Add switch to turn adaptivity on and off in configuration (#93)

docs/configuration.md

@@ -107,7 +107,7 @@ The Micro Manager can adaptively control micro simulations. The adaptivity strat
 
 All the adaptivity parameters are chosen from the second publication.
 
-To turn on adaptivity, the following options need to be set in `simulation_params` under the sub-heading `adaptivity`:
+To turn on adaptivity, set `"adaptivity": True` in `simulation_params`. Then under `adaptivity_settings` set the following variables:
 
 Parameter | Description
 --- | ---
@@ -119,12 +119,13 @@ Parameter | Description
 `every_implicit_iteration` | If True, adaptivity is calculated in every implicit iteration. <br> If False, adaptivity is calculated once at the start of the time window and then reused in every implicit time iteration.
 `similarity_measure`| Similarity measure to be used for adaptivity. Can be either `L1`, `L2`, `L1rel` or `L2rel`. By default, `L1` is used. The `rel` variants calculate the respective relative norms. This parameter is *optional*.
 
-Example of adaptivity configuration
+Example of adaptivity configuration is
 
 ```json
 "simulation_params": {
     "macro_domain_bounds": [0, 1, 0, 1, 0, 1],
-    "adaptivity" {
+    "adaptivity": "True",
+    "adaptivity_settings" {
         "type": "local",
         "data": ["temperature", "porosity"],
         "history_param": 0.5,

examples/micro-manager-adaptivity-config.json

@@ -8,7 +8,8 @@
     },
     "simulation_params": {
         "macro_domain_bounds": [0.0, 25.0, 0.0, 25.0, 0.0, 25.0],
-        "adaptivity": {
+        "adaptivity": "True",
+        "adaptivity_settings": {
             "type": "local",
             "data": ["macro-scalar-data", "macro-vector-data"],
             "history_param": 0.5,

micro_manager/config.py

@@ -124,25 +124,33 @@ def read_json(self, config_filename):
             )
 
         try:
-            if data["simulation_params"]["adaptivity"]:
+            if data["simulation_params"]["adaptivity"] == "True":
                 self._adaptivity = True
+                if not data["simulation_params"]["adaptivity_settings"]:
+                    raise Exception(
+                        "Adaptivity is turned on but no adaptivity settings are provided."
+                    )
             else:
                 self._adaptivity = False
+                if data["simulation_params"]["adaptivity_settings"]:
+                    raise Exception(
+                        "Adaptivity settings are provided but adaptivity is turned off."
+                    )
         except BaseException:
             self._logger.info(
-                "Micro Manager will not adaptively run micro simulations, but instead will run all micro simulations in all time steps."
+                "Micro Manager will not adaptively run micro simulations, but instead will run all micro simulations."
             )
 
         if self._adaptivity:
-            if data["simulation_params"]["adaptivity"]["type"] == "local":
+            if data["simulation_params"]["adaptivity_settings"]["type"] == "local":
                 self._adaptivity_type = "local"
-            elif data["simulation_params"]["adaptivity"]["type"] == "global":
+            elif data["simulation_params"]["adaptivity_settings"]["type"] == "global":
                 self._adaptivity_type = "global"
             else:
                 raise Exception("Adaptivity type can be either local or global.")
 
             exchange_data = {**self._read_data_names, **self._write_data_names}
-            for dname in data["simulation_params"]["adaptivity"]["data"]:
+            for dname in data["simulation_params"]["adaptivity_settings"]["data"]:
                 self._data_for_adaptivity[dname] = exchange_data[dname]
 
             if self._data_for_adaptivity.keys() == self._write_data_names.keys():
@@ -152,19 +160,19 @@ def read_json(self, config_filename):
                     " please include macro simulation data as well."
                 )
 
-            self._adaptivity_history_param = data["simulation_params"]["adaptivity"][
-                "history_param"
-            ]
+            self._adaptivity_history_param = data["simulation_params"][
+                "adaptivity_settings"
+            ]["history_param"]
             self._adaptivity_coarsening_constant = data["simulation_params"][
-                "adaptivity"
+                "adaptivity_settings"
             ]["coarsening_constant"]
             self._adaptivity_refining_constant = data["simulation_params"][
-                "adaptivity"
+                "adaptivity_settings"
             ]["refining_constant"]
 
-            if "similarity_measure" in data["simulation_params"]["adaptivity"]:
+            if "similarity_measure" in data["simulation_params"]["adaptivity_settings"]:
                 self._adaptivity_similarity_measure = data["simulation_params"][
-                    "adaptivity"
+                    "adaptivity_settings"
                 ]["similarity_measure"]
             else:
                 self._logger.info(
@@ -173,7 +181,7 @@ def read_json(self, config_filename):
                 self._adaptivity_similarity_measure = "L1"
 
             adaptivity_every_implicit_iteration = data["simulation_params"][
-                "adaptivity"
+                "adaptivity_settings"
             ]["every_implicit_iteration"]
 
             if adaptivity_every_implicit_iteration == "True":

tests/integration/test_unit_cube/micro-manager-config-global-adaptivity-parallel.json

@@ -9,7 +9,8 @@
     "simulation_params": {
         "macro_domain_bounds": [0, 1, 0, 1, 0, 1],
         "decomposition": [2, 1, 1],
-        "adaptivity": {
+        "adaptivity": "True",
+        "adaptivity_settings": {
             "type": "global",
             "data": ["macro-scalar-data", "micro-vector-data"],
             "history_param": 0.5,

tests/integration/test_unit_cube/micro-manager-config-global-adaptivity.json

@@ -8,7 +8,8 @@
     },
     "simulation_params": {
         "macro_domain_bounds": [0, 1, 0, 1, 0, 1],
-        "adaptivity": {
+        "adaptivity": "True",
+        "adaptivity_settings": {
             "type": "global",
             "data": ["macro-scalar-data", "macro-vector-data"],
             "history_param": 0.5,

tests/integration/test_unit_cube/micro-manager-config-local-adaptivity.json

@@ -8,7 +8,8 @@
     },
     "simulation_params": {
         "macro_domain_bounds": [0, 1, 0, 1, 0, 1],
-        "adaptivity": {
+        "adaptivity": "True",
+        "adaptivity_settings": {
             "type": "local",
             "data": ["macro-scalar-data", "macro-vector-data"],
             "history_param": 0.5,

tests/unit/micro-manager-config.json

@@ -8,7 +8,8 @@
     },
     "simulation_params": {
         "macro_domain_bounds": [0.0, 25.0, 0.0, 25.0, 0.0, 25.0],
-        "adaptivity": {
+        "adaptivity": "True",
+        "adaptivity_settings": {
             "type": "local",
             "data": ["macro-scalar-data", "macro-vector-data"],
             "history_param": 0.5,