Refactor DomainDecomposer class and add new functionality to decompose the macro-scale coordinates

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## latest
 
+- Refactored `DomainDecomposer` class and added a new variant of non-uniform decomposition [#243](https://github.com/precice/micro-manager/pull/243)
 - Fixed load balancing configuration `partitioning` parameter setting [#245](https://github.com/precice/micro-manager/pull/245)
 - Fixed comparison of zero values of type float32 and float64 in simulation deactivation [#244](https://github.com/precice/micro-manager/pull/244)
 - Optimized norm calculations and further fixed lazy initialization [#241](https://github.com/precice/micro-manager/pull/241)

docs/configuration.md

@@ -34,16 +34,20 @@ Apart from the base settings, there are three main sections in the configuration
 
 ## Simulation Parameters
 
-| Parameter             | Description                                                                                                                                          | Default                 |
-|-----------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------|
-| `macro_domain_bounds` | Minimum and maximum bounds of the macro-domain, having the format `[xmin, xmax, ymin, ymax, zmin, zmax]` in 3D and `[xmin, xmax, ymin, ymax]` in 2D. | -                       |
-| `decomposition`       | List of number of ranks in each axis with format `[xranks, yranks, zranks]` in 3D and `[xranks, yranks]` in 2D.                                      | `[1, 1, 1]` or `[1, 1]` |
-| `micro_dt`            | Initial time window size (dt) of the micro simulation.                                                                                               | -                       |
-| `adaptivity`          | Set `true` for simulations with adaptivity. See section on [adaptivity](#adaptivity).                                                                | `false`                 |
-| `load_balancing`      | Set `true` for load balancing. See section on [load balancing](#load-balancing).                                                                     | `false`                 |
+| Parameter | Description | Default |
+| --- | --- | --- |
+| `macro_domain_bounds` | Minimum and maximum bounds of the macro-domain, having the format `[xmin, xmax, ymin, ymax, zmin, zmax]` in 3D and `[xmin, xmax, ymin, ymax]` in 2D. | - |
+| `decomposition` | List of number of ranks in each axis with format `[xranks, yranks, zranks]` in 3D and `[xranks, yranks]` in 2D. | `[1, 1, 1]` or `[1, 1]` |
+| `decomposition_type` | Type of domain decomposition. Either `uniform` or `nonuniform`. | `uniform` |
+| `minimum_access_region_size` | If `nonuniform` decomposition, optionally set a minimum domain width in each axis. Format `[xmin, ymin, zmin]` | - |
+| `micro_dt` | Initial time window size (dt) of the micro simulation. | - |
+| `adaptivity` | Set `true` for simulations with adaptivity. See section on [adaptivity](#adaptivity). | `false` |
+| `load_balancing` | Set `true` for load balancing. See section on [load balancing](#load-balancing). | `false` |
 
 The total number of partitions ranks in the `decomposition` list should be the same as the number of ranks in the `mpirun` or `mpiexec` command.
 
+Non-uniform domain decomposition is based on a geometric progression.
+
 ## Diagnostics
 
 | Parameter              | Description                                                                                                                                | Default |

micro_manager/config.py

@@ -33,8 +33,12 @@ def __init__(self, config_file_name):
         self._write_data_names = None
         self._micro_dt = None
 
+        # Domain decomposition information
         self._macro_domain_bounds = None
         self._ranks_per_axis = None
+        self._decomposition_type = "uniform"
+        self._minimum_access_region_size: list = []
+
         self._micro_output_n = 1
         self._diagnostics_data_names = None
 
@@ -258,6 +262,30 @@ def read_json_micro_manager(self):
             self._logger.log_info_rank_zero(
                 "Axis-wise domain decomposition: " + str(self._ranks_per_axis)
             )
+            if self._data["simulation_params"]["decomposition_type"]:
+                self._decomposition_type = self._data["simulation_params"][
+                    "decomposition_type"
+                ]
+                if self._decomposition_type not in ["uniform", "nonuniform"]:
+                    raise Exception(
+                        "Decomposition type can be either 'uniform' or 'nonuniform'."
+                    )
+                if (
+                    self._data["simulation_params"]["decomposition_type"]
+                    == "nonuniform"
+                ):
+                    if self._data["simulation_params"]["minimum_access_region_size"]:
+                        self._minimum_access_region_size = self._data[
+                            "simulation_params"
+                        ]["minimum_access_region_size"]
+                    else:
+                        self._logger.log_info_rank_zero(
+                            "Minimum access region size is not specified. Calculating it as 1 / (2^ranks_per_axis - 1) of the macro domain size in each axis."
+                        )
+
+            self._logger.log_info_rank_zero(
+                "Domain decomposition type: " + self._decomposition_type
+            )
         except BaseException:
             self._logger.log_info_rank_zero(
                 "Domain decomposition is not specified, so the Micro Manager will expect to be run in serial."
@@ -743,6 +771,28 @@ def get_ranks_per_axis(self):
         """
         return self._ranks_per_axis
 
+    def get_decomposition_type(self):
+        """
+        Get the type of domain decomposition.
+
+        Returns
+        -------
+        decomposition_type : str
+            Type of domain decomposition, can be either "uniform" or "non-uniform".
+        """
+        return self._decomposition_type
+
+    def get_minimum_access_region_size(self):
+        """
+        Get the minimum access region size for non-uniform domain decomposition.
+
+        Returns
+        -------
+        minimum_access_region_size : list
+            List containing the minimum access region size in each axis for non-uniform domain decomposition.
+        """
+        return self._minimum_access_region_size
+
     def get_micro_file_name(self):
         """
         Get the path to the Python script of the micro-simulation.