IPKM/mdevaluate
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  • d97863e356 added fake _xdr attributes in case the trajectory was constructed by other means than reading a gromacs xtc file feature/compatibility_robin 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
  • b66e920758 Updated type hints skloth 2023-12-28 12:00:40 +01:00