
d_ss	Union[List[float], float, None]	Vector of particle diameter. Used if settling is 3.	None
rho_ss	Union[List[float], float, None]	Vector of particle density. Used if settling is 3.	None
resuspension	Union[int, None]	Resuspension sub-model. 0 for none, 1 for constant, 2 for constant adjusted, 3 for Stokes.	None
fs	Union[List[float], float, None]	Vector of particle fraction within the sediment. Must be of length num_tracers.	None
epsilon	Union[List[float], float, None]	Vector of resuspension rate coefficient.	None
tau_0	Union[List[float], float, None]	Vector of critical shear stress for resuspension.	None
tau_r	Union[List[float], float, None]	Reference shear stress.	None
ktau_0	Union[List[float], float, None]	Coefficient determining the effect of macrophyte_link_var on tau_0.	None
macrophyte_link_var	Union[str, None]	AED2 benthic variable on which the critical shear stress depends.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

ZooplanktonBlock

Bases: NMLBlock

aed_zooplankton block.

Simulates different size classes of zooplankton, accounting for carbon and nutrient assimilation from grazing, carbon loss via respiration, excretion of DOM, faecal pellet production, mortality, and predation by larger organisms.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(num_zoops=None, the_zoops=None, dn_target_variable=None, pn_target_variable=None, dp_target_variable=None, pp_target_variable=None, dc_target_variable=None, pc_target_variable=None, dbase=None, simzoopfeedback=None)

Parameters:

Name	Type	Description	Default
num_zoops	Union[int, None]	Number of zooplankton groups.	None
the_zoops	Union[List[int], int, None]	List of ID's of groups in aed_zoo_pars database. Length must equal num_phyto.	None
dn_target_variable	Union[str, None]	Undocumented parameter.	None
pn_target_variable	Union[str, None]	Undocumented parameter.	None
dp_target_variable	Union[str, None]	Undocumented parameter.	None
pp_target_variable	Union[str, None]	Undocumented parameter.	None
dc_target_variable	Union[str, None]	Undocumented parameter.	None
pc_target_variable	Union[str, None]	Undocumented parameter.	None
dbase	Union[str, None]	Undocumented parameter.	None
simzoopfeedback	Union[bool, None]	Undocumented parameter.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

glm_nml

BirdModelBlock

Bases: NMLBlock

NMLBlock subclass for the bird_model block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(ap=None, oz=None, watvap=None, aod500=None, aod380=None, albedo=None)

Parameters:

Name	Type	Description	Default
ap	Union[float, None]	Atmospheric pressure (hPa).	None
oz	Union[float, None]	Ozone concentration (atm-cm).	None
watvap	Union[float, None]	Total Precipitable water vapor (atm-cm).	None
aod500	Union[float, None]	Dimensionless Aerosol Optical Depth at wavelength 500 nm.	None
aod380	Union[float, None]	Dimensionless Aerosol Optical Depth at wavelength 380 nm.	None
albedo	Union[float, None]	Albedo of the surface used for Bird Model insolation calculation.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

GLMNML

Bases: NML

NML subclass for the glm .NML file.

Attributes:

Name	Type	Description
blocks	Dict[str, NMLBlock]	Dictionary of NMLBlock objects.
strict	bool	Switch to turn on or off block and parameter validation.

__init__(glm_setup=GLMSetupBlock(), time=TimeBlock(), morphometry=MorphometryBlock(), init_profiles=InitProfilesBlock(), mixing=MixingBlock(), wq_setup=WQSetupBlock(), output=OutputBlock(), light=LightBlock(), bird_model=BirdModelBlock(), sediment=SedimentBlock(), snowice=SnowIceBlock(), meteorology=MeteorologyBlock(), inflow=InflowBlock(), outflow=OutflowBlock())

Parameters:

Name	Type	Description	Default
glm_setup	GLMSetupBlock		GLMSetupBlock()
time	TimeBlock		TimeBlock()
morphometry	MorphometryBlock		MorphometryBlock()
init_profiles	InitProfilesBlock		InitProfilesBlock()
mixing	MixingBlock		MixingBlock()
wq_setup	WQSetupBlock		WQSetupBlock()
output	OutputBlock		OutputBlock()
light	LightBlock		LightBlock()
bird_model	BirdModelBlock		BirdModelBlock()
sediment	SedimentBlock		SedimentBlock()
snowice	SnowIceBlock		SnowIceBlock()
meteorology	MeteorologyBlock		MeteorologyBlock()
inflow	InflowBlock		InflowBlock()
outflow	OutflowBlock		OutflowBlock()

from_dict(nml_dict) classmethod

Initialise class instance from a dictionary.

Returns an instance of the class that has been initialised with a nested dictionary of NML parameters.

Parameters:

Name	Type	Description	Default
nml_dict	dict	A dictionary where the keys are the block names and the values are dictionaries of parameter names (keys) and parameter values (values).	required

from_file(nml_path) classmethod

Initialise class instance from a NML file.

Returns an instance of the class that has been initialised with parameters from a NML file.

Parameters:

Name	Type	Description	Default
nml_path	dict	Path to the NML file.	required

get_block(block_name)

Get a NML Block.

Returns an instance of a NMLBlock subclass from the NML.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required

get_block_names()

List the block names.

Returns a list of the name attribute for all NMLBlock subclass instances.

get_param_names(block_name)

List the parameter names in a block.

Returns a list of the name attribute for all NMLParam instances.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required

get_param_units(block_name, param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required
param_name	str	The name of the parameter to return the value for.	required

get_param_value(block_name, param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required
param_name	str	The name of the parameter to return the value for.	required

init_blocks(*args)

Populate the blocks dictionary with instances of NMLBlock subclasses.

is_none_nml()

Test if all NML parameter values are None.

Returns True if is_none_block() is True for all subclassed NMLBlock instances in the blocks dictionary.

iter_blocks()

Iterate over all NMLBlock objects.

iter_params()

Iterate over all NMLParam objects.

set_block(block_name, block)

Set a NML Block.

Overrides, or adds a new block, to a NML.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required
block	NMLBlock	The block to set.	required

set_param_value(block_name, param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_blocks=True, none_params=True)

Nested dictionary of parameters.

Returns a nested dictionary where the keys are the block names and the values a dictionary of parameter values.

Parameters:

Name	Type	Description	Default
none_blocks	bool	Whether to include blocks where all parameter values are None.	True
none_params	bool	Whether to include parameter values that are None.	True

to_nml(nml_path='glm3.nml')

Write a NML file.

Parameters with values of None are omitted.

Parameters:

Name	Type	Description	Default
nml_path	str	Path to the NML file	'glm3.nml'

GLMSetupBlock

Bases: NMLBlock

NMLBlock subclass for the glm_setup block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(sim_name=None, max_layers=None, min_layer_vol=None, min_layer_thick=None, max_layer_thick=None, density_model=None, non_avg=None)

Parameters:

Name	Type	Description	Default
sim_name	Union[str, None]	Title of simulation.	None
max_layers	Union[int, None]	Maximum number of layers.	None
min_layer_vol	Union[float, None]	Minimum layer volume (m^3).	None
min_layer_thick	Union[float, None]	Minimum thickness of a layer (m).	None
max_layer_thick	Union[float, None]	Maximum thickness of a layer (m).	None
density_model	Union[int, None]	Switch to set the density equation. Options are 1 for TEOS-10, 2 for UNESCO(1981), and 3 for a custom implementation.	None
non_avg	Union[bool, None]	Switch to configure flow boundary condition temporal interpolation.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

InflowBlock

Bases: NMLBlock

NMLBlock subclass for the inflow block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(num_inflows=None, names_of_strms=None, subm_flag=None, subm_elev=None, strm_hf_angle=None, strmbd_slope=None, strmbd_drag=None, coef_inf_entrain=None, inflow_factor=None, inflow_fl=None, inflow_varnum=None, inflow_vars=None, time_fmt=None)

Parameters:

Name	Type	Description	Default
num_inflows	Union[int, None]	Number of inflows to be simulated in this simulation.	None
names_of_strms	Union[List[str], str, None]	Names of each inflow. A list if num_inflows > 1.	None
subm_flag	Union[List[bool], bool, None]	Switch indicating if the inflow is entering as a submerged input. A list if num_inflows > 1.	None
subm_elev	Union[List[float], float, None]	Elevation of the submerged inflow. A list if num_inflows > 1.	None
strm_hf_angle	Union[List[float], float, None]	Angle describing the width of an inflow river channel ("half angle"). A list if num_inflows > 1.	None
strmbd_slope	Union[List[float], float, None]	Slope of the streambed / river thalweg for each river (degrees). A list if num_inflows > 1.	None
strmbd_drag	Union[List[float], float, None]	Drag coefficient of the river inflow thalweg, to calculate entrainment during insertion. A list if num_inflows > 1.	None
coef_inf_entrain	Union[List[float], float, None]	Undocumented parameter. A list if num_inflows > 1.	None
inflow_factor	Union[List[float], float, None]	Scaling factor that can be applied to adjust the provided input data. A list if num_inflows > 1.	None
inflow_fl	Union[List[str], str, None]	Filename(s) of the inflow CSV boundary condition files. A list if num_inflows > 1.	None
inflow_varnum	Union[int, None]	Number of variables being listed in the columns of inflow_fl. Can include GLM variables.	None
inflow_vars	Union[List[str], str, None]	Names of the variables in the inflow_fl. Provide variables in the order as they are in the file.	None
time_fmt	Union[str, None]	Time format of the 1st column in the inflow_fl. For example, 'YYYY-MM-DD hh:mm:ss'.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

InitProfilesBlock

Bases: NMLBlock

NMLBlock subclass for the init_profiles block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(lake_depth=None, num_depths=None, the_depths=None, the_temps=None, the_sals=None, num_wq_vars=None, wq_names=None, wq_init_vals=None, snow_thickness=None, white_ice_thickness=None, blue_ice_thickness=None, avg_surf_temp=None, restart_variables=None)

Parameters:

Name	Type	Description	Default
lake_depth	Union[float, None]	Initial lake height/depth (m).	None
num_depths	Union[int, None]	Number of depths provided for initial profiles.	None
the_depths	Union[List[float], float, None]	The depths of the initial profile points (m).	None
the_temps	Union[List[float], float, None]	The temperature (°C) at each of the initial profile points.	None
the_sals	Union[List[float], float, None]	The salinity (ppt) at each of the initial profile points.	None
num_wq_vars	Union[int, None]	Number of non-GLM (i.e., FABM or AED2) variables to be initialised.	None
wq_names	Union[List[str], str, None]	Names of non-GLM (i.e., FABM or AED2) variables to be initialised.	None
wq_init_vals	Union[List[float], float, None]	List of water quality variable initial data.	None
snow_thickness	Union[float, None]	Thickness of snow (m).	None
white_ice_thickness	Union[float, None]	Thickness of white ice (m).	None
blue_ice_thickness	Union[float, None]	Thickness of blue ice (m).	None
restart_variables	Union[List[float], float, None]	Restart variables to restart model from a previous saved state.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

LightBlock

Bases: NMLBlock

NMLBlock subclass for the light block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(light_mode=None, kw=None, kw_file=None, n_bands=None, light_extc=None, energy_frac=None, benthic_imin=None)

Parameters:

Name	Type	Description	Default
light_mode	Union[int, None]	Switch to configure the approach to light penetration. Options are 0 or 1.	None
kw	Union[float, None]	Light extinction coefficient (m^{-1}). Used when light_mode=0.	None
kw_file	Union[str, None]	Name of file with Kw time-series included.	None
n_bands	Union[int, None]	Number of light bandwidths to simulate. Used when light_mode=1.	None
light_extc	Union[List[float], float, None]	Comma-separated list of light extinction coefficients for each waveband.	None
energy_frac	Union[List[float], float, None]	Comma-separated list of energy fraction captured by each waveband.	None
benthic_imin	Union[float, None]	Critical fraction of incident light reaching the benthos.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

MeteorologyBlock

Bases: NMLBlock

NMLBlock subclass for the meteorology block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(met_sw=None, meteo_fl=None, subdaily=None, time_fmt=None, rad_mode=None, albedo_mode=None, sw_factor=None, lw_type=None, cloud_mode=None, lw_factor=None, lw_offset=None, atm_stab=None, rh_factor=None, at_factor=None, ce=None, ch=None, rain_sw=None, rain_factor=None, catchrain=None, rain_threshold=None, runoff_coef=None, cd=None, wind_factor=None, fetch_mode=None, aws=None, xws=None, num_dir=None, wind_dir=None, fetch_scale=None)

Parameters:

Name	Type	Description	Default
met_sw	Union[bool, None]	Switch to enable the surface heating module.	None
meteo_fl	Union[str, None]	Filename of the meterological file. Include path and filename.	None
subdaily	Union[bool, None]	Switch to indicate the meteorological data is provided with sub-daily resolution, at an interval equivalent to dt from TimeBlock (Δt).	None
time_fmt	Union[str, None]	Time format of the 1st column in the inflow_fl. For example, 'YYYY-MM-DD hhss'.	None
rad_mode	Union[int, None]	Switch to configure which incoming radiation option to use. Options are 1, 2, 3, 4, or 5.	None
albedo_mode	Union[int, None]	Switch to configure which albedo calculation option is used. Options are 1 for Hamilton & Schladow, 2 for Briegleb et al., or 3 for Yajima & Yamamoto.	None
sw_factor	Union[float, None]	Scaling factor to adjust the shortwave radiation data provided in the meteo_fl.	None
lw_type	Union[str, None]	Switch to configure which input approach is being used for longwave/cloud data in the meteo_fl. Options are 'LW_IN' for incident longwave, 'LW_NET' for net longwave, or 'LW_CC' for cloud cover.	None
cloud_mode	Union[int, None]	Switch to configure which atmospheric emmissivity calculation option is used. Options are 1 for Idso and Jackson, 2 for Swinbank, 3 for Brutsaert, 4 for Yajima & Yamamoto.	None
lw_factor	Union[float, None]	Scaling factor to adjust the longwave (or cloud) data provided in the meteo_fl.	None
atm_stab	Union[int, None]	Switch to configure which approach to atmospheric stability is used. 0 for neutral conditions, 1 for an undocumented use case, and 2 for an undocumented use case.	None
rh_factor	Union[float, None]	Scaling factor to adjust the relative humidity data provided in the meteo_fl.	None
at_factor	Union[float, None]	Scaling factor to adjust the air temperature data provided in the meteo_fl.	None
ce	Union[float, None]	Bulk aerodynamic transfer coefficient for latent heat flux.	None
ch	Union[float, None]	Bulk aerodynamic transfer coefficient for sensible heat flux.	None
rain_sw	Union[bool, None]	Switch to configure rainfall input concentrations.	None
rain_factor	Union[float, None]	Scaling factor to adjust the rainfall data provided in the meteo_fl.	None
catchrain	Union[bool, None]	Switch that configures runoff from exposed banks of lake area.	None
rain_threshold	Union[float, None]	Daily rainfall amount (m) required before runoff from exposed banks occurs.	None
runoff_coef	Union[float, None]	Conversion fraction of infiltration excess rainfall to runoff in exposed lake banks.	None
cd	Union[float, None]	Bulk aerodynamic transfer coefficient for momentum.	None
wind_factor	Union[float, None]	Scaling factor to adjust the windspeed data provided in the meteo_fl.	None
fetch_mode	Union[int, None]	Switch to configure which wind-sheltering/fetch option to use. Options are 0 for no sheltering, 1 for area-based scaling, 2 for Markfort length-scale, or 3 for user input scaling table.	None
aws	Union[float, None]	Undocumented parameter. Required if fetch_mode is 1.	None
xws	Union[float, None]	Undocumented parameter. Required if fetch_mode is 2.	None
num_dir	Union[int, None]	Number of wind direction reference points being read in. Required if fetch_mode is 2 or fetch_mode is 3.	None
wind_dir	Union[float, None]	Wind directions used for wind-sheltering effects. Required if fetch_mode=2 or fetch_mode=3.	None
fetch_scale	Union[float, None]	Direction specific wind-sheltering scaling factors. Required if fetch_mode=2 or fetch_mode=3.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

MixingBlock

Bases: NMLBlock

NMLBlock subclass for the mixing block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(surface_mixing=None, coef_mix_conv=None, coef_wind_stir=None, coef_mix_shear=None, coef_mix_turb=None, coef_mix_kh=None, deep_mixing=None, coef_mix_hyp=None, coef_mix_shreq=None, diff=None)

Parameters:

Name	Type	Description	Default
surface_mixing	Union[int, None]	Switch to select the options of the surface mixing model. Options are 0 for no surface mixing, 1, and 2.	None
coef_mix_conv	Union[float, None]	Mixing efficiency - convective overturn.	None
coef_wind_stir	Union[float, None]	Mixing efficiency - wind stirring.	None
coef_mix_shear	Union[float, None]	Mixing efficiency - shear production.	None
coef_mix_turb	Union[float, None]	Mixing efficiency - unsteady turbulence effects.	None
coef_mix_kh	Union[float, None]	Mixing efficiency - Kelvin-Helmholtz billowing.	None
deep_mixing	Union[int, None]	Switch to select the options of the deep (hypolimnetic) mixing model. Options are 0 for no deep mixing, 1 for constant diffusivity, and 2 for the Weinstock model.	None
coef_mix_hyp	Union[float, None]	Mixing efficiency - hypolimnetic turbulence.	None
coef_mix_shreq	Union[int, None]	Undocumented parameter.	None
diff	Union[float, None]	Background (molecular) diffusivity in the hypolimnion.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

MorphometryBlock

Bases: NMLBlock

NMLBlock subclass for the morphometry block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(lake_name=None, latitude=None, longitude=None, base_elev=None, crest_elev=None, bsn_len=None, bsn_wid=None, bsn_vals=None, h=None, a=None)

Parameters:

Name	Type	Description	Default
lake_name	Union[str, None]	Site name.	None
latitude	Union[float, None]	Latitude, positive North (°N).	None
longitude	Union[float, None]	Longitude, positive East (°E).	None
base_elev	Union[float, None]	Elevation of the bottom-most point of the lake (m above datum).	None
crest_elev	Union[float, None]	Elevation of a weir crest, where overflow begins (m above datum).	None
bsn_len	Union[float, None]	Length of the lake basin, at crest height (m).	None
bsn_wid	Union[float, None]	Width of the lake basin, at crest height (m).	None
bsn_vals	Union[int, None]	Number of points being provided to described the hyposgraphic details.	None
h	Union[List[float], None]	Comma-separated list of lake elevations (m above datum).	None
a	Union[List[float], None]	Comma-separated list of lake areas (m^2).	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

OutflowBlock

Bases: NMLBlock

NMLBlock subclass for the outflow block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(num_outlet=None, outflow_fl=None, time_fmt=None, outflow_factor=None, outflow_thick_limit=None, single_layer_draw=None, flt_off_sw=None, outlet_type=None, outl_elvs=None, bsn_len_outl=None, bsn_wid_outl=None, crit_o2=None, crit_o2_dep=None, crit_o2_days=None, outlet_crit=None, o2name=None, o2idx=None, target_temp=None, min_lake_temp=None, fac_range_upper=None, fac_range_lower=None, mix_withdraw=None, coupl_oxy_sw=None, withdrtemp_fl=None, seepage=None, seepage_rate=None, crest_width=None, crest_factor=None)

Parameters:

Name	Type	Description	Default
num_outlet	Union[int, None]	Number of outflows (including withdrawals, outlets or offtakes) to be included in this simulation.	None
outflow_fl	Union[List[str], str, None]	Filename of the file containing the outflow time-series. A list if num_outlet > 1.	None
time_fmt	Union[str, None]	Time format of the 1st column in the outflow_fl.	None
outflow_factor	Union[List[float], float, None]	Scaling factor used as a multiplier for outflows. A list if num_outlet > 1.	None
outflow_thick_limit	Union[List[float], float, None]	Maximum vertical limit of withdrawal entrainment. A list if num_outlet > 1.	None
single_layer_draw	Union[List[bool], bool, None]	Switch to only limit withdrawal entrainment and force outflows from layer at the outlet elevation height. A list if num_outlet > 1.	None
flt_off_sw	Union[List[bool], bool, None]	Switch to indicate if the outflows are floating offtakes (taking water from near the surface). A list if num_outlet > 1.	None
outlet_type	Union[List[int], int, None]	Switch to configure approach of each withdrawal. Options are 1 for fixed outlet height, 2 for floating offtake, 3 for adaptive offtake/low oxy avoidance, 4 for adaptive offtake/isotherm following, or 5 for adaptive offtake/temp time-series. A list if num_outlet > 1.	None
outl_elvs	Union[List[float], float, None]	Outlet elevations (m). A list if num_outlet > 1.	None
bsn_len_outl	Union[List[float], float, None]	Basin length at the outlet height(s) (m). A list if num_outlet > 1.	None
bsn_wid_outl	Union[List[float], float, None]	Basin width at the outlet heights (m). A list if num_outlet > 1.	None
crit_o2	Union[int, None]	Undocumented parameter.	None
crit_o2_dep	Union[int, None]	Undocumented parameter.	None
crit_o2_days	Union[int, None]	Undocumented parameter.	None
outlet_crit	Union[int, None]	Undocumented parameter.	None
o2name	Union[str, None]	Undocumented parameter.	None
o2idx	Union[str, None]	Undocumented parameter.	None
target_temp	Union[float, None]	Undocumented parameter.	None
min_lake_temp	Union[float, None]	Undocumented parameter.	None
fac_range_upper	Union[float, None]	Undocumented parameter.	None
fac_range_lower	Union[float, None	Undocumented parameter.	None
mix_withdraw	Union[bool, None]	Undocumented parameter.	None
coupl_oxy_sw	Union[bool, None]	Undocumented parameter.	None
withdrtemp_fl	Union[str, None]	Filename of the file containing the temperature time-series the adaptive withdrawal is targeting. Required if outlet_type=5.	None
seepage	Union[bool, None]	Switch to enable the seepage of water from the lake bottom.	None
seepage_rate	Union[float, None]	Seepage rate of water, or, soil hydraulic conductivity (m day^{-1}).	None
crest_width	Union[float, None]	Width of weir (at crest height) where lake overflows (m).	None
crest_factor	Union[float, None]	Drag coefficient associated with the weir crest, used to compute the overflow discharge rate. Applies only when the crest elevation is configured to be less than the maximum elevation of the domain.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

OutputBlock

Bases: NMLBlock

NMLBlock subclass for the output block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(out_dir=None, out_fn=None, nsave=None, csv_lake_fname=None, csv_point_nlevs=None, csv_point_fname=None, csv_point_frombot=None, csv_point_at=None, csv_point_nvars=None, csv_point_vars=None, csv_outlet_allinone=None, csv_outlet_fname=None, csv_outlet_nvars=None, csv_outlet_vars=None, csv_ovrflw_fname=None)

Parameters:

Name	Type	Description	Default
out_dir	Union[str, None]	Directory to write the output files.	None
out_fn	Union[str, None]	Filename of the main NetCDF output file.	None
nsave	Union[int, None]	Frequency to write to the NetCDF and CSV point files.	None
csv_lake_fname	Union[str, None]	Filename for the daily summary file.	None
csv_point_nlevs	Union[int, None]	Number of specific level/depth CSV files to be created.	None
csv_point_fname	Union[str, None]	Name to be appended to specified depth CSV files.	None
csv_point_frombot	Union[List[bool], bool, None]	Comma separated list identify whether each output point listed in csv_point_at is relative to the bottom (i.e., heights) or the surface (i.e., depths).	None
csv_point_at	Union[List[float], float, None]	Height or Depth of points to output at (comma-separated list).	None
csv_point_nvars	Union[int, None]	Number of variables to output into the csv files.	None
csv_point_vars	Union[List[str], str, None]	Comma separated list of variable names.	None
csv_outlet_allinone	Union[bool, None]	Switch to create an optional outlet file combining all outlets.	None
csv_outlet_fname	Union[str, None]	Name to be appended to each of the outlet CSV files.	None
csv_outlet_nvars	Union[int, None]	Number of variables to be written into the outlet file(s).	None
csv_outlet_vars	Union[List[str], str, None]	Comma separated list of variable names to be included in the output file(s).	None
csv_ovrflw_fname	Union[str, None]	Filename to be used for recording the overflow details.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

SedimentBlock

Bases: NMLBlock

NMLBlock subclass for the sediment block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(benthic_mode=None, sed_heat_model=None, n_zones=None, sed_heat_ksoil=None, sed_temp_depth=None, sed_temp_mean=None, sed_temp_amplitude=None, sed_temp_peak_doy=None, zone_heights=None, sed_reflectivity=None, sed_roughness=None)

Parameters:

Name	Type	Description	Default
benthic_mode	Union[int, None]	Switch to configure which mode of benthic interaction to apply. Options are 0 for bottom layer only, 1 for bottom layer and layer flanks, 2 for sediment zones, and 3 for an undocumented use case.	None
sed_heat_model	Union[int, None]	Undocumented parameter.	None
n_zones	Union[int, None]	Number of sediment zones to simulate. Required if benthic_mode=2 or benthic_mode=3.	None
sed_heat_ksoil	Union[float, None]	Heat conductivity of soil/sediment.	None
sed_temp_depth	Union[float, None]	Depth of soil/sediment layer below the lake bottom, used for heat flux calculation.	None
sed_temp_mean	Union[List[float], float, None]	Annual mean sediment temperature. A list if n_zones > 1.	None
sed_temp_amplitude	Union[List[float], float, None]	Amplitude of temperature variation experienced in the sediment over one year. A list if n_zones > 1.	None
sed_temp_peak_doy	Union[List[int], int, None]	Day of the year where the sediment temperature peaks. A list if n_zones > 1.	None
zone_heights	Union[List[float], float, None]	Upper height of zone boundary. Required if benthic_mode=2 or benthic_mode=3.	None
sed_reflectivity	Union[List[float], float, None]	Sediment reflectivity.	None
sed_roughness	Union[List[float], float, None]	Undocumented parameter.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

SnowIceBlock

Bases: NMLBlock

snowice block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.

__init__(snow_albedo_factor=None, snow_rho_min=None, snow_rho_max=None, min_ice_thickness=None, dt_iceon_avg=None, avg_surf_temp_thres=None)

Paramters

snow_albedo_factor : Union[float, None] Scaling factor used to as a multiplier to scale the snow/ice albedo estimate. snow_rho_min : Union[float, None] Maximum snow density allowable (kg m^{-3}). snow_rho_max : Union[float, None] Minimum snow density allowable (kg m^{-3}). min_ice_thickness : Union[float, None] Undocumented parameter. dt_iceon_avg : Union[float, None] Undocumented parameter. avg_surf_temp_thres : Union[float, None] Undocumented parameter.

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

TimeBlock

Bases: NMLBlock

NMLBlock subclass for the time block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(timefmt=None, start=None, stop=None, dt=None, num_days=None, timezone=None)

Parameters:

Name	Type	Description	Default
timefmt	Union[int, None]	Time configuration switch. Options are 2 when using start and stop parameters or 3 when using num_days.	None
start	Union[str, None]	Start time/date of simulation in format 'yyyy-mm-dd hhss'.	None
stop	Union[str, None]	End time/date of simulation in format 'yyyy-mm-dd hhss'. Used when timefmt=2.	None
dt	Union[float, None]	Time step (seconds).	None
num_days	Union[int, None]	Number of days to simulate. Used when timefmt=3.	None
timezone	Union[float, None]	UTC time zone.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

WQSetupBlock

Bases: NMLBlock

NMLBlock subclass for the wq_setup block.

Attributes:

Name	Type	Description
params	Dict[str, NMLParam]	Dictionary of NMLParam objects.
strict	bool	Switch to turn on or off parameter validation.

__init__(wq_lib=None, wq_nml_file=None, bioshade_feedback=None, mobility_off=None, ode_method=None, split_factor=None, repair_state=None)

Parameters:

Name	Type	Description	Default
wq_lib	Union[str, None]	Water quality model selection. Options are "aed2" and "fabm".	None
wq_nml_file	Union[str, None]	Filename of water quality configuration file, e.g., "./aed2.nml".	None
bioshade_feedback	Union[bool, None]	Switch to enable K_{w} to be updated by the WQ model.	None
mobility_off	Union[bool, None]	Switch to enable settling within the WQ model.	None
ode_method	Union[int, None]	Method to use for ODE solution of water quality module.	None
split_factor	Union[float, None]	Factor weighting implicit vs explicit numerical solution of the WQ model. split_factor has a valid range between 0.0 and 1.0.	None
repair_state	Union[bool, None]	Switch to correct negative or out of range WQ variables.	None

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

nml

NML

Bases: ABC

Base class for all NML classes.

Attributes:

Name	Type	Description
blocks	NMLDict[str, NMLParam]	Dictionary of NMLBlock subclass instances.
strict	bool	Toggles strict for each instance of NMLBlock in the blocksdictionary.

from_dict(nml_dict) classmethod

Initialise class instance from a dictionary.

Returns an instance of the class that has been initialised with a nested dictionary of NML parameters.

Parameters:

Name	Type	Description	Default
nml_dict	dict	A dictionary where the keys are the block names and the values are dictionaries of parameter names (keys) and parameter values (values).	required

from_file(nml_path) classmethod

Initialise class instance from a NML file.

Returns an instance of the class that has been initialised with parameters from a NML file.

Parameters:

Name	Type	Description	Default
nml_path	dict	Path to the NML file.	required

get_block(block_name)

Get a NML Block.

Returns an instance of a NMLBlock subclass from the NML.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required

get_block_names()

List the block names.

Returns a list of the name attribute for all NMLBlock subclass instances.

get_param_names(block_name)

List the parameter names in a block.

Returns a list of the name attribute for all NMLParam instances.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required

get_param_units(block_name, param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required
param_name	str	The name of the parameter to return the value for.	required

get_param_value(block_name, param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required
param_name	str	The name of the parameter to return the value for.	required

init_blocks(*args)

Populate the blocks dictionary with instances of NMLBlock subclasses.

is_none_nml()

Test if all NML parameter values are None.

Returns True if is_none_block() is True for all subclassed NMLBlock instances in the blocks dictionary.

iter_blocks()

Iterate over all NMLBlock objects.

iter_params()

Iterate over all NMLParam objects.

set_block(block_name, block)

Set a NML Block.

Overrides, or adds a new block, to a NML.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required
block	NMLBlock	The block to set.	required

set_param_value(block_name, param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
block_name	str	The block name.	required
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_blocks=True, none_params=True)

Nested dictionary of parameters.

Returns a nested dictionary where the keys are the block names and the values a dictionary of parameter values.

Parameters:

Name	Type	Description	Default
none_blocks	bool	Whether to include blocks where all parameter values are None.	True
none_params	bool	Whether to include parameter values that are None.	True

to_nml(nml_path='glm3.nml')

Write a NML file.

Parameters with values of None are omitted.

Parameters:

Name	Type	Description	Default
nml_path	str	Path to the NML file	'glm3.nml'

validate() abstractmethod

Validation tests for cross-block dependencies.

Must be implemented for all subclasses of NML. Implement your own validation tests or use available methods, e.g.,val_required_block(). Raise a ValueError when validation fails.

NMLBlock

Bases: ABC

Base class for all NML block classes.

Attributes:

Name	Type	Description
params	NMLDict[str, NMLParam]	Dictionary of NMLParams.
strict	bool	Toggles strict for each instance of NMLParam in the params dictionary.

get_param_names()

List the parameter names.

Returns a list of the name attribute for all NMLParam instances.

get_param_units(param_name)

Get a parameter's units.

Returns the units attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

get_param_value(param_name)

Get a parameter value.

Returns the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The name of the parameter to return the value for.	required

init_params(*args)

Populate the params dictionary with instances of NMLParam.

is_none_block()

Test if all NML parameter values are None.

Returns True if NMLParam.value is None for all instances of NMLParam in the params dictionary.

iter_params()

Iterate over all NMLParam objects.

set_param_value(param_name, value)

Set a parameter value.

Sets the value attribute of a NMLParam instance.

Parameters:

Name	Type	Description	Default
param_name	str	The parameter name.	required
value	Any	The parameter value to set.	required

to_dict(none_params=True)

Dictionary of parameters.

Returns a dictionary of the block's parameters.

Parameters:

Name	Type	Description	Default
none_params	bool	Whether to include parameter values that are None.	True

validate() abstractmethod

Validation tests for cross-parameter dependencies.

Must be implemented for all subclasses of NMLBlock. Implement your own validation tests or use available methods, e.g.,val_incompat_param_values() and val_list_len_params(). Raise a ValueError when validation fails.

NMLDict

Bases: OrderedDict[K, T], Generic[K, T]

Ordered dictionary for storing collections of NMLParam, NMLBlock, or NML.

Attributes:

Name	Type	Description
strict	bool	Set strict for all values in the dictionary.

validate()

Call validate for each value in the dictionary.

NMLParam

NML Parameter.

Class for representing an individual parameter in a NML file. Stores the parameter name, value, type, units, and value validation logic.

Attributes:

Name	Type	Description
name	str	The parameter name.
type	Any	Expected data type of the parameter value. For list parameters, type is the type of the list elements.
value	Any	The parameter value.
units	Union[str, None]	The parameter units. If the parameter is unitless, units is None.
is_list	bool	Whether the parameter value is a list of values.
is_bcs_fl	bool	Whether the parameter value represents a bcs file path.
is_dbase_fl	bool	Whether the parameter value represents a dbase file path.

__init__(name, type, value=None, units=None, is_list=False, is_bcs_fl=False, is_dbase_fl=False, val_gt=None, val_gte=None, val_lt=None, val_lte=None, val_switch=None, val_datetime=None, val_type=True)

Initialise a new NML parameter.

Parameters:

Name	Type	Description	Default
name	str	The parameter name.	required
type	Any	Expected data type of the parameter value. For list parameters, type is the type of the list elements.	required
value	Any	The parameter value.	None
units	Union[str, None]	The parameter units. If the parameter is unitless, units is None.	None
is_list	bool	Whether the parameter value is a list of elements.	False
is_bcs_fl	bool	Whether the parameter value represents a bcs file path.	False
is_dbase_fl	bool	Whether the parameter value represents a dbase file path.	False
val_gt	Union[None, int, float]	value must be greater than val_gt. If val_gt is None, no validation occurs.	None
val_gte	Union[None, int, float]	value must be greater than or equal to val_gte. If val_gte is None, no validation occurs.	None
val_lt	Union[None, int, float]	value must be less than val_lt. If val_lt is None, no validation occurs.	None
val_lte	Union[None, int, float]	value must be less than or equal to val_lte. If val_lte is None, no validation occurs.	None
val_switch	Union[None, List[Any]] = None	value must be one of val_switch. If val_switch is None, no validation occurs.	None
val_datetime	Union[None, List[str]] = None	value must be one of val_datetime. If val_datetime is None, no validation occurs.	None
val_type	bool	If True, value must have type type. If False, no type validation occurs.	True

validate()

Validate parameter value.

Runs parameter value validation logic. If strict is False, no validation occurs.

NMLReader

Read a NML file.

Provides methods that convert a NML file, or a JSON representation of a NML file, to either a dictionary or an instance of a NML subclass.

Attributes:

Name	Type	Description
nml_path	str	Path either a NML file or a JSON representation of a NML file.

to_dict()

Return a dictionary of the NML file.

to_nml_obj(nml_cls)

Return an instance of a NML subclass that has been initialised with the parameters in the NML file.

Parameters:

Name	Type	Description	Default
nml_cls	NML	Class type to construct, e.g., GLMNML or AEDNML.	required

NMLRegistry

Register NMLBlock and NML subclasses.

A registry that maps block_name and nml_name to the respective NMLBlock and NML subclasses.

__init__(name)

Initialise the registry.

Multiple instances of NMLRegistry should not be needed.

Parameters:

Name	Type	Description	Default
name	str	The name of the registry.	required

get_block_cls(nml_name, block_name)

Return a registered NMLBlock subclass type.

Parameters:

Name	Type	Description	Default
nml_name	str	Name of the NML.	required
block_name	str	Name of the NML block.	required

get_nml_cls(nml_name)

Return a registered NML subclass type.

Parameters:

Name	Type	Description	Default
nml_name	str	Name of the NML.	required

register_block()

Register a NMLBlock subclass under the name cls.block_name. Used as a decorator.

register_nml()

Register a NML subclass under the name cls.nml_name. Used as a decorator.

NMLWriter

Write a NML file.

Provides methods to write a dictionary as either a NML file or a JSON representation of a NML file.

Attributes:

Name	Type	Description
nml_dict	dict	Nested dictionary of the NML file. Keys are the block names, values are dictionaries of parameter names/values.

to_json(json_path)

Write the dictionary to a JSON file.

Parameters:

Name	Type	Description	Default
json_path	str	JSON file path to write.	required

to_nml(nml_path)

Write the dictionary to a NML file.

Parameters:

Name	Type	Description	Default
nml_path	str	NML file path to write.	required