feat: reads potentions from ljc file

diceplayer/dice/dice_handler.py

@@ -1,10 +1,14 @@
-import shutil
-
-from diceplayer.dice.dice_input import NVTTerConfig, NVTEqConfig, NPTEqConfig, NPTTerConfig
+from diceplayer.dice.dice_input import (
+    NPTEqConfig,
+    NPTTerConfig,
+    NVTEqConfig,
+    NVTTerConfig,
+)
 from diceplayer.dice.dice_wrapper import DiceWrapper
 from diceplayer.logger import logger
 from diceplayer.state.state_model import StateModel
 
+import shutil
 from pathlib import Path
 from threading import Thread
 
@@ -15,7 +19,9 @@ class DiceHandler:
 
     def run(self, state: StateModel, cycle: int) -> StateModel:
         if self.dice_directory.exists():
-            logger.info(f"Found dice directory: {self.dice_directory}, this directory will be purged for a clean state")
+            logger.info(
+                f"Found dice directory: {self.dice_directory}, this directory will be purged for a clean state"
+            )
             shutil.rmtree(self.dice_directory)
         self.dice_directory.mkdir(parents=True)
 
@@ -38,7 +44,9 @@ class DiceHandler:
             t.join()
 
         if len(results) != state.config.dice.nprocs:
-            raise RuntimeError(f"Expected {state.config.dice.nprocs} simulation results, but got {len(results)}")
+            raise RuntimeError(
+                f"Expected {state.config.dice.nprocs} simulation results, but got {len(results)}"
+            )
 
         return results
 
@@ -47,21 +55,23 @@ class DiceHandler:
     def commit_simulation_state(self, state: StateModel, result: dict) -> StateModel:
         return state
 
-    def _simulation_process(self, state: StateModel, cycle: int, proc: int, results: list[dict]) -> None:
+    def _simulation_process(
+        self, state: StateModel, cycle: int, proc: int, results: list[dict]
+    ) -> None:
         proc_directory = self.dice_directory / f"{proc:02d}"
         if proc_directory.exists():
             shutil.rmtree(proc_directory)
         proc_directory.mkdir(parents=True)
 
-        dice = DiceWrapper(
-            state.config.dice, proc_directory
-        )
+        dice = DiceWrapper(state.config.dice, proc_directory)
 
-        if state.config.dice.randominit == "first" and cycle == 0:
+        self._generate_phb_file(state, proc_directory)
+
+        if state.config.dice.randominit == "first" and cycle >= 0:
+            self._generate_last_xyz(state, proc_directory)
+        else:
             nvt_ter_config = NVTTerConfig.from_config(state.config)
             dice.run(nvt_ter_config)
-        else:
-            self._generate_last_xyz(state, proc_directory)
 
         if len(state.config.dice.nstep) == 2:
             nvt_eq_config = NVTEqConfig.from_config(state.config)
@@ -76,5 +86,30 @@ class DiceHandler:
 
         results.append(dice.extract_results())
 
-    def _generate_last_xyz(self, state: StateModel, proc_directory: Path) -> None:
-        ...
+    @staticmethod
+    def _generate_phb_file(state: StateModel, proc_directory: Path) -> None:
+        fstr = "{:<3d} {:>3d}  {:>10.5f} {:>10.5f} {:>10.5f}  {:>10.6f} {:>9.5f} {:>7.4f}\n"
+
+        phb_file = proc_directory / state.config.dice.ljname
+
+        with open(phb_file, "w") as f:
+            f.write(f"{state.config.dice.combrule}\n")
+            f.write(f"{len(state.config.dice.nmol)}\n")
+
+            for molecule in state.system.molecule:
+                f.write(f"{len(molecule.atom)} {molecule.molname}\n")
+                for atom in molecule.atom:
+                    f.write(
+                        fstr.format(
+                            atom.lbl,
+                            atom.na,
+                            atom.rx,
+                            atom.ry,
+                            atom.rz,
+                            atom.chg,
+                            atom.eps,
+                            atom.sig,
+                        )
+                    )
+
+    def _generate_last_xyz(self, state: StateModel, proc_directory: Path) -> None: ...