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Balgae Testing (and one Nitrogen Test) #85

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May 13, 2024
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Balgae Testing (and one Nitrogen Test) #85

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1efe7ff
balgae tests
kewalak May 8, 2024
e1e363d
Nitrogen Test
kewalak May 9, 2024
0ff1eff
Update to Nitrogen Tests
kewalak May 9, 2024
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0 ...er_modules/nsm1/CBOD/dynamic_variables.py → ...odules/nsm1/old/CBOD/dynamic_variables.py
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0 ...clearwater_modules/nsm1/CBOD/processes.py → ...rwater_modules/nsm1/old/CBOD/processes.py
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0 ...ter_modules/nsm1/DOX/dynamic_variables.py → ...modules/nsm1/old/DOX/dynamic_variables.py
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0 ...r_modules/nsm1/algae/dynamic_variables.py → ...dules/nsm1/old/algae/dynamic_variables.py
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0 ...learwater_modules/nsm1/algae/processes.py → ...water_modules/nsm1/old/algae/processes.py
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0 ...er_modules/nsm1/algae/static_variables.py → ...odules/nsm1/old/algae/static_variables.py
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0 ...ules/nsm1/alkalinity/dynamic_variables.py → .../nsm1/old/alkalinity/dynamic_variables.py
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0 ...ater_modules/nsm1/alkalinity/processes.py → ..._modules/nsm1/old/alkalinity/processes.py
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0 ..._modules/nsm1/balgae/dynamic_variables.py → ...ules/nsm1/old/balgae/dynamic_variables.py
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8 changes: 4 additions & 4 deletions ...earwater_modules/nsm1/balgae/processes.py → ...ater_modules/nsm1/old/balgae/processes.py
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Expand Up @@ -15,7 +15,7 @@ def mub_max_tc(
"""Calculate mub_max_tc: Maximum benthic algal growth rate with temperature correction (1/d).

Args:
mu_max_20: Maximum benthic algal growth rate at 20C (1/d)
mub_max_20: Maximum benthic algal growth rate at 20C (1/d)
TwaterC: Water temperature (C)
"""
return arrhenius_correction(TwaterC, mub_max_20, 1.047)
Expand Down Expand Up @@ -162,7 +162,7 @@ def FNb(
"""
FNb = xr.where(use_NH4 or use_NO3, (NH4 + NO3) / (KsNb + NH4 + NO3),1)
FNb = xr.where(math.isnan(FNb),0.0,
xr.where(FNb < 1.0, 1, FNb))
xr.where(FNb > 1.0, 1, FNb))

return FNb

Expand Down Expand Up @@ -230,12 +230,12 @@ def mub(
FPb: Benthic algae phosphorous limitation (unitless)
FNb: Benthic algae nitrogen limitation (unitless)
FSb: Benthic density attenuation (unitless),
"""
"""

# Benthic Local Specific Growth Rate
return xr.where(b_growth_rate_option == 1, mub_max_tc * FLb * FPb * FNb * FSb, mub_max_tc * FLb * FSb * min(FPb, FNb))


#TODO RAS WQ has an option for harmonic which the FORTAN code does not have

@numba.njit
def AbGrowth(
Expand Down
0 ...r_modules/nsm1/balgae/static_variables.py → ...dules/nsm1/old/balgae/static_variables.py
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0 ..._modules/nsm1/carbon/dynamic_variables.py → ...ules/nsm1/old/carbon/dynamic_variables.py
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0 ...earwater_modules/nsm1/carbon/processes.py → ...ater_modules/nsm1/old/carbon/processes.py
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0 ...r_modules/nsm1/carbon/static_variables.py → ...dules/nsm1/old/carbon/static_variables.py
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0 ...ater_modules/nsm1/n2/dynamic_variables.py → ..._modules/nsm1/old/n2/dynamic_variables.py
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0 src/clearwater_modules/nsm1/n2/processes.py → ...earwater_modules/nsm1/old/n2/processes.py
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0 ...water_modules/nsm1/n2/static_variables.py → ...r_modules/nsm1/old/n2/static_variables.py
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0 ...odules/nsm1/nitrogen/dynamic_variables.py → ...es/nsm1/old/nitrogen/dynamic_variables.py
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0 ...rwater_modules/nsm1/nitrogen/processes.py → ...er_modules/nsm1/old/nitrogen/processes.py
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0 ...modules/nsm1/nitrogen/static_variables.py → ...les/nsm1/old/nitrogen/static_variables.py
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0 ...dules/nsm1/pathogens/dynamic_variables.py → ...s/nsm1/old/pathogens/dynamic_variables.py
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0 ...water_modules/nsm1/pathogens/processes.py → ...r_modules/nsm1/old/pathogens/processes.py
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0 ...odules/nsm1/pathogens/static_variables.py → ...es/nsm1/old/pathogens/static_variables.py
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0 ...ules/nsm1/phosphorus/dynamic_variables.py → .../nsm1/old/phosphorus/dynamic_variables.py
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0 ...ater_modules/nsm1/phosphorus/processes.py → ..._modules/nsm1/old/phosphorus/processes.py
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0 ...dules/nsm1/phosphorus/static_variables.py → ...s/nsm1/old/phosphorus/static_variables.py
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0 ...modules/nsm1/sedflux/dynamic_variables.py → ...les/nsm1/old/sedflux/dynamic_variables.py
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0 ...arwater_modules/nsm1/sedflux/processes.py → ...ter_modules/nsm1/old/sedflux/processes.py
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10 changes: 7 additions & 3 deletions src/clearwater_modules/nsm1/processes.py
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Expand Up @@ -704,7 +704,7 @@ def mub_max_tc(
"""Calculate mub_max_tc: Maximum benthic algal growth rate with temperature correction (1/d).

Args:
mu_max_20: Maximum benthic algal growth rate at 20C (1/d)
mub_max_20: Maximum benthic algal growth rate at 20C (1/d)
TwaterC: Water temperature (C)
"""
return arrhenius_correction(TwaterC, mub_max_20, 1.047)
Expand Down Expand Up @@ -1169,7 +1169,7 @@ def kon_tc(
kon_20: Decay rate of OrgN to NH4 (1/d)
"""

return arrhenius_correction(TwaterC, kon_20, 1.074)
return arrhenius_correction(TwaterC, kon_20, 1.047)



Expand Down Expand Up @@ -1490,6 +1490,8 @@ def NH4_ApGrowth(
def NH4_AbRespiration(
use_Balgae: bool,
rnb: xr.DataArray,
Fb: xr.DataArray,
depth: xr.DataArray,
AbRespiration: xr.DataArray,

) -> xr.DataArray:
Expand All @@ -1499,10 +1501,12 @@ def NH4_AbRespiration(
use_Balgae: true/false to use benthic algae module (unitless),
rnb: xr.DataArray,
AbRespiration: Benthic algal respiration rate (g/m^2/d),
depth: water depth (m),
Fb: Fraction of bottom area for benthic algae (unitless),
"""
# TODO changed the calculation for respiration from the inital FORTRAN due to conflict with the reference guide

return xr.where(use_Balgae, rnb * AbRespiration, 0.0 )
return xr.where(use_Balgae, (rnb * AbRespiration*Fb)/depth, 0.0 )

def NH4_AbGrowth(
use_Balgae: bool,
Expand Down
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