refactor: update dice handling and optimization flow to return structured results

diceplayer/dice/dice_handler.py

@@ -4,7 +4,7 @@ from diceplayer.dice.dice_input import (
     NVTEqConfig,
     NVTTerConfig,
 )
-from diceplayer.dice.dice_wrapper import DiceWrapper
+from diceplayer.dice.dice_wrapper import DiceWrapper, DiceEnvironment
 from diceplayer.logger import logger
 from diceplayer.state.state_model import StateModel
 
@@ -17,7 +17,7 @@ class DiceHandler:
     def __init__(self, step_directory: Path):
         self.dice_directory = step_directory / "dice"
 
-    def run(self, state: StateModel, cycle: int) -> StateModel:
+    def run(self, state: StateModel, cycle: int) -> list[DiceEnvironment]:
         if self.dice_directory.exists():
             logger.info(
                 f"Found dice directory: {self.dice_directory}, this directory will be purged for a clean state"
@@ -25,13 +25,9 @@ class DiceHandler:
             shutil.rmtree(self.dice_directory)
         self.dice_directory.mkdir(parents=True)
 
-        simulation_results = self.run_simulations(state, cycle)
+        return self.run_simulations(state, cycle)
 
-        result = self.aggregate_results(simulation_results)
-
-        return self.commit_simulation_state(state, result)
-
-    def run_simulations(self, state: StateModel, cycle: int) -> list[dict]:
+    def run_simulations(self, state: StateModel, cycle: int) -> list[DiceEnvironment]:
         results = []
 
         threads = []
@@ -48,15 +44,12 @@ class DiceHandler:
                 f"Expected {state.config.dice.nprocs} simulation results, but got {len(results)}"
             )
 
-        return results
-
-    def aggregate_results(self, simulation_results: list[dict]) -> dict: ...
-
-    def commit_simulation_state(self, state: StateModel, result: dict) -> StateModel:
-        return state
+        return [
+            i for i in [r for r in results]
+        ]
 
     def _simulation_process(
-        self, state: StateModel, cycle: int, proc: int, results: list[dict]
+        self, state: StateModel, cycle: int, proc: int, results: list[list[DiceEnvironment]]
     ) -> None:
         proc_directory = self.dice_directory / f"{proc:02d}"
         if proc_directory.exists():

diceplayer/dice/dice_wrapper.py

@@ -1,3 +1,5 @@
+from pydantic import TypeAdapter
+
 import diceplayer.dice.dice_input as dice_input
 from diceplayer.config import DiceConfig
 from diceplayer.environment import System
@@ -7,6 +9,10 @@ from pathlib import Path
 from typing import Final
 
 
+type DiceEnvironment = tuple[str, int, int, int]
+DiceEnvironmentAdapter = TypeAdapter(DiceEnvironment)
+
+
 DICE_FLAG_LINE: Final[int] = -2
 DICE_END_FLAG: Final[str] = "End of simulation"
 
@@ -35,9 +41,22 @@ class DiceWrapper:
 
         raise RuntimeError(f"Dice simulation failed with exit status {exit_status}")
 
-    def parse_results(self, system: System) -> dict:
-        results = {}
+    def parse_results(self, system: System) -> list[DiceEnvironment]:
+        NUMBER_OF_HEADER_LINES = 2
+        NUMBER_OF_PRIMARY_ATOMS = len(system.molecule[0].atom)
+
+        results = []
         for output_file in sorted(self.working_directory.glob("phb*.xyz")):
-            ...
+            with open(output_file, "r") as f:
+                for _ in range(NUMBER_OF_HEADER_LINES + NUMBER_OF_PRIMARY_ATOMS):
+                    next(f, None)
+
+                for line in f:
+                    if line.strip() == "":
+                        break
+
+                    results.append(
+                        DiceEnvironmentAdapter.validate_python(line.split())
+                    )
 
         return results