Merge pull request #18 from HideyoshiNakazone/feature/refactors-environment

Feature/refactors environment

.github/workflows/python-test-and-build.yml

@@ -1,7 +1,7 @@
                                                                                                                                                       # This workflow will install Python dependencies, run tests and lint with a single version of Python
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 
-name: Upload DicePlayer to PyPI
+name: build and upload
 
 on:
     push
@@ -13,24 +13,35 @@ jobs:
 
     test:
         runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                python-version:
+                    - "3.10"
         steps:
             -   uses: actions/checkout@v3
                 with:
                     fetch-depth: 0
-            -   name: Install poetry
-                run: pipx install poetry
 
             -   name: Set up Python 3.10
                 uses: actions/setup-python@v3
                 with:
                     python-version: "3.10"
-            -   name: Install dependencies
-                run: |
-                    poetry self add "poetry-dynamic-versioning[plugin]"
-                    if [ -f pyproject.toml ]; then poetry install; fi
-            -   name: Run unittest
-                run: |
-                    poetry run python -m unittest
+
+            - name: Install uv
+              uses: astral-sh/setup-uv@v5
+              with:
+                  # Install a specific version of uv.
+                  version: "0.9.15"
+                  enable-cache: true
+                  cache-dependency-glob: "uv.lock"
+                  python-version: ${{ matrix.python-version }}
+
+            - name: Install dependencies
+              run: uv sync --all-extras --dev
+
+            - name: Run unittest
+              run: |
+                  uv run python -m unittest
 
     pypi-upload:
         needs: [test]
@@ -40,26 +51,27 @@ jobs:
             -   uses: actions/checkout@v3
                 with:
                     fetch-depth: 0
-            -   name: Install poetry
-                run: pipx install poetry
 
             -   name: Set up Python 3.10
                 uses: actions/setup-python@v3
                 with:
                     python-version: "3.10"
-            -   name: Install dependencies
-                run: |
-                    poetry self add "poetry-dynamic-versioning[plugin]"
-                    if [ -f pyproject.toml ]; then poetry install; fi
-            -   name: Build Python Package
-                run: |
-                    poetry build -f sdist
-                    poetry install
-                    echo "Builded DicePlayer - $(poetry version)"
-            -   name: Configure PyPI
-                run: |
-                    poetry config repositories.pypi https://upload.pypi.org/legacy/
-                    poetry config pypi-token.pypi ${{secrets.PYPI_TOKEN}}
-            -   name: Upload Python Package
-                run: |
-                    poetry publish --repository pypi
+
+            - name: Install uv
+              uses: astral-sh/setup-uv@v5
+              with:
+                  # Install a specific version of uv.
+                  version: "0.9.15"
+                  enable-cache: true
+                  cache-dependency-glob: "uv.lock"
+                  python-version: ${{ matrix.python-version }}
+
+            - name: Install dependencies
+              run: uv sync
+
+            - name: Build source distribution
+              run: uv build --sdist
+
+            - name: Upload Python Package
+              run: |
+                  uv publish -t ${{ secrets.PYPI_TOKEN }}

.gitignore

@@ -1,20 +1,184 @@
-### Python ###
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
 *$py.class
-.vscode/settings.json
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# IDE
+.idea/
+.vscode
 
 *.ljc
-*.log
 *.log.backup
-
 simfiles/*
-
-.vscode/*
-.idea/*
 *.pkl
-
 *.xyz
-
-dist/

.pre-commit-config.yaml

@@ -1,13 +1,9 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 24.4.2
-    hooks:
-    - id: black
-      args: [--config=pyproject.toml]
-
-  - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
-    hooks:
-    - id: isort
-      files: "\\.(py)$"
-      args: [--settings-path=pyproject.toml]
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+        # Ruff version.
+      rev: v0.14.7
+      hooks:
+          # Run the linter.
+          - id: ruff
+          # Run the formatter.
+          - id: ruff-format

.python-version

@@ -0,0 +1 @@
+3.10

diceplayer/__init__.py

@@ -1,7 +1,8 @@
-from diceplayer.shared.utils.logger import Logger
+from diceplayer.utils import Logger
 
 from importlib import metadata
 
+
 VERSION = metadata.version("diceplayer")
 
 logger = Logger(__name__)

diceplayer/config/dice_config.py

@@ -0,0 +1,40 @@
+from pydantic import BaseModel, Field
+from typing_extensions import List, Literal
+
+
+class DiceConfig(BaseModel):
+    """
+    Data Transfer Object for the Dice configuration.
+    """
+
+    ljname: str = 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(
+        ..., description="List of the number of molecules for each component"
+    )
+    nstep: List[int] = Field(
+        ...,
+        description="List of the number of steps for each component",
+        min_length=2,
+        max_length=3,
+    )
+
+    upbuf: int = Field(
+        360, description="Buffer size for the potential energy calculations"
+    )
+    combrule: Literal["+", "*"] = Field(
+        "*", description="Combination rule for the Lennard-Jones potential"
+    )
+    isave: int = Field(1000, description="Frequency of saving the simulation results")
+    press: float = Field(1.0, description="Pressure of the system")
+    temp: float = Field(300.0, description="Temperature of the system")
+    progname: str = Field(
+        "dice", description="Name of the program to run the simulation"
+    )
+    randominit: str = Field(
+        "first", description="Method for initializing the random number generator"
+    )
+    seed: int | None = Field(None, description="Seed for the random number generator")

diceplayer/config/gaussian_config.py

@@ -0,0 +1,25 @@
+from pydantic import BaseModel, Field
+from typing_extensions import Literal
+
+
+class GaussianConfig(BaseModel):
+    """
+    Data Transfer Object for the Gaussian configuration.
+    """
+
+    level: str = Field(..., description="Level of theory for the QM calculations")
+    qmprog: Literal["g03", "g09", "g16"] = Field(
+        "g16", description="QM program to use for the calculations"
+    )
+
+    chgmult: list[int] = Field(
+        default_factory=lambda: [0, 1],
+        description="List of charge and multiplicity for the QM calculations",
+    )
+    pop: str = Field(
+        "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(
+        None, description="Additional keywords for the QM calculations"
+    )

diceplayer/config/player_config.py

@@ -0,0 +1,48 @@
+from diceplayer.config.dice_config import DiceConfig
+from diceplayer.config.gaussian_config import GaussianConfig
+
+from pydantic import BaseModel, Field, model_validator
+from typing_extensions import Self
+
+from pathlib import Path
+
+
+MIN_STEP = 20000
+
+
+class PlayerConfig(BaseModel):
+    """
+    Data Transfer Object for the player configuration.
+    """
+
+    opt: bool = Field(..., description="Whether to perform geometry optimization")
+    maxcyc: int = Field(
+        ..., description="Maximum number of cycles for the geometry optimization"
+    )
+    nprocs: int = Field(
+        ..., description="Number of processors to use for the QM calculations"
+    )
+    ncores: int = Field(
+        ..., description="Number of cores to use for the QM calculations"
+    )
+
+    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"
+    )
+    simulation_dir: Path = Field(
+        "simfiles", description="Directory name for the simulation files"
+    )
+
+    @model_validator(mode="after")
+    def validate_altsteps(self) -> Self:
+        self.altsteps = round(max(MIN_STEP, self.altsteps) / 1000) * 1000
+        return self

diceplayer/environment/__init__.py

@@ -0,0 +1,6 @@
+from .atom import Atom
+from .molecule import Molecule
+from .system import System
+
+
+__all__ = ["Atom", "Molecule", "System"]

diceplayer/environment/atom.py

@@ -0,0 +1,27 @@
+from diceplayer.utils.ptable import AtomInfo, PTable
+
+from dataclasses import dataclass
+
+
+@dataclass
+class Atom:
+    """
+    Atom class declaration. This class is used throughout the DicePlayer program to represent atoms.
+    """
+
+    lbl: int
+    na: int
+    rx: float
+    ry: float
+    rz: float
+    chg: float
+    eps: float
+    sig: float
+
+    @property
+    def mass(self) -> float:
+        return PTable.get_atomic_mass(self.na)
+
+    @property
+    def atom_info(self) -> AtomInfo:
+        return PTable.get_from_atomic_number(self.na)

diceplayer/environment/molecule.py

@@ -0,0 +1,316 @@
+from __future__ import annotations
+
+from diceplayer import logger
+from diceplayer.environment import Atom
+from diceplayer.utils.cache import invalidate_computed_properties
+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
+from typing_extensions import List, Self, Tuple
+
+import math
+from copy import deepcopy
+from dataclasses import dataclass, field
+from functools import cached_property
+
+
+@dataclass
+class Molecule:
+    """
+    Molecule class declaration. This class is used throughout the DicePlayer program to represent molecules.
+
+    Atributes:
+        molname (str): The name of the represented molecule
+        atom (List[Atom]): List of atoms of the represented molecule
+        total_mass (int): The total mass of the molecule
+        com (npt.NDArray[np.float64]): The center of mass of the molecule
+        inertia_tensor (npt.NDArray[np.float64]): The inertia tensor of the molecule
+    """
+
+    molname: str
+    atom: List[Atom] = field(default_factory=list)
+
+    @cached_property
+    def total_mass(self) -> float:
+        return sum(atom.mass for atom in self.atom)
+
+    @cached_property
+    def com(self) -> npt.NDArray[np.float64]:
+        com = np.zeros(3)
+
+        for atom in self.atom:
+            com += atom.mass * np.array([atom.rx, atom.ry, atom.rz])
+
+        com = com / self.total_mass
+
+        return com
+
+    @cached_property
+    def inertia_tensor(self) -> npt.NDArray[np.float64]:
+        """
+        Calculates the inertia tensor of the molecule.
+
+        Returns:
+            npt.NDArray[np.float64]: inertia tensor of the molecule.
+        """
+        inertia_tensor = np.zeros((3, 3), dtype=np.float64)
+
+        for atom in self.atom:
+            dx = atom.rx - self.com[0]
+            dy = atom.ry - self.com[1]
+            dz = atom.rz - self.com[2]
+
+            inertia_tensor[0, 0] += atom.mass * (dy**2 + dz**2)
+            inertia_tensor[1, 1] += atom.mass * (dz**2 + dx**2)
+            inertia_tensor[2, 2] += atom.mass * (dx**2 + dy**2)
+
+            inertia_tensor[0, 1] -= atom.mass * dx * dy
+            inertia_tensor[0, 2] -= atom.mass * dx * dz
+            inertia_tensor[1, 2] -= atom.mass * dy * dz
+
+        # enforce symmetry
+        inertia_tensor[1, 0] = inertia_tensor[0, 1]
+        inertia_tensor[2, 0] = inertia_tensor[0, 2]
+        inertia_tensor[2, 1] = inertia_tensor[1, 2]
+
+        return inertia_tensor
+
+    @invalidate_computed_properties()
+    def add_atom(self, a: Atom) -> None:
+        """
+        Adds Atom instance to the molecule.
+
+        Args:
+            a (Atom): Atom instance to be added to atom list.
+        """
+
+        self.atom.append(a)
+
+    @invalidate_computed_properties()
+    def remove_atom(self, a: Atom) -> None:
+        """
+        Removes Atom instance from the molecule.
+
+        Args:
+            a (Atom): Atom instance to be removed from atom list.
+        """
+
+        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
+        """
+        for atom in self.atom:
+            atom.rx -= self.com[0]
+            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
+        """
+
+        self.move_center_of_mass_to_origin()
+        evals, evecs = self.principal_axes()
+
+        if np.isclose(linalg.det(evecs), -1):
+            evecs[:, 2] *= -1
+
+        if not np.isclose(linalg.det(evecs), 1):
+            raise RuntimeError(
+                "Error: could not make a rotation matrix while adopting the standard orientation"
+            )
+
+        coords = np.array([(a.rx, a.ry, a.rz) for a in self.atom])
+        rotated = coords @ evecs.T
+
+        for atom, pos in zip(self.atom, rotated):
+            atom.rx, atom.ry, atom.rz = pos
+
+    def charges_and_dipole(self) -> List[float]:
+        """
+        Calculates the charges and dipole of the molecule atoms
+
+        Returns:
+            List[float]: Respectivly magnitude of the: charge magnitude, first dipole,
+            second dipole, third dipole and total dipole.
+        """
+
+        charge = 0
+        dipole = np.zeros(3)
+        for atom in self.atom:
+            position = np.array([atom.rx, atom.ry, atom.rz])
+            dipole += atom.chg * position
+            charge += atom.chg
+
+        dipole *= EA_2_DEBYE
+        total_dipole = math.sqrt(dipole[0] ** 2 + dipole[1] ** 2 + dipole[2] ** 2)
+
+        return [charge, dipole[0], dipole[1], dipole[2], total_dipole]
+
+    def distances_between_atoms(self) -> npt.NDArray[np.float64]:
+        """
+        Calculates distances between the atoms of the molecule
+
+        Returns:
+           NDArray[Shape["Any,Any"],Float]: distances between the atoms.
+        """
+        coords = np.array([(a.rx, a.ry, a.rz) for a in self.atom], dtype=np.float64)
+        diff = coords[:, None, :] - coords[None, :, :]
+        return np.linalg.norm(diff, axis=-1)
+
+    def principal_axes(self) -> Tuple[npt.NDArray[np.float64], npt.NDArray[np.float64]]:
+        """
+        Calculates the principal axes of the molecule
+
+        Returns:
+            Tuple[np.ndarray, np.ndarray]: Tuple where the first value is the Eigen Values and the second is the Eigen Vectors,
+             representing the principal axes of the molecule.
+        """
+
+        try:
+            evals, evecs = linalg.eigh(self.inertia_tensor)
+
+            idx = np.argsort(evals)
+            evals = evals[idx]
+            evecs = evecs[:, idx]
+        except ValueError:
+            raise RuntimeError(
+                "Error: diagonalization of inertia tensor did not converge"
+            )
+
+        return evals, evecs
+
+    def read_position(self) -> npt.NDArray[np.float64]:
+        """Reads the position of the molecule from the position values of the atoms
+
+        Returns:
+            np.ndarray: internal position relative to atoms of the molecule
+        """
+        coords = np.array([(a.rx, a.ry, a.rz) for a in self.atom], dtype=np.float64)
+        return coords.ravel() * BOHR2ANG
+
+    def update_charges(self, charges: npt.NDArray[np.float64]) -> int:
+        """
+        Updates the charges of the atoms of the molecule and
+        returns the max difference between the new and old charges
+        """
+        diff = 0
+        for i, atom in enumerate(self.atom):
+            diff = max(diff, abs(atom.chg - charges[i]))
+            atom.chg = charges[i]
+
+        return diff
+
+    def sizes_of_molecule(self) -> List[float]:
+        """
+        Calculates sides of the smallest box that the molecule could fit
+
+        Returns:
+            List[float]: list of the sizes of the molecule
+        """
+        coords = np.array([(a.rx, a.ry, a.rz) for a in self.atom], dtype=np.float64)
+        return (coords.max(axis=0) - coords.min(axis=0)).tolist()
+
+    def translate(self, vector: np.ndarray) -> Self:
+        """
+        Creates a new Molecule object where its' atoms has been translated by a vector
+
+        Args:
+            vector (np.ndarray): translation vector
+
+        Returns:
+            Molecule: new Molecule object translated by a vector
+        """
+        vec = np.asarray(vector, dtype=np.float64)
+        if vec.shape != (3,):
+            raise ValueError("translation vector must be shape (3,)")
+
+        new_molecule = deepcopy(self)
+
+        for atom in new_molecule.atom:
+            atom.rx += vector[0]
+            atom.ry += vector[1]
+            atom.rz += vector[2]
+
+        return new_molecule
+
+    def print_mol_info(self) -> None:
+        """
+        Prints the Molecule information into a Output File
+        """
+
+        logger.info(
+            "    Center of mass = ( {:>10.4f} , {:>10.4f} , {:>10.4f} )".format(
+                self.com[0], self.com[1], self.com[2]
+            )
+        )
+        evals, evecs = self.principal_axes()
+
+        logger.info(
+            "    Moments of inertia =  {:>9E}  {:>9E}  {:>9E}".format(
+                evals[0], evals[1], evals[2]
+            )
+        )
+
+        logger.info(
+            "    Major principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )".format(
+                evecs[0, 0], evecs[1, 0], evecs[2, 0]
+            )
+        )
+        logger.info(
+            "    Inter principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )".format(
+                evecs[0, 1], evecs[1, 1], evecs[2, 1]
+            )
+        )
+        logger.info(
+            "    Minor principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )".format(
+                evecs[0, 2], evecs[1, 2], evecs[2, 2]
+            )
+        )
+
+        sizes = self.sizes_of_molecule()
+        logger.info(
+            "    Characteristic lengths = ( {:>6.2f} , {:>6.2f} , {:>6.2f} )".format(
+                sizes[0], sizes[1], sizes[2]
+            )
+        )
+        logger.info("    Total mass = {:>8.2f} au".format(self.total_mass))
+
+        chg_dip = self.charges_and_dipole()
+        logger.info("    Total charge = {:>8.4f} e".format(chg_dip[0]))
+        logger.info(
+            "    Dipole moment = ( {:>9.4f} , {:>9.4f} , {:>9.4f} )     Total = {:>9.4f} Debye".format(
+                chg_dip[1], chg_dip[2], chg_dip[3], chg_dip[4]
+            )
+        )
+
+    def minimum_distance(self, molec: Self) -> float:
+        """
+        Return the minimum distance between two molecules
+
+        Args:
+            molec (Molecule): Molecule object to be compared
+
+        Returns:
+            float: minimum distance between the two molecules
+        """
+        coords_a = np.array(
+            [(a.rx, a.ry, a.rz) for a in self.atom if a.na != GHOST_NUMBER]
+        )
+        coords_b = np.array(
+            [(a.rx, a.ry, a.rz) for a in molec.atom if a.na != GHOST_NUMBER]
+        )
+
+        if len(coords_a) == 0 or len(coords_b) == 0:
+            raise ValueError("No real atoms to compare")
+
+        diff = coords_a[:, None, :] - coords_b[None, :, :]
+        d2 = np.sum(diff**2, axis=-1)
+        return np.sqrt(d2.min())

diceplayer/environment/system.py

@@ -0,0 +1,30 @@
+from diceplayer.environment.molecule import Molecule
+
+from typing_extensions import List
+
+from dataclasses import dataclass, field
+
+
+@dataclass
+class System:
+    """
+    System class declaration. This class is used throughout the DicePlayer program to represent the system containing the molecules.
+
+    Atributes:
+        molecule (List[Molecule]): List of molecules of the system
+        nmols (List[int]): List of number of molecules in the system
+    """
+
+    nmols: List[int] = field(default_factory=list)
+    molecule: List[Molecule] = field(default_factory=list)
+
+    def add_type(self, m: Molecule) -> None:
+        """
+        Adds a new molecule type to the system
+
+        Args:
+            m (Molecule): The instance of the new type of molecule
+        """
+        if not isinstance(m, Molecule):
+            raise TypeError("Error: molecule is not a Molecule instance")
+        self.molecule.append(m)

diceplayer/interface/__init__.py

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

diceplayer/interface/__interface.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
-from diceplayer.shared.config.player_config import PlayerConfig
-from diceplayer.shared.environment.system import System
+from diceplayer.config.player_config import PlayerConfig
+from diceplayer.environment.system import System
 
 from abc import ABC, abstractmethod
 

diceplayer/interface/dice_interface.py

@@ -1,11 +1,12 @@
 from __future__ import annotations
 
 from diceplayer import logger
-from diceplayer.shared.config.player_config import PlayerConfig
-from diceplayer.shared.environment.system import System
-from diceplayer.shared.interface import Interface
+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
@@ -15,7 +16,7 @@ import sys
 import time
 from multiprocessing import Process, connection
 from pathlib import Path
-from typing import Final, TextIO
+
 
 DICE_END_FLAG: Final[str] = "End of simulation"
 DICE_FLAG_LINE: Final[int] = -2
@@ -206,10 +207,10 @@ class DiceInterface(Interface):
             f.write(f"temp = {self.step.dice.temp}\n")
 
             if self.step.dice.randominit == "first" and cycle > 1:
-                f.write(f"init = yesreadxyz\n")
+                f.write("init = yesreadxyz\n")
                 f.write(f"nstep = {self.step.altsteps}\n")
             else:
-                f.write(f"init = yes\n")
+                f.write("init = yes\n")
                 f.write(f"nstep = {self.step.dice.nstep[0]}\n")
 
             f.write("vstep = 0\n")
@@ -301,7 +302,7 @@ class DiceInterface(Interface):
             f.write(f"press = {self.step.dice.press}\n")
             f.write(f"temp = {self.step.dice.temp}\n")
 
-            f.write(f"nstep = 5\n")
+            f.write("nstep = 5\n")
 
             f.write(f"vstep = {int(self.step.dice.nstep[2] / 5)}\n")
             f.write("init = no\n")
@@ -356,9 +357,10 @@ class DiceInterface(Interface):
                     )
 
     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:
+        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(
                     [

diceplayer/interface/gaussian_interface.py

@@ -1,23 +1,23 @@
 from __future__ import annotations
 
 from diceplayer import logger
-from diceplayer.shared.config.player_config import PlayerConfig
-from diceplayer.shared.environment.atom import Atom
-from diceplayer.shared.environment.molecule import Molecule
-from diceplayer.shared.environment.system import System
-from diceplayer.shared.interface import Interface
-from diceplayer.shared.utils.misc import date_time
-from diceplayer.shared.utils.ptable import atomsymb
+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
-from nptyping import NDArray
+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
-from typing import Any, Dict, List, Tuple
 
 
 class GaussianInterface(Interface):
@@ -60,13 +60,13 @@ class GaussianInterface(Interface):
 
     def _copy_chk_file_from_previous_step(self, cycle: int):
         current_chk_file_path = Path(
-            self.step.simulation_dir, f"step{cycle:02d}", "qm", f"asec.chk"
+            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", f"asec.chk"
+            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.")
@@ -139,7 +139,7 @@ class GaussianInterface(Interface):
             charges_nsites = int(charges.pop(0))
             if int(charges_nsites) != total_nsites:
                 raise ValueError(
-                    f"Number of sites does not match total number of sites."
+                    "Number of sites does not match total number of sites."
                 )
 
             thickness.append(self._calculate_proc_thickness(charges))
@@ -161,12 +161,12 @@ class GaussianInterface(Interface):
 
                         if (
                             line[0].title()
-                            != atomsymb[
+                            != PTable.get_atomic_symbol(
                                 self.system.molecule[type].atom[site].na
-                            ].strip()
+                            ).strip()
                         ):
                             raise SyntaxError(
-                                f"Error: Invalid Dice Output. Atom type does not match."
+                                "Error: Invalid Dice Output. Atom type does not match."
                             )
 
                         new_molecule.add_atom(
@@ -188,7 +188,7 @@ class GaussianInterface(Interface):
                         for atom in new_molecule.atom:
                             asec_charges.append(
                                 {
-                                    "lbl": atomsymb[atom.na],
+                                    "lbl": PTable.get_atomic_symbol(atom.na),
                                     "rx": atom.rx,
                                     "ry": atom.ry,
                                     "rz": atom.rz,
@@ -216,7 +216,7 @@ class GaussianInterface(Interface):
 
     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", f"asec.gjf"
+            self.step.simulation_dir, f"step{cycle:02d}", "qm", "asec.gjf"
         )
 
         with open(gaussian_input_file_path, "w") as gaussian_input_file:
@@ -258,7 +258,7 @@ class GaussianInterface(Interface):
         )
 
         for atom in self.system.molecule[0].atom:
-            symbol = atomsymb[atom.na]
+            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

diceplayer/player.py

@@ -1,24 +1,18 @@
 from diceplayer import VERSION, logger
-from diceplayer.shared.config.dice_config import DiceConfig
-from diceplayer.shared.config.gaussian_config import GaussianDTO
-from diceplayer.shared.config.player_config import PlayerConfig
-from diceplayer.shared.environment.atom import Atom
-from diceplayer.shared.environment.molecule import Molecule
-from diceplayer.shared.environment.system import System
-from diceplayer.shared.interface.dice_interface import DiceInterface
-from diceplayer.shared.interface.gaussian_interface import GaussianInterface
-from diceplayer.shared.utils.dataclass_protocol import Dataclass
-from diceplayer.shared.utils.misc import weekday_date_time
-from diceplayer.shared.utils.ptable import atomsymb
+from diceplayer.config.player_config import PlayerConfig
+from diceplayer.environment import Atom, Molecule, System
+from diceplayer.interface import DiceInterface, GaussianInterface
+from diceplayer.utils import PTable, weekday_date_time
 
 import yaml
+from pydantic import BaseModel
+from typing_extensions import Tuple
 
 import os
 import pickle
 import sys
-from dataclasses import fields
 from pathlib import Path
-from typing import Tuple, Type
+
 
 ENV = ["OMP_STACKSIZE"]
 
@@ -82,7 +76,7 @@ class Player:
                 "\n    Translating and rotating molecule to standard orientation..."
             )
 
-            mol.standard_orientation()
+            mol.rotate_to_standard_orientation()
             logger.info("\n Done")
             logger.info("\nNew values:\n")
             mol.print_mol_info()
@@ -108,14 +102,15 @@ class Player:
         geoms_file_path.touch()
 
     def print_keywords(self) -> None:
-        def log_keywords(config: Dataclass, dto: Type[Dataclass]):
-            for key in sorted(list(map(lambda f: f.name, fields(dto)))):
-                if getattr(config, key) is not None:
-                    if isinstance(getattr(config, key), list):
-                        string = " ".join(str(x) for x in getattr(config, key))
-                        logger.info(f"{key} = [ {string} ]")
-                    else:
-                        logger.info(f"{key} = {getattr(config, key)}")
+        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"
@@ -138,7 +133,7 @@ class Player:
             "------------------------------------------------------------------------------------------\n"
         )
 
-        log_keywords(self.config.dice, DiceConfig)
+        log_keywords(self.config.dice)
 
         logger.info(
             "------------------------------------------------------------------------------------------\n"
@@ -146,7 +141,7 @@ class Player:
             "------------------------------------------------------------------------------------------\n"
         )
 
-        log_keywords(self.config.gaussian, GaussianDTO)
+        log_keywords(self.config.gaussian)
 
         logger.info("\n")
 
@@ -272,8 +267,6 @@ class Player:
             if "position" not in result:
                 raise RuntimeError("Optimization failed. No position found in result.")
 
-            self.system.update_molecule(result["position"])
-
         else:
             if "charges" not in result:
                 raise RuntimeError(
@@ -282,19 +275,43 @@ class Player:
 
             diff = self.system.molecule[0].update_charges(result["charges"])
 
-            self.system.print_charges_and_dipole(cycle)
+            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 = atomsymb[atom.na]
+                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"
                 )
@@ -412,7 +429,7 @@ class Player:
             with open("latest-step.pkl", "wb") as pickle_file:
                 pickle.dump((self.config, self.system, cycle), pickle_file)
         except Exception:
-            raise RuntimeError(f"Could not save pickle file latest-step.pkl.")
+            raise RuntimeError("Could not save pickle file latest-step.pkl.")
 
     @staticmethod
     def load_run_from_pickle() -> Tuple[PlayerConfig, System, int]:
@@ -427,7 +444,7 @@ class Player:
 
     @staticmethod
     def set_config(data: dict) -> PlayerConfig:
-        return PlayerConfig.from_dict(data)
+        return PlayerConfig.model_validate(data)
 
     @staticmethod
     def read_keywords(infile) -> dict:

diceplayer/shared/config/dice_config.py

@@ -1,51 +0,0 @@
-from diceplayer.shared.utils.dataclass_protocol import Dataclass
-
-from dataclasses import dataclass, fields
-from typing import List
-
-
-@dataclass
-class DiceConfig(Dataclass):
-    """
-    Data Transfer Object for the Dice configuration.
-    """
-
-    ljname: str
-    outname: str
-    dens: float
-    nmol: List[int]
-    nstep: List[int]
-
-    upbuf = 360
-    combrule = "*"
-    isave: int = 1000
-    press: float = 1.0
-    temp: float = 300.0
-    progname: str = "dice"
-    randominit: str = "first"
-
-    def __post_init__(self):
-        if not isinstance(self.ljname, str):
-            raise ValueError("Error: 'ljname' keyword not specified in config file")
-
-        if not isinstance(self.outname, str):
-            raise ValueError("Error: 'outname' keyword not specified in config file")
-
-        if not isinstance(self.dens, float):
-            raise ValueError("Error: 'dens' keyword not specified in config file")
-
-        if not isinstance(self.nmol, list):
-            raise ValueError(
-                "Error: 'nmol' keyword not defined appropriately in config file"
-            )
-
-        if not isinstance(self.nstep, list) or len(self.nstep) not in (2, 3):
-            raise ValueError(
-                "Error: 'nstep' keyword not defined appropriately in config file"
-            )
-
-    @classmethod
-    def from_dict(cls, params: dict):
-        params = {f.name: params[f.name] for f in fields(cls) if f.name in params}
-
-        return cls(**params)

diceplayer/shared/config/gaussian_config.py

@@ -1,30 +0,0 @@
-from diceplayer.shared.utils.dataclass_protocol import Dataclass
-
-from dataclasses import dataclass, fields
-
-
-@dataclass
-class GaussianDTO(Dataclass):
-    """
-    Data Transfer Object for the Gaussian configuration.
-    """
-
-    level: str
-    qmprog: str
-
-    chgmult = [0, 1]
-    pop: str = "chelpg"
-    chg_tol: float = 0.01
-    keywords: str = None
-
-    def __post_init__(self):
-        if self.qmprog not in ("g03", "g09", "g16"):
-            raise ValueError("Error: invalid qmprog value.")
-        if self.level is None:
-            raise ValueError("Error: 'level' keyword not specified in config file.")
-
-    @classmethod
-    def from_dict(cls, params: dict):
-        params = {f.name: params[f.name] for f in fields(cls) if f.name in params}
-
-        return cls(**params)

diceplayer/shared/config/player_config.py

@@ -1,46 +0,0 @@
-from diceplayer.shared.config.dice_config import DiceConfig
-from diceplayer.shared.config.gaussian_config import GaussianDTO
-from diceplayer.shared.utils.dataclass_protocol import Dataclass
-
-from dataclasses import dataclass, fields
-
-
-@dataclass
-class PlayerConfig(Dataclass):
-    """
-    Data Transfer Object for the player configuration.
-    """
-
-    opt: bool
-    maxcyc: int
-    nprocs: int
-    ncores: int
-
-    dice: DiceConfig
-    gaussian: GaussianDTO
-
-    mem: int = None
-    switchcyc: int = 3
-    qmprog: str = "g16"
-    altsteps: int = 20000
-    geoms_file = "geoms.xyz"
-    simulation_dir = "simfiles"
-
-    def __post_init__(self):
-        MIN_STEP = 20000
-        # altsteps value is always the nearest multiple of 1000
-        self.altsteps = round(max(MIN_STEP, self.altsteps) / 1000) * 1000
-
-    @classmethod
-    def from_dict(cls, params: dict):
-        if params["dice"] is None:
-            raise ValueError("Error: 'dice' keyword not specified in config file.")
-        params["dice"] = DiceConfig.from_dict(params["dice"])
-
-        if params["gaussian"] is None:
-            raise ValueError("Error: 'gaussian' keyword not specified in config file.")
-        params["gaussian"] = GaussianDTO.from_dict(params["gaussian"])
-
-        params = {f.name: params[f.name] for f in fields(cls) if f.name in params}
-
-        return cls(**params)

diceplayer/shared/environment/atom.py

@@ -1,52 +0,0 @@
-from diceplayer.shared.utils.ptable import atommass
-
-
-class Atom:
-    """
-    Atom class declaration. This class is used throughout the DicePlayer program to represent atoms.
-
-    Atributes:
-        lbl (int): Dice derived variable used to represent atoms with identical energies and simetric positions.
-        na (int): Atomic number of the represented atom.
-        rx (float): x cartesian coordinates of the represented atom.
-        ry (float): y cartesian coordinates of the represented atom.
-        rz (float): z cartesian coordinates of the represented atom.
-        chg (float): charge of the represented atom.
-        eps (float): quantum number epsilon of the represented atom.
-        sig (float): quantum number sigma of the represented atom.
-    """
-
-    def __init__(
-        self,
-        lbl: int,
-        na: int,
-        rx: float,
-        ry: float,
-        rz: float,
-        chg: float,
-        eps: float,
-        sig: float,
-    ) -> None:
-        """
-        The constructor function __init__ is used to create new instances of the Atom class.
-
-        Args:
-            lbl (int): Dice derived variable used to represent atoms with identical energies and simetric positions.
-            na (int): Atomic number of the represented atom.
-            rx (float): x cartesian coordinates of the represented atom.
-            ry (float): y cartesian coordinates of the represented atom.
-            rz (float): z cartesian coordinates of the represented atom.
-            chg (float): charge of the represented atom.
-            eps (float): quantum number epsilon of the represented atom.
-            sig (float): quantum number sigma of the represented atom.
-        """
-
-        self.lbl = lbl
-        self.na = na
-        self.rx = rx
-        self.ry = ry
-        self.rz = rz
-        self.chg = chg
-        self.eps = eps
-        self.sig = sig
-        self.mass = atommass[self.na]

diceplayer/shared/environment/molecule.py

@@ -1,384 +0,0 @@
-from __future__ import annotations
-
-from typing import TYPE_CHECKING
-
-if TYPE_CHECKING:
-    from nptyping import Float, NDArray, Shape
-
-from diceplayer import logger
-from diceplayer.shared.environment.atom import Atom
-from diceplayer.shared.utils.misc import BOHR2ANG
-from diceplayer.shared.utils.ptable import ghost_number
-
-import numpy as np
-from numpy.linalg import linalg
-
-import math
-from copy import deepcopy
-from typing import Any, List, Tuple, Union
-
-
-class Molecule:
-    """
-    Molecule class declaration. This class is used throughout the DicePlayer program to represent molecules.
-
-    Atributes:
-        molname (str): The name of the represented molecule
-        atom (List[Atom]): List of atoms of the represented molecule
-        position (NDArray[Any, Any]): The position relative to the internal atoms of the represented molecule
-        energy (NDArray[Any, Any]): The energy of the represented molecule
-        gradient (NDArray[Any, Any]): The first derivative of the energy relative to the position
-        hessian (NDArray[Any, Any]): The second derivative of the energy relative to the position
-        total_mass (int): The total mass of the molecule
-        com (NDArray[Any, Any]): The center of mass of the molecule
-    """
-
-    def __init__(self, molname: str) -> None:
-        """
-        The constructor function __init__ is used to create new instances of the Molecule class.
-
-        Args:
-            molname (str): Molecule name
-        """
-        self.molname: str = molname
-
-        self.atom: List[Atom] = []
-        self.position: NDArray[Any, Any]
-        self.energy: NDArray[Any, Any]
-        self.gradient: NDArray[Any, Any]
-        self.hessian: NDArray[Any, Any]
-
-        self.ghost_atoms: List[Atom] = []
-        self.lp_atoms: List[Atom] = []
-
-        self.total_mass: int = 0
-        self.com: Union[None, NDArray[Any, Any]] = None
-
-    def add_atom(self, a: Atom) -> None:
-        """
-        Adds Atom instance to the molecule.
-
-        Args:
-            a (Atom): Atom instance to be added to atom list.
-        """
-
-        self.atom.append(a)
-        self.total_mass += a.mass
-
-        self.center_of_mass()
-
-    def center_of_mass(self) -> NDArray[Any, Any]:
-        """
-        Calculates the center of mass of the molecule
-        """
-
-        self.com = np.zeros(3)
-
-        for atom in self.atom:
-            self.com += atom.mass * np.array([atom.rx, atom.ry, atom.rz])
-
-        self.com = self.com / self.total_mass
-
-        return self.com
-
-    def center_of_mass_to_origin(self) -> None:
-        """
-        Updated positions based on the center of mass of the molecule
-        """
-        for atom in self.atom:
-            atom.rx -= self.com[0]
-            atom.ry -= self.com[1]
-            atom.rz -= self.com[2]
-
-        self.center_of_mass()
-
-    def charges_and_dipole(self) -> List[float]:
-        """
-        Calculates the charges and dipole of the molecule atoms
-
-        Returns:
-            List[float]: Respectivly magnitude of the: charge magnitude, first dipole,
-            second dipole, third dipole and total dipole.
-        """
-
-        eA_to_Debye = 1 / 0.20819434
-        charge = 0
-        dipole = np.zeros(3)
-        for atom in self.atom:
-            position = np.array([atom.rx, atom.ry, atom.rz])
-            dipole += atom.chg * position
-            charge += atom.chg
-
-        dipole *= eA_to_Debye
-        total_dipole = math.sqrt(dipole[0] ** 2 + dipole[1] ** 2 + dipole[2] ** 2)
-
-        return [charge, dipole[0], dipole[1], dipole[2], total_dipole]
-
-    def distances_between_atoms(self) -> NDArray[Shape["Any,Any"], Float]:
-        """
-        Calculates distances between the atoms of the molecule
-
-        Returns:
-           NDArray[Shape["Any,Any"],Float]: distances between the atoms.
-        """
-
-        distances = []
-        dim = len(self.atom)
-        for index1, atom1 in enumerate(self.atom):
-            for index2, atom2 in enumerate(self.atom):
-                if index1 != index2:
-                    dx = atom1.rx - atom2.rx
-                    dy = atom1.ry - atom2.ry
-                    dz = atom1.rz - atom2.rz
-                    distances.append(math.sqrt(dx**2 + dy**2 + dz**2))
-
-        return np.array(distances).reshape(dim, dim - 1)
-
-    def inertia_tensor(self) -> NDArray[Shape["3, 3"], Float]:
-        """
-        Calculates the inertia tensor of the molecule.
-
-        Returns:
-            NDArray[Shape["3, 3"], Float]: inertia tensor of the molecule.
-        """
-
-        self.center_of_mass()
-        Ixx = Ixy = Ixz = Iyy = Iyz = Izz = 0.0
-
-        for atom in self.atom:
-            dx = atom.rx - self.com[0]
-            dy = atom.ry - self.com[1]
-            dz = atom.rz - self.com[2]
-
-            Ixx += atom.mass * (dy**2 + dz**2)
-            Iyy += atom.mass * (dz**2 + dx**2)
-            Izz += atom.mass * (dx**2 + dy**2)
-
-            Ixy += atom.mass * dx * dy * -1
-            Ixz += atom.mass * dx * dz * -1
-            Iyz += atom.mass * dy * dz * -1
-
-        return np.array([[Ixx, Ixy, Ixz], [Ixy, Iyy, Iyz], [Ixz, Iyz, Izz]])
-
-    def principal_axes(self) -> Tuple[np.ndarray, np.ndarray]:
-        """
-        Calculates the principal axes of the molecule
-
-        Returns:
-            Tuple[np.ndarray, np.ndarray]: Tuple where the first value is the Eigen Values and the second is the Eigen Vectors,
-             representing the principal axes of the molecule.
-        """
-
-        try:
-            evals, evecs = linalg.eigh(self.inertia_tensor())
-        except ValueError:
-            raise RuntimeError(
-                "Error: diagonalization of inertia tensor did not converge"
-            )
-
-        return evals, evecs
-
-    def read_position(self) -> np.ndarray:
-        """Reads the position of the molecule from the position values of the atoms
-
-        Returns:
-            np.ndarray: internal position relative to atoms of the molecule
-        """
-
-        position_list = []
-        for atom in self.atom:
-            position_list.extend([atom.rx, atom.ry, atom.rz])
-        position = np.array(position_list)
-        position *= BOHR2ANG
-
-        return position
-
-    def update_charges(self, charges: NDArray) -> int:
-        """
-        Updates the charges of the atoms of the molecule and
-        returns the max difference between the new and old charges
-        """
-        diff = 0
-        for i, atom in enumerate(self.atom):
-            diff = max(diff, abs(atom.chg - charges[i]))
-            atom.chg = charges[i]
-
-        return diff
-
-    # @staticmethod
-    # def update_hessian(
-    #         step: np.ndarray,
-    #         cur_gradient: np.ndarray,
-    #         old_gradient: np.ndarray,
-    #         hessian: np.ndarray,
-    # ) -> np.ndarray:
-    #     """
-    #     Updates the Hessian of the molecule based on the current hessian, the current gradient and the previous gradient
-    #
-    #     Args:
-    #         step (np.ndarray): step value of the iteration
-    #         cur_gradient (np.ndarray): current gradient
-    #         old_gradient (np.ndarray): previous gradient
-    #         hessian (np.ndarray): current hessian
-    #
-    #     Returns:
-    #         np.ndarray: updated hessian of the molecule
-    #     """
-    #
-    #     dif_gradient = cur_gradient - old_gradient
-    #
-    #     mat1 = 1 / np.dot(dif_gradient, step) * np.matmul(dif_gradient.T, dif_gradient)
-    #     mat2 = 1 / np.dot(step, np.matmul(hessian, step.T).T)
-    #     mat2 *= np.matmul(np.matmul(hessian, step.T), np.matmul(step, hessian))
-    #
-    #     return hessian + mat1 - mat2
-
-    def sizes_of_molecule(self) -> List[float]:
-        """
-        Calculates sides of the smallest box that the molecule could fit
-
-        Returns:
-            List[float]: list of the sizes of the molecule
-        """
-
-        x_list = []
-        y_list = []
-        z_list = []
-
-        for atom in self.atom:
-            x_list.append(atom.rx)
-            y_list.append(atom.ry)
-            z_list.append(atom.rz)
-
-        x_max = max(x_list)
-        x_min = min(x_list)
-        y_max = max(y_list)
-        y_min = min(y_list)
-        z_max = max(z_list)
-        z_min = min(z_list)
-
-        sizes = [x_max - x_min, y_max - y_min, z_max - z_min]
-
-        return sizes
-
-    def standard_orientation(self) -> None:
-        """
-        Rotates the molecule to the standard orientation
-        """
-
-        self.center_of_mass_to_origin()
-        evals, evecs = self.principal_axes()
-
-        if round(linalg.det(evecs)) == -1:
-            evecs[0, 2] *= -1
-            evecs[1, 2] *= -1
-            evecs[2, 2] *= -1
-
-        if round(linalg.det(evecs)) != 1:
-            raise RuntimeError(
-                "Error: could not make a rotation matrix while adopting the standard orientation"
-            )
-
-        rot_matrix = evecs.T
-
-        for atom in self.atom:
-            position = np.array([atom.rx, atom.ry, atom.rz])
-            new_position = np.matmul(rot_matrix, position.T).T
-
-            atom.rx = new_position[0]
-            atom.ry = new_position[1]
-            atom.rz = new_position[2]
-
-    def translate(self, vector: np.ndarray) -> "Molecule":
-        """
-        Creates a new Molecule object where its' atoms has been translated by a vector
-
-        Args:
-            vector (np.ndarray): translation vector
-
-        Returns:
-            Molecule: new Molecule object translated by a vector
-        """
-
-        new_molecule = deepcopy(self)
-
-        for atom in new_molecule.atom:
-            atom.rx += vector[0]
-            atom.ry += vector[1]
-            atom.rz += vector[2]
-
-        return new_molecule
-
-    def print_mol_info(self) -> None:
-        """
-        Prints the Molecule information into a Output File
-        """
-
-        logger.info(
-            "    Center of mass = ( {:>10.4f} , {:>10.4f} , {:>10.4f} )".format(
-                self.com[0], self.com[1], self.com[2]
-            )
-        )
-        inertia = self.inertia_tensor()
-        evals, evecs = self.principal_axes()
-
-        logger.info(
-            "    Moments of inertia =  {:>9E}  {:>9E}  {:>9E}".format(
-                evals[0], evals[1], evals[2]
-            )
-        )
-
-        logger.info(
-            "    Major principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )".format(
-                evecs[0, 0], evecs[1, 0], evecs[2, 0]
-            )
-        )
-        logger.info(
-            "    Inter principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )".format(
-                evecs[0, 1], evecs[1, 1], evecs[2, 1]
-            )
-        )
-        logger.info(
-            "    Minor principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )".format(
-                evecs[0, 2], evecs[1, 2], evecs[2, 2]
-            )
-        )
-
-        sizes = self.sizes_of_molecule()
-        logger.info(
-            "    Characteristic lengths = ( {:>6.2f} , {:>6.2f} , {:>6.2f} )".format(
-                sizes[0], sizes[1], sizes[2]
-            )
-        )
-        logger.info("    Total mass = {:>8.2f} au".format(self.total_mass))
-
-        chg_dip = self.charges_and_dipole()
-        logger.info("    Total charge = {:>8.4f} e".format(chg_dip[0]))
-        logger.info(
-            "    Dipole moment = ( {:>9.4f} , {:>9.4f} , {:>9.4f} )     Total = {:>9.4f} Debye".format(
-                chg_dip[1], chg_dip[2], chg_dip[3], chg_dip[4]
-            )
-        )
-
-    def minimum_distance(self, molec: "Molecule") -> float:
-        """
-        Return the minimum distance between two molecules
-
-        Args:
-            molec (Molecule): Molecule object to be compared
-
-        Returns:
-            float: minimum distance between the two molecules
-        """
-
-        distances = []
-        for atom1 in self.atom:
-            if atom1.na != ghost_number:
-                for atom2 in molec.atom:
-                    if atom2.na != ghost_number:
-                        dx = atom1.rx - atom2.rx
-                        dy = atom1.ry - atom2.ry
-                        dz = atom1.rz - atom2.rz
-                        distances.append(math.sqrt(dx**2 + dy**2 + dz**2))
-
-        return min(distances)

diceplayer/shared/environment/system.py

@@ -1,237 +0,0 @@
-from diceplayer import logger
-from diceplayer.shared.environment.molecule import Molecule
-from diceplayer.shared.utils.misc import BOHR2ANG
-from diceplayer.shared.utils.ptable import atomsymb
-
-import numpy as np
-from numpy import linalg
-
-import math
-from copy import deepcopy
-from typing import List, TextIO, Tuple
-
-
-class System:
-    """
-    System class declaration. This class is used throughout the DicePlayer program to represent the system containing the molecules.
-
-    Atributes:
-        molecule (List[Molecule]): List of molecules of the system
-        nmols (List[int]): List of number of molecules in the system
-    """
-
-    def __init__(self) -> None:
-        """
-        Initializes an empty system object that will be populated afterwards
-        """
-        self.nmols: List[int] = []
-        self.molecule: List[Molecule] = []
-
-    def add_type(self, m: Molecule) -> None:
-        """
-        Adds a new molecule type to the system
-
-        Args:
-            m (Molecule): The instance of the new type of molecule
-        """
-        if isinstance(m, Molecule) is False:
-            raise TypeError("Error: molecule is not a Molecule instance")
-        self.molecule.append(m)
-
-    def update_molecule(self, position: np.ndarray) -> None:
-        """Updates the position of the molecule in the Output file
-
-        Args:
-            position (np.ndarray): numpy position vector
-        """
-
-        position_in_ang = (position * BOHR2ANG).tolist()
-        self.add_type(deepcopy(self.molecule[0]))
-
-        for atom in self.molecule[-1].atom:
-            atom.rx = position_in_ang.pop(0)
-            atom.ry = position_in_ang.pop(0)
-            atom.rz = position_in_ang.pop(0)
-
-        rmsd, self.molecule[0] = self.rmsd_fit(-1, 0)
-        self.molecule.pop(-1)
-
-        logger.info("Projected new conformation of reference molecule with RMSD fit")
-        logger.info(f"RMSD = {rmsd:>8.5f} Angstrom")
-
-    def rmsd_fit(self, p_index: int, r_index: int) -> Tuple[float, Molecule]:
-        projecting_mol = self.molecule[p_index]
-        reference_mol = self.molecule[r_index]
-
-        if len(projecting_mol.atom) != len(reference_mol.atom):
-            raise RuntimeError(
-                "Error in RMSD fit procedure: molecules have different number of atoms"
-            )
-        dim = len(projecting_mol.atom)
-
-        new_projecting_mol = deepcopy(projecting_mol)
-        new_reference_mol = deepcopy(reference_mol)
-
-        new_projecting_mol.center_of_mass_to_origin()
-        new_reference_mol.center_of_mass_to_origin()
-
-        x = []
-        y = []
-
-        for atom in new_projecting_mol.atom:
-            x.extend([atom.rx, atom.ry, atom.rz])
-
-        for atom in new_reference_mol.atom:
-            y.extend([atom.rx, atom.ry, atom.rz])
-
-        x = np.array(x).reshape(dim, 3)
-        y = np.array(y).reshape(dim, 3)
-
-        r = np.matmul(y.T, x)
-        rr = np.matmul(r.T, r)
-
-        try:
-            evals, evecs = linalg.eigh(rr)
-        except:
-            raise RuntimeError("Error: diagonalization of RR matrix did not converge")
-
-        a1 = evecs[:, 2].T
-        a2 = evecs[:, 1].T
-        a3 = np.cross(a1, a2)
-
-        A = np.array([a1[0], a1[1], a1[2], a2[0], a2[1], a2[2], a3[0], a3[1], a3[2]])
-        A = A.reshape(3, 3)
-
-        b1 = np.matmul(r, a1.T).T  # or np.dot(r, a1)
-        b1 /= linalg.norm(b1)
-        b2 = np.matmul(r, a2.T).T  # or np.dot(r, a2)
-        b2 /= linalg.norm(b2)
-        b3 = np.cross(b1, b2)
-
-        B = np.array([b1[0], b1[1], b1[2], b2[0], b2[1], b2[2], b3[0], b3[1], b3[2]])
-        B = B.reshape(3, 3).T
-
-        rot_matrix = np.matmul(B, A)
-        x = np.matmul(rot_matrix, x.T).T
-
-        rmsd = 0
-        for i in range(dim):
-            rmsd += (
-                (x[i, 0] - y[i, 0]) ** 2
-                + (x[i, 1] - y[i, 1]) ** 2
-                + (x[i, 2] - y[i, 2]) ** 2
-            )
-        rmsd = math.sqrt(rmsd / dim)
-
-        for i in range(dim):
-            new_projecting_mol.atom[i].rx = x[i, 0]
-            new_projecting_mol.atom[i].ry = x[i, 1]
-            new_projecting_mol.atom[i].rz = x[i, 2]
-
-        reference_mol.center_of_mass()
-
-        projected_mol = new_projecting_mol.translate(reference_mol.com)
-
-        return rmsd, projected_mol
-
-    # def center_of_mass_distance(self, a: int, b: int) -> float:
-    #     """
-    #     Calculates the distance between the center of mass of two molecules
-    #
-    #     Args:
-    #         a (Molecule): First Molecule Instance
-    #         b (Molecule): Second Molecule Instance
-    #
-    #     Returns:
-    #         float: module of the distance between the two center of masses
-    #     """
-    #
-    #     com1 = self.molecule[a].center_of_mass()
-    #     com2 = self.molecule[b].center_of_mass()
-    #     dx = com1[0] - com2[0]
-    #     dy = com1[1] - com2[1]
-    #     dz = com1[2] - com2[2]
-    #     distance = math.sqrt(dx**2 + dy**2 + dz**2)
-    #
-    #     return distance
-
-    # def nearest_image(
-    #     self,
-    #     index_r: int,
-    #     index_m: int,
-    #     lx: float,
-    #     ly: float,
-    #     lz: float,
-    #     criterium=None,
-    # ) -> Tuple[float, Molecule]:
-    #
-    #     if criterium in None:
-    #         criterium = "com"
-    #
-    #     if criterium != "com" and criterium != "min":
-    #         raise RuntimeError("Error in value passed to function nearest_image")
-    #
-    #     min_dist = 1e20
-    #
-    #     for i in range(-1, 2):
-    #         for j in range(-1, 2):
-    #             for k in range(-1, 2):
-    #
-    #                 tr_vector = [i * lx, j * ly, k * lz]
-    #                 self.add_molecule(self.molecule[index_m].translate(tr_vector))
-    #
-    #                 if criterium == "com":
-    #                     dist = self.center_of_mass_distance(index_r, -1)
-    #                 else:
-    #                     dist = self.minimum_distance(index_r, -1)
-    #
-    #                 if dist < min_dist:
-    #                     min_dist = dist
-    #                     nearestmol = deepcopy(self.molecule[-1])
-    #
-    #     self.molecule.pop(-1)
-    #
-    #     return min_dist, nearestmol
-
-    # def print_geom(self, cycle: int, fh: TextIO) -> None:
-    #     """
-    #             Print the geometry of the molecule in the Output file
-    #
-    #             Args:
-    #                 cycle (int): Number of the cycle
-    #                 fh (TextIO): Output file
-    #             """
-    #
-    #     fh.write("Cycle # {}\n".format(cycle))
-    #     fh.write("Number of site: {}\n".format(len(self.molecule[0].atom)))
-    #     for atom in self.molecule[0].atom:
-    #         symbol = atomsymb[atom.na]
-    #         fh.write(
-    #             "{:<2s}    {:>10.6f}  {:>10.6f}  {:>10.6f}\n".format(
-    #                 symbol, atom.rx, atom.ry, atom.rz
-    #             )
-    #         )
-    #
-    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.molecule[0].atom)))
-
-        chargesAndDipole = self.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],
-            )
-        )

diceplayer/shared/interface/__init__.py

@@ -1 +0,0 @@
-from .__interface import Interface

diceplayer/shared/utils/ptable.py

@@ -1,223 +0,0 @@
-####  Label used in Dice for a ghost atom
-dice_ghost_label = "Xx"
-
-####  Tuple of atom symbols
-atomsymb = (
-    "00",
-    "H ",
-    "He",
-    "Li",
-    "Be",
-    "B ",
-    "C ",
-    "N ",
-    "O ",
-    "F ",
-    "Ne",
-    "Na",
-    "Mg",
-    "Al",
-    "Si",
-    "P ",
-    "S ",
-    "Cl",
-    "Ar",
-    "K ",
-    "Ca",
-    "Sc",
-    "Ti",
-    "V ",
-    "Cr",
-    "Mn",
-    "Fe",
-    "Co",
-    "Ni",
-    "Cu",
-    "Zn",
-    "Ga",
-    "Ge",
-    "As",
-    "Se",
-    "Br",
-    "Kr",
-    "Rb",
-    "Sr",
-    "Y ",
-    "Zr",
-    "Nb",
-    "Mo",
-    "Tc",
-    "Ru",
-    "Rh",
-    "Pd",
-    "Ag",
-    "Cd",
-    "In",
-    "Sn",
-    "Sb",
-    "Te",
-    "I ",
-    "Xe",
-    "Cs",
-    "Ba",
-    "La",
-    "Ce",
-    "Pr",
-    "Nd",
-    "Pm",
-    "Sm",
-    "Eu",
-    "Gd",
-    "Tb",
-    "Dy",
-    "Ho",
-    "Er",
-    "Tm",
-    "Yb",
-    "Lu",
-    "Hf",
-    "Ta",
-    "W ",
-    "Re",
-    "Os",
-    "Ir",
-    "Pt",
-    "Au",
-    "Hg",
-    "Ti",
-    "Pb",
-    "Bi",
-    "Po",
-    "At",
-    "Rn",
-    "Fr",
-    "Ra",
-    "Ac",
-    "Th",
-    "Pa",
-    "U ",
-    "Np",
-    "Pu",
-    "Am",
-    "Cm",
-    "Bk",
-    "Cf",
-    "Es",
-    "Fm",
-    "Md",
-    "No",
-    "Lr",
-    dice_ghost_label,
-)
-
-####  Tuple of atom masses
-atommass = (
-    0.0,
-    1.0079,
-    4.0026,
-    6.9410,
-    9.0122,
-    10.811,
-    12.011,
-    14.007,
-    15.999,
-    18.998,
-    20.180,
-    22.990,
-    24.305,
-    26.982,
-    28.086,
-    30.974,
-    32.065,
-    35.453,
-    39.948,
-    39.098,
-    40.078,
-    44.956,
-    47.867,
-    50.942,
-    51.996,
-    54.938,
-    55.845,
-    58.933,
-    58.693,
-    63.546,
-    65.409,
-    69.723,
-    72.640,
-    74.922,
-    78.960,
-    79.904,
-    83.798,
-    85.468,
-    87.620,
-    88.906,
-    91.224,
-    92.906,
-    95.940,
-    98.000,
-    101.07,
-    102.91,
-    106.42,
-    107.87,
-    112.41,
-    114.82,
-    118.71,
-    121.76,
-    127.60,
-    126.90,
-    131.29,
-    132.91,
-    137.33,
-    138.91,
-    140.12,
-    140.91,
-    144.24,
-    145.00,
-    150.36,
-    151.96,
-    157.25,
-    158.93,
-    162.50,
-    164.93,
-    167.26,
-    168.93,
-    173.04,
-    174.97,
-    178.49,
-    180.95,
-    183.84,
-    186.21,
-    190.23,
-    192.22,
-    195.08,
-    196.97,
-    200.59,
-    204.38,
-    207.20,
-    208.98,
-    209.00,
-    210.00,
-    222.00,
-    223.00,
-    226.00,
-    227.00,
-    232.04,
-    231.04,
-    238.03,
-    237.00,
-    244.00,
-    243.00,
-    247.00,
-    247.00,
-    251.00,
-    252.00,
-    257.00,
-    258.00,
-    259.00,
-    262.00,
-    0.000,
-)
-
-####  Number of the ghost atom
-ghost_number = len(atomsymb) - 1

diceplayer/utils/__init__.py

@@ -0,0 +1,22 @@
+from .logger import Logger, valid_logger
+from .misc import (
+    compress_files_1mb,
+    date_time,
+    make_qm_dir,
+    make_step_dir,
+    weekday_date_time,
+)
+from .ptable import AtomInfo, PTable
+
+
+__all__ = [
+    "Logger",
+    "valid_logger",
+    "PTable",
+    "AtomInfo",
+    "weekday_date_time",
+    "date_time",
+    "compress_files_1mb",
+    "make_step_dir",
+    "make_qm_dir",
+]

diceplayer/utils/cache.py

@@ -0,0 +1,29 @@
+from functools import cached_property
+
+
+def invalidate_computed_properties():
+    """
+    Decorator function to invalidate the cached properties of the molecule when a new atom is added
+
+    Args:
+        properties (list[str]): list of the names of the properties to be invalidated
+    """
+
+    def get_cached_properies(cls: type) -> set[str]:
+        return {
+            name
+            for name, value in cls.__dict__.items()
+            if isinstance(value, cached_property)
+        }
+
+    def decorator(func):
+        def wrapper(self, *args, **kwargs):
+            result = func(self, *args, **kwargs)
+            for prop in get_cached_properies(self.__class__):
+                if hasattr(self, prop):
+                    delattr(self, prop)
+            return result
+
+        return wrapper
+
+    return decorator

diceplayer/utils/dataclass_protocol.py

@@ -1,4 +1,4 @@
-from typing import Protocol, runtime_checkable
+from typing_extensions import Protocol, runtime_checkable
 
 
 @runtime_checkable

diceplayer/utils/misc.py

@@ -1,9 +1,11 @@
+from typing_extensions import Final
+
 import gzip
 import os
 import shutil
 import sys
 import time
-from typing import Final
+
 
 #######################################  constants  ######################################
 
@@ -11,6 +13,8 @@ from typing import Final
 BOHR2ANG: Final[float] = 0.52917721092
 ANG2BOHR: Final[float] = 1 / BOHR2ANG
 
+EA_2_DEBYE = 1 / 0.20819434
+
 
 #######################################  functions  ######################################
 
@@ -35,7 +39,7 @@ def compress_files_1mb(path):
                 with open(file, "rb") as f_in:
                     with gzip.open(filegz, "wb") as f_out:
                         shutil.copyfileobj(f_in, f_out)
-            except:
+            except Exception as _:
                 sys.exit("Error: cannot compress file {}".format(file))
 
     os.chdir(working_dir)
@@ -51,7 +55,7 @@ def make_step_dir(cycle):
         sys.exit("Error: a file or directory {} already exists".format(step_dir))
     try:
         os.makedirs(path)
-    except:
+    except Exception as _:
         sys.exit("Error: cannot make directory {}".format(step_dir))
 
 
@@ -61,5 +65,5 @@ def make_qm_dir(cycle):
     path = sim_dir + os.sep + step_dir + os.sep + "qm"
     try:
         os.makedirs(path)
-    except:
+    except Exception as _:
         sys.exit("Error: cannot make directory {}".format(path))

diceplayer/utils/ptable.py

@@ -0,0 +1,143 @@
+from dataclasses import dataclass
+from enum import Enum
+
+
+DICE_GHOST_LABEL = "Xx"
+
+####  Number of the ghost atom
+GHOST_NUMBER = 0
+
+
+@dataclass(frozen=True, slots=True)
+class AtomInfo:
+    atomic_number: int
+    symbol: str
+    mass: float
+
+
+class PTable(Enum):
+    Xx = AtomInfo(GHOST_NUMBER, DICE_GHOST_LABEL, 0.0)
+    H = AtomInfo(1, "H", 1.0079)
+    He = AtomInfo(2, "He", 4.0026)
+    Li = AtomInfo(3, "Li", 6.9410)
+    Be = AtomInfo(4, "Be", 9.0122)
+    B = AtomInfo(5, "B", 10.811)
+    C = AtomInfo(6, "C", 12.011)
+    N = AtomInfo(7, "N", 14.007)
+    O = AtomInfo(8, "O", 15.999)
+    F = AtomInfo(9, "F", 18.998)
+    Ne = AtomInfo(10, "Ne", 20.180)
+    Na = AtomInfo(11, "Na", 22.990)
+    Mg = AtomInfo(12, "Mg", 24.305)
+    Al = AtomInfo(13, "Al", 26.982)
+    Si = AtomInfo(14, "Si", 28.086)
+    P = AtomInfo(15, "P", 30.974)
+    S = AtomInfo(16, "S", 32.065)
+    Cl = AtomInfo(17, "Cl", 35.453)
+    Ar = AtomInfo(18, "Ar", 39.948)
+    K = AtomInfo(19, "K", 39.098)
+    Ca = AtomInfo(20, "Ca", 40.078)
+    Sc = AtomInfo(21, "Sc", 44.956)
+    Ti = AtomInfo(22, "Ti", 47.867)
+    V = AtomInfo(23, "V", 50.942)
+    Cr = AtomInfo(24, "Cr", 51.996)
+    Mn = AtomInfo(25, "Mn", 54.938)
+    Fe = AtomInfo(26, "Fe", 55.845)
+    Co = AtomInfo(27, "Co", 58.933)
+    Ni = AtomInfo(28, "Ni", 58.693)
+    Cu = AtomInfo(29, "Cu", 63.546)
+    Zn = AtomInfo(30, "Zn", 65.409)
+    Ga = AtomInfo(31, "Ga", 69.723)
+    Ge = AtomInfo(32, "Ge", 72.640)
+    As = AtomInfo(33, "As", 74.922)
+    Se = AtomInfo(34, "Se", 78.960)
+    Br = AtomInfo(35, "Br", 79.904)
+    Kr = AtomInfo(36, "Kr", 83.798)
+    Rb = AtomInfo(37, "Rb", 85.468)
+    Sr = AtomInfo(38, "Sr", 87.620)
+    Y = AtomInfo(39, "Y", 88.906)
+    Zr = AtomInfo(40, "Zr", 91.224)
+    Nb = AtomInfo(41, "Nb", 92.906)
+    Mo = AtomInfo(42, "Mo", 95.940)
+    Tc = AtomInfo(43, "Tc", 98.000)
+    Ru = AtomInfo(44, "Ru", 101.07)
+    Rh = AtomInfo(45, "Rh", 102.91)
+    Pd = AtomInfo(46, "Pd", 106.42)
+    Ag = AtomInfo(47, "Ag", 107.87)
+    Cd = AtomInfo(48, "Cd", 112.41)
+    In = AtomInfo(49, "In", 114.82)
+    Sn = AtomInfo(50, "Sn", 118.71)
+    Sb = AtomInfo(51, "Sb", 121.76)
+    Te = AtomInfo(52, "Te", 127.60)
+    I = AtomInfo(53, "I", 126.90)
+    Xe = AtomInfo(54, "Xe", 131.29)
+    Cs = AtomInfo(55, "Cs", 132.91)
+    Ba = AtomInfo(56, "Ba", 137.33)
+    La = AtomInfo(57, "La", 138.91)
+    Ce = AtomInfo(58, "Ce", 140.12)
+    Pr = AtomInfo(59, "Pr", 140.91)
+    Nd = AtomInfo(60, "Nd", 144.24)
+    Pm = AtomInfo(61, "Pm", 145.00)
+    Sm = AtomInfo(62, "Sm", 150.36)
+    Eu = AtomInfo(63, "Eu", 151.96)
+    Gd = AtomInfo(64, "Gd", 157.25)
+    Tb = AtomInfo(65, "Tb", 158.93)
+    Dy = AtomInfo(66, "Dy", 162.50)
+    Ho = AtomInfo(67, "Ho", 164.93)
+    Er = AtomInfo(68, "Er", 167.26)
+    Tm = AtomInfo(69, "Tm", 168.93)
+    Yb = AtomInfo(70, "Yb", 173.04)
+    Lu = AtomInfo(71, "Lu", 174.97)
+    Hf = AtomInfo(72, "Hf", 178.49)
+    Ta = AtomInfo(73, "Ta", 180.95)
+    W = AtomInfo(74, "W", 183.84)
+    Re = AtomInfo(75, "Re", 186.21)
+    Os = AtomInfo(76, "Os", 190.23)
+    Ir = AtomInfo(77, "Ir", 192.22)
+    Pt = AtomInfo(78, "Pt", 195.08)
+    Au = AtomInfo(79, "Au", 196.97)
+    Hg = AtomInfo(80, "Hg", 200.59)
+    Tl = AtomInfo(81, "Tl", 204.38)
+    Pb = AtomInfo(82, "Pb", 207.20)
+    Bi = AtomInfo(83, "Bi", 208.98)
+    Po = AtomInfo(84, "Po", 209.00)
+    At = AtomInfo(85, "At", 210.00)
+    Rn = AtomInfo(86, "Rn", 222.00)
+    Fr = AtomInfo(87, "Fr", 223.00)
+    Ra = AtomInfo(88, "Ra", 226.00)
+    Ac = AtomInfo(89, "Ac", 227.00)
+    Th = AtomInfo(90, "Th", 232.04)
+    Pa = AtomInfo(91, "Pa", 231.04)
+    U = AtomInfo(92, "U", 238.03)
+    Np = AtomInfo(93, "Np", 237.00)
+    Pu = AtomInfo(94, "Pu", 244.00)
+    Am = AtomInfo(95, "Am", 243.00)
+    Cm = AtomInfo(96, "Cm", 247.00)
+    Bk = AtomInfo(97, "Bk", 247.00)
+    Cf = AtomInfo(98, "Cf", 251.00)
+    Es = AtomInfo(99, "Es", 252.00)
+    Fm = AtomInfo(100, "Fm", 257.00)
+    Md = AtomInfo(101, "Md", 258.00)
+    No = AtomInfo(102, "No", 259.00)
+    Lr = AtomInfo(103, "Lr", 262.00)
+
+    @classmethod
+    def get_atomic_symbol(cls, atomic_number: int) -> str:
+        for element in cls:
+            if element.value.atomic_number == atomic_number:
+                return element.value.symbol
+        raise ValueError(f"Atomic number {atomic_number} not found in PTable.")
+
+    @classmethod
+    def get_atomic_mass(cls, atomic_number: int) -> float:
+        for element in cls:
+            if element.value.atomic_number == atomic_number:
+                return element.value.mass
+        raise ValueError(f"Atomic number {atomic_number} not found in PTable.")
+
+    @classmethod
+    def get_from_atomic_number(cls, atomic_number: int) -> AtomInfo:
+        for element in cls:
+            if element.value.atomic_number == atomic_number:
+                return element.value
+        raise ValueError(f"Atomic number {atomic_number} not found in PTable.")

poetry.lock

@@ -1,594 +0,0 @@
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pyproject.toml

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-authors = ["Vitor Hideyoshi <vitor.h.n.batista@gmail.com>", "Herbert Georg <hcgeorg@ufg.br>"]
-license = "GPL-2.0-only"
+description = "Python Program for Molecular Optimization in Non-Vacuum Mediums"
+authors = [
+    { name = "Vitor Hideyoshi", email = "vitor.h.n.batista@gmail.com" },
+    { name = "Herbert Georg", email = "hcgeorg@ufg.br" }
+]
 readme = "README.md"
+license = "GPL-2.0-only"
+scripts = { diceplayer = "diceplayer.__main__:main" }
+requires-python = ">=3.10"
+dynamic = ["version"]
 
-[tool.poetry.dependencies]
-python = ">=3.9,<4.0"
-numpy = "^1.26.4"
-argparse = "^1.4.0"
-setproctitle = "^1.3.2"
-pyyaml = "^6.0"
-nptyping = "^2.5.0"
 
-[tool.poetry.scripts]
-diceplayer = "diceplayer.__main__:main"
+dependencies = [
+    "numpy>=2.2.0",
+    "argparse>=1.4.0",
+    "setproctitle>=1.3.2",
+    "pyyaml>=6.0",
+    "pydantic>=2.12.5",
+    "typing-extensions>=4.15.0"
+]
 
-[tool.poetry.group.dev.dependencies]
-coverage = "^7.2.7"
-isort = "^5.13.2"
-black = "^24.4.2"
-pre-commit = "^3.7.1"
-poethepoet = "^0.27.0"
 
-[tool.poetry-dynamic-versioning]
-enable = true
-vcs = "git"
+[dependency-groups]
+dev = [
+    "coverage>=7.2.7",
+    "isort>=5.13.2",
+    "black>=24.4.2",
+    "pre-commit>=3.7.1",
+    "poethepoet>=0.27.0",
+    "ruff>=0.15.2"
+]
+
+
+# Build system
+[tool.hatch.version]
+source = "vcs"
 
 [build-system]
-requires = ["poetry-core"]
-build-backend = "poetry_dynamic_versioning.backend"
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
 
+
+# POE Tasks
 [tool.poe.tasks]
-hooks = "pre-commit install --config .pre-commit-config.yaml"
+create-hooks        = "bash .githooks/set-hooks.sh"
+tests               = "python -m coverage run -m unittest discover -v"
+tests-report        = "python -m coverage xml"
 
-[tool.isort]
-profile = "black"
-line_length = 79
-sections=[
-    "FUTURE",
-    "FIRSTPARTY",
-    "LOCALFOLDER",
-    "THIRDPARTY",
-    "STDLIB",
+
+
+# Tests
+[tool.coverage.run]
+omit = [
+    "tests/*",
 ]
+
+
+
+# Linters
+[tool.ruff.lint]
+extend-select = ["I"]
+ignore = [
+    "E741" # ambiguous variable name 'l', 'O', or 'I'
+]
+
+[tool.ruff.lint.isort]
+known-first-party = ["jambo"]
+section-order=[
+    "future",
+    "first-party",
+    "local-folder",
+    "third-party",
+    "standard-library",
+]
+lines-after-imports = 2
+
+
+[tool.pyright]
+venvPath = "."
+venv = ".venv"

tests/config/test_dice_dto.py

@@ -1,4 +1,4 @@
-from diceplayer.shared.config.dice_config import DiceConfig
+from diceplayer.config.dice_config import DiceConfig
 
 import unittest
 
@@ -83,7 +83,7 @@ class TestDiceDto(unittest.TestCase):
             )
 
     def test_from_dict(self):
-        dice_dto = DiceConfig.from_dict(
+        dice_dto = DiceConfig.model_validate(
             {
                 "ljname": "test",
                 "outname": "test",

tests/config/test_gaussian_dto.py

@@ -1,21 +1,21 @@
-from diceplayer.shared.config.gaussian_config import GaussianDTO
+from diceplayer.config.gaussian_config import GaussianConfig
 
 import unittest
 
 
 class TestGaussianDTO(unittest.TestCase):
     def test_class_instantiation(self):
-        gaussian_dto = GaussianDTO(
+        gaussian_dto = GaussianConfig(
             level="test",
             qmprog="g16",
             keywords="test",
         )
 
-        self.assertIsInstance(gaussian_dto, GaussianDTO)
+        self.assertIsInstance(gaussian_dto, GaussianConfig)
 
     def test_is_valid_qmprog(self):
         with self.assertRaises(ValueError):
-            gaussian_dto = GaussianDTO(
+            GaussianConfig(
                 level="test",
                 qmprog="test",
                 keywords="test",
@@ -23,14 +23,14 @@ class TestGaussianDTO(unittest.TestCase):
 
     def test_is_valid_level(self):
         with self.assertRaises(ValueError):
-            gaussian_dto = GaussianDTO(
+            GaussianConfig(
                 level=None,
                 qmprog="g16",
                 keywords="test",
             )
 
     def test_from_dict(self):
-        gaussian_dto = GaussianDTO.from_dict(
+        gaussian_dto = GaussianConfig.model_validate(
             {
                 "level": "test",
                 "qmprog": "g16",
@@ -38,7 +38,7 @@ class TestGaussianDTO(unittest.TestCase):
             }
         )
 
-        self.assertIsInstance(gaussian_dto, GaussianDTO)
+        self.assertIsInstance(gaussian_dto, GaussianConfig)
 
 
 if __name__ == "__main__":

tests/config/test_player_dto.py

@@ -1,6 +1,6 @@
-from diceplayer.shared.config.dice_config import DiceConfig
-from diceplayer.shared.config.gaussian_config import GaussianDTO
-from diceplayer.shared.config.player_config import PlayerConfig
+from diceplayer.config.dice_config import DiceConfig
+from diceplayer.config.gaussian_config import GaussianConfig
+from diceplayer.config.player_config import PlayerConfig
 
 import unittest
 
@@ -36,7 +36,7 @@ class TestPlayerDTO(unittest.TestCase):
             nmol=[1],
             nstep=[1, 1],
         )
-        self.gaussian_dto = GaussianDTO(
+        self.gaussian_dto = GaussianConfig(
             level="test",
             qmprog="g16",
             keywords="test",
@@ -55,7 +55,7 @@ class TestPlayerDTO(unittest.TestCase):
 
         self.assertIsInstance(player_dto, PlayerConfig)
         self.assertIsInstance(player_dto.dice, DiceConfig)
-        self.assertIsInstance(player_dto.gaussian, GaussianDTO)
+        self.assertIsInstance(player_dto.gaussian, GaussianConfig)
 
     def test_min_altsteps(self):
         player_dto = PlayerConfig(
@@ -72,11 +72,11 @@ class TestPlayerDTO(unittest.TestCase):
         self.assertEqual(player_dto.altsteps, 20000)
 
     def test_from_dict(self):
-        player_dto = PlayerConfig.from_dict(get_config_dict())
+        player_dto = PlayerConfig.model_validate(get_config_dict())
 
         self.assertIsInstance(player_dto, PlayerConfig)
         self.assertIsInstance(player_dto.dice, DiceConfig)
-        self.assertIsInstance(player_dto.gaussian, GaussianDTO)
+        self.assertIsInstance(player_dto.gaussian, GaussianConfig)
 
 
 if __name__ == "__main__":

tests/mocks/mock_proc.py

@@ -1,5 +1,6 @@
+from typing_extensions import List
+
 import itertools
-from typing import List
 
 
 class MockProc:

tests/shared/environment/test_atom.py

@@ -1,4 +1,4 @@
-from diceplayer.shared.environment.atom import Atom
+from diceplayer.environment import Atom
 
 import unittest
 

tests/shared/environment/test_molecule.py

@@ -1,5 +1,4 @@
-from diceplayer.shared.environment.atom import Atom
-from diceplayer.shared.environment.molecule import Molecule
+from diceplayer.environment import Atom, Molecule
 
 import numpy as np
 import numpy.testing as npt
@@ -42,7 +41,7 @@ class TestMolecule(unittest.TestCase):
             Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
         )
 
-        mol.center_of_mass_to_origin()
+        mol.move_center_of_mass_to_origin()
 
         npt.assert_equal(mol.com, [0, 0, 0])
 
@@ -69,12 +68,10 @@ class TestMolecule(unittest.TestCase):
             Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
         )
 
-        expected_distance_between_atoms = [[1.73205081], [1.73205081]]
-        actual_distance_between_atoms = mol.distances_between_atoms()
+        expected = [[0.0, 1.73205081], [1.73205081, 0.0]]
+        actual = mol.distances_between_atoms()
 
-        npt.assert_almost_equal(
-            expected_distance_between_atoms, actual_distance_between_atoms
-        )
+        npt.assert_almost_equal(expected, actual)
 
     def test_inertia_tensor(self):
         mol = Molecule("test")
@@ -92,7 +89,7 @@ class TestMolecule(unittest.TestCase):
             [-0.50395, -0.50395, 1.0079],
         ]
 
-        actual_inertia_tensor = mol.inertia_tensor()
+        actual_inertia_tensor = mol.inertia_tensor
 
         npt.assert_equal(expected_inertia_tensor, actual_inertia_tensor)
 
@@ -103,11 +100,14 @@ class TestMolecule(unittest.TestCase):
             Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
         )
 
-        expected_evals, expected_evecs = [0.0, 0.0, 0.0], [
-            [1.0, 0.0, 0.0],
-            [0.0, 1.0, 0.0],
-            [0.0, 0.0, 1.0],
-        ]
+        expected_evals, expected_evecs = (
+            [0.0, 0.0, 0.0],
+            [
+                [1.0, 0.0, 0.0],
+                [0.0, 1.0, 0.0],
+                [0.0, 0.0, 1.0],
+            ],
+        )
 
         evals, evecs = mol.principal_axes()
 
@@ -161,7 +161,7 @@ class TestMolecule(unittest.TestCase):
             Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
         )
 
-        mol.standard_orientation()
+        mol.rotate_to_standard_orientation()
 
         expected_position = [0.0, 0.0, 0.0]
 

tests/shared/environment/test_system.py

@@ -1,6 +1,4 @@
-from diceplayer.shared.environment.atom import Atom
-from diceplayer.shared.environment.molecule import Molecule
-from diceplayer.shared.environment.system import System
+from diceplayer.environment import Molecule, System
 
 import unittest
 

tests/shared/interface/test_dice_interface.py

@@ -1,9 +1,7 @@
 from diceplayer import logger
-from diceplayer.shared.config.player_config import PlayerConfig
-from diceplayer.shared.environment.atom import Atom
-from diceplayer.shared.environment.molecule import Molecule
-from diceplayer.shared.environment.system import System
-from diceplayer.shared.interface.dice_interface import DiceInterface
+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
 
@@ -19,7 +17,7 @@ class TestDiceInterface(unittest.TestCase):
         logger.set_logger(stream=io.StringIO())
 
         config = yaml.load(get_config_example(), Loader=yaml.Loader)
-        self.config = PlayerConfig.from_dict(config["diceplayer"])
+        self.config = PlayerConfig.model_validate(config["diceplayer"])
 
     def test_class_instantiation(self):
         dice = DiceInterface()
@@ -51,18 +49,16 @@ class TestDiceInterface(unittest.TestCase):
         self.assertFalse(hasattr(dice, "step"))
         self.assertFalse(hasattr(dice, "system"))
 
-    @mock.patch("diceplayer.shared.interface.dice_interface.Process", MockProc())
-    @mock.patch("diceplayer.shared.interface.dice_interface.connection", MockConnection)
+    @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.shared.interface.dice_interface.connection", MockConnection)
-    @mock.patch(
-        "diceplayer.shared.interface.dice_interface.Process", MockProc(exitcode=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())
@@ -76,13 +72,9 @@ class TestDiceInterface(unittest.TestCase):
         with self.assertRaises(SystemExit):
             dice._simulation_process(1, 1)
 
-    @mock.patch(
-        "diceplayer.shared.interface.dice_interface.DiceInterface._make_proc_dir"
-    )
-    @mock.patch(
-        "diceplayer.shared.interface.dice_interface.DiceInterface._make_dice_inputs"
-    )
-    @mock.patch("diceplayer.shared.interface.dice_interface.DiceInterface._run_dice")
+    @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
     ):
@@ -94,8 +86,8 @@ class TestDiceInterface(unittest.TestCase):
         self.assertTrue(dice._make_dice_inputs.called)
         self.assertTrue(dice._run_dice.called)
 
-    @mock.patch("diceplayer.shared.interface.dice_interface.Path.mkdir")
-    @mock.patch("diceplayer.shared.interface.dice_interface.Path.exists")
+    @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())
@@ -106,8 +98,8 @@ class TestDiceInterface(unittest.TestCase):
 
         self.assertEqual(mock_path_mkdir.call_count, 2)
 
-    @mock.patch("diceplayer.shared.interface.dice_interface.Path.mkdir")
-    @mock.patch("diceplayer.shared.interface.dice_interface.Path.exists")
+    @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
     ):
@@ -155,9 +147,7 @@ class TestDiceInterface(unittest.TestCase):
         self.assertFalse(dice._make_npt_eq.called)
 
     @mock.patch("builtins.open", new_callable=mock.mock_open, read_data="test")
-    @mock.patch(
-        "diceplayer.shared.interface.dice_interface.Path.exists", return_value=True
-    )
+    @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
     ):
@@ -189,9 +179,7 @@ class TestDiceInterface(unittest.TestCase):
         self.assertFalse(dice._make_npt_ter.called)
         self.assertFalse(dice._make_npt_eq.called)
 
-    @mock.patch(
-        "diceplayer.shared.interface.dice_interface.Path.exists", return_value=False
-    )
+    @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
     ):
@@ -240,11 +228,9 @@ class TestDiceInterface(unittest.TestCase):
         self.assertTrue(dice._make_npt_ter.called)
         self.assertTrue(dice._make_npt_eq.called)
 
-    @mock.patch("diceplayer.shared.interface.dice_interface.os")
-    @mock.patch("diceplayer.shared.interface.dice_interface.shutil")
-    @mock.patch(
-        "diceplayer.shared.interface.dice_interface.Path.exists", return_value=True
-    )
+    @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
     ):
@@ -278,11 +264,9 @@ class TestDiceInterface(unittest.TestCase):
         self.assertEqual(dice.run_dice_file.call_count, 2)
         self.assertTrue(mock_shutils.copy.called)
 
-    @mock.patch("diceplayer.shared.interface.dice_interface.os")
-    @mock.patch("diceplayer.shared.interface.dice_interface.shutil")
-    @mock.patch(
-        "diceplayer.shared.interface.dice_interface.Path.exists", return_value=True
-    )
+    @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
     ):
@@ -309,15 +293,13 @@ class TestDiceInterface(unittest.TestCase):
         self.assertTrue(mock_os.getcwd.called)
         self.assertTrue(mock_os.chdir.called)
 
-        self.assertEqual(dice.run_dice_file.call_count, 1)
+        self.assertEqual(dice.run_dice_file.call_count, 2)
         self.assertTrue(mock_shutils.copy.called)
 
-    @mock.patch("diceplayer.shared.interface.dice_interface.os")
-    @mock.patch("diceplayer.shared.interface.dice_interface.shutil")
-    @mock.patch(
-        "diceplayer.shared.interface.dice_interface.Path.exists", return_value=False
-    )
-    def test_run_dice_on_second_cycle_run_successful(
+    @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()
@@ -424,7 +406,7 @@ class TestDiceInterface(unittest.TestCase):
         self.assertEqual(density, 85.35451545000001)
 
     @mock.patch("builtins.open", new_callable=mock.mock_open)
-    @mock.patch("diceplayer.shared.interface.dice_interface.random")
+    @mock.patch("diceplayer.interface.dice_interface.random")
     def test_make_nvt_ter(self, mock_random, mock_open):
         mock_random.random.return_value = 1
 
@@ -461,7 +443,7 @@ class TestDiceInterface(unittest.TestCase):
         self.assertEqual(lines, expected_lines)
 
     @mock.patch("builtins.open", new_callable=mock.mock_open)
-    @mock.patch("diceplayer.shared.interface.dice_interface.random")
+    @mock.patch("diceplayer.interface.dice_interface.random")
     def test_make_nvt_eq(self, mock_random, mock_open):
         mock_random.random.return_value = 1
 
@@ -497,7 +479,7 @@ class TestDiceInterface(unittest.TestCase):
         self.assertEqual(lines, expected_lines)
 
     @mock.patch("builtins.open", new_callable=mock.mock_open)
-    @mock.patch("diceplayer.shared.interface.dice_interface.random")
+    @mock.patch("diceplayer.interface.dice_interface.random")
     def test_make_npt_ter(self, mock_random, mock_open):
         mock_random.random.return_value = 1
 
@@ -533,7 +515,7 @@ class TestDiceInterface(unittest.TestCase):
         self.assertEqual(lines, expected_lines)
 
     @mock.patch("builtins.open", new_callable=mock.mock_open)
-    @mock.patch("diceplayer.shared.interface.dice_interface.random")
+    @mock.patch("diceplayer.interface.dice_interface.random")
     def test_make_npt_eq(self, mock_random, mock_open):
         mock_random.random.return_value = 1
 
@@ -612,7 +594,7 @@ class TestDiceInterface(unittest.TestCase):
 
         self.assertEqual(lines, expected_lines)
 
-    @mock.patch("diceplayer.shared.interface.dice_interface.subprocess")
+    @mock.patch("diceplayer.interface.dice_interface.subprocess")
     @mock.patch(
         "builtins.open",
         new_callable=mock.mock_open,
@@ -628,7 +610,7 @@ class TestDiceInterface(unittest.TestCase):
         self.assertTrue(mock_subprocess.call.called)
         self.assertTrue(mock_open.called)
 
-    @mock.patch("diceplayer.shared.interface.dice_interface.subprocess")
+    @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
@@ -640,7 +622,7 @@ class TestDiceInterface(unittest.TestCase):
         with self.assertRaises(RuntimeError):
             dice.run_dice_file(1, 1, "test")
 
-    @mock.patch("diceplayer.shared.interface.dice_interface.subprocess")
+    @mock.patch("diceplayer.interface.dice_interface.subprocess")
     @mock.patch(
         "builtins.open",
         new_callable=mock.mock_open,

tests/shared/interface/test_gaussian_interface.py

@@ -1,7 +1,7 @@
 from diceplayer import logger
-from diceplayer.shared.config.player_config import PlayerConfig
-from diceplayer.shared.environment.system import System
-from diceplayer.shared.interface.gaussian_interface import GaussianInterface
+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
@@ -16,7 +16,7 @@ class TestGaussianInterface(unittest.TestCase):
         logger.set_logger(stream=io.StringIO())
 
         config = yaml.load(get_config_example(), Loader=yaml.Loader)
-        self.config = PlayerConfig.from_dict(config["diceplayer"])
+        self.config = PlayerConfig.model_validate(config["diceplayer"])
 
     def test_class_instantiation(self):
         gaussian_interface = GaussianInterface()
@@ -46,8 +46,8 @@ class TestGaussianInterface(unittest.TestCase):
         self.assertFalse(hasattr(gaussian_interface, "step"))
         self.assertFalse(hasattr(gaussian_interface, "system"))
 
-    @mock.patch("diceplayer.shared.interface.gaussian_interface.Path.mkdir")
-    @mock.patch("diceplayer.shared.interface.gaussian_interface.Path.exists")
+    @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
 
@@ -59,8 +59,8 @@ class TestGaussianInterface(unittest.TestCase):
         mock_exists.assert_called_once()
         mock_mkdir.assert_called_once()
 
-    @mock.patch("diceplayer.shared.interface.gaussian_interface.shutil.copy")
-    @mock.patch("diceplayer.shared.interface.gaussian_interface.Path.exists")
+    @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())
@@ -72,8 +72,8 @@ class TestGaussianInterface(unittest.TestCase):
         self.assertTrue(mock_exists.called)
         self.assertTrue(mock_copy.called)
 
-    @mock.patch("diceplayer.shared.interface.gaussian_interface.shutil.copy")
-    @mock.patch("diceplayer.shared.interface.gaussian_interface.Path.exists")
+    @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
     ):
@@ -85,8 +85,8 @@ class TestGaussianInterface(unittest.TestCase):
         with self.assertRaises(FileNotFoundError):
             gaussian_interface._copy_chk_file_from_previous_step(2)
 
-    @mock.patch("diceplayer.shared.interface.gaussian_interface.shutil.copy")
-    @mock.patch("diceplayer.shared.interface.gaussian_interface.Path.exists")
+    @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
     ):

tests/shared/utils/test_logger.py

@@ -1,4 +1,4 @@
-from diceplayer.shared.utils.logger import Logger, valid_logger
+from diceplayer.utils import Logger, valid_logger
 
 import io
 import logging
@@ -53,8 +53,8 @@ class TestLogger(unittest.TestCase):
         self.assertEqual(logger._logger.name, "test")
 
     @mock.patch("builtins.open", mock.mock_open())
-    @mock.patch("diceplayer.shared.utils.logger.Path.exists")
-    @mock.patch("diceplayer.shared.utils.logger.Path.rename")
+    @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")
 
@@ -66,8 +66,8 @@ class TestLogger(unittest.TestCase):
         self.assertEqual(logger._logger.name, "test")
 
     @mock.patch("builtins.open", mock.mock_open())
-    @mock.patch("diceplayer.shared.utils.logger.Path.exists")
-    @mock.patch("diceplayer.shared.utils.logger.Path.rename")
+    @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")
 

tests/test_player.py

@@ -1,4 +1,4 @@
-from diceplayer import VERSION, logger
+from diceplayer import logger
 from diceplayer.player import Player
 from tests.mocks.mock_inputs import mock_open
 
@@ -71,6 +71,7 @@ class TestPlayer(unittest.TestCase):
             "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",
@@ -81,8 +82,10 @@ class TestPlayer(unittest.TestCase):
             "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",

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