hillclimber 0.1.6__cp314-cp314t-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl

plumedCommunications.pyi

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+"""Type stubs for plumedCommunications module.
+
+This module is a pybind11 C++ extension that provides Python bindings
+for PLUMED's PythonCVInterface and PythonFunction classes.
+
+See: https://joss.theoj.org/papers/10.21105/joss.01773
+"""
+
+from typing import Any
+
+import numpy as np
+import numpy.typing as npt
+
+class defaults:
+    """Default definitions for PLUMED components."""
+
+    COMPONENT: dict[str, Any]
+    """Default component settings with derivative=True and period=None."""
+
+    COMPONENT_NODEV: dict[str, Any]
+    """Component settings with derivative=False and period=None."""
+
+class Pbc:
+    """Interface to PLUMED periodic boundary conditions."""
+
+    def apply(self, deltas: npt.NDArray[np.float64]) -> npt.NDArray[np.float64]:
+        """Apply PBC to a set of positions or distance vectors.
+
+        Parameters
+        ----------
+        deltas : np.ndarray
+            Array of shape (n, 3) containing distance vectors.
+
+        Returns
+        -------
+        np.ndarray
+            The input array with PBC applied (modified in-place).
+        """
+        ...
+
+    def getBox(self) -> npt.NDArray[np.float64]:
+        """Get the simulation box vectors.
+
+        Returns
+        -------
+        np.ndarray
+            Array of shape (3, 3) with the box vectors.
+        """
+        ...
+
+    def getInvBox(self) -> npt.NDArray[np.float64]:
+        """Get the inverted box vectors.
+
+        Returns
+        -------
+        np.ndarray
+            Array of shape (3, 3) with the inverted box vectors.
+        """
+        ...
+
+class NeighborList:
+    """Interface to PLUMED neighbor list."""
+
+    @property
+    def size(self) -> int:
+        """The number of atom pairs in the neighbor list."""
+        ...
+
+    def __len__(self) -> int:
+        """Return the number of atom pairs."""
+        ...
+
+    def getClosePairs(self) -> npt.NDArray[np.uint64]:
+        """Get the list of close atom pairs.
+
+        Returns
+        -------
+        np.ndarray
+            Array of shape (n_pairs, 2) with atom pair indices.
+        """
+        ...
+
+class PythonCVInterface:
+    """Interface for defining collective variables in Python.
+
+    This class provides access to atomic data and simulation information
+    when implementing custom collective variables via PYCVINTERFACE.
+    """
+
+    data: dict[str, Any]
+    """Persistent dictionary that survives across simulation steps."""
+
+    @property
+    def label(self) -> str:
+        """The label of this action."""
+        ...
+
+    @property
+    def nat(self) -> int:
+        """The number of atoms requested by this action."""
+        ...
+
+    def getStep(self) -> int:
+        """Get the current simulation step.
+
+        Returns
+        -------
+        int
+            The current step number.
+        """
+        ...
+
+    def getTime(self) -> float:
+        """Get the current simulation time.
+
+        Returns
+        -------
+        float
+            The current time.
+        """
+        ...
+
+    def getTimeStep(self) -> float:
+        """Get the simulation timestep.
+
+        Returns
+        -------
+        float
+            The timestep.
+        """
+        ...
+
+    def isRestart(self) -> bool:
+        """Check if this is a restart simulation.
+
+        Returns
+        -------
+        bool
+            True if restarting from a previous simulation.
+        """
+        ...
+
+    def isExchangeStep(self) -> bool:
+        """Check if this is a replica exchange step.
+
+        Returns
+        -------
+        bool
+            True if on an exchange step.
+        """
+        ...
+
+    def log(self, s: object) -> None:
+        """Write a message to the PLUMED log.
+
+        Parameters
+        ----------
+        s : object
+            Message to write (will be converted to string).
+        """
+        ...
+
+    def lognl(self, s: object) -> None:
+        """Write a message to the PLUMED log with newline.
+
+        Parameters
+        ----------
+        s : object
+            Message to write (will be converted to string).
+        """
+        ...
+
+    def getPosition(self, i: int) -> npt.NDArray[np.float64]:
+        """Get the position of atom i.
+
+        Parameters
+        ----------
+        i : int
+            Atom index (0-based, relative to atoms requested by action).
+
+        Returns
+        -------
+        np.ndarray
+            Array of shape (3,) with x, y, z coordinates.
+        """
+        ...
+
+    def getPositions(self) -> npt.NDArray[np.float64]:
+        """Get positions of all atoms requested by this action.
+
+        Returns
+        -------
+        np.ndarray
+            Array of shape (n_atoms, 3) with atomic positions.
+        """
+        ...
+
+    def getPbc(self) -> Pbc:
+        """Get the periodic boundary conditions interface.
+
+        Returns
+        -------
+        Pbc
+            Interface to the current PBC.
+        """
+        ...
+
+    def getNeighbourList(self) -> NeighborList:
+        """Get the neighbor list interface.
+
+        Returns
+        -------
+        NeighborList
+            Interface to the current neighbor list.
+        """
+        ...
+
+    def makeWhole(self) -> None:
+        """Make atoms whole across periodic boundaries.
+
+        Assumes atoms are in proper order.
+        """
+        ...
+
+    def absoluteIndexes(self) -> npt.NDArray[np.uint32]:
+        """Get the absolute atom indices.
+
+        Returns
+        -------
+        np.ndarray
+            Array of absolute atom indices in the full system.
+        """
+        ...
+
+    def charge(self, i: int) -> float:
+        """Get the charge of atom i.
+
+        Parameters
+        ----------
+        i : int
+            Atom index.
+
+        Returns
+        -------
+        float
+            The atomic charge.
+        """
+        ...
+
+    def mass(self, i: int) -> float:
+        """Get the mass of atom i.
+
+        Parameters
+        ----------
+        i : int
+            Atom index.
+
+        Returns
+        -------
+        float
+            The atomic mass.
+        """
+        ...
+
+    def masses(self) -> npt.NDArray[np.float64]:
+        """Get masses of all atoms.
+
+        Returns
+        -------
+        np.ndarray
+            Array of atomic masses.
+        """
+        ...
+
+    def charges(self) -> npt.NDArray[np.float64]:
+        """Get charges of all atoms.
+
+        Returns
+        -------
+        np.ndarray
+            Array of atomic charges.
+        """
+        ...
+
+class PythonFunction:
+    """Interface for defining functions of collective variables in Python.
+
+    This class provides access to CV arguments when implementing
+    custom functions via PYFUNCTION.
+    """
+
+    @property
+    def label(self) -> str:
+        """The label of this action."""
+        ...
+
+    @property
+    def nargs(self) -> int:
+        """The number of arguments passed to this function."""
+        ...
+
+    def getStep(self) -> int:
+        """Get the current simulation step.
+
+        Returns
+        -------
+        int
+            The current step number.
+        """
+        ...
+
+    def getTime(self) -> float:
+        """Get the current simulation time.
+
+        Returns
+        -------
+        float
+            The current time.
+        """
+        ...
+
+    def getTimeStep(self) -> float:
+        """Get the simulation timestep.
+
+        Returns
+        -------
+        float
+            The timestep.
+        """
+        ...
+
+    def isRestart(self) -> bool:
+        """Check if this is a restart simulation.
+
+        Returns
+        -------
+        bool
+            True if restarting from a previous simulation.
+        """
+        ...
+
+    def isExchangeStep(self) -> bool:
+        """Check if this is a replica exchange step.
+
+        Returns
+        -------
+        bool
+            True if on an exchange step.
+        """
+        ...
+
+    def log(self, s: object) -> None:
+        """Write a message to the PLUMED log.
+
+        Parameters
+        ----------
+        s : object
+            Message to write (will be converted to string).
+        """
+        ...
+
+    def lognl(self, s: object) -> None:
+        """Write a message to the PLUMED log with newline.
+
+        Parameters
+        ----------
+        s : object
+            Message to write (will be converted to string).
+        """
+        ...
+
+    def argument(self, i: int) -> float:
+        """Get the value of argument i.
+
+        Parameters
+        ----------
+        i : int
+            Argument index.
+
+        Returns
+        -------
+        float
+            The argument value.
+        """
+        ...
+
+    def arguments(self) -> npt.NDArray[np.float64]:
+        """Get all argument values.
+
+        Returns
+        -------
+        np.ndarray
+            Array of argument values.
+        """
+        ...
+
+    def difference(self, i: int, x: float, y: float) -> float:
+        """Compute difference accounting for periodicity.
+
+        Parameters
+        ----------
+        i : int
+            Argument index (for periodicity info).
+        x : float
+            First value.
+        y : float
+            Second value.
+
+        Returns
+        -------
+        float
+            The difference y - x accounting for periodicity.
+        """
+        ...
+
+    def bringBackInPbc(self, i: int, x: float) -> float:
+        """Bring a value back into the periodic domain.
+
+        Parameters
+        ----------
+        i : int
+            Argument index (for periodicity info).
+        x : float
+            Value to wrap.
+
+        Returns
+        -------
+        float
+            The value wrapped into the periodic domain.
+        """
+        ...