From b73a84c8e7f41819a6b14eafbdfd7242354688b9 Mon Sep 17 00:00:00 2001
From: Knut-Frode Dagestad <knutfd@met.no>
Date: Fri, 15 Mar 2024 09:47:18 +0100
Subject: [PATCH] Oil biodegradation decay is now specified with half time in
 days, instead of decay rate

---
 examples/example_biodegradation.py  | 10 +++++-----
 examples/example_chemicaldrift.py   |  2 +-
 opendrift/models/openoil/openoil.py | 24 +++++++++++++-----------
 3 files changed, 19 insertions(+), 17 deletions(-)

diff --git a/examples/example_biodegradation.py b/examples/example_biodegradation.py
index daca5a864..45c6ab8a2 100755
--- a/examples/example_biodegradation.py
+++ b/examples/example_biodegradation.py
@@ -15,19 +15,19 @@
 # No motion is needed for this test
 o.set_config('environment:constant', {k: 0 for k in
              ['x_wind', 'y_wind', 'x_sea_water_velocity', 'y_sea_water_velocity']})
-o.set_config('drift', {'current_uncertainty': 0, 'wind_uncertainty': 0, 'horizontal_diffusivity': 100})
+o.set_config('drift', {'current_uncertainty': 0, 'wind_uncertainty': 0, 'horizontal_diffusivity': 10})
 
 #%%
 # Seeding some particles
 o.set_config('drift:vertical_mixing', True)
 o.set_config('processes:biodegradation', True)
-o.set_config('biodegradation:method', 'decay_rate')
+o.set_config('biodegradation:method', 'half_time')
 
 #%%
 # Fast decay for droplets, and slow decay for slick 
-decay = {'biodegradation_decay_rate_slick': np.log(2)/timedelta(days=5).total_seconds(),
-         'biodegradation_decay_rate_droplet': np.log(2)/timedelta(days=1).total_seconds(),
-         'oil_type': 'GENERIC MEDIUM CRUDE', 'm3_per_hour': .5, 'diameter': 1e-9}  # small droplets
+decay = {'biodegradation_half_time_slick': 5, # days
+         'biodegradation_half_time_droplet': 1, # days,
+         'oil_type': 'GENERIC MEDIUM CRUDE', 'm3_per_hour': .5, 'diameter': 1e-5}  # small droplets
 
 #%%
 # Seed 500 oil elements at surface, and 500 elements at 50m depth
diff --git a/examples/example_chemicaldrift.py b/examples/example_chemicaldrift.py
index e350d1c30..8100e6fd8 100755
--- a/examples/example_chemicaldrift.py
+++ b/examples/example_chemicaldrift.py
@@ -101,7 +101,7 @@
 
 o.animation(color='specie',
             markersize='mass',
-            markersize_scaling=30,
+            markersize_scaling=100,
             alpha=.5,
             vmin=0,vmax=o.nspecies-1,
             colorbar=False,
diff --git a/opendrift/models/openoil/openoil.py b/opendrift/models/openoil/openoil.py
index c340655d0..0caccbdee 100644
--- a/opendrift/models/openoil/openoil.py
+++ b/opendrift/models/openoil/openoil.py
@@ -171,10 +171,12 @@ class Oil(Lagrangian3DArray):
             'seed': False,
             'default': 0
         }),
-        ('biodegradation_decay_rate_droplet',  # TODO: should have valid_min and valid_max for element properties
-                {'dtype': np.float32, 'units': 'kg', 'seed': False, 'default': np.log(2)/(3600*24)}),  # 1 day default
-        ('biodegradation_decay_rate_slick',
-                {'dtype': np.float32, 'units': 'kg', 'seed': False, 'default': np.log(2)/(3600*24*3)}),  # 3 days default
+        ('biodegradation_half_time_droplet',
+                {'dtype': np.float32, 'units': 'days', 'seed': False, 'default': 1,
+                 'description': 'Biodegradation half time in days for submerged oil droplets'}),
+        ('biodegradation_half_time_slick',
+                {'dtype': np.float32, 'units': 'days', 'seed': False, 'default': 3,
+                 'description': 'Biodegradation half time in days for surface oil slick'}),
         ('fraction_evaporated', {
             'dtype': np.float32,
             'units': '%',  # TODO: should be fraction and not percent
@@ -436,7 +438,7 @@ def __init__(self, weathering_model='noaa', *args, **kwargs):
             },
             'biodegradation:method': {
                 'type': 'enum',
-                'enum': ['Adcroft', 'decay_rate'],
+                'enum': ['Adcroft', 'half_time'],
                 'default': 'Adcroft', 'level': CONFIG_LEVEL_ADVANCED,
                 'description': 'Alogorithm to be used for biodegradation of oil'
             },
@@ -552,17 +554,17 @@ def biodegradation(self):
             logger.debug(f'Calculating: biodegradation ({method})')
             if method == 'Adcroft':
                 self.biodegradation_adcroft()
-            elif method == 'decay_rate':
-                self.biodegradation_decay_rate()
+            elif method == 'half_time':
+                self.biodegradation_half_time()
 
-    def biodegradation_decay_rate(self):
+    def biodegradation_half_time(self):
         '''Oil biodegradation with exponential decay'''
 
         surface = np.where(self.elements.z == 0)[0]  # of active elements
-        age0 = self.time_step.total_seconds()
+        age0 = self.time_step.total_seconds()/(3600*24)  # days
 
-        half_time = np.log(2) / self.elements.biodegradation_decay_rate_droplet
-        half_time[surface] = np.log(2) / self.elements.biodegradation_decay_rate_slick[surface]
+        half_time = self.elements.biodegradation_half_time_droplet.copy()
+        half_time[surface] = self.elements.biodegradation_half_time_slick[surface]
 
         fraction_biodegraded = (1 - np.exp(-age0 / half_time))
         biodegraded_now = self.elements.mass_oil * fraction_biodegraded