Merge test_molecular_dynamics

ISISNeutronMuon · Feb 25, 2025 · e063d2c · e063d2c
1 parent 0a9f7ee
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Showing 2 changed files with 14 additions and 111 deletions.
diff --git a/MDANSE/Tests/UnitTests/test_analysis.py b/MDANSE/Tests/UnitTests/test_analysis.py
@@ -1,4 +1,3 @@
-
 import numpy as np
 import pytest
 from MDANSE.MolecularDynamics.Analysis import (AnalysisError,
@@ -8,16 +7,22 @@
                                                radius_of_gyration)
 
 COORDS = [
-    np.array([[0, 0, 0], [0, 0, 0], [0, 0, 0]]),
-    np.array([[1, 1, 1], [2, 1, 1], [3, 1, 1]]),
-    np.array([[1, 1, 1], [2, 1, 1], [8, 1, 1]]),
-    np.array([[1, 2, 1], [2, 1, 1], [10, 5, 5], [1, 1, 2]]),
+    np.array([[0, 0, 0], [0, 0, 0], [0, 0, 0]], dtype=float),
+    np.array([[1, 1, 1], [2, 1, 1], [3, 1, 1]], dtype=float),
+    np.array([[1, 1, 1], [2, 1, 1], [8, 1, 1]], dtype=float),
+    np.array([[1, 2, 1], [2, 1, 1], [10, 5, 5], [1, 1, 2]], dtype=float),
+    np.array([[0, 0, 0], [1, 0, 0], [1, 1, 0], [0, 1, 0],
+              [0, 0, 1], [1, 0, 1], [1, 1, 1], [0, 1, 1]], dtype=float),
+    np.array([[1, 1, 1], [2, 1, 1], [2, 2, 1], [1, 2, 1],
+              [1, 1, 2], [2, 1, 2], [2, 2, 2], [1, 2, 2]], dtype=float),
 ]
 
 @pytest.mark.parametrize("coords,masses,root,expected", [
     ((COORDS[1], COORDS[0]), None, False, 20/3),
     ((COORDS[1], COORDS[0]), [3, 10, 1], False, 80/14),
     ((COORDS[2], COORDS[0]), None, True, 5),
+    ((COORDS[4], COORDS[5]), None, True, np.sqrt(3))
+    ((COORDS[4], COORDS[5]), None, False, 3)
     ])
 def test_mean_square_deviation(coords, masses, root, expected):
     msd = mean_square_deviation(*coords, masses, root)
@@ -40,6 +45,7 @@ def test_mean_square_displacement(coords, n_configs, expected):
 @pytest.mark.parametrize("coords, root, expected", [
     (COORDS[3], False, 19.625),
     (COORDS[3], True, np.sqrt(19.625)),
+    (COORDS[4], False, 0.75),
 ])
 def test_mean_square_fluctuation(coords, root, expected):
     msf = mean_square_fluctuation(coords, root=root)
@@ -50,7 +56,9 @@ def test_mean_square_fluctuation(coords, root, expected):
     (COORDS[3], [1, 1, 5, 1], False, 24.15625),
     (COORDS[3], None, True, np.sqrt(19.625)),
     (COORDS[3], [1, 1, 5, 1], True, np.sqrt(24.15625)),
+    (COORDS[4], None, True, np.sqrt(0.75)),
+    (COORDS[4], [1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0], True, np.sqrt(0.5))
 ])
-def test_radius_of_gyration_no_masses_no_root(coords, masses, root, expected):
+def test_radius_of_gyration(coords, masses, root, expected):
     rog = radius_of_gyration(coords, masses, root=root)
     assert rog == expected
diff --git a/MDANSE/Tests/UnitTests/test_molecular_dynamics.py b/MDANSE/Tests/UnitTests/test_molecular_dynamics.py