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Adding organic phosphorus flows #653

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merged 10 commits into from
Jan 8, 2025
Merged

Adding organic phosphorus flows #653

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ba68185
Added organic P pools into the soil model
jacobcook1995 Dec 4, 2024
d5eb80a
Added phosphorus decay from litter into the soil model
jacobcook1995 Dec 4, 2024
ae04bfc
Added leaching of dissolved organic phosphorus to the soil model
jacobcook1995 Dec 4, 2024
a339c0c
Added phosphorus flow due to soil organic matter mineralisation
jacobcook1995 Dec 4, 2024
504cf6f
Added phosphorus flow associated with microbial death
jacobcook1995 Dec 5, 2024
e126743
Added microbial uptake of phosphorus to set of nutrients determining …
jacobcook1995 Dec 9, 2024
6d8507f
Added tracking of phosphorus associated with microbial necromass deca…
jacobcook1995 Jan 6, 2025
54bbb2d
Added phosphorus component to LMWC to MAOM flow
jacobcook1995 Jan 6, 2025
f129175
Merge branch 'develop' into feature/organic_phosphorus
jacobcook1995 Jan 6, 2025
41d5f1b
Merge branch 'develop' into feature/organic_phosphorus
jacobcook1995 Jan 8, 2025
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5 changes: 5 additions & 0 deletions tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -265,11 +265,16 @@ def dummy_carbon_data(fixture_core_components):
"soil_n_pool_particulate": [0.00714285, 0.00071425, 0.00285714, 0.01428571],
"soil_n_pool_necromass": [0.00288462, 0.01788462, 0.02019231, 0.01115385],
"soil_n_pool_maom": [0.86538462, 0.48076923, 0.32692308, 0.09615385],
"soil_p_pool_dop": [5.714e-6, 2.2857120e-5, 5.7142800e-5, 1.1428568e-4],
"soil_p_pool_particulate": [2.857e-5, 2.85714e-4, 1.142856e-4, 5.714284e-4],
"soil_p_pool_necromass": [0.00080769, 0.00011538, 0.00071538, 0.00044615],
"soil_p_pool_maom": [0.01307692, 0.03461538, 0.01923077, 0.00384615],
"pH": [3.0, 7.5, 9.0, 5.7],
"bulk_density": [1350.0, 1800.0, 1000.0, 1500.0],
"clay_fraction": [0.8, 0.3, 0.1, 0.9],
"litter_C_mineralisation_rate": [0.00212106, 0.00106053, 0.00049000, 0.0055],
"litter_N_mineralisation_rate": [3.5351e-5, 7.0702e-5, 0.000183, 1.63333e-5],
"litter_P_mineralisation_rate": [7.32e-6, 1.41404e-6, 2.82808e-6, 6.53332e-7],
"vertical_flow": [0.1, 0.5, 2.5, 1.59],
}

Expand Down
4 changes: 4 additions & 0 deletions tests/core/test_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -978,6 +978,10 @@ def test_output_current_state(mocker, dummy_carbon_data, time_index):
"soil_n_pool_particulate",
"soil_n_pool_necromass",
"soil_n_pool_maom",
"soil_p_pool_dop",
"soil_p_pool_particulate",
"soil_p_pool_necromass",
"soil_p_pool_maom",
],
time_index,
)
Expand Down
1 change: 1 addition & 0 deletions tests/models/soil/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -115,6 +115,7 @@ def microbial_changes(
return calculate_microbial_changes(
soil_c_pool_lmwc=dummy_carbon_data["soil_c_pool_lmwc"],
soil_n_pool_don=dummy_carbon_data["soil_n_pool_don"],
soil_p_pool_dop=dummy_carbon_data["soil_p_pool_dop"],
soil_c_pool_microbe=dummy_carbon_data["soil_c_pool_microbe"],
soil_enzyme_pom=dummy_carbon_data["soil_enzyme_pom"],
soil_enzyme_maom=dummy_carbon_data["soil_enzyme_maom"],
Expand Down
115 changes: 75 additions & 40 deletions tests/models/soil/test_pools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,17 +36,21 @@ def test_calculate_all_pool_updates(dummy_carbon_data, fixture_core_components):
soil_pools = SoilPools(data=dummy_carbon_data, pools=pools, constants=SoilConsts)

change_in_pools = {
"soil_c_pool_lmwc": [0.0129365, 0.0060499, 0.03697928, 0.02425546],
"soil_c_pool_lmwc": [0.01510858, 0.01400719, 0.03697928, 0.02426899],
"soil_c_pool_maom": [0.038767651, 0.00829848, 0.05982197, 0.07277182],
"soil_c_pool_microbe": [-0.05362396, -0.02020101, -0.11965575, -0.00719517],
"soil_c_pool_microbe": [-0.0544059, -0.02282691, -0.11965575, -0.00720166],
"soil_c_pool_pom": [0.00177803841, -0.007860960795, -0.012016245, 0.00545032],
"soil_c_pool_necromass": [0.001137474, 0.009172067, 0.033573266, -0.08978050],
"soil_enzyme_pom": [1.18e-8, 1.67e-8, 1.8e-9, -1.12e-8],
"soil_enzyme_maom": [-0.00031009, -5.09593e-5, 0.0005990658, -3.72112e-5],
"soil_n_pool_don": [0.00104884, 0.00419763, 0.00496839, 0.00251317],
"soil_n_pool_don": [0.00119921, 0.00470261, 0.00496839, 0.00251442],
"soil_n_pool_particulate": [1.102338e-5, 6.422491e-5, 0.000131687, 1.461799e-5],
"soil_n_pool_necromass": [0.00786114, -0.01209909, 0.00432363, -0.00891218],
"soil_n_pool_maom": [0.00148604, 0.01179891, 0.01365197, 0.0077315],
"soil_p_pool_dop": [1.92918032e-4, 6.24454858e-5, 1.57222238e-4, 9.94118894e-5],
"soil_p_pool_particulate": [7.22218e-6, -1.13464e-6, 7.86083e-7, 5.85634364e-7],
"soil_p_pool_necromass": [2.674836e-3, 1.333056e-3, 6.8090685e-3, 4.1429847e-5],
"soil_p_pool_maom": [5.52086672e-4, 3.68566732e-5, 4.7566130e-4, 3.09257058e-4],
}

# Make order of pools object
Expand All @@ -72,16 +76,18 @@ def test_calculate_microbial_changes(

from virtual_ecosystem.models.soil.pools import calculate_microbial_changes

expected_lmwc_uptake = [2.241176e-3, 8.433524e-3, 1.556094e-3, 5.7736357e-5]
expected_don_uptake = [1.5515837e-4, 5.3520443e-4, 8.97746776e-5, 5.3295099e-6]
expected_microbe = [-0.05362396, -0.02020101, -0.11965575, -0.00719517]
expected_lmwc_uptake = [6.90989514e-5, 4.76229800e-4, 1.55609440e-3, 4.42097002e-5]
expected_don_uptake = [4.78377356e-6, 3.02222758e-5, 8.97746767e-5, 4.08089540e-6]
expected_dop_uptake = [1.55472641e-6, 9.82223962e-6, 2.91767699e-5, 1.32629101e-6]
expected_microbe = [-0.0544059, -0.02282691, -0.11965575, -0.00720166]
expected_pom_enzyme = [1.17571917e-8, 1.67442231e-8, 1.83311362e-9, -1.11675865e-8]
expected_maom_enzyme = [-3.1009224e-4, -5.0959256e-5, 5.9906583e-4, -3.7211168e-5]
expected_necromass = [0.05474086, 0.02303502, 0.11952352, 0.00726011]

mic_changes = calculate_microbial_changes(
soil_c_pool_lmwc=dummy_carbon_data["soil_c_pool_lmwc"],
soil_n_pool_don=dummy_carbon_data["soil_n_pool_don"],
soil_p_pool_dop=dummy_carbon_data["soil_p_pool_dop"],
soil_c_pool_microbe=dummy_carbon_data["soil_c_pool_microbe"],
soil_enzyme_pom=dummy_carbon_data["soil_enzyme_pom"],
soil_enzyme_maom=dummy_carbon_data["soil_enzyme_maom"],
Expand All @@ -95,6 +101,7 @@ def test_calculate_microbial_changes(
# Check that each rate matches expectation
assert np.allclose(mic_changes.lmwc_uptake, expected_lmwc_uptake)
assert np.allclose(mic_changes.don_uptake, expected_don_uptake)
assert np.allclose(mic_changes.dop_uptake, expected_dop_uptake)
assert np.allclose(mic_changes.microbe_change, expected_microbe)
assert np.allclose(mic_changes.pom_enzyme_change, expected_pom_enzyme)
assert np.allclose(mic_changes.maom_enzyme_change, expected_maom_enzyme)
Expand Down Expand Up @@ -225,27 +232,36 @@ def test_calculate_nutrient_uptake_rates(
calculate_nutrient_uptake_rates,
)

expected_carbon_gain = [8.06823526e-4, 2.78306304e-3, 4.66828324e-4, 2.77134516e-5]
expected_nitrogen_gain = [1.5515837e-4, 5.3520443e-4, 8.97746776e-5, 5.3295099e-6]
expected_carbon_consumption = [2.241176e-3, 8.433524e-3, 1.556094e-3, 5.7736357e-5]

actual_carbon_gain, actual_carbon_consumption, actual_nitrogen_gain = (
calculate_nutrient_uptake_rates(
soil_c_pool_lmwc=dummy_carbon_data["soil_c_pool_lmwc"],
soil_n_pool_don=dummy_carbon_data["soil_n_pool_don"],
soil_c_pool_microbe=dummy_carbon_data["soil_c_pool_microbe"],
water_factor=environmental_factors.water,
pH_factor=environmental_factors.pH,
soil_temp=dummy_carbon_data["soil_temperature"][
fixture_core_components.layer_structure.index_topsoil_scalar
].to_numpy(),
constants=SoilConsts,
)
expected_carbon_gain = [2.48756225e-5, 1.57155834e-4, 4.66828319e-4, 2.12206561e-5]
expected_consumption_rates = {
"nitrogen": [4.78377356e-6, 3.02222758e-5, 8.97746767e-5, 4.08089540e-6],
"phosphorus": [1.55472641e-6, 9.82223962e-6, 2.91767699e-5, 1.32629101e-6],
"carbon": [6.90989514e-5, 4.76229800e-4, 1.55609440e-3, 4.42097002e-5],
}

actual_carbon_gain, actual_consumption_rates = calculate_nutrient_uptake_rates(
soil_c_pool_lmwc=dummy_carbon_data["soil_c_pool_lmwc"],
soil_n_pool_don=dummy_carbon_data["soil_n_pool_don"],
soil_p_pool_dop=dummy_carbon_data["soil_p_pool_dop"],
soil_c_pool_microbe=dummy_carbon_data["soil_c_pool_microbe"],
water_factor=environmental_factors.water,
pH_factor=environmental_factors.pH,
soil_temp=dummy_carbon_data["soil_temperature"][
fixture_core_components.layer_structure.index_topsoil_scalar
].to_numpy(),
constants=SoilConsts,
)

assert np.allclose(actual_carbon_gain, expected_carbon_gain)
assert np.allclose(actual_nitrogen_gain, expected_nitrogen_gain)
assert np.allclose(actual_carbon_consumption, expected_carbon_consumption)

assert set(expected_consumption_rates.keys()) == set(
actual_consumption_rates.keys()
)

for key in expected_consumption_rates.keys():
assert np.allclose(
expected_consumption_rates[key], actual_consumption_rates[key]
)


def test_calculate_highest_achievable_nutrient_uptake(
Expand Down Expand Up @@ -409,52 +425,71 @@ def test_calculate_nutrient_flows_to_necromass(microbial_changes):
)

expected_n_flow_to_necromass = [0.01052709, 0.00442981, 0.02298529, 0.00139617]
expected_p_flow_to_necromass = [0.0034213, 0.00143969, 0.00747022, 0.00045376]

actual_n_flow_to_necromass = calculate_nutrient_flows_to_necromass(
microbial_changes=microbial_changes, constants=SoilConsts
actual_n_flow_to_necromass, actual_p_flow_to_necromass = (
calculate_nutrient_flows_to_necromass(
microbial_changes=microbial_changes, constants=SoilConsts
)
)

assert np.allclose(actual_n_flow_to_necromass, expected_n_flow_to_necromass)
assert np.allclose(actual_p_flow_to_necromass, expected_p_flow_to_necromass)


def test_find_necromass_nitrogen_outflows(
def test_find_necromass_nutrient_outflows(
dummy_carbon_data, necromass_breakdown, necromass_sorption
):
"""Test that function to find necromass nitrogen losses works correctly."""
from virtual_ecosystem.models.soil.pools import find_necromass_nitrogen_outflows

expected_decay = [0.00066649, 0.00413222, 0.00466541, 0.00257709]
expected_sorption = [0.00199947, 0.01239667, 0.01399624, 0.00773126]
"""Test that function to find necromass nutrient losses works correctly."""
from virtual_ecosystem.models.soil.pools import find_necromass_nutrient_outflows

expected_rates = {
"decay_nitrogen": [0.00066649, 0.00413222, 0.00466541, 0.00257709],
"sorption_nitrogen": [0.00199947, 0.01239667, 0.01399624, 0.00773126],
"decay_phosphorus": [1.86616016e-4, 2.6658441e-5, 1.65287877e-4, 1.03082538e-4],
"sorption_phosphorus": [5.5984805e-4, 7.9975322e-5, 4.958636e-4, 3.0924762e-4],
}

actual_decay, actual_sorption = find_necromass_nitrogen_outflows(
actual_rates = find_necromass_nutrient_outflows(
necromass_carbon=dummy_carbon_data["soil_c_pool_necromass"],
necromass_nitrogen=dummy_carbon_data["soil_n_pool_necromass"],
necromass_phosphorus=dummy_carbon_data["soil_p_pool_necromass"],
necromass_decay=necromass_breakdown,
necromass_sorption=necromass_sorption,
)

assert np.allclose(actual_decay, expected_decay)
assert np.allclose(actual_sorption, expected_sorption)
assert set(expected_rates.keys()) == set(actual_rates.keys())

for key in expected_rates.keys():
assert np.allclose(expected_rates[key], actual_rates[key])

def test_calculate_net_nitrogen_transfer_from_maom_to_don(

def test_calculate_net_nutrient_transfers_from_maom_to_lmwc(
dummy_carbon_data, enzyme_mediated_rates, lmwc_sorption, maom_desorption
):
"""Test function to find net exchange of nitrogen between maom and don."""
from virtual_ecosystem.models.soil.pools import (
calculate_net_nitrogen_transfer_from_maom_to_don,
calculate_net_nutrient_transfers_from_maom_to_lmwc,
)

expected_transfer = [5.13427177e-4, 5.97759087e-4, 3.44268148e-4, -2.36081562e-7]
expected_transfers = {
"nitrogen": [5.13427177e-4, 5.97759087e-4, 3.44268148e-4, -2.36081562e-7],
"phosphorus": [7.76137416e-6, 4.31186485e-5, 2.02023283e-5, -9.44337153e-9],
}

actual_transfer = calculate_net_nitrogen_transfer_from_maom_to_don(
actual_transfers = calculate_net_nutrient_transfers_from_maom_to_lmwc(
lmwc_carbon=dummy_carbon_data["soil_c_pool_lmwc"],
lmwc_nitrogen=dummy_carbon_data["soil_n_pool_don"],
lmwc_phosphorus=dummy_carbon_data["soil_p_pool_dop"],
maom_carbon=dummy_carbon_data["soil_c_pool_maom"],
maom_nitrogen=dummy_carbon_data["soil_n_pool_maom"],
maom_phosphorus=dummy_carbon_data["soil_p_pool_maom"],
maom_breakdown=enzyme_mediated_rates.maom_to_lmwc,
maom_desorption=maom_desorption,
lmwc_sorption=lmwc_sorption,
)

assert np.allclose(actual_transfer, expected_transfer)
assert set(expected_transfers.keys()) == set(actual_transfers.keys())

for key in expected_transfers.keys():
assert np.allclose(expected_transfers[key], actual_transfers[key])
63 changes: 49 additions & 14 deletions tests/models/soil/test_soil_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,10 @@
(DEBUG, "soil model: required var 'soil_n_pool_particulate' checked"),
(DEBUG, "soil model: required var 'soil_n_pool_necromass' checked"),
(DEBUG, "soil model: required var 'soil_n_pool_maom' checked"),
(DEBUG, "soil model: required var 'soil_p_pool_dop' checked"),
(DEBUG, "soil model: required var 'soil_p_pool_particulate' checked"),
(DEBUG, "soil model: required var 'soil_p_pool_necromass' checked"),
(DEBUG, "soil model: required var 'soil_p_pool_maom' checked"),
(DEBUG, "soil model: required var 'pH' checked"),
(DEBUG, "soil model: required var 'bulk_density' checked"),
(DEBUG, "soil model: required var 'clay_fraction' checked"),
Expand Down Expand Up @@ -285,20 +289,20 @@ def test_update(mocker, fixture_soil_model, dummy_carbon_data):
Dataset(
data_vars=dict(
soil_c_pool_lmwc=DataArray(
[0.0558832, 0.02294602, 0.11309406, 0.01485682], dims="cell_id"
[0.0571695, 0.02695769, 0.11767019, 0.01488859], dims="cell_id"
),
soil_c_pool_maom=DataArray(
[2.5194618, 1.70483236, 4.53238116, 0.52968038], dims="cell_id"
),
soil_c_pool_microbe=DataArray(
[5.77347072, 2.29002259, 11.24219185, 0.99642319],
[5.77300855, 2.28870164, 11.24082106, 0.99640795],
dims="cell_id",
),
soil_c_pool_pom=DataArray(
[0.10088826, 0.99607827, 0.69401858, 0.35272508], dims="cell_id"
),
soil_c_pool_necromass=DataArray(
[0.05840173, 0.01865113, 0.10631256, 0.06904725], dims="cell_id"
[0.05840079, 0.01864821, 0.10630987, 0.06904723], dims="cell_id"
),
soil_enzyme_pom=DataArray(
[0.02267842, 0.00957576, 0.05004963, 0.00300993], dims="cell_id"
Expand All @@ -307,17 +311,31 @@ def test_update(mocker, fixture_soil_model, dummy_carbon_data):
[0.0354453, 0.01167442, 0.02538637, 0.00454144], dims="cell_id"
),
soil_n_pool_don=DataArray(
[0.00124825, 0.00320679, 0.00236633, 0.00388298], dims="cell_id"
[0.00133728, 0.00346121, 0.00262946, 0.0038859], dims="cell_id"
),
soil_n_pool_particulate=DataArray(
[0.00714836, 0.00074629, 0.00292269, 0.01429302], dims="cell_id"
),
soil_n_pool_necromass=DataArray(
[0.00602181, 0.01303618, 0.02189848, 0.00758444], dims="cell_id"
[0.00602163, 0.01303562, 0.02189796, 0.00758443], dims="cell_id"
),
soil_n_pool_maom=DataArray(
[0.86671423, 0.48576345, 0.33406677, 0.09935391], dims="cell_id"
),
soil_p_pool_dop=DataArray(
[1.59404568e-4, 8.17510225e-5, 2.73598058e-4, 1.64590927e-4],
dims="cell_id",
),
soil_p_pool_particulate=DataArray(
[3.21780215e-5, 2.85147941e-4, 1.14676885e-4, 5.71721209e-4],
dims="cell_id",
),
soil_p_pool_necromass=DataArray(
[0.00187526, 0.00064761, 0.00343342, 0.00046239], dims="cell_id"
),
soil_p_pool_maom=DataArray(
[0.01355237, 0.03473323, 0.01997613, 0.00400384], dims="cell_id"
),
)
),
(),
Expand Down Expand Up @@ -398,6 +416,7 @@ def test_order_independance(
"clay_fraction",
"litter_C_mineralisation_rate",
"litter_N_mineralisation_rate",
"litter_P_mineralisation_rate",
]
for not_pool in not_pools:
new_data[not_pool] = dummy_carbon_data[not_pool]
Expand Down Expand Up @@ -436,18 +455,18 @@ def test_construct_full_soil_model(dummy_carbon_data, fixture_core_components):
)

delta_pools = [
0.0129365,
0.0060499,
0.01510858,
0.01400719,
0.03697928,
0.02425546,
0.02426899,
0.038767651,
0.00829848,
0.05982197,
0.07277182,
-0.05362396,
-0.02020101,
-0.0544059,
-0.02282691,
-0.11965575,
-0.00719517,
-0.00720166,
0.00177803841,
-0.007860960795,
-0.012016245,
Expand All @@ -464,10 +483,10 @@ def test_construct_full_soil_model(dummy_carbon_data, fixture_core_components):
-5.09593e-5,
0.0005990658,
-3.72112e-5,
0.00104884,
0.00419763,
0.00119921,
0.00470261,
0.00496839,
0.00251317,
0.00251442,
1.102338e-5,
6.422491e-5,
0.000131687,
Expand All @@ -480,6 +499,22 @@ def test_construct_full_soil_model(dummy_carbon_data, fixture_core_components):
0.01179891,
0.01365197,
0.0077315,
1.92918032e-4,
6.24454858e-5,
1.57222238e-4,
9.94118894e-5,
7.22218e-6,
-1.13464e-6,
7.86083e-7,
5.85634364e-7,
2.674836e-3,
1.333056e-3,
6.8090685e-3,
4.1429847e-5,
5.52086672e-4,
3.68566732e-5,
4.7566130e-4,
3.09257058e-4,
]

# make pools
Expand Down
4 changes: 4 additions & 0 deletions tests/test_main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,10 @@
(DEBUG, "soil model: required var 'soil_n_pool_particulate' checked"),
(DEBUG, "soil model: required var 'soil_n_pool_necromass' checked"),
(DEBUG, "soil model: required var 'soil_n_pool_maom' checked"),
(DEBUG, "soil model: required var 'soil_p_pool_dop' checked"),
(DEBUG, "soil model: required var 'soil_p_pool_particulate' checked"),
(DEBUG, "soil model: required var 'soil_p_pool_necromass' checked"),
(DEBUG, "soil model: required var 'soil_p_pool_maom' checked"),
(DEBUG, "soil model: required var 'pH' checked"),
(DEBUG, "soil model: required var 'bulk_density' checked"),
(DEBUG, "soil model: required var 'clay_fraction' checked"),
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