switched joined prerequisites for jumps to seperate prerequisites (#247)

src/gemdat/jumps.py

@@ -39,7 +39,6 @@ def _generic_transitions_to_jumps(transitions: Transitions,
     fromevent = None
     candidate_jump = None
 
-    # Only take jumps which hit the inner radius
     for _, event in events.iterrows():
         # If we are jumping, but we go to the next atom index, reset
         if fromevent is not None:
@@ -57,6 +56,7 @@ def _generic_transitions_to_jumps(transitions: Transitions,
                     'stop time'] >= minimal_residence:
                 jumps.append(candidate_jump)
                 candidate_jump = None
+                fromevent = None
             elif candidate_jump['destination site'] != event[
                     'destination site']:
                 candidate_jump = None
@@ -66,18 +66,28 @@ def _generic_transitions_to_jumps(transitions: Transitions,
             if event['start site'] != event['destination site']:
                 fromevent = event
 
-        # Check if we have a candidate jump to the inner site
-        # (only residence time still has to be checked)
         if fromevent is not None:
+            # if we jump back, remove fromevent
             if fromevent['start site'] == event['destination site']:
                 fromevent = None
+                candidate_jump = None
                 continue
-            if event['destination inner site'] == -1:
+
+            # Check if jump to the inner site, add it to the jumps immediately
+            if event['destination inner site'] != -1:
+                event['start site'] = fromevent['start site']
+                event['start time'] = fromevent['start time']
+                fromevent = None
+                candidate_jump = None
+                jumps.append(event)
                 continue
-            event['start site'] = fromevent['start site']
-            event['start time'] = fromevent['start time']
-            fromevent = None
-            candidate_jump = event
+
+            # If we enter another site, create a candidate jump
+            if candidate_jump is None:
+                if event['destination site'] != -1:
+                    event['start site'] = fromevent['start site']
+                    event['start time'] = fromevent['start time']
+                    candidate_jump = event
 
     # Also add a last candidate jump (if there is one
     if candidate_jump is not None:

tests/integration/jumps_test.py

@@ -16,12 +16,14 @@ def test_site_inner_fraction(self, vasp_traj, vasp_sites, structure):
                                                   structure=structure,
                                                   floating_specie='Li',
                                                   site_inner_fraction=0.5)
-        jumps = Jumps(transitions=transitions, sites=vasp_sites)
+        jumps = Jumps(transitions=transitions,
+                      sites=vasp_sites,
+                      minimal_residence=100)
 
-        assert len(jumps.data) == 256
+        assert len(jumps.data) == 267
         assert np.all(jumps.data[::100].to_numpy() == np.array([[
             0, 94, 0, 282, 303
-        ], [16, 64, 42, 2106, 2179], [35, 77, 15, 2559, 2603]]))
+        ], [15, 74, 8, 1271, 1286], [34, 49, 33, 3141, 3296]]))
 
     def test_minimal_residency(self, vasp_traj, vasp_sites, structure):
         transitions = Transitions.from_trajectory(trajectory=vasp_traj,
@@ -31,7 +33,7 @@ def test_minimal_residency(self, vasp_traj, vasp_sites, structure):
                       sites=vasp_sites,
                       minimal_residence=3)
 
-        assert len(jumps.data) == 457
+        assert len(jumps.data) == 462
         assert np.all(jumps.data[::200].to_numpy() == np.array([[
             0, 94, 0, 282, 284
-        ], [18, 54, 24, 3336, 3368], [41, 67, 41, 2886, 2893]]))
+        ], [18, 54, 24, 2937, 3015], [41, 41, 67, 849, 851]]))