Algae Module Tests

examples/dev_sandbox/prof_nsm.py

@@ -0,0 +1,217 @@
+"""A script to allow for debugging of the NSM module."""
+import time
+import sys
+import clearwater_modules as cwm
+from clearwater_modules.nsm1.model import NutrientBudget
+
+
+
+
+initial_state_values = {
+    'Ap': 1,
+    'Ab': 1,
+    'NH4': 1,
+    'NO3': 1,
+    'OrgN': 1,
+    'N2': 1,
+    'TIP': 1,
+    'OrgP': 1,
+    'POC': 1,
+    'DOC': 1,
+    'DIC': 1,
+    'POM': 1,
+    'CBOD': 1,
+    'DOX': 1,
+    'PX': 1,
+    'Alk': 1
+}
+
+algae_parameters = {
+    'AWd': 100,
+    'AWc': 40,
+    'AWn': 7.2,
+    'AWp': 1,
+    'AWa': 1000,
+    'KL': 10,
+    'KsN': 0.04,
+    'KsP': 0.0012,
+    'mu_max_20': 1,
+    'kdp_20': 0.15,
+    'krp_20': 0.2,
+    'vsap': 0.15,
+    'growth_rate_option': 1,
+    'light_limitation_option': 1,
+    'lambda0': .5,
+    'lambda1': .5,
+    'lambda2': .5,
+    'lambdas': .5,
+    'lambdam': .5, 
+    'Fr_PAR': .5  
+}
+
+balgae_parameters = {
+    'BWd': 100,
+    'BWc': 40,
+    'BWn': 7.2,
+    'BWp': 1,
+    'BWa': 3500,
+
+    'KLb': 10,
+    'KsNb': 0.25,
+    'KsPb': 0.125,
+    'Ksb': 10,
+    'mub_max_20': 0.4,
+    'krb_20': 0.2,
+    'kdb_20': 0.3,
+    'b_growth_rate_option': 1,
+    'b_light_limitation_option': 1,
+    'Fw': 0.9,
+    'Fb': 0.9
+}
+
+nitrogen_parameters = {
+    'KNR': 0.6,
+    'knit_20': 0.1,
+    'kon_20': 0.1,
+    'kdnit_20': 0.002,
+    'rnh4_20': 0,
+    'vno3_20': 0,
+    'KsOxdn': 0.1,
+    'PN': 0.5,
+    'PNb': 0.5
+}
+
+phosphorus_parameters = {
+    'kop_20': 0.1,
+    'rpo4_20': 0
+}
+
+POM_parameters = {
+    'kpom_20': 0.1
+}
+
+CBOD_parameters = {
+    'KsOxbod': 0.5,
+    'kbod_20': 0.12,
+    'ksbod_20': 0
+}
+
+carbon_parameters = {
+    'f_pocp': 0.9,
+    'kdoc_20': 0.01,
+    'f_pocb': 0.9,
+    'kpoc_20': 0.005,
+    'K_sOxmc': 1,
+    'pCO2': 383,
+    'FCO2': 0.2
+}
+
+pathogen_parameters = {
+    'kdx': 0.8,
+    'apx': 1,
+    'vx': 1
+}
+
+alkalinity_parameters = {
+    'r_alkaa': 1,
+    'r_alkan': 1,
+    'r_alkn': 1,
+    'r_alkden': 1,
+    'r_alkba': 1,
+    'r_alkbn': 1 
+}
+
+global_parameters = {
+    'use_NH4': True,
+    'use_NO3': True, 
+    'use_OrgN': True,
+    'use_TIP': True,  
+    'use_SedFlux': False,
+    'use_DOX': True,
+    'use_Algae': True,
+    'use_Balgae': True,
+    'use_OrgP': True,
+    'use_POC': True,
+    'use_DOC': True,
+    'use_DIC': True,
+    'use_N2': True,
+    'use_Pathogen': True,
+    'use_Alk': True,
+    'use_POM': True 
+}
+
+
+global_vars = {
+    'vson': 0.01,
+    'vsoc': 0.01,
+    'vsop': 999,
+    'vs': 999,
+    'SOD_20': 999,
+    '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,    
+    'timestep': 86400,
+    'depth': 1,
+    'TwaterC': 20,
+    'theta': 1.047,
+    'velocity': 1,
+    'flow': 2,
+    'topwidth': 1,
+    'slope': 2,
+    'shear_velocity': 4,
+    'pressure_atm': 2,
+    'wind_speed': 4,
+    'q_solar': 4,
+    'Solid': 1, 
+}
+
+DOX_parameters = {
+    'DOX': 6.5,
+}
+N2_parameters = {}
+
+def main(iters: int):
+    ti = time.time()
+    # define starting state values
+    nsm_model = NutrientBudget(
+        initial_state_values=initial_state_values,  # mandatory
+        algae_parameters=algae_parameters,
+        alkalinity_parameters=alkalinity_parameters,
+        balgae_parameters=balgae_parameters,
+        carbon_parameters=carbon_parameters,
+        CBOD_parameters=CBOD_parameters,
+        DOX_parameters=DOX_parameters,
+        nitrogen_parameters=nitrogen_parameters,
+        POM_parameters=POM_parameters,
+        N2_parameters=N2_parameters,
+        phosphorus_parameters=phosphorus_parameters,
+        pathogen_parameters=pathogen_parameters,
+        global_parameters=global_parameters,
+        global_vars=global_vars,  
+        track_dynamic_variables=True,  # default is true
+        hotstart_dataset=None,  # default is None
+        time_dim='year',  # default is "timestep"
+    )
+    # print(nsm_model.get_variable_names())
+    print(nsm_model.dynamic_variables_names)
+
+    for _ in range(iters):
+        nsm_model.increment_timestep()
+
+
+if __name__ == '__main__':
+    if len(sys.argv) > 1:
+        try:
+            iters = int(sys.argv[1])
+            print(f'Running {iters} iterations.')
+        except ValueError:
+            raise ValueError('Argument must be an integer # of iterations.')
+    else:
+        print('No argument given, defaulting to 100 iteration.')
+        iters = 100
+
+    main(iters=iters)

src/clearwater_modules/nsm1/__init__.py

@@ -1,36 +1,4 @@
-"""
-=======================================================================================
-Nutrient Simulation Module 1 (NSM1)
-=======================================================================================
-
-Developed by:
-* Dr. Todd E. Steissberg (ERDC-EL)
-* Dr. Billy E. Johnson (ERDC-EL, LimnoTech)
-* Dr. Zhonglong Zhang (Portland State University)
-* Mr. Mark Jensen (HEC)
-
-This module computes the water quality of a single computational cell. The algorithms 
-and structure of this program were adapted from the Fortran 95 version of this module, 
-developed by:
-* Dr. Billy E. Johnson (ERDC-EL)
-* Dr. Zhonglong Zhang (Portland State University)
-* Mr. Mark Jensen (HEC)
-
-Version 1.0
-
-Initial Version: June 5, 2021
-"""
-
-from clearwater_modules.nsm1 import algae
-from clearwater_modules.nsm1 import alkalinity
-from clearwater_modules.nsm1 import balgae
-from clearwater_modules.nsm1 import carbon
-from clearwater_modules.nsm1 import CBOD
-from clearwater_modules.nsm1 import DOX
-from clearwater_modules.nsm1 import nitrogen
-from clearwater_modules.nsm1 import POM
-
-
-class NSM1:
-    def __init__(self):
-        pass
+from clearwater_modules.nsm1 import state_variables
+from clearwater_modules.nsm1 import dynamic_variables
+from clearwater_modules.nsm1 import static_variables
+from clearwater_modules.nsm1.model import NutrientBudget

src/clearwater_modules/nsm1/algae/processes.py

@@ -3,6 +3,7 @@
 """
 import numba
 import xarray as xr
+import numpy as np
 from clearwater_modules.shared.processes import arrhenius_correction
 import math
 
@@ -116,7 +117,7 @@ def FL(
     Ap: xr.DataArray,
     PAR: xr.DataArray,
     light_limitation_option: int,
-    KL: xr.DataArray,
+    KL: int,
 ) -> xr.DataArray:
     """Calculate Algal light limitation: FL (unitless).
 
@@ -131,12 +132,13 @@ def FL(
 
     KEXT = L * depth
 
+
     FL = xr.where(Ap <= 0.0 or KEXT <= 0.0 or PAR <= 0.0, 0, 
          xr.where(light_limitation_option==1, (1.0 / KEXT) * math.log((KL + PAR) /(KL + PAR * math.exp(-KEXT))),
          xr.where(light_limitation_option==2,
-         xr.where(abs(KL)<0.0000000001, 1, (1.0 / KEXT) * math.log( (PAR / KL + ((1.0 + (PAR / KL)**2.0)**0.5)) / (PAR * math.exp(-KEXT) / KL + ((1.0 + (PAR * math.exp(-KEXT) / KL)**2.0)**0.5)))), 
+         xr.where(abs(KL)< 0.0000000001, 1, (1.0 / KEXT) * math.log( (PAR / KL + ((1.0 + (PAR / KL)**2.0)**0.5)) / (PAR * math.exp(-KEXT) / KL + ((1.0 + (PAR * math.exp(-KEXT) / KL)**2.0)**0.5)))), 
          xr.where(light_limitation_option==3,
-         xr.where(abs(KL)<0.0000000001,0,(2.718/KEXT) * (math.exp(-PAR/KL * math.exp(-KEXT)) - math.exp(-PAR/KL))), "NaN"))))
+         xr.where(abs(KL)< 0.0000000001,0,(2.718/KEXT) * (math.exp(-PAR/KL * math.exp(-KEXT)) - math.exp(-PAR/KL))), "NaN"))))
 
 
     FL= xr.where(FL > 1.0, 1.0,

src/clearwater_modules/nsm1/balgae/dynamic_variables.py

@@ -12,7 +12,6 @@
 class Variable(base.Variable):
     ...
 
-
 Variable(
     name='mub_max_tc',
     long_name='Maximum benthic algal growth rate',

src/clearwater_modules/nsm1/carbon/static_variables.py

@@ -72,6 +72,6 @@ class Variable(base.Variable):
     name='roc',
     long_name='O2:C ratio for carbon oxidation',
     units='mg-O2/mg-C',
-    description='32/12',
+    description='O2:C ratio for carbon oxidation (32/12)',
     use='static'
 )