Merge branch 'develop' into parallize_rdf

Author: p-j-smith

.github/actions/setup-deps/action.yaml

@@ -64,6 +64,8 @@ inputs:
     default: 'h5py>=2.10'
   hole2:
     default: 'hole2'
+  imdclient:
+    default: 'imdclient>=0.2.2'
   joblib:
     default: 'joblib>=0.12'
   netcdf4:
@@ -138,6 +140,7 @@ runs:
           ${{ inputs.gsd }}
           ${{ inputs.h5py }}
           ${{ inputs.hole2 }}
+          ${{ inputs.imdclient }}
           ${{ inputs.joblib }}
           ${{ inputs.netcdf4 }}
           ${{ inputs.networkx }}

azure-pipelines.yml

@@ -113,6 +113,8 @@ jobs:
       pytng>=0.2.3
       rdkit>=2024.03.4
       tidynamics>=1.0.0
+      imdclient>=0.2.2
+
     # remove from azure to avoid test hanging #4707
     # "gsd>3.0.0"
     displayName: 'Install additional dependencies for 64-bit tests'

maintainer/conda/environment.yml

@@ -30,6 +30,7 @@ dependencies:
   - sphinxcontrib-bibtex
   - mdaencore
   - waterdynamics
+  - imdclient>=0.2.2
   - pip:
       - mdahole2
       - pathsimanalysis

package/AUTHORS

@@ -259,7 +259,8 @@ Chronological list of authors
   - Tulga-Erdene Sodjargal
   - Gareth Elliott
   - Marc Schuh
-
+  - Sirsha Ganguly
+  - Amruthesh Thirumalaiswamy
 
 External code
 -------------

package/CHANGELOG

@@ -16,7 +16,7 @@ The rules for this file:
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, orbeckst, BHM-Bob, TRY-ER, Abdulrahman-PROG, pbuslaev,
          yuxuanzhuang, yuyuan871111, tanishy7777, tulga-rdn, Gareth-elliott,
-         hmacdope, tylerjereddy, cbouy, talagayev, DrDomenicoMarson
+         hmacdope, tylerjereddy, cbouy, talagayev, DrDomenicoMarson, amruthesht
 
 
  * 2.10.0
@@ -42,6 +42,14 @@ Fixes
    directly passing them. (Issue #3520, PR #5006)
 
 Enhancements
+ * Added support for reading and processing streamed data in `coordinates.base`
+   with new `StreamFrameIteratorSliced` and `StreamReaderBase` (Issue #4827, PR #4923)
+ * New coordinate reader: Added `IMDReader` for reading real-time streamed
+   molecular dynamics simulation data using the IMDv3 protocol - requires
+   `imdclient` package (Issue #4827, PR #4923)
+ * Added capability to calculate MSD from frames with irregular (non-linear)
+   time spacing in analysis.msd.EinsteinMSD with keyword argument
+   `non_linear=True` (Issue #5028, PR #5066)
  * Support has been added for reading positions and velocities
    from GROMACS TPR files, between GROMACS version 4.x and 2025
    (Issue #464, PR #4873)
@@ -67,7 +75,7 @@ Enhancements
    so that it gets passed through from the calling functions and classes
    (PR #5038)
  * Moved distopia checking function to common import location in
-   MDAnalysisTest.util (PR #5038)
+   MDAnalysisTest.util (PR #5038)  
  * Enables parallelization for `analysis.polymer.PersistenceLength` (Issue #4671, PR #5074)
 
 

package/MDAnalysis/analysis/msd.py

@@ -63,15 +63,23 @@
 the normal MDAnalysis citations.
 
 .. warning::
-    To correctly compute the MSD using this analysis module, you must supply
-    coordinates in the **unwrapped** convention. That is, when atoms pass
-    the periodic boundary, they must not be **wrapped** back into the primary
-    simulation cell. MDAnalysis does not currently offer this functionality in
-    the ``MDAnalysis.transformations`` API despite having functions with
-    similar names. We plan to implement the appropriate transformations in the
-    future. In the meantime, various simulation packages provide utilities to
-    convert coordinates to the unwrapped convention. In GROMACS for example,
-    this can be done using ``gmx trjconv`` with the ``-pbc nojump`` flag.
+   To correctly compute the MSD using this analysis module, you must supply
+   coordinates in the **unwrapped** convention, also known as **no-jump**. 
+   That is, when atoms pass the periodic boundary, they must not be wrapped 
+   back into the primary simulation cell.
+   
+   In MDAnalysis you can use the 
+   :class:`~MDAnalysis.transformations.nojump.NoJump`
+   transformation. 
+   
+   In GROMACS, for example, this can be done using `gmx trjconv`_ with the
+   ``-pbc nojump`` flag.
+
+.. _`gmx trjconv`: https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html
+
+.. SeeAlso::
+   :mod:`MDAnalysis.transformations.nojump`
+
 
 Computing an MSD
 ----------------
@@ -102,16 +110,14 @@
 .. code-block:: python
 
     msd =  MSD.results.timeseries
+    lagtimes = MSD.results.delta_t_values
 
-Visual inspection of the MSD is important, so let's take a look at it with a
- simple plot.
+Visual inspection of the MSD is important, so let's take a look at it with a simple plot.
 
 .. code-block:: python
 
     import matplotlib.pyplot as plt
     nframes = MSD.n_frames
-    timestep = 1 # this needs to be the actual time between frames
-    lagtimes = np.arange(nframes)*timestep # make the lag-time axis
     fig = plt.figure()
     ax = plt.axes()
     # plot the actual MSD
@@ -172,8 +178,7 @@
     start_time = 20
     start_index = int(start_time/timestep)
     end_time = 60
-    linear_model = linregress(lagtimes[start_index:end_index],
-    				  		  msd[start_index:end_index])
+    linear_model = linregress(lagtimes[start_index:end_index], msd[start_index:end_index])
     slope = linear_model.slope
     error = linear_model.stderr
     # dim_fac is 3 as we computed a 3D msd with 'xyz'
@@ -245,6 +250,7 @@
 from .base import AnalysisBase
 from ..core import groups
 from tqdm import tqdm
+import collections
 
 logger = logging.getLogger("MDAnalysis.analysis.msd")
 
@@ -281,15 +287,32 @@ class EinsteinMSD(AnalysisBase):
         the MSD. Otherwise, use the simple "windowed" algorithm.
         The tidynamics package is required for `fft=True`.
         Defaults to ``True``.
+    non_linear : bool
+        If ``True``, calculates MSD for trajectory where frames are
+        non-linearly dumped. To use this set `fft=False`.
+        Defaults to ``False``.
+
+        .. versionadded:: 2.10.0
+
 
     Attributes
     ----------
     dim_fac : int
         Dimensionality :math:`d` of the MSD.
     results.timeseries : :class:`numpy.ndarray`
-        The averaged MSD over all the particles with respect to lag-time.
+        The averaged MSD over all the particles with respect to constant lag-time or
+        unique Δt intervals.
     results.msds_by_particle : :class:`numpy.ndarray`
-        The MSD of each individual particle with respect to lag-time.
+        The MSD of each individual particle with respect to constant lag-time or
+        unique Δt intervals.
+            - for `non_linear=False`: a 2D array of shape (n_lagtimes, n_atoms)
+            - for `non_linear=True`: a 2D array of shape (n_delta_t_values, n_atoms)
+    results.delta_t_values : :class:`numpy.ndarray`
+        Array of unique Δt (time differences) at which time-averaged MSD values are
+        computed.
+
+        .. versionadded:: 2.10.0
+
     ag : :class:`AtomGroup`
         The :class:`AtomGroup` resulting from your selection
     n_frames : int
@@ -299,27 +322,23 @@ class EinsteinMSD(AnalysisBase):
 
 
     .. versionadded:: 2.0.0
+    .. versionchanged:: 2.10.0
+       Added ability to calculate MSD from samples that are not linearly spaced with the
+       new `non_linear` keyword argument.
     """
 
-    def __init__(self, u, select="all", msd_type="xyz", fft=True, **kwargs):
-        r"""
-        Parameters
-        ----------
-        u : Universe or AtomGroup
-            An MDAnalysis :class:`Universe` or :class:`AtomGroup`.
-        select : str
-            A selection string. Defaults to "all" in which case
-            all atoms are selected.
-        msd_type : {'xyz', 'xy', 'yz', 'xz', 'x', 'y', 'z'}
-            Desired dimensions to be included in the MSD.
-        fft : bool
-            If ``True``, uses a fast FFT based algorithm for computation of
-            the MSD. Otherwise, use the simple "windowed" algorithm.
-            The tidynamics package is required for `fft=True`.
-        """
+    def __init__(
+        self,
+        u,
+        select="all",
+        msd_type="xyz",
+        fft=True,
+        non_linear=False,
+        **kwargs,
+    ):
         if isinstance(u, groups.UpdatingAtomGroup):
             raise TypeError(
-                "UpdatingAtomGroups are not valid for MSD " "computation"
+                "UpdatingAtomGroups are not valid for MSD computation"
             )
 
         super(EinsteinMSD, self).__init__(u.universe.trajectory, **kwargs)
@@ -329,6 +348,7 @@ def __init__(self, u, select="all", msd_type="xyz", fft=True, **kwargs):
         self.msd_type = msd_type
         self._parse_msd_type()
         self.fft = fft
+        self.non_linear = non_linear
 
         # local
         self.ag = u.select_atoms(self.select)
@@ -338,6 +358,7 @@ def __init__(self, u, select="all", msd_type="xyz", fft=True, **kwargs):
         # result
         self.results.msds_by_particle = None
         self.results.timeseries = None
+        self.results.delta_t_values = None
 
     def _prepare(self):
         # self.n_frames only available here
@@ -383,10 +404,13 @@ def _single_frame(self):
         ]
 
     def _conclude(self):
-        if self.fft:
-            self._conclude_fft()
+        if self.non_linear:
+            self._conclude_non_linear()
         else:
-            self._conclude_simple()
+            if self.fft:
+                self._conclude_fft()
+            else:
+                self._conclude_simple()
 
     def _conclude_simple(self):
         r"""Calculates the MSD via the simple "windowed" algorithm."""
@@ -397,6 +421,9 @@ def _conclude_simple(self):
             sqdist = np.square(disp).sum(axis=-1)
             self.results.msds_by_particle[lag, :] = np.mean(sqdist, axis=0)
         self.results.timeseries = self.results.msds_by_particle.mean(axis=1)
+        self.results.delta_t_values = np.arange(self.n_frames) * (
+            self.times[1] - self.times[0]
+        )
 
     def _conclude_fft(self):  # with FFT, np.float64 bit prescision required.
         r"""Calculates the MSD via the FCA fast correlation algorithm."""
@@ -421,3 +448,44 @@ def _conclude_fft(self):  # with FFT, np.float64 bit prescision required.
                 positions[:, n, :]
             )
         self.results.timeseries = self.results.msds_by_particle.mean(axis=1)
+        self.results.delta_t_values = np.arange(self.n_frames) * (
+            self.times[1] - self.times[0]
+        )
+
+    def _conclude_non_linear(self):
+
+        n_frames = self.n_frames
+        n_atoms = self.n_particles
+        positions = self._position_array.astype(np.float64)
+        # Dictionary to collect MSDs: {Δt: [msd1, msd2, ...]}
+        msd_dict = collections.defaultdict(list)
+        msds_by_particle_dict = collections.defaultdict(list)
+
+        # TODO: optimize the code
+        # Looping over all the frames as if the referenced gets shifted frame to frame
+        for i in range(n_frames):
+            for j in range(i + 1, n_frames):
+                delta_t = self.times[j] - self.times[i]
+                # Compute displacement and squared displacement
+                disp = positions[j] - positions[i]
+                squared_disp = np.sum(disp**2, axis=1)
+                msd = np.mean(squared_disp)
+                # Store MSD under corresponding Δt
+                msd_dict[delta_t].append(msd)
+                msds_by_particle_dict[delta_t].append(squared_disp)
+
+        msd_dict[0] = [0]
+        msds_by_particle_dict[0.0] = [np.zeros(n_atoms)]
+
+        # For each delta_t, stacked all squared_disp arrays and averaging over axis=0 (time origins)
+        delta_t_values = sorted(msd_dict.keys())
+        avg_msds = [np.mean(msd_dict[dt]) for dt in delta_t_values]
+        msds_by_particle_array = np.zeros((len(delta_t_values), n_atoms))
+        for idx, dt in enumerate(delta_t_values):
+            # Stack list of arrays like -- (n_time_origins, n_atoms)
+            arr = np.vstack(msds_by_particle_dict[dt])
+            msds_by_particle_array[idx, :] = np.mean(arr, axis=0)
+
+        self.results.timeseries = np.array(avg_msds)
+        self.results.delta_t_values = np.array(delta_t_values)
+        self.results.msds_by_particle = msds_by_particle_array