refactor: restructure dice environment handling and update Python version requirement

.python-version

@@ -1 +1 @@
-3.10
+3.12

control.example.yml

@@ -1,23 +1,26 @@
 diceplayer:
-    opt: no
+    type: both
+    switch_cyc: 3
+    max_cyc: 5
     mem: 24
-    maxcyc: 5
+    ncores: 20
-    ncores: 5
-    nprocs: 4
     qmprog: 'g16'
     lps: no
     ghosts: no
     altsteps: 2000
 
     dice:
-        nmol: [1, 100]
+        nprocs: 1
+        nmol: [1, 200]
         dens: 1.5
-        nstep: [2000, 3000]
+        nstep: [200, 200]
-        isave: 1000
+        vstep: 1000
+        isave: 30
         outname: 'phb'
-        progname: '~/.local/bin/dice'
+        progname: '/home/hideyoshi/.local/bin/dice'
-        ljname: 'phb.ljc'
+        ljname: 'phb.ljc.example'
         randominit: 'always'
+        seed: 12345
 
     gaussian:
         qmprog: 'g16'

diceplayer/__init__.py

@@ -1,8 +0,0 @@
-from diceplayer.utils import Logger
-
-from importlib import metadata
-
-
-VERSION = metadata.version("diceplayer")
-
-logger = Logger(__name__)

diceplayer/__main__.py

@@ -1,22 +1,22 @@
-from diceplayer import VERSION, logger
+from diceplayer.cli import ArgsModel, read_input
+from diceplayer.config import PlayerConfig
+from diceplayer.logger import logger
 from diceplayer.player import Player
 
 import argparse
-import logging
+from importlib import metadata
+
+
+VERSION = metadata.version("diceplayer")
 
 
 def main():
-    """
-    Read and store the arguments passed to the program
-    and set the usage and help messages
-    """
-
     parser = argparse.ArgumentParser(prog="Diceplayer")
     parser.add_argument(
-        "-c", "--continue", dest="opt_continue", default=False, action="store_true"
+        "-v", "--version", action="version", version="diceplayer-" + VERSION
     )
     parser.add_argument(
-        "-v", "--version", action="version", version="diceplayer-" + VERSION
+        "-c", "--continue", dest="continuation", default=False, action="store_true"
     )
     parser.add_argument(
         "-i",
@@ -34,36 +34,26 @@ def main():
         metavar="OUTFILE",
         help="output file of diceplayer [default = run.log]",
     )
-    args = parser.parse_args()
+    parser.add_argument(
+        "-f",
+        "--force",
+        dest="force",
+        default=False,
+        action="store_true",
+        help="force overwrite existing state file if it exists [default = False]",
+    )
+    args = ArgsModel.from_args(parser.parse_args())
 
-    # Open OUTFILE for writing and print keywords and initial info
+    logger.set_output_file(args.outfile)
-    logger.set_logger(args.outfile, logging.INFO)
 
-    if args.opt_continue:
+    config: PlayerConfig
-        player = Player.from_save()
+    try:
-    else:
+        config = read_input(args.infile)
-        player = Player.from_file(args.infile)
+    except Exception as e:
+        logger.error(f"Failed to read input file: {e}")
+        return
 
-        player.read_potentials()
+    Player(config).play(continuation=args.continuation, force=args.force)
-
-        player.create_simulation_dir()
-        player.create_geoms_file()
-
-    player.print_keywords()
-
-    player.print_potentials()
-
-    player.prepare_system()
-
-    player.start()
-
-    logger.info("\n+" + 88 * "-" + "+\n")
-
-    player.print_results()
-
-    logger.info("\n+" + 88 * "-" + "+\n")
-
-    logger.info("Diceplayer finished successfully \n")
 
 
 if __name__ == "__main__":

diceplayer/cli/__init__.py

@@ -0,0 +1,5 @@
+from .args_model import ArgsModel
+from .read_input_file import read_input
+
+
+__all__ = ["ArgsModel", "read_input"]

diceplayer/cli/args_model.py

@@ -0,0 +1,12 @@
+from pydantic import BaseModel
+
+
+class ArgsModel(BaseModel):
+    outfile: str
+    infile: str
+    continuation: bool
+    force: bool
+
+    @classmethod
+    def from_args(cls, args):
+        return cls(**vars(args))

diceplayer/cli/read_input_file.py

@@ -0,0 +1,9 @@
+from diceplayer.config import PlayerConfig
+
+import yaml
+
+
+def read_input(infile) -> PlayerConfig:
+    with open(infile, "r") as f:
+        values = yaml.safe_load(f)
+        return PlayerConfig.model_validate(values["diceplayer"])

diceplayer/config/__init__.py

@@ -0,0 +1,10 @@
+from .dice_config import DiceConfig
+from .gaussian_config import GaussianConfig
+from .player_config import PlayerConfig
+
+
+__all__ = [
+    "DiceConfig",
+    "GaussianConfig",
+    "PlayerConfig",
+]

diceplayer/config/dice_config.py

@@ -1,5 +1,8 @@
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, ConfigDict, Field
-from typing_extensions import List, Literal
+from typing_extensions import Literal
+
+import random
+from pathlib import Path
 
 
 class DiceConfig(BaseModel):
@@ -7,15 +10,22 @@ class DiceConfig(BaseModel):
     Data Transfer Object for the Dice configuration.
     """
 
-    ljname: str = Field(..., description="Name of the Lennard-Jones potential file")
+    model_config = ConfigDict(
+        frozen=True,
+    )
+    nprocs: int = Field(
+        ..., description="Number of processes to use for the DICE simulations"
+    )
+
+    ljname: Path = Field(..., description="Name of the Lennard-Jones potential file")
     outname: str = Field(
         ..., description="Name of the output file for the simulation results"
     )
     dens: float = Field(..., description="Density of the system")
-    nmol: List[int] = Field(
+    nmol: list[int] = Field(
         ..., description="List of the number of molecules for each component"
     )
-    nstep: List[int] = Field(
+    nstep: list[int] = Field(
         ...,
         description="List of the number of steps for each component",
         min_length=2,
@@ -25,6 +35,13 @@ class DiceConfig(BaseModel):
     upbuf: int = Field(
         360, description="Buffer size for the potential energy calculations"
     )
+    irdf: int = Field(
+        0,
+        description="Controls the interval of Monte Carlo steps at which configurations are used at computation of radial distribution functions",
+    )
+    vstep: int = Field(
+        5000, description="Frequency of volume change moves in NPT simulations"
+    )
     combrule: Literal["+", "*"] = Field(
         "*", description="Combination rule for the Lennard-Jones potential"
     )
@@ -37,4 +54,7 @@ class DiceConfig(BaseModel):
     randominit: str = Field(
         "first", description="Method for initializing the random number generator"
     )
-    seed: int | None = Field(None, 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/config/gaussian_config.py

@@ -1,4 +1,4 @@
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, ConfigDict, Field
 from typing_extensions import Literal
 
 
@@ -7,10 +7,14 @@ class GaussianConfig(BaseModel):
     Data Transfer Object for the Gaussian configuration.
     """
 
-    level: str = Field(..., description="Level of theory for the QM calculations")
+    model_config = ConfigDict(
+        frozen=True,
+    )
+
     qmprog: Literal["g03", "g09", "g16"] = Field(
         "g16", description="QM program to use for the calculations"
     )
+    level: str = Field(..., description="Level of theory for the QM calculations")
 
     chgmult: list[int] = Field(
         default_factory=lambda: [0, 1],
@@ -20,6 +24,6 @@ class GaussianConfig(BaseModel):
         "chelpg", description="Population analysis method for the QM calculations"
     )
     chg_tol: float = Field(0.01, description="Charge tolerance for the QM calculations")
-    keywords: str = Field(
+    keywords: str | None = Field(
         None, description="Additional keywords for the QM calculations"
     )

diceplayer/config/player_config.py

@@ -1,27 +1,52 @@
 from diceplayer.config.dice_config import DiceConfig
 from diceplayer.config.gaussian_config import GaussianConfig
 
-from pydantic import BaseModel, Field, model_validator
+from pydantic import BaseModel, ConfigDict, Field, model_validator
-from typing_extensions import Self
+from typing_extensions import Any
 
+from enum import Enum
 from pathlib import Path
 
 
 MIN_STEP = 20000
+STEP_INCREMENT = 1000
+
+
+class RoutineType(str, Enum):
+    CHARGE = "charge"
+    GEOMETRY = "geometry"
+    BOTH = "both"
 
 
 class PlayerConfig(BaseModel):
     """
-    Data Transfer Object for the player configuration.
+    Configuration for DICEPlayer simulations.
+
+    Attributes:
+        type: Type of simulation to perform (charge, geometry, or both).
+        max_cyc: Maximum number of cycles for the geometry optimization.
+        switch_cyc: Cycle at which to switch from charge to geometry optimization (if type is "both").
+        mem: Memory configuration for QM calculations.
+        nprocs: Number of processors to use for QM calculations.
+        ncores: Number of cores to use for QM calculations.
+        dice: Configuration parameters specific to DICE simulations.
+        gaussian: Configuration parameters specific to Gaussian calculations.
+        altsteps: Number of steps for the alternate simulation (default: 20000).
+        geoms_file: File name for the geometries output (default: "geoms.xyz").
+        simulation_dir: Directory name for the simulation files (default: "simfiles").
     """
 
-    opt: bool = Field(..., description="Whether to perform geometry optimization")
+    model_config = ConfigDict(
-    maxcyc: int = Field(
+        frozen=True,
-        ..., description="Maximum number of cycles for the geometry optimization"
     )
-    nprocs: int = Field(
+
-        ..., description="Number of processors to use for the QM calculations"
+    type: RoutineType = Field(..., description="Type of simulation to perform")
+    max_cyc: int = Field(
+        ..., description="Maximum number of cycles for the geometry optimization", gt=0
     )
+    switch_cyc: int = Field(..., description="Switch cycle configuration")
+
+    mem: int = Field(None, description="Memory configuration")
     ncores: int = Field(
         ..., description="Number of cores to use for the QM calculations"
     )
@@ -29,20 +54,37 @@ class PlayerConfig(BaseModel):
     dice: DiceConfig = Field(..., description="Dice configuration")
     gaussian: GaussianConfig = Field(..., description="Gaussian configuration")
 
-    mem: int = Field(None, description="Memory configuration")
-    switchcyc: int = Field(3, description="Switch cycle configuration")
-    qmprog: str = Field("g16", description="QM program to use for the calculations")
     altsteps: int = Field(
         20000, description="Number of steps for the alternate simulation"
     )
     geoms_file: Path = Field(
-        "geoms.xyz", description="File name for the geometries output"
+        Path("geoms.xyz"), description="File name for the geometries output"
     )
     simulation_dir: Path = Field(
-        "simfiles", description="Directory name for the simulation files"
+        Path("simfiles"), description="Directory name for the simulation files"
     )
 
-    @model_validator(mode="after")
+    @model_validator(mode="before")
-    def validate_altsteps(self) -> Self:
+    @staticmethod
-        self.altsteps = round(max(MIN_STEP, self.altsteps) / 1000) * 1000
+    def validate_altsteps(fields) -> dict[str, Any]:
-        return self
+        altsteps = fields.pop("altsteps", MIN_STEP)
+        fields["altsteps"] = (
+            round(max(MIN_STEP, altsteps) / STEP_INCREMENT) * STEP_INCREMENT
+        )
+        return fields
+
+    @model_validator(mode="before")
+    @staticmethod
+    def validate_switch_cyc(fields: dict[str, Any]) -> dict[str, Any]:
+        max_cyc = int(fields.get("max_cyc", 0))
+        switch_cyc = int(fields.get("switch_cyc", max_cyc))
+
+        if fields.get("type") == "both" and not switch_cyc < max_cyc:
+            raise ValueError("switch_cyc must be less than max_cyc when type='both'.")
+
+        if fields.get("type") != "both" and switch_cyc != max_cyc:
+            raise ValueError(
+                "switch_cyc must be equal to max_cyc when type is not 'both'."
+            )
+
+        return fields

diceplayer/dice/__init__.py

@@ -0,0 +1,174 @@
+"""
+DICE Monte Carlo Simulation Interface
+=====================================
+
+This package provides utilities for configuring and running simulations with
+the DICE Monte Carlo molecular simulation program.
+
+DICE performs statistical sampling of molecular systems using the Metropolis
+Monte Carlo algorithm. Simulations are defined by text input files containing
+keywords that control the thermodynamic ensemble, system composition, and
+simulation parameters.
+
+---------------------------------------------------------------------
+
+Simulation Ensembles
+--------------------
+
+DICE supports multiple statistical ensembles.
+
+NVT
+    Canonical ensemble where the following properties remain constant:
+
+    - N: number of molecules
+    - V: system volume
+    - T: temperature
+
+    The system density is fixed and the simulation box volume does not change
+    during the simulation.
+
+NPT
+    Isothermal–isobaric ensemble where the following properties remain constant:
+
+    - N: number of molecules
+    - P: pressure
+    - T: temperature
+
+    The simulation box volume is allowed to fluctuate in order to maintain the
+    target pressure.
+
+---------------------------------------------------------------------
+
+Simulation Stages
+-----------------
+
+Simulations are typically executed in multiple stages.
+
+Thermalization (TER)
+    Initial phase where the system relaxes to the desired thermodynamic
+    conditions. Molecular configurations stabilize and the system reaches
+    equilibrium.
+
+    During this stage statistical properties are **not accumulated**.
+
+Production / Equilibration (EQ)
+    Main sampling phase after the system has equilibrated.
+
+    Statistical properties such as energies, densities, and radial
+    distribution functions are collected and configurations may be saved
+    for later analysis.
+
+---------------------------------------------------------------------
+
+Typical Simulation Pipeline
+---------------------------
+
+Two common execution workflows are used.
+
+NVT Simulation
+    Used when the system density is known.
+
+    1. NVT.ter  → thermalization at constant density
+    2. NVT.eq   → production sampling
+
+NPT Simulation
+    Used when the equilibrium density is unknown.
+
+    1. NVT.ter  → initial thermalization at approximate density
+    2. NPT.ter  → pressure relaxation (volume adjustment)
+    3. NPT.eq   → production sampling at target pressure
+
+---------------------------------------------------------------------
+
+DICE Input Keywords
+-------------------
+
+The following keywords are used in the generated input files.
+
+title
+    Descriptive title printed in the simulation output.
+
+ncores
+    Number of CPU cores used by the DICE executable.
+
+ljname
+    File containing Lennard-Jones parameters and molecular topology.
+
+outname
+    Prefix used for simulation output files.
+
+nmol
+    Number of molecules of each species in the system.
+
+dens
+    System density (g/cm³). Used only in NVT simulations or for
+    initialization of NPT runs.
+
+press
+    Target pressure used in NPT simulations.
+
+temp
+    Simulation temperature.
+
+nstep
+    Number of Monte Carlo cycles executed in the simulation stage.
+
+init
+    Defines how the simulation initializes molecular coordinates.
+
+    yes
+        Random initial configuration.
+
+    no
+        Continue from a previous configuration.
+
+    yesreadxyz
+        Read coordinates from a previously saved XYZ configuration.
+
+vstep
+    Frequency of volume-change moves in NPT simulations.
+
+mstop
+    Molecule displacement control flag used internally by DICE.
+
+accum
+    Enables or disables accumulation of statistical averages.
+
+iprint
+    Frequency of simulation information printed to the output.
+
+isave
+    Frequency at which configurations are written to trajectory files.
+
+irdf
+    Controls calculation of radial distribution functions.
+
+seed
+    Random number generator seed used by the Monte Carlo algorithm.
+
+upbuf
+    Buffer size parameter used internally by DICE during thermalization.
+
+---------------------------------------------------------------------
+
+Output Files
+------------
+
+Important output files produced during the simulation include:
+
+phb.xyz
+    XYZ trajectory containing sampled molecular configurations.
+
+last.xyz
+    Final configuration of the simulation, often used as the starting
+    configuration for the next simulation cycle.
+
+---------------------------------------------------------------------
+
+References
+----------
+
+DICE is a Monte Carlo molecular simulation program developed primarily
+by researchers at the University of São Paulo (USP) for studying liquids,
+solutions, and solvation phenomena.
+"""

diceplayer/dice/dice_handler.py

@@ -0,0 +1,186 @@
+import warnings
+
+from diceplayer.dice.dice_input import (
+    NPTEqConfig,
+    NPTTerConfig,
+    NVTEqConfig,
+    NVTTerConfig,
+)
+from diceplayer.dice.dice_wrapper import (
+    DiceEnvironment,
+    DiceWrapper,
+)
+from diceplayer.environment import Atom, Molecule
+from diceplayer.logger import logger
+from diceplayer.state.state_model import StateModel
+
+import shutil
+from itertools import batched, chain, islice
+from pathlib import Path
+from threading import Thread
+
+
+class DiceHandler:
+    def __init__(self, step_directory: Path):
+        self.dice_directory = step_directory / "dice"
+
+    def run(self, state: StateModel, cycle: int) -> list[Atom]:
+        if self.dice_directory.exists():
+            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)
+
+        return self.run_simulations(state, cycle)
+
+    def run_simulations(self, state: StateModel, cycle: int) -> list[Atom]:
+        results: list[list[Atom]] = []
+
+        threads = []
+        for p in range(state.config.dice.nprocs):
+            t = Thread(target=self._simulation_process, args=(state, cycle, p, results))
+            threads.append(t)
+            t.start()
+
+        for t in threads:
+            t.join()
+
+        if len(results) != state.config.dice.nprocs:
+            raise RuntimeError(
+                f"Expected {state.config.dice.nprocs} simulation results, but got {len(results)}"
+            )
+
+        return self._aggregate_results(state, results)
+
+    def _simulation_process(
+        self,
+        state: StateModel,
+        cycle: int,
+        proc: int,
+        results: list[list[Atom]],
+    ) -> 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)
+
+        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)
+
+        if len(state.config.dice.nstep) == 2:
+            nvt_eq_config = NVTEqConfig.from_config(state.config)
+            dice.run(nvt_eq_config)
+
+        elif len(state.config.dice.nstep) == 3:
+            npt_ter_config = NPTTerConfig.from_config(state.config)
+            dice.run(npt_ter_config)
+
+            npt_eq_config = NPTEqConfig.from_config(state.config)
+            dice.run(npt_eq_config)
+
+        results.extend(
+            [
+                self._filter_environment_sites(state, environment)
+                for environment in dice.parse_results()
+            ]
+        )
+
+    @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: ...
+
+    @staticmethod
+    def _filter_environment_sites(
+        state: StateModel, environment: DiceEnvironment
+    ) -> list[Atom]:
+        picked_environment = []
+
+        ref_molecule = state.system.molecule[0]
+        ref_molecule_sizes = ref_molecule.sizes_of_molecule()
+        ref_n_sites = len(ref_molecule.atom) * state.config.dice.nmol[0]
+
+        min_distance = min(
+            (environment.thickness[i] - ref_molecule_sizes[i]) / 2 for i in range(3)
+        )
+
+        site_iter = iter(environment.items)
+        _ = list(islice(site_iter, ref_n_sites))
+
+        for molecule_index, molecule in enumerate(state.system.molecule[1:], start=1):
+            molecule_n_atoms = len(molecule.atom)
+            molecule_n_sites = molecule_n_atoms * state.config.dice.nmol[molecule_index]
+
+            sites = list(islice(site_iter, molecule_n_sites))
+
+            for molecule_sites in batched(sites, molecule_n_atoms):
+                new_molecule = Molecule("ASEC TMP MOLECULE")
+
+                for site_index, atom_site in enumerate(molecule_sites):
+                    new_molecule.add_atom(
+                        Atom(
+                            molecule.atom[site_index].lbl,
+                            molecule.atom[site_index].na,
+                            atom_site.x,
+                            atom_site.y,
+                            atom_site.z,
+                            molecule.atom[site_index].chg,
+                            molecule.atom[site_index].eps,
+                            molecule.atom[site_index].sig,
+                        )
+                    )
+
+                if molecule.signature() != new_molecule.signature():
+                    _message = f"Skipping sites because the molecule signature does not match the reference molecule. Expected {molecule.signature()} but got {new_molecule.signature()}"
+                    warnings.warn(_message)
+                    logger.warning(_message)
+                    continue
+
+                if ref_molecule.minimum_distance(new_molecule) >= min_distance:
+                    continue
+
+                picked_environment.extend(new_molecule.atom)
+
+        return picked_environment
+
+    @staticmethod
+    def _aggregate_results(state: StateModel, results: list[list[Atom]]) -> list[Atom]:
+        norm_factor = round(state.config.dice.nstep[-1] / state.config.dice.isave)
+
+        agg_results = []
+        for atom in chain(*[r for r in results]):
+            atom.chg = atom.chg * norm_factor
+            agg_results.append(atom)
+
+        return agg_results

diceplayer/dice/dice_input.py

@@ -0,0 +1,257 @@
+from diceplayer.config import PlayerConfig
+from diceplayer.logger import logger
+
+from pydantic import BaseModel, Field
+from typing_extensions import Self
+
+import random
+from enum import StrEnum
+from pathlib import Path
+from typing import Annotated, Any, Literal, TextIO
+
+
+_ALLOWED_DICE_KEYWORD_IN_ORDER = [
+    "title",
+    "ncores",
+    "ljname",
+    "outname",
+    "nmol",
+    "dens",
+    "temp",
+    "press",
+    "seed",
+    "init",
+    "nstep",
+    "vstep",
+    "mstop",
+    "accum",
+    "iprint",
+    "isave",
+    "irdf",
+    "upbuf",
+]
+
+
+class DiceRoutineType(StrEnum):
+    NVT_TER = "nvt.ter"
+    NVT_EQ = "nvt.eq"
+    NPT_TER = "npt.ter"
+    NPT_EQ = "npt.eq"
+
+
+def get_nstep(config, idx: int) -> int:
+    if len(config.dice.nstep) > idx:
+        return config.dice.nstep[idx]
+    return config.dice.nstep[-1]
+
+
+def get_seed(config) -> int:
+    return config.dice.seed or random.randint(0, 2**32 - 1)
+
+
+def get_ncores(config) -> int:
+    return max(1, int(config.ncores / config.dice.nprocs))
+
+
+# -----------------------------------------------------
+# NVT THERMALIZATION
+# -----------------------------------------------------
+class NVTTerConfig(BaseModel):
+    type: Literal[DiceRoutineType.NVT_TER] = DiceRoutineType.NVT_TER
+
+    title: str = "NVT Thermalization"
+    ncores: int
+    ljname: str
+    outname: str
+    nmol: list[int]
+    dens: float
+    temp: float
+    seed: int
+    init: Literal["yes"] = "yes"
+    nstep: int
+    vstep: Literal[0] = 0
+    isave: int
+    upbuf: int
+
+    @classmethod
+    def from_config(cls, config: PlayerConfig, **kwargs) -> Self:
+        return cls(
+            ncores=get_ncores(config),
+            ljname=str(config.dice.ljname),
+            outname=config.dice.outname,
+            nmol=config.dice.nmol,
+            dens=config.dice.dens,
+            temp=config.dice.temp,
+            seed=get_seed(config),
+            nstep=get_nstep(config, 0),
+            isave=config.dice.isave,
+            upbuf=config.dice.upbuf,
+            **kwargs,
+        )
+
+
+# -----------------------------------------------------
+# NVT PRODUCTION
+# -----------------------------------------------------
+class NVTEqConfig(BaseModel):
+    type: Literal[DiceRoutineType.NVT_EQ] = DiceRoutineType.NVT_EQ
+
+    title: str = "NVT Production"
+    ncores: int
+    ljname: str
+    outname: str
+    nmol: list[int]
+    dens: float
+    temp: float
+    seed: int
+    init: Literal["no", "yesreadxyz"] = "no"
+    nstep: int
+    vstep: int
+    isave: int
+    irdf: Literal[0] = 0
+    upbuf: int
+
+    @classmethod
+    def from_config(cls, config: PlayerConfig, **kwargs) -> Self:
+        return cls(
+            ncores=get_ncores(config),
+            ljname=str(config.dice.ljname),
+            outname=config.dice.outname,
+            nmol=config.dice.nmol,
+            dens=config.dice.dens,
+            temp=config.dice.temp,
+            seed=get_seed(config),
+            nstep=get_nstep(config, 1),
+            vstep=config.dice.vstep,
+            isave=max(1, get_nstep(config, 1) // 10),
+            upbuf=config.dice.upbuf,
+            **kwargs,
+        )
+
+
+# -----------------------------------------------------
+# NPT THERMALIZATION
+# -----------------------------------------------------
+class NPTTerConfig(BaseModel):
+    type: Literal[DiceRoutineType.NPT_TER] = DiceRoutineType.NPT_TER
+
+    title: str = "NPT Thermalization"
+    ncores: int
+    ljname: str
+    outname: str
+    nmol: list[int]
+    dens: float
+    temp: float
+    press: float
+    seed: int
+    init: Literal["yes", "yesreadxyz"] = "yes"
+    nstep: int
+    vstep: int
+    isave: int
+    upbuf: int
+
+    @classmethod
+    def from_config(cls, config: PlayerConfig, **kwargs) -> Self:
+        return cls(
+            ncores=get_ncores(config),
+            ljname=str(config.dice.ljname),
+            outname=config.dice.outname,
+            nmol=config.dice.nmol,
+            dens=config.dice.dens,
+            temp=config.dice.temp,
+            press=config.dice.press,
+            seed=get_seed(config),
+            nstep=get_nstep(config, 1),
+            vstep=max(1, config.dice.vstep),
+            isave=config.dice.isave,
+            upbuf=config.dice.upbuf,
+            **kwargs,
+        )
+
+
+# -----------------------------------------------------
+# NPT PRODUCTION
+# -----------------------------------------------------
+class NPTEqConfig(BaseModel):
+    type: Literal[DiceRoutineType.NPT_EQ] = DiceRoutineType.NPT_EQ
+
+    title: str = "NPT Production"
+    ncores: int
+    ljname: str
+    outname: str
+    nmol: list[int]
+    dens: float
+    temp: float
+    press: float
+    seed: int
+    init: Literal["yes", "yesreadxyz"] = "yes"
+    nstep: int
+    vstep: int
+    isave: int
+    irdf: Literal[0] = 0
+    upbuf: int
+
+    @classmethod
+    def from_config(cls, config: PlayerConfig, **kwargs) -> Self:
+        return cls(
+            ncores=get_ncores(config),
+            ljname=str(config.dice.ljname),
+            outname=config.dice.outname,
+            nmol=config.dice.nmol,
+            dens=config.dice.dens,
+            temp=config.dice.temp,
+            press=config.dice.press,
+            seed=get_seed(config),
+            nstep=get_nstep(config, 2),
+            vstep=config.dice.vstep,
+            isave=max(1, get_nstep(config, 2) // 10),
+            upbuf=config.dice.upbuf,
+            **kwargs,
+        )
+
+
+DiceInputConfig = Annotated[
+    NVTTerConfig | NVTEqConfig | NPTTerConfig | NPTEqConfig,
+    Field(discriminator="type"),
+]
+
+
+def _serialize_value(value: Any) -> str:
+    if value is None:
+        raise ValueError("DICE configuration cannot serialize None values")
+
+    if isinstance(value, bool):
+        return "yes" if value else "no"
+
+    if isinstance(value, (list, tuple)):
+        return " ".join(str(v) for v in value)
+
+    return str(value)
+
+
+def write_dice_config(obj: DiceInputConfig, io_writer: TextIO) -> None:
+    values = {f: getattr(obj, f) for f in obj.__class__.model_fields}
+
+    for key in _ALLOWED_DICE_KEYWORD_IN_ORDER:
+        value = values.pop(key, None)
+        if value is None:
+            continue
+        io_writer.write(f"{key} = {_serialize_value(value)}\n")
+
+    io_writer.write("$end\n")
+
+
+def write_config(config: DiceInputConfig, directory: Path) -> Path:
+    input_path = directory / config.type
+
+    if input_path.exists():
+        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)
+
+    with open(input_path, "w") as io:
+        write_dice_config(config, io)
+
+    return input_path

diceplayer/dice/dice_wrapper.py

@@ -0,0 +1,103 @@
+import diceplayer.dice.dice_input as dice_input
+from diceplayer.config import DiceConfig
+
+from pydantic import TypeAdapter
+from pydantic.dataclasses import dataclass
+
+import subprocess
+from itertools import islice
+from pathlib import Path
+from typing import Final, List, Self
+
+
+@dataclass(slots=True, frozen=True)
+class DiceEnvironmentItem:
+    atom: str
+    x: float
+    y: float
+    z: float
+
+
+DiceEnvironmentItemAdapter = TypeAdapter(DiceEnvironmentItem)
+
+
+@dataclass(slots=True)
+class DiceEnvironment:
+    number_of_sites: int
+    thickness: List[float]
+    items: List[DiceEnvironmentItem]
+
+    @classmethod
+    def new(cls, thickness: List[float]) -> Self:
+        return cls(number_of_sites=0, thickness=thickness, items=[])
+
+    def add_site(self, site: DiceEnvironmentItem):
+        self.items.append(site)
+        self.number_of_sites += 1
+
+
+DICE_FLAG_LINE: Final[int] = -2
+DICE_END_FLAG: Final[str] = "End of simulation"
+
+
+class DiceWrapper:
+    def __init__(self, dice_config: DiceConfig, working_directory: Path):
+        self.dice_config = dice_config
+        self.working_directory = working_directory
+
+    def run(self, dice_config: dice_input.DiceInputConfig) -> None:
+        input_path = dice_input.write_config(dice_config, self.working_directory)
+        output_path = input_path.parent / (input_path.name + ".out")
+
+        with open(output_path, "w") as outfile, open(input_path, "r") as infile:
+            exit_status = subprocess.call(
+                self.dice_config.progname,
+                stdin=infile,
+                stdout=outfile,
+                cwd=self.working_directory,
+            )
+
+        if exit_status != 0:
+            raise RuntimeError(f"Dice simulation failed with exit status {exit_status}")
+
+        with open(output_path, "r") as outfile:
+            line = outfile.readlines()[DICE_FLAG_LINE]
+            if line.strip() == DICE_END_FLAG:
+                return
+
+        raise RuntimeError(f"Dice simulation failed with exit status {exit_status}")
+
+    def parse_results(self) -> list[DiceEnvironment]:
+        results = []
+
+        positions_file = self.working_directory / "phb.xyz"
+        if not positions_file.exists():
+            raise RuntimeError(f"Positions file not found at {self.working_directory}")
+
+        with open(positions_file, "r") as f:
+            while True:
+                line = f.readline()
+                if not line.startswith("    "):
+                    break
+
+                environment = DiceEnvironment(
+                    number_of_sites=int(line.strip()),
+                    thickness=[float(n) for n in f.readline().split()[-3:]],
+                    items=[],
+                )
+
+                # Skip the comment line
+
+                environment.items.extend(
+                    [
+                        DiceEnvironmentItemAdapter.validate_python(
+                            {"atom": site[0], "x": site[1], "y": site[2], "z": site[3]}
+                        )
+                        for atom in islice(f, environment.number_of_sites)
+                        if (site := atom.strip().split()) and len(site) == 4
+                    ]
+                )
+
+                results.append(environment)
+
+        return results

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

@@ -1,20 +1,19 @@
 from __future__ import annotations
 
-from diceplayer import logger
 from diceplayer.environment import Atom
-from diceplayer.utils.cache import invalidate_computed_properties
+from diceplayer.logger import logger
 from diceplayer.utils.misc import BOHR2ANG, EA_2_DEBYE
 from diceplayer.utils.ptable import GHOST_NUMBER
 
 import numpy as np
-import numpy.typing as npt
 import numpy.linalg as linalg
+import numpy.typing as npt
+from pydantic.dataclasses import dataclass
 from typing_extensions import List, Self, Tuple
 
 import math
 from copy import deepcopy
-from dataclasses import dataclass, field
+from dataclasses import field
-from functools import cached_property
 
 
 @dataclass
@@ -33,11 +32,11 @@ class Molecule:
     molname: str
     atom: List[Atom] = field(default_factory=list)
 
-    @cached_property
+    @property
     def total_mass(self) -> float:
         return sum(atom.mass for atom in self.atom)
 
-    @cached_property
+    @property
     def com(self) -> npt.NDArray[np.float64]:
         com = np.zeros(3)
 
@@ -48,7 +47,7 @@ class Molecule:
 
         return com
 
-    @cached_property
+    @property
     def inertia_tensor(self) -> npt.NDArray[np.float64]:
         """
         Calculates the inertia tensor of the molecule.
@@ -78,7 +77,6 @@ class Molecule:
 
         return inertia_tensor
 
-    @invalidate_computed_properties()
     def add_atom(self, a: Atom) -> None:
         """
         Adds Atom instance to the molecule.
@@ -89,7 +87,6 @@ class Molecule:
 
         self.atom.append(a)
 
-    @invalidate_computed_properties()
     def remove_atom(self, a: Atom) -> None:
         """
         Removes Atom instance from the molecule.
@@ -100,7 +97,6 @@ class Molecule:
 
         self.atom.remove(a)
 
-    @invalidate_computed_properties()
     def move_center_of_mass_to_origin(self) -> None:
         """
         Updated positions based on the center of mass of the molecule
@@ -110,7 +106,6 @@ class Molecule:
             atom.ry -= self.com[1]
             atom.rz -= self.com[2]
 
-    @invalidate_computed_properties()
     def rotate_to_standard_orientation(self) -> None:
         """
         Rotates the molecule to the standard orientation
@@ -314,3 +309,12 @@ class Molecule:
         diff = coords_a[:, None, :] - coords_b[None, :, :]
         d2 = np.sum(diff**2, axis=-1)
         return np.sqrt(d2.min())
+
+    def signature(self) -> List[int]:
+        """
+        Returns the signature of the molecule, which is a list of the number of atoms of each type in the molecule.
+
+        Returns:
+            List[int]: signature of the molecule
+        """
+        return [a.lbl for a in self.atom]

diceplayer/interface/__init__.py

@@ -1,6 +0,0 @@
-from .__interface import Interface
-from .dice_interface import DiceInterface
-from .gaussian_interface import GaussianInterface
-
-
-__all__ = ["Interface", "DiceInterface", "GaussianInterface"]

diceplayer/interface/__interface.py

@@ -1,26 +0,0 @@
-from __future__ import annotations
-
-from diceplayer.config.player_config import PlayerConfig
-from diceplayer.environment.system import System
-
-from abc import ABC, abstractmethod
-
-
-class Interface(ABC):
-    __slots__ = ["step", "system"]
-
-    def __init__(self):
-        self.system: System | None = None
-        self.step: PlayerConfig | None = None
-
-    @abstractmethod
-    def configure(self, step: PlayerConfig, system: System):
-        pass
-
-    @abstractmethod
-    def start(self, cycle: int):
-        pass
-
-    @abstractmethod
-    def reset(self):
-        pass

diceplayer/interface/dice_interface.py

@@ -1,389 +0,0 @@
-from __future__ import annotations
-
-from diceplayer import logger
-from diceplayer.config.player_config import PlayerConfig
-from diceplayer.environment.system import System
-from diceplayer.interface import Interface
-
-from setproctitle import setproctitle
-from typing_extensions import Final, TextIO
-
-import os
-import random
-import shutil
-import subprocess
-import sys
-import time
-from multiprocessing import Process, connection
-from pathlib import Path
-
-
-DICE_END_FLAG: Final[str] = "End of simulation"
-DICE_FLAG_LINE: Final[int] = -2
-UMAANG3_TO_GCM3: Final[float] = 1.6605
-
-MAX_SEED: Final[int] = 4294967295
-
-
-class DiceInterface(Interface):
-    title = "Diceplayer run"
-
-    def configure(self, step: PlayerConfig, system: System):
-        self.step = step
-        self.system = system
-
-    def start(self, cycle: int):
-        procs = []
-        sentinels = []
-
-        for proc in range(1, self.step.nprocs + 1):
-            p = Process(target=self._simulation_process, args=(cycle, proc))
-            p.start()
-
-            procs.append(p)
-            sentinels.append(p.sentinel)
-
-        while procs:
-            finished = connection.wait(sentinels)
-            for proc_sentinel in finished:
-                i = sentinels.index(proc_sentinel)
-                status = procs[i].exitcode
-                procs.pop(i)
-                sentinels.pop(i)
-                if status != 0:
-                    for p in procs:
-                        p.terminate()
-                    sys.exit(status)
-
-        logger.info("\n")
-
-    def reset(self):
-        del self.step
-        del self.system
-
-    def _simulation_process(self, cycle: int, proc: int):
-        setproctitle(f"diceplayer-step{cycle:0d}-p{proc:0d}")
-
-        try:
-            self._make_proc_dir(cycle, proc)
-            self._make_dice_inputs(cycle, proc)
-            self._run_dice(cycle, proc)
-        except Exception as err:
-            sys.exit(err)
-
-    def _make_proc_dir(self, cycle, proc):
-        simulation_dir = Path(self.step.simulation_dir)
-        if not simulation_dir.exists():
-            simulation_dir.mkdir(parents=True)
-
-        proc_dir = Path(simulation_dir, f"step{cycle:02d}", f"p{proc:02d}")
-        proc_dir.mkdir(parents=True, exist_ok=True)
-
-    def _make_dice_inputs(self, cycle, proc):
-        proc_dir = Path(self.step.simulation_dir, f"step{cycle:02d}", f"p{proc:02d}")
-
-        self._make_potentials(proc_dir)
-
-        random.seed(self._make_dice_seed())
-
-        # This is logic is used to make the initial configuration file
-        # for the next cycle using the last.xyz file from the previous cycle.
-        if self.step.dice.randominit == "first" and cycle > 1:
-            last_xyz = Path(
-                self.step.simulation_dir,
-                f"step{(cycle - 1):02d}",
-                f"p{proc:02d}",
-                "last.xyz",
-            )
-            if not last_xyz.exists():
-                raise FileNotFoundError(f"File {last_xyz} not found.")
-
-            with open(last_xyz, "r") as last_xyz_file:
-                self._make_init_file(proc_dir, last_xyz_file)
-                last_xyz_file.seek(0)
-                self.step.dice.dens = self._new_density(last_xyz_file)
-
-        else:
-            self._make_nvt_ter(cycle, proc_dir)
-
-        if len(self.step.dice.nstep) == 2:
-            self._make_nvt_eq(cycle, proc_dir)
-
-        elif len(self.step.dice.nstep) == 3:
-            self._make_npt_ter(cycle, proc_dir)
-            self._make_npt_eq(proc_dir)
-
-    def _run_dice(self, cycle: int, proc: int):
-        working_dir = os.getcwd()
-
-        proc_dir = Path(self.step.simulation_dir, f"step{cycle:02d}", f"p{proc:02d}")
-
-        logger.info(
-            f"Simulation process {str(proc_dir)} initiated with pid {os.getpid()}"
-        )
-
-        os.chdir(proc_dir)
-
-        if not (self.step.dice.randominit == "first" and cycle > 1):
-            self.run_dice_file(cycle, proc, "NVT.ter")
-
-        if len(self.step.dice.nstep) == 2:
-            self.run_dice_file(cycle, proc, "NVT.eq")
-
-        elif len(self.step.dice.nstep) == 3:
-            self.run_dice_file(cycle, proc, "NPT.ter")
-            self.run_dice_file(cycle, proc, "NPT.eq")
-
-        os.chdir(working_dir)
-
-        xyz_file = Path(proc_dir, "phb.xyz")
-        last_xyz_file = Path(proc_dir, "last.xyz")
-
-        if xyz_file.exists():
-            shutil.copy(xyz_file, last_xyz_file)
-        else:
-            raise FileNotFoundError(f"File {xyz_file} not found.")
-
-    @staticmethod
-    def _make_dice_seed() -> int:
-        num = time.time()
-        num = (num - int(num)) * 1e6
-
-        num = int((num - int(num)) * 1e6)
-
-        return (os.getpid() * num) % (MAX_SEED + 1)
-
-    def _make_init_file(self, proc_dir: Path, last_xyz_file: TextIO):
-        xyz_lines = last_xyz_file.readlines()
-
-        SECONDARY_MOLECULE_LENGTH = 0
-        for i in range(1, len(self.step.dice.nmol)):
-            SECONDARY_MOLECULE_LENGTH += self.step.dice.nmol[i] * len(
-                self.system.molecule[i].atom
-            )
-
-        xyz_lines = xyz_lines[-SECONDARY_MOLECULE_LENGTH:]
-
-        input_file = Path(proc_dir, self.step.dice.outname + ".xy")
-        with open(input_file, "w") as f:
-            for atom in self.system.molecule[0].atom:
-                f.write(f"{atom.rx:>10.6f}  {atom.ry:>10.6f}  {atom.rz:>10.6f}\n")
-
-            for line in xyz_lines:
-                atom = line.split()
-                rx = float(atom[1])
-                ry = float(atom[2])
-                rz = float(atom[3])
-                f.write(f"{rx:>10.6f}  {ry:>10.6f}  {rz:>10.6f}\n")
-
-            f.write("$end")
-
-    def _new_density(self, last_xyz_file: TextIO):
-        last_xyz_lines = last_xyz_file.readlines()
-
-        box = last_xyz_lines[1].split()
-        volume = float(box[-3]) * float(box[-2]) * float(box[-1])
-
-        total_mass = 0
-        for i in range(len(self.system.molecule)):
-            total_mass += self.system.molecule[i].total_mass * self.step.dice.nmol[i]
-
-        density = (total_mass / volume) * UMAANG3_TO_GCM3
-
-        return density
-
-    def _make_nvt_ter(self, cycle, proc_dir):
-        file = Path(proc_dir, "NVT.ter")
-        with open(file, "w") as f:
-            f.write(f"title = {self.title} - NVT Thermalization\n")
-            f.write(f"ncores = {self.step.ncores}\n")
-            f.write(f"ljname = {self.step.dice.ljname}\n")
-            f.write(f"outname = {self.step.dice.outname}\n")
-
-            mol_string = " ".join(str(x) for x in self.step.dice.nmol)
-            f.write(f"nmol = {mol_string}\n")
-
-            f.write(f"dens = {self.step.dice.dens}\n")
-            f.write(f"temp = {self.step.dice.temp}\n")
-
-            if self.step.dice.randominit == "first" and cycle > 1:
-                f.write("init = yesreadxyz\n")
-                f.write(f"nstep = {self.step.altsteps}\n")
-            else:
-                f.write("init = yes\n")
-                f.write(f"nstep = {self.step.dice.nstep[0]}\n")
-
-            f.write("vstep = 0\n")
-            f.write("mstop = 1\n")
-            f.write("accum = no\n")
-            f.write("iprint = 1\n")
-            f.write("isave = 0\n")
-            f.write("irdf = 0\n")
-
-            seed = int(1e6 * random.random())
-            f.write(f"seed = {seed}\n")
-            f.write(f"upbuf = {self.step.dice.upbuf}")
-
-    def _make_nvt_eq(self, cycle, proc_dir):
-        file = Path(proc_dir, "NVT.eq")
-        with open(file, "w") as f:
-            f.write(f"title = {self.title} - NVT Production\n")
-            f.write(f"ncores = {self.step.ncores}\n")
-            f.write(f"ljname = {self.step.dice.ljname}\n")
-            f.write(f"outname = {self.step.dice.outname}\n")
-
-            mol_string = " ".join(str(x) for x in self.step.dice.nmol)
-            f.write(f"nmol = {mol_string}\n")
-
-            f.write(f"dens = {self.step.dice.dens}\n")
-            f.write(f"temp = {self.step.dice.temp}\n")
-
-            if self.step.dice.randominit == "first" and cycle > 1:
-                f.write("init = yesreadxyz\n")
-            else:
-                f.write("init = no\n")
-
-            f.write(f"nstep = {self.step.dice.nstep[1]}\n")
-
-            f.write("vstep = 0\n")
-            f.write("mstop = 1\n")
-            f.write("accum = no\n")
-            f.write("iprint = 1\n")
-
-            f.write(f"isave = {self.step.dice.isave}\n")
-            f.write(f"irdf = {10 * self.step.nprocs}\n")
-
-            seed = int(1e6 * random.random())
-            f.write("seed = {}\n".format(seed))
-
-    def _make_npt_ter(self, cycle, proc_dir):
-        file = Path(proc_dir, "NPT.ter")
-        with open(file, "w") as f:
-            f.write(f"title = {self.title} - NPT Thermalization\n")
-            f.write(f"ncores = {self.step.ncores}\n")
-            f.write(f"ljname = {self.step.dice.ljname}\n")
-            f.write(f"outname = {self.step.dice.outname}\n")
-
-            mol_string = " ".join(str(x) for x in self.step.dice.nmol)
-            f.write(f"nmol = {mol_string}\n")
-
-            f.write(f"press = {self.step.dice.press}\n")
-            f.write(f"temp = {self.step.dice.temp}\n")
-
-            if self.step.dice.randominit == "first" and cycle > 1:
-                f.write("init = yesreadxyz\n")
-                f.write(f"dens = {self.step.dice.dens:<8.4f}\n")
-                f.write(f"vstep = {int(self.step.altsteps / 5)}\n")
-            else:
-                f.write("init = no\n")
-                f.write(f"vstep = {int(self.step.dice.nstep[1] / 5)}\n")
-
-            f.write("nstep = 5\n")
-            f.write("mstop = 1\n")
-            f.write("accum = no\n")
-            f.write("iprint = 1\n")
-            f.write("isave = 0\n")
-            f.write("irdf = 0\n")
-
-            seed = int(1e6 * random.random())
-            f.write(f"seed = {seed}\n")
-
-    def _make_npt_eq(self, proc_dir):
-        file = Path(proc_dir, "NPT.eq")
-        with open(file, "w") as f:
-            f.write(f"title = {self.title} - NPT Production\n")
-            f.write(f"ncores = {self.step.ncores}\n")
-            f.write(f"ljname = {self.step.dice.ljname}\n")
-            f.write(f"outname = {self.step.dice.outname}\n")
-
-            mol_string = " ".join(str(x) for x in self.step.dice.nmol)
-            f.write(f"nmol = {mol_string}\n")
-
-            f.write(f"press = {self.step.dice.press}\n")
-            f.write(f"temp = {self.step.dice.temp}\n")
-
-            f.write("nstep = 5\n")
-
-            f.write(f"vstep = {int(self.step.dice.nstep[2] / 5)}\n")
-            f.write("init = no\n")
-            f.write("mstop = 1\n")
-            f.write("accum = no\n")
-            f.write("iprint = 1\n")
-            f.write(f"isave = {self.step.dice.isave}\n")
-            f.write(f"irdf = {10 * self.step.nprocs}\n")
-
-            seed = int(1e6 * random.random())
-            f.write(f"seed = {seed}\n")
-
-    def _make_potentials(self, proc_dir):
-        fstr = "{:<3d} {:>3d}  {:>10.5f} {:>10.5f} {:>10.5f}  {:>10.6f} {:>9.5f} {:>7.4f}\n"
-
-        file = Path(proc_dir, self.step.dice.ljname)
-        with open(file, "w") as f:
-            f.write(f"{self.step.dice.combrule}\n")
-            f.write(f"{len(self.step.dice.nmol)}\n")
-
-            nsites_qm = len(self.system.molecule[0].atom)
-            f.write(f"{nsites_qm} {self.system.molecule[0].molname}\n")
-
-            for atom in self.system.molecule[0].atom:
-                f.write(
-                    fstr.format(
-                        atom.lbl,
-                        atom.na,
-                        atom.rx,
-                        atom.ry,
-                        atom.rz,
-                        atom.chg,
-                        atom.eps,
-                        atom.sig,
-                    )
-                )
-
-            for mol in self.system.molecule[1:]:
-                f.write(f"{len(mol.atom)} {mol.molname}\n")
-                for atom in mol.atom:
-                    f.write(
-                        fstr.format(
-                            atom.lbl,
-                            atom.na,
-                            atom.rx,
-                            atom.ry,
-                            atom.rz,
-                            atom.chg,
-                            atom.eps,
-                            atom.sig,
-                        )
-                    )
-
-    def run_dice_file(self, cycle: int, proc: int, file_name: str):
-        with (
-            open(Path(file_name), "r") as infile,
-            open(Path(file_name + ".out"), "w") as outfile,
-        ):
-            if shutil.which("bash") is not None:
-                exit_status = subprocess.call(
-                    [
-                        "bash",
-                        "-c",
-                        f"exec -a dice-step{cycle}-p{proc} {self.step.dice.progname} < {infile.name} > {outfile.name}",
-                    ]
-                )
-            else:
-                exit_status = subprocess.call(
-                    self.step.dice.progname, stdin=infile, stdout=outfile
-                )
-
-        if exit_status != 0:
-            raise RuntimeError(
-                f"Dice process step{cycle:02d}-p{proc:02d} did not exit properly"
-            )
-
-        with open(Path(file_name + ".out"), "r") as outfile:
-            flag = outfile.readlines()[DICE_FLAG_LINE].strip()
-            if flag != DICE_END_FLAG:
-                raise RuntimeError(
-                    f"Dice process step{cycle:02d}-p{proc:02d} did not exit properly"
-                )
-
-        logger.info(f"Dice {file_name} - step{cycle:02d}-p{proc:02d} exited properly")

diceplayer/interface/gaussian_interface.py

@@ -1,359 +0,0 @@
-from __future__ import annotations
-
-from diceplayer import logger
-from diceplayer.config.player_config import PlayerConfig
-from diceplayer.environment import Atom
-from diceplayer.environment.molecule import Molecule
-from diceplayer.environment.system import System
-from diceplayer.interface import Interface
-from diceplayer.utils.misc import date_time
-from diceplayer.utils.ptable import PTable
-
-import numpy as np
-import numpy.typing as npt
-from typing_extensions import Any, Dict, List, Tuple
-
-import os
-import shutil
-import subprocess
-import textwrap
-from pathlib import Path
-
-
-class GaussianInterface(Interface):
-    def configure(self, step_dto: PlayerConfig, system: System):
-        self.system = system
-        self.step = step_dto
-
-    def start(self, cycle: int) -> Dict[str, NDArray]:
-        self._make_qm_dir(cycle)
-
-        if cycle > 1:
-            self._copy_chk_file_from_previous_step(cycle)
-
-        asec_charges = self.populate_asec_vdw(cycle)
-        self._make_gaussian_input_file(cycle, asec_charges)
-
-        self._run_gaussian(cycle)
-        self._run_formchk(cycle)
-
-        return_value = {}
-        if self.step.opt:
-            # return_value['position'] = np.array(
-            #     self._run_optimization(cycle)
-            # )
-            raise NotImplementedError("Optimization not implemented yet.")
-
-        else:
-            return_value["charges"] = np.array(self._read_charges_from_fchk(cycle))
-
-        return return_value
-
-    def reset(self):
-        del self.step
-        del self.system
-
-    def _make_qm_dir(self, cycle: int):
-        qm_dir_path = Path(self.step.simulation_dir, f"step{cycle:02d}", "qm")
-        if not qm_dir_path.exists():
-            qm_dir_path.mkdir()
-
-    def _copy_chk_file_from_previous_step(self, cycle: int):
-        current_chk_file_path = Path(
-            self.step.simulation_dir, f"step{cycle:02d}", "qm", "asec.chk"
-        )
-        if current_chk_file_path.exists():
-            raise FileExistsError(f"File {current_chk_file_path} already exists.")
-
-        previous_chk_file_path = Path(
-            self.step.simulation_dir, f"step{(cycle - 1):02d}", "qm", "asec.chk"
-        )
-        if not previous_chk_file_path.exists():
-            raise FileNotFoundError(f"File {previous_chk_file_path} does not exist.")
-
-        shutil.copy(previous_chk_file_path, current_chk_file_path)
-
-    def populate_asec_vdw(self, cycle: int) -> list[dict]:
-        norm_factor = self._calculate_norm_factor()
-
-        nsitesref = len(self.system.molecule[0].atom)
-
-        nsites_total = self._calculate_total_number_of_sites(nsitesref)
-
-        proc_charges = []
-        for proc in range(1, self.step.nprocs + 1):
-            proc_charges.append(self._read_charges_from_last_step(cycle, proc))
-
-        asec_charges, thickness, picked_mols = self._evaluate_proc_charges(
-            nsites_total, proc_charges
-        )
-
-        logger.info(
-            f"In average, {(sum(picked_mols) / norm_factor):^7.2f} molecules\n"
-            f"were selected from each of the {len(picked_mols)} configurations\n"
-            f"of the production simulations to form the ASEC, comprising a shell with\n"
-            f"minimum thickness of {(sum(thickness) / norm_factor):>6.2f} Angstrom\n"
-        )
-
-        for charge in asec_charges:
-            charge["chg"] = charge["chg"] / norm_factor
-
-        return asec_charges
-
-    def _calculate_norm_factor(self) -> int:
-        if self.step.dice.nstep[-1] % self.step.dice.isave == 0:
-            nconfigs = round(self.step.dice.nstep[-1] / self.step.dice.isave)
-        else:
-            nconfigs = int(self.step.dice.nstep[-1] / self.step.dice.isave)
-
-        return nconfigs * self.step.nprocs
-
-    def _calculate_total_number_of_sites(self, nsitesref) -> int:
-        nsites_total = self.step.dice.nmol[0] * nsitesref
-        for i in range(1, len(self.step.dice.nmol)):
-            nsites_total += self.step.dice.nmol[i] * len(self.system.molecule[i].atom)
-
-        return nsites_total
-
-    def _read_charges_from_last_step(self, cycle: int, proc: int) -> list[str]:
-        last_xyz_file_path = Path(
-            self.step.simulation_dir, f"step{cycle:02d}", f"p{proc:02d}", "last.xyz"
-        )
-        if not last_xyz_file_path.exists():
-            raise FileNotFoundError(f"File {last_xyz_file_path} does not exist.")
-
-        with open(last_xyz_file_path, "r") as last_xyz_file:
-            lines = last_xyz_file.readlines()
-
-        return lines
-
-    def _evaluate_proc_charges(
-        self, total_nsites: int, proc_charges: list[list[str]]
-    ) -> Tuple[List[Dict[str, float | Any]], List[float], List[int]]:
-        asec_charges = []
-
-        thickness = []
-        picked_mols = []
-
-        for charges in proc_charges:
-            charges_nsites = int(charges.pop(0))
-            if int(charges_nsites) != total_nsites:
-                raise ValueError(
-                    "Number of sites does not match total number of sites."
-                )
-
-            thickness.append(self._calculate_proc_thickness(charges))
-            nsites_ref_mol = len(self.system.molecule[0].atom)
-            charges = charges[nsites_ref_mol:]
-
-            mol_count = 0
-            for type in range(len(self.step.dice.nmol)):
-                if type == 0:
-                    # Reference Molecule must be ignored from type 0
-                    nmols = self.step.dice.nmol[type] - 1
-                else:
-                    nmols = self.step.dice.nmol[type]
-
-                for mol in range(nmols):
-                    new_molecule = Molecule("ASEC TMP MOLECULE")
-                    for site in range(len(self.system.molecule[type].atom)):
-                        line = charges.pop(0).split()
-
-                        if (
-                            line[0].title()
-                            != PTable.get_atomic_symbol(
-                                self.system.molecule[type].atom[site].na
-                            ).strip()
-                        ):
-                            raise SyntaxError(
-                                "Error: Invalid Dice Output. Atom type does not match."
-                            )
-
-                        new_molecule.add_atom(
-                            Atom(
-                                self.system.molecule[type].atom[site].lbl,
-                                self.system.molecule[type].atom[site].na,
-                                float(line[1]),
-                                float(line[2]),
-                                float(line[3]),
-                                self.system.molecule[type].atom[site].chg,
-                                self.system.molecule[type].atom[site].eps,
-                                self.system.molecule[type].atom[site].sig,
-                            )
-                        )
-
-                    distance = self.system.molecule[0].minimum_distance(new_molecule)
-
-                    if distance < thickness[-1]:
-                        for atom in new_molecule.atom:
-                            asec_charges.append(
-                                {
-                                    "lbl": PTable.get_atomic_symbol(atom.na),
-                                    "rx": atom.rx,
-                                    "ry": atom.ry,
-                                    "rz": atom.rz,
-                                    "chg": atom.chg,
-                                }
-                            )
-                        mol_count += 1
-
-            picked_mols.append(mol_count)
-
-        return asec_charges, thickness, picked_mols
-
-    def _calculate_proc_thickness(self, charges: list[str]) -> float:
-        box = charges.pop(0).split()[-3:]
-        box = [float(box[0]), float(box[1]), float(box[2])]
-        sizes = self.system.molecule[0].sizes_of_molecule()
-
-        return min(
-            [
-                (box[0] - sizes[0]) / 2,
-                (box[1] - sizes[1]) / 2,
-                (box[2] - sizes[2]) / 2,
-            ]
-        )
-
-    def _make_gaussian_input_file(self, cycle: int, asec_charges: list[dict]) -> None:
-        gaussian_input_file_path = Path(
-            self.step.simulation_dir, f"step{cycle:02d}", "qm", "asec.gjf"
-        )
-
-        with open(gaussian_input_file_path, "w") as gaussian_input_file:
-            gaussian_input_file.writelines(
-                self._generate_gaussian_input(cycle, asec_charges)
-            )
-
-    def _generate_gaussian_input(
-        self, cycle: int, asec_charges: list[dict]
-    ) -> list[str]:
-        gaussian_input = ["%Chk=asec.chk\n"]
-
-        if self.step.mem is not None:
-            gaussian_input.append(f"%Mem={self.step.mem}GB\n")
-
-        gaussian_input.append(f"%Nprocs={self.step.nprocs * self.step.ncores}\n")
-
-        kwords_line = f"#P {self.step.gaussian.level}"
-
-        if self.step.gaussian.keywords:
-            kwords_line += " " + self.step.gaussian.keywords
-
-        if self.step.opt == "yes":
-            kwords_line += " Force"
-
-        kwords_line += " NoSymm"
-        kwords_line += f" Pop={self.step.gaussian.pop} Density=Current"
-
-        if cycle > 1:
-            kwords_line += " Guess=Read"
-
-        gaussian_input.append(textwrap.fill(kwords_line, 90))
-        gaussian_input.append("\n")
-
-        gaussian_input.append("\nForce calculation - Cycle number {}\n".format(cycle))
-        gaussian_input.append("\n")
-        gaussian_input.append(
-            f"{self.step.gaussian.chgmult[0]},{self.step.gaussian.chgmult[1]}\n"
-        )
-
-        for atom in self.system.molecule[0].atom:
-            symbol = PTable.get_atomic_symbol(atom.na)
-            gaussian_input.append(
-                "{:<2s}    {:>10.5f}   {:>10.5f}   {:>10.5f}\n".format(
-                    symbol, atom.rx, atom.ry, atom.rz
-                )
-            )
-
-        gaussian_input.append("\n")
-
-        for charge in asec_charges:
-            gaussian_input.append(
-                "{:>10.5f}   {:>10.5f}   {:>10.5f}     {:>11.8f}\n".format(
-                    charge["rx"], charge["ry"], charge["rz"], charge["chg"]
-                )
-            )
-
-        gaussian_input.append("\n")
-
-        return gaussian_input
-
-    def _run_gaussian(self, cycle: int) -> None:
-        qm_dir = Path(self.step.simulation_dir, f"step{(cycle):02d}", "qm")
-
-        working_dir = os.getcwd()
-        os.chdir(qm_dir)
-
-        infile = "asec.gjf"
-
-        operation = None
-        if self.step.opt:
-            operation = "forces"
-        else:
-            operation = "charges"
-
-        logger.info(
-            f"Calculation of {operation} initiated with Gaussian on {date_time()}\n"
-        )
-
-        if shutil.which("bash") is not None:
-            exit_status = subprocess.call(
-                [
-                    "bash",
-                    "-c",
-                    "exec -a {}-step{} {} {}".format(
-                        self.step.gaussian.qmprog,
-                        cycle,
-                        self.step.gaussian.qmprog,
-                        infile,
-                    ),
-                ]
-            )
-        else:
-            exit_status = subprocess.call([self.step.gaussian.qmprog, infile])
-
-        if exit_status != 0:
-            raise SystemError("Gaussian process did not exit properly")
-
-        logger.info(f"Calculation of {operation} finished on {date_time()}")
-
-        os.chdir(working_dir)
-
-    def _run_formchk(self, cycle: int):
-        qm_dir = Path(self.step.simulation_dir, f"step{(cycle):02d}", "qm")
-
-        work_dir = os.getcwd()
-        os.chdir(qm_dir)
-
-        logger.info("Formatting the checkpoint file... \n")
-
-        exit_status = subprocess.call(
-            ["formchk", "asec.chk"], stdout=subprocess.DEVNULL
-        )
-
-        if exit_status != 0:
-            raise SystemError("Formchk process did not exit properly")
-
-        logger.info("Done\n")
-
-        os.chdir(work_dir)
-
-    def _read_charges_from_fchk(self, cycle: int):
-        fchk_file_path = Path("simfiles", f"step{cycle:02d}", "qm", "asec.fchk")
-        with open(fchk_file_path) as fchk:
-            fchkfile = fchk.readlines()
-
-        if self.step.gaussian.pop in ["chelpg", "mk"]:
-            CHARGE_FLAG = "ESP Charges"
-        else:
-            CHARGE_FLAG = "ESP Charges"
-
-        start = fchkfile.pop(0).strip()
-        while start.find(CHARGE_FLAG) != 0:  # expression in begining of line
-            start = fchkfile.pop(0).strip()
-
-        charges: List[float] = []
-        while len(charges) < len(self.system.molecule[0].atom):
-            charges.extend([float(x) for x in fchkfile.pop(0).split()])
-
-        return charges

diceplayer/logger.py

@@ -0,0 +1,4 @@
+from diceplayer.utils import RunLogger
+
+
+logger = RunLogger("diceplayer")

diceplayer/optimization/optimization_handler.py

@@ -0,0 +1,37 @@
+from diceplayer.config.player_config import RoutineType
+from diceplayer.dice.dice_wrapper import DiceEnvironmentItem
+from diceplayer.environment import Atom
+from diceplayer.logger import logger
+from diceplayer.state.state_model import StateModel
+
+from pathlib import Path
+
+
+class OptimizationHandler:
+    def __init__(self, step_directory: Path):
+        self.optimization_directory = step_directory / "optimization"
+
+    def run(
+        self,
+        state: StateModel,
+        current_cycle: int,
+        dice_environment: list[Atom],
+    ) -> StateModel:
+        routine = self._fetch_current_routine(state, current_cycle)
+        logger.info(
+            f"Running Optimization - {current_cycle} - {routine} - {self.optimization_directory}"
+        )
+
+        logger.info(dice_environment)
+
+        return state
+
+    @staticmethod
+    def _fetch_current_routine(state: StateModel, current_cycle: int) -> RoutineType:
+        if state.config.type != RoutineType.BOTH:
+            return state.config.type
+
+        if current_cycle < state.config.switch_cyc:
+            return RoutineType.CHARGE
+
+        return RoutineType.GEOMETRY

diceplayer/player.py

@@ -1,465 +1,60 @@
-from diceplayer import VERSION, logger
 from diceplayer.config.player_config import PlayerConfig
-from diceplayer.environment import Atom, Molecule, System
+from diceplayer.dice.dice_handler import DiceHandler
-from diceplayer.interface import DiceInterface, GaussianInterface
+from diceplayer.logger import logger
-from diceplayer.utils import PTable, weekday_date_time
+from diceplayer.optimization.optimization_handler import OptimizationHandler
+from diceplayer.state.state_handler import StateHandler
+from diceplayer.state.state_model import StateModel
+from diceplayer.utils.potential import read_system_from_phb
 
-import yaml
+from typing_extensions import TypedDict, Unpack
-from pydantic import BaseModel
-from typing_extensions import Tuple
-
-import os
-import pickle
-import sys
-from pathlib import Path
 
 
-ENV = ["OMP_STACKSIZE"]
+class PlayerFlags(TypedDict):
+    continuation: bool
+    force: bool
 
 
 class Player:
-    def __init__(self, infile: str = None, optimization: bool = False):
+    def __init__(self, config: PlayerConfig):
-        if infile is None and optimization is False:
+        self.config = config
-            raise ValueError("Must specify either infile or optimization")
+        self._state_handler = StateHandler(config.simulation_dir)
 
-        elif infile is not None:
+    def play(self, **flags: Unpack[PlayerFlags]):
-            self.config = self.set_config(self.read_keywords(infile))
+        continuation = flags.get("continuation", False)
+        force = flags.get("force", False)
 
-            self.system = System()
+        state = self._state_handler.get(self.config, force=force)
-
+        if not continuation and state is not None:
-            self.initial_cycle = 1
+            logger.info(
-
+                "Continuation flag is not set. Starting a new simulation and deleting any existing state."
-        elif optimization is True:
+            )
-            save = self.load_run_from_pickle()
+            self._state_handler.delete()
-
+            state = None
-            self.config = save[0]
-
-            self.system = save[1]
-
-            self.initial_cycle = save[2] + 1
 
+        if state is None:
+            system = read_system_from_phb(self.config)
+            state = StateModel(config=self.config, system=system)
         else:
-            raise ValueError("Must specify either infile or config")
+            logger.info("Resuming from existing state.")
 
-        self.dice_interface = DiceInterface()
+        while state.current_cycle < self.config.max_cyc:
-        self.gaussian_interface = GaussianInterface()
-
-    def start(self):
-        logger.info(
-            "==========================================================================================\n"
-            "Starting the iterative process.\n"
-            "==========================================================================================\n"
-        )
-
-        for cycle in range(self.initial_cycle, self.initial_cycle + self.config.maxcyc):
             logger.info(
-                f"------------------------------------------------------------------------------------------\n"
+                f"Starting cycle {state.current_cycle + 1} of {self.config.max_cyc}."
-                f"                                         Step # {cycle}\n"
-                f"------------------------------------------------------------------------------------------\n"
             )
 
-            self.dice_start(cycle)
+            step_directory = self.config.simulation_dir / f"{state.current_cycle:02d}"
+            if not step_directory.exists():
+                step_directory.mkdir(parents=True)
 
-            try:
+            dice_environment = DiceHandler(step_directory).run(
-                self.gaussian_start(cycle)
+                state, state.current_cycle
-            except StopIteration:
-                break
-
-            self.save_run_in_pickle(cycle)
-
-    def prepare_system(self):
-        for i, mol in enumerate(self.system.molecule):
-            logger.info(f"Molecule {i + 1} - {mol.molname}")
-
-            mol.print_mol_info()
-            logger.info(
-                "\n    Translating and rotating molecule to standard orientation..."
             )
 
-            mol.rotate_to_standard_orientation()
+            state = OptimizationHandler(step_directory).run(
-            logger.info("\n Done")
+                state, state.current_cycle, dice_environment
-            logger.info("\nNew values:\n")
-            mol.print_mol_info()
-
-            logger.info("\n")
-
-    def create_simulation_dir(self):
-        simulation_dir_path = Path(self.config.simulation_dir)
-        if simulation_dir_path.exists():
-            raise FileExistsError(
-                f"Error: a file or a directory {self.config.simulation_dir} already exists,"
-                f" move or delete the simfiles directory to continue."
-            )
-        simulation_dir_path.mkdir()
-
-    def create_geoms_file(self):
-        geoms_file_path = Path(self.config.geoms_file)
-        if geoms_file_path.exists():
-            raise FileExistsError(
-                f"Error: a file or a directory {self.config.geoms_file} already exists,"
-                f" move or delete the simfiles directory to continue."
-            )
-        geoms_file_path.touch()
-
-    def print_keywords(self) -> None:
-        def log_keywords(config: BaseModel):
-            for key, value in sorted(config.model_dump().items()):
-                if value is None:
-                    continue
-                if isinstance(value, list):
-                    string = " ".join(str(x) for x in value)
-                    logger.info(f"{key} = [ {string} ]")
-                else:
-                    logger.info(f"{key} = {value}")
-
-        logger.info(
-            f"##########################################################################################\n"
-            f"#############               Welcome to DICEPLAYER version {VERSION}                #############\n"
-            f"##########################################################################################\n"
-        )
-        logger.info("Your python version is {}\n".format(sys.version))
-        logger.info("Program started on {}\n".format(weekday_date_time()))
-        logger.info("Environment variables:")
-        for var in ENV:
-            logger.info(
-                "{} = {}\n".format(
-                    var, (os.environ[var] if var in os.environ else "Not set")
-                )
             )
 
-        logger.info(
+            state.current_cycle += 1
-            "------------------------------------------------------------------------------------------\n"
+            self._state_handler.save(state)
-            "                         DICE variables being used in this run:\n"
-            "------------------------------------------------------------------------------------------\n"
-        )
 
-        log_keywords(self.config.dice)
+        logger.info("Reached maximum number of cycles. Simulation complete.")
-
-        logger.info(
-            "------------------------------------------------------------------------------------------\n"
-            "                         GAUSSIAN variables being used in this run:\n"
-            "------------------------------------------------------------------------------------------\n"
-        )
-
-        log_keywords(self.config.gaussian)
-
-        logger.info("\n")
-
-    def read_potentials(self):
-        ljname_path = Path(self.config.dice.ljname)
-        if ljname_path.exists():
-            with open(self.config.dice.ljname) as file:
-                ljc_data = file.readlines()
-        else:
-            raise RuntimeError(f"Potential file {self.config.dice.ljname} not found.")
-
-        combrule = ljc_data.pop(0).split()[0]
-        if combrule not in ("*", "+"):
-            sys.exit(
-                "Error: expected a '*' or a '+' sign in 1st line of file {}".format(
-                    self.config.dice.ljname
-                )
-            )
-        self.config.dice.combrule = combrule
-
-        ntypes = ljc_data.pop(0).split()[0]
-        if not ntypes.isdigit():
-            sys.exit(
-                "Error: expected an integer in the 2nd line of file {}".format(
-                    self.config.dice.ljname
-                )
-            )
-        ntypes = int(ntypes)
-
-        if ntypes != len(self.config.dice.nmol):
-            sys.exit(
-                f"Error: number of molecule types in file {self.config.dice.ljname} "
-                f"must match that of 'nmol' keyword in config file"
-            )
-
-        for i in range(ntypes):
-            try:
-                nsites, molname = ljc_data.pop(0).split()[:2]
-            except ValueError:
-                raise ValueError(
-                    f"Error: expected nsites and molname for the molecule type {i + 1}"
-                )
-
-            if not nsites.isdigit():
-                raise ValueError(
-                    f"Error: expected nsites to be an integer for molecule type {i + 1}"
-                )
-
-            nsites = int(nsites)
-            self.system.add_type(Molecule(molname))
-
-            atom_fields = ["lbl", "na", "rx", "ry", "rz", "chg", "eps", "sig"]
-            for j in range(nsites):
-                new_atom = dict(zip(atom_fields, ljc_data.pop(0).split()))
-                self.system.molecule[i].add_atom(
-                    Atom(**self.validate_atom_dict(i, j, new_atom))
-                )
-
-    def print_potentials(self) -> None:
-        formatstr = "{:<3d} {:>3d}  {:>10.5f} {:>10.5f} {:>10.5f}  {:>10.6f} {:>9.5f} {:>7.4f} {:>9.4f}"
-        logger.info(
-            "==========================================================================================\n"
-            f"                    Potential parameters from file {self.config.dice.ljname}:\n"
-            "------------------------------------------------------------------------------------------"
-            "\n"
-        )
-
-        logger.info(f"Combination rule: {self.config.dice.combrule}")
-        logger.info(f"Types of molecules: {len(self.system.molecule)}\n")
-
-        i = 0
-        for mol in self.system.molecule:
-            i += 1
-            logger.info("{} atoms in molecule type {}:".format(len(mol.atom), i))
-            logger.info(
-                "---------------------------------------------------------------------------------"
-            )
-            logger.info(
-                "Lbl  AN       X          Y          Z         Charge    Epsilon   Sigma     Mass"
-            )
-            logger.info(
-                "---------------------------------------------------------------------------------"
-            )
-
-            for atom in mol.atom:
-                logger.info(
-                    formatstr.format(
-                        atom.lbl,
-                        atom.na,
-                        atom.rx,
-                        atom.ry,
-                        atom.rz,
-                        atom.chg,
-                        atom.eps,
-                        atom.sig,
-                        atom.mass,
-                    )
-                )
-
-            logger.info("\n")
-
-    def dice_start(self, cycle: int):
-        self.dice_interface.configure(
-            self.config,
-            self.system,
-        )
-
-        self.dice_interface.start(cycle)
-
-        self.dice_interface.reset()
-
-    def gaussian_start(self, cycle: int):
-        self.gaussian_interface.configure(
-            self.config,
-            self.system,
-        )
-
-        result = self.gaussian_interface.start(cycle)
-
-        self.gaussian_interface.reset()
-
-        if self.config.opt:
-            if "position" not in result:
-                raise RuntimeError("Optimization failed. No position found in result.")
-
-        else:
-            if "charges" not in result:
-                raise RuntimeError(
-                    "Charges optimization failed. No charges found in result."
-                )
-
-            diff = self.system.molecule[0].update_charges(result["charges"])
-
-            self.print_charges_and_dipole(cycle)
-            self.print_geoms(cycle)
-
-            if diff < self.config.gaussian.chg_tol:
-                logger.info(f"Charges converged after {cycle} cycles.")
-                raise StopIteration()
-
-    def print_charges_and_dipole(self, cycle: int) -> None:
-        """
-        Print the charges and dipole of the molecule in the Output file
-
-        Args:
-            cycle (int): Number of the cycle
-            fh (TextIO): Output file
-        """
-
-        logger.info("Cycle # {}\n".format(cycle))
-        logger.info("Number of site: {}\n".format(len(self.system.molecule[0].atom)))
-
-        chargesAndDipole = self.system.molecule[0].charges_and_dipole()
-
-        logger.info(
-            "{:>10.6f}  {:>10.6f}  {:>10.6f}  {:>10.6f}  {:>10.6f}\n".format(
-                chargesAndDipole[0],
-                chargesAndDipole[1],
-                chargesAndDipole[2],
-                chargesAndDipole[3],
-                chargesAndDipole[4],
-            )
-        )
-
-    def print_geoms(self, cycle: int):
-        with open(self.config.geoms_file, "a") as file:
-            file.write(f"Cycle # {cycle}\n")
-
-            for atom in self.system.molecule[0].atom:
-                symbol = PTable.get_atomic_symbol(atom.na)
-                file.write(
-                    f"{symbol:<2s}    {atom.rx:>10.6f}  {atom.ry:>10.6f}  {atom.rz:>10.6f}\n"
-                )
-
-            file.write("\n")
-
-    @staticmethod
-    def validate_atom_dict(molecule_type, molecule_site, atom_dict: dict) -> dict:
-        molecule_type += 1
-        molecule_site += 1
-
-        if len(atom_dict) < 8:
-            raise ValueError(
-                f"Invalid number of fields for site {molecule_site} for molecule type {molecule_type}."
-            )
-
-        try:
-            atom_dict["lbl"] = int(atom_dict["lbl"])
-        except Exception:
-            raise ValueError(
-                f"Invalid lbl fields for site {molecule_site} for molecule type {molecule_type}."
-            )
-
-        try:
-            atom_dict["na"] = int(atom_dict["na"])
-        except Exception:
-            raise ValueError(
-                f"Invalid na fields for site {molecule_site} for molecule type {molecule_type}."
-            )
-
-        try:
-            atom_dict["rx"] = float(atom_dict["rx"])
-        except Exception:
-            raise ValueError(
-                f"Invalid rx fields for site {molecule_site} for molecule type {molecule_type}. "
-                f"Value must be a float."
-            )
-
-        try:
-            atom_dict["ry"] = float(atom_dict["ry"])
-        except Exception:
-            raise ValueError(
-                f"Invalid ry fields for site {molecule_site} for molecule type {molecule_type}. "
-                f"Value must be a float."
-            )
-
-        try:
-            atom_dict["rz"] = float(atom_dict["rz"])
-        except Exception:
-            raise ValueError(
-                f"Invalid rz fields for site {molecule_site} for molecule type {molecule_type}. "
-                f"Value must be a float."
-            )
-
-        try:
-            atom_dict["chg"] = float(atom_dict["chg"])
-        except Exception:
-            raise ValueError(
-                f"Invalid chg fields for site {molecule_site} for molecule type {molecule_type}. "
-                f"Value must be a float."
-            )
-
-        try:
-            atom_dict["eps"] = float(atom_dict["eps"])
-        except Exception:
-            raise ValueError(
-                f"Invalid eps fields for site {molecule_site} for molecule type {molecule_type}. "
-                f"Value must be a float."
-            )
-
-        try:
-            atom_dict["sig"] = float(atom_dict["sig"])
-        except Exception:
-            raise ValueError(
-                f"Invalid sig fields for site {molecule_site} for molecule type {molecule_type}. "
-                f"Value must be a float."
-            )
-
-        return atom_dict
-
-    def print_results(self):
-        formatstr = "{:<3d} {:>3d}  {:>10.5f} {:>10.5f} {:>10.5f}  {:>10.6f} {:>9.5f} {:>7.4f} {:>9.4f}"
-
-        mol = self.system.molecule[0]
-        logger.info("{} atoms in molecule type {}:".format(len(mol.atom), 1))
-        logger.info(
-            "---------------------------------------------------------------------------------"
-        )
-        logger.info(
-            "Lbl  AN       X          Y          Z         Charge    Epsilon   Sigma     Mass"
-        )
-        logger.info(
-            "---------------------------------------------------------------------------------"
-        )
-
-        for atom in mol.atom:
-            logger.info(
-                formatstr.format(
-                    atom.lbl,
-                    atom.na,
-                    atom.rx,
-                    atom.ry,
-                    atom.rz,
-                    atom.chg,
-                    atom.eps,
-                    atom.sig,
-                    atom.mass,
-                )
-            )
-
-        logger.info("\n")
-
-    def save_run_in_pickle(self, cycle):
-        try:
-            with open("latest-step.pkl", "wb") as pickle_file:
-                pickle.dump((self.config, self.system, cycle), pickle_file)
-        except Exception:
-            raise RuntimeError("Could not save pickle file latest-step.pkl.")
-
-    @staticmethod
-    def load_run_from_pickle() -> Tuple[PlayerConfig, System, int]:
-        pickle_path = Path("latest-step.pkl")
-        try:
-            with open(pickle_path, "rb") as pickle_file:
-                save = pickle.load(pickle_file)
-            return save[0], save[1], save[2] + 1
-
-        except Exception:
-            raise RuntimeError(f"Could not load pickle file {pickle_path}.")
-
-    @staticmethod
-    def set_config(data: dict) -> PlayerConfig:
-        return PlayerConfig.model_validate(data)
-
-    @staticmethod
-    def read_keywords(infile) -> dict:
-        with open(infile, "r") as yml_file:
-            config = yaml.load(yml_file, Loader=yaml.SafeLoader)
-
-        if "diceplayer" in config:
-            return config.get("diceplayer")
-
-        raise RuntimeError(f"Could not find diceplayer section in {infile}.")
-
-    @classmethod
-    def from_file(cls, infile: str) -> "Player":
-        return cls(infile=infile)
-
-    @classmethod
-    def from_save(cls):
-        return cls(optimization=True)

diceplayer/state/state_handler.py

@@ -0,0 +1,37 @@
+from diceplayer.config import PlayerConfig
+from diceplayer.logger import logger
+from diceplayer.state.state_model import StateModel
+
+import pickle
+from pathlib import Path
+
+
+class StateHandler:
+    def __init__(self, sim_dir: Path, state_file: str = "state.pkl"):
+        if not sim_dir.exists():
+            sim_dir.mkdir(parents=True, exist_ok=True)
+        self._state_file = sim_dir / state_file
+
+    def get(self, config: PlayerConfig, force=False) -> StateModel | None:
+        if not self._state_file.exists():
+            return None
+
+        with open(self._state_file, mode="rb") as file:
+            data = pickle.load(file)
+            model = StateModel.model_validate(data)
+
+            if config != model.config and not force:
+                logger.warning(
+                    "The configuration in the state file does not match the provided configuration."
+                )
+                return None
+
+            return model
+
+    def save(self, state: StateModel) -> None:
+        with self._state_file.open(mode="wb") as f:
+            pickle.dump(state.model_dump(), f)
+
+    def delete(self) -> None:
+        if self._state_file.exists():
+            self._state_file.unlink()

diceplayer/state/state_model.py

@@ -0,0 +1,19 @@
+from diceplayer.config import PlayerConfig
+from diceplayer.environment import System
+
+from pydantic import BaseModel
+from typing_extensions import Self
+
+
+class StateModel(BaseModel):
+    config: PlayerConfig
+    system: System
+    current_cycle: int = 0
+
+    @classmethod
+    def from_config(cls, config: PlayerConfig) -> Self:
+        return cls(
+            config=config,
+            system=System(),
+            current_cycle=0,
+        )

diceplayer/utils/__init__.py

@@ -1,4 +1,4 @@
-from .logger import Logger, valid_logger
+from .logger import RunLogger
 from .misc import (
     compress_files_1mb,
     date_time,
@@ -10,8 +10,7 @@ from .ptable import AtomInfo, PTable
 
 
 __all__ = [
-    "Logger",
+    "RunLogger",
-    "valid_logger",
     "PTable",
     "AtomInfo",
     "weekday_date_time",

diceplayer/utils/dataclass_protocol.py

@@ -1,6 +0,0 @@
-from typing_extensions import Protocol, runtime_checkable
-
-
-@runtime_checkable
-class Dataclass(Protocol):
-    __dataclass_fields__: dict

diceplayer/utils/logger.py

@@ -1,72 +1,44 @@
+from typing_extensions import TypeVar
+
 import logging
+import sys
 from pathlib import Path
 
 
-def valid_logger(func):
+H = TypeVar("H", bound=logging.Handler)
-    def wrapper(*args, **kwargs):
-        logger = args[0]
-        assert logger._was_set, "Logger is not set. Please call set_logger() first."
-
-        return func(*args, **kwargs)
-
-    return wrapper
 
 
-class Logger:
+class RunLogger(logging.Logger):
-    outfile = None
+    def __init__(self, name, level=logging.INFO, stream=sys.stdout):
+        super().__init__(name, level)
 
-    _logger = None
+        self.handlers.clear()
 
-    _was_set = False
+        self.handlers.append(
+            self._configure_handler(logging.StreamHandler(stream), level)
+        )
 
-    def __init__(self, logger_name):
+    def set_output_file(self, outfile: Path, level=logging.INFO):
-        if self._logger is None:
+        for handler in list(self.handlers):
-            self._logger = logging.getLogger(logger_name)
+            if not isinstance(handler, logging.FileHandler):
+                continue
+            self.handlers.remove(handler)
 
-    def set_logger(self, outfile="run.log", level=logging.INFO, stream=None):
+        self.handlers.append(self._create_file_handler(outfile, level))
-        outfile_path = None
-        if outfile is not None and stream is None:
-            outfile_path = Path(outfile)
-            if outfile_path.exists():
-                outfile_path.rename(str(outfile_path) + ".backup")
 
-        if level is not None:
+    @staticmethod
-            self._logger.setLevel(level)
+    def _create_file_handler(file: str | Path, level) -> logging.FileHandler:
+        file = Path(file)
 
-        self._create_handlers(outfile_path, stream)
+        if file.exists():
+            file.rename(file.with_suffix(".log.backup"))
 
-        self._was_set = True
+        handler = logging.FileHandler(file)
+        return RunLogger._configure_handler(handler, level)
 
-    @valid_logger
+    @staticmethod
-    def info(self, message):
+    def _configure_handler(handler: H, level) -> H:
-        self._logger.info(message)
+        handler.setLevel(level)
-
+        formatter = logging.Formatter("%(message)s")
-    @valid_logger
+        handler.setFormatter(formatter)
-    def debug(self, message):
+        return handler
-        self._logger.debug(message)
-
-    @valid_logger
-    def warning(self, message):
-        self._logger.warning(message)
-
-    @valid_logger
-    def error(self, message):
-        self._logger.error(message)
-
-    def _create_handlers(self, outfile_path: Path, stream):
-        handlers = []
-        if outfile_path is not None:
-            handlers.append(logging.FileHandler(outfile_path, mode="a+"))
-        elif stream is not None:
-            handlers.append(logging.StreamHandler(stream))
-        else:
-            handlers.append(logging.StreamHandler())
-
-        for handler in handlers:
-            handler.setFormatter(logging.Formatter("%(message)s"))
-            self._logger.addHandler(handler)
-
-    def close(self):
-        for handler in self._logger.handlers:
-            handler.close()
-            self._logger.removeHandler(handler)

diceplayer/utils/potential.py

@@ -0,0 +1,55 @@
+from diceplayer.config import PlayerConfig
+from diceplayer.environment import Atom, Molecule, System
+
+from pathlib import Path
+
+
+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")

pyproject.toml

@@ -8,7 +8,7 @@ authors = [
 readme = "README.md"
 license = "GPL-2.0-only"
 scripts = { diceplayer = "diceplayer.__main__:main" }
-requires-python = ">=3.10"
+requires-python = ">=3.12"
 dynamic = ["version"]
 
 
@@ -29,7 +29,8 @@ dev = [
     "black>=24.4.2",
     "pre-commit>=3.7.1",
     "poethepoet>=0.27.0",
-    "ruff>=0.15.2"
+    "ruff>=0.15.2",
+    "pytest>=9.0.2",
 ]
 
 

tests/_assets/__init__.py

@@ -0,0 +1,4 @@
+from pathlib import Path
+
+
+ASSETS_DIR = Path(__file__).parent

tests/cli/test_read_input_file.py

@@ -0,0 +1,30 @@
+import diceplayer
+from diceplayer.cli import read_input
+from diceplayer.config import PlayerConfig
+
+import pytest
+
+from pathlib import Path
+
+
+class TestReadInputFile:
+    @pytest.fixture
+    def example_config(self) -> Path:
+        return Path(diceplayer.__path__[0]).parent / "control.example.yml"
+
+    def test_read_input_file(self, example_config: Path):
+        config = read_input(example_config)
+
+        assert config is not None
+        assert isinstance(config, PlayerConfig)
+
+    def test_read_input_non_existing_file(self):
+        with pytest.raises(FileNotFoundError):
+            read_input("nonexistent_file.yml")
+
+    def test_read_input_invalid_yaml(self, tmp_path: Path):
+        invalid_yaml_file = tmp_path / "invalid.yml"
+        invalid_yaml_file.write_text("This is not valid YAML: [unbalanced brackets")
+
+        with pytest.raises(Exception):
+            read_input(invalid_yaml_file)

tests/config/test_dice_config.py

@@ -1,11 +1,12 @@
 from diceplayer.config.dice_config import DiceConfig
 
-import unittest
+import pytest
 
 
-class TestDiceDto(unittest.TestCase):
+class TestDiceConfig:
     def test_class_instantiation(self):
         dice_dto = DiceConfig(
+            nprocs=1,
             ljname="test",
             outname="test",
             dens=1.0,
@@ -13,78 +14,77 @@ class TestDiceDto(unittest.TestCase):
             nstep=[1, 1],
         )
 
-        self.assertIsInstance(dice_dto, DiceConfig)
+        assert isinstance(dice_dto, DiceConfig)
 
     def test_validate_jname(self):
-        with self.assertRaises(ValueError) as ex:
+        with pytest.raises(ValueError) as ex:
             DiceConfig(
+                nprocs=1,
                 ljname=None,
                 outname="test",
                 dens=1.0,
                 nmol=[1],
                 nstep=[1, 1],
             )
-            self.assertEqual(
+
-                ex.exception, "Error: 'ljname' keyword not specified in config file"
+            assert ex.value == "Error: 'ljname' keyword not specified in config file"
-            )
 
     def test_validate_outname(self):
-        with self.assertRaises(ValueError) as ex:
+        with pytest.raises(ValueError) as ex:
             DiceConfig(
+                nprocs=1,
                 ljname="test",
                 outname=None,
                 dens=1.0,
                 nmol=[1],
                 nstep=[1, 1],
             )
-            self.assertEqual(
+
-                ex.exception, "Error: 'outname' keyword not specified in config file"
+            assert ex.value == "Error: 'outname' keyword not specified in config file"
-            )
 
     def test_validate_dens(self):
-        with self.assertRaises(ValueError) as ex:
+        with pytest.raises(ValueError) as ex:
             DiceConfig(
+                nprocs=1,
                 ljname="test",
                 outname="test",
                 dens=None,
                 nmol=[1],
                 nstep=[1, 1],
             )
-            self.assertEqual(
+
-                ex.exception, "Error: 'dens' keyword not specified in config file"
+            assert ex.value == "Error: 'dens' keyword not specified in config file"
-            )
 
     def test_validate_nmol(self):
-        with self.assertRaises(ValueError) as ex:
+        with pytest.raises(ValueError) as ex:
             DiceConfig(
+                nprocs=1,
                 ljname="test",
                 outname="test",
                 dens=1.0,
                 nmol=0,
                 nstep=[1, 1],
             )
-            self.assertEqual(
+
-                ex.exception,
+            assert ex.value == "Error: 'nmol' keyword not specified in config file"
-                "Error: 'nmol' keyword not defined appropriately in config file",
-            )
 
     def test_validate_nstep(self):
-        with self.assertRaises(ValueError) as ex:
+        with pytest.raises(ValueError) as ex:
             DiceConfig(
+                nprocs=1,
                 ljname="test",
                 outname="test",
                 dens=1.0,
                 nmol=[1],
                 nstep=0,
             )
-            self.assertEqual(
+
-                ex.exception,
+            assert ex.value == "Error: 'nstep' keyword not specified in config file"
-                "Error: 'nstep' keyword not defined appropriately in config file",
-            )
 
     def test_from_dict(self):
         dice_dto = DiceConfig.model_validate(
             {
+                "nprocs": 1,
                 "ljname": "test",
                 "outname": "test",
                 "dens": 1.0,
@@ -93,4 +93,4 @@ class TestDiceDto(unittest.TestCase):
             }
         )
 
-        self.assertIsInstance(dice_dto, DiceConfig)
+        assert isinstance(dice_dto, DiceConfig)

tests/config/test_gaussian_config.py

@@ -1,9 +1,9 @@
 from diceplayer.config.gaussian_config import GaussianConfig
 
-import unittest
+import pytest
 
 
-class TestGaussianDTO(unittest.TestCase):
+class TestGaussianConfig:
     def test_class_instantiation(self):
         gaussian_dto = GaussianConfig(
             level="test",
@@ -11,10 +11,10 @@ class TestGaussianDTO(unittest.TestCase):
             keywords="test",
         )
 
-        self.assertIsInstance(gaussian_dto, GaussianConfig)
+        assert isinstance(gaussian_dto, GaussianConfig)
 
     def test_is_valid_qmprog(self):
-        with self.assertRaises(ValueError):
+        with pytest.raises(ValueError):
             GaussianConfig(
                 level="test",
                 qmprog="test",
@@ -22,7 +22,7 @@ class TestGaussianDTO(unittest.TestCase):
             )
 
     def test_is_valid_level(self):
-        with self.assertRaises(ValueError):
+        with pytest.raises(ValueError):
             GaussianConfig(
                 level=None,
                 qmprog="g16",
@@ -38,8 +38,4 @@ class TestGaussianDTO(unittest.TestCase):
             }
         )
 
-        self.assertIsInstance(gaussian_dto, GaussianConfig)
+        assert isinstance(gaussian_dto, GaussianConfig)
-
-
-if __name__ == "__main__":
-    unittest.main()

tests/config/test_player_config.py

@@ -0,0 +1,90 @@
+from diceplayer.config.dice_config import DiceConfig
+from diceplayer.config.gaussian_config import GaussianConfig
+from diceplayer.config.player_config import PlayerConfig, RoutineType
+
+import pytest
+
+from typing import Any
+
+
+class TestPlayerConfig:
+    @pytest.fixture
+    def dice_payload(self) -> dict[str, Any]:
+        return {
+            "nprocs": 4,
+            "ljname": "test",
+            "outname": "test",
+            "dens": 1.0,
+            "nmol": [1],
+            "nstep": [1, 1],
+        }
+
+    @pytest.fixture
+    def gaussian_payload(self) -> dict[str, Any]:
+        return {
+            "level": "test",
+            "qmprog": "g16",
+            "keywords": "test",
+        }
+
+    @pytest.fixture
+    def player_payload(
+        self, dice_payload: dict[str, Any], gaussian_payload: dict[str, Any]
+    ) -> dict[str, Any]:
+        return {
+            "type": "both",
+            "mem": 12,
+            "max_cyc": 100,
+            "switch_cyc": 50,
+            "ncores": 4,
+            "dice": dice_payload,
+            "gaussian": gaussian_payload,
+        }
+
+    @pytest.fixture
+    def dice_config(self, dice_payload: dict[str, Any]) -> DiceConfig:
+        return DiceConfig.model_validate(dice_payload)
+
+    @pytest.fixture
+    def gaussian_config(self, gaussian_payload: dict[str, Any]):
+        return GaussianConfig.model_validate(gaussian_payload)
+
+    def test_class_instantiation(
+        self, dice_config: DiceConfig, gaussian_config: GaussianConfig
+    ):
+        player_dto = PlayerConfig(
+            type=RoutineType.BOTH,
+            mem=12,
+            max_cyc=100,
+            switch_cyc=50,
+            ncores=4,
+            dice=dice_config,
+            gaussian=gaussian_config,
+        )
+
+        assert isinstance(player_dto, PlayerConfig)
+        assert isinstance(player_dto.dice, DiceConfig)
+        assert isinstance(player_dto.gaussian, GaussianConfig)
+
+    def test_min_altsteps(
+        self, dice_config: DiceConfig, gaussian_config: GaussianConfig
+    ):
+        player_dto = PlayerConfig(
+            type=RoutineType.BOTH,
+            mem=12,
+            max_cyc=100,
+            switch_cyc=50,
+            ncores=4,
+            altsteps=0,
+            dice=dice_config,
+            gaussian=gaussian_config,
+        )
+
+        assert player_dto.altsteps == 20000
+
+    def test_from_dict(self, player_payload: dict[str, Any]):
+        player_dto = PlayerConfig.model_validate(player_payload)
+
+        assert isinstance(player_dto, PlayerConfig)
+        assert isinstance(player_dto.dice, DiceConfig)
+        assert isinstance(player_dto.gaussian, GaussianConfig)

tests/config/test_player_dto.py

@@ -1,83 +0,0 @@
-from diceplayer.config.dice_config import DiceConfig
-from diceplayer.config.gaussian_config import GaussianConfig
-from diceplayer.config.player_config import PlayerConfig
-
-import unittest
-
-
-def get_config_dict():
-    return {
-        "opt": True,
-        "mem": 12,
-        "maxcyc": 100,
-        "nprocs": 4,
-        "ncores": 4,
-        "dice": {
-            "ljname": "test",
-            "outname": "test",
-            "dens": 1.0,
-            "nmol": [1],
-            "nstep": [1, 1],
-        },
-        "gaussian": {
-            "level": "test",
-            "qmprog": "g16",
-            "keywords": "test",
-        },
-    }
-
-
-class TestPlayerDTO(unittest.TestCase):
-    def setUp(self) -> None:
-        self.dice_dto = DiceConfig(
-            ljname="test",
-            outname="test",
-            dens=1.0,
-            nmol=[1],
-            nstep=[1, 1],
-        )
-        self.gaussian_dto = GaussianConfig(
-            level="test",
-            qmprog="g16",
-            keywords="test",
-        )
-
-    def test_class_instantiation(self):
-        player_dto = PlayerConfig(
-            opt=True,
-            mem=12,
-            maxcyc=100,
-            nprocs=4,
-            ncores=4,
-            dice=self.dice_dto,
-            gaussian=self.gaussian_dto,
-        )
-
-        self.assertIsInstance(player_dto, PlayerConfig)
-        self.assertIsInstance(player_dto.dice, DiceConfig)
-        self.assertIsInstance(player_dto.gaussian, GaussianConfig)
-
-    def test_min_altsteps(self):
-        player_dto = PlayerConfig(
-            opt=True,
-            mem=12,
-            maxcyc=100,
-            nprocs=4,
-            ncores=4,
-            altsteps=100,
-            dice=self.dice_dto,
-            gaussian=self.gaussian_dto,
-        )
-
-        self.assertEqual(player_dto.altsteps, 20000)
-
-    def test_from_dict(self):
-        player_dto = PlayerConfig.model_validate(get_config_dict())
-
-        self.assertIsInstance(player_dto, PlayerConfig)
-        self.assertIsInstance(player_dto.dice, DiceConfig)
-        self.assertIsInstance(player_dto.gaussian, GaussianConfig)
-
-
-if __name__ == "__main__":
-    unittest.main()

tests/dice/test_dice_handler.py

@@ -0,0 +1,92 @@
+from diceplayer.config import DiceConfig, GaussianConfig, PlayerConfig
+from diceplayer.dice.dice_handler import DiceHandler
+from diceplayer.dice.dice_wrapper import DiceWrapper
+from diceplayer.state.state_model import StateModel
+from diceplayer.utils.potential import read_system_from_phb
+from tests._assets import ASSETS_DIR
+
+import pytest
+
+from pathlib import Path
+
+
+class TestDiceHandler:
+    @pytest.fixture
+    def working_directory(self) -> Path:
+        return ASSETS_DIR
+
+    @pytest.fixture
+    def player_config(self, working_directory: Path) -> PlayerConfig:
+        return PlayerConfig(
+            type="both",
+            mem=12,
+            max_cyc=100,
+            switch_cyc=50,
+            ncores=4,
+            dice=DiceConfig(
+                nprocs=4,
+                ljname=working_directory / "phb.ljc",
+                outname="test",
+                dens=1.0,
+                nmol=[1, 200],
+                nstep=[1000, 1000],
+            ),
+            gaussian=GaussianConfig(
+                level="test",
+                qmprog="g16",
+                keywords="test",
+            ),
+        )
+
+    @pytest.fixture
+    def state_model(self, player_config: PlayerConfig) -> StateModel:
+        return StateModel(
+            config=player_config,
+            system=read_system_from_phb(player_config),
+            current_cycle=0,
+        )
+
+    @pytest.fixture
+    def dice_wrapper(
+        self, player_config: PlayerConfig, working_directory: Path
+    ) -> DiceWrapper:
+        return DiceWrapper(player_config.dice, working_directory)
+
+    @pytest.fixture
+    def dice_handler(self, tmp_path) -> DiceHandler:
+        return DiceHandler(tmp_path)
+
+    def test_filter_environment_sites(
+        self,
+        dice_handler: DiceHandler,
+        dice_wrapper: DiceWrapper,
+        state_model: StateModel,
+    ) -> None:
+        environment = dice_wrapper.parse_results()[0]
+
+        filtered_environment = dice_handler._filter_environment_sites(
+            state_model, environment
+        )
+
+        assert len(filtered_environment) < environment.number_of_sites
+
+    def test_aggregate_results(
+        self,
+        dice_handler: DiceHandler,
+        dice_wrapper: DiceWrapper,
+        state_model: StateModel,
+    ) -> None:
+        environments = dice_wrapper.parse_results()
+
+        picked_environments = [
+            dice_handler._filter_environment_sites(state_model, env)
+            for env in environments
+        ]
+
+        aggregated_environment = dice_handler._aggregate_results(
+            state_model, picked_environments
+        )
+
+        assert len(aggregated_environment) == sum(
+            len(env) for env in picked_environments
+        )

tests/dice/test_dice_input.py

@@ -0,0 +1,67 @@
+from diceplayer.config import PlayerConfig
+from diceplayer.dice.dice_input import (
+    NPTEqConfig,
+    NPTTerConfig,
+    NVTEqConfig,
+    NVTTerConfig,
+    write_config,
+)
+
+import pytest
+
+from pathlib import Path
+
+
+class TestDiceInput:
+    @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": "test",
+                    "outname": "test",
+                    "dens": 1.0,
+                    "nmol": [1],
+                    "nstep": [1, 1],
+                },
+                "gaussian": {
+                    "level": "test",
+                    "qmprog": "g16",
+                    "keywords": "test",
+                },
+            }
+        )
+
+    def test_generate_nvt_ter_input(self, player_config: PlayerConfig):
+        dice_input = NVTTerConfig.from_config(player_config)
+
+        assert isinstance(dice_input, NVTTerConfig)
+
+    def test_generate_nvt_eq_input(self, player_config: PlayerConfig):
+        dice_input = NVTEqConfig.from_config(player_config)
+
+        assert isinstance(dice_input, NVTEqConfig)
+
+    def test_generate_npt_ter_input(self, player_config: PlayerConfig):
+        dice_input = NPTTerConfig.from_config(player_config)
+
+        assert isinstance(dice_input, NPTTerConfig)
+
+    def test_generate_npt_eq_input(self, player_config: PlayerConfig):
+        dice_input = NPTEqConfig.from_config(player_config)
+
+        assert isinstance(dice_input, NPTEqConfig)
+
+    def test_write_dice_config(self, player_config: PlayerConfig, tmp_path: Path):
+        dice_input = NVTTerConfig.from_config(player_config)
+
+        output_file = tmp_path / dice_input.type
+        write_config(dice_input, tmp_path)
+
+        assert output_file.exists()

tests/dice/test_dice_wrapper.py

@@ -0,0 +1,38 @@
+from diceplayer.config import DiceConfig
+from diceplayer.dice.dice_wrapper import DiceEnvironment, DiceWrapper
+from tests._assets import ASSETS_DIR
+
+import pytest
+
+from pathlib import Path
+
+
+class TestDiceWrapper:
+    @pytest.fixture(autouse=True)
+    def dice_config(self) -> DiceConfig:
+        return DiceConfig.model_validate(
+            {
+                "nprocs": 4,
+                "ljname": "test",
+                "outname": "test",
+                "dens": 1.0,
+                "nmol": [1],
+                "nstep": [1, 1],
+            }
+        )
+
+    @pytest.fixture(autouse=True)
+    def working_directory(self) -> Path:
+        return ASSETS_DIR
+
+    @pytest.fixture(autouse=True)
+    def dice_wrapper(
+        self, dice_config: DiceConfig, working_directory: Path
+    ) -> DiceWrapper:
+        return DiceWrapper(dice_config, working_directory)
+
+    def test_parse_results(self, dice_wrapper: DiceWrapper) -> None:
+        results = dice_wrapper.parse_results()
+
+        assert isinstance(results, list)
+        assert all(isinstance(env, DiceEnvironment) for env in results)

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/shared/interface/test_dice_interface.py

@@ -1,643 +0,0 @@
-from diceplayer import logger
-from diceplayer.config.player_config import PlayerConfig
-from diceplayer.environment import Atom, Molecule, System
-from diceplayer.interface import DiceInterface
-from tests.mocks.mock_inputs import get_config_example
-from tests.mocks.mock_proc import MockConnection, MockProc
-
-import yaml
-
-import io
-import unittest
-from unittest import mock
-
-
-class TestDiceInterface(unittest.TestCase):
-    def setUp(self):
-        logger.set_logger(stream=io.StringIO())
-
-        config = yaml.load(get_config_example(), Loader=yaml.Loader)
-        self.config = PlayerConfig.model_validate(config["diceplayer"])
-
-    def test_class_instantiation(self):
-        dice = DiceInterface()
-
-        self.assertIsInstance(dice, DiceInterface)
-
-    def test_configure(self):
-        dice = DiceInterface()
-
-        self.assertIsNone(dice.step)
-        self.assertIsNone(dice.system)
-
-        # Ignoring the types for testing purposes
-        dice.configure(self.config, System())
-
-        self.assertIsNotNone(dice.step)
-        self.assertIsNotNone(dice.system)
-
-    def test_reset(self):
-        dice = DiceInterface()
-
-        dice.configure(self.config, System())
-
-        self.assertTrue(hasattr(dice, "step"))
-        self.assertTrue(hasattr(dice, "system"))
-
-        dice.reset()
-
-        self.assertFalse(hasattr(dice, "step"))
-        self.assertFalse(hasattr(dice, "system"))
-
-    @mock.patch("diceplayer.interface.dice_interface.Process", MockProc())
-    @mock.patch("diceplayer.interface.dice_interface.connection", MockConnection)
-    def test_start(self):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.start(1)
-
-    @mock.patch("diceplayer.interface.dice_interface.connection", MockConnection)
-    @mock.patch("diceplayer.interface.dice_interface.Process", MockProc(exitcode=1))
-    def test_start_with_process_error(self):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        with self.assertRaises(SystemExit):
-            dice.start(1)
-
-    def test_simulation_process_raises_exception(self):
-        dice = DiceInterface()
-
-        with self.assertRaises(SystemExit):
-            dice._simulation_process(1, 1)
-
-    @mock.patch("diceplayer.interface.dice_interface.DiceInterface._make_proc_dir")
-    @mock.patch("diceplayer.interface.dice_interface.DiceInterface._make_dice_inputs")
-    @mock.patch("diceplayer.interface.dice_interface.DiceInterface._run_dice")
-    def test_simulation_process(
-        self, mock_run_dice, mock_make_dice_inputs, mock_make_proc_dir
-    ):
-        dice = DiceInterface()
-
-        dice._simulation_process(1, 1)
-
-        self.assertTrue(dice._make_proc_dir.called)
-        self.assertTrue(dice._make_dice_inputs.called)
-        self.assertTrue(dice._run_dice.called)
-
-    @mock.patch("diceplayer.interface.dice_interface.Path.mkdir")
-    @mock.patch("diceplayer.interface.dice_interface.Path.exists")
-    def test_make_proc_dir_if_simdir_exists(self, mock_path_exists, mock_path_mkdir):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        mock_path_exists.return_value = False
-
-        dice._make_proc_dir(1, 1)
-
-        self.assertEqual(mock_path_mkdir.call_count, 2)
-
-    @mock.patch("diceplayer.interface.dice_interface.Path.mkdir")
-    @mock.patch("diceplayer.interface.dice_interface.Path.exists")
-    def test_make_proc_dir_if_simdir_doesnt_exists(
-        self, mock_path_exists, mock_path_mkdir
-    ):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        mock_path_exists.return_value = False
-
-        dice._make_proc_dir(1, 1)
-
-        self.assertEqual(mock_path_mkdir.call_count, 2)
-
-    def test_make_dice_seed(self):
-        seed = DiceInterface._make_dice_seed()
-
-        self.assertIsInstance(seed, int)
-
-    def test_make_dice_inputs_nstep_len_two_with_randoninit_first_cycle_one(self):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.step.dice.nstep = [1, 1]
-
-        dice._make_potentials = mock.Mock()
-
-        dice._make_init_file = mock.Mock()
-        dice._new_density = mock.Mock()
-
-        dice._make_nvt_ter = mock.Mock()
-        dice._make_nvt_eq = mock.Mock()
-        dice._make_npt_ter = mock.Mock()
-        dice._make_npt_eq = mock.Mock()
-
-        dice._make_dice_inputs(1, 1)
-
-        self.assertTrue(dice._make_potentials.called)
-
-        self.assertFalse(dice._make_init_file.called)
-        self.assertFalse(dice._new_density.called)
-
-        self.assertTrue(dice._make_nvt_ter.called)
-        self.assertTrue(dice._make_nvt_eq.called)
-
-        self.assertFalse(dice._make_npt_ter.called)
-        self.assertFalse(dice._make_npt_eq.called)
-
-    @mock.patch("builtins.open", new_callable=mock.mock_open, read_data="test")
-    @mock.patch("diceplayer.interface.dice_interface.Path.exists", return_value=True)
-    def test_make_dice_inputs_nstep_len_two_with_randoninit_first_cycle_two(
-        self, mock_path_exists, mock_open
-    ):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.step.dice.nstep = [1, 1]
-
-        dice._make_potentials = mock.Mock()
-
-        dice._make_init_file = mock.Mock()
-        dice._new_density = mock.Mock()
-
-        dice._make_nvt_ter = mock.Mock()
-        dice._make_nvt_eq = mock.Mock()
-        dice._make_npt_ter = mock.Mock()
-        dice._make_npt_eq = mock.Mock()
-
-        dice._make_dice_inputs(2, 1)
-
-        self.assertTrue(dice._make_potentials.called)
-
-        self.assertTrue(dice._make_init_file.called)
-        self.assertTrue(dice._new_density.called)
-
-        self.assertFalse(dice._make_nvt_ter.called)
-        self.assertTrue(dice._make_nvt_eq.called)
-
-        self.assertFalse(dice._make_npt_ter.called)
-        self.assertFalse(dice._make_npt_eq.called)
-
-    @mock.patch("diceplayer.interface.dice_interface.Path.exists", return_value=False)
-    def test_make_dice_inputs_raises_exception_on_last_not_found(
-        self, mock_path_exists
-    ):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.step.dice.nstep = [1, 1]
-
-        dice._make_potentials = mock.Mock()
-
-        dice._make_init_file = mock.Mock()
-        dice._new_density = mock.Mock()
-
-        dice._make_nvt_ter = mock.Mock()
-        dice._make_nvt_eq = mock.Mock()
-        dice._make_npt_ter = mock.Mock()
-        dice._make_npt_eq = mock.Mock()
-
-        with self.assertRaises(FileNotFoundError):
-            dice._make_dice_inputs(2, 1)
-
-    def test_make_dice_inputs_nstep_len_three_with_randoninit_first_cycle_one(self):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice._make_potentials = mock.Mock()
-
-        dice._make_init_file = mock.Mock()
-        dice._new_density = mock.Mock()
-
-        dice._make_nvt_ter = mock.Mock()
-        dice._make_nvt_eq = mock.Mock()
-        dice._make_npt_ter = mock.Mock()
-        dice._make_npt_eq = mock.Mock()
-
-        dice._make_dice_inputs(1, 1)
-
-        self.assertTrue(dice._make_potentials.called)
-
-        self.assertFalse(dice._make_init_file.called)
-        self.assertFalse(dice._new_density.called)
-
-        self.assertTrue(dice._make_nvt_ter.called)
-        self.assertFalse(dice._make_nvt_eq.called)
-
-        self.assertTrue(dice._make_npt_ter.called)
-        self.assertTrue(dice._make_npt_eq.called)
-
-    @mock.patch("diceplayer.interface.dice_interface.os")
-    @mock.patch("diceplayer.interface.dice_interface.shutil")
-    @mock.patch("diceplayer.interface.dice_interface.Path.exists", return_value=True)
-    def test_run_dice_on_first_cycle_run_successful(
-        self, mock_path_exists, mock_shutils, mock_os
-    ):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.step.dice.nstep = [1, 1, 1]
-
-        dice.run_dice_file = mock.Mock()
-
-        dice._run_dice(1, 1)
-
-        self.assertTrue(mock_os.getcwd.called)
-        self.assertTrue(mock_os.chdir.called)
-
-        self.assertEqual(dice.run_dice_file.call_count, 3)
-        self.assertTrue(mock_shutils.copy.called)
-
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.step.dice.nstep = [1, 1]
-
-        dice.run_dice_file = mock.Mock()
-
-        dice._run_dice(1, 1)
-
-        self.assertTrue(mock_os.getcwd.called)
-        self.assertTrue(mock_os.chdir.called)
-
-        self.assertEqual(dice.run_dice_file.call_count, 2)
-        self.assertTrue(mock_shutils.copy.called)
-
-    @mock.patch("diceplayer.interface.dice_interface.os")
-    @mock.patch("diceplayer.interface.dice_interface.shutil")
-    @mock.patch("diceplayer.interface.dice_interface.Path.exists", return_value=True)
-    def test_run_dice_on_second_cycle_run_successful(
-        self, mock_path_exists, mock_shutils, mock_os
-    ):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.run_dice_file = mock.Mock()
-
-        dice._run_dice(2, 1)
-
-        self.assertTrue(mock_os.getcwd.called)
-        self.assertTrue(mock_os.chdir.called)
-
-        self.assertEqual(dice.run_dice_file.call_count, 2)
-        self.assertTrue(mock_shutils.copy.called)
-
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.run_dice_file = mock.Mock()
-
-        dice._run_dice(2, 1)
-
-        self.assertTrue(mock_os.getcwd.called)
-        self.assertTrue(mock_os.chdir.called)
-
-        self.assertEqual(dice.run_dice_file.call_count, 2)
-        self.assertTrue(mock_shutils.copy.called)
-
-    @mock.patch("diceplayer.interface.dice_interface.os")
-    @mock.patch("diceplayer.interface.dice_interface.shutil")
-    @mock.patch("diceplayer.interface.dice_interface.Path.exists", return_value=False)
-    def test_run_dice_raises_filenotfound_on_invalid_file(
-        self, mock_path_exists, mock_shutils, mock_os
-    ):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.run_dice_file = mock.Mock()
-
-        with self.assertRaises(FileNotFoundError):
-            dice._run_dice(1, 1)
-
-    @mock.patch("builtins.open", new_callable=mock.mock_open)
-    def test_make_init_file(self, mock_open):
-        example_atom = Atom(
-            lbl=1,
-            na=1,
-            rx=1.0,
-            ry=1.0,
-            rz=1.0,
-            chg=1.0,
-            eps=1.0,
-            sig=1.0,
-        )
-
-        main_molecule = Molecule("main_molecule")
-        main_molecule.add_atom(example_atom)
-
-        secondary_molecule = Molecule("secondary_molecule")
-        secondary_molecule.add_atom(example_atom)
-
-        system = System()
-        system.add_type(main_molecule)
-        system.add_type(secondary_molecule)
-
-        dice = DiceInterface()
-        dice.configure(self.config, system)
-
-        dice.step.dice.nmol = [1, 1]
-
-        last_xyz_file = io.StringIO()
-        last_xyz_file.writelines(
-            [
-                "   TEST\n",
-                " Configuration number :     TEST =   TEST  TEST  TEST\n",
-                "   H     1.00000     1.00000     1.00000\n",
-                "   H     1.00000     1.00000     1.00000\n",
-            ]
-        )
-        last_xyz_file.seek(0)
-
-        dice._make_init_file("test", last_xyz_file)
-
-        mock_handler = mock_open()
-        calls = mock_handler.write.call_args_list
-
-        lines = list(map(lambda x: x[0][0], calls))
-
-        expected_lines = [
-            "  1.000000    1.000000    1.000000\n",
-            "  1.000000    1.000000    1.000000\n",
-            "$end",
-        ]
-
-        self.assertEqual(lines, expected_lines)
-
-    @mock.patch("builtins.open", new_callable=mock.mock_open)
-    def test_new_density(self, mock_open):
-        example_atom = Atom(
-            lbl=1,
-            na=1,
-            rx=1.0,
-            ry=1.0,
-            rz=1.0,
-            chg=1.0,
-            eps=1.0,
-            sig=1.0,
-        )
-
-        main_molecule = Molecule("main_molecule")
-        main_molecule.add_atom(example_atom)
-
-        secondary_molecule = Molecule("secondary_molecule")
-        secondary_molecule.add_atom(example_atom)
-
-        system = System()
-        system.add_type(main_molecule)
-        system.add_type(secondary_molecule)
-
-        dice = DiceInterface()
-        dice.configure(self.config, system)
-
-        last_xyz_file = io.StringIO()
-        last_xyz_file.writelines(
-            [
-                "   TEST\n",
-                " Configuration number :     TEST =   1  1  1\n",
-                "   H     1.00000     1.00000     1.00000\n",
-                "   H     1.00000     1.00000     1.00000\n",
-            ]
-        )
-        last_xyz_file.seek(0)
-
-        density = dice._new_density(last_xyz_file)
-
-        self.assertEqual(density, 85.35451545000001)
-
-    @mock.patch("builtins.open", new_callable=mock.mock_open)
-    @mock.patch("diceplayer.interface.dice_interface.random")
-    def test_make_nvt_ter(self, mock_random, mock_open):
-        mock_random.random.return_value = 1
-
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice._make_nvt_ter(1, "test")
-
-        mock_handler = mock_open()
-        calls = mock_handler.write.call_args_list
-
-        lines = list(map(lambda x: x[0][0], calls))
-
-        expected_lines = [
-            "title = Diceplayer run - NVT Thermalization\n",
-            "ncores = 4\n",
-            "ljname = phb.ljc\n",
-            "outname = phb\n",
-            "nmol = 1 50\n",
-            "dens = 0.75\n",
-            "temp = 300.0\n",
-            "init = yes\n",
-            "nstep = 2000\n",
-            "vstep = 0\n",
-            "mstop = 1\n",
-            "accum = no\n",
-            "iprint = 1\n",
-            "isave = 0\n",
-            "irdf = 0\n",
-            "seed = 1000000\n",
-            "upbuf = 360",
-        ]
-
-        self.assertEqual(lines, expected_lines)
-
-    @mock.patch("builtins.open", new_callable=mock.mock_open)
-    @mock.patch("diceplayer.interface.dice_interface.random")
-    def test_make_nvt_eq(self, mock_random, mock_open):
-        mock_random.random.return_value = 1
-
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice._make_nvt_eq(1, "test")
-
-        mock_handler = mock_open()
-        calls = mock_handler.write.call_args_list
-
-        lines = list(map(lambda x: x[0][0], calls))
-
-        expected_lines = [
-            "title = Diceplayer run - NVT Production\n",
-            "ncores = 4\n",
-            "ljname = phb.ljc\n",
-            "outname = phb\n",
-            "nmol = 1 50\n",
-            "dens = 0.75\n",
-            "temp = 300.0\n",
-            "init = no\n",
-            "nstep = 3000\n",
-            "vstep = 0\n",
-            "mstop = 1\n",
-            "accum = no\n",
-            "iprint = 1\n",
-            "isave = 1000\n",
-            "irdf = 40\n",
-            "seed = 1000000\n",
-        ]
-
-        self.assertEqual(lines, expected_lines)
-
-    @mock.patch("builtins.open", new_callable=mock.mock_open)
-    @mock.patch("diceplayer.interface.dice_interface.random")
-    def test_make_npt_ter(self, mock_random, mock_open):
-        mock_random.random.return_value = 1
-
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice._make_npt_ter(1, "test")
-
-        mock_handler = mock_open()
-        calls = mock_handler.write.call_args_list
-
-        lines = list(map(lambda x: x[0][0], calls))
-
-        expected_lines = [
-            "title = Diceplayer run - NPT Thermalization\n",
-            "ncores = 4\n",
-            "ljname = phb.ljc\n",
-            "outname = phb\n",
-            "nmol = 1 50\n",
-            "press = 1.0\n",
-            "temp = 300.0\n",
-            "init = no\n",
-            "vstep = 600\n",
-            "nstep = 5\n",
-            "mstop = 1\n",
-            "accum = no\n",
-            "iprint = 1\n",
-            "isave = 0\n",
-            "irdf = 0\n",
-            "seed = 1000000\n",
-        ]
-
-        self.assertEqual(lines, expected_lines)
-
-    @mock.patch("builtins.open", new_callable=mock.mock_open)
-    @mock.patch("diceplayer.interface.dice_interface.random")
-    def test_make_npt_eq(self, mock_random, mock_open):
-        mock_random.random.return_value = 1
-
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice._make_npt_eq("test")
-
-        mock_handler = mock_open()
-        calls = mock_handler.write.call_args_list
-
-        lines = list(map(lambda x: x[0][0], calls))
-
-        expected_lines = [
-            "title = Diceplayer run - NPT Production\n",
-            "ncores = 4\n",
-            "ljname = phb.ljc\n",
-            "outname = phb\n",
-            "nmol = 1 50\n",
-            "press = 1.0\n",
-            "temp = 300.0\n",
-            "nstep = 5\n",
-            "vstep = 800\n",
-            "init = no\n",
-            "mstop = 1\n",
-            "accum = no\n",
-            "iprint = 1\n",
-            "isave = 1000\n",
-            "irdf = 40\n",
-            "seed = 1000000\n",
-        ]
-
-        self.assertEqual(lines, expected_lines)
-
-    @mock.patch("builtins.open", new_callable=mock.mock_open)
-    def test_make_potentials(self, mock_open):
-        example_atom = Atom(
-            lbl=1,
-            na=1,
-            rx=1.0,
-            ry=1.0,
-            rz=1.0,
-            chg=1.0,
-            eps=1.0,
-            sig=1.0,
-        )
-
-        main_molecule = Molecule("main_molecule")
-        main_molecule.add_atom(example_atom)
-
-        secondary_molecule = Molecule("secondary_molecule")
-        secondary_molecule.add_atom(example_atom)
-
-        system = System()
-        system.add_type(main_molecule)
-        system.add_type(secondary_molecule)
-
-        dice = DiceInterface()
-        dice.configure(self.config, system)
-
-        dice._make_potentials("test")
-
-        mock_handler = mock_open()
-        calls = mock_handler.write.call_args_list
-
-        lines = list(map(lambda x: x[0][0], calls))
-
-        expected_lines = [
-            "*\n",
-            "2\n",
-            "1 main_molecule\n",
-            "1     1     1.00000    1.00000    1.00000    1.000000   1.00000  1.0000\n",
-            "1 secondary_molecule\n",
-            "1     1     1.00000    1.00000    1.00000    1.000000   1.00000  1.0000\n",
-        ]
-
-        self.assertEqual(lines, expected_lines)
-
-    @mock.patch("diceplayer.interface.dice_interface.subprocess")
-    @mock.patch(
-        "builtins.open",
-        new_callable=mock.mock_open,
-        read_data="End of simulation\nBLABLA",
-    )
-    def test_run_dice_file(self, mock_open, mock_subprocess):
-        mock_subprocess.call.return_value = 0
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.run_dice_file(1, 1, "test")
-
-        self.assertTrue(mock_subprocess.call.called)
-        self.assertTrue(mock_open.called)
-
-    @mock.patch("diceplayer.interface.dice_interface.subprocess")
-    @mock.patch("builtins.open", new_callable=mock.mock_open, read_data="Error\nBLABLA")
-    def test_run_dice_file_raises_runtime_error_on_dice_file(
-        self, mock_open, mock_subprocess
-    ):
-        mock_subprocess.call.return_value = 0
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        with self.assertRaises(RuntimeError):
-            dice.run_dice_file(1, 1, "test")
-
-    @mock.patch("diceplayer.interface.dice_interface.subprocess")
-    @mock.patch(
-        "builtins.open",
-        new_callable=mock.mock_open,
-        read_data="End of simulation\nBLABLA",
-    )
-    def test_run_dice_file_raises_runtime_error_of_dice_exit_code(
-        self, mock_open, mock_subprocess
-    ):
-        mock_subprocess.call.return_value = 1
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        with self.assertRaises(RuntimeError):
-            dice.run_dice_file(1, 1, "test")
-
-
-if __name__ == "__main__":
-    unittest.main()

tests/shared/interface/test_gaussian_interface.py

@@ -1,115 +0,0 @@
-from diceplayer import logger
-from diceplayer.config.player_config import PlayerConfig
-from diceplayer.environment import System
-from diceplayer.interface import GaussianInterface
-from tests.mocks.mock_inputs import get_config_example
-
-import yaml
-
-import io
-import unittest
-from unittest import mock
-
-
-class TestGaussianInterface(unittest.TestCase):
-    def setUp(self) -> None:
-        logger.set_logger(stream=io.StringIO())
-
-        config = yaml.load(get_config_example(), Loader=yaml.Loader)
-        self.config = PlayerConfig.model_validate(config["diceplayer"])
-
-    def test_class_instantiation(self):
-        gaussian_interface = GaussianInterface()
-        self.assertIsInstance(gaussian_interface, GaussianInterface)
-
-    def test_configure(self):
-        gaussian_interface = GaussianInterface()
-
-        self.assertIsNone(gaussian_interface.step)
-        self.assertIsNone(gaussian_interface.system)
-
-        gaussian_interface.configure(self.config, System())
-
-        self.assertIsNotNone(gaussian_interface.step)
-        self.assertIsNotNone(gaussian_interface.system)
-
-    def test_reset(self):
-        gaussian_interface = GaussianInterface()
-
-        gaussian_interface.configure(self.config, System())
-
-        self.assertIsNotNone(gaussian_interface.step)
-        self.assertIsNotNone(gaussian_interface.system)
-
-        gaussian_interface.reset()
-
-        self.assertFalse(hasattr(gaussian_interface, "step"))
-        self.assertFalse(hasattr(gaussian_interface, "system"))
-
-    @mock.patch("diceplayer.interface.gaussian_interface.Path.mkdir")
-    @mock.patch("diceplayer.interface.gaussian_interface.Path.exists")
-    def test_make_qm_dir(self, mock_exists, mock_mkdir):
-        mock_exists.return_value = False
-
-        gaussian_interface = GaussianInterface()
-        gaussian_interface.configure(self.config, System())
-
-        gaussian_interface._make_qm_dir(1)
-
-        mock_exists.assert_called_once()
-        mock_mkdir.assert_called_once()
-
-    @mock.patch("diceplayer.interface.gaussian_interface.shutil.copy")
-    @mock.patch("diceplayer.interface.gaussian_interface.Path.exists")
-    def test_copy_chk_file_from_previous_step(self, mock_exists, mock_copy):
-        gaussian_interface = GaussianInterface()
-        gaussian_interface.configure(self.config, System())
-
-        mock_exists.side_effect = [False, True]
-
-        gaussian_interface._copy_chk_file_from_previous_step(2)
-
-        self.assertTrue(mock_exists.called)
-        self.assertTrue(mock_copy.called)
-
-    @mock.patch("diceplayer.interface.gaussian_interface.shutil.copy")
-    @mock.patch("diceplayer.interface.gaussian_interface.Path.exists")
-    def test_copy_chk_file_from_previous_step_no_previous_step(
-        self, mock_exists, mock_copy
-    ):
-        gaussian_interface = GaussianInterface()
-        gaussian_interface.configure(self.config, System())
-
-        mock_exists.side_effect = [False, False]
-
-        with self.assertRaises(FileNotFoundError):
-            gaussian_interface._copy_chk_file_from_previous_step(2)
-
-    @mock.patch("diceplayer.interface.gaussian_interface.shutil.copy")
-    @mock.patch("diceplayer.interface.gaussian_interface.Path.exists")
-    def test_copy_chk_file_from_previous_step_current_exists(
-        self, mock_exists, mock_copy
-    ):
-        gaussian_interface = GaussianInterface()
-        gaussian_interface.configure(self.config, System())
-
-        mock_exists.side_effect = [True, True]
-
-        with self.assertRaises(FileExistsError):
-            gaussian_interface._copy_chk_file_from_previous_step(2)
-
-    # def test_start(self):
-    #     gaussian_interface = GaussianInterface()
-    #     gaussian_interface.configure(self.config, System())
-    #
-    #     gaussian_interface._make_qm_dir = mock.Mock()
-    #     gaussian_interface._copy_chk_file_from_previous_step = mock.Mock()
-    #
-    #     gaussian_interface.start(2)
-    #
-    #     gaussian_interface._make_qm_dir.assert_called_once_with(2)
-    #     gaussian_interface._copy_chk_file_from_previous_step.assert_called_once_with(2)
-
-
-if __name__ == "__main__":
-    unittest.main()

tests/shared/utils/test_logger.py

@@ -1,132 +0,0 @@
-from diceplayer.utils import Logger, valid_logger
-
-import io
-import logging
-import unittest
-from unittest import mock
-
-
-class TestValidateLogger(unittest.TestCase):
-    def test_validate_logger(self):
-        class MockLogger:
-            _was_set = True
-
-            @valid_logger
-            def test_func(self):
-                pass
-
-        MockLogger().test_func()
-
-    def test_validate_logger_exception(self):
-        class MockLogger:
-            _was_set = False
-
-            @valid_logger
-            def test_func(self):
-                pass
-
-        with self.assertRaises(AssertionError):
-            MockLogger().test_func()
-
-
-class TestLogger(unittest.TestCase):
-    def test_class_instantiation(self):
-        logger = Logger("test")
-
-        self.assertIsInstance(logger, Logger)
-
-    @mock.patch("builtins.open", mock.mock_open())
-    def test_set_logger_to_file(self):
-        logger = Logger("test")
-
-        logger.set_logger(stream=io.StringIO())
-
-        self.assertIsNotNone(logger._logger)
-        self.assertEqual(logger._logger.name, "test")
-
-    def test_set_logger_to_stream(self):
-        logger = Logger("test")
-
-        logger.set_logger(stream=io.StringIO())
-
-        self.assertIsNotNone(logger._logger)
-        self.assertEqual(logger._logger.name, "test")
-
-    @mock.patch("builtins.open", mock.mock_open())
-    @mock.patch("diceplayer.utils.logger.Path.exists")
-    @mock.patch("diceplayer.utils.logger.Path.rename")
-    def test_set_logger_if_file_exists(self, mock_rename, mock_exists):
-        logger = Logger("test")
-
-        mock_exists.return_value = True
-        logger.set_logger()
-
-        self.assertTrue(mock_rename.called)
-        self.assertIsNotNone(logger._logger)
-        self.assertEqual(logger._logger.name, "test")
-
-    @mock.patch("builtins.open", mock.mock_open())
-    @mock.patch("diceplayer.utils.logger.Path.exists")
-    @mock.patch("diceplayer.utils.logger.Path.rename")
-    def test_set_logger_if_file_not_exists(self, mock_rename, mock_exists):
-        logger = Logger("test")
-
-        mock_exists.return_value = False
-        logger.set_logger()
-
-        self.assertFalse(mock_rename.called)
-        self.assertIsNotNone(logger._logger)
-        self.assertEqual(logger._logger.name, "test")
-
-    @mock.patch("builtins.open", mock.mock_open())
-    def test_close(self):
-        logger = Logger("test")
-
-        logger.set_logger()
-        logger.close()
-
-        self.assertEqual(len(logger._logger.handlers), 0)
-
-    @mock.patch("builtins.open", mock.mock_open())
-    def test_info(self):
-        logger = Logger("test")
-        logger.set_logger(stream=io.StringIO())
-
-        with self.assertLogs(level="INFO") as cm:
-            logger.info("test")
-
-        self.assertEqual(cm.output, ["INFO:test:test"])
-
-    @mock.patch("builtins.open", mock.mock_open())
-    def test_debug(self):
-        logger = Logger("test")
-        logger.set_logger(stream=io.StringIO(), level=logging.DEBUG)
-
-        with self.assertLogs(level="DEBUG") as cm:
-            logger.debug("test")
-
-        self.assertEqual(cm.output, ["DEBUG:test:test"])
-
-    @mock.patch("builtins.open", mock.mock_open())
-    def test_warning(self):
-        logger = Logger("test")
-        logger.set_logger(stream=io.StringIO())
-
-        with self.assertLogs(level="WARNING") as cm:
-            logger.warning("test")
-
-        self.assertEqual(cm.output, ["WARNING:test:test"])
-
-    @mock.patch("builtins.open", mock.mock_open())
-    def test_error(self):
-        logger = Logger("test")
-        logger.set_logger(stream=io.StringIO())
-
-        with self.assertLogs(level="ERROR") as cm:
-            logger.error("test")
-
-        self.assertEqual(cm.output, ["ERROR:test:test"])
-
-
-if __name__ == "__main__":
-    unittest.main()

tests/state/test_state_handler.py

@@ -0,0 +1,118 @@
+from diceplayer.config import DiceConfig, GaussianConfig, PlayerConfig
+from diceplayer.environment import System
+from diceplayer.state.state_handler import StateHandler
+from diceplayer.state.state_model import StateModel
+
+import pytest
+
+from pathlib import Path
+
+
+class TestStateHandler:
+    @pytest.fixture
+    def player_config(self) -> PlayerConfig:
+        return PlayerConfig(
+            type="both",
+            mem=12,
+            max_cyc=100,
+            switch_cyc=50,
+            ncores=4,
+            dice=DiceConfig(
+                nprocs=4,
+                ljname="test",
+                outname="test",
+                dens=1.0,
+                nmol=[1],
+                nstep=[1, 1],
+            ),
+            gaussian=GaussianConfig(
+                level="test",
+                qmprog="g16",
+                keywords="test",
+            ),
+        )
+
+    def test_initialization(self, tmp_path: Path):
+        state_handler = StateHandler(tmp_path)
+
+        assert isinstance(state_handler, StateHandler)
+
+    def test_save(self, tmp_path: Path, player_config: PlayerConfig):
+        state_handler = StateHandler(tmp_path)
+
+        state = StateModel(
+            config=player_config,
+            system=System(),
+            current_cycle=0,
+        )
+
+        state_handler.save(state)
+
+        assert (tmp_path / "state.pkl").exists()
+
+    def test_get_when_empty(self, tmp_path: Path, player_config: PlayerConfig):
+        state_handler = StateHandler(tmp_path)
+
+        state = state_handler.get(player_config)
+
+        assert state is None
+
+    def test_get(self, tmp_path: Path, player_config: PlayerConfig):
+        state_handler = StateHandler(tmp_path)
+
+        state = StateModel(
+            config=player_config,
+            system=System(),
+            current_cycle=0,
+        )
+
+        state_handler.save(state)
+
+        retrieved_state = state_handler.get(player_config)
+
+        assert retrieved_state is not None
+        assert retrieved_state.config == state.config
+        assert retrieved_state.system == state.system
+        assert retrieved_state.current_cycle == state.current_cycle
+
+    def test_get_with_different_config(
+        self, tmp_path: Path, player_config: PlayerConfig
+    ):
+        state_handler = StateHandler(tmp_path)
+
+        state = StateModel(
+            config=player_config,
+            system=System(),
+            current_cycle=0,
+        )
+
+        state_handler.save(state)
+
+        different_config = player_config.model_copy(update={"max_cyc": 200})
+
+        retrieved_state = state_handler.get(different_config)
+
+        assert retrieved_state is None
+
+    def test_get_with_different_config_force(
+        self, tmp_path: Path, player_config: PlayerConfig
+    ):
+        state_handler = StateHandler(tmp_path)
+
+        state = StateModel(
+            config=player_config,
+            system=System(),
+            current_cycle=0,
+        )
+
+        state_handler.save(state)
+
+        different_config = player_config.model_copy(update={"max_cyc": 200})
+
+        retrieved_state = state_handler.get(different_config, force=True)
+
+        assert retrieved_state is not None
+        assert retrieved_state.config == state.config
+        assert retrieved_state.config != different_config
+        assert retrieved_state.system == state.system
+        assert retrieved_state.current_cycle == state.current_cycle

tests/test_player.py

@@ -1,396 +0,0 @@
-from diceplayer import logger
-from diceplayer.player import Player
-from tests.mocks.mock_inputs import mock_open
-
-import io
-import unittest
-from unittest import mock
-
-
-class TestPlayer(unittest.TestCase):
-    def setUp(self):
-        logger.set_logger(stream=io.StringIO())
-
-    @mock.patch("builtins.open", mock_open)
-    def test_class_instantiation(self):
-        # This file does not exist and it will be mocked
-        player = Player("control.test.yml")
-
-        self.assertIsInstance(player, Player)
-
-    @mock.patch("builtins.open", mock_open)
-    def test_start(self):
-        player = Player("control.test.yml")
-
-        player.gaussian_start = mock.MagicMock()
-        player.dice_start = mock.MagicMock()
-
-        player.start()
-
-        self.assertEqual(player.dice_start.call_count, 3)
-        self.assertEqual(player.gaussian_start.call_count, 3)
-
-    @mock.patch("builtins.open", mock_open)
-    @mock.patch("diceplayer.player.Path")
-    def test_create_simulation_dir_if_already_exists(self, mock_path):
-        player = Player("control.test.yml")
-        mock_path.return_value.exists.return_value = True
-
-        with self.assertRaises(FileExistsError):
-            player.create_simulation_dir()
-
-        self.assertTrue(mock_path.called)
-
-    @mock.patch("builtins.open", mock_open)
-    @mock.patch("diceplayer.player.Path")
-    def test_create_simulation_dir_if_not_exists(self, mock_path):
-        player = Player("control.test.yml")
-        mock_path.return_value.exists.return_value = False
-
-        player.create_simulation_dir()
-
-        self.assertTrue(mock_path.called)
-
-    @mock.patch("builtins.open", mock_open)
-    @mock.patch("diceplayer.player.VERSION", "test")
-    @mock.patch("diceplayer.player.sys")
-    @mock.patch("diceplayer.player.weekday_date_time")
-    def test_print_keywords(self, mock_date_func, mock_sys):
-        player = Player("control.test.yml")
-
-        mock_sys.version = "TEST"
-        mock_date_func.return_value = "00 Test 0000 at 00:00:00"
-
-        with self.assertLogs() as cm:
-            player.print_keywords()
-
-        expected_output = [
-            "INFO:diceplayer:##########################################################################################\n#############               Welcome to DICEPLAYER version test                #############\n##########################################################################################\n",
-            "INFO:diceplayer:Your python version is TEST\n",
-            "INFO:diceplayer:Program started on 00 Test 0000 at 00:00:00\n",
-            "INFO:diceplayer:Environment variables:",
-            "INFO:diceplayer:OMP_STACKSIZE = Not set\n",
-            "INFO:diceplayer:------------------------------------------------------------------------------------------\n                         DICE variables being used in this run:\n------------------------------------------------------------------------------------------\n",
-            "INFO:diceplayer:combrule = *",
-            "INFO:diceplayer:dens = 0.75",
-            "INFO:diceplayer:isave = 1000",
-            "INFO:diceplayer:ljname = phb.ljc",
-            "INFO:diceplayer:nmol = [ 1 50 ]",
-            "INFO:diceplayer:nstep = [ 2000 3000 4000 ]",
-            "INFO:diceplayer:outname = phb",
-            "INFO:diceplayer:press = 1.0",
-            "INFO:diceplayer:progname = ~/.local/bin/dice",
-            "INFO:diceplayer:randominit = first",
-            "INFO:diceplayer:temp = 300.0",
-            "INFO:diceplayer:upbuf = 360",
-            "INFO:diceplayer:------------------------------------------------------------------------------------------\n                         GAUSSIAN variables being used in this run:\n------------------------------------------------------------------------------------------\n",
-            "INFO:diceplayer:chg_tol = 0.01",
-            "INFO:diceplayer:chgmult = [ 0 1 ]",
-            "INFO:diceplayer:keywords = freq",
-            "INFO:diceplayer:level = MP2/aug-cc-pVDZ",
-            "INFO:diceplayer:pop = chelpg",
-            "INFO:diceplayer:qmprog = g16",
-            "INFO:diceplayer:\n",
-        ]
-
-        self.assertEqual(cm.output, expected_output)
-
-    def test_validate_atom_dict(self):
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": 0,
-                    "na": 1,
-                    "rx": 1.0,
-                    "ry": 1.0,
-                    "rz": 1.0,
-                    "chg": 1.0,
-                    "eps": 1.0,
-                },
-            )
-        self.assertEqual(
-            str(context.exception),
-            "Invalid number of fields for site 1 for molecule type 1.",
-        )
-
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": "",
-                    "na": 1,
-                    "rx": 1.0,
-                    "ry": 1.0,
-                    "rz": 1.0,
-                    "chg": 1.0,
-                    "eps": 1.0,
-                    "sig": 1.0,
-                },
-            )
-        self.assertEqual(
-            str(context.exception), "Invalid lbl fields for site 1 for molecule type 1."
-        )
-
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": 1.0,
-                    "na": "",
-                    "rx": 1.0,
-                    "ry": 1.0,
-                    "rz": 1.0,
-                    "chg": 1.0,
-                    "eps": 1.0,
-                    "sig": 1.0,
-                },
-            )
-        self.assertEqual(
-            str(context.exception), "Invalid na fields for site 1 for molecule type 1."
-        )
-
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": 1.0,
-                    "na": 1,
-                    "rx": "",
-                    "ry": 1.0,
-                    "rz": 1.0,
-                    "chg": 1.0,
-                    "eps": 1.0,
-                    "sig": 1.0,
-                },
-            )
-        self.assertEqual(
-            str(context.exception),
-            "Invalid rx fields for site 1 for molecule type 1. Value must be a float.",
-        )
-
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": 1.0,
-                    "na": 1,
-                    "rx": 1.0,
-                    "ry": "",
-                    "rz": 1.0,
-                    "chg": 1.0,
-                    "eps": 1.0,
-                    "sig": 1.0,
-                },
-            )
-        self.assertEqual(
-            str(context.exception),
-            "Invalid ry fields for site 1 for molecule type 1. Value must be a float.",
-        )
-
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": 1.0,
-                    "na": 1,
-                    "rx": 1.0,
-                    "ry": 1.0,
-                    "rz": "",
-                    "chg": 1.0,
-                    "eps": 1.0,
-                    "sig": 1.0,
-                },
-            )
-        self.assertEqual(
-            str(context.exception),
-            "Invalid rz fields for site 1 for molecule type 1. Value must be a float.",
-        )
-
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": 1.0,
-                    "na": 1,
-                    "rx": 1.0,
-                    "ry": 1.0,
-                    "rz": 1.0,
-                    "chg": "",
-                    "eps": 1.0,
-                    "sig": 1.0,
-                },
-            )
-        self.assertEqual(
-            str(context.exception),
-            "Invalid chg fields for site 1 for molecule type 1. Value must be a float.",
-        )
-
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": 1.0,
-                    "na": 1,
-                    "rx": 1.0,
-                    "ry": 1.0,
-                    "rz": 1.0,
-                    "chg": 1.0,
-                    "eps": "",
-                    "sig": 1.0,
-                },
-            )
-        self.assertEqual(
-            str(context.exception),
-            "Invalid eps fields for site 1 for molecule type 1. Value must be a float.",
-        )
-
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": 1.0,
-                    "na": 1,
-                    "rx": 1.0,
-                    "ry": 1.0,
-                    "rz": 1.0,
-                    "chg": 1.0,
-                    "eps": 1.0,
-                    "sig": "",
-                },
-            )
-        self.assertEqual(
-            str(context.exception),
-            "Invalid sig fields for site 1 for molecule type 1. Value must be a float.",
-        )
-
-    @mock.patch("builtins.open", mock_open)
-    @mock.patch("diceplayer.player.Path.exists", return_value=True)
-    def test_read_potentials(self, mock_path_exists):
-        player = Player("control.test.yml")
-
-        player.read_potentials()
-
-        self.assertEqual(player.system.molecule[0].molname, "TEST")
-        self.assertEqual(len(player.system.molecule[0].atom), 1)
-
-        self.assertEqual(player.system.molecule[1].molname, "PLACEHOLDER")
-        self.assertEqual(len(player.system.molecule[1].atom), 1)
-
-    @mock.patch("builtins.open", mock_open)
-    @mock.patch("diceplayer.player.Path.exists")
-    def test_read_potentials_error(self, mock_path_exists):
-        player = Player("control.test.yml")
-
-        # Testing file not found error
-        mock_path_exists.return_value = False
-        with self.assertRaises(RuntimeError) as context:
-            player.read_potentials()
-
-        self.assertEqual(str(context.exception), "Potential file phb.ljc not found.")
-
-        # Enabling file found for next tests
-        mock_path_exists.return_value = True
-
-        # Testing combrule error
-        with self.assertRaises(SystemExit) as context:
-            player.config.dice.ljname = "phb.error.combrule.ljc"
-            player.read_potentials()
-
-        self.assertEqual(
-            str(context.exception),
-            "Error: expected a '*' or a '+' sign in 1st line of file phb.error.combrule.ljc",
-        )
-
-        # Testing ntypes error
-        with self.assertRaises(SystemExit) as context:
-            player.config.dice.ljname = "phb.error.ntypes.ljc"
-            player.read_potentials()
-
-        self.assertEqual(
-            str(context.exception),
-            "Error: expected an integer in the 2nd line of file phb.error.ntypes.ljc",
-        )
-
-        # Testing ntypes error on config
-        with self.assertRaises(SystemExit) as context:
-            player.config.dice.ljname = "phb.error.ntypes.config.ljc"
-            player.read_potentials()
-
-        self.assertEqual(
-            str(context.exception),
-            "Error: number of molecule types in file phb.error.ntypes.config.ljc "
-            "must match that of 'nmol' keyword in config file",
-        )
-
-        # Testing nsite error
-        with self.assertRaises(ValueError) as context:
-            player.config.dice.ljname = "phb.error.nsites.ljc"
-            player.read_potentials()
-
-        self.assertEqual(
-            str(context.exception),
-            "Error: expected nsites to be an integer for molecule type 1",
-        )
-
-        # Testing molname error
-        with self.assertRaises(ValueError) as context:
-            player.config.dice.ljname = "phb.error.molname.ljc"
-            player.read_potentials()
-
-        self.assertEqual(
-            str(context.exception),
-            "Error: expected nsites and molname for the molecule type 1",
-        )
-
-    @mock.patch("builtins.open", mock_open)
-    @mock.patch("diceplayer.player.Path.exists", return_value=True)
-    def test_print_potentials(self, mock_path_exists):
-        player = Player("control.test.yml")
-        player.read_potentials()
-
-        with self.assertLogs(level="INFO") as context:
-            player.print_potentials()
-
-        expected_output = [
-            "INFO:diceplayer:==========================================================================================\n                    Potential parameters from file phb.ljc:\n------------------------------------------------------------------------------------------\n",
-            "INFO:diceplayer:Combination rule: *",
-            "INFO:diceplayer:Types of molecules: 2\n",
-            "INFO:diceplayer:1 atoms in molecule type 1:",
-            "INFO:diceplayer:---------------------------------------------------------------------------------",
-            "INFO:diceplayer:Lbl  AN       X          Y          Z         Charge    Epsilon   Sigma     Mass",
-            "INFO:diceplayer:---------------------------------------------------------------------------------",
-            "INFO:diceplayer:1     1     0.00000    0.00000    0.00000    0.000000   0.00000  0.0000    1.0079",
-            "INFO:diceplayer:\n",
-            "INFO:diceplayer:1 atoms in molecule type 2:",
-            "INFO:diceplayer:---------------------------------------------------------------------------------",
-            "INFO:diceplayer:Lbl  AN       X          Y          Z         Charge    Epsilon   Sigma     Mass",
-            "INFO:diceplayer:---------------------------------------------------------------------------------",
-            "INFO:diceplayer:1     1     0.00000    0.00000    0.00000    0.000000   0.00000  0.0000    1.0079",
-            "INFO:diceplayer:\n",
-        ]
-
-        self.assertEqual(context.output, expected_output)
-
-    @mock.patch("builtins.open", mock_open)
-    def test_dice_start(self):
-        player = Player("control.test.yml")
-        player.dice_interface = mock.MagicMock()
-        player.dice_interface.start = mock.MagicMock()
-
-        player.dice_start(1)
-
-        player.dice_interface.start.assert_called_once()
-
-
-if __name__ == "__main__":
-    unittest.main()

tests/utils/test_potential.py

@@ -0,0 +1,37 @@
+from diceplayer.config import PlayerConfig
+from diceplayer.environment import System
+from diceplayer.utils.potential import read_system_from_phb
+
+import pytest
+
+
+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)

uv.lock

@@ -1,10 +1,6 @@
 version = 1
 revision = 3
-requires-python = ">=3.10"
+requires-python = ">=3.12"
-resolution-markers = [
-    "python_full_version >= '3.11'",
-    "python_full_version < '3.11'",
-]
 
 [[package]]
 name = "annotated-types"
@@ -35,21 +31,9 @@ dependencies = [
     { name = "pathspec" },
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     { name = "poethepoet" },
     { name = "pre-commit" },
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