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mdeval_dev

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• adae920527 Fixed formatting mdeval_dev Sebastian Kloth 2024-06-14 10:12:50 +0200
• 11793d7960 Added autosave to shifted_correlation Sebastian Kloth 2024-06-14 10:12:18 +0200
• 55b06fa61d Improved performance and split up shifted_correlation Sebastian Kloth 2024-06-14 10:11:20 +0200
• 3aa91d7482 Updated version number and type hint Sebastian Kloth 2024-06-14 10:10:58 +0200
• 7d8c5d849d Added tests for shifted_correlation Sebastian Kloth 2024-06-14 10:10:37 +0200
• c09549902a Added Robins adjustments for FEL main Sebastian Kloth 2024-05-27 14:27:09 +0200
• b7bb8cb379 Merge branch 'refs/heads/mdeval_dev' Sebastian Kloth 2024-05-02 16:18:18 +0200
• 33c4756e34 Fixed frame-index selection in occupancy calculation. Sebastian Kloth 2024-05-02 16:17:54 +0200
• 7b9f8b6773 Merge branch 'mdeval_dev' Sebastian Kloth 2024-03-05 13:58:15 +0100
• c89cead81c Moved KDTree build up in its own function and made find_maxima query for each point separately. Sebastian Kloth 2024-03-05 13:57:55 +0100
• 31eb145a13 Merge branch 'mdeval_dev' Sebastian Kloth 2024-02-26 14:20:12 +0100
• af3758cbef Fixed iter in Coordinates Sebastian Kloth 2024-02-26 14:18:23 +0100
• 93d020a4de Updated fel test to run faster Sebastian Kloth 2024-02-26 14:14:29 +0100
• b5395098ce Fixed iter of Coordinates after last change Sebastian Kloth 2024-02-26 13:57:44 +0100
• 5e80701562 Coordinates returns now correct length after slicing Sebastian Kloth 2024-02-26 13:50:46 +0100
• 363e420cd8 Fixed chill ice_cluster_traj() function Sebastian Kloth 2024-02-16 11:11:17 +0100
• 6b77ef78e1 Fixed chill selector_ice() function Sebastian Kloth 2024-02-15 11:49:20 +0100
• 0c940115af Fixed LSI Sebastian Kloth 2024-02-08 17:24:44 +0100
• b0f29907df Updated fel to triclinic box case Sebastian Kloth 2024-02-08 17:24:22 +0100
• 37bf496b21 Fixed reading nojump_matrices from non-writable directories Sebastian Kloth 2024-02-06 13:29:38 +0100
• befaef2dfa Fixed van Hove calculation in plane Sebastian Kloth 2024-02-06 09:38:38 +0100
• 8ea7da5d2f Removed prints from number_of_neighbors Sebastian Kloth 2024-01-31 15:36:51 +0100
• b405842452 Changed version number Sebastian Kloth 2024-01-31 11:32:52 +0100
• f5cf453d61 Fixed isf for 2d case Sebastian Kloth 2024-01-31 11:32:29 +0100
• 4394f70530 Fixed pyproject.toml Sebastian Kloth 2024-01-31 09:02:57 +0100
• 298da3818d Changed parameter normed to density in np.histogram Sebastian Kloth 2024-01-31 09:02:36 +0100
• d9278eed83 Removed prints from rdf Sebastian Kloth 2024-01-31 08:59:39 +0100
• 787882810c Added pyedr in requirements.txt Sebastian Kloth 2024-01-30 17:03:57 +0100
• f527d25864 Changed dynamic calculations to include 2D cases Sebastian Kloth 2024-01-30 16:46:11 +0100
• 77771738ab Fixed parse jumps for triclinic box case Sebastian Kloth 2024-01-30 16:27:59 +0100
• 3e8fd04726 Fixed construction of nojump trajectory for triclinic box case Sebastian Kloth 2024-01-29 18:21:36 +0100
• 02fed343f0 Fixed rdf Sebastian Kloth 2024-01-23 11:01:43 +0100
• 5c17e04b38 Added tables to dependencies Sebastian Kloth 2024-01-23 10:09:11 +0100
• 16233e2f2c Merge branch 'mdeval_dev' Sebastian Kloth 2024-01-16 16:54:54 +0100
• 87ffa1e67e Fixed to find dimension of selector output Sebastian Kloth 2024-01-16 13:39:48 +0100
• 5fdc9c8698 Adjusted type hints Sebastian Kloth 2024-01-16 13:38:44 +0100
• 95b46c43be Changed input of hbonds to atom_indices Sebastian Kloth 2024-01-16 13:38:13 +0100
• 9200d31af6 Fixed spelling Sebastian Kloth 2024-01-16 13:37:49 +0100
• 5d16c7de5e Cleaned up imports and renamed T to temperature Sebastian Kloth 2024-01-16 13:36:56 +0100
• cf865930a5 Added pytest as a requirement Sebastian Kloth 2024-01-10 15:50:42 +0100
• 13532b3db1 Added time_distribution function Sebastian Kloth 2024-01-10 15:44:55 +0100
• 25cb3d38b3 Added type hints Sebastian Kloth 2024-01-10 15:11:42 +0100
• 9e9c865cf9 Adjusted tests Sebastian Kloth 2024-01-10 12:41:18 +0100
• ba893881a3 Removed deprecated code Sebastian Kloth 2024-01-10 12:41:06 +0100
• a559f72221 Selector now checks for to many dimensions. Sebastian Kloth 2024-01-09 13:46:46 +0100
• 0870a94b44 Selector now also works correctly on lists. Sebastian Kloth 2024-01-09 13:43:04 +0100
• 7dd2074ee5 Renamed matrixes to matrices Sebastian Kloth 2024-01-09 13:00:12 +0100
• 949ed877fb Added module for water structure parameters Sebastian Kloth 2024-01-08 07:42:04 +0100
• 4f17cfe876 Added type hints and removed number_of_next_neighbors Sebastian Kloth 2024-01-05 16:36:34 +0100
• b39dd3c45f Changed type hint for pbc_points Sebastian Kloth 2024-01-05 16:34:18 +0100
• 76db85d628 Added optional argument box to pbc_points Sebastian Kloth 2024-01-05 16:30:47 +0100
• b1cb9d99cf Marked old code as deprecated Sebastian Kloth 2024-01-05 16:10:46 +0100
• 0968ff214c Completed new functions for free energy landscape calculations Sebastian Kloth 2024-01-05 16:04:14 +0100
• 9d8965ace9 Added new function for adding distances from the pore center Sebastian Kloth 2024-01-04 16:25:23 +0100
• ec3f6b1c67 Added new function for energy calculations Sebastian Kloth 2024-01-02 15:54:43 +0100
• c9c4ffcc59 Updated version number Sebastian Kloth 2024-01-02 10:17:27 +0100
• 62d05423c5 Added new function for finding maxima of occupation Sebastian Kloth 2023-12-29 16:59:56 +0100
• f48dff2ede Fixed imports in init files Sebastian Kloth 2023-12-28 15:18:08 +0100
• 218574d50c Fixed circular import Sebastian Kloth 2023-12-28 14:40:11 +0100
• dffd06d3c0 Removed docs and example from repo since documentation will be done in the wiki Sebastian Kloth 2023-12-28 14:16:07 +0100
• 4ace860436 Adjusted examples Sebastian Kloth 2023-12-28 14:10:30 +0100
• 608cdb12eb Added type hints, refactored and deleted some functions Sebastian Kloth 2023-12-28 14:10:16 +0100
• f2806ca3ca Changed from len(index.shape) to index.ndim Sebastian Kloth 2023-12-28 13:33:47 +0100
• 4a6c02627a Added tables to requirements.txt Sebastian Kloth 2023-12-28 13:30:05 +0100
• b4f9b98876 Switched to numpy histogram Sebastian Kloth 2023-12-28 13:29:43 +0100
• 0dd6daa941 Reorganized imports Sebastian Kloth 2023-12-28 12:43:06 +0100
• 94d67496ba Added type hints Sebastian Kloth 2023-12-28 12:42:43 +0100
• cc08f5ae50 Added type hints Sebastian Kloth 2023-12-28 12:13:53 +0100
• b66e920758 Updated type hints Sebastian Kloth 2023-12-28 12:00:40 +0100
• 3cfdf79777 Added type hints Sebastian Kloth 2023-12-28 11:52:58 +0100
• bffcd56cdc Changed gr to work with time_average and use next_neighbors Sebastian Kloth 2023-12-27 12:43:05 +0100
• cc3768925a Changed time_average to work similar to shifted_correlation Sebastian Kloth 2023-12-26 16:57:53 +0100
• 32e3541c4b Changed type hint for version from int to str Sebastian Kloth 2023-12-26 16:40:43 +0100
• e91de71787 Combined selector and multi_selector in shifted_correlation and added type hints Sebastian Kloth 2023-12-26 16:38:55 +0100
• 476f7167b4 Moved functions around to circumvent a circular import Sebastian Kloth 2023-12-26 16:06:38 +0100
• cedfd24bb3 Updated regex test for atom_subsets Sebastian Kloth 2023-12-26 16:05:42 +0100
• cc185546d6 Small changes to type hints Sebastian Kloth 2023-12-26 15:24:01 +0100
• eed94cfca6 Added type hints, adjusted imports, and doc strings Sebastian Kloth 2023-12-26 12:55:53 +0100
• c00fc78f23 Added type hints, moved imports and classes around Sebastian Kloth 2023-12-26 11:50:16 +0100
• 8bad2861fa Updated doc strings and added type hints Sebastian Kloth 2023-12-26 11:33:59 +0100
• aca9ba0723 Updated doc strings and added type hints Sebastian Kloth 2023-12-26 11:29:21 +0100
• 2615798088 Added dnn to next_neighbors Sebastian Kloth 2023-12-26 11:07:30 +0100
• 97e29e6de3 Refactored next_neighbors and added type hints Sebastian Kloth 2023-12-26 11:05:16 +0100
• fd60cae3b8 Added type hints for return values Sebastian Kloth 2023-12-26 11:04:17 +0100
• f48e037936 Started rewriting, adding type hints Sebastian Kloth 2023-12-22 14:22:25 +0100
• 2d7905315d Added cleanup_h5 to utils.py Sebastian Kloth 2023-12-21 16:39:30 +0100
• 21dcc7641b Adjusted van_hove_self to better work with shifted_correlation Sebastian Kloth 2023-12-18 17:02:22 +0100
• 62705da6f3 Moved files and reformatted some Sebastian Kloth 2023-12-18 14:47:22 +0100
• e91defdc7a Added range for van Hove histogram Sebastian Kloth 2023-12-13 13:49:47 +0100
• 43ac510e7d renamed time from time package to pytime Sebastian Kloth 2023-12-09 15:52:15 +0100
• c40ea052b8 Added new function for calculating the occupation matrix Sebastian Kloth 2023-12-08 17:20:06 +0100
• 5267f6abac Updated version Sebastian Kloth 2023-12-06 15:47:20 +0100
• b4486ff265 Added slices to CoordinatesMap Sebastian Kloth 2023-12-06 15:44:33 +0100
• 4efb221a80 Reworked while loops to for loops in free_energy_landscape.py Sebastian Kloth 2023-12-06 15:38:15 +0100
• fa2e793354 Added test for get_fel Sebastian Kloth 2023-12-06 10:55:55 +0100
• d8154d3c38 Initial commit of free_energy_landscape Sebastian Kloth 2023-12-05 17:08:57 +0100
• 9b45a1a7bd Applied black formatter Sebastian Kloth 2023-12-05 16:44:26 +0100
• a7da9d7ec8 Merge remote-tracking branch 'origin/mdeval_dev' into mdeval_dev Sebastian Kloth 2023-11-19 12:19:06 +0100
• ab3d9497d9 Added NoSuchNodeError to except in load_and_concat_data Sebastian Kloth 2023-11-19 12:18:52 +0100
• 57a492cb48 Fixed normal_vectors() and removed old pbc_diff Sebastian Kloth 2023-11-13 16:26:06 +0100