What's Changed
New features
- New script
discretization/correct_intermittent_dtrj.py
that corrects the intermittent behavior of a discrete trajectory by @andthum in #202 - Scripts
discretization/back_jump_prob.py
anddiscretization/back_jump_prob_discrete.py
: Return normalization factors by @andthum in #201 - Functions
mdtools.dtrj.back_jump_prob
andmdtools.dtrj.back_jump_prob_discrete
: Add a new argument return_norm that allows the user to return the normalization factor of the back-jump probability by @andthum in #192 misc/dtrj_lifetimes/compare_dtrj_lifetime_methods.py
: Additionally calculate lifetimes from the Kaplan-Meier estimate of the survival function by @andthum in #189
Bug fixes
- Scripts scripts/dynamics/msd_layer_serial.py and scripts/dynamics/msd_layer_parallel.py: Bin the wrapped particle positions in box coordinates instead of Cartesian coordinates to account for potentially fluctuating simulation boxes by @andthum in #203
- Functions
mdtools.dtrj.kaplan_meier
andmdtools.dtrj.leave_prob
: Fix consistency checks by @andthum in #199 - Scripts
axial_hex_distribution_1nn.py
andaxial_hex_distribution_2nn.py
: Fix the search algorithms for finding the first column(s) and row(s) of a hexagonal lattice when the lattice faces lie (almost) exactly on the edges of the simulation box by @andthum in #197, #198 - Script
dynamics/extract_renewal_events.py
: The information about the reference group in the output file was not about the reference but the selection group. Fixed by @andthum in #187 - Include information about memory consumption in progress bars of some functions in the module
mdtools.dtrj
by @andthum in #186
Code refactoring
- Add more consistency checks to the functions
mdtools.dtrj.back_jump_prob
andmdtools.dtrj.back_jump_prob_discrete
by @andthum in #190, #191, #193, #195, #196
Full Changelog: v0.0.7.0...v0.0.8.0