Refactor simulation

MDMC/MD/__init__.py

@@ -34,6 +34,7 @@
 from pkgutil import iter_modules
 
 from . import ase, engine_facades, force_fields, solvents
+from .constraints import Rattle, Shake
 from .interaction_functions import (
     Buckingham,
     Coulomb,
@@ -55,14 +56,10 @@
     Interaction,
     NonBondedInteraction,
 )
+from .kspace_solvers import PPPM, Ewald, KSpaceSolver
 from .parameters import Parameter, Parameters
 from .simulation import (
-    PPPM,
     ConstraintAlgorithm,
-    Ewald,
-    KSpaceSolver,
-    Rattle,
-    Shake,
     Simulation,
     Universe,
 )

MDMC/MD/constraints.py

@@ -0,0 +1,108 @@
+# MDMC is a package for the optimisation of classical potentials with experimental data
+# Copyright (C) 2026 MDMC Developers
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+"""Constraint solvers."""
+
+
+class ConstraintAlgorithm:
+    """
+    Class describing the algorithm and parameters which are applied to
+    constrain ``BondedInteraction`` objects
+
+    Parameters
+    ----------
+    accuracy : float
+        The accuracy (tolerance) of the applied constraints
+    max_iterations : int
+        The maximum number of iterations that can be used when calculating the
+        additional force that is required to constrain the atoms to satisfy the
+        constraints on the bonded interactions
+
+    Attributes
+    ----------
+    accuracy : float
+        The accuracy (tolerance) of the applied constraints
+    """
+
+    def __init__(self, accuracy: float, max_iterations: int):
+
+        self.accuracy = accuracy
+        self.max_iterations = max_iterations
+
+    @property
+    def name(self) -> str:
+        """
+        Get the name of the class
+
+        Returns
+        -------
+        str
+            The name of the class
+        """
+
+        return self.__class__.__name__
+
+    @property
+    def max_iterations(self) -> int:
+        """
+        Get or set the maximum number of iterations that can be used when
+        calculating the additional force that is required to constrain the atoms
+        to satisfy the constraints on the bonded interactions
+
+        Returns
+        -------
+        int
+            The maximum number of iterations
+        """
+
+        return self._max_iterations
+
+    @max_iterations.setter
+    def max_iterations(self, value: int) -> None:
+
+        self._max_iterations = int(value)
+
+
+class Shake(ConstraintAlgorithm):
+    """
+    Holds the parameters which are required for the SHAKE algorithm to be
+    applied to the constrained interactions
+
+    Parameters
+    ----------
+    accuracy : float
+        The accuracy (tolerance) of the applied constraints
+    max_iterations : int
+        The maximum number of iterations that can be used when calculating the
+        additional force that is required to constrain the atoms to satisfy the
+        constraints on the bonded interactions
+    """
+
+
+class Rattle(ConstraintAlgorithm):
+    """
+    Holds the parameters which are required for the RATTLE algorithm to be
+    applied to the constrained interactions
+
+    Parameters
+    ----------
+    accuracy : float
+        The accuracy (tolerance) of the applied constraints
+    max_iterations : int
+        The maximum number of iterations that can be used when calculating the
+        additional force that is required to constrain the atoms to satisfy the
+        constraints on the bonded interactions
+    """

MDMC/MD/engine_facades/lammps_engine.py

@@ -72,7 +72,8 @@
     Interaction,
     NonBondedInteraction,
 )
-from MDMC.MD.simulation import ConstraintAlgorithm, KSpaceSolver, Universe
+from MDMC.MD.kspace_solvers import KSpaceSolver
+from MDMC.MD.simulation import ConstraintAlgorithm, Universe
 from MDMC.MD.structures import Atom
 from MDMC.trajectory_analysis.compact_trajectory import CompactTrajectory
 from MDMC.utilities.partitioning import partition, partition_interactions

MDMC/MD/kspace_solvers.py

@@ -0,0 +1,94 @@
+# MDMC is a package for the optimisation of classical potentials with experimental data
+# Copyright (C) 2026 MDMC Developers
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+"""k-Space models for long range forces."""
+
+
+class KSpaceSolver:
+    """
+    Class describing the k-space solver that is applied to electrostatic and/or
+    dispersion interactions
+
+    Different ``MDEngine`` require different parameters to be specified for a
+    k-space solver to be used. These parameters are specified in settings.
+
+    Parameters
+    ----------
+    **settings
+        ``accuracy`` (`float`)
+            The relative RMS error in per-atom forces
+
+    Attributes
+    ----------
+    accuracy : float
+        The relative RMS error in per-atom forces
+    """
+
+    def __init__(self, *, accuracy: float | None = None):
+
+        self.accuracy = accuracy
+
+    @property
+    def name(self):
+        """
+        Get the name of the class
+
+        Returns
+        -------
+        str
+            The name of the class
+        """
+
+        return self.__class__.__name__
+
+
+class Ewald(KSpaceSolver):
+    """
+    Holds the parameters that are required for the Ewald solver to be applied to
+    both/either the electrostatic and/or dispersion interactions
+
+    Parameters
+    ----------
+    **settings
+        ``accuracy`` (`float`)
+            The relative RMS error in per-atom forces
+    """
+
+
+class PPPM(KSpaceSolver):
+    """
+    Holds the parameters that are required for the PPPM solver to be applied to
+    both/either the electrostatic and/or dispersion interactions
+
+    Parameters
+    ----------
+    **settings
+        ``accuracy`` (`float`)
+            The relative RMS error in per-atom forces
+    """
+
+    def __eq__(self, other) -> bool:
+        """
+        Two KSpaceSolvers are equal if their __dict__ are equal
+        """
+
+        if not isinstance(other, self.__class__):
+            return False
+        return all(v == getattr(other, k) for k, v in self.__dict__.items())
+
+    def __ne__(self, other) -> bool:
+
+        return not self.__eq__(other)