Merge branch 'KW_Variables' into IJM_NSM_nb

Author: imscw95

src/clearwater_modules/nsm1/CBOD/dynamic_variables.py

@@ -1,4 +1,6 @@
-# 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
@@ -12,21 +14,21 @@ class Variable(base.Variable):
 
 
 Variable(
-    name='kbod_T',
+    name='kbod_tc',
     long_name='Temperature adjusted oxidation rate',
     units='1/d',
     description='Temperature adjusted oxidation rate',
     use='dynamic',
-    process=processes.kbod_T
+    process=processes.kbod_tc
 )
 
 Variable(
-    name='ksbod_T',
+    name='ksbod_tc',
     long_name='Temperature adjusted sedimentation rate',
     units='m/d',
     description='Temperature adjusted sedimentation rate',
     use='dynamic',
-    process=processes.ksbod_T
+    process=processes.ksbod_tc
 )
 
 Variable(

src/clearwater_modules/nsm1/CBOD/processes.py

@@ -1,52 +1,49 @@
-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_T(
-    water_temp_c: xr.DataArray,
+def kbod_tc(
+    TwaterC: xr.DataArray,
     kbod_20: xr.DataArray,
-    theta: xr.DataArray
 ) -> xr.DataArray:
     """Calculate the temperature adjusted CBOD oxidation rate (1/d)
 
     Args:
-        water_temp_c: water temperature in Celsius
+        TwaterC: water temperature in Celsius
         kbod_20: CBOD oxidation rate at 20 degrees Celsius (1/d)
-        theta: Arrhenius coefficient
     """
 
-    kbod_T = arrhenius_correction(water_temp_c, kbod_20, theta)
-    return kbod_T
+    kbod_tc = arrhenius_correction(TwaterC, kbod_20, 1.047)
+    return kbod_tc
 
 
 @numba.njit
-def ksbod_T(
-    water_temp_c: xr.DataArray,
+def ksbod_tc(
+    TwaterC: xr.DataArray,
     ksbod_20: xr.DataArray,
-    theta: xr.DataArray
 ) -> xr.DataArray:
     """Calculate the temperature adjusted CBOD sedimentation rate (m/d)
 
     Args:
-        water_temp_c: water temperature in Celsius
+        TwaterC: water temperature in Celsius
         ksbod_20: CBOD sedimentation rate at 20 degrees Celsius (m/d)
-        theta: Arrhenius coefficient
     """
 
-    ksbod_T = arrhenius_correction(water_temp_c, ksbod_20, theta)
-    return ksbod_T
+    ksbod_tc = arrhenius_correction(TwaterC, ksbod_20, 1.024)
+    return ksbod_tc
 
 
 
 def CBOD_oxidation(
     DOX: xr.DataArray,
     CBOD: xr.DataArray,
-    kbod_T: xr.DataArray,
+    kbod_tc: xr.DataArray,
     KsOxbod: xr.DataArray,
     use_DOX: xr.DataArray
 ) -> xr.DataArray:
@@ -55,28 +52,28 @@ def CBOD_oxidation(
     Args:
         DOX: Dissolved oxygen concentration (mg-O2/L)
         CBOD: Carbonaceous biochemical oxygen demand (mg-O2/L)
-        kbod_T: Temperature adjusted CBOD oxidation rate (1/d)
+        kbod_tc: Temperature adjusted CBOD oxidation rate (1/d)
         KsOxbod: Half-saturation oxygen attenuation for CBOD oxidation (mg-O2/L)
         use_DOX: Option to consider DOX concentration in calculation of CBOD oxidation
     """
-    da: xr.DataArray = xr.where(use_DOX == True, (DOX / (KsOxbod + DOX)) * kbod_T * CBOD, kbod_T * CBOD)
+    da: xr.DataArray = xr.where(use_DOX == True, (DOX / (KsOxbod + DOX)) * kbod_tc * CBOD, kbod_tc * CBOD)
 
     return da
 
 
 @numba.njit
 def CBOD_sedimentation(
     CBOD: xr.DataArray,
-    ksbod_T: xr.DataArray
+    ksbod_tc: xr.DataArray
 ) -> xr.DataArray:
     """Calculates CBOD sedimentation for each group
 
     Args:
         CBOD: CBOD concentration (mg-O2/L)
-        ksbod_T: Temperature adjusted sedimentation rate (m/d)
+        ksbod_tc: Temperature adjusted sedimentation rate (m/d)
     """
 
-    CBOD_sedimentation = CBOD * ksbod_T
+    CBOD_sedimentation = CBOD * ksbod_tc
     return CBOD_sedimentation
 
 
@@ -95,7 +92,7 @@ def dCBODdt(
 
 
 @numba.njit
-def CBOD_new(
+def CBOD(
     CBOD: xr.DataArray,
     dCBODdt: xr.DataArray,
     timestep: xr.DataArray

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',
@@ -26,9 +28,10 @@ class Variable(base.Variable):
 )
 
 Variable(
-    name='ksOxbod',
+    name='KsOxbod',
     long_name='Half saturation oxygen attenuation constant for CBOD oxidation',
     units='mg-O2/L',
     description='Half saturation oxygen attenuation constant for CBOD oxidation',
     use='static'
 )
+

src/clearwater_modules/nsm1/DOX/processes.py

@@ -1,74 +1,76 @@
-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...
 @numba.njit
 def pwv(
-    t_water_k: xr.DataArray
+    TwaterK: xr.DataArray
 ) -> xr.DataArray:
     """Calculate partial pressure of water vapor
 
     Args:
-        t_water_k: Water temperature kelvin
+        TwaterK: Water temperature kelvin
     """
-    return np.exp(11.8571 - 3840.70 / t_water_k - 216961 / t_water_k ** 2)
+    return np.exp(11.8571 - 3840.70 / TwaterK - 216961 / TwaterK ** 2)
 
 
 @numba.njit
 def DOs_atm_alpha(
-    t_water_k: xr.DataArray
+    TwaterK: xr.DataArray
 ) -> xr.DataArray:
     """Calculate DO saturation atmospheric correction coefficient
 
     Args:
-        t_water_k: Water temperature kelvin
+        TwaterK: Water temperature kelvin
     """
-    return .000975 - 1.426 * 10 ** -5 * t_water_k + 6.436 * 10 ** -8 * t_water_k ** 2
+    return .000975 - 1.426 * 10 ** -5 * TwaterK + 6.436 * 10 ** -8 * TwaterK ** 2
 
 
 @numba.njit
 def DOX_sat(
-    t_water_k: xr.DataArray,
-    patm: xr.DataArray,
+    TwaterK: xr.DataArray,
+    pressure_atm: xr.DataArray,
     pwv: xr.DataArray,
     DOs_atm_alpha: xr.DataArray
 ) -> xr.DataArray:
     """Calculate DO saturation value
 
     Args:
-        t_water_k: Water temperature kelvin
-        patm: Atmospheric pressure (atm)
+        TwaterK: Water temperature kelvin
+        pressure_atm: Atmospheric pressure (atm)
         pwv: Patrial pressure of water vapor (atm)
         DOs_atm_alpha: DO saturation atmospheric correction coefficient
     """
-    DOX_sat_uncorrected = np.exp(-139.34410 + 1.575701 * 10 ** 5 / t_water_k - 6.642308 * 10 ** 7 / t_water_k ** 2
-                                 + 1.243800 * 10 ** 10 / t_water_k - 8.621949 * 10 ** 11 / t_water_k)
+    DOX_sat_uncorrected = np.exp(-139.34410 + 1.575701 * 10 ** 5 / TwaterK - 6.642308 * 10 ** 7 / TwaterK ** 2
+                                 + 1.243800 * 10 ** 10 / TwaterK - 8.621949 * 10 ** 11 / TwaterK)
 
-    DOX_sat_corrected = DOX_sat_uncorrected * patm * \
-        (1 - pwv / patm) * (1 - DOs_atm_alpha * patm) / \
+    DOX_sat_corrected = DOX_sat_uncorrected * pressure_atm * \
+        (1 - pwv / pressure_atm) * (1 - DOs_atm_alpha * pressure_atm) / \
         ((1 - pwv) * (1 - DOs_atm_alpha))
     return DOX_sat_corrected
 
 
 @numba.njit
 def Atm_O2_reaeration(
-    ka_T: xr.DataArray,
+    ka_tc: xr.DataArray,
     DOX_sat: xr.DataArray,
     DOX: xr.DataArray
 ) -> xr.DataArray:
     """Compute the atmospheric O2 reaeration flux
 
     Args: 
-        ka_T: Oxygen reaeration rate adjusted for temperature (1/d)
+        ka_tc: Oxygen reaeration rate adjusted for temperature (1/d)
         DOX_sat: Dissolved oxygen saturation concentration (mg/L)
         DOX: Dissolved oxygen concentration (mg/L)
     """
-    return ka_T * (DOX_sat - DOX)
+    return ka_tc * (DOX_sat - DOX)
 
 
 def DOX_ApGrowth(
@@ -258,7 +260,7 @@ def dDOXdt(
 
 
 @numba.njit
-def DOX_new(
+def DOX(
     DOX: xr.DataArray,
     dDOXdt: xr.DataArray,
     timestep: xr.DataArray

src/clearwater_modules/nsm1/DOX/static_variables.py

@@ -1,10 +1,76 @@
-# 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',
+    units='mg-O2/mg-N',
+    description='2*32/14',
+    use='static'
+)
+
+Variable(
+    name='SOD_20',
+    long_name='Sediment oxygen demand at 20C',
+    units='mg-O2/m2/d',
+    description='Sediment oxygen demand at 20C',
+    use='static'
+)
+
+Variable(
+    name='kaw_20_user',
+    long_name='Wind oxygen reaeration velocity at 20C',
+    units='m/d',
+    description='Wind oxygen reaeration velocity at 20C',
+    use='static'
+)
+
+Variable(
+    name='kah_20_user',
+    long_name='Hydraulic oxygen reaeration rate at 20C',
+    units='1/d',
+    description='Hydraulic oxygen reaeration rate at 20C',
+    use='static'
+)
+
+Variable(
+    name='hydraulic_reaeration_option',
+    long_name='Option for chosing the method by which O2 reaeration rate is calculated',
+    units='unitless',
+    description='Selects method for computing O2 reaeration rate',
+    use='static'
+)
+
+Variable(
+    name='wind_reaeration_option',
+    long_name='Option for chosing the method by which wind reaeration is calculated',
+    units='unitless',
+    description='Selects method for computing O2 reaeration due to wind',
+    use='static'
+)
+
+Variable(
+    name='patm',
+    long_name='Atmospheric pressure',
+    units='atm',
+    description='Atmospheric pressure',
+    use='static'
+)
+
+Variable(
+    name='KsSOD',
+    long_name='half saturation oxygen attenuation constant for SOD',
+    units='mg/L',
+    description='half saturation oxygen attenuation constant for SOD',
+    use='static'
+)