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Improve jump specification criteria#228

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v1kko merged 34 commits intomainGEMDAT-repos/GEMDAT:mainfrom jumps_updateGEMDAT-repos/GEMDAT:jumps_updateCopy head branch name to clipboardJan 23, 2024

+835-510

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Commits on Jan 9, 2024

• tools/flake.lock: Update

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• add site_radius parameter, which fixes the site radius for analysis

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• Fix the start time of a transition to be at the leaving time of the starting site.

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• Added Jumps class

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• distance to check for collective jumps by default reduced to 1 angstrom

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Commits on Jan 11, 2024

• updated jump plots and tests

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• tools/flake.lock: Update

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• removed dashboard

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• updated legacy.py

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• fix last plots

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• update changed test

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Commits on Jan 15, 2024

• Added site_inner_fraction parameter

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• Added minimal residence parameter

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• Added tests for jumps

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• updated documentation

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• updated notebooks

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Commits on Jan 16, 2024

• updated notebooks

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Commits on Jan 18, 2024

• cleaned up jumps a bit and added comments

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Commits on Jan 22, 2024

• Update src/gemdat/collective.py

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• Update src/gemdat/jumps.py

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• Update src/gemdat/jumps.py

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• Update src/gemdat/jumps.py

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• Update src/gemdat/jumps.py

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• Update src/gemdat/jumps.py

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• Update src/gemdat/jumps.py

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• Update src/gemdat/jumps.py

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• Update src/gemdat/transitions.py

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• Update src/gemdat/transitions.py

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• Fixed all suggestions

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• fix collective jumps plot

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Commits on Jan 23, 2024

• remove transitions from sites

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• fix rdf call in legacy

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• xfail rdf plot

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• fix plot_rdf xfail

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