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jumps calculation: switched joined prerequisites to independent prerequisites #247

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Jan 24, 2024
Merged

jumps calculation: switched joined prerequisites to independent prerequisites #247

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26 changes: 18 additions & 8 deletions src/gemdat/jumps.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand All @@ -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
Expand All @@ -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:
Expand Down
12 changes: 7 additions & 5 deletions tests/integration/jumps_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand All @@ -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]]))