working out interaction between cytosim and medyan

simularium · Mar 15, 2022 · 4c8a9c7 · 4c8a9c7
1 parent a4ac9b1
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Showing 6 changed files with 83 additions and 73 deletions.
diff --git a/in/cytosim-buckling.cym b/in/cytosim-buckling.cym
diff --git a/in/medyan_Chandrasekaran_2019_no_tread_2mUNI_alphaA_0.1_MA_0.675/filaments.txt b/in/medyan_Chandrasekaran_2019_no_tread_2mUNI_alphaA_0.1_MA_0.675/filaments.txt
diff --git a/...UNI_alphaA_0.1_MA_0.675/medyan_Chandrasekaran_2019_no_tread_2mUNI_alphaA_0.1_MA_0.675.txt b/...UNI_alphaA_0.1_MA_0.675/medyan_Chandrasekaran_2019_no_tread_2mUNI_alphaA_0.1_MA_0.675.txt
@@ -66,7 +66,7 @@ CHEMISTRYFILE:               chemistryinput.txt
 
 CALGORITHM:                  NRM
 NUMTOTALSTEPS:		     	 
-RUNTIME:                     4.999999900000001
+RUNTIME:                     1.0
 
 NUMSTEPSPERS:		    
 SNAPSHOTTIME:                1.0

diff --git a/vivarium_models/composites/filament_alternatives.py b/vivarium_models/composites/filament_alternatives.py
@@ -8,13 +8,21 @@
 from vivarium_models.processes.medyan import MedyanProcess
 from vivarium_models.processes.cytosim import CytosimProcess
 
-ALTERNATOR_PERIODS = [5.0, 5.0]
+ALTERNATOR_PERIODS = [2.0, 2.0]
 
 class FilamentAlternatives(Composer):
     defaults = {
         "periodic_event": {"periods": ALTERNATOR_PERIODS},
-        "medyan": {"time_step": 5.0, "_condition": ("choices", "medyan_active")},
-        "cytosim": {"time_step": 5.0, "_condition": ("choices", "cytosim_active")},
+        "medyan": {
+            "time_step": 1.0,
+            "_condition": ("choices", "medyan_active")},
+        "cytosim": {
+            "time_step": 1.0,
+            "_condition": ("choices", "cytosim_active"),
+            'confine': {
+                'side': 'inside',
+                'force': 100,
+                'space': 'cell'}},
         "alternator": {"choices": ["medyan_active", "cytosim_active"]},
     }
 
@@ -282,7 +290,7 @@ def test_filament_alternatives():
 
     medyan_config = {
         "medyan_executable": args.medyan_executable_path,  # "...../medyan/build/medyan"
-        "transform_points": [0, 0, 0],
+        "transform_points": [2000, 1000, 1000],
     }
 
     filament_alternatives_config = {'medyan': medyan_config}
@@ -301,7 +309,7 @@ def test_filament_alternatives():
 
     import ipdb; ipdb.set_trace()
 
-    engine.update(30)
+    engine.update(10)
 
     engine.emitter.get_data()
 

diff --git a/vivarium_models/processes/cytosim.py b/vivarium_models/processes/cytosim.py
@@ -29,6 +29,7 @@
 NAME = "CYTOSIM"
 
 RELATIVE_MICRON = 0.001
+BOUNDARY_BUFFER = 0.95
 
 def fiber_section(id, fiber):
     points = fiber['points']
@@ -103,18 +104,10 @@ def __init__(self, parameters=None):
 
     def ports_schema(self):
         ports = fibers_schema()
-        ports['choices'] = {
-            'medyan_active': {
-                '_default': True,
-                '_emit': True},
-            'readdy_active': {
-                '_default': False,
-                '_emit': True}}
-
         return ports
 
-    def calculate_timestep(self, state):
-        return 0.1
+    # def calculate_timestep(self, state):
+    #     return 0.1
 
     def initial_state(self, config):
         return {}
@@ -125,7 +118,7 @@ def next_update(self, timestep, state):
 
         fiber_sections = [fiber_section(id, fiber) for id, fiber in initial_fibers.items()]
 
-        box_extent = state['fibers_box_extent'] * RELATIVE_MICRON
+        box_extent = state['fibers_box_extent'] * RELATIVE_MICRON * BOUNDARY_BUFFER
 
         template = env.get_template(self.parameters['cytosim_template'])
         cytosim_config = template.render(

diff --git a/vivarium_models/processes/medyan.py b/vivarium_models/processes/medyan.py
@@ -44,7 +44,7 @@ class MedyanProcess(Process):
     def __init__(self, parameters=None):
         super().__init__(parameters)
 
-        assert self.parameters["time_step"] > self.parameters["snapshot"]
+        assert self.parameters["time_step"] >= self.parameters["snapshot"]
 
     def ports_schema(self):
         return fibers_schema()