Verifying that the fix succeeded

This notebook tests that the fix to the litter integration model has successfully fixed the bugs identified in the bug identification notebook.

%%bash
# Install the example data directory from the Virtual Ecosystem package
# This is currently using my desktop, but this should change in future (probably)
ve_run --install-example /Users/jc2017/Desktop

# Rename config (and out) to original_config to make it clearer that it is unchanged
mv /Users/jc2017/Desktop/ve_example/config /Users/jc2017/Desktop/ve_example/original_config
mv /Users/jc2017/Desktop/ve_example/out /Users/jc2017/Desktop/ve_example/original_out

Example directory created at:
/Users/jc2017/Desktop/ve_example

Setting up models (again)

The same steps are taken to set up the model runs as in the previous notebook.

import tomllib

import tomli_w

with open("/Users/jc2017/Desktop/ve_example/original_config/ve_run.toml", "rb") as f:
    general_config = tomllib.load(f)

general_config["abiotic_simple"]["static"] = True
general_config["hydrology"]["static"] = True
general_config["soil"]["static"] = True
general_config["animal"]["static"] = True

with open("/Users/jc2017/Desktop/ve_example/original_config/ve_run.toml", "wb") as f:
    tomli_w.dump(general_config, f)

with open(
    "/Users/jc2017/Desktop/ve_example/original_config/plant_config.toml", "rb"
) as f:
    plant_config = tomllib.load(f)

plant_config["plants"]["static"] = True
plant_config["plants"].setdefault("constants", {})
plant_config["plants"]["constants"].setdefault("PlantsConsts", {})
plant_config["plants"]["constants"]["PlantsConsts"][
    "per_stem_annual_mortality_probability"
] = 0.0

with open(
    "/Users/jc2017/Desktop/ve_example/original_config/plant_config.toml", "wb"
) as f:
    tomli_w.dump(plant_config, f)

Doubling the above-ground metabolic litter decay rate

Again we double the decay rate of the above ground metabolic litter pool to see how this changes the simulation results.

%%bash
cp -r /Users/jc2017/Desktop/ve_example/original_config /Users/jc2017/Desktop/ve_example/increased_meta_decay_config

mkdir /Users/jc2017/Desktop/ve_example/increased_meta_decay_out

with open(
    "/Users/jc2017/Desktop/ve_example/increased_meta_decay_config/ve_run.toml", "rb"
) as f:
    general_config = tomllib.load(f)

general_config["litter"].setdefault("constants", {})
general_config["litter"]["constants"].setdefault("LitterConsts", {})
general_config["litter"]["constants"]["LitterConsts"][
    "litter_decay_constant_metabolic_above"
] = 0.16

with open(
    "/Users/jc2017/Desktop/ve_example/increased_meta_decay_config/ve_run.toml", "wb"
) as f:
    tomli_w.dump(general_config, f)

%%bash
ve_run /Users/jc2017/Desktop/ve_example/original_config \
    --outpath /Users/jc2017/Desktop/ve_example/original_out \
    --logfile /Users/jc2017/Desktop/ve_example/original_out/original.log

Starting Virtual Ecosystem simulation.
Logging to: /Users/jc2017/Desktop/ve_example/original_out/original.log
* Loading configuration
* Saved compiled configuration: /Users/jc2017/Desktop/ve_example/original_out/ve_full_model_configuration.toml
* Built core model components
* Initial data loaded
* Models initialised: soil, hydrology, abiotic_simple, animal, litter, plants
* Saved model initial state
* Starting simulation
100%|██████████| 24/24 [00:02<00:00,  8.58it/s]
* Simulation completed
* Merged time series data
* Saved final model state
Virtual Ecosystem run complete.

%%bash
ve_run /Users/jc2017/Desktop/ve_example/increased_meta_decay_config \
    --outpath /Users/jc2017/Desktop/ve_example/increased_meta_decay_out \
    --logfile /Users/jc2017/Desktop/ve_example/increased_meta_decay_out/increased_decay.log

Starting Virtual Ecosystem simulation.
Logging to: /Users/jc2017/Desktop/ve_example/increased_meta_decay_out/increased_decay.log
* Loading configuration
* Saved compiled configuration: /Users/jc2017/Desktop/ve_example/increased_meta_decay_out/ve_full_model_configuration.toml
* Built core model components
* Initial data loaded
* Models initialised: soil, hydrology, abiotic_simple, animal, litter, plants
* Saved model initial state
* Starting simulation
100%|██████████| 24/24 [00:02<00:00,  8.68it/s]
* Simulation completed
* Merged time series data
* Saved final model state
Virtual Ecosystem run complete.

We start by (again) checking the total mineralisation of carbon. This now works and values are always positive

import matplotlib.pyplot as plt
import xarray

original = xarray.load_dataset(
    "/Users/jc2017/Desktop/ve_example/original_out/all_continuous_data.nc"
)
increased_above_meta_decay = xarray.load_dataset(
    "/Users/jc2017/Desktop/ve_example/increased_meta_decay_out/all_continuous_data.nc"
)

fig, (ax1, ax2) = plt.subplots(ncols=2, figsize=(12, 5))


ax1.plot(original["time_index"], original["litter_C_mineralisation_rate"])
ax1.set_title("litter_C_mineralisation_rate (original config)")
ax1.set_ylabel("litter_C_mineralisation_rate")
ax1.set_xlabel("Time step (months)")

ax2.plot(
    increased_above_meta_decay["time_index"],
    increased_above_meta_decay["litter_C_mineralisation_rate"],
)
ax2.set_title("litter_C_mineralisation_rate (changed config)")
ax2.set_ylabel("litter_C_mineralisation_rate")
ax2.set_xlabel("Time step (months)")

plt.tight_layout()

The carbon nitrogen ratios also now show plausible behaviours for the increased decay rate case.

fig, (ax1, ax2) = plt.subplots(ncols=2, figsize=(12, 5))


ax1.plot(original["time_index"], original["c_n_ratio_above_metabolic"])
ax1.set_title("c_n_ratio_above_metabolic (original config)")
ax1.set_ylabel("c_n_ratio_above_metabolic")
ax1.set_xlabel("Time step (months)")

ax2.plot(
    increased_above_meta_decay["time_index"],
    increased_above_meta_decay["c_n_ratio_above_metabolic"],
)
ax2.set_title("c_n_ratio_above_metabolic (changed config)")
ax2.set_ylabel("c_n_ratio_above_metabolic")
ax2.set_xlabel("Time step (months)")

plt.tight_layout()

Finally, the above ground metabolic litter pools now all show trajectories that don’t include impossible (i.e. negative values)

fig, (ax1, ax2) = plt.subplots(ncols=2, figsize=(12, 5))


ax1.plot(original["time_index"], original["litter_pool_above_metabolic"])
ax1.set_title("Above metabolic litter pool against time (original config)")
ax1.set_ylabel("Above metabolic litter pool ($kg C m^{-2}$)")
ax1.set_xlabel("Time step (months)")

ax2.plot(
    increased_above_meta_decay["time_index"],
    increased_above_meta_decay["litter_pool_above_metabolic"],
)
ax2.set_title("Above metabolic litter pool against time (changed config)")
ax2.set_ylabel("Above metabolic litter pool ($kg C m^{-2}$)")
ax2.set_xlabel("Time step (months)")

plt.tight_layout()