Merge pull request #19 from mcgalcode/dev

Dev

paper/paper.md

@@ -74,7 +74,7 @@ The result of a simulation run is an instance of `SimulationResult`, which store
 
 ## Overview
 
-![\label{fig_1}Diagram showing relationships between `pylattica` entities.](./flowchart.png)
+![\label{fig_1}Diagram showing relationships between `pylattica` entities.](./flowchart.png){width=1080}
 
 \autoref{fig_1} shows the relationship between the entities discussed so far, and how they are connected in producing a `SimulationResult`. To summarize, a `Lattice` is used to create a `Structure`, which is paired with an initial `SimulationState` to create a `Simulation`, or the starting point for simulation execution. The `Structure` is also fed to a `NeighborhoodBuilder` to construct a `Neighborhood` object, which is used in the update rule implemented by the `Controller` to determine how the simulation evolves. Finally, the `Simulation` and `Controller` are passed to a `Runner`, which applies the update rule repeatedly, producing a series of `SimulationState`s, which are concatenated to form a `SimulationResult`.
 

src/pylattica/core/simulation_state.py

@@ -156,7 +156,7 @@ def batch_update(self, update_batch: Dict) -> None:
         """
 
         if GENERAL in update_batch:
-            for site_id, updates in update_batch[SITES].items():
+            for site_id, updates in update_batch.get(SITES, {}).items():
                 self.set_site_state(site_id, updates)
 
             self.set_general_state(update_batch[GENERAL])

src/pylattica/structures/square_grid/grid_setup.py

@@ -50,6 +50,21 @@ def _build_blank_state(
             state.set_site_state(site[SITE_ID], {DISCRETE_OCCUPANCY: fill})
         return state
 
+    def build_structure(self, size: int) -> PeriodicStructure:
+        """Constructs a structure without a state of the specified size
+
+        Parameters
+        ----------
+        size : int
+            The size of the structure to build
+
+        Returns
+        -------
+        PeriodicStructure
+            The resulting structure.
+        """
+        return self._builder.build(size)
+
     def setup_solid_phase(
         self, structure: PeriodicStructure, phase_name: str
     ) -> SimulationState: