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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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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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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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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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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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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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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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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0c940115af
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Fixed LSI
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2024-02-08 17:24:44 +01:00 |
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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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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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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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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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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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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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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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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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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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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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02fed343f0
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Fixed rdf
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2024-01-23 11:01:43 +01:00 |
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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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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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5fdc9c8698
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Adjusted type hints
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2024-01-16 13:38:44 +01:00 |
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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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9200d31af6
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Fixed spelling
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2024-01-16 13:37:49 +01:00 |
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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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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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25cb3d38b3
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Added type hints
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2024-01-10 15:11:42 +01:00 |
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ba893881a3
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Removed deprecated code
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2024-01-10 12:41:06 +01:00 |
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