Bug fixes for demo (#207)

* fix missing last set of conditions

* allow user-defined reactions in mechanism

* add air density to output

* adjust next time step to not pass output or updates to conditions

* fix timestepping

---------

Co-authored-by: Kyle Shores <[email protected]>

src/acom_music_box/music_box.py

@@ -199,7 +199,9 @@ def generateConfig(self, directory):
             elif reaction_rate.reaction.reaction_type == "LOSS":
                 name = "LOSS." + reaction_rate.reaction.name + ".s-1"
             elif reaction_rate.reaction.reaction_type == "EMISSION":
-                name = "EMISSION." + reaction_rate.reaction.name + ".s-1"
+                name = "EMIS." + reaction_rate.reaction.name + ".s-1"
+            elif reaction_rate.reaction.reaction_type == "USER_DEFINED":
+                name = "USER." + reaction_rate.reaction.name + ".s-1"
 
             reaction_names.append(name)
             reaction_rates.append(reaction_rate.rate)
@@ -469,6 +471,7 @@ def solve(self, output_path=None):
         headers.append("time")
         headers.append("ENV.temperature")
         headers.append("ENV.pressure")
+        headers.append("ENV.number_density_air")
 
         if (self.solver is None):
             raise Exception("Error: MusicBox object {} has no solver."
@@ -500,33 +503,21 @@ def solve(self, output_path=None):
 
         while (curr_time <= self.box_model_options.simulation_length):
 
-            # outputs to output_array if enough time has elapsed
-            if (next_output_time <= curr_time):
-                row = []
-                row.append(next_output_time)
-                row.append(curr_conditions.temperature)
-                row.append(curr_conditions.pressure)
-                for conc in ordered_concentrations:
-                    row.append(conc)
-                output_array.append(row)
-                next_output_time += self.box_model_options.output_step_time
 
             # iterates evolving  conditions if enough time has elapsed
             while (
                     next_conditions is not None and next_conditions_time <= curr_time):
 
                 curr_conditions.update_conditions(next_conditions)
-
+                ordered_rate_constants = self.order_reaction_rates(
+                        curr_conditions, rate_constant_ordering)
+
                 # iterates next_conditions if there are remaining evolving
                 # conditions
                 if (len(self.evolving_conditions) > next_conditions_index + 1):
                     next_conditions_index += 1
                     next_conditions = self.evolving_conditions.conditions[next_conditions_index]
                     next_conditions_time = self.evolving_conditions.times[next_conditions_index]
-
-                    ordered_rate_constants = self.order_reaction_rates(
-                        curr_conditions, rate_constant_ordering)
-
                 else:
                     next_conditions = None
 
@@ -537,20 +528,40 @@ def solve(self, output_path=None):
             air_density = curr_conditions.pressure / \
                 (GAS_CONSTANT * curr_conditions.temperature)
 
+            # outputs to output_array if enough time has elapsed
+            if (next_output_time <= curr_time):
+                row = []
+                row.append(next_output_time)
+                row.append(curr_conditions.temperature)
+                row.append(curr_conditions.pressure)
+                row.append(air_density)
+                for conc in ordered_concentrations:
+                    row.append(conc)
+                output_array.append(row)
+                next_output_time += self.box_model_options.output_step_time
+
+            # ensure the time step is not greater than the next update to the
+            # evolving conditions or the next output time
+            time_step = self.box_model_options.chem_step_time
+            if (next_conditions is not None and next_conditions_time > curr_time):
+                time_step = min(time_step, next_conditions_time - curr_time)
+            if (next_output_time > curr_time):
+                time_step = min(time_step, next_output_time - curr_time)
+
             # solves and updates concentration values in concentration array
             if (not ordered_concentrations):
                 logger.info("Warning: ordered_concentrations list is empty.")
             musica.micm_solve(
                 self.solver,
-                self.box_model_options.chem_step_time,
+                time_step,
                 curr_conditions.temperature,
                 curr_conditions.pressure,
                 air_density,
                 ordered_concentrations,
                 ordered_rate_constants)
 
             # increments time
-            curr_time += self.box_model_options.chem_step_time
+            curr_time += time_step
 
         df = pd.DataFrame(output_array[1:], columns=output_array[0])
         # outputs to file if output is present
@@ -721,6 +732,8 @@ def order_reaction_rates(self, curr_conditions, rate_constant_ordering):
                 key = "LOSS." + rate.reaction.name
             elif (rate.reaction.reaction_type == "EMISSION"):
                 key = "EMIS." + rate.reaction.name
+            elif (rate.reaction.reaction_type == "USER_DEFINED"):
+                key = "USER." + rate.reaction.name
             rate_constants[key] = rate.rate
 
         ordered_rate_constants = len(rate_constants.keys()) * [0.0]

src/acom_music_box/reaction.py

@@ -75,6 +75,7 @@ def short_type(self):
             "ARRHENIUS": "ARRH",
             "TUNNELING": "TUNN",
             "TROE_TERNARY": "TROE",
+            "USER_DEFINED": "USER",
         }
         return type_map.get(self.reaction_type, "UNKNOWN")
 

tests/test_chapman.py

@@ -58,7 +58,7 @@ def test_run(self):
                 assert math.isclose(
                     float(model_output_concs[i][j]),
                     float(test_output_concs[i][j]),
-                    rel_tol=1e-8,
+                    rel_tol=1e-7,
                     abs_tol=1e-15,
                 ), f"Arrays differ at index ({i}, {j}) for species {concs_to_test[j]}"