refactor: restructure dice environment handling and update Python version requirement

Feature/refactors environment

.github/workflows/build-and-uplod.yml

@@ -1,47 +0,0 @@
-                                                                                                                                                      # 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: Build and Upload to PyPI
-
-on:
-    push:
-        tags:
-            - 'v*'
-
-permissions:
-    contents: read
-
-jobs:
-    pypi-upload:
-        needs: [test]
-        if: github.ref == 'refs/heads/main'
-        runs-on: ubuntu-latest
-        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 install
-
-            -   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

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

@@ -0,0 +1,77 @@
+                                                                                                                                                      # 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: build and upload
+
+on:
+    push
+
+permissions:
+    contents: read
+
+jobs:
+
+    test:
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                python-version:
+                    - "3.10"
+        steps:
+            -   uses: actions/checkout@v3
+                with:
+                    fetch-depth: 0
+
+            -   name: Set up Python 3.10
+                uses: actions/setup-python@v3
+                with:
+                    python-version: "3.10"
+
+            - 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]
+        if: startsWith(github.ref, 'refs/tags/v')
+        runs-on: ubuntu-latest
+        steps:
+            -   uses: actions/checkout@v3
+                with:
+                    fetch-depth: 0
+
+            -   name: Set up Python 3.10
+                uses: actions/setup-python@v3
+                with:
+                    python-version: "3.10"
+
+            - 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 }}

.github/workflows/run-tests.yml

@@ -1,36 +0,0 @@
-# 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: Run Tests
-
-on:
-  push
-
-permissions:
-  contents: read
-
-jobs:
-
-  test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python: ["3.10", "3.11", "3.12", "3.13"]
-    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: ${{ matrix.python }}
-      -   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

.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 @@
+3.12

control.example.yml

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

diceplayer/__init__.py

@@ -1,7 +0,0 @@
-from diceplayer.shared.utils.logger import Logger
-
-from importlib import metadata
-
-VERSION = metadata.version("diceplayer")
-
-logger = Logger(__name__)

diceplayer/__main__.py

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

diceplayer/cli/__init__.py

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

diceplayer/cli/args_model.py

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

diceplayer/cli/read_input_file.py

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

diceplayer/config/__init__.py

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

diceplayer/config/dice_config.py

@@ -0,0 +1,60 @@
+from pydantic import BaseModel, ConfigDict, Field
+from typing_extensions import Literal
+
+import random
+from pathlib import Path
+
+
+class DiceConfig(BaseModel):
+    """
+    Data Transfer Object for the Dice configuration.
+    """
+
+    model_config = ConfigDict(
+        frozen=True,
+    )
+    nprocs: int = Field(
+        ..., description="Number of processes to use for the DICE simulations"
+    )
+
+    ljname: Path = Field(..., description="Name of the Lennard-Jones potential file")
+    outname: str = Field(
+        ..., description="Name of the output file for the simulation results"
+    )
+    dens: float = Field(..., description="Density of the system")
+    nmol: list[int] = Field(
+        ..., 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"
+    )
+    irdf: int = Field(
+        0,
+        description="Controls the interval of Monte Carlo steps at which configurations are used at computation of radial distribution functions",
+    )
+    vstep: int = Field(
+        5000, description="Frequency of volume change moves in NPT simulations"
+    )
+    combrule: Literal["+", "*"] = Field(
+        "*", description="Combination rule for the Lennard-Jones potential"
+    )
+    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 = Field(
+        default_factory=lambda: int(1e6 * random.random()),
+        description="Seed for the random number generator",
+    )

diceplayer/config/gaussian_config.py

@@ -0,0 +1,29 @@
+from pydantic import BaseModel, ConfigDict, Field
+from typing_extensions import Literal
+
+
+class GaussianConfig(BaseModel):
+    """
+    Data Transfer Object for the Gaussian configuration.
+    """
+
+    model_config = ConfigDict(
+        frozen=True,
+    )
+
+    qmprog: Literal["g03", "g09", "g16"] = Field(
+        "g16", description="QM program to use for the calculations"
+    )
+    level: str = Field(..., description="Level of theory for the QM calculations")
+
+    chgmult: list[int] = Field(
+        default_factory=lambda: [0, 1],
+        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 | None = Field(
+        None, description="Additional keywords for the QM calculations"
+    )

diceplayer/config/player_config.py

@@ -0,0 +1,90 @@
+from diceplayer.config.dice_config import DiceConfig
+from diceplayer.config.gaussian_config import GaussianConfig
+
+from pydantic import BaseModel, ConfigDict, Field, model_validator
+from typing_extensions import Any
+
+from enum import Enum
+from pathlib import Path
+
+
+MIN_STEP = 20000
+STEP_INCREMENT = 1000
+
+
+class RoutineType(str, Enum):
+    CHARGE = "charge"
+    GEOMETRY = "geometry"
+    BOTH = "both"
+
+
+class PlayerConfig(BaseModel):
+    """
+    Configuration for DICEPlayer simulations.
+
+    Attributes:
+        type: Type of simulation to perform (charge, geometry, or both).
+        max_cyc: Maximum number of cycles for the geometry optimization.
+        switch_cyc: Cycle at which to switch from charge to geometry optimization (if type is "both").
+        mem: Memory configuration for QM calculations.
+        nprocs: Number of processors to use for QM calculations.
+        ncores: Number of cores to use for QM calculations.
+        dice: Configuration parameters specific to DICE simulations.
+        gaussian: Configuration parameters specific to Gaussian calculations.
+        altsteps: Number of steps for the alternate simulation (default: 20000).
+        geoms_file: File name for the geometries output (default: "geoms.xyz").
+        simulation_dir: Directory name for the simulation files (default: "simfiles").
+    """
+
+    model_config = ConfigDict(
+        frozen=True,
+    )
+
+    type: RoutineType = Field(..., description="Type of simulation to perform")
+    max_cyc: int = Field(
+        ..., description="Maximum number of cycles for the geometry optimization", gt=0
+    )
+    switch_cyc: int = Field(..., description="Switch cycle configuration")
+
+    mem: int = Field(None, description="Memory configuration")
+    ncores: int = Field(
+        ..., description="Number of cores to use for the QM calculations"
+    )
+
+    dice: DiceConfig = Field(..., description="Dice configuration")
+    gaussian: GaussianConfig = Field(..., description="Gaussian configuration")
+
+    altsteps: int = Field(
+        20000, description="Number of steps for the alternate simulation"
+    )
+    geoms_file: Path = Field(
+        Path("geoms.xyz"), description="File name for the geometries output"
+    )
+    simulation_dir: Path = Field(
+        Path("simfiles"), description="Directory name for the simulation files"
+    )
+
+    @model_validator(mode="before")
+    @staticmethod
+    def validate_altsteps(fields) -> dict[str, Any]:
+        altsteps = fields.pop("altsteps", MIN_STEP)
+        fields["altsteps"] = (
+            round(max(MIN_STEP, altsteps) / STEP_INCREMENT) * STEP_INCREMENT
+        )
+        return fields
+
+    @model_validator(mode="before")
+    @staticmethod
+    def validate_switch_cyc(fields: dict[str, Any]) -> dict[str, Any]:
+        max_cyc = int(fields.get("max_cyc", 0))
+        switch_cyc = int(fields.get("switch_cyc", max_cyc))
+
+        if fields.get("type") == "both" and not switch_cyc < max_cyc:
+            raise ValueError("switch_cyc must be less than max_cyc when type='both'.")
+
+        if fields.get("type") != "both" and switch_cyc != max_cyc:
+            raise ValueError(
+                "switch_cyc must be equal to max_cyc when type is not 'both'."
+            )
+
+        return fields

diceplayer/dice/__init__.py

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

diceplayer/dice/dice_handler.py

@@ -0,0 +1,186 @@
+import warnings
+
+from diceplayer.dice.dice_input import (
+    NPTEqConfig,
+    NPTTerConfig,
+    NVTEqConfig,
+    NVTTerConfig,
+)
+from diceplayer.dice.dice_wrapper import (
+    DiceEnvironment,
+    DiceWrapper,
+)
+from diceplayer.environment import Atom, Molecule
+from diceplayer.logger import logger
+from diceplayer.state.state_model import StateModel
+
+import shutil
+from itertools import batched, chain, islice
+from pathlib import Path
+from threading import Thread
+
+
+class DiceHandler:
+    def __init__(self, step_directory: Path):
+        self.dice_directory = step_directory / "dice"
+
+    def run(self, state: StateModel, cycle: int) -> list[Atom]:
+        if self.dice_directory.exists():
+            logger.info(
+                f"Found dice directory: {self.dice_directory}, this directory will be purged for a clean state"
+            )
+            shutil.rmtree(self.dice_directory)
+        self.dice_directory.mkdir(parents=True)
+
+        return self.run_simulations(state, cycle)
+
+    def run_simulations(self, state: StateModel, cycle: int) -> list[Atom]:
+        results: list[list[Atom]] = []
+
+        threads = []
+        for p in range(state.config.dice.nprocs):
+            t = Thread(target=self._simulation_process, args=(state, cycle, p, results))
+            threads.append(t)
+            t.start()
+
+        for t in threads:
+            t.join()
+
+        if len(results) != state.config.dice.nprocs:
+            raise RuntimeError(
+                f"Expected {state.config.dice.nprocs} simulation results, but got {len(results)}"
+            )
+
+        return self._aggregate_results(state, results)
+
+    def _simulation_process(
+        self,
+        state: StateModel,
+        cycle: int,
+        proc: int,
+        results: list[list[Atom]],
+    ) -> None:
+        proc_directory = self.dice_directory / f"{proc:02d}"
+        if proc_directory.exists():
+            shutil.rmtree(proc_directory)
+        proc_directory.mkdir(parents=True)
+
+        dice = DiceWrapper(state.config.dice, proc_directory)
+
+        self._generate_phb_file(state, proc_directory)
+
+        if state.config.dice.randominit == "first" and cycle >= 0:
+            self._generate_last_xyz(state, proc_directory)
+        else:
+            nvt_ter_config = NVTTerConfig.from_config(state.config)
+            dice.run(nvt_ter_config)
+
+        if len(state.config.dice.nstep) == 2:
+            nvt_eq_config = NVTEqConfig.from_config(state.config)
+            dice.run(nvt_eq_config)
+
+        elif len(state.config.dice.nstep) == 3:
+            npt_ter_config = NPTTerConfig.from_config(state.config)
+            dice.run(npt_ter_config)
+
+            npt_eq_config = NPTEqConfig.from_config(state.config)
+            dice.run(npt_eq_config)
+
+        results.extend(
+            [
+                self._filter_environment_sites(state, environment)
+                for environment in dice.parse_results()
+            ]
+        )
+
+    @staticmethod
+    def _generate_phb_file(state: StateModel, proc_directory: Path) -> None:
+        fstr = "{:<3d} {:>3d}  {:>10.5f} {:>10.5f} {:>10.5f}  {:>10.6f} {:>9.5f} {:>7.4f}\n"
+
+        phb_file = proc_directory / state.config.dice.ljname
+
+        with open(phb_file, "w") as f:
+            f.write(f"{state.config.dice.combrule}\n")
+            f.write(f"{len(state.config.dice.nmol)}\n")
+
+            for molecule in state.system.molecule:
+                f.write(f"{len(molecule.atom)} {molecule.molname}\n")
+                for atom in molecule.atom:
+                    f.write(
+                        fstr.format(
+                            atom.lbl,
+                            atom.na,
+                            atom.rx,
+                            atom.ry,
+                            atom.rz,
+                            atom.chg,
+                            atom.eps,
+                            atom.sig,
+                        )
+                    )
+
+    def _generate_last_xyz(self, state: StateModel, proc_directory: Path) -> None: ...
+
+    @staticmethod
+    def _filter_environment_sites(
+        state: StateModel, environment: DiceEnvironment
+    ) -> list[Atom]:
+        picked_environment = []
+
+        ref_molecule = state.system.molecule[0]
+        ref_molecule_sizes = ref_molecule.sizes_of_molecule()
+        ref_n_sites = len(ref_molecule.atom) * state.config.dice.nmol[0]
+
+        min_distance = min(
+            (environment.thickness[i] - ref_molecule_sizes[i]) / 2 for i in range(3)
+        )
+
+        site_iter = iter(environment.items)
+        _ = list(islice(site_iter, ref_n_sites))
+
+        for molecule_index, molecule in enumerate(state.system.molecule[1:], start=1):
+            molecule_n_atoms = len(molecule.atom)
+            molecule_n_sites = molecule_n_atoms * state.config.dice.nmol[molecule_index]
+
+            sites = list(islice(site_iter, molecule_n_sites))
+
+            for molecule_sites in batched(sites, molecule_n_atoms):
+                new_molecule = Molecule("ASEC TMP MOLECULE")
+
+                for site_index, atom_site in enumerate(molecule_sites):
+                    new_molecule.add_atom(
+                        Atom(
+                            molecule.atom[site_index].lbl,
+                            molecule.atom[site_index].na,
+                            atom_site.x,
+                            atom_site.y,
+                            atom_site.z,
+                            molecule.atom[site_index].chg,
+                            molecule.atom[site_index].eps,
+                            molecule.atom[site_index].sig,
+                        )
+                    )
+
+                if molecule.signature() != new_molecule.signature():
+                    _message = f"Skipping sites because the molecule signature does not match the reference molecule. Expected {molecule.signature()} but got {new_molecule.signature()}"
+                    warnings.warn(_message)
+                    logger.warning(_message)
+                    continue
+
+                if ref_molecule.minimum_distance(new_molecule) >= min_distance:
+                    continue
+
+                picked_environment.extend(new_molecule.atom)
+
+        return picked_environment
+
+    @staticmethod
+    def _aggregate_results(state: StateModel, results: list[list[Atom]]) -> list[Atom]:
+        norm_factor = round(state.config.dice.nstep[-1] / state.config.dice.isave)
+
+        agg_results = []
+        for atom in chain(*[r for r in results]):
+            atom.chg = atom.chg * norm_factor
+            agg_results.append(atom)
+
+        return agg_results

diceplayer/dice/dice_input.py

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

diceplayer/dice/dice_wrapper.py

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

diceplayer/environment/__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 pydantic.dataclasses import dataclass
+
+
+@dataclass(slots=True)
+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 +1,320 @@
+from __future__ import annotations
+
+from diceplayer.environment import Atom
+from diceplayer.logger import logger
+from diceplayer.utils.misc import BOHR2ANG, EA_2_DEBYE
+from diceplayer.utils.ptable import GHOST_NUMBER
+
+import numpy as np
+import numpy.linalg as linalg
+import numpy.typing as npt
+from pydantic.dataclasses import dataclass
+from typing_extensions import List, Self, Tuple
+
+import math
+from copy import deepcopy
+from dataclasses import field
+
+
+@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)
+
+    @property
+    def total_mass(self) -> float:
+        return sum(atom.mass for atom in self.atom)
+
+    @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
+
+    @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
+
+    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)
+
+    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)
+
+    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]
+
+    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())
+
+    def signature(self) -> List[int]:
+        """
+        Returns the signature of the molecule, which is a list of the number of atoms of each type in the molecule.
+
+        Returns:
+            List[int]: signature of the molecule
+        """
+        return [a.lbl for a in self.atom]

diceplayer/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/logger.py

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

diceplayer/optimization/optimization_handler.py

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

diceplayer/player.py

@@ -1,448 +1,60 @@
-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.dice.dice_handler import DiceHandler
+from diceplayer.logger import logger
+from diceplayer.optimization.optimization_handler import OptimizationHandler
+from diceplayer.state.state_handler import StateHandler
+from diceplayer.state.state_model import StateModel
+from diceplayer.utils.potential import read_system_from_phb
 
-import yaml
+from typing_extensions import TypedDict, Unpack
 
-import os
-import pickle
-import sys
-from dataclasses import fields
-from pathlib import Path
-from typing import Tuple, Type
 
-ENV = ["OMP_STACKSIZE"]
+class PlayerFlags(TypedDict):
+    continuation: bool
+    force: bool
 
 
 class Player:
-    def __init__(self, infile: str = None, optimization: bool = False):
-        if infile is None and optimization is False:
-            raise ValueError("Must specify either infile or optimization")
+    def __init__(self, config: PlayerConfig):
+        self.config = config
+        self._state_handler = StateHandler(config.simulation_dir)
 
-        elif infile is not None:
-            self.config = self.set_config(self.read_keywords(infile))
+    def play(self, **flags: Unpack[PlayerFlags]):
+        continuation = flags.get("continuation", False)
+        force = flags.get("force", False)
 
-            self.system = System()
-
-            self.initial_cycle = 1
-
-        elif optimization is True:
-            save = self.load_run_from_pickle()
-
-            self.config = save[0]
-
-            self.system = save[1]
-
-            self.initial_cycle = save[2] + 1
+        state = self._state_handler.get(self.config, force=force)
+        if not continuation and state is not None:
+            logger.info(
+                "Continuation flag is not set. Starting a new simulation and deleting any existing state."
+            )
+            self._state_handler.delete()
+            state = None
 
+        if state is None:
+            system = read_system_from_phb(self.config)
+            state = StateModel(config=self.config, system=system)
         else:
-            raise ValueError("Must specify either infile or config")
+            logger.info("Resuming from existing state.")
 
-        self.dice_interface = DiceInterface()
-        self.gaussian_interface = GaussianInterface()
-
-    def start(self):
-        logger.info(
-            "==========================================================================================\n"
-            "Starting the iterative process.\n"
-            "==========================================================================================\n"
-        )
-
-        for cycle in range(self.initial_cycle, self.initial_cycle + self.config.maxcyc):
+        while state.current_cycle < self.config.max_cyc:
             logger.info(
-                f"------------------------------------------------------------------------------------------\n"
-                f"                                         Step # {cycle}\n"
-                f"------------------------------------------------------------------------------------------\n"
+                f"Starting cycle {state.current_cycle + 1} of {self.config.max_cyc}."
             )
 
-            self.dice_start(cycle)
+            step_directory = self.config.simulation_dir / f"{state.current_cycle:02d}"
+            if not step_directory.exists():
+                step_directory.mkdir(parents=True)
 
-            try:
-                self.gaussian_start(cycle)
-            except StopIteration:
-                break
-
-            self.save_run_in_pickle(cycle)
-
-    def prepare_system(self):
-        for i, mol in enumerate(self.system.molecule):
-            logger.info(f"Molecule {i + 1} - {mol.molname}")
-
-            mol.print_mol_info()
-            logger.info(
-                "\n    Translating and rotating molecule to standard orientation..."
+            dice_environment = DiceHandler(step_directory).run(
+                state, state.current_cycle
             )
 
-            mol.standard_orientation()
-            logger.info("\n Done")
-            logger.info("\nNew values:\n")
-            mol.print_mol_info()
-
-            logger.info("\n")
-
-    def create_simulation_dir(self):
-        simulation_dir_path = Path(self.config.simulation_dir)
-        if simulation_dir_path.exists():
-            raise FileExistsError(
-                f"Error: a file or a directory {self.config.simulation_dir} already exists,"
-                f" move or delete the simfiles directory to continue."
-            )
-        simulation_dir_path.mkdir()
-
-    def create_geoms_file(self):
-        geoms_file_path = Path(self.config.geoms_file)
-        if geoms_file_path.exists():
-            raise FileExistsError(
-                f"Error: a file or a directory {self.config.geoms_file} already exists,"
-                f" move or delete the simfiles directory to continue."
-            )
-        geoms_file_path.touch()
-
-    def print_keywords(self) -> None:
-        def log_keywords(config: 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)}")
-
-        logger.info(
-            f"##########################################################################################\n"
-            f"#############               Welcome to DICEPLAYER version {VERSION}                #############\n"
-            f"##########################################################################################\n"
-        )
-        logger.info("Your python version is {}\n".format(sys.version))
-        logger.info("Program started on {}\n".format(weekday_date_time()))
-        logger.info("Environment variables:")
-        for var in ENV:
-            logger.info(
-                "{} = {}\n".format(
-                    var, (os.environ[var] if var in os.environ else "Not set")
-                )
+            state = OptimizationHandler(step_directory).run(
+                state, state.current_cycle, dice_environment
             )
 
-        logger.info(
-            "------------------------------------------------------------------------------------------\n"
-            "                         DICE variables being used in this run:\n"
-            "------------------------------------------------------------------------------------------\n"
-        )
+            state.current_cycle += 1
+            self._state_handler.save(state)
 
-        log_keywords(self.config.dice, DiceConfig)
-
-        logger.info(
-            "------------------------------------------------------------------------------------------\n"
-            "                         GAUSSIAN variables being used in this run:\n"
-            "------------------------------------------------------------------------------------------\n"
-        )
-
-        log_keywords(self.config.gaussian, GaussianDTO)
-
-        logger.info("\n")
-
-    def read_potentials(self):
-        ljname_path = Path(self.config.dice.ljname)
-        if ljname_path.exists():
-            with open(self.config.dice.ljname) as file:
-                ljc_data = file.readlines()
-        else:
-            raise RuntimeError(f"Potential file {self.config.dice.ljname} not found.")
-
-        combrule = ljc_data.pop(0).split()[0]
-        if combrule not in ("*", "+"):
-            sys.exit(
-                "Error: expected a '*' or a '+' sign in 1st line of file {}".format(
-                    self.config.dice.ljname
-                )
-            )
-        self.config.dice.combrule = combrule
-
-        ntypes = ljc_data.pop(0).split()[0]
-        if not ntypes.isdigit():
-            sys.exit(
-                "Error: expected an integer in the 2nd line of file {}".format(
-                    self.config.dice.ljname
-                )
-            )
-        ntypes = int(ntypes)
-
-        if ntypes != len(self.config.dice.nmol):
-            sys.exit(
-                f"Error: number of molecule types in file {self.config.dice.ljname} "
-                f"must match that of 'nmol' keyword in config file"
-            )
-
-        for i in range(ntypes):
-            try:
-                nsites, molname = ljc_data.pop(0).split()[:2]
-            except ValueError:
-                raise ValueError(
-                    f"Error: expected nsites and molname for the molecule type {i + 1}"
-                )
-
-            if not nsites.isdigit():
-                raise ValueError(
-                    f"Error: expected nsites to be an integer for molecule type {i + 1}"
-                )
-
-            nsites = int(nsites)
-            self.system.add_type(Molecule(molname))
-
-            atom_fields = ["lbl", "na", "rx", "ry", "rz", "chg", "eps", "sig"]
-            for j in range(nsites):
-                new_atom = dict(zip(atom_fields, ljc_data.pop(0).split()))
-                self.system.molecule[i].add_atom(
-                    Atom(**self.validate_atom_dict(i, j, new_atom))
-                )
-
-    def print_potentials(self) -> None:
-        formatstr = "{:<3d} {:>3d}  {:>10.5f} {:>10.5f} {:>10.5f}  {:>10.6f} {:>9.5f} {:>7.4f} {:>9.4f}"
-        logger.info(
-            "==========================================================================================\n"
-            f"                    Potential parameters from file {self.config.dice.ljname}:\n"
-            "------------------------------------------------------------------------------------------"
-            "\n"
-        )
-
-        logger.info(f"Combination rule: {self.config.dice.combrule}")
-        logger.info(f"Types of molecules: {len(self.system.molecule)}\n")
-
-        i = 0
-        for mol in self.system.molecule:
-            i += 1
-            logger.info("{} atoms in molecule type {}:".format(len(mol.atom), i))
-            logger.info(
-                "---------------------------------------------------------------------------------"
-            )
-            logger.info(
-                "Lbl  AN       X          Y          Z         Charge    Epsilon   Sigma     Mass"
-            )
-            logger.info(
-                "---------------------------------------------------------------------------------"
-            )
-
-            for atom in mol.atom:
-                logger.info(
-                    formatstr.format(
-                        atom.lbl,
-                        atom.na,
-                        atom.rx,
-                        atom.ry,
-                        atom.rz,
-                        atom.chg,
-                        atom.eps,
-                        atom.sig,
-                        atom.mass,
-                    )
-                )
-
-            logger.info("\n")
-
-    def dice_start(self, cycle: int):
-        self.dice_interface.configure(
-            self.config,
-            self.system,
-        )
-
-        self.dice_interface.start(cycle)
-
-        self.dice_interface.reset()
-
-    def gaussian_start(self, cycle: int):
-        self.gaussian_interface.configure(
-            self.config,
-            self.system,
-        )
-
-        result = self.gaussian_interface.start(cycle)
-
-        self.gaussian_interface.reset()
-
-        if self.config.opt:
-            if "position" not in result:
-                raise RuntimeError("Optimization failed. No position found in result.")
-
-            self.system.update_molecule(result["position"])
-
-        else:
-            if "charges" not in result:
-                raise RuntimeError(
-                    "Charges optimization failed. No charges found in result."
-                )
-
-            diff = self.system.molecule[0].update_charges(result["charges"])
-
-            self.system.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_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]
-                file.write(
-                    f"{symbol:<2s}    {atom.rx:>10.6f}  {atom.ry:>10.6f}  {atom.rz:>10.6f}\n"
-                )
-
-            file.write("\n")
-
-    @staticmethod
-    def validate_atom_dict(molecule_type, molecule_site, atom_dict: dict) -> dict:
-        molecule_type += 1
-        molecule_site += 1
-
-        if len(atom_dict) < 8:
-            raise ValueError(
-                f"Invalid number of fields for site {molecule_site} for molecule type {molecule_type}."
-            )
-
-        try:
-            atom_dict["lbl"] = int(atom_dict["lbl"])
-        except Exception:
-            raise ValueError(
-                f"Invalid lbl fields for site {molecule_site} for molecule type {molecule_type}."
-            )
-
-        try:
-            atom_dict["na"] = int(atom_dict["na"])
-        except Exception:
-            raise ValueError(
-                f"Invalid na fields for site {molecule_site} for molecule type {molecule_type}."
-            )
-
-        try:
-            atom_dict["rx"] = float(atom_dict["rx"])
-        except Exception:
-            raise ValueError(
-                f"Invalid rx fields for site {molecule_site} for molecule type {molecule_type}. "
-                f"Value must be a float."
-            )
-
-        try:
-            atom_dict["ry"] = float(atom_dict["ry"])
-        except Exception:
-            raise ValueError(
-                f"Invalid ry fields for site {molecule_site} for molecule type {molecule_type}. "
-                f"Value must be a float."
-            )
-
-        try:
-            atom_dict["rz"] = float(atom_dict["rz"])
-        except Exception:
-            raise ValueError(
-                f"Invalid rz fields for site {molecule_site} for molecule type {molecule_type}. "
-                f"Value must be a float."
-            )
-
-        try:
-            atom_dict["chg"] = float(atom_dict["chg"])
-        except Exception:
-            raise ValueError(
-                f"Invalid chg fields for site {molecule_site} for molecule type {molecule_type}. "
-                f"Value must be a float."
-            )
-
-        try:
-            atom_dict["eps"] = float(atom_dict["eps"])
-        except Exception:
-            raise ValueError(
-                f"Invalid eps fields for site {molecule_site} for molecule type {molecule_type}. "
-                f"Value must be a float."
-            )
-
-        try:
-            atom_dict["sig"] = float(atom_dict["sig"])
-        except Exception:
-            raise ValueError(
-                f"Invalid sig fields for site {molecule_site} for molecule type {molecule_type}. "
-                f"Value must be a float."
-            )
-
-        return atom_dict
-
-    def print_results(self):
-        formatstr = "{:<3d} {:>3d}  {:>10.5f} {:>10.5f} {:>10.5f}  {:>10.6f} {:>9.5f} {:>7.4f} {:>9.4f}"
-
-        mol = self.system.molecule[0]
-        logger.info("{} atoms in molecule type {}:".format(len(mol.atom), 1))
-        logger.info(
-            "---------------------------------------------------------------------------------"
-        )
-        logger.info(
-            "Lbl  AN       X          Y          Z         Charge    Epsilon   Sigma     Mass"
-        )
-        logger.info(
-            "---------------------------------------------------------------------------------"
-        )
-
-        for atom in mol.atom:
-            logger.info(
-                formatstr.format(
-                    atom.lbl,
-                    atom.na,
-                    atom.rx,
-                    atom.ry,
-                    atom.rz,
-                    atom.chg,
-                    atom.eps,
-                    atom.sig,
-                    atom.mass,
-                )
-            )
-
-        logger.info("\n")
-
-    def save_run_in_pickle(self, cycle):
-        try:
-            with open("latest-step.pkl", "wb") as pickle_file:
-                pickle.dump((self.config, self.system, cycle), pickle_file)
-        except Exception:
-            raise RuntimeError(f"Could not save pickle file latest-step.pkl.")
-
-    @staticmethod
-    def load_run_from_pickle() -> Tuple[PlayerConfig, System, int]:
-        pickle_path = Path("latest-step.pkl")
-        try:
-            with open(pickle_path, "rb") as pickle_file:
-                save = pickle.load(pickle_file)
-            return save[0], save[1], save[2] + 1
-
-        except Exception:
-            raise RuntimeError(f"Could not load pickle file {pickle_path}.")
-
-    @staticmethod
-    def set_config(data: dict) -> PlayerConfig:
-        return PlayerConfig.from_dict(data)
-
-    @staticmethod
-    def read_keywords(infile) -> dict:
-        with open(infile, "r") as yml_file:
-            config = yaml.load(yml_file, Loader=yaml.SafeLoader)
-
-        if "diceplayer" in config:
-            return config.get("diceplayer")
-
-        raise RuntimeError(f"Could not find diceplayer section in {infile}.")
-
-    @classmethod
-    def from_file(cls, infile: str) -> "Player":
-        return cls(infile=infile)
-
-    @classmethod
-    def from_save(cls):
-        return cls(optimization=True)
+        logger.info("Reached maximum number of cycles. Simulation complete.")

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

@@ -1,381 +0,0 @@
-# from __future__ import annotations
-
-import numpy.typing as npt
-
-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 (npt.NDArray[Any, Any]): The position relative to the internal atoms of the represented molecule
-        energy (npt.NDArray[Any, Any]): The energy of the represented molecule
-        gradient (npt.NDArray[Any, Any]): The first derivative of the energy relative to the position
-        hessian (npt.NDArray[Any, Any]): The second derivative of the energy relative to the position
-        total_mass (int): The total mass of the molecule
-        com (npt.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: npt.NDArray[Any, Any]
-        self.energy: npt.NDArray[Any, Any]
-        self.gradient: npt.NDArray[Any, Any]
-        self.hessian: npt.NDArray[Any, Any]
-
-        self.ghost_atoms: List[Atom] = []
-        self.lp_atoms: List[Atom] = []
-
-        self.total_mass: int = 0
-        self.com: Union[None, npt.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) -> npt.NDArray[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[npt.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) -> npt.NDArray[np.float64]:
-        """
-        Calculates distances between the atoms of the molecule
-
-        Returns:
-           npt.NDArray[npt.Shape["Any,Any"],npt.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) -> npt.NDArray[np.float64]:
-        """
-        Calculates the inertia tensor of the molecule.
-
-        Returns:
-            npt.NDArray[npt.Shape["3, 3"], npt.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[npt.NDArray, npt.NDArray]:
-        """
-        Calculates the principal axes of the molecule
-
-        Returns:
-            Tuple[npt.NDArray, npt.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) -> npt.NDArray:
-        """Reads the position of the molecule from the position values of the atoms
-
-        Returns:
-            npt.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: npt.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: npt.NDArray,
-    #         cur_gradient: npt.NDArray,
-    #         old_gradient: npt.NDArray,
-    #         hessian: npt.NDArray,
-    # ) -> npt.NDArray:
-    #     """
-    #     Updates the Hessian of the molecule based on the current hessian, the current gradient and the previous gradient
-    #
-    #     Args:
-    #         step (npt.NDArray): step value of the iteration
-    #         cur_gradient (npt.NDArray): current gradient
-    #         old_gradient (npt.NDArray): previous gradient
-    #         hessian (npt.NDArray): current hessian
-    #
-    #     Returns:
-    #         npt.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[npt.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: npt.NDArray) -> "Molecule":
-        """
-        Creates a new Molecule object where its' atoms has been translated by a vector
-
-        Args:
-            vector (npt.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:
-            npt.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/interface/__interface.py

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

diceplayer/shared/interface/dice_interface.py

@@ -1,387 +0,0 @@
-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 setproctitle import setproctitle
-
-import os
-import random
-import shutil
-import subprocess
-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
-UMAANG3_TO_GCM3: Final[float] = 1.6605
-
-MAX_SEED: Final[int] = 4294967295
-
-
-class DiceInterface(Interface):
-    title = "Diceplayer run"
-
-    def configure(self, step: PlayerConfig, system: System):
-        self.step = step
-        self.system = system
-
-    def start(self, cycle: int):
-        procs = []
-        sentinels = []
-
-        for proc in range(1, self.step.nprocs + 1):
-            p = Process(target=self._simulation_process, args=(cycle, proc))
-            p.start()
-
-            procs.append(p)
-            sentinels.append(p.sentinel)
-
-        while procs:
-            finished = connection.wait(sentinels)
-            for proc_sentinel in finished:
-                i = sentinels.index(proc_sentinel)
-                status = procs[i].exitcode
-                procs.pop(i)
-                sentinels.pop(i)
-                if status != 0:
-                    for p in procs:
-                        p.terminate()
-                    sys.exit(status)
-
-        logger.info("\n")
-
-    def reset(self):
-        del self.step
-        del self.system
-
-    def _simulation_process(self, cycle: int, proc: int):
-        setproctitle(f"diceplayer-step{cycle:0d}-p{proc:0d}")
-
-        try:
-            self._make_proc_dir(cycle, proc)
-            self._make_dice_inputs(cycle, proc)
-            self._run_dice(cycle, proc)
-        except Exception as err:
-            sys.exit(err)
-
-    def _make_proc_dir(self, cycle, proc):
-        simulation_dir = Path(self.step.simulation_dir)
-        if not simulation_dir.exists():
-            simulation_dir.mkdir(parents=True)
-
-        proc_dir = Path(simulation_dir, f"step{cycle:02d}", f"p{proc:02d}")
-        proc_dir.mkdir(parents=True, exist_ok=True)
-
-    def _make_dice_inputs(self, cycle, proc):
-        proc_dir = Path(self.step.simulation_dir, f"step{cycle:02d}", f"p{proc:02d}")
-
-        self._make_potentials(proc_dir)
-
-        random.seed(self._make_dice_seed())
-
-        # This is logic is used to make the initial configuration file
-        # for the next cycle using the last.xyz file from the previous cycle.
-        if self.step.dice.randominit == "first" and cycle > 1:
-            last_xyz = Path(
-                self.step.simulation_dir,
-                f"step{(cycle - 1):02d}",
-                f"p{proc:02d}",
-                "last.xyz",
-            )
-            if not last_xyz.exists():
-                raise FileNotFoundError(f"File {last_xyz} not found.")
-
-            with open(last_xyz, "r") as last_xyz_file:
-                self._make_init_file(proc_dir, last_xyz_file)
-                last_xyz_file.seek(0)
-                self.step.dice.dens = self._new_density(last_xyz_file)
-
-        else:
-            self._make_nvt_ter(cycle, proc_dir)
-
-        if len(self.step.dice.nstep) == 2:
-            self._make_nvt_eq(cycle, proc_dir)
-
-        elif len(self.step.dice.nstep) == 3:
-            self._make_npt_ter(cycle, proc_dir)
-            self._make_npt_eq(proc_dir)
-
-    def _run_dice(self, cycle: int, proc: int):
-        working_dir = os.getcwd()
-
-        proc_dir = Path(self.step.simulation_dir, f"step{cycle:02d}", f"p{proc:02d}")
-
-        logger.info(
-            f"Simulation process {str(proc_dir)} initiated with pid {os.getpid()}"
-        )
-
-        os.chdir(proc_dir)
-
-        if not (self.step.dice.randominit == "first" and cycle > 1):
-            self.run_dice_file(cycle, proc, "NVT.ter")
-
-        if len(self.step.dice.nstep) == 2:
-            self.run_dice_file(cycle, proc, "NVT.eq")
-
-        elif len(self.step.dice.nstep) == 3:
-            self.run_dice_file(cycle, proc, "NPT.ter")
-            self.run_dice_file(cycle, proc, "NPT.eq")
-
-        os.chdir(working_dir)
-
-        xyz_file = Path(proc_dir, "phb.xyz")
-        last_xyz_file = Path(proc_dir, "last.xyz")
-
-        if xyz_file.exists():
-            shutil.copy(xyz_file, last_xyz_file)
-        else:
-            raise FileNotFoundError(f"File {xyz_file} not found.")
-
-    @staticmethod
-    def _make_dice_seed() -> int:
-        num = time.time()
-        num = (num - int(num)) * 1e6
-
-        num = int((num - int(num)) * 1e6)
-
-        return (os.getpid() * num) % (MAX_SEED + 1)
-
-    def _make_init_file(self, proc_dir: Path, last_xyz_file: TextIO):
-        xyz_lines = last_xyz_file.readlines()
-
-        SECONDARY_MOLECULE_LENGTH = 0
-        for i in range(1, len(self.step.dice.nmol)):
-            SECONDARY_MOLECULE_LENGTH += self.step.dice.nmol[i] * len(
-                self.system.molecule[i].atom
-            )
-
-        xyz_lines = xyz_lines[-SECONDARY_MOLECULE_LENGTH:]
-
-        input_file = Path(proc_dir, self.step.dice.outname + ".xy")
-        with open(input_file, "w") as f:
-            for atom in self.system.molecule[0].atom:
-                f.write(f"{atom.rx:>10.6f}  {atom.ry:>10.6f}  {atom.rz:>10.6f}\n")
-
-            for line in xyz_lines:
-                atom = line.split()
-                rx = float(atom[1])
-                ry = float(atom[2])
-                rz = float(atom[3])
-                f.write(f"{rx:>10.6f}  {ry:>10.6f}  {rz:>10.6f}\n")
-
-            f.write("$end")
-
-    def _new_density(self, last_xyz_file: TextIO):
-        last_xyz_lines = last_xyz_file.readlines()
-
-        box = last_xyz_lines[1].split()
-        volume = float(box[-3]) * float(box[-2]) * float(box[-1])
-
-        total_mass = 0
-        for i in range(len(self.system.molecule)):
-            total_mass += self.system.molecule[i].total_mass * self.step.dice.nmol[i]
-
-        density = (total_mass / volume) * UMAANG3_TO_GCM3
-
-        return density
-
-    def _make_nvt_ter(self, cycle, proc_dir):
-        file = Path(proc_dir, "NVT.ter")
-        with open(file, "w") as f:
-            f.write(f"title = {self.title} - NVT Thermalization\n")
-            f.write(f"ncores = {self.step.ncores}\n")
-            f.write(f"ljname = {self.step.dice.ljname}\n")
-            f.write(f"outname = {self.step.dice.outname}\n")
-
-            mol_string = " ".join(str(x) for x in self.step.dice.nmol)
-            f.write(f"nmol = {mol_string}\n")
-
-            f.write(f"dens = {self.step.dice.dens}\n")
-            f.write(f"temp = {self.step.dice.temp}\n")
-
-            if self.step.dice.randominit == "first" and cycle > 1:
-                f.write(f"init = yesreadxyz\n")
-                f.write(f"nstep = {self.step.altsteps}\n")
-            else:
-                f.write(f"init = yes\n")
-                f.write(f"nstep = {self.step.dice.nstep[0]}\n")
-
-            f.write("vstep = 0\n")
-            f.write("mstop = 1\n")
-            f.write("accum = no\n")
-            f.write("iprint = 1\n")
-            f.write("isave = 0\n")
-            f.write("irdf = 0\n")
-
-            seed = int(1e6 * random.random())
-            f.write(f"seed = {seed}\n")
-            f.write(f"upbuf = {self.step.dice.upbuf}")
-
-    def _make_nvt_eq(self, cycle, proc_dir):
-        file = Path(proc_dir, "NVT.eq")
-        with open(file, "w") as f:
-            f.write(f"title = {self.title} - NVT Production\n")
-            f.write(f"ncores = {self.step.ncores}\n")
-            f.write(f"ljname = {self.step.dice.ljname}\n")
-            f.write(f"outname = {self.step.dice.outname}\n")
-
-            mol_string = " ".join(str(x) for x in self.step.dice.nmol)
-            f.write(f"nmol = {mol_string}\n")
-
-            f.write(f"dens = {self.step.dice.dens}\n")
-            f.write(f"temp = {self.step.dice.temp}\n")
-
-            if self.step.dice.randominit == "first" and cycle > 1:
-                f.write("init = yesreadxyz\n")
-            else:
-                f.write("init = no\n")
-
-            f.write(f"nstep = {self.step.dice.nstep[1]}\n")
-
-            f.write("vstep = 0\n")
-            f.write("mstop = 1\n")
-            f.write("accum = no\n")
-            f.write("iprint = 1\n")
-
-            f.write(f"isave = {self.step.dice.isave}\n")
-            f.write(f"irdf = {10 * self.step.nprocs}\n")
-
-            seed = int(1e6 * random.random())
-            f.write("seed = {}\n".format(seed))
-
-    def _make_npt_ter(self, cycle, proc_dir):
-        file = Path(proc_dir, "NPT.ter")
-        with open(file, "w") as f:
-            f.write(f"title = {self.title} - NPT Thermalization\n")
-            f.write(f"ncores = {self.step.ncores}\n")
-            f.write(f"ljname = {self.step.dice.ljname}\n")
-            f.write(f"outname = {self.step.dice.outname}\n")
-
-            mol_string = " ".join(str(x) for x in self.step.dice.nmol)
-            f.write(f"nmol = {mol_string}\n")
-
-            f.write(f"press = {self.step.dice.press}\n")
-            f.write(f"temp = {self.step.dice.temp}\n")
-
-            if self.step.dice.randominit == "first" and cycle > 1:
-                f.write("init = yesreadxyz\n")
-                f.write(f"dens = {self.step.dice.dens:<8.4f}\n")
-                f.write(f"vstep = {int(self.step.altsteps / 5)}\n")
-            else:
-                f.write("init = no\n")
-                f.write(f"vstep = {int(self.step.dice.nstep[1] / 5)}\n")
-
-            f.write("nstep = 5\n")
-            f.write("mstop = 1\n")
-            f.write("accum = no\n")
-            f.write("iprint = 1\n")
-            f.write("isave = 0\n")
-            f.write("irdf = 0\n")
-
-            seed = int(1e6 * random.random())
-            f.write(f"seed = {seed}\n")
-
-    def _make_npt_eq(self, proc_dir):
-        file = Path(proc_dir, "NPT.eq")
-        with open(file, "w") as f:
-            f.write(f"title = {self.title} - NPT Production\n")
-            f.write(f"ncores = {self.step.ncores}\n")
-            f.write(f"ljname = {self.step.dice.ljname}\n")
-            f.write(f"outname = {self.step.dice.outname}\n")
-
-            mol_string = " ".join(str(x) for x in self.step.dice.nmol)
-            f.write(f"nmol = {mol_string}\n")
-
-            f.write(f"press = {self.step.dice.press}\n")
-            f.write(f"temp = {self.step.dice.temp}\n")
-
-            f.write(f"nstep = 5\n")
-
-            f.write(f"vstep = {int(self.step.dice.nstep[2] / 5)}\n")
-            f.write("init = no\n")
-            f.write("mstop = 1\n")
-            f.write("accum = no\n")
-            f.write("iprint = 1\n")
-            f.write(f"isave = {self.step.dice.isave}\n")
-            f.write(f"irdf = {10 * self.step.nprocs}\n")
-
-            seed = int(1e6 * random.random())
-            f.write(f"seed = {seed}\n")
-
-    def _make_potentials(self, proc_dir):
-        fstr = "{:<3d} {:>3d}  {:>10.5f} {:>10.5f} {:>10.5f}  {:>10.6f} {:>9.5f} {:>7.4f}\n"
-
-        file = Path(proc_dir, self.step.dice.ljname)
-        with open(file, "w") as f:
-            f.write(f"{self.step.dice.combrule}\n")
-            f.write(f"{len(self.step.dice.nmol)}\n")
-
-            nsites_qm = len(self.system.molecule[0].atom)
-            f.write(f"{nsites_qm} {self.system.molecule[0].molname}\n")
-
-            for atom in self.system.molecule[0].atom:
-                f.write(
-                    fstr.format(
-                        atom.lbl,
-                        atom.na,
-                        atom.rx,
-                        atom.ry,
-                        atom.rz,
-                        atom.chg,
-                        atom.eps,
-                        atom.sig,
-                    )
-                )
-
-            for mol in self.system.molecule[1:]:
-                f.write(f"{len(mol.atom)} {mol.molname}\n")
-                for atom in mol.atom:
-                    f.write(
-                        fstr.format(
-                            atom.lbl,
-                            atom.na,
-                            atom.rx,
-                            atom.ry,
-                            atom.rz,
-                            atom.chg,
-                            atom.eps,
-                            atom.sig,
-                        )
-                    )
-
-    def run_dice_file(self, cycle: int, proc: int, file_name: str):
-        with open(Path(file_name), "r") as infile, open(
-            Path(file_name + ".out"), "w"
-        ) as outfile:
-            if shutil.which("bash") is not None:
-                exit_status = subprocess.call(
-                    [
-                        "bash",
-                        "-c",
-                        f"exec -a dice-step{cycle}-p{proc} {self.step.dice.progname} < {infile.name} > {outfile.name}",
-                    ]
-                )
-            else:
-                exit_status = subprocess.call(
-                    self.step.dice.progname, stdin=infile, stdout=outfile
-                )
-
-        if exit_status != 0:
-            raise RuntimeError(
-                f"Dice process step{cycle:02d}-p{proc:02d} did not exit properly"
-            )
-
-        with open(Path(file_name + ".out"), "r") as outfile:
-            flag = outfile.readlines()[DICE_FLAG_LINE].strip()
-            if flag != DICE_END_FLAG:
-                raise RuntimeError(
-                    f"Dice process step{cycle:02d}-p{proc:02d} did not exit properly"
-                )
-
-        logger.info(f"Dice {file_name} - step{cycle:02d}-p{proc:02d} exited properly")

diceplayer/shared/interface/gaussian_interface.py

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

diceplayer/shared/utils/dataclass_protocol.py

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

diceplayer/shared/utils/logger.py

@@ -1,72 +0,0 @@
-import logging
-from pathlib import Path
-
-
-def valid_logger(func):
-    def wrapper(*args, **kwargs):
-        logger = args[0]
-        assert logger._was_set, "Logger is not set. Please call set_logger() first."
-
-        return func(*args, **kwargs)
-
-    return wrapper
-
-
-class Logger:
-    outfile = None
-
-    _logger = None
-
-    _was_set = False
-
-    def __init__(self, logger_name):
-        if self._logger is None:
-            self._logger = logging.getLogger(logger_name)
-
-    def set_logger(self, outfile="run.log", level=logging.INFO, stream=None):
-        outfile_path = None
-        if outfile is not None and stream is None:
-            outfile_path = Path(outfile)
-            if outfile_path.exists():
-                outfile_path.rename(str(outfile_path) + ".backup")
-
-        if level is not None:
-            self._logger.setLevel(level)
-
-        self._create_handlers(outfile_path, stream)
-
-        self._was_set = True
-
-    @valid_logger
-    def info(self, message):
-        self._logger.info(message)
-
-    @valid_logger
-    def debug(self, message):
-        self._logger.debug(message)
-
-    @valid_logger
-    def warning(self, message):
-        self._logger.warning(message)
-
-    @valid_logger
-    def error(self, message):
-        self._logger.error(message)
-
-    def _create_handlers(self, outfile_path: Path, stream):
-        handlers = []
-        if outfile_path is not None:
-            handlers.append(logging.FileHandler(outfile_path, mode="a+"))
-        elif stream is not None:
-            handlers.append(logging.StreamHandler(stream))
-        else:
-            handlers.append(logging.StreamHandler())
-
-        for handler in handlers:
-            handler.setFormatter(logging.Formatter("%(message)s"))
-            self._logger.addHandler(handler)
-
-    def close(self):
-        for handler in self._logger.handlers:
-            handler.close()
-            self._logger.removeHandler(handler)

diceplayer/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/state/state_handler.py

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

diceplayer/state/state_model.py

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

diceplayer/utils/__init__.py

@@ -0,0 +1,21 @@
+from .logger import RunLogger
+from .misc import (
+    compress_files_1mb,
+    date_time,
+    make_qm_dir,
+    make_step_dir,
+    weekday_date_time,
+)
+from .ptable import AtomInfo, PTable
+
+
+__all__ = [
+    "RunLogger",
+    "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/logger.py

@@ -0,0 +1,44 @@
+from typing_extensions import TypeVar
+
+import logging
+import sys
+from pathlib import Path
+
+
+H = TypeVar("H", bound=logging.Handler)
+
+
+class RunLogger(logging.Logger):
+    def __init__(self, name, level=logging.INFO, stream=sys.stdout):
+        super().__init__(name, level)
+
+        self.handlers.clear()
+
+        self.handlers.append(
+            self._configure_handler(logging.StreamHandler(stream), level)
+        )
+
+    def set_output_file(self, outfile: Path, level=logging.INFO):
+        for handler in list(self.handlers):
+            if not isinstance(handler, logging.FileHandler):
+                continue
+            self.handlers.remove(handler)
+
+        self.handlers.append(self._create_file_handler(outfile, level))
+
+    @staticmethod
+    def _create_file_handler(file: str | Path, level) -> logging.FileHandler:
+        file = Path(file)
+
+        if file.exists():
+            file.rename(file.with_suffix(".log.backup"))
+
+        handler = logging.FileHandler(file)
+        return RunLogger._configure_handler(handler, level)
+
+    @staticmethod
+    def _configure_handler(handler: H, level) -> H:
+        handler.setLevel(level)
+        formatter = logging.Formatter("%(message)s")
+        handler.setFormatter(formatter)
+        return handler

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/potential.py

@@ -0,0 +1,55 @@
+from diceplayer.config import PlayerConfig
+from diceplayer.environment import Atom, Molecule, System
+
+from pathlib import Path
+
+
+def read_system_from_phb(config: PlayerConfig) -> System:
+    phb_file = Path(config.dice.ljname)
+    if not phb_file.exists():
+        raise FileNotFoundError
+
+    ljc_data = phb_file.read_text(encoding="utf-8").splitlines()
+
+    combrule = ljc_data.pop(0).strip()
+    if combrule != config.dice.combrule:
+        raise ValueError(
+            f"Invalid combrule defined in {phb_file}. Expected the same value configured in the config file"
+        )
+
+    ntypes = ljc_data.pop(0).strip()
+    if not ntypes.isdigit():
+        raise ValueError(f"Invalid ntypes defined in {phb_file}")
+
+    nmol = int(ntypes)
+    if nmol != len(config.dice.nmol):
+        raise ValueError(f"Invalid nmol defined in {phb_file}")
+
+    sys = System()
+
+    for i in range(nmol):
+        nsites, molname = ljc_data.pop(0).split()
+
+        if not nsites.isdigit():
+            raise ValueError(f"Invalid nsites defined in {phb_file}")
+        nsites = int(nsites)
+
+        mol = Molecule(molname)
+
+        for j in range(nsites):
+            _fields = ljc_data.pop(0).split()
+            mol.add_atom(Atom(*_fields))
+
+        sys.add_type(mol)
+
+    return sys
+
+
+# def write_phb(phb_file: Path, state: StateModel) -> None:
+#     if phb_file.exists():
+#        raise RuntimeError(f"File {phb_file} already exists")
+#
+#     with open(phb_file, "w") as f:
+#         f.write(f"{state.config.dice.combrule}\n")
+#         f.write(f"{len(state.system.nmols)}\n")
+#         f.write(f"{state.config.dice.nmol}\n")

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

@@ -1,706 +0,0 @@
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-    {file = "tomli-2.2.1-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a92ef1a44547e894e2a17d24e7557a5e85a9e1d0048b0b5e7541f76c5032cb13"},
-    {file = "tomli-2.2.1-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9316dc65bed1684c9a98ee68759ceaed29d229e985297003e494aa825ebb0281"},
-    {file = "tomli-2.2.1-cp313-cp313-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:e85e99945e688e32d5a35c1ff38ed0b3f41f43fad8df0bdf79f72b2ba7bc5272"},
-    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_aarch64.whl", hash = "sha256:ac065718db92ca818f8d6141b5f66369833d4a80a9d74435a268c52bdfa73140"},
-    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_i686.whl", hash = "sha256:d920f33822747519673ee656a4b6ac33e382eca9d331c87770faa3eef562aeb2"},
-    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:a198f10c4d1b1375d7687bc25294306e551bf1abfa4eace6650070a5c1ae2744"},
-    {file = "tomli-2.2.1-cp313-cp313-win32.whl", hash = "sha256:d3f5614314d758649ab2ab3a62d4f2004c825922f9e370b29416484086b264ec"},
-    {file = "tomli-2.2.1-cp313-cp313-win_amd64.whl", hash = "sha256:a38aa0308e754b0e3c67e344754dff64999ff9b513e691d0e786265c93583c69"},
-    {file = "tomli-2.2.1-py3-none-any.whl", hash = "sha256:cb55c73c5f4408779d0cf3eef9f762b9c9f147a77de7b258bef0a5628adc85cc"},
-    {file = "tomli-2.2.1.tar.gz", hash = "sha256:cd45e1dc79c835ce60f7404ec8119f2eb06d38b1deba146f07ced3bbc44505ff"},
-]
-
-[[package]]
-name = "typing-extensions"
-version = "4.15.0"
-description = "Backported and Experimental Type Hints for Python 3.9+"
-optional = false
-python-versions = ">=3.9"
-groups = ["dev"]
-markers = "python_version == \"3.10\""
-files = [
-    {file = "typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548"},
-    {file = "typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466"},
-]
-
-[[package]]
-name = "virtualenv"
-version = "20.34.0"
-description = "Virtual Python Environment builder"
-optional = false
-python-versions = ">=3.8"
-groups = ["dev"]
-files = [
-    {file = "virtualenv-20.34.0-py3-none-any.whl", hash = "sha256:341f5afa7eee943e4984a9207c025feedd768baff6753cd660c857ceb3e36026"},
-    {file = "virtualenv-20.34.0.tar.gz", hash = "sha256:44815b2c9dee7ed86e387b842a84f20b93f7f417f95886ca1996a72a4138eb1a"},
-]
-
-[package.dependencies]
-distlib = ">=0.3.7,<1"
-filelock = ">=3.12.2,<4"
-platformdirs = ">=3.9.1,<5"
-typing-extensions = {version = ">=4.13.2", markers = "python_version < \"3.11\""}
-
-[package.extras]
-docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
-test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8) ; platform_python_implementation == \"PyPy\" or platform_python_implementation == \"GraalVM\" or platform_python_implementation == \"CPython\" and sys_platform == \"win32\" and python_version >= \"3.13\"", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10) ; platform_python_implementation == \"CPython\""]
-
-[metadata]
-lock-version = "2.1"
-python-versions = ">=3.10,<4.0"
-content-hash = "f90241137e4e1197ca6a78485387f4227bbcb8ab61f83955c23cb2479ad3c8c4"

poetry.toml

@@ -1,2 +0,0 @@
-[virtualenvs]
-in-project = true

pyproject.toml

@@ -1,66 +1,83 @@
 [project]
 name = "diceplayer"
-description = ""
+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"}
+    { name = "Vitor Hideyoshi", email = "vitor.h.n.batista@gmail.com" },
+    { name = "Herbert Georg", email = "hcgeorg@ufg.br" }
 ]
-license = "GPL-2.0-only"
 readme = "README.md"
-dynamic = [
-    "version",
-    "dependencies",
-    "requires-python"
+license = "GPL-2.0-only"
+scripts = { diceplayer = "diceplayer.__main__:main" }
+requires-python = ">=3.12"
+dynamic = ["version"]
+
+
+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"
 ]
 
-[project.scripts]
-diceplayer = "diceplayer.__main__:main"
 
-
-# POETRY
-[tool.poetry]
-packages = [
-    { include = "diceplayer" }
+[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",
+    "pytest>=9.0.2",
 ]
-version = "0.0.0"
 
-[tool.poetry.dependencies]
-python = ">=3.10,<4.0"
-numpy = "^2.2.6"
-argparse = "^1.4.0"
-setproctitle = "^1.3.2"
-pyyaml = "^6.0"
 
-[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.requires-plugins]
-poetry-dynamic-versioning = { version = ">=1.0.0,<2.0.0", extras = ["plugin"] }
-
-[tool.poetry-dynamic-versioning]
-enable = true
-vcs = "git"
+# Build system
+[tool.hatch.version]
+source = "vcs"
 
 [build-system]
-requires = ["poetry-core", "poetry-dynamic-versioning>=1.0.0,<2.0.0"]
-build-backend = "poetry_dynamic_versioning.backend"
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
 
 
-# UTILS
+# 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/_assets/__init__.py

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

tests/cli/test_read_input_file.py

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

tests/config/test_dice_config.py

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

tests/config/test_gaussian_config.py

@@ -1,36 +1,36 @@
-from diceplayer.shared.config.gaussian_config import GaussianDTO
+from diceplayer.config.gaussian_config import GaussianConfig
 
-import unittest
+import pytest
 
 
-class TestGaussianDTO(unittest.TestCase):
+class TestGaussianConfig:
     def test_class_instantiation(self):
-        gaussian_dto = GaussianDTO(
+        gaussian_dto = GaussianConfig(
             level="test",
             qmprog="g16",
             keywords="test",
         )
 
-        self.assertIsInstance(gaussian_dto, GaussianDTO)
+        assert isinstance(gaussian_dto, GaussianConfig)
 
     def test_is_valid_qmprog(self):
-        with self.assertRaises(ValueError):
-            gaussian_dto = GaussianDTO(
+        with pytest.raises(ValueError):
+            GaussianConfig(
                 level="test",
                 qmprog="test",
                 keywords="test",
             )
 
     def test_is_valid_level(self):
-        with self.assertRaises(ValueError):
-            gaussian_dto = GaussianDTO(
+        with pytest.raises(ValueError):
+            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",
@@ -38,8 +38,4 @@ class TestGaussianDTO(unittest.TestCase):
             }
         )
 
-        self.assertIsInstance(gaussian_dto, GaussianDTO)
-
-
-if __name__ == "__main__":
-    unittest.main()
+        assert isinstance(gaussian_dto, GaussianConfig)

tests/config/test_player_config.py

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

tests/dice/test_dice_handler.py

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

tests/dice/test_dice_input.py

@@ -0,0 +1,67 @@
+from diceplayer.config import PlayerConfig
+from diceplayer.dice.dice_input import (
+    NPTEqConfig,
+    NPTTerConfig,
+    NVTEqConfig,
+    NVTTerConfig,
+    write_config,
+)
+
+import pytest
+
+from pathlib import Path
+
+
+class TestDiceInput:
+    @pytest.fixture
+    def player_config(self) -> PlayerConfig:
+        return PlayerConfig.model_validate(
+            {
+                "type": "both",
+                "mem": 12,
+                "max_cyc": 100,
+                "switch_cyc": 50,
+                "ncores": 4,
+                "dice": {
+                    "nprocs": 4,
+                    "ljname": "test",
+                    "outname": "test",
+                    "dens": 1.0,
+                    "nmol": [1],
+                    "nstep": [1, 1],
+                },
+                "gaussian": {
+                    "level": "test",
+                    "qmprog": "g16",
+                    "keywords": "test",
+                },
+            }
+        )
+
+    def test_generate_nvt_ter_input(self, player_config: PlayerConfig):
+        dice_input = NVTTerConfig.from_config(player_config)
+
+        assert isinstance(dice_input, NVTTerConfig)
+
+    def test_generate_nvt_eq_input(self, player_config: PlayerConfig):
+        dice_input = NVTEqConfig.from_config(player_config)
+
+        assert isinstance(dice_input, NVTEqConfig)
+
+    def test_generate_npt_ter_input(self, player_config: PlayerConfig):
+        dice_input = NPTTerConfig.from_config(player_config)
+
+        assert isinstance(dice_input, NPTTerConfig)
+
+    def test_generate_npt_eq_input(self, player_config: PlayerConfig):
+        dice_input = NPTEqConfig.from_config(player_config)
+
+        assert isinstance(dice_input, NPTEqConfig)
+
+    def test_write_dice_config(self, player_config: PlayerConfig, tmp_path: Path):
+        dice_input = NVTTerConfig.from_config(player_config)
+
+        output_file = tmp_path / dice_input.type
+        write_config(dice_input, tmp_path)
+
+        assert output_file.exists()

tests/dice/test_dice_wrapper.py

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

tests/environment/test_atom.py

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

tests/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/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/mocks/mock_inputs.py

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

tests/mocks/mock_proc.py

@@ -1,31 +0,0 @@
-import itertools
-from typing import List
-
-
-class MockProc:
-    pid_counter = itertools.count()
-
-    def __init__(self, *args, **kwargs):
-        self.pid = next(MockProc.pid_counter)
-
-        if "exitcode" in kwargs:
-            self.exitcode = kwargs["exitcode"]
-        else:
-            self.exitcode = 0
-
-        self.sentinel = self.pid
-
-    def __call__(self, *args, **kwargs):
-        return self
-
-    def start(self):
-        pass
-
-    def terminate(self):
-        pass
-
-
-class MockConnection:
-    @staticmethod
-    def wait(sentinels: List[int]):
-        return sentinels

tests/shared/config/test_player_dto.py

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

tests/shared/interface/test_dice_interface.py

@@ -1,661 +0,0 @@
-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 tests.mocks.mock_inputs import get_config_example
-from tests.mocks.mock_proc import MockConnection, MockProc
-
-import yaml
-
-import io
-import unittest
-from unittest import mock
-
-
-class TestDiceInterface(unittest.TestCase):
-    def setUp(self):
-        logger.set_logger(stream=io.StringIO())
-
-        config = yaml.load(get_config_example(), Loader=yaml.Loader)
-        self.config = PlayerConfig.from_dict(config["diceplayer"])
-
-    def test_class_instantiation(self):
-        dice = DiceInterface()
-
-        self.assertIsInstance(dice, DiceInterface)
-
-    def test_configure(self):
-        dice = DiceInterface()
-
-        self.assertIsNone(dice.step)
-        self.assertIsNone(dice.system)
-
-        # Ignoring the types for testing purposes
-        dice.configure(self.config, System())
-
-        self.assertIsNotNone(dice.step)
-        self.assertIsNotNone(dice.system)
-
-    def test_reset(self):
-        dice = DiceInterface()
-
-        dice.configure(self.config, System())
-
-        self.assertTrue(hasattr(dice, "step"))
-        self.assertTrue(hasattr(dice, "system"))
-
-        dice.reset()
-
-        self.assertFalse(hasattr(dice, "step"))
-        self.assertFalse(hasattr(dice, "system"))
-
-    @mock.patch("diceplayer.shared.interface.dice_interface.Process", MockProc())
-    @mock.patch("diceplayer.shared.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)
-    )
-    def test_start_with_process_error(self):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        with self.assertRaises(SystemExit):
-            dice.start(1)
-
-    def test_simulation_process_raises_exception(self):
-        dice = DiceInterface()
-
-        with self.assertRaises(SystemExit):
-            dice._simulation_process(1, 1)
-
-    @mock.patch(
-        "diceplayer.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")
-    def test_simulation_process(
-        self, mock_run_dice, mock_make_dice_inputs, mock_make_proc_dir
-    ):
-        dice = DiceInterface()
-
-        dice._simulation_process(1, 1)
-
-        self.assertTrue(dice._make_proc_dir.called)
-        self.assertTrue(dice._make_dice_inputs.called)
-        self.assertTrue(dice._run_dice.called)
-
-    @mock.patch("diceplayer.shared.interface.dice_interface.Path.mkdir")
-    @mock.patch("diceplayer.shared.interface.dice_interface.Path.exists")
-    def test_make_proc_dir_if_simdir_exists(self, mock_path_exists, mock_path_mkdir):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        mock_path_exists.return_value = False
-
-        dice._make_proc_dir(1, 1)
-
-        self.assertEqual(mock_path_mkdir.call_count, 2)
-
-    @mock.patch("diceplayer.shared.interface.dice_interface.Path.mkdir")
-    @mock.patch("diceplayer.shared.interface.dice_interface.Path.exists")
-    def test_make_proc_dir_if_simdir_doesnt_exists(
-        self, mock_path_exists, mock_path_mkdir
-    ):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        mock_path_exists.return_value = False
-
-        dice._make_proc_dir(1, 1)
-
-        self.assertEqual(mock_path_mkdir.call_count, 2)
-
-    def test_make_dice_seed(self):
-        seed = DiceInterface._make_dice_seed()
-
-        self.assertIsInstance(seed, int)
-
-    def test_make_dice_inputs_nstep_len_two_with_randoninit_first_cycle_one(self):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.step.dice.nstep = [1, 1]
-
-        dice._make_potentials = mock.Mock()
-
-        dice._make_init_file = mock.Mock()
-        dice._new_density = mock.Mock()
-
-        dice._make_nvt_ter = mock.Mock()
-        dice._make_nvt_eq = mock.Mock()
-        dice._make_npt_ter = mock.Mock()
-        dice._make_npt_eq = mock.Mock()
-
-        dice._make_dice_inputs(1, 1)
-
-        self.assertTrue(dice._make_potentials.called)
-
-        self.assertFalse(dice._make_init_file.called)
-        self.assertFalse(dice._new_density.called)
-
-        self.assertTrue(dice._make_nvt_ter.called)
-        self.assertTrue(dice._make_nvt_eq.called)
-
-        self.assertFalse(dice._make_npt_ter.called)
-        self.assertFalse(dice._make_npt_eq.called)
-
-    @mock.patch("builtins.open", new_callable=mock.mock_open, read_data="test")
-    @mock.patch(
-        "diceplayer.shared.interface.dice_interface.Path.exists", return_value=True
-    )
-    def test_make_dice_inputs_nstep_len_two_with_randoninit_first_cycle_two(
-        self, mock_path_exists, mock_open
-    ):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.step.dice.nstep = [1, 1]
-
-        dice._make_potentials = mock.Mock()
-
-        dice._make_init_file = mock.Mock()
-        dice._new_density = mock.Mock()
-
-        dice._make_nvt_ter = mock.Mock()
-        dice._make_nvt_eq = mock.Mock()
-        dice._make_npt_ter = mock.Mock()
-        dice._make_npt_eq = mock.Mock()
-
-        dice._make_dice_inputs(2, 1)
-
-        self.assertTrue(dice._make_potentials.called)
-
-        self.assertTrue(dice._make_init_file.called)
-        self.assertTrue(dice._new_density.called)
-
-        self.assertFalse(dice._make_nvt_ter.called)
-        self.assertTrue(dice._make_nvt_eq.called)
-
-        self.assertFalse(dice._make_npt_ter.called)
-        self.assertFalse(dice._make_npt_eq.called)
-
-    @mock.patch(
-        "diceplayer.shared.interface.dice_interface.Path.exists", return_value=False
-    )
-    def test_make_dice_inputs_raises_exception_on_last_not_found(
-        self, mock_path_exists
-    ):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.step.dice.nstep = [1, 1]
-
-        dice._make_potentials = mock.Mock()
-
-        dice._make_init_file = mock.Mock()
-        dice._new_density = mock.Mock()
-
-        dice._make_nvt_ter = mock.Mock()
-        dice._make_nvt_eq = mock.Mock()
-        dice._make_npt_ter = mock.Mock()
-        dice._make_npt_eq = mock.Mock()
-
-        with self.assertRaises(FileNotFoundError):
-            dice._make_dice_inputs(2, 1)
-
-    def test_make_dice_inputs_nstep_len_three_with_randoninit_first_cycle_one(self):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice._make_potentials = mock.Mock()
-
-        dice._make_init_file = mock.Mock()
-        dice._new_density = mock.Mock()
-
-        dice._make_nvt_ter = mock.Mock()
-        dice._make_nvt_eq = mock.Mock()
-        dice._make_npt_ter = mock.Mock()
-        dice._make_npt_eq = mock.Mock()
-
-        dice._make_dice_inputs(1, 1)
-
-        self.assertTrue(dice._make_potentials.called)
-
-        self.assertFalse(dice._make_init_file.called)
-        self.assertFalse(dice._new_density.called)
-
-        self.assertTrue(dice._make_nvt_ter.called)
-        self.assertFalse(dice._make_nvt_eq.called)
-
-        self.assertTrue(dice._make_npt_ter.called)
-        self.assertTrue(dice._make_npt_eq.called)
-
-    @mock.patch("diceplayer.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
-    )
-    def test_run_dice_on_first_cycle_run_successful(
-        self, mock_path_exists, mock_shutils, mock_os
-    ):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.step.dice.nstep = [1, 1, 1]
-
-        dice.run_dice_file = mock.Mock()
-
-        dice._run_dice(1, 1)
-
-        self.assertTrue(mock_os.getcwd.called)
-        self.assertTrue(mock_os.chdir.called)
-
-        self.assertEqual(dice.run_dice_file.call_count, 3)
-        self.assertTrue(mock_shutils.copy.called)
-
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.step.dice.nstep = [1, 1]
-
-        dice.run_dice_file = mock.Mock()
-
-        dice._run_dice(1, 1)
-
-        self.assertTrue(mock_os.getcwd.called)
-        self.assertTrue(mock_os.chdir.called)
-
-        self.assertEqual(dice.run_dice_file.call_count, 2)
-        self.assertTrue(mock_shutils.copy.called)
-
-    @mock.patch("diceplayer.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
-    )
-    def test_run_dice_on_second_cycle_run_successful(
-        self, mock_path_exists, mock_shutils, mock_os
-    ):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.run_dice_file = mock.Mock()
-
-        dice._run_dice(2, 1)
-
-        self.assertTrue(mock_os.getcwd.called)
-        self.assertTrue(mock_os.chdir.called)
-
-        self.assertEqual(dice.run_dice_file.call_count, 2)
-        self.assertTrue(mock_shutils.copy.called)
-
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.run_dice_file = mock.Mock()
-
-        dice._run_dice(2, 1)
-
-        self.assertTrue(mock_os.getcwd.called)
-        self.assertTrue(mock_os.chdir.called)
-
-        self.assertEqual(dice.run_dice_file.call_count, 1)
-        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(
-        self, mock_path_exists, mock_shutils, mock_os
-    ):
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.run_dice_file = mock.Mock()
-
-        with self.assertRaises(FileNotFoundError):
-            dice._run_dice(1, 1)
-
-    @mock.patch("builtins.open", new_callable=mock.mock_open)
-    def test_make_init_file(self, mock_open):
-        example_atom = Atom(
-            lbl=1,
-            na=1,
-            rx=1.0,
-            ry=1.0,
-            rz=1.0,
-            chg=1.0,
-            eps=1.0,
-            sig=1.0,
-        )
-
-        main_molecule = Molecule("main_molecule")
-        main_molecule.add_atom(example_atom)
-
-        secondary_molecule = Molecule("secondary_molecule")
-        secondary_molecule.add_atom(example_atom)
-
-        system = System()
-        system.add_type(main_molecule)
-        system.add_type(secondary_molecule)
-
-        dice = DiceInterface()
-        dice.configure(self.config, system)
-
-        dice.step.dice.nmol = [1, 1]
-
-        last_xyz_file = io.StringIO()
-        last_xyz_file.writelines(
-            [
-                "   TEST\n",
-                " Configuration number :     TEST =   TEST  TEST  TEST\n",
-                "   H     1.00000     1.00000     1.00000\n",
-                "   H     1.00000     1.00000     1.00000\n",
-            ]
-        )
-        last_xyz_file.seek(0)
-
-        dice._make_init_file("test", last_xyz_file)
-
-        mock_handler = mock_open()
-        calls = mock_handler.write.call_args_list
-
-        lines = list(map(lambda x: x[0][0], calls))
-
-        expected_lines = [
-            "  1.000000    1.000000    1.000000\n",
-            "  1.000000    1.000000    1.000000\n",
-            "$end",
-        ]
-
-        self.assertEqual(lines, expected_lines)
-
-    @mock.patch("builtins.open", new_callable=mock.mock_open)
-    def test_new_density(self, mock_open):
-        example_atom = Atom(
-            lbl=1,
-            na=1,
-            rx=1.0,
-            ry=1.0,
-            rz=1.0,
-            chg=1.0,
-            eps=1.0,
-            sig=1.0,
-        )
-
-        main_molecule = Molecule("main_molecule")
-        main_molecule.add_atom(example_atom)
-
-        secondary_molecule = Molecule("secondary_molecule")
-        secondary_molecule.add_atom(example_atom)
-
-        system = System()
-        system.add_type(main_molecule)
-        system.add_type(secondary_molecule)
-
-        dice = DiceInterface()
-        dice.configure(self.config, system)
-
-        last_xyz_file = io.StringIO()
-        last_xyz_file.writelines(
-            [
-                "   TEST\n",
-                " Configuration number :     TEST =   1  1  1\n",
-                "   H     1.00000     1.00000     1.00000\n",
-                "   H     1.00000     1.00000     1.00000\n",
-            ]
-        )
-        last_xyz_file.seek(0)
-
-        density = dice._new_density(last_xyz_file)
-
-        self.assertEqual(density, 85.35451545000001)
-
-    @mock.patch("builtins.open", new_callable=mock.mock_open)
-    @mock.patch("diceplayer.shared.interface.dice_interface.random")
-    def test_make_nvt_ter(self, mock_random, mock_open):
-        mock_random.random.return_value = 1
-
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice._make_nvt_ter(1, "test")
-
-        mock_handler = mock_open()
-        calls = mock_handler.write.call_args_list
-
-        lines = list(map(lambda x: x[0][0], calls))
-
-        expected_lines = [
-            "title = Diceplayer run - NVT Thermalization\n",
-            "ncores = 4\n",
-            "ljname = phb.ljc\n",
-            "outname = phb\n",
-            "nmol = 1 50\n",
-            "dens = 0.75\n",
-            "temp = 300.0\n",
-            "init = yes\n",
-            "nstep = 2000\n",
-            "vstep = 0\n",
-            "mstop = 1\n",
-            "accum = no\n",
-            "iprint = 1\n",
-            "isave = 0\n",
-            "irdf = 0\n",
-            "seed = 1000000\n",
-            "upbuf = 360",
-        ]
-
-        self.assertEqual(lines, expected_lines)
-
-    @mock.patch("builtins.open", new_callable=mock.mock_open)
-    @mock.patch("diceplayer.shared.interface.dice_interface.random")
-    def test_make_nvt_eq(self, mock_random, mock_open):
-        mock_random.random.return_value = 1
-
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice._make_nvt_eq(1, "test")
-
-        mock_handler = mock_open()
-        calls = mock_handler.write.call_args_list
-
-        lines = list(map(lambda x: x[0][0], calls))
-
-        expected_lines = [
-            "title = Diceplayer run - NVT Production\n",
-            "ncores = 4\n",
-            "ljname = phb.ljc\n",
-            "outname = phb\n",
-            "nmol = 1 50\n",
-            "dens = 0.75\n",
-            "temp = 300.0\n",
-            "init = no\n",
-            "nstep = 3000\n",
-            "vstep = 0\n",
-            "mstop = 1\n",
-            "accum = no\n",
-            "iprint = 1\n",
-            "isave = 1000\n",
-            "irdf = 40\n",
-            "seed = 1000000\n",
-        ]
-
-        self.assertEqual(lines, expected_lines)
-
-    @mock.patch("builtins.open", new_callable=mock.mock_open)
-    @mock.patch("diceplayer.shared.interface.dice_interface.random")
-    def test_make_npt_ter(self, mock_random, mock_open):
-        mock_random.random.return_value = 1
-
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice._make_npt_ter(1, "test")
-
-        mock_handler = mock_open()
-        calls = mock_handler.write.call_args_list
-
-        lines = list(map(lambda x: x[0][0], calls))
-
-        expected_lines = [
-            "title = Diceplayer run - NPT Thermalization\n",
-            "ncores = 4\n",
-            "ljname = phb.ljc\n",
-            "outname = phb\n",
-            "nmol = 1 50\n",
-            "press = 1.0\n",
-            "temp = 300.0\n",
-            "init = no\n",
-            "vstep = 600\n",
-            "nstep = 5\n",
-            "mstop = 1\n",
-            "accum = no\n",
-            "iprint = 1\n",
-            "isave = 0\n",
-            "irdf = 0\n",
-            "seed = 1000000\n",
-        ]
-
-        self.assertEqual(lines, expected_lines)
-
-    @mock.patch("builtins.open", new_callable=mock.mock_open)
-    @mock.patch("diceplayer.shared.interface.dice_interface.random")
-    def test_make_npt_eq(self, mock_random, mock_open):
-        mock_random.random.return_value = 1
-
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice._make_npt_eq("test")
-
-        mock_handler = mock_open()
-        calls = mock_handler.write.call_args_list
-
-        lines = list(map(lambda x: x[0][0], calls))
-
-        expected_lines = [
-            "title = Diceplayer run - NPT Production\n",
-            "ncores = 4\n",
-            "ljname = phb.ljc\n",
-            "outname = phb\n",
-            "nmol = 1 50\n",
-            "press = 1.0\n",
-            "temp = 300.0\n",
-            "nstep = 5\n",
-            "vstep = 800\n",
-            "init = no\n",
-            "mstop = 1\n",
-            "accum = no\n",
-            "iprint = 1\n",
-            "isave = 1000\n",
-            "irdf = 40\n",
-            "seed = 1000000\n",
-        ]
-
-        self.assertEqual(lines, expected_lines)
-
-    @mock.patch("builtins.open", new_callable=mock.mock_open)
-    def test_make_potentials(self, mock_open):
-        example_atom = Atom(
-            lbl=1,
-            na=1,
-            rx=1.0,
-            ry=1.0,
-            rz=1.0,
-            chg=1.0,
-            eps=1.0,
-            sig=1.0,
-        )
-
-        main_molecule = Molecule("main_molecule")
-        main_molecule.add_atom(example_atom)
-
-        secondary_molecule = Molecule("secondary_molecule")
-        secondary_molecule.add_atom(example_atom)
-
-        system = System()
-        system.add_type(main_molecule)
-        system.add_type(secondary_molecule)
-
-        dice = DiceInterface()
-        dice.configure(self.config, system)
-
-        dice._make_potentials("test")
-
-        mock_handler = mock_open()
-        calls = mock_handler.write.call_args_list
-
-        lines = list(map(lambda x: x[0][0], calls))
-
-        expected_lines = [
-            "*\n",
-            "2\n",
-            "1 main_molecule\n",
-            "1     1     1.00000    1.00000    1.00000    1.000000   1.00000  1.0000\n",
-            "1 secondary_molecule\n",
-            "1     1     1.00000    1.00000    1.00000    1.000000   1.00000  1.0000\n",
-        ]
-
-        self.assertEqual(lines, expected_lines)
-
-    @mock.patch("diceplayer.shared.interface.dice_interface.subprocess")
-    @mock.patch(
-        "builtins.open",
-        new_callable=mock.mock_open,
-        read_data="End of simulation\nBLABLA",
-    )
-    def test_run_dice_file(self, mock_open, mock_subprocess):
-        mock_subprocess.call.return_value = 0
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        dice.run_dice_file(1, 1, "test")
-
-        self.assertTrue(mock_subprocess.call.called)
-        self.assertTrue(mock_open.called)
-
-    @mock.patch("diceplayer.shared.interface.dice_interface.subprocess")
-    @mock.patch("builtins.open", new_callable=mock.mock_open, read_data="Error\nBLABLA")
-    def test_run_dice_file_raises_runtime_error_on_dice_file(
-        self, mock_open, mock_subprocess
-    ):
-        mock_subprocess.call.return_value = 0
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        with self.assertRaises(RuntimeError):
-            dice.run_dice_file(1, 1, "test")
-
-    @mock.patch("diceplayer.shared.interface.dice_interface.subprocess")
-    @mock.patch(
-        "builtins.open",
-        new_callable=mock.mock_open,
-        read_data="End of simulation\nBLABLA",
-    )
-    def test_run_dice_file_raises_runtime_error_of_dice_exit_code(
-        self, mock_open, mock_subprocess
-    ):
-        mock_subprocess.call.return_value = 1
-        dice = DiceInterface()
-        dice.configure(self.config, System())
-
-        with self.assertRaises(RuntimeError):
-            dice.run_dice_file(1, 1, "test")
-
-
-if __name__ == "__main__":
-    unittest.main()

tests/shared/interface/test_gaussian_interface.py

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

tests/shared/utils/test_logger.py

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

tests/state/test_state_handler.py

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

tests/test_player.py

@@ -1,393 +0,0 @@
-from diceplayer import VERSION, logger
-from diceplayer.player import Player
-from tests.mocks.mock_inputs import mock_open
-
-import io
-import unittest
-from unittest import mock
-
-
-class TestPlayer(unittest.TestCase):
-    def setUp(self):
-        logger.set_logger(stream=io.StringIO())
-
-    @mock.patch("builtins.open", mock_open)
-    def test_class_instantiation(self):
-        # This file does not exist and it will be mocked
-        player = Player("control.test.yml")
-
-        self.assertIsInstance(player, Player)
-
-    @mock.patch("builtins.open", mock_open)
-    def test_start(self):
-        player = Player("control.test.yml")
-
-        player.gaussian_start = mock.MagicMock()
-        player.dice_start = mock.MagicMock()
-
-        player.start()
-
-        self.assertEqual(player.dice_start.call_count, 3)
-        self.assertEqual(player.gaussian_start.call_count, 3)
-
-    @mock.patch("builtins.open", mock_open)
-    @mock.patch("diceplayer.player.Path")
-    def test_create_simulation_dir_if_already_exists(self, mock_path):
-        player = Player("control.test.yml")
-        mock_path.return_value.exists.return_value = True
-
-        with self.assertRaises(FileExistsError):
-            player.create_simulation_dir()
-
-        self.assertTrue(mock_path.called)
-
-    @mock.patch("builtins.open", mock_open)
-    @mock.patch("diceplayer.player.Path")
-    def test_create_simulation_dir_if_not_exists(self, mock_path):
-        player = Player("control.test.yml")
-        mock_path.return_value.exists.return_value = False
-
-        player.create_simulation_dir()
-
-        self.assertTrue(mock_path.called)
-
-    @mock.patch("builtins.open", mock_open)
-    @mock.patch("diceplayer.player.VERSION", "test")
-    @mock.patch("diceplayer.player.sys")
-    @mock.patch("diceplayer.player.weekday_date_time")
-    def test_print_keywords(self, mock_date_func, mock_sys):
-        player = Player("control.test.yml")
-
-        mock_sys.version = "TEST"
-        mock_date_func.return_value = "00 Test 0000 at 00:00:00"
-
-        with self.assertLogs() as cm:
-            player.print_keywords()
-
-        expected_output = [
-            "INFO:diceplayer:##########################################################################################\n#############               Welcome to DICEPLAYER version test                #############\n##########################################################################################\n",
-            "INFO:diceplayer:Your python version is TEST\n",
-            "INFO:diceplayer:Program started on 00 Test 0000 at 00:00:00\n",
-            "INFO:diceplayer:Environment variables:",
-            "INFO:diceplayer:OMP_STACKSIZE = Not set\n",
-            "INFO:diceplayer:------------------------------------------------------------------------------------------\n                         DICE variables being used in this run:\n------------------------------------------------------------------------------------------\n",
-            "INFO:diceplayer:dens = 0.75",
-            "INFO:diceplayer:isave = 1000",
-            "INFO:diceplayer:ljname = phb.ljc",
-            "INFO:diceplayer:nmol = [ 1 50 ]",
-            "INFO:diceplayer:nstep = [ 2000 3000 4000 ]",
-            "INFO:diceplayer:outname = phb",
-            "INFO:diceplayer:press = 1.0",
-            "INFO:diceplayer:progname = ~/.local/bin/dice",
-            "INFO:diceplayer:randominit = first",
-            "INFO:diceplayer:temp = 300.0",
-            "INFO:diceplayer:------------------------------------------------------------------------------------------\n                         GAUSSIAN variables being used in this run:\n------------------------------------------------------------------------------------------\n",
-            "INFO:diceplayer:chg_tol = 0.01",
-            "INFO:diceplayer:keywords = freq",
-            "INFO:diceplayer:level = MP2/aug-cc-pVDZ",
-            "INFO:diceplayer:pop = chelpg",
-            "INFO:diceplayer:qmprog = g16",
-            "INFO:diceplayer:\n",
-        ]
-
-        self.assertEqual(cm.output, expected_output)
-
-    def test_validate_atom_dict(self):
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": 0,
-                    "na": 1,
-                    "rx": 1.0,
-                    "ry": 1.0,
-                    "rz": 1.0,
-                    "chg": 1.0,
-                    "eps": 1.0,
-                },
-            )
-        self.assertEqual(
-            str(context.exception),
-            "Invalid number of fields for site 1 for molecule type 1.",
-        )
-
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": "",
-                    "na": 1,
-                    "rx": 1.0,
-                    "ry": 1.0,
-                    "rz": 1.0,
-                    "chg": 1.0,
-                    "eps": 1.0,
-                    "sig": 1.0,
-                },
-            )
-        self.assertEqual(
-            str(context.exception), "Invalid lbl fields for site 1 for molecule type 1."
-        )
-
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": 1.0,
-                    "na": "",
-                    "rx": 1.0,
-                    "ry": 1.0,
-                    "rz": 1.0,
-                    "chg": 1.0,
-                    "eps": 1.0,
-                    "sig": 1.0,
-                },
-            )
-        self.assertEqual(
-            str(context.exception), "Invalid na fields for site 1 for molecule type 1."
-        )
-
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": 1.0,
-                    "na": 1,
-                    "rx": "",
-                    "ry": 1.0,
-                    "rz": 1.0,
-                    "chg": 1.0,
-                    "eps": 1.0,
-                    "sig": 1.0,
-                },
-            )
-        self.assertEqual(
-            str(context.exception),
-            "Invalid rx fields for site 1 for molecule type 1. Value must be a float.",
-        )
-
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": 1.0,
-                    "na": 1,
-                    "rx": 1.0,
-                    "ry": "",
-                    "rz": 1.0,
-                    "chg": 1.0,
-                    "eps": 1.0,
-                    "sig": 1.0,
-                },
-            )
-        self.assertEqual(
-            str(context.exception),
-            "Invalid ry fields for site 1 for molecule type 1. Value must be a float.",
-        )
-
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": 1.0,
-                    "na": 1,
-                    "rx": 1.0,
-                    "ry": 1.0,
-                    "rz": "",
-                    "chg": 1.0,
-                    "eps": 1.0,
-                    "sig": 1.0,
-                },
-            )
-        self.assertEqual(
-            str(context.exception),
-            "Invalid rz fields for site 1 for molecule type 1. Value must be a float.",
-        )
-
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": 1.0,
-                    "na": 1,
-                    "rx": 1.0,
-                    "ry": 1.0,
-                    "rz": 1.0,
-                    "chg": "",
-                    "eps": 1.0,
-                    "sig": 1.0,
-                },
-            )
-        self.assertEqual(
-            str(context.exception),
-            "Invalid chg fields for site 1 for molecule type 1. Value must be a float.",
-        )
-
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": 1.0,
-                    "na": 1,
-                    "rx": 1.0,
-                    "ry": 1.0,
-                    "rz": 1.0,
-                    "chg": 1.0,
-                    "eps": "",
-                    "sig": 1.0,
-                },
-            )
-        self.assertEqual(
-            str(context.exception),
-            "Invalid eps fields for site 1 for molecule type 1. Value must be a float.",
-        )
-
-        with self.assertRaises(ValueError) as context:
-            Player.validate_atom_dict(
-                molecule_type=0,
-                molecule_site=0,
-                atom_dict={
-                    "lbl": 1.0,
-                    "na": 1,
-                    "rx": 1.0,
-                    "ry": 1.0,
-                    "rz": 1.0,
-                    "chg": 1.0,
-                    "eps": 1.0,
-                    "sig": "",
-                },
-            )
-        self.assertEqual(
-            str(context.exception),
-            "Invalid sig fields for site 1 for molecule type 1. Value must be a float.",
-        )
-
-    @mock.patch("builtins.open", mock_open)
-    @mock.patch("diceplayer.player.Path.exists", return_value=True)
-    def test_read_potentials(self, mock_path_exists):
-        player = Player("control.test.yml")
-
-        player.read_potentials()
-
-        self.assertEqual(player.system.molecule[0].molname, "TEST")
-        self.assertEqual(len(player.system.molecule[0].atom), 1)
-
-        self.assertEqual(player.system.molecule[1].molname, "PLACEHOLDER")
-        self.assertEqual(len(player.system.molecule[1].atom), 1)
-
-    @mock.patch("builtins.open", mock_open)
-    @mock.patch("diceplayer.player.Path.exists")
-    def test_read_potentials_error(self, mock_path_exists):
-        player = Player("control.test.yml")
-
-        # Testing file not found error
-        mock_path_exists.return_value = False
-        with self.assertRaises(RuntimeError) as context:
-            player.read_potentials()
-
-        self.assertEqual(str(context.exception), "Potential file phb.ljc not found.")
-
-        # Enabling file found for next tests
-        mock_path_exists.return_value = True
-
-        # Testing combrule error
-        with self.assertRaises(SystemExit) as context:
-            player.config.dice.ljname = "phb.error.combrule.ljc"
-            player.read_potentials()
-
-        self.assertEqual(
-            str(context.exception),
-            "Error: expected a '*' or a '+' sign in 1st line of file phb.error.combrule.ljc",
-        )
-
-        # Testing ntypes error
-        with self.assertRaises(SystemExit) as context:
-            player.config.dice.ljname = "phb.error.ntypes.ljc"
-            player.read_potentials()
-
-        self.assertEqual(
-            str(context.exception),
-            "Error: expected an integer in the 2nd line of file phb.error.ntypes.ljc",
-        )
-
-        # Testing ntypes error on config
-        with self.assertRaises(SystemExit) as context:
-            player.config.dice.ljname = "phb.error.ntypes.config.ljc"
-            player.read_potentials()
-
-        self.assertEqual(
-            str(context.exception),
-            "Error: number of molecule types in file phb.error.ntypes.config.ljc "
-            "must match that of 'nmol' keyword in config file",
-        )
-
-        # Testing nsite error
-        with self.assertRaises(ValueError) as context:
-            player.config.dice.ljname = "phb.error.nsites.ljc"
-            player.read_potentials()
-
-        self.assertEqual(
-            str(context.exception),
-            "Error: expected nsites to be an integer for molecule type 1",
-        )
-
-        # Testing molname error
-        with self.assertRaises(ValueError) as context:
-            player.config.dice.ljname = "phb.error.molname.ljc"
-            player.read_potentials()
-
-        self.assertEqual(
-            str(context.exception),
-            "Error: expected nsites and molname for the molecule type 1",
-        )
-
-    @mock.patch("builtins.open", mock_open)
-    @mock.patch("diceplayer.player.Path.exists", return_value=True)
-    def test_print_potentials(self, mock_path_exists):
-        player = Player("control.test.yml")
-        player.read_potentials()
-
-        with self.assertLogs(level="INFO") as context:
-            player.print_potentials()
-
-        expected_output = [
-            "INFO:diceplayer:==========================================================================================\n                    Potential parameters from file phb.ljc:\n------------------------------------------------------------------------------------------\n",
-            "INFO:diceplayer:Combination rule: *",
-            "INFO:diceplayer:Types of molecules: 2\n",
-            "INFO:diceplayer:1 atoms in molecule type 1:",
-            "INFO:diceplayer:---------------------------------------------------------------------------------",
-            "INFO:diceplayer:Lbl  AN       X          Y          Z         Charge    Epsilon   Sigma     Mass",
-            "INFO:diceplayer:---------------------------------------------------------------------------------",
-            "INFO:diceplayer:1     1     0.00000    0.00000    0.00000    0.000000   0.00000  0.0000    1.0079",
-            "INFO:diceplayer:\n",
-            "INFO:diceplayer:1 atoms in molecule type 2:",
-            "INFO:diceplayer:---------------------------------------------------------------------------------",
-            "INFO:diceplayer:Lbl  AN       X          Y          Z         Charge    Epsilon   Sigma     Mass",
-            "INFO:diceplayer:---------------------------------------------------------------------------------",
-            "INFO:diceplayer:1     1     0.00000    0.00000    0.00000    0.000000   0.00000  0.0000    1.0079",
-            "INFO:diceplayer:\n",
-        ]
-
-        self.assertEqual(context.output, expected_output)
-
-    @mock.patch("builtins.open", mock_open)
-    def test_dice_start(self):
-        player = Player("control.test.yml")
-        player.dice_interface = mock.MagicMock()
-        player.dice_interface.start = mock.MagicMock()
-
-        player.dice_start(1)
-
-        player.dice_interface.start.assert_called_once()
-
-
-if __name__ == "__main__":
-    unittest.main()

tests/utils/test_potential.py

@@ -0,0 +1,37 @@
+from diceplayer.config import PlayerConfig
+from diceplayer.environment import System
+from diceplayer.utils.potential import read_system_from_phb
+
+import pytest
+
+
+class TestPotential:
+    @pytest.fixture
+    def player_config(self) -> PlayerConfig:
+        return PlayerConfig.model_validate(
+            {
+                "type": "both",
+                "mem": 12,
+                "max_cyc": 100,
+                "switch_cyc": 50,
+                "ncores": 4,
+                "dice": {
+                    "nprocs": 4,
+                    "ljname": "phb.ljc.example",
+                    "outname": "test",
+                    "dens": 1.0,
+                    "nmol": [12, 16],
+                    "nstep": [1, 1],
+                },
+                "gaussian": {
+                    "level": "test",
+                    "qmprog": "g16",
+                    "keywords": "test",
+                },
+            }
+        )
+
+    def test_read_phb(self, player_config: PlayerConfig):
+        system = read_system_from_phb(player_config)
+
+        assert isinstance(system, System)

uv.lock

@@ -0,0 +1,727 @@
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