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Merge pull request #78 from EcohydrologyTeam/KW_testing
Algae Module Tests
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‎examples/dev_sandbox/prof_nsm.py

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"""A script to allow for debugging of the NSM module."""
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import time
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import sys
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import clearwater_modules as cwm
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from clearwater_modules.nsm1.model import NutrientBudget
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initial_state_values = {
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'Ap': 1,
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'Ab': 1,
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'NH4': 1,
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'NO3': 1,
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'OrgN': 1,
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'N2': 1,
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'TIP': 1,
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'OrgP': 1,
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'POC': 1,
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'DOC': 1,
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'DIC': 1,
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'POM': 1,
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'CBOD': 1,
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'DOX': 1,
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'PX': 1,
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'Alk': 1
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}
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algae_parameters = {
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'AWd': 100,
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'AWc': 40,
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'AWn': 7.2,
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'AWp': 1,
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'AWa': 1000,
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'KL': 10,
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'KsN': 0.04,
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'KsP': 0.0012,
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'mu_max_20': 1,
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'kdp_20': 0.15,
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'krp_20': 0.2,
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'vsap': 0.15,
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'growth_rate_option': 1,
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'light_limitation_option': 1,
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'lambda0': .5,
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'lambda1': .5,
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'lambda2': .5,
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'lambdas': .5,
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'lambdam': .5,
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'Fr_PAR': .5
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}
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balgae_parameters = {
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'BWd': 100,
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'BWc': 40,
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'BWn': 7.2,
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'BWp': 1,
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'BWa': 3500,
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'KLb': 10,
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'KsNb': 0.25,
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'KsPb': 0.125,
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'Ksb': 10,
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'mub_max_20': 0.4,
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'krb_20': 0.2,
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'kdb_20': 0.3,
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'b_growth_rate_option': 1,
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'b_light_limitation_option': 1,
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'Fw': 0.9,
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'Fb': 0.9
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}
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nitrogen_parameters = {
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'KNR': 0.6,
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'knit_20': 0.1,
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'kon_20': 0.1,
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'kdnit_20': 0.002,
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'rnh4_20': 0,
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'vno3_20': 0,
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'KsOxdn': 0.1,
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'PN': 0.5,
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'PNb': 0.5
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}
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phosphorus_parameters = {
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'kop_20': 0.1,
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'rpo4_20': 0
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}
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POM_parameters = {
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'kpom_20': 0.1
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}
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CBOD_parameters = {
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'KsOxbod': 0.5,
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'kbod_20': 0.12,
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'ksbod_20': 0
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}
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carbon_parameters = {
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'f_pocp': 0.9,
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'kdoc_20': 0.01,
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'f_pocb': 0.9,
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'kpoc_20': 0.005,
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'K_sOxmc': 1,
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'pCO2': 383,
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'FCO2': 0.2
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}
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pathogen_parameters = {
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'kdx': 0.8,
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'apx': 1,
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'vx': 1
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}
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alkalinity_parameters = {
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'r_alkaa': 1,
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'r_alkan': 1,
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'r_alkn': 1,
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'r_alkden': 1,
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'r_alkba': 1,
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'r_alkbn': 1
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}
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global_parameters = {
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'use_NH4': True,
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'use_NO3': True,
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'use_OrgN': True,
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'use_TIP': True,
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'use_SedFlux': False,
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'use_DOX': True,
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'use_Algae': True,
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'use_Balgae': True,
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'use_OrgP': True,
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'use_POC': True,
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'use_DOC': True,
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'use_DIC': True,
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'use_N2': True,
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'use_Pathogen': True,
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'use_Alk': True,
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'use_POM': True
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}
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global_vars = {
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'vson': 0.01,
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'vsoc': 0.01,
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'vsop': 999,
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'vs': 999,
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'SOD_20': 999,
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'SOD_theta': 999,
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'vb': 0.01,
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'fcom': 0.4,
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'kaw_20_user': 999,
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'kah_20_user': 999,
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'hydraulic_reaeration_option': 2,
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'wind_reaeration_option': 2,
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'timestep': 86400,
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'depth': 1,
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'TwaterC': 20,
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'theta': 1.047,
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'velocity': 1,
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'flow': 2,
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'topwidth': 1,
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'slope': 2,
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'shear_velocity': 4,
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'pressure_atm': 2,
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'wind_speed': 4,
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'q_solar': 4,
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'Solid': 1,
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}
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DOX_parameters = {
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'DOX': 6.5,
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}
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N2_parameters = {}
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def main(iters: int):
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ti = time.time()
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# define starting state values
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nsm_model = NutrientBudget(
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initial_state_values=initial_state_values, # mandatory
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algae_parameters=algae_parameters,
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alkalinity_parameters=alkalinity_parameters,
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balgae_parameters=balgae_parameters,
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carbon_parameters=carbon_parameters,
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CBOD_parameters=CBOD_parameters,
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DOX_parameters=DOX_parameters,
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nitrogen_parameters=nitrogen_parameters,
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POM_parameters=POM_parameters,
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N2_parameters=N2_parameters,
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phosphorus_parameters=phosphorus_parameters,
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pathogen_parameters=pathogen_parameters,
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global_parameters=global_parameters,
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global_vars=global_vars,
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track_dynamic_variables=True, # default is true
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hotstart_dataset=None, # default is None
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time_dim='year', # default is "timestep"
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)
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# print(nsm_model.get_variable_names())
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print(nsm_model.dynamic_variables_names)
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for _ in range(iters):
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nsm_model.increment_timestep()
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if __name__ == '__main__':
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if len(sys.argv) > 1:
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try:
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iters = int(sys.argv[1])
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print(f'Running {iters} iterations.')
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except ValueError:
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raise ValueError('Argument must be an integer # of iterations.')
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else:
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print('No argument given, defaulting to 100 iteration.')
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iters = 100
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main(iters=iters)

‎examples/model_architecture.ipynb

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‎examples/model_architecture_nsm.ipynb

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‎src/clearwater_modules/nsm1/__init__.py

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

‎src/clearwater_modules/nsm1/algae/processes.py

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

‎src/clearwater_modules/nsm1/balgae/dynamic_variables.py

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class Variable(base.Variable):
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...
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Variable(
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name='mub_max_tc',
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long_name='Maximum benthic algal growth rate',

‎src/clearwater_modules/nsm1/carbon/static_variables.py

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name='roc',
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long_name='O2:C ratio for carbon oxidation',
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units='mg-O2/mg-C',
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description='32/12',
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description='O2:C ratio for carbon oxidation (32/12)',
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use='static'
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)

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