 robrobo
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303bdbf9d2
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parse jumps now correctly uses fractional coordinates and should work for triclinic boxes. this should lead to correct behavior in all cases except for maybe changing angles in triclinic boxes. old behavior can still be used
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2026-04-23 14:34:05 +02:00 |
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robrobo
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d97863e356
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added fake _xdr attributes in case the trajectory was constructed by other means than reading a gromacs xtc file
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2026-04-11 17:22:39 +02:00 |
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robrobo
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ddf7d42c27
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extended the has checksum case for edge cases that caused problems
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2026-04-11 17:21:57 +02:00 |
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robrobo
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715deea1e0
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norm in quick fit
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2025-10-16 17:44:30 +02:00 |
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robrobo
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6b7641f152
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stop reading many frames to get times for shifted_correlation
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2025-09-05 14:47:53 +02:00 |
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robrobo
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cd7097ad46
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remove print
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2025-08-14 16:43:56 +02:00 |
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robrobo
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a0ca2d8657
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Merge branch 'fix/nojump_and_npt_caching' into feature/compatibility_robin
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2025-08-14 16:35:12 +02:00 |
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robrobo
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9ff3badab1
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have to wrap delta with np.array to make sure it is ndarray and result stays CoordinateFrame
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2025-08-14 16:33:37 +02:00 |
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robrobo
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0f47475f22
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quick version of center_of_masses for equal weights
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2025-08-14 15:20:16 +02:00 |
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robrobo
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f6ff7606ad
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decorator for autosave_data now consumes and autosave_dir_overwrite. this can enable autosave by itself and takes precedence over the enable(dir) value. provided the same way as the description
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2025-08-09 18:43:50 +02:00 |
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robrobo
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96c624efee
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Merge branch 'fix/nojump_and_npt_caching' into feature/compatibility_robin
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2025-08-09 16:11:42 +02:00 |
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robrobo
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492098fe01
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apply selection and scaling with current box after delta in jumps has been cached or calculated directly. this should fix using nojump on NPT simulations
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2025-08-09 16:11:24 +02:00 |
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robrobo
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9f6af2af11
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corrected spelling
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2025-07-17 20:21:43 +02:00 |
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robrobo
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0ffce2f17a
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added full_output option to non gaussian parameter so that correct statistics can be done afterwards
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2025-07-17 18:45:11 +02:00 |
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robrobo
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0eff84910b
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simplified quick non gaussian fit function so that it is more robust
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2025-07-17 18:44:20 +02:00 |
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robrobo
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dae2d6ed95
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created wrappers around the isf to allow for access of more raw data and the variance for accurate kai4 calculation
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2025-07-17 12:50:49 +02:00 |
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robrobo
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ec4094cd92
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added quick estimation for peak tau and height of non Gaussian
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2025-07-17 12:34:43 +02:00 |
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robrobo
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4047db209c
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using pbc_diff now in tetrahedral_order parameter calculation, since reference positions will not be periodic images in the default use case
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2025-07-11 20:59:30 +02:00 |
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robrobo
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00043637e9
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added a _seen set to avoid infinite recursions due to function arguments; also, applied pbc_diff to neighbors in tetrahedral order
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2025-07-11 20:54:27 +02:00 |
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robrobo
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7585e598dc
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dedent before ast.parse for non-toplevel functions
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2025-06-17 01:02:15 +02:00 |
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robrobo
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6d8b86c1ef
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extended checksum.strip_comments function to work with prefixed docstrings and other small features
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2025-06-16 22:15:22 +02:00 |
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robrobo
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a2a0ae8d7b
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renamed logging to loggin_util to avoid circular import with python logging in some cases; added two raw strings to docstrings and fixed a sphinx syntax in one
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2025-06-16 21:00:42 +02:00 |
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robrobo
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67d3e70a66
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Added some ordering to checksums from FunctionType since these could depending on input fail to be deterministic
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2025-06-16 20:09:50 +02:00 |
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 skloth
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c09549902a
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Added Robins adjustments for FEL
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2024-05-27 14:27:09 +02:00 |
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skloth
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33c4756e34
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Fixed frame-index selection in occupancy calculation.
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2024-05-02 16:17:54 +02:00 |
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skloth
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c89cead81c
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Moved KDTree build up in its own function and made find_maxima query for each point separately.
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2024-03-05 13:57:55 +01:00 |
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skloth
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af3758cbef
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Fixed iter in Coordinates
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2024-02-26 14:18:23 +01:00 |
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skloth
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5e80701562
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Coordinates returns now correct length after slicing
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2024-02-26 13:50:46 +01:00 |
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skloth
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363e420cd8
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Fixed chill ice_cluster_traj() function
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2024-02-16 11:11:17 +01:00 |
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skloth
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6b77ef78e1
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Fixed chill selector_ice() function
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2024-02-15 11:49:20 +01:00 |
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skloth
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0c940115af
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Fixed LSI
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2024-02-08 17:24:44 +01:00 |
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skloth
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b0f29907df
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Updated fel to triclinic box case
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2024-02-08 17:24:22 +01:00 |
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skloth
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37bf496b21
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Fixed reading nojump_matrices from non-writable directories
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2024-02-06 13:29:38 +01:00 |
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skloth
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befaef2dfa
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Fixed van Hove calculation in plane
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2024-02-06 09:38:38 +01:00 |
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skloth
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8ea7da5d2f
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Removed prints from number_of_neighbors
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2024-01-31 15:36:51 +01:00 |
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skloth
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f5cf453d61
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Fixed isf for 2d case
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2024-01-31 11:32:29 +01:00 |
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skloth
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298da3818d
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Changed parameter normed to density in np.histogram
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2024-01-31 09:02:36 +01:00 |
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skloth
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d9278eed83
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Removed prints from rdf
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2024-01-31 08:59:39 +01:00 |
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skloth
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f527d25864
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Changed dynamic calculations to include 2D cases
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2024-01-30 16:46:11 +01:00 |
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skloth
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77771738ab
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Fixed parse jumps for triclinic box case
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2024-01-30 16:27:59 +01:00 |
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skloth
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3e8fd04726
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Fixed construction of nojump trajectory for triclinic box case
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2024-01-29 18:21:36 +01:00 |
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skloth
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02fed343f0
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Fixed rdf
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2024-01-23 11:01:43 +01:00 |
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skloth
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16233e2f2c
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Merge branch 'mdeval_dev'
# Conflicts:
# .gitignore
# doc/conf.py
# examples/plot_chi4.py
# examples/plot_isf.py
# examples/plot_spatialisf.py
# examples/plot_temperature.py
# src/mdevaluate/cli.py
# src/mdevaluate/correlation.py
# src/mdevaluate/distribution.py
# src/mdevaluate/functions.py
# test/test_atoms.py
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2024-01-16 16:54:54 +01:00 |
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skloth
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87ffa1e67e
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Fixed to find dimension of selector output
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2024-01-16 13:39:48 +01:00 |
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skloth
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5fdc9c8698
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Adjusted type hints
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2024-01-16 13:38:44 +01:00 |
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skloth
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95b46c43be
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Changed input of hbonds to atom_indices
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2024-01-16 13:38:13 +01:00 |
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skloth
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9200d31af6
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Fixed spelling
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2024-01-16 13:37:49 +01:00 |
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skloth
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5d16c7de5e
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Cleaned up imports and renamed T to temperature
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2024-01-16 13:36:56 +01:00 |
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skloth
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13532b3db1
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Added time_distribution function
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2024-01-10 15:44:55 +01:00 |
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skloth
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25cb3d38b3
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Added type hints
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2024-01-10 15:11:42 +01:00 |
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