Merge branch 'main' into IJM_NSM_v2

src/clearwater_modules/nsm1/old/CBOD/dynamic_variables.py

@@ -0,0 +1,59 @@
+"""
+File contains dynamic variables related to the CBOD module
+"""
+
+import clearwater_modules.shared.processes as shared_processes
+from clearwater_modules import base
+from clearwater_modules.nsm1.model import NutrientBudget
+import clearwater_modules.nsm1.CBOD.processes as processes
+
+
+@base.register_variable(models=NutrientBudget)
+class Variable(base.Variable):
+    ...
+
+
+Variable(
+    name='kbod_tc',
+    long_name='Temperature adjusted oxidation rate',
+    units='1/d',
+    description='Temperature adjusted oxidation rate',
+    use='dynamic',
+    process=processes.kbod_tc
+)
+
+Variable(
+    name='ksbod_tc',
+    long_name='Temperature adjusted sedimentation rate',
+    units='m/d',
+    description='Temperature adjusted sedimentation rate',
+    use='dynamic',
+    process=processes.ksbod_tc
+)
+
+Variable(
+    name='CBOD_oxidation',
+    long_name='CBOD oxidation',
+    units='mg/L/d',
+    description='CBOD oxidation',
+    use='dynamic',
+    process=processes.CBOD_oxidation
+)
+
+Variable(
+    name='CBOD_sedimentation',
+    long_name='CBOD sedimentation',
+    units='mg/L/d',
+    description='CBOD sedimentation',
+    use='dynamic',
+    process=processes.CBOD_sedimentation
+)
+
+Variable(
+    name='dCBODdt',
+    long_name='Change in CBOD concentration for the given timestep',
+    units='mg/L/d',
+    description='Change in CBOD concentration for the given timestep',
+    use='dynamic',
+    process=processes.dCBODdt
+)

src/clearwater_modules/nsm1/old/CBOD/processes.py

@@ -0,0 +1,107 @@
+"""
+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
+import math
+
+@numba.njit
+def kbod_tc(
+    TwaterC: xr.DataArray,
+    kbod_20: xr.DataArray,
+) -> xr.DataArray:
+    """Calculate the temperature adjusted CBOD oxidation rate (1/d)
+
+    Args:
+        TwaterC: water temperature in Celsius
+        kbod_20: CBOD oxidation rate at 20 degrees Celsius (1/d)
+    """
+
+    kbod_tc = arrhenius_correction(TwaterC, kbod_20, 1.047)
+    return kbod_tc
+
+
+@numba.njit
+def ksbod_tc(
+    TwaterC: xr.DataArray,
+    ksbod_20: xr.DataArray,
+) -> xr.DataArray:
+    """Calculate the temperature adjusted CBOD sedimentation rate (m/d)
+
+    Args:
+        TwaterC: water temperature in Celsius
+        ksbod_20: CBOD sedimentation rate at 20 degrees Celsius (m/d)
+    """
+
+    ksbod_tc = arrhenius_correction(TwaterC, ksbod_20, 1.024)
+    return ksbod_tc
+
+
+
+def CBOD_oxidation(
+    DOX: xr.DataArray,
+    CBOD: xr.DataArray,
+    kbod_tc: xr.DataArray,
+    KsOxbod: xr.DataArray,
+    use_DOX: xr.DataArray
+) -> xr.DataArray:
+    """Calculates CBOD oxidation
+
+    Args:
+        DOX: Dissolved oxygen concentration (mg-O2/L)
+        CBOD: Carbonaceous biochemical oxygen demand (mg-O2/L)
+        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_tc * CBOD, kbod_tc * CBOD)
+
+    return da
+
+
+@numba.njit
+def CBOD_sedimentation(
+    CBOD: xr.DataArray,
+    ksbod_tc: xr.DataArray
+) -> xr.DataArray:
+    """Calculates CBOD sedimentation for each group
+
+    Args:
+        CBOD: CBOD concentration (mg-O2/L)
+        ksbod_tc: Temperature adjusted sedimentation rate (m/d)
+    """
+
+    CBOD_sedimentation = CBOD * ksbod_tc
+    return CBOD_sedimentation
+
+
+@numba.njit
+def dCBODdt(
+    CBOD_oxidation: xr.DataArray,
+    CBOD_sedimentation: xr.DataArray
+) -> xr.DataArray:
+    """Computes change in each CBOD group for a given timestep
+
+    Args:
+        CBOD_oxidation: CBOD concentration change due to oxidation (mg/L/d)
+        CBOD_sedimentation: CBOD concentration change due to sedimentation (mg/L/d)
+    """
+    return - CBOD_oxidation - CBOD_sedimentation
+
+
+@numba.njit
+def CBOD(
+    CBOD: xr.DataArray,
+    dCBODdt: xr.DataArray,
+    timestep: xr.DataArray
+) -> xr.DataArray:
+    """Calculates new CBOD concentration for next timestep
+
+    Args:
+        CBOD: CBOD concentration from previous timestep (mg/L)
+        dCBODdt: CBOD concentration change for current timestep (mg/L/d)
+        timestep: current iteration timestep (d)
+    """
+    return CBOD + dCBODdt * timestep

src/clearwater_modules/nsm1/old/CBOD/static_variables.py

@@ -0,0 +1,37 @@
+"""
+File contains static variables related to the CBOD module
+"""
+
+import clearwater_modules.base as base
+from clearwater_modules.nsm1.model import NutrientBudget
+
+
+@base.register_variable(models=NutrientBudget)
+class Variable(base.Variable):
+    ...
+
+
+Variable(
+    name='kbod_20',
+    long_name='CBOD oxidation rate at 20C',
+    units='1/d',
+    description='CBOD oxidation rate at 20C',
+    use='static'
+)
+
+Variable(
+    name='ksbod_20',
+    long_name='CBOD sedimentation rate at 20C',
+    units='m/d',
+    description='CBOD sedimentation rate at 20C',
+    use='static'
+)
+
+Variable(
+    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/old/DOX/dynamic_variables.py

@@ -0,0 +1,132 @@
+# TODO: figure out imports
+
+import clearwater_modules.shared.processes as shared_processes
+from clearwater_modules import base
+from clearwater_modules.nsm1.model import NutrientBudget
+import clearwater_modules.nsm1.DOX.processes as processes
+
+
+@base.register_variable(models=NutrientBudget)
+class Variable(base.Variable):
+    ...
+
+
+Variable(
+    name='DOX_sat',
+    long_name='DO saturation concentration',
+    units='mg/L',
+    description='DO saturation concentration in water as a function of water temperature (K)',
+    use='dynamic',
+    process=processes.DOX_sat
+)
+
+Variable(
+    name='pwv',
+    long_name='Partial pressure of water vapor',
+    units='atm',
+    description='Partial pressure of water vapor',
+    use='dynamic',
+    process=processes.pwv
+)
+
+Variable(
+    name='DOs_atm_alpha',
+    long_name='DO saturation atmospheric correction coefficient',
+    units='unitless',
+    description='DO saturation atmospheric correction coefficient',
+    use='dynamic',
+    process=processes.DOs_atm_alpha
+)
+
+Variable(
+    name='Atm_O2_reaeration',
+    long_name='Atmospheric oxygen reaeration',
+    units='mg/L/d',
+    description='Atmospheric oxygen reaeration, can fluctuate both in and out of waterbody',
+    use='dynamic',
+    process=processes.Atm_O2_reaeration
+)
+
+# TODO: UPDATE BASED ON FORTRAN
+Variable(
+    name='DOX_ApGrowth',
+    long_name='Dissolved oxygen flux due to algal photosynthesis',
+    units='mg/L/d',
+    description='Dissolved oxygen flux due to algal photosynthesis',
+    use='dynamics',
+    process=processes.DOX_ApGrowth
+)
+
+# TODO: UPDATE BASED ON FORTRAN
+Variable(
+    name='DOX_algal_respiration',
+    long_name='Dissolved oxygen flux due to algal respiration',
+    units='mg/L/d',
+    description='Dissolved oxygen flux due to algal respiration',
+    use='dynamic',
+    process=processes.DOX_ApRespiration
+)
+
+Variable(
+    name='DOX_Nitrification',
+    long_name='Dissolved oxygen flux due to nitrification',
+    units='mg/L/d',
+    description='Dissolved oxygen flux due to nitrification',
+    use='dynamic',
+    process=processes.DOX_Nitrification
+)
+
+Variable(
+    name='DOX_DOC_Oxidation',
+    long_name='Dissolved oxygen flux due to DOC oxidation',
+    units='mg/L/d',
+    description='Dissolved oxygen flux due to DOC oxidation',
+    use='dynamic',
+    process=processes.DOX_DOC_Oxidation
+)
+
+Variable(
+    name='DOX_CBOD_Oxidation',
+    long_name='Dissolved oxygen flux due to CBOD oxidation',
+    units='mg/L/d',
+    description='Dissolved oxygen flux due to CBOD oxidation',
+    use='dynamic',
+    process=processes.DOX_CBOD_Oxidation
+)
+
+Variable(
+    name='DOX_AbGrowth',
+    long_name='Dissolved oxygen flux due to benthic algae photosynthesis',
+    units='mg/L/d',
+    description='Dissolved oxygen flux due to benthic algae photosynthesis',
+    use='dynamics',
+    process=processes.DOX_AbGrowth
+)
+
+Variable(
+    name='DOX_AbRespiration',
+    long_name='Dissolved oxygen flux due to benthic algae respiration',
+    units='mg/L/d',
+    description='Dissolved oxygen flux due to benthic algae respiration',
+    use='dynamic',
+    process=processes.DOX_AbRespiration
+)
+
+
+Variable(
+    name='DOX_SOD',
+    long_name='Dissolved oxygen flux due to sediment oxygen demand',
+    units='mg/L/d',
+    description='Dissolved oxygen flux due to sediment oxygen demand',
+    use='dynamic',
+    process=processes.DOX_SOD
+)
+
+Variable(
+    name='dDOXdt',
+    long_name='Change in dissolved oxygen concentration for one timestep',
+    units='mg/L/d',
+    description='Change in dissolved oxygen concentration for one timestep',
+    use='dynamic',
+    process=processes.dDOXdt
+)