SSA reaction rate in CN space

tests/multialgorithm/submodels/test_submodels.py

@@ -99,7 +99,8 @@ def test_get_specie_concentrations(self):
             "dynamic submodel .* cannot compute concentration in compartment .* with volume=0")
 
     def test_calc_reaction_rates(self):
-        expected_rates = {'reaction_2': 0.0, 'reaction_4': 2.0}
+        # reaction_4 is adjusted w V*NA factor to account for calculating rxn rate in copy space         
+        expected_rates = {'reaction_2': 0.0, 'reaction_4': 13791.0}
         for dynamic_submodel in self.dynamic_submodels.values():
             rates = dynamic_submodel.calc_reaction_rates()
             for index,rxn in enumerate(dynamic_submodel.reactions):

tests/multialgorithm/test_multialgorithm_simulation.py

@@ -358,6 +358,7 @@ def setUp(self):
         self.model = MakeModels.make_test_model('2 species, 1 reaction, with rates given by reactant population',
             specie_copy_numbers={'spec_type_0[compt_1]':10, 'spec_type_1[compt_1]':10})
 
+    @unittest.skip('Disable temporarily, while A finishes "incomplete-updates" branch')        
     def test_nan_propensities(self):
         self.model.species_types.get_one(id='spec_type_0').molecular_weight = float('NaN')
         multialgorithm_simulation = MultialgorithmSimulation(self.model, {})

wc_sim.core.debug.cfg

@@ -0,0 +1,43 @@
+# log config for the core WC simulator
+[debug_logs]
+    [[formatters]]
+        [[[default]]]
+            template = {timestamp}; {name:s}; {level:s}; {src:s}:{func:s}:{line:d}; {sim_time:f}; {message:s}
+
+        [[[plot]]]
+            template = {timestamp}; {message:s}
+
+    [[handlers]]
+        [[[debug.file]]]
+            class = FileHandler
+            filename = ~/tmp/logs/wc/debug.log
+            mode = a
+
+        [[[plot.file]]]
+            class = FileHandler
+            filename = ~/tmp/logs/wc/plot.log
+            mode = w
+
+        [[[debug.console]]]
+            class = StreamHandler
+            stream = stdout
+
+    [[loggers]]
+        [[[wc.debug.file]]]
+            level = DEBUG
+            formatters = default,
+            handlers = debug.file,
+            [[[[additional_context]]]]
+                sim_time = get_sim_time
+
+        [[[wc.debug.console]]]
+            level = INFO
+            formatters = default,
+            handlers = debug.console,
+            [[[[additional_context]]]]
+                sim_time = get_sim_time
+
+        [[[wc.plot.file]]]
+            level = INFO
+            formatters = default, plot,
+            handlers = plot.file,

wc_sim/core/config/wc_sim.core.debug.cfg

@@ -0,0 +1,43 @@
+# log config for the core WC simulator
+[debug_logs]
+    [[formatters]]
+        [[[default]]]
+            template = {timestamp}; {name:s}; {level:s}; {src:s}:{func:s}:{line:d}; {sim_time:f}; {message:s}
+
+        [[[plot]]]
+            template = {timestamp}; {message:s}
+
+    [[handlers]]
+        [[[debug.file]]]
+            class = FileHandler
+            filename = ~/tmp/logs/wc/debug.log
+            mode = a
+
+        [[[plot.file]]]
+            class = FileHandler
+            filename = ~/tmp/logs/wc/plot.log
+            mode = w
+
+        [[[debug.console]]]
+            class = StreamHandler
+            stream = stdout
+
+    [[loggers]]
+        [[[wc.debug.file]]]
+            level = DEBUG
+            formatters = default,
+            handlers = debug.file,
+            [[[[additional_context]]]]
+                sim_time = get_sim_time
+
+        [[[wc.debug.console]]]
+            level = INFO
+            formatters = default,
+            handlers = debug.console,
+            [[[[additional_context]]]]
+                sim_time = get_sim_time
+
+        [[[wc.plot.file]]]
+            level = INFO
+            formatters = default, plot,
+            handlers = plot.file,

wc_sim/multialgorithm/submodels/dynamic_submodel.py

@@ -154,11 +154,20 @@ def calc_reaction_rates(self):
             :obj:`np.ndarray`: a numpy array of reaction rates, indexed by reaction index
         """
         # TODO(Arthur): optimization: get concentrations only for modifiers in the reactions
-        species_concentrations = self.get_specie_concentrations()
-        for idx_reaction, rxn in enumerate(self.reactions):            
+        # species_concentrations = self.get_specie_concentrations()
+        species_counts = self.get_specie_counts()
+
+        for idx_reaction, rxn in enumerate(self.reactions):
             if rxn.rate_laws:
                 parameter_values = {param.id: param.value for param in rxn.rate_laws[0].equation.parameters}
-                self.rates[idx_reaction] = RateLawUtils.eval_rate_law(rxn.rate_laws[0], species_concentrations, parameter_values)
+                self.rates[idx_reaction] = RateLawUtils.eval_rate_law(rxn.rate_laws[0], species_counts, parameter_values)
+
+                #Balazs debug
+                #if rxn.id=='transcription_tu_1_1' or rxn.id=='degrad_tu_1_1' :
+                #    if random.random() > 0.95:
+                #        print('Rate of reaction {}: {}'.format(rxn.id, self.rates[idx_reaction]))
+
+
         # TODO(Arthur): optimization: get this if to work:
         # if self.logger.isEnabledFor(self.logger.getEffectiveLevel()):
         # print('self.logger.getEffectiveLevel())', self.logger.getEffectiveLevel())