Test Suit

Added back in algae, balgae, and nitogen. Adapted all tests to new theta variable. One failing test change kbod in Carbon and Alkalinity. Incomplete suit for PX and N2. Questions on DOX_Sat concentration.

src/clearwater_modules/nsm1/constants.py

@@ -98,7 +98,7 @@ class BalgaeStaticVariables(TypedDict):
     krb_20=0.2,
     kdb_20=0.3,
     mub_max_theta = 1.047,
-    krb_theta = 1.047,
+    krb_theta = 1.06,
     kdb_theta = 1.047,
     b_growth_rate_option=1,
     b_light_limitation_option=1,
@@ -130,11 +130,11 @@ class NitrogenStaticVariables(TypedDict):
     kdnit_20=0.002,
     rnh4_20=0,
     vno3_20=0,
-    knit_theta= 1.047, ## Check values RAS/Kelsey's
-    kon_theta= 1.047,
-    kdnit_theta= 1.047,
+    knit_theta= 1.083,
+    kon_theta= 1.074,
+    kdnit_theta= 1.08,
     rnh4_theta= 1.047,
-    vno3_theta= 1.047,
+    vno3_theta= 1.045,
     KsOxdn=0.1,
     PN=0.5,
     PNb=0.5
@@ -156,10 +156,10 @@ class CarbonStaticVariables(TypedDict):
 DEFAULT_CARBON = CarbonStaticVariables(
     f_pocp = 0.9,
     kdoc_20= 0.01,
-    kdoc_theta = 1.047,
     f_pocb=0.9,
     kpoc_20= 0.005,
     kpoc_theta = 1.047,
+    kdoc_theta = 1.047,
     KsOxmc=1.0,
     pCO2 = 383.0,
     FCO2 = 0.2,
@@ -218,7 +218,7 @@ class PathogenStaticVariables(TypedDict):
 
 DEFAULT_PATHOGEN = PathogenStaticVariables(
     kdx_20=0.8,
-    kdx_theta = 1.047,
+    kdx_theta = 1.07,
     apx=1,
     vx=1
 )
@@ -234,7 +234,7 @@ class PhosphorusStaticVariables(TypedDict):
     kop_20 = 0.1,
     rpo4_20 =0,
     kop_theta = 1.047,
-    rpo4_theta = 1.047,
+    rpo4_theta = 1.074,
     kdpo4 = 0.0,
 )
 
@@ -321,18 +321,18 @@ class GlobalVars(TypedDict):
     vs = 999,
     SOD_20 = 999,
     SOD_theta = 999,
+    theta=1.047,
     vb = 0.01,
     fcom = 0.4,
     kaw_20_user = 999,
     kah_20_user = 999,
-    kaw_theta = 1.047,
-    kah_theta = 1.047,
-    hydraulic_reaeration_option = 2,
-    wind_reaeration_option = 2,  
+    kaw_theta = 1.024,
+    kah_theta = 1.024,
+    hydraulic_reaeration_option = 1,
+    wind_reaeration_option = 1,  
     dt = 1,    #TODO Dynamic or static?
     depth = 1.5,         #TODO Dynamic or static?
     TwaterC = 20,
-    theta = 1.047,
     velocity = 1,
     flow = 2,
     topwidth = 1,

src/clearwater_modules/nsm1/dynamic_variables.py

@@ -1371,14 +1371,6 @@ class Variable(base.Variable):
     process=processes.KHN2_tc
 )
 
-Variable(
-    name='P_wv',
-    long_name='Partial pressure water vapor',
-    units='atm',
-    description='Partial pressure water vapor',
-    use='dynamic',
-    process=processes.P_wv
-)
 
 Variable(
     name='N2sat',

src/clearwater_modules/nsm1/processes.py

@@ -12,7 +12,7 @@ def celsius_to_kelvin(tempc: xr.DataArray) -> xr.DataArray:
 
 
 def kelvin_to_celsius(tempk: xr.DataArray) -> xr.DataArray:
-    return tempk - 273.16
+    return tempk - 273.15
 
 
 def arrhenius_correction(
@@ -1512,6 +1512,8 @@ def NH4_ApGrowth(
 def NH4_AbRespiration(
     use_Balgae: bool,
     rnb: xr.DataArray,
+    Fb: xr.DataArray,
+    depth: xr.DataArray,
     AbRespiration: xr.DataArray,
 
 ) -> xr.DataArray:
@@ -1521,10 +1523,12 @@ 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,
@@ -3469,36 +3473,21 @@ def KHN2_tc(
     return 0.00065 * np.exp(1300.0 * (1.0 / TwaterK - 1 / 298.15))   
 
 
-def P_wv(
-    TwaterK : xr.DataArray,
-) -> xr.DataArray :
-
-    """Calculate partial pressure water vapor (atm)
-
-    Constant values found in documentation
-
-    Args:
-        TwaterK: water temperature kelvin (K)
-
-    """
-    return np.exp(11.8571  - (3840.70 / TwaterK) - (216961.0 / (TwaterK**2)))
-
-
 def N2sat(
     KHN2_tc : xr.DataArray,
     pressure_atm: xr.DataArray,
-    P_wv: xr.DataArray
+    pwv: xr.DataArray
 ) -> xr.DataArray:
 
     """Calculate N2 at saturation f(Twater and atm pressure) (mg-N/L)
 
     Args:
         KHN2_tc: Henry's law constant (mol/L/atm)
         pressure_atm: atmosphric pressure in atm (atm)
-        P_wv: Partial pressure of water vapor (atm)
+        pwv: Partial pressure of water vapor (atm)
     """
 
-    N2sat = 2.8E+4 * KHN2_tc * 0.79 * (pressure_atm - P_wv)  
+    N2sat = 2.8E+4 * KHN2_tc * 0.79 * (pressure_atm - pwv)  
     N2sat = xr.where(N2sat < 0.0,0.000001,N2sat) #Trap saturation concentration to ensure never negative
 
     return N2sat

tests/test_14_nsm_phosphrous_calculations.py

@@ -74,6 +74,9 @@ def default_algae_params() -> AlgaeStaticVariables:
         vsap= 0.15,
         growth_rate_option = 1,
         light_limitation_option = 1,
+        mu_max_theta= 1.047,
+        kdp_theta= 1.047,
+        krp_theta= 1.047,
     )
 
 @pytest.fixture(scope='function')
@@ -119,7 +122,10 @@ def default_balgae_params() -> BalgaeStaticVariables:
         b_growth_rate_option=1,
         b_light_limitation_option=1,
         Fw=0.9,
-        Fb=0.9
+        Fb=0.9,
+        mub_max_theta = 1.047,
+        krb_theta = 1.06,
+        kdb_theta = 1.047,
     )
 
 @pytest.fixture(scope='function')
@@ -140,7 +146,12 @@ def default_nitrogen_params() -> NitrogenStaticVariables:
         vno3_20=0,
         KsOxdn=0.1,
         PN=0.5,
-        PNb=0.5
+        PNb=0.5,
+        knit_theta= 1.083,
+        kon_theta= 1.047,
+        kdnit_theta= 1.045,
+        rnh4_theta= 1.074,
+        vno3_theta= 1.08,
     )
 
 @pytest.fixture(scope='function')
@@ -160,7 +171,9 @@ def default_carbon_params() -> CarbonStaticVariables:
         KsOxmc=1.0,
         pCO2 = 383.0,
         FCO2 = 0.2,
-        roc = 32.0/12.0
+        roc = 32.0/12.0,
+        kpoc_theta = 1.047,
+        kdoc_theta = 1.047,
     )
 
 @pytest.fixture(scope='function')
@@ -175,7 +188,9 @@ def default_CBOD_params() -> CBODStaticVariables:
     return CBODStaticVariables(
         KsOxbod = 0.5,
         kbod_20 =  0.12,
-        ksbod_20 = 0.0
+        ksbod_20 = 0.0,
+        kbod_theta =  1.047,
+        ksbod_theta = 1.047
     )
 
 @pytest.fixture(scope='function')
@@ -215,7 +230,9 @@ def default_POM_params() -> POMStaticVariables:
     Returns a typed dictionary, with string keys and float values.
     """
     return POMStaticVariables(
-        kpom_20 = 0.1
+        kpom_20 = 0.1,
+        h2 = 0.1,
+        kpom_theta = 1.047
     )
 
 @pytest.fixture(scope='function')
@@ -230,7 +247,8 @@ def default_pathogen_params() -> PathogenStaticVariables:
     return PathogenStaticVariables(
         kdx_20=0.8,
         apx=1,
-        vx=1
+        vx=1,
+        kdx_theta = 1.07,
     )
 
 @pytest.fixture(scope='function')
@@ -246,6 +264,8 @@ def default_phosphorus_params() -> PhosphorusStaticVariables:
         kop_20 = 0.1,
         rpo4_20 =0,
         kdpo4 = 0.0,
+        kop_theta = 1.047,
+        rpo4_theta = 1.074,
     )
 
 @pytest.fixture(scope='function')
@@ -294,14 +314,15 @@ def default_gvars_params() -> GlobalVars:
         SOD_theta = 999,
         vb = 0.01,
         fcom = 0.4,
-        kaw_20_user = 999,
-        kah_20_user = 999,
-        hydraulic_reaeration_option = 2,
-        wind_reaeration_option = 2,  
+        kaw_20_user = 0,
+        kah_20_user = 1,
+        hydraulic_reaeration_option = 1,
+        wind_reaeration_option = 1,  
         timestep = 1,    #TODO Dynamic or static?
         depth = 1.5,         #TODO Dynamic or static?
         TwaterC = 25,
-        theta = 1.047,
+        kaw_theta = 1.024,
+        kah_theta = 1.024,
         velocity = 1,
         flow = 150,
         topwidth = 100,

tests/test_15_nsm_POM_calculations.py

@@ -34,7 +34,7 @@ def initial_nsm1_state() -> dict[str, float]:
         'OrgN': 1.726,
         'N2': 1, 
         'TIP': 0.071,
-        'OrgP': 0.24,
+        'OrgP': 0.25,
         'POC': 4.356,
         'DOC': 1,
         'DIC': 1,
@@ -74,6 +74,9 @@ def default_algae_params() -> AlgaeStaticVariables:
         vsap= 0.15,
         growth_rate_option = 1,
         light_limitation_option = 1,
+        mu_max_theta= 1.047,
+        kdp_theta= 1.047,
+        krp_theta= 1.047,
     )
 
 @pytest.fixture(scope='function')
@@ -119,7 +122,10 @@ def default_balgae_params() -> BalgaeStaticVariables:
         b_growth_rate_option=1,
         b_light_limitation_option=1,
         Fw=0.9,
-        Fb=0.9
+        Fb=0.9,
+        mub_max_theta = 1.047,
+        krb_theta = 1.06,
+        kdb_theta = 1.047,
     )
 
 @pytest.fixture(scope='function')
@@ -140,7 +146,12 @@ def default_nitrogen_params() -> NitrogenStaticVariables:
         vno3_20=0,
         KsOxdn=0.1,
         PN=0.5,
-        PNb=0.5
+        PNb=0.5,
+        knit_theta= 1.083,
+        kon_theta= 1.047,
+        kdnit_theta= 1.045,
+        rnh4_theta= 1.074,
+        vno3_theta= 1.08,
     )
 
 @pytest.fixture(scope='function')
@@ -160,7 +171,9 @@ def default_carbon_params() -> CarbonStaticVariables:
         KsOxmc=1.0,
         pCO2 = 383.0,
         FCO2 = 0.2,
-        roc = 32.0/12.0
+        roc = 32.0/12.0,
+        kpoc_theta = 1.047,
+        kdoc_theta = 1.047,
     )
 
 @pytest.fixture(scope='function')
@@ -175,7 +188,9 @@ def default_CBOD_params() -> CBODStaticVariables:
     return CBODStaticVariables(
         KsOxbod = 0.5,
         kbod_20 =  0.12,
-        ksbod_20 = 0.0
+        ksbod_20 = 0.0,
+        kbod_theta =  1.047,
+        ksbod_theta = 1.047
     )
 
 @pytest.fixture(scope='function')
@@ -216,7 +231,8 @@ def default_POM_params() -> POMStaticVariables:
     """
     return POMStaticVariables(
         kpom_20 = 0.1,
-        h2 = 0.1
+        h2 = 0.1,
+        kpom_theta = 1.047
     )
 
 @pytest.fixture(scope='function')
@@ -231,7 +247,8 @@ def default_pathogen_params() -> PathogenStaticVariables:
     return PathogenStaticVariables(
         kdx_20=0.8,
         apx=1,
-        vx=1
+        vx=1,
+        kdx_theta = 1.07,
     )
 
 @pytest.fixture(scope='function')
@@ -247,8 +264,9 @@ def default_phosphorus_params() -> PhosphorusStaticVariables:
         kop_20 = 0.1,
         rpo4_20 =0,
         kdpo4 = 0.0,
+        kop_theta = 1.047,
+        rpo4_theta = 1.074,
     )
-
 @pytest.fixture(scope='function')
 def default_gp_params() -> GlobalParameters:
     """Returns default global parameter static variable values for the model.
@@ -295,14 +313,15 @@ def default_gvars_params() -> GlobalVars:
         SOD_theta = 999,
         vb = 0.01,
         fcom = 0.4,
-        kaw_20_user = 999,
-        kah_20_user = 999,
-        hydraulic_reaeration_option = 2,
-        wind_reaeration_option = 2,  
+        kaw_20_user = 0,
+        kah_20_user = 1,
+        hydraulic_reaeration_option = 1,
+        wind_reaeration_option = 1,  
         timestep = 1,    #TODO Dynamic or static?
         depth = 1.5,         #TODO Dynamic or static?
         TwaterC = 25,
-        theta = 1.047,
+        kaw_theta = 1.024,
+        kah_theta = 1.024,
         velocity = 1,
         flow = 150,
         topwidth = 100,