feat: reads potentions from ljc file

control.example.yml

@@ -3,7 +3,7 @@ diceplayer:
     switch_cyc: 3
     max_cyc: 5
     mem: 24
-    ncores: 5
+    ncores: 20
     qmprog: 'g16'
     lps: no
     ghosts: no
@@ -11,14 +11,15 @@ diceplayer:
 
     dice:
         nprocs: 4
-        nmol: [1, 100]
+        nmol: [1, 1000]
         dens: 1.5
         nstep: [2000, 3000]
-        isave: 1000
+        isave: 0
         outname: 'phb'
         progname: '~/.local/bin/dice'
-        ljname: 'phb.ljc'
+        ljname: 'phb.ljc.example'
         randominit: 'always'
+        seed: 12345
 
     gaussian:
         qmprog: 'g16'

diceplayer/config/dice_config.py

@@ -1,3 +1,5 @@
+from pathlib import Path
+
 from pydantic import BaseModel, ConfigDict, Field
 from typing_extensions import Literal
 
@@ -16,7 +18,7 @@ class DiceConfig(BaseModel):
         ..., description="Number of processes to use for the DICE simulations"
     )
 
-    ljname: str = Field(..., description="Name of the Lennard-Jones potential file")
+    ljname: Path = Field(..., description="Name of the Lennard-Jones potential file")
     outname: str = Field(
         ..., description="Name of the output file for the simulation results"
     )
@@ -47,10 +49,13 @@ class DiceConfig(BaseModel):
     isave: int = Field(1000, description="Frequency of saving the simulation results")
     press: float = Field(1.0, description="Pressure of the system")
     temp: float = Field(300.0, description="Temperature of the system")
-    progname: str = Field(
+    progname: Path = Field(
         "dice", description="Name of the program to run the simulation"
     )
     randominit: str = Field(
         "first", description="Method for initializing the random number generator"
     )
-    seed: int = Field(default_factory=lambda: random.randint(0, 2**32 - 1), description="Seed for the random number generator")
+    seed: int = Field(
+        default_factory=lambda: int(1e6 * random.random()),
+        description="Seed for the random number generator",
+    )

diceplayer/dice/dice_handler.py

@@ -1,10 +1,14 @@
-import shutil
+from diceplayer.dice.dice_input import (
-
+    NPTEqConfig,
-from diceplayer.dice.dice_input import NVTTerConfig, NVTEqConfig, NPTEqConfig, NPTTerConfig
+    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(
+        dice = DiceWrapper(state.config.dice, proc_directory)
-            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: ...

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):
+        values = {f.name: getattr(self, f.name) for f in fields(self)}
-            key = field.name
-            value = getattr(self, key)
 
+        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
+    dens: float = ...
-    nstep: int = 0
+    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(
+        return super(NVTTerConfig, self).write(directory, filename)
-            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(
+        return super(NVTEqConfig, self).write(directory, filename)
-            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(
+        return super(NPTTerConfig, self).write(directory, filename)
-            directory, filename
-        )
 
 
 # -----------------------------------------------------
@@ -209,6 +248,4 @@ class NPTEqConfig(NPTConfig):
         )
 
     def write(self, directory: Path, filename: str = "npt.eq") -> Path:
-        return super(NPTEqConfig, self).write(
+        return super(NPTEqConfig, self).write(directory, filename)
-            directory, filename
-        )

diceplayer/dice/dice_wrapper.py

@@ -1,12 +1,10 @@
-import subprocess
-from typing import Final
-
 import diceplayer.dice.dice_input as dice_input
-
-from pathlib import Path
-
 from diceplayer.config import DiceConfig
 
+import subprocess
+from pathlib import Path
+from typing import Final
+
 
 DICE_FLAG_LINE: Final[int] = -2
 DICE_END_FLAG: Final[str] = "End of simulation"
@@ -22,8 +20,9 @@ class DiceWrapper:
         output_path = input_path.parent / (input_path.name + ".out")
 
         with open(output_path, "w") as outfile, open(input_path, "r") as infile:
+            bin_path = self.dice_config.progname.expanduser()
             exit_status = subprocess.call(
-                self.dice_config.progname, stdin=infile, stdout=outfile
+                bin_path, stdin=infile, stdout=outfile, cwd=self.working_directory
             )
 
         if exit_status != 0:
@@ -38,4 +37,3 @@ class DiceWrapper:
 
     def extract_results(self) -> dict:
         return {}
-

diceplayer/environment/atom.py

@@ -1,9 +1,9 @@
 from diceplayer.utils.ptable import AtomInfo, PTable
 
-from dataclasses import dataclass
+from pydantic.dataclasses import dataclass
 
 
-@dataclass
+@dataclass(slots=True)
 class Atom:
     """
     Atom class declaration. This class is used throughout the DicePlayer program to represent atoms.

diceplayer/environment/molecule.py

@@ -10,10 +10,11 @@ import numpy as np
 import numpy.linalg as linalg
 import numpy.typing as npt
 from typing_extensions import List, Self, Tuple
+from pydantic.dataclasses import dataclass
 
 import math
 from copy import deepcopy
-from dataclasses import dataclass, field
+from dataclasses import field
 from functools import cached_property
 
 

diceplayer/optimization/optimization_handler.py

@@ -16,4 +16,4 @@ class OptimizationHandler:
         if current_cycle < state.config.switch_cyc:
             return RoutineType.CHARGE
 
-        return RoutineType.GEOMETRY
+        return RoutineType.GEOMETRY

diceplayer/player.py

@@ -1,12 +1,13 @@
 from diceplayer.config.player_config import PlayerConfig
 from diceplayer.dice.dice_handler import DiceHandler
 from diceplayer.logger import logger
-from diceplayer.optimization.optimization_handler import OptimizationHandler
 from diceplayer.state.state_handler import StateHandler
 from diceplayer.state.state_model import StateModel
 
 from typing_extensions import TypedDict, Unpack
 
+from diceplayer.utils.potential import read_system_from_phb
+
 
 class PlayerFlags(TypedDict):
     continuation: bool
@@ -30,9 +31,11 @@ class Player:
             self._state_handler.delete()
             state = None
 
-
         if state is None:
-            state = StateModel.from_config(self.config)
+            system = read_system_from_phb(self.config)
+            state = StateModel(
+                config=self.config, system=system
+            )
         else:
             logger.info("Resuming from existing state.")
 

diceplayer/state/state_model.py

@@ -8,7 +8,7 @@ from typing_extensions import Self
 class StateModel(BaseModel):
     config: PlayerConfig
     system: System
-    current_cycle: int
+    current_cycle: int = 0
 
     @classmethod
     def from_config(cls, config: PlayerConfig) -> Self:

diceplayer/utils/potential.py

@@ -0,0 +1,62 @@
+from diceplayer.config import PlayerConfig
+from diceplayer.environment import System, Molecule, Atom
+
+from pathlib import Path
+
+from diceplayer.logger import logger
+from diceplayer.state.state_model import StateModel
+
+
+def read_system_from_phb(config: PlayerConfig) -> System:
+    phb_file = Path(config.dice.ljname)
+    if not phb_file.exists():
+        raise FileNotFoundError
+
+    ljc_data = phb_file.read_text(encoding="utf-8").splitlines()
+
+    combrule = ljc_data.pop(0).strip()
+    if combrule != config.dice.combrule:
+        raise ValueError(
+            f"Invalid combrule defined in {phb_file}. Expected the same value configured in the config file"
+        )
+
+    ntypes = ljc_data.pop(0).strip()
+    if not ntypes.isdigit():
+        raise ValueError(f"Invalid ntypes defined in {phb_file}")
+
+    nmol = int(ntypes)
+    if nmol != len(config.dice.nmol):
+        raise ValueError(f"Invalid nmol defined in {phb_file}")
+
+    sys = System()
+
+    for i in range(nmol):
+        nsites, molname = ljc_data.pop(0).split()
+
+        if not nsites.isdigit():
+            raise ValueError(f"Invalid nsites defined in {phb_file}")
+        nsites = int(nsites)
+
+        mol = Molecule(molname)
+
+        for j in range(nsites):
+            _fields = ljc_data.pop(0).split()
+            mol.add_atom(
+                Atom(*_fields)
+            )
+
+        sys.add_type(mol)
+
+    return sys
+
+
+# def write_phb(phb_file: Path, state: StateModel) -> None:
+#     if phb_file.exists():
+#        raise RuntimeError(f"File {phb_file} already exists")
+#
+#     with open(phb_file, "w") as f:
+#         f.write(f"{state.config.dice.combrule}\n")
+#         f.write(f"{len(state.system.nmols)}\n")
+#         f.write(f"{state.config.dice.nmol}\n")
+
+

tests/config/test_dice_config.py

@@ -6,6 +6,7 @@ import pytest
 class TestDiceConfig:
     def test_class_instantiation(self):
         dice_dto = DiceConfig(
+                nprocs=1,
             ljname="test",
             outname="test",
             dens=1.0,
@@ -18,6 +19,7 @@ class TestDiceConfig:
     def test_validate_jname(self):
         with pytest.raises(ValueError) as ex:
             DiceConfig(
+                nprocs=1,
                 ljname=None,
                 outname="test",
                 dens=1.0,
@@ -30,6 +32,7 @@ class TestDiceConfig:
     def test_validate_outname(self):
         with pytest.raises(ValueError) as ex:
             DiceConfig(
+                nprocs=1,
                 ljname="test",
                 outname=None,
                 dens=1.0,
@@ -42,6 +45,7 @@ class TestDiceConfig:
     def test_validate_dens(self):
         with pytest.raises(ValueError) as ex:
             DiceConfig(
+                nprocs=1,
                 ljname="test",
                 outname="test",
                 dens=None,
@@ -54,6 +58,7 @@ class TestDiceConfig:
     def test_validate_nmol(self):
         with pytest.raises(ValueError) as ex:
             DiceConfig(
+                nprocs=1,
                 ljname="test",
                 outname="test",
                 dens=1.0,
@@ -66,6 +71,7 @@ class TestDiceConfig:
     def test_validate_nstep(self):
         with pytest.raises(ValueError) as ex:
             DiceConfig(
+                nprocs=1,
                 ljname="test",
                 outname="test",
                 dens=1.0,
@@ -78,6 +84,7 @@ class TestDiceConfig:
     def test_from_dict(self):
         dice_dto = DiceConfig.model_validate(
             {
+                "nprocs": 1,
                 "ljname": "test",
                 "outname": "test",
                 "dens": 1.0,

tests/config/test_player_config.py

@@ -11,6 +11,7 @@ class TestPlayerConfig:
     @pytest.fixture
     def dice_payload(self) -> dict[str, Any]:
         return {
+            "nprocs": 4,
             "ljname": "test",
             "outname": "test",
             "dens": 1.0,
@@ -35,7 +36,6 @@ class TestPlayerConfig:
             "mem": 12,
             "max_cyc": 100,
             "switch_cyc": 50,
-            "nprocs": 4,
             "ncores": 4,
             "dice": dice_payload,
             "gaussian": gaussian_payload,
@@ -57,7 +57,6 @@ class TestPlayerConfig:
             mem=12,
             max_cyc=100,
             switch_cyc=50,
-            nprocs=4,
             ncores=4,
             dice=dice_config,
             gaussian=gaussian_config,
@@ -75,7 +74,6 @@ class TestPlayerConfig:
             mem=12,
             max_cyc=100,
             switch_cyc=50,
-            nprocs=4,
             ncores=4,
             altsteps=0,
             dice=dice_config,

tests/dice/test_dice_input.py

@@ -20,9 +20,9 @@ class TestDiceInput:
                 "mem": 12,
                 "max_cyc": 100,
                 "switch_cyc": 50,
-                "nprocs": 4,
                 "ncores": 4,
                 "dice": {
+                    "nprocs": 4,
                     "ljname": "test",
                     "outname": "test",
                     "dens": 1.0,

tests/mocks/mock_inputs.py

@@ -1,113 +0,0 @@
-from unittest import mock
-
-
-def get_config_example():
-    return """
-diceplayer:
-    opt: no
-    mem: 12
-    maxcyc: 3
-    ncores: 4
-    nprocs: 4
-    qmprog: 'g16'
-    lps: no
-    ghosts: no
-    altsteps: 20000
-
-    dice:
-        nmol: [1, 50]
-        dens: 0.75
-        nstep: [2000, 3000, 4000]
-        isave: 1000
-        outname: 'phb'
-        progname: '~/.local/bin/dice'
-        ljname: 'phb.ljc'
-        randominit: 'first'
-
-    gaussian:
-        qmprog: 'g16'
-        level: 'MP2/aug-cc-pVDZ'
-        keywords: 'freq'
-"""
-
-
-def get_potentials_exemple():
-    return """\
-*
-2
-1 TEST
- 1   1   0.000000   0.000000   0.000000   0.000000  0.0000  0.0000
-1 PLACEHOLDER
- 1   1   0.000000   0.000000   0.000000   0.000000  0.0000  0.0000
-"""
-
-
-def get_potentials_error_combrule():
-    return """\
-.
-2
-1 TEST
- 1   1   0.000000   0.000000   0.000000   0.000000  0.0000  0.0000
-1 PLACEHOLDER
- 1   1   0.000000   0.000000   0.000000   0.000000  0.0000  0.0000
-"""
-
-
-def get_potentials_error_ntypes():
-    return """\
-*
-a
-1 TEST
- 1   1   0.000000   0.000000   0.000000   0.000000  0.0000  0.0000
-1 PLACEHOLDER
- 1   1   0.000000   0.000000   0.000000   0.000000  0.0000  0.0000
-"""
-
-
-def get_potentials_error_ntypes_config():
-    return """\
-*
-3
-1 TEST
- 1   1   0.000000   0.000000   0.000000   0.000000  0.0000  0.0000
-1 PLACEHOLDER
- 1   1   0.000000   0.000000   0.000000   0.000000  0.0000  0.0000
-"""
-
-
-def get_potentials_error_nsites():
-    return """\
-*
-2
-. TEST
- 1   1   0.000000   0.000000   0.000000   0.000000  0.0000  0.0000
-1 PLACEHOLDER
- 1   1   0.000000   0.000000   0.000000   0.000000  0.0000  0.0000
-"""
-
-
-def get_potentials_error_molname():
-    return """\
-*
-2
-1
- 1   1   0.000000   0.000000   0.000000   0.000000  0.0000  0.0000
-1 PLACEHOLDER
- 1   1   0.000000   0.000000   0.000000   0.000000  0.0000  0.0000
-"""
-
-
-def mock_open(file, *args, **kwargs):
-    values = {
-        "control.test.yml": get_config_example(),
-        "phb.ljc": get_potentials_exemple(),
-        "phb.error.combrule.ljc": get_potentials_error_combrule(),
-        "phb.error.ntypes.ljc": get_potentials_error_ntypes(),
-        "phb.error.ntypes.config.ljc": get_potentials_error_ntypes_config(),
-        "phb.error.nsites.ljc": get_potentials_error_nsites(),
-        "phb.error.molname.ljc": get_potentials_error_molname(),
-    }
-    if file in values:
-        return mock.mock_open(read_data=values[file])()
-
-    return mock.mock_open(read_data="")()

tests/mocks/mock_proc.py

@@ -1,32 +0,0 @@
-from typing_extensions import List
-
-import itertools
-
-
-class MockProc:
-    pid_counter = itertools.count()
-
-    def __init__(self, *args, **kwargs):
-        self.pid = next(MockProc.pid_counter)
-
-        if "exitcode" in kwargs:
-            self.exitcode = kwargs["exitcode"]
-        else:
-            self.exitcode = 0
-
-        self.sentinel = self.pid
-
-    def __call__(self, *args, **kwargs):
-        return self
-
-    def start(self):
-        pass
-
-    def terminate(self):
-        pass
-
-
-class MockConnection:
-    @staticmethod
-    def wait(sentinels: List[int]):
-        return sentinels

tests/state/test_state_handler.py

@@ -16,9 +16,9 @@ class TestStateHandler:
             mem=12,
             max_cyc=100,
             switch_cyc=50,
-            nprocs=4,
             ncores=4,
             dice=DiceConfig(
+                nprocs=4,
                 ljname="test",
                 outname="test",
                 dens=1.0,

tests/utils/test_potential.py

@@ -0,0 +1,38 @@
+from pathlib import Path
+from typing import Any
+
+import pytest
+
+from diceplayer.config import PlayerConfig
+from diceplayer.environment import System
+from diceplayer.utils.potential import read_system_from_phb
+
+
+class TestPotential:
+    @pytest.fixture
+    def player_config(self) -> PlayerConfig:
+        return PlayerConfig.model_validate({
+            "type": "both",
+            "mem": 12,
+            "max_cyc": 100,
+            "switch_cyc": 50,
+            "ncores": 4,
+            "dice": {
+                "nprocs": 4,
+                "ljname": "phb.ljc.example",
+                "outname": "test",
+                "dens": 1.0,
+                "nmol": [12, 16],
+                "nstep": [1, 1],
+            },
+            "gaussian": {
+                "level": "test",
+                "qmprog": "g16",
+                "keywords": "test",
+            },
+        })
+
+    def test_read_phb(self, player_config: PlayerConfig):
+        system = read_system_from_phb(player_config)
+
+        assert isinstance(system, System)