Feature non linear time averaged msd

benchmarks/benchmarks/analysis/rms.py

@@ -28,7 +28,9 @@ def setup(self, num_atoms, use_weights, center, superposition):
         self.u.trajectory[-1]
         self.B = self.u.atoms.positions.copy()[:num_atoms]
         self.atoms = self.u.atoms[:num_atoms]
-        self.weights = self.atoms.masses/np.sum(self.atoms.masses) if use_weights else None
+        self.weights = (
+            self.atoms.masses / np.sum(self.atoms.masses) if use_weights else None
+        )
 
     def time_rmsd(self, num_atoms, weights, center, superposition):
         """Benchmark rmsd function using a setup similar to

package/AUTHORS

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

package/CHANGELOG

@@ -63,6 +63,11 @@ Enhancements
    (PR #5038)
  * Moved distopia checking function to common import location in
    MDAnalysisTest.util (PR #5038)
+ * Added new method '_conclude_non_linear` to calculate time-averaged
+   mean square displacement in `package/MDAnalysis/analysis/msd.py`,
+   new bool keyword argument `non_linear=True` under `EinsteinMSD`
+   enables execution of this method.
+   (Issue #5028, PR #5066)
 
 Changes
  * Refactored the RDKit converter code to move the inferring code in a separate

package/MDAnalysis/__init__.py

@@ -179,9 +179,7 @@
 _CONVERTERS: Dict = {}
 # Registry of TopologyAttributes
 _TOPOLOGY_ATTRS: Dict = {}  # {attrname: cls}
-_TOPOLOGY_TRANSPLANTS: Dict = (
-    {}
-)  # {name: [attrname, method, transplant class]}
+_TOPOLOGY_TRANSPLANTS: Dict = {}  # {name: [attrname, method, transplant class]}
 _TOPOLOGY_ATTRNAMES: Dict = {}  # {lower case name w/o _ : name}
 _GUESSERS: Dict = {}
 
@@ -204,9 +202,7 @@
 del logging
 
 # only MDAnalysis DeprecationWarnings are loud by default
-warnings.filterwarnings(
-    action="once", category=DeprecationWarning, module="MDAnalysis"
-)
+warnings.filterwarnings(action="once", category=DeprecationWarning, module="MDAnalysis")
 
 
 from . import units