feat: reads potentions from ljc file

diceplayer/dice/dice_input.py

@@ -9,6 +9,30 @@ from pathlib import Path
 from typing import Any, Sequence, TextIO
 
 
+
+DICE_KEYWORD_ORDER = [
+    "title",
+    "ncores",
+    "ljname",
+    "outname",
+    "nmol",
+    "dens",
+    "temp",
+    "press",
+    "seed",
+    "init",
+    "nstep",
+    "vstep",
+    "mstop",
+    "accum",
+    "iprint",
+    "isave",
+    "irdf",
+    "upbuf",
+]
+
+
+
 @dataclass(slots=True)
 class BaseConfig(ABC):
     ncores: int
@@ -18,13 +42,14 @@ class BaseConfig(ABC):
     temp: float
     seed: int
     isave: int
-    press: float = 1.0
 
     def write(self, directory: Path, filename: str = "input") -> Path:
         input_path = directory / filename
 
         if input_path.exists():
-            logger.info(f"Dice input file {input_path} already exists and will be overwritten")
+            logger.info(
+                f"Dice input file {input_path} already exists and will be overwritten"
+            )
             input_path.unlink()
         input_path.parent.mkdir(parents=True, exist_ok=True)
 
@@ -34,13 +59,18 @@ class BaseConfig(ABC):
         return input_path
 
     def write_dice_config(self, io_writer: TextIO) -> None:
-        for field in fields(self):
-            key = field.name
-            value = getattr(self, key)
+        values = {f.name: getattr(self, f.name) for f in fields(self)}
 
+        for key in DICE_KEYWORD_ORDER:
+            value = values.pop(key, None)
             if value is None:
                 continue
+            io_writer.write(f"{key} = {self._serialize_value(value)}\n")
 
+        # write any remaining fields (future extensions)
+        for key, value in values.items():
+            if value is None:
+                continue
             io_writer.write(f"{key} = {self._serialize_value(value)}\n")
 
         io_writer.write("$end\n")
@@ -48,7 +78,7 @@ class BaseConfig(ABC):
     @classmethod
     def from_config(cls, config: PlayerConfig, **kwargs) -> Self:
         base_fields = cls._extract_base_fields(config)
-        return cls(**base_fields, **kwargs)
+        return cls(**(base_fields | kwargs))
 
     @staticmethod
     def _extract_base_fields(config: PlayerConfig) -> dict[str, Any]:
@@ -60,7 +90,6 @@ class BaseConfig(ABC):
             temp=config.dice.temp,
             seed=config.dice.seed,
             isave=config.dice.isave,
-            press=config.dice.press,
         )
 
     @staticmethod
@@ -91,10 +120,18 @@ class BaseConfig(ABC):
 @dataclass(slots=True)
 class NVTConfig(BaseConfig):
     title: str = "Diceplayer Run - NVT"
-    dens: float = 0.0
-    nstep: int = 0
+    dens: float = ...
+    nstep: int = ...
     vstep: int = 0
 
+    @classmethod
+    def from_config(cls, config: PlayerConfig, **kwargs) -> Self:
+        return super(NVTConfig, cls).from_config(
+            config,
+            dens=config.dice.dens,
+            nstep=cls._get_nstep(config, 0),
+        )
+
 
 # -----------------------------------------------------
 # NVT THERMALIZATION
@@ -105,12 +142,12 @@ class NVTConfig(BaseConfig):
 class NVTTerConfig(NVTConfig):
     title: str = "Diceplayer Run - NVT Thermalization"
     upbuf: int = 360
+    init: str = "yes"
 
     @classmethod
     def from_config(cls, config: PlayerConfig, **kwargs) -> Self:
         return super(NVTTerConfig, cls).from_config(
             config,
-            dens=config.dice.dens,
             nstep=cls._get_nstep(config, 0),
             upbuf=config.dice.upbuf,
             vstep=0,
@@ -118,9 +155,7 @@ class NVTTerConfig(NVTConfig):
         )
 
     def write(self, directory: Path, filename: str = "nvt.ter") -> Path:
-        return super(NVTTerConfig, self).write(
-            directory, filename
-        )
+        return super(NVTTerConfig, self).write(directory, filename)
 
 
 # -----------------------------------------------------
@@ -132,12 +167,12 @@ class NVTTerConfig(NVTConfig):
 class NVTEqConfig(NVTConfig):
     title: str = "Diceplayer Run - NVT Production"
     irdf: int = 0
+    init: str = "yesreadxyz"
 
     @classmethod
     def from_config(cls, config: PlayerConfig, **kwargs) -> Self:
         return super(NVTEqConfig, cls).from_config(
             config,
-            dens=config.dice.dens,
             nstep=cls._get_nstep(config, 1),
             irdf=config.dice.irdf,
             vstep=0,
@@ -145,9 +180,7 @@ class NVTEqConfig(NVTConfig):
         )
 
     def write(self, directory: Path, filename: str = "nvt.eq") -> Path:
-        return super(NVTEqConfig, self).write(
-            directory, filename
-        )
+        return super(NVTEqConfig, self).write(directory, filename)
 
 
 # -----------------------------------------------------
@@ -160,6 +193,14 @@ class NPTConfig(BaseConfig):
     title: str = "Diceplayer Run - NPT"
     nstep: int = 0
     vstep: int = 5000
+    press: float = 1.0
+
+    @classmethod
+    def from_config(cls, config: PlayerConfig, **kwargs) -> Self:
+        return super(NPTConfig, cls).from_config(
+            config,
+            press=config.dice.press,
+        )
 
 
 # -----------------------------------------------------
@@ -183,9 +224,7 @@ class NPTTerConfig(NPTConfig):
         )
 
     def write(self, directory: Path, filename: str = "npt.ter") -> Path:
-        return super(NPTTerConfig, self).write(
-            directory, filename
-        )
+        return super(NPTTerConfig, self).write(directory, filename)
 
 
 # -----------------------------------------------------
@@ -209,6 +248,4 @@ class NPTEqConfig(NPTConfig):
         )
 
     def write(self, directory: Path, filename: str = "npt.eq") -> Path:
-        return super(NPTEqConfig, self).write(
-            directory, filename
-        )
+        return super(NPTEqConfig, self).write(directory, filename)