Constants and Headers

src/clearwater_modules/nsm1/CBOD/dynamic_variables.py

@@ -1,12 +1,14 @@
-# TODO: figure out imports...
+"""
+File contains dynamic variables related to the CBOD module
+"""
 
 import clearwater_modules.shared.processes as shared_processes
 from clearwater_modules import base
-from clearwater_modules.tsm.model import EnergyBudget
+from clearwater_modules.nsm1.model import NutrientBudget
 from clearwater_modules.nsm1.CBOD import processes
 
 
-@base.register_variable(models=EnergyBudget)
+@base.register_variable(models=NutrientBudget)
 class Variable(base.Variable):
     ...
 

src/clearwater_modules/nsm1/CBOD/processes.py

@@ -1,10 +1,11 @@
-import numpy as np
+"""
+File contains process to calculate new CBOD concentration and associated dependent variables
+"""
+
 import numba
 import xarray as xr
-from clearwater_modules.shared.processes import (
-    arrhenius_correction,
-)
-
+from clearwater_modules.shared.processes import arrhenius_correction
+import math
 
 @numba.njit
 def kbod_tc(

src/clearwater_modules/nsm1/CBOD/static_variables.py

@@ -1,14 +1,16 @@
-# TODO: figure out what 'model' to import
+"""
+File contains static variables related to the CBOD module
+"""
+
 import clearwater_modules.base as base
-from clearwater_modules.tsm.model import EnergyBudget
+from clearwater_modules.nsm1.model import NutrientBudget
 
 
-@base.register_variable(models=EnergyBudget)
+@base.register_variable(models=NutrientBudget)
 class Variable(base.Variable):
     ...
 
 
-# CBOD variables for each CBOD group - array
 Variable(
     name='kbod_20',
     long_name='CBOD oxidation rate at 20C',

src/clearwater_modules/nsm1/DOX/dynamic_variables.py

@@ -2,11 +2,10 @@
 
 import clearwater_modules.shared.processes as shared_processes
 from clearwater_modules import base
-from clearwater_modules.tsm.model import EnergyBudget
+from clearwater_modules.nsm1.model import NutrientBudget
 from clearwater_modules.nsm1.DOX import processes
 
-
-@base.register_variable(models=EnergyBudget)
+@base.register_variable(models=NutrientBudget)
 class Variable(base.Variable):
     ...
 

src/clearwater_modules/nsm1/DOX/processes.py

@@ -1,9 +1,11 @@
-import numpy as np
+"""
+File contains dynamic variables related to the DOX module
+"""
+
 import numba
 import xarray as xr
-from clearwater_modules.shared.processes import (
-    arrhenius_correction,
-)
+from clearwater_modules.shared.processes import arrhenius_correction
+import math
 
 
 #TODO: make sure np.exp will work here...

src/clearwater_modules/nsm1/DOX/static_variables.py

@@ -1,12 +1,16 @@
-# TODO: figure out what 'model' to import
+"""
+File contains static variables related to the DOX module
+"""
+
 import clearwater_modules.base as base
-from clearwater_modules.tsm.model import EnergyBudget
+from clearwater_modules.nsm1.model import NutrientBudget
 
 
-@base.register_variable(models=EnergyBudget)
+@base.register_variable(models=NutrientBudget)
 class Variable(base.Variable):
     ...
 
+
 Variable(
     name='ron',
     long_name='O2:N ratio for nitrification',

src/clearwater_modules/nsm1/POM/dynamic_variables.py

@@ -1,10 +1,14 @@
+"""
+File contains dynamic variables related to the POM module
+"""
+
 import clearwater_modules.shared.processes as shared_processes
 from clearwater_modules import base
-from clearwater_modules.nsm1.carbon.model import CarbonBudget
+from clearwater_modules.nsm1.model import NutrientBudget
 from clearwater_modules.nsm1.POM import processes
 
 
-@base.register_variable(models=CarbonBudget)
+@base.register_variable(models=NutrientBudget)
 class Variable(base.Variable):
     ...
 

src/clearwater_modules/nsm1/POM/processes.py

@@ -1,14 +1,10 @@
+"""
+File contains process to calculate new POM concentration and associated dependent variables
+"""
 import numba
-import math
-from clearwater_modules.shared.processes import (
-    arrhenius_correction
-)
 import xarray as xr
-from clearwater_modules.nsm1.POM import dynamic_variables
-from clearwater_modules.nsm1.POM import static_variables
-from clearwater_modules.nsm1 import static_variables_global
-from clearwater_modules.nsm1 import dynamic_variables_global
-from clearwater_modules.nsm1 import state_variables
+from clearwater_modules.shared.processes import arrhenius_correction
+import math
 
 @numba.njit
 def kpom_tc(

src/clearwater_modules/nsm1/POM/static_variables.py

@@ -1,12 +1,17 @@
+"""
+File contains static variables related to the POM module
+"""
+
 import clearwater_modules.base as base
-from clearwater_modules.tsm.model import EnergyBudget
+from clearwater_modules.nsm1.model import NutrientBudget
 
 
-@base.register_variable(models=EnergyBudget)
+@base.register_variable(models=NutrientBudget)
 class Variable(base.Variable):
     ...
 
 
+
 Variable(
     name='kpom_20',
     long_name='POM dissolution rate at 20C',

src/clearwater_modules/nsm1/algae/dynamic_variables.py

@@ -1,5 +1,5 @@
 """
-File includes dynamic variables computed in Algae module. Dynamic variables may be accessed by other modules.
+File contains dynamic variables related to the Algae module
 """
 
 import clearwater_modules.shared.processes as shared_processes

src/clearwater_modules/nsm1/algae/processes.py

@@ -1,12 +1,10 @@
 """
 File contains process to calculate new algae biomass concentration and associated dependent variables
 """
-
-# TODO calculate lambda?
-import math
-from clearwater_modules.shared.processes import arrhenius_correction
 import numba
 import xarray as xr
+from clearwater_modules.shared.processes import arrhenius_correction
+import math
 
 
 @numba.njit

src/clearwater_modules/nsm1/algae/static_variables.py

@@ -1,18 +1,14 @@
 """
-File includes static variables only used in Algae module
+File contains static variables related to the Algae module
 """
 
 import clearwater_modules.base as base
 from clearwater_modules.nsm1.model import NutrientBudget
-import clearwater_modules.nsm1.algae.processes as processes
 
 
 @base.register_variable(models=NutrientBudget)
 class Variable(base.Variable):
     ...
-# TODO: verify all these values
-
-# Only Algae Variables
 
 
 Variable(

src/clearwater_modules/nsm1/alkalinity/dynamic_variables.py

@@ -1,33 +1,16 @@
-# TODO: figure out imports
+"""
+File contains dynamic variables related to the alkalinity module
+"""
 
 import clearwater_modules.shared.processes as shared_processes
 from clearwater_modules import base
-from clearwater_modules.nsm1.carbon.model import CarbonBudget
+from clearwater_modules.nsm1.model import NutrientBudget
 from clearwater_modules.nsm1.alkalinity import processes
 
-
-@base.register_variable(models=CarbonBudget)
+@base.register_variable(models=NutrientBudget)
 class Variable(base.Variable):
     ...
 
-Variable(
-    name='knit_tc',
-    long_name='Nitrification rate corrected for temperature',
-    units='1/d',
-    description='Nitrification rate corrected for temperature',
-    use='dynamic',
-    process=processes.knit_tc
-)
-
-Variable(
-    name='kdnit_tc',
-    long_name='Denitrification rate corrected for temperature',
-    units='1/d',
-    description='Denitrification rate corrected for temperature',
-    use='dynamic',
-    process=processes.kdnit_tc
-)
-
 Variable(
     name='Alk_denitrification',
     long_name='Alkalinity change due to denitrification',

src/clearwater_modules/nsm1/alkalinity/processes.py

@@ -1,44 +1,11 @@
+"""
+File contains process to calculate new alkalinity concentration and associated dependent variables
+"""
+
 import numba
-import math
-from clearwater_modules.shared.processes import (
-    arrhenius_correction
-)
 import xarray as xr
-from clearwater_modules.nsm1.alkalinity import dynamic_variables
-from clearwater_modules.nsm1.alkalinity import static_variables
-from clearwater_modules.nsm1 import static_variables_global
-from clearwater_modules.nsm1 import dynamic_variables_global
-from clearwater_modules.nsm1 import state_variables
-
-@numba.njit
-def kdnit_tc( 
-    TwaterC: float,
-    kdnit_20: float
-) -> float:
-    """Calculate kdnit_tc: Denitrification rate temperature correction (1/d). #TODO only if use_NO3 = true
-
-    Args:
-        TwaterC: Water temperature (C)
-        kdnit_20: Denitrification rate (1/d)
-    """
-
-    return arrhenius_correction(TwaterC, kdnit_20, 1.045)
-
-
-@numba.njit
-def knit_tc( ##Theta variable??
-    TwaterC: float,
-    knit_20: float
-) -> float:
-    """Calculate knit_tc: Denitrification rate temperature correction (1/d). #TODO only if use_NO3 = true
-
-    Args:
-        TwaterC: Water temperature (C)
-        knit_20: Nitrification rate (1/d)
-    """
-
-    return arrhenius_correction(TwaterC, knit_20, 1.045)
-
+from clearwater_modules.shared.processes import arrhenius_correction
+import math
 
 def Alk_denitrification(
     DOX: xr.DataArray,

src/clearwater_modules/nsm1/alkalinity/static_variables.py

@@ -1,35 +1,16 @@
+"""
+File contains static variables related to the Alkalinity module
+"""
+
 import clearwater_modules.base as base
-from clearwater_modules.tsm.model import EnergyBudget
+from clearwater_modules.nsm1.model import NutrientBudget
 
 
-@base.register_variable(models=EnergyBudget)
+@base.register_variable(models=NutrientBudget)
 class Variable(base.Variable):
     ...
 
 
-Variable(
-    name='kdnit_20',
-    long_name='Denitrification rate at 20C',
-    units='1/d',
-    description='Denitrification rate at 20C',
-    use='static',
-)
-
-Variable(
-    name='knit_20',
-    long_name='Nitrification Rate Ammonia decay at 20C',
-    units='1/d',
-    description='Nitrification Rate Ammonia NH4 -> NO3 decay at 20C',
-    use='static',
-)
-
-Variable(
-    name='KNR',
-    long_name='Oxygen inhabitation factor for nitrification',
-    units='mg-O2/L',
-    description='Oxygen inhabitation factor for nitrification',
-    use='static',
-)
 
 Variable(
     name='r_alkaa',

src/clearwater_modules/nsm1/balgae/dynamic_variables.py

@@ -1,5 +1,5 @@
 """
-File includes dynamic variables computed in Balgae module. Dynamic variables may be accessed by other modules.
+File contains dynamic variables related to the benthic algae module
 """
 
 import clearwater_modules.shared.processes as shared_processes

src/clearwater_modules/nsm1/balgae/processes.py

@@ -2,11 +2,10 @@
 File contains process to calculate new benthic algae biomass concentration and associated dependent variables
 """
 
-import math
-from clearwater_modules.shared.processes import arrhenius_correction
 import numba
 import xarray as xr
-
+from clearwater_modules.shared.processes import arrhenius_correction
+import math
 
 @numba.njit
 def mub_max_tc(

src/clearwater_modules/nsm1/balgae/static_variables.py

@@ -1,18 +1,14 @@
 """
-File includes static variables only used in Algae module
+File contains static variables related to the Benthic Algae module
 """
 
 import clearwater_modules.base as base
 from clearwater_modules.nsm1.model import NutrientBudget
-import clearwater_modules.nsm1.algae.processes as processes
 
 
 @base.register_variable(models=NutrientBudget)
 class Variable(base.Variable):
     ...
-# TODO: verify all these values
-
-#Only Balgae Variables 
 
 Variable(
     name='Fw',
@@ -138,7 +134,7 @@ class Variable(base.Variable):
     name='b_light_limitation_option',
     long_name='Benthic Algal light limitation rate options',
     units='unitless',
-    description='Benthic Algal light limitation rate with three options: 1) Half-saturation formulation, 2) Smiths Model, 3) Steeles Model'
+    description='Benthic Algal light limitation rate with three options: 1) Half-saturation formulation, 2) Smiths Model, 3) Steeles Model',
     use='static',
 )