still good params

ihmeuw · Jan 1, 2025 · 21ed796 · 21ed796
1 parent 14434bb
commit 21ed796
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Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/src/vivarium_eye_vessels/components/particles.py b/src/vivarium_eye_vessels/components/particles.py
@@ -605,7 +605,7 @@ def dla_freeze(self, pop: pd.DataFrame) -> None:
         near_frozen_indices = self.freezer.query_radius(
             not_frozen, self.near_radius
         )
-
+        # FIXME: should only use particles with path_id < 0 (i.e. in frozen DataFrame, not all in freezer object )
         near_particles = np.array([len(indices) > 0 for indices in near_frozen_indices])
         stickiness_probabilities = self.randomness.get_draw(
             not_frozen.index, additional_key="stickiness"

diff --git a/src/vivarium_eye_vessels/model_specifications/model_spec.yaml b/src/vivarium_eye_vessels/model_specifications/model_spec.yaml
@@ -25,7 +25,7 @@ configuration:
             day: 1
         step_size: .05 # Days
     population:
-        population_size: 2000
+        population_size: 5000
 
     # Base particle configuration
     particles:
@@ -43,29 +43,29 @@ configuration:
 
     # Path splitting configuration
     path_splitter:
-        split_interval: 100     # Steps between checking for splits
+        split_interval: 50     # Steps between checking for splits
         split_angle: 60         # Angle in degrees between split paths
         split_probability: .2  # Probability of eligible path splitting
 
     path_extinction:
-        check_interval: 100
-        extinction_start_time: '2025-03-01'
-        extinction_end_time: '2025-05-02'
+        check_interval: 50
+        extinction_start_time: '2025-05-01'
+        extinction_end_time: '2025-06-02'
         initial_freeze_probability: 0.2
         final_freeze_probability: 1.0
         force_threshold: 5.0
 
     path_dla:
-        dla_start_time: '2025-05-01'
+        dla_start_time: '2025-06-01'
         dla_end_time: '2025-09-01'
         stickiness: 1.0                   # Probability of sticking when near frozen particle
-        initial_near_radius: 0.05         # Distance for checking proximity to frozen particles
-        final_near_radius: 0.02           # Distance for checking proximity to frozen particles
+        initial_near_radius: 0.04         # Distance for checking proximity to frozen particles
+        final_near_radius: 0.01           # Distance for checking proximity to frozen particles
 
     ellipsoid_containment:
         a: 2    # Ellipsoid x semi-major axis
         b: 1    # Ellipsoid y semi-major axis
-        c: 0.025  # Ellipsoid z semi-major axis
+        c: 0.05  # Ellipsoid z semi-major axis
         force_type: hookean
         spring_constant: 10