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feature/compatibility_robin

fix/nojump_and_npt_caching

fix/tetrahedral_order_pbc

fix_nondeterministic_checksum

main

mdeval_dev

refactor_logging

#2

#4

#5

#6

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• 303bdbf9d2 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 feature/compatibility_robin robrobo 2026-04-23 13:28:42 +02:00
• d97863e356 added fake _xdr attributes in case the trajectory was constructed by other means than reading a gromacs xtc file robrobo 2026-04-11 17:22:39 +02:00
• ddf7d42c27 extended the has checksum case for edge cases that caused problems robrobo 2026-04-11 17:21:57 +02:00
• 715deea1e0 norm in quick fit robrobo 2025-10-16 17:44:30 +02:00
• 6b7641f152 stop reading many frames to get times for shifted_correlation robrobo 2025-09-05 14:47:53 +02:00
• 4f35a234c3 updated readme main markusro 2025-08-19 15:10:02 +02:00
• 893bf31292 added install script for mdevaluate for shared /nfsopt markusro 2025-08-19 15:07:52 +02:00
• cf7ef06c67 Merge pull request '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' (#6) from fix/nojump_and_npt_caching into main markusro 2025-08-19 12:55:43 +00:00
• cd7097ad46 remove print robrobo 2025-08-14 16:43:56 +02:00
• a0ca2d8657 Merge branch 'fix/nojump_and_npt_caching' into feature/compatibility_robin robrobo 2025-08-14 16:35:12 +02:00
• 9ff3badab1 have to wrap delta with np.array to make sure it is ndarray and result stays CoordinateFrame fix/nojump_and_npt_caching robrobo 2025-08-14 16:33:37 +02:00
• 0f47475f22 quick version of center_of_masses for equal weights robrobo 2025-08-14 15:20:16 +02:00
• f6ff7606ad 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 robrobo 2025-08-09 18:43:50 +02:00
• 96c624efee Merge branch 'fix/nojump_and_npt_caching' into feature/compatibility_robin robrobo 2025-08-09 16:11:42 +02:00
• 492098fe01 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 robrobo 2025-08-09 16:11:24 +02:00
• accb43d7e6 Merge branch 'refactor_logging' into feature/compatibility_robin robrobo 2025-08-09 13:58:15 +02:00
• 07b14a6cd6 Merge branch 'main' into feature/compatibility_robin robrobo 2025-08-09 13:57:29 +02:00
• e124506d10 fixed typo in logging output refactor_logging robrobo 2025-08-09 13:54:23 +02:00
• 8169e76964 Merge branch 'main' into refactor_logging robrobo 2025-08-09 13:52:58 +02:00
• 65ac6e9143 Merge pull request 'using pbc_diff now in tetrahedral_order parameter calcul since reference positions will not be periodic images in the default use case' (ation,#5) from fix/tetrahedral_order_pbc into main markusro 2025-07-21 11:57:15 +00:00
• 9f6af2af11 corrected spelling robrobo 2025-07-17 20:21:43 +02:00
• 0ffce2f17a added full_output option to non gaussian parameter so that correct statistics can be done afterwards robrobo 2025-07-17 18:45:11 +02:00
• 0eff84910b simplified quick non gaussian fit function so that it is more robust robrobo 2025-07-17 18:44:20 +02:00
• dae2d6ed95 created wrappers around the isf to allow for access of more raw data and the variance for accurate kai4 calculation robrobo 2025-07-17 12:50:49 +02:00
• ec4094cd92 added quick estimation for peak tau and height of non Gaussian robrobo 2025-07-17 12:34:43 +02:00
• 4047db209c using pbc_diff now in tetrahedral_order parameter calculation, since reference positions will not be periodic images in the default use case fix/tetrahedral_order_pbc robrobo 2025-07-11 20:59:30 +02:00
• 00043637e9 added a _seen set to avoid infinite recursions due to function arguments; also, applied pbc_diff to neighbors in tetrahedral order robrobo 2025-07-11 20:54:27 +02:00
• 7585e598dc dedent before ast.parse for non-toplevel functions robrobo 2025-06-17 01:02:15 +02:00
• 6d8b86c1ef extended checksum.strip_comments function to work with prefixed docstrings and other small features robrobo 2025-06-16 22:15:22 +02:00
• a2a0ae8d7b 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 robrobo 2025-06-16 21:00:42 +02:00
• 90bd90a608 Merge pull request 'Added some ordering to checksums from FunctionType since these could depending on input fail to be deterministic' (#2) from fix_nondeterministic_checksum into main robin 2025-06-16 18:45:48 +00:00
• 67d3e70a66 Added some ordering to checksums from FunctionType since these could depending on input fail to be deterministic fix_nondeterministic_checksum robrobo 2025-06-16 20:09:50 +02:00
• adae920527 Fixed formatting mdeval_dev skloth 2024-06-14 10:12:50 +02:00
• 11793d7960 Added autosave to shifted_correlation skloth 2024-06-14 10:12:18 +02:00
• 55b06fa61d Improved performance and split up shifted_correlation skloth 2024-06-14 10:11:20 +02:00
• 3aa91d7482 Updated version number and type hint skloth 2024-06-14 10:10:58 +02:00
• 7d8c5d849d Added tests for shifted_correlation skloth 2024-06-14 10:10:37 +02:00
• c09549902a Added Robins adjustments for FEL skloth 2024-05-27 14:27:09 +02:00
• b7bb8cb379 Merge branch 'refs/heads/mdeval_dev' skloth 2024-05-02 16:18:18 +02:00
• 33c4756e34 Fixed frame-index selection in occupancy calculation. skloth 2024-05-02 16:17:54 +02:00
• 7b9f8b6773 Merge branch 'mdeval_dev' skloth 2024-03-05 13:58:15 +01:00
• c89cead81c Moved KDTree build up in its own function and made find_maxima query for each point separately. skloth 2024-03-05 13:57:55 +01:00
• 31eb145a13 Merge branch 'mdeval_dev' skloth 2024-02-26 14:20:12 +01:00
• af3758cbef Fixed iter in Coordinates skloth 2024-02-26 14:18:23 +01:00
• 93d020a4de Updated fel test to run faster skloth 2024-02-26 14:14:29 +01:00
• b5395098ce Fixed iter of Coordinates after last change skloth 2024-02-26 13:57:44 +01:00
• 5e80701562 Coordinates returns now correct length after slicing skloth 2024-02-26 13:50:46 +01:00
• 363e420cd8 Fixed chill ice_cluster_traj() function skloth 2024-02-16 11:11:17 +01:00
• 6b77ef78e1 Fixed chill selector_ice() function skloth 2024-02-15 11:49:20 +01:00
• 0c940115af Fixed LSI skloth 2024-02-08 17:24:44 +01:00
• b0f29907df Updated fel to triclinic box case skloth 2024-02-08 17:24:22 +01:00
• 37bf496b21 Fixed reading nojump_matrices from non-writable directories skloth 2024-02-06 13:29:38 +01:00
• befaef2dfa Fixed van Hove calculation in plane skloth 2024-02-06 09:38:38 +01:00
• 8ea7da5d2f Removed prints from number_of_neighbors skloth 2024-01-31 15:36:51 +01:00
• b405842452 Changed version number skloth 2024-01-31 11:32:52 +01:00
• f5cf453d61 Fixed isf for 2d case skloth 2024-01-31 11:32:29 +01:00
• 4394f70530 Fixed pyproject.toml skloth 2024-01-31 09:02:57 +01:00
• 298da3818d Changed parameter normed to density in np.histogram skloth 2024-01-31 09:02:36 +01:00
• d9278eed83 Removed prints from rdf skloth 2024-01-31 08:59:39 +01:00
• 787882810c Added pyedr in requirements.txt skloth 2024-01-30 17:03:57 +01:00
• f527d25864 Changed dynamic calculations to include 2D cases skloth 2024-01-30 16:46:11 +01:00
• 77771738ab Fixed parse jumps for triclinic box case skloth 2024-01-30 16:27:59 +01:00
• 3e8fd04726 Fixed construction of nojump trajectory for triclinic box case skloth 2024-01-29 18:21:36 +01:00
• 02fed343f0 Fixed rdf skloth 2024-01-23 11:01:43 +01:00
• 5c17e04b38 Added tables to dependencies skloth 2024-01-23 10:09:11 +01:00
• 16233e2f2c Merge branch 'mdeval_dev' skloth 2024-01-16 16:54:54 +01:00
• 87ffa1e67e Fixed to find dimension of selector output skloth 2024-01-16 13:39:48 +01:00
• 5fdc9c8698 Adjusted type hints skloth 2024-01-16 13:38:44 +01:00
• 95b46c43be Changed input of hbonds to atom_indices skloth 2024-01-16 13:38:13 +01:00
• 9200d31af6 Fixed spelling skloth 2024-01-16 13:37:49 +01:00
• 5d16c7de5e Cleaned up imports and renamed T to temperature skloth 2024-01-16 13:36:56 +01:00
• cf865930a5 Added pytest as a requirement skloth 2024-01-10 15:50:42 +01:00
• 13532b3db1 Added time_distribution function skloth 2024-01-10 15:44:55 +01:00
• 25cb3d38b3 Added type hints skloth 2024-01-10 15:11:42 +01:00
• 9e9c865cf9 Adjusted tests skloth 2024-01-10 12:41:18 +01:00
• ba893881a3 Removed deprecated code skloth 2024-01-10 12:41:06 +01:00
• a559f72221 Selector now checks for to many dimensions. skloth 2024-01-09 13:46:46 +01:00
• 0870a94b44 Selector now also works correctly on lists. skloth 2024-01-09 13:43:04 +01:00
• 7dd2074ee5 Renamed matrixes to matrices skloth 2024-01-09 13:00:12 +01:00
• 949ed877fb Added module for water structure parameters skloth 2024-01-08 07:42:04 +01:00
• 4f17cfe876 Added type hints and removed number_of_next_neighbors skloth 2024-01-05 16:36:34 +01:00
• b39dd3c45f Changed type hint for pbc_points skloth 2024-01-05 16:34:18 +01:00
• 76db85d628 Added optional argument box to pbc_points skloth 2024-01-05 16:30:47 +01:00
• b1cb9d99cf Marked old code as deprecated skloth 2024-01-05 16:10:46 +01:00
• 0968ff214c Completed new functions for free energy landscape calculations skloth 2024-01-05 16:04:14 +01:00
• 9d8965ace9 Added new function for adding distances from the pore center skloth 2024-01-04 16:25:23 +01:00
• ec3f6b1c67 Added new function for energy calculations skloth 2024-01-02 15:54:43 +01:00
• c9c4ffcc59 Updated version number skloth 2024-01-02 10:17:27 +01:00
• 62d05423c5 Added new function for finding maxima of occupation skloth 2023-12-29 16:59:56 +01:00
• f48dff2ede Fixed imports in init files skloth 2023-12-28 15:18:08 +01:00
• 218574d50c Fixed circular import skloth 2023-12-28 14:40:11 +01:00
• dffd06d3c0 Removed docs and example from repo since documentation will be done in the wiki skloth 2023-12-28 14:16:07 +01:00
• 4ace860436 Adjusted examples skloth 2023-12-28 14:10:30 +01:00
• 608cdb12eb Added type hints, refactored and deleted some functions skloth 2023-12-28 14:10:16 +01:00
• f2806ca3ca Changed from len(index.shape) to index.ndim skloth 2023-12-28 13:33:47 +01:00
• 4a6c02627a Added tables to requirements.txt skloth 2023-12-28 13:30:05 +01:00
• b4f9b98876 Switched to numpy histogram skloth 2023-12-28 13:29:43 +01:00
• 0dd6daa941 Reorganized imports skloth 2023-12-28 12:43:06 +01:00
• 94d67496ba Added type hints skloth 2023-12-28 12:42:43 +01:00
• cc08f5ae50 Added type hints skloth 2023-12-28 12:13:53 +01:00