chore: release v1.4.0

.gitignore

@@ -3,6 +3,13 @@ build/
 **/PQAnalysis.egg-info/
 **/__pycache*
 
+# generated Cython artifacts (the .pyx sources stay tracked)
+*.cpython-*.so
+PQAnalysis/analysis/msd/_msd_kernel.c
+PQAnalysis/analysis/vacf/_vacf_kernel.c
+PQAnalysis/analysis/rdf/_rdf_kernel.c
+PQAnalysis/io/traj_file/_slab_parser.c
+
 _version.py
 **/*.ipynb
 

MANIFEST.in

@@ -3,3 +3,7 @@ include README.md
 include CHANGELOG.md
 recursive-include PQAnalysis/grammar *.lark
 include PQAnalysis/io/traj_file/process_lines.pyx
+include PQAnalysis/io/traj_file/_slab_parser.pyx
+include PQAnalysis/analysis/msd/_msd_kernel.pyx
+include PQAnalysis/analysis/vacf/_vacf_kernel.pyx
+include PQAnalysis/analysis/rdf/_rdf_kernel.pyx

PQAnalysis/analysis/__init__.py

@@ -2,4 +2,13 @@
 This is a collection of analysis subpackages.
 """
 
+from .momentum import Momentum, check_momentum
+from .msd import MSD, MSDDiffusionFit, MSDInputFileReader, msd
 from .rdf import RDF, RDFInputFileReader, RDFDataWriter, RDFLogWriter, rdf
+from .spectrum_broadening import broaden, build_spectrum
+from .vacf import VACF, VACFInputFileReader, vacf, vacf_spectrum
+from .vibrational import (
+    VibrationalAnalysisInputFileReader,
+    VibrationalAnalysisResult,
+    vibrations,
+)

PQAnalysis/analysis/momentum/__init__.py

@@ -0,0 +1,28 @@
+"""
+A package containing classes and functions to check the total linear
+momentum of velocity trajectories.
+
+Classes
+-------
+:py:class:`~PQAnalysis.analysis.momentum.momentum.Momentum`
+    A class to calculate the norm of the total linear momentum of a
+    selection of atoms for every frame of a velocity trajectory.
+:py:class:`~PQAnalysis.analysis.momentum.momentum_output_file_writer.MomentumDataWriter`
+    A class to write momentum data to output files.
+
+Functions
+---------
+:py:func:`~PQAnalysis.analysis.momentum.api.check_momentum`
+    A function to calculate and write the total linear momentum norm
+    per frame of a velocity trajectory.
+"""
+
+from .api import check_momentum
+from .momentum import Momentum
+from .momentum_output_file_writer import MomentumDataWriter
+
+__all__ = [
+    "Momentum",
+    "MomentumDataWriter",
+    "check_momentum",
+]

PQAnalysis/analysis/momentum/api.py

@@ -0,0 +1,84 @@
+"""
+API functions for the momentum analysis.
+"""
+
+from beartype.typing import List
+
+from PQAnalysis.io import TrajectoryReader
+from PQAnalysis.io.formats import FileWritingMode
+from PQAnalysis.topology import SelectionCompatible
+from PQAnalysis.traj import MDEngineFormat
+from PQAnalysis.type_checking import runtime_type_checking
+from PQAnalysis.types import Np1DNumberArray, PositiveReal
+
+from .momentum import Momentum
+from .momentum_output_file_writer import MomentumDataWriter
+
+
+
+@runtime_type_checking
+def check_momentum(
+    trajectory_files: str | List[str],
+    output: str | None = None,
+    selection: SelectionCompatible = None,
+    use_full_atom_info: bool = False,
+    scale: PositiveReal | None = None,
+    md_format: MDEngineFormat | str = MDEngineFormat.PQ,
+    mode: str | FileWritingMode = "w",
+) -> Np1DNumberArray:
+    """
+    Calculate the total linear momentum norm per frame and write it.
+
+    Reads the given velocity trajectory file(s) frame by frame,
+    calculates the norm of the total linear momentum
+    ``P = sum_i m_i * v_i`` of the selected atoms for every frame and
+    writes one row per frame containing the one-based frame index and
+    the scaled momentum norm. This is a port of the legacy
+    ``equipartition.jl`` tool.
+
+    Parameters
+    ----------
+    trajectory_files : str | List[str]
+        The velocity trajectory file(s) to read.
+    output : str | None, optional
+        The output file. If None, the output is printed to stdout,
+        by default None.
+    selection : SelectionCompatible, optional
+        The selection of atoms to include in the total momentum,
+        by default None (all atoms).
+    use_full_atom_info : bool, optional
+        Whether to use the full atom information of the trajectory
+        for the selection or not, by default False.
+    scale : PositiveReal | None, optional
+        The scaling factor applied to the momentum norm before
+        output, by default None (1e-15, which converts
+        amu*Angstrom/s to amu*Angstrom/fs).
+    md_format : MDEngineFormat | str, optional
+        The format of the trajectory, by default MDEngineFormat.PQ.
+        Use ``qmcfc`` for legacy trajectories with a leading dummy
+        'X' atom.
+    mode : str | FileWritingMode, optional
+        The writing mode of the output file, by default "w".
+
+    Returns
+    -------
+    Np1DNumberArray
+        The scaled norms of the total linear momentum, one value
+        per frame.
+    """
+    reader = TrajectoryReader(trajectory_files, md_format=md_format)
+
+    momentum = Momentum(
+        reader,
+        selection=selection,
+        use_full_atom_info=use_full_atom_info,
+        scale=scale,
+    )
+
+    data_writer = MomentumDataWriter(output, mode=mode)
+
+    momentum_norms = momentum.run()
+
+    data_writer.write(momentum_norms)
+
+    return momentum_norms

PQAnalysis/analysis/momentum/exceptions.py

@@ -0,0 +1,13 @@
+"""
+Exceptions for the momentum analysis.
+"""
+
+from PQAnalysis.exceptions import PQException
+
+
+
+class MomentumError(PQException):
+
+    """
+    Exception raised for momentum analysis errors.
+    """