Snapshot: Add possibility to have only one micro simulation object (#123

)

* Allow to compute snapshots on single object

* Update snapshot documentation and CHANGELOG

* Apply suggestions from code review

Co-authored-by: Ishaan Desai <[email protected]>

* Add note when to use a single object

---------

Co-authored-by: Ishaan Desai <[email protected]>

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## latest
 
+- Add option to use only one micro simulation object in the snapshot computation https://github.com/precice/micro-manager/pull/123
 - Explicitly check if time window has converged using the API function `is_time_window_complete()` https://github.com/precice/micro-manager/pull/118
 - Add `MicroManagerSnapshot` enabling snapshot computation and storage of microdata in HDF5 format https://github.com/precice/micro-manager/pull/101
 - Make `sklearn` an optional dependency

docs/snapshot_configuration.md

@@ -74,6 +74,7 @@ Parameter | Description
 Parameter | Description
 --- | ---
 `post_processing_file_name`| Path to the post-processing Python script from the current working directory. Providing a post-processing script is optional. The script must contain a class `PostProcessing` with a method `postprocessing(sim_output)` that takes the simulation output as an argument. The method can be used to post-process the simulation output before writing it to the database.
+`initialize_once` | If `True`, only one micro simulation is initialized and solved for all macro inputs per rank. If `False` a new micro simulation is initialized and solved for each macro input in the parameter space. Default is `False`. This option can be True if the micro simulation is not history-dependent and the same setup is shared across all micro simulations.
 
 ## Diagnostics
 

micro_manager/config.py

@@ -53,6 +53,7 @@ def __init__(self, logger, config_filename):
         # Snapshot information
         self._parameter_file_name = None
         self._postprocessing_file_name = None
+        self._initialize_once = False
 
         self._output_micro_sim_time = False
 
@@ -301,6 +302,14 @@ def read_json_snapshot(self):
                 "No diagnostics data is defined. Snapshot computation will not output any diagnostics data."
             )
 
+        try:
+            if self._data["snapshot_params"]["initialize_once"] == "True":
+                self._initialize_once = True
+        except BaseException:
+            self._logger.info(
+                "For each snapshot a new micro simulation object will be created"
+            )
+
     def get_config_file_name(self):
         """
         Get the name of the JSON configuration file.
@@ -544,3 +553,14 @@ def interpolate_crashed_micro_sim(self):
             True if crashed micro simulations need to be interpolated, False otherwise.
         """
         return self._interpolate_crash
+
+    def create_single_sim_object(self):
+        """
+        Check if multiple snapshots can be computed on a single micro simulation object.
+
+        Returns
+        -------
+        initialize_once : bool
+            True if initialization is done only once, False otherwise.
+        """
+        return self._initialize_once

micro_manager/snapshot/snapshot.py

@@ -40,6 +40,9 @@ def __init__(self, config_file: str) -> None:
         self._parameter_file = self._config.get_parameter_file_name()
         # Get name of pos-processing script
         self._post_processing_file_name = self._config.get_postprocessing_file_name()
+
+        # Check if simulation object can be re-used.
+        self._initialize_once = self._config.create_single_sim_object()
         # Collect crashed indices
         self._crashed_snapshots = []  # Declaration
 
@@ -58,10 +61,16 @@ def solve(self) -> None:
 
         # Loop over all macro parameters
         for elems in range(self._local_number_of_sims):
-            # Create micro simulation object
-            self._micro_sims = create_simulation_class(self._micro_problem)(
-                self._global_ids_of_local_sims[elems]
-            )
+            # initialize micro simulation
+            if elems == 0:
+                self._micro_sims = create_simulation_class(self._micro_problem)(
+                    self._global_ids_of_local_sims[0]
+                )
+            else:
+                if not self._initialize_once:
+                    self._micro_sims = create_simulation_class(self._micro_problem)(
+                        self._global_ids_of_local_sims[elems]
+                    )
 
             micro_sims_input = self._macro_parameters[elems]
             # Solve micro simulation

tests/unit/snapshot-config.json

@@ -9,6 +9,7 @@
         "micro_dt": 1.0
     },
     "snapshot_params": {
-        "post_processing_file_name": "snapshot_post_processing"
+        "post_processing_file_name": "snapshot_post_processing",
+        "initialize_once": "True"
     }
 }

tests/unit/test_snapshot_computation.py

@@ -11,9 +11,6 @@ class MicroSimulation:
     def __init__(self, sim_id):
         self.very_important_value = 0
 
-    def initialize(self):
-        pass
-
     def solve(self, macro_data, dt):
         assert macro_data["macro-scalar-data"] == 1
         assert macro_data["macro-vector-data"].tolist() == [0, 1, 2]
@@ -149,6 +146,7 @@ def test_config(self):
         self.assertDictEqual(config._read_data_names, self.fake_read_data_names)
         self.assertDictEqual(config._write_data_names, self.fake_write_data_names)
         self.assertEqual(config._postprocessing_file_name, "snapshot_post_processing")
+        self.assertTrue(config._initialize_once)
 
 
 if __name__ == "__main__":