Merge pull request #73 from EcohydrologyTeam/KW_CleanUp

Moving global variables and removing repeats

src/clearwater_modules/nsm1/DOX/static_variables.py

@@ -19,53 +19,6 @@ class Variable(base.Variable):
     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',

src/clearwater_modules/nsm1/algae/dynamic_variables.py

@@ -12,24 +12,6 @@
 class Variable(base.Variable):
     ...
 
-Variable(
-    name='L',
-    long_name='Light attenuation coefficient',
-    units='unitless',
-    description='Light attenuation coefficient',
-    use='dynamic',
-    process=processes.L
-)
-
-Variable(
-    name='PAR',
-    long_name='surface light intensity',
-    units='W/m2',
-    description='surface light intensity',
-    use='dynamic',
-    process=processes.PAR
-)
-
 Variable(
     name='rna',
     long_name='Algal N:Chla Ratio',

src/clearwater_modules/nsm1/algae/processes.py

@@ -108,58 +108,6 @@ def kdp_tc(
 
     return arrhenius_correction(TwaterC, kdp_20, 1.047)
 
-@numba.njit
-def L(
-    lambda0: xr.DataArray,
-    lambda1: xr.DataArray,
-    lambda2: xr.DataArray,
-    lambdas: xr.DataArray,
-    lambdam: xr.DataArray,
-    Solid: xr.DataArray,
-    POC: xr.DataArray,
-    focm: xr.DataArray,
-    use_Algae: xr.DataArray,
-    use_POC: xr.DataArray,
-    Ap: xr.DataArray,
-
-) -> xr.DataArray:
-    """Compute L: lambda: light extinction coefficient (unitless)
-
-    Args:
-        lambda0: background portion (1/m)
-        lambda1: linear self shading (1/m/(ug Chla/L))
-        lambda2: non-linear (unitless),
-        lambdas: ISS portion (L/mg/m),
-        lambdam: POM portion (L/mg/m)
-        Solid: #TODO define this
-        POC: particulate organic carbon (mg-C/L)
-        focm: ratio of carbon to organic matter (mg-C/mg-D)
-        use_Algae: true/false use algae module (t/f)
-        use_POC: true/falseo use particulate organic carbon module (t/f)
-        Ap: algae concentration (ug-Chla/L)
-    """
-    L=lambda0 + lambdas * Solid
-
-    L=xr.where (use_POC, L+lambdam*POC/focm, L)
-    L=xr.where (use_Algae, L+lambda1*Ap + lambda2*Ap**0.66667, L)
-
-    return L
-
-@numba.njit
-def PAR(
-    use_Algae : bool,
-    use_Balgae: bool,
-    q_solar: xr.DataArray,
-    Fr_PAR: xr.DataArray,
-) -> xr.DataArray :
-    """Calculate temperature in kelvin (K)
-    Args:
-        use_Algae : true/false use algae module (t/f)
-        use_Balgae: true/falsoe use balgae module (t/f)
-        q_solar: solar radiation (1/d),
-        Fr_PAR: fraction of soalr radiation within the PAR of the spectrum
-    """
-    return xr.where (use_Algae or use_Balgae, q_solar * Fr_PAR)
 
 @numba.njit
 def FL(

src/clearwater_modules/nsm1/balgae/processes.py

@@ -298,7 +298,7 @@ def dAbdt(
     return AbGrowth - AbRespiration - AbDeath
 
 @numba.njit
-def Ab_new(
+def Ab(
     Ab: xr.DataArray,
     dAbdt: xr.DataArray
 

src/clearwater_modules/nsm1/carbon/processes.py

@@ -118,7 +118,7 @@ def dPOCdt(
 
 
 @numba.njit
-def POC_new(
+def POC(
     POC: xr.DataArray,
     dPOCdt: xr.DataArray,
     timestep: xr.DataArray
@@ -265,7 +265,7 @@ def Henrys_k(
 
 @numba.njit
 def Atmospheric_CO2_reaeration(
-    ka_T: xr.DataArray,
+    ka_tc: xr.DataArray,
     K_H: xr.DataArray,
     pCO2: xr.DataArray,
     FCO2: xr.DataArray,
@@ -274,13 +274,13 @@ def Atmospheric_CO2_reaeration(
     """Calculates the atmospheric input of CO2 into the waterbody
 
     Args:
-        ka_T: CO2 reaeration rate adjusted for temperature, same as O2 reaeration rate (1/d)
+        ka_tc: CO2 reaeration rate adjusted for temperature, same as O2 reaeration rate (1/d)
         K_H: Henry's Law constant (mol/L/atm)
         pCO2: Partial pressure of CO2 in the atmosphere (ppm)
         FCO2: Fraction of CO2 in total inorganic carbon
         DIC: Dissolved inorganic carbon concentration (mg/L)
     """
-    return 12 * ka_T * (10**-3 * K_H * pCO2 - 10**3 * FCO2 * DIC)
+    return 12 * ka_tc * (10**-3 * K_H * pCO2 - 10**3 * FCO2 * DIC)
 
 
 def DIC_algal_respiration(
@@ -385,7 +385,7 @@ def DIC_CBOD_oxidation(
 
 
 def DIC_sed_release(
-    SOD_tcc: xr.DataArray,
+    SOD_tc: xr.DataArray,
     roc: xr.DataArray,
     depth: xr.DataArray,
     JDIC: xr.DataArray,
@@ -394,13 +394,13 @@ def DIC_sed_release(
     """Computes the sediment release of DIC
 
     Args:
-        SOD_tcc: Sediment oxygen demand adjusted for water temperature (mg-O2/L/d)
+        SOD_tc: Sediment oxygen demand adjusted for water temperature (mg-O2/L/d)
         roc: Ratio of O2 to carbon for carbon oxidation (mg-O2/mg-C)
         depth: Water depth (m)
         JDIC: Sediment-water flux of dissolved inorganic carbon (g-C/m2/d)
         use_SedFlux: Option to consider full sediment flux budget in DIC sediment contribution (bool)
     """
-    da: xr.DataArray = xr.where(use_SedFlux == True, JDIC / depth, SOD_tcc / roc / depth)
+    da: xr.DataArray = xr.where(use_SedFlux == True, JDIC / depth, SOD_tc / roc / depth)
 
     return da
 

src/clearwater_modules/nsm1/dynamic_variables_global.py

@@ -57,12 +57,12 @@ class Variable(base.Variable):
 )
 
 Variable(
-    name='kah_T',
+    name='kah_tc',
     long_name='Hydraulic oxygen reaeration rate adjusted for temperature',
     units='1/d',
     description='Hydraulic oxygen reaeration rate adjusted for temperature',
     use='dynamic',
-    process=shared_processes.kah_T
+    process=shared_processes.kah_tc
 )
 
 Variable(
@@ -75,19 +75,38 @@ class Variable(base.Variable):
 )
 
 Variable(
-    name='kaw_T',
+    name='kaw_tc',
     long_name='Wind oxygen reaeration velocity adjusted for temperature',
     units='m/d',
     description='Wind oxygen reaeration velocity adjusted for temperature',
     use='dynamic',
-    process=shared_processes.kaw_T
+    process=shared_processes.kaw_tc
 )
 
 Variable(
-    name='ka_T',
+    name='ka_tc',
     long_name='Oxygen reaeration rate',
     units='1/d',
     description='Oxygen reaeration rate',
     use='dynamic',
     process=shared_processes.ka_T
 )
+
+
+Variable(
+    name='L',
+    long_name='Light attenuation coefficient',
+    units='unitless',
+    description='Light attenuation coefficient',
+    use='dynamic',
+    process=processes.L
+)
+
+Variable(
+    name='PAR',
+    long_name='surface light intensity',
+    units='W/m2',
+    description='surface light intensity',
+    use='dynamic',
+    process=processes.PAR
+)

src/clearwater_modules/nsm1/nitrogen/processes.py

@@ -556,7 +556,7 @@ def NO3_AbGrowth(
     return xr.where(use_Balgae, (AbUptakeFr_NO3 * rnb * Fb * AbGrowth) / depth, 0.0)
 
 @numba.njit
-def NH4_new(
+def NH4(
     dNH4dt: xr.DataArray,
     NH4: xr.DataArray
 
@@ -621,7 +621,7 @@ def NO3(
     return NO3 + dNO3dt*timestep
 
 @numba.njit
-def NO3_new(
+def NO3(
     dNO3dt: xr.DataArray,
     NO3: xr.DataArray
 

src/clearwater_modules/nsm1/nitrogen/static_variables.py

@@ -84,11 +84,3 @@ class Variable(base.Variable):
     description='NH4 preference factor benthic algae (1=full NH4, 0=full NO3)',
     use='static',
 )
-
-Variable(
-    name='vson',
-    long_name='OrgN settling velocity',
-    units='m/d',
-    description='OrgN settling velocity',
-    use='static',
-)

src/clearwater_modules/nsm1/pathogens/dynamic_variables.py

@@ -58,10 +58,10 @@ class Variable(base.Variable):
 )
 
 Variable(
-    name='PX_new',
+    name='PX',
     long_name='New pathogen concentration',
     units='cfu/100mL',
     description='New pathogen concentration',
     use='dynamic',
-    process=processes.PX_new
+    process=processes.PX
 )

src/clearwater_modules/nsm1/phosphorus/processes.py

@@ -7,22 +7,6 @@
 import math
 
 
-@numba.njit
-def fdp(
-    use_TIP: bool,
-    Solid : xr.DataArray,
-    kdop4: xr.DataArray
-) -> xr.DataArray :
-
-    """Calculate kop_tc: Decay rate of organic P to DIP temperature correction (1/d).
-
-    Args:
-        use_TIP: true/false use total inorganic phosphrous,
-        Solid : #TODO define this
-        kdop4: solid partitioning coeff. of PO4 (L/kg)
-    """
-
-    return xr.where(use_TIP, 1/(1+kdop4 * Solid/0.000001), 0)
 
 @numba.njit
 def kop_tc(

src/clearwater_modules/nsm1/phosphorus/static_variables.py

@@ -26,22 +26,6 @@ class Variable(base.Variable):
     use='static',
 )
 
-Variable(
-    name='vsop',
-    long_name='Orgnaic P settling velocity',
-    units='m/d',
-    description='Orgnaic P settling velocity',
-    use='static',
-)
-
-
-Variable(
-    name='vs',
-    long_name='Sediment settling velocity',
-    units='m/d',
-    description='Sediment settling velocity',
-    use='static',
-)
 
 Variable(
     name='kdop4',

src/clearwater_modules/nsm1/state_variables.py

@@ -31,7 +31,7 @@ def mock_equation(water_temp_c: float) -> float:
     units='ug-Chla/L',
     description='Algal Concentration',
     use='state',
-    process=algae_processes.Ap_new 
+    process=algae_processes.Ap 
 )
 
 Variable(

src/clearwater_modules/nsm1/static_variables_global.py

@@ -330,14 +330,6 @@ class Variable(base.Variable):
     use='static',
 )
 
-Variable(
-    name='wind_reaeration_option',
-    long_name='wind reaeration option',
-    units='unitless',
-    description='Integer value which selects method for computing wind oxygen reaeration velocity',
-    use='static',
-)
-
 #TODO figure out what Solid is
 Variable(
     name='Solid',