Fix RDF test

tests/integration/conftest.py

@@ -76,9 +76,13 @@ def vasp_rdf_data(vasp_traj, structure, vasp_transitions):
                       trajectory=trajectory,
                       floating_specie='Li')
 
+    transitions = Transitions.from_trajectory(trajectory=trajectory,
+                                              structure=structure,
+                                              floating_specie='Li')
+
     rdfs = radial_distribution(
         sites=sites,
-        transitions=vasp_transitions,
+        transitions=transitions,
         max_dist=5,
     )
 
@@ -87,13 +91,13 @@ def vasp_rdf_data(vasp_traj, structure, vasp_transitions):
 
 @pytest.fixture(scope='module')
 def vasp_shape_data(vasp_traj):
-    trajectory = vasp_traj[-1000:]
+    trajectory = vasp_traj[-250:]
     trajectory.filter('Li')
 
     # shape analysis needs structure without supercell
-    structure = load_known_material('argyrodite')
+    sites = load_known_material('argyrodite')
 
-    sa = ShapeAnalyzer.from_structure(structure)
+    sa = ShapeAnalyzer.from_structure(sites)
 
     shapes = sa.analyze_trajectory(trajectory, supercell=(2, 1, 1))
 

tests/integration/plot_test.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import pytest
 from helpers import image_comparison2
 
 from gemdat.io import load_known_material
@@ -61,7 +60,6 @@ def test_jumps_3d_animation(vasp_jumps):
     plots.jumps_3d_animation(jumps=vasp_jumps, t_start=1000, t_stop=1001)
 
 
-@pytest.mark.xfail(reason='Needs to be checked')
 @image_comparison2(baseline_images=['rdf1', 'rdf2', 'rdf3'])
 def test_rdf23(vasp_rdf_data):
     assert len(vasp_rdf_data) == 3
@@ -78,7 +76,7 @@ def test_shape(vasp_shape_data):
 
 @image_comparison2(baseline_images=['msd'])
 def test_msd_per_element(vasp_traj):
-    plots.msd_per_element(trajectory=vasp_traj)
+    plots.msd_per_element(trajectory=vasp_traj[-500:])
 
 
 @image_comparison2(baseline_images=['path_energy'])

tests/integration/shape_test.py

@@ -11,7 +11,7 @@ def test_shape(vasp_shape_data):
     for shape in vasp_shape_data:
         assert isinstance(shape, ShapeData)
         assert shape.name == '48h'
-        assert shape.coords.shape == (76610, 3)
+        assert shape.coords.shape == (19284, 3)
 
         # coords may not exceed threshold
         assert np.all(shape.coords > -1)

tests/integration/trajectory_test.py

@@ -119,9 +119,9 @@ def test_vibration_metrics(vasp_traj):
 
 @pytest.vaspxml_available  # type: ignore
 def test_msd(vasp_traj):
-    msd = vasp_traj.mean_squared_displacement()
+    msd = vasp_traj[-100:].mean_squared_displacement()
 
-    assert msd.shape == (104, 3750)
-    assert np.isclose(msd[10, -1], 0.03396214706964429)
-    assert np.isclose(msd[52, -1], 0.30140820020960746)
-    assert np.isclose(msd[85, -1], 11.927261505164097)
+    assert msd.shape == (104, 100)
+    assert np.isclose(msd[10, -1], 0.0711843146266915)
+    assert np.isclose(msd[52, -1], 0.597740065985704)
+    assert np.isclose(msd[85, -1], 1.1881148711032665)