6.13.0 (2024-10-23)
- 495 (#496) (e1d3700)
- delete last atom of a chain (9ca51e3)
- need parametrization after delete (c3b5793)
- only check gmx version if applicable (0d7e96c)
- search for radicals only in REACTIVE molecule (e0cd397)
6.12.0 (2024-09-16)
- copy gro to setup (#487) (25ac265)
- do not log empty edissoc lines (774d338)
- link residuetypedat (#488) (2576440)
- truncate time in plumed output to 1 fs (#484) (b73104a)
- use correct distances.dat when starting from existing traj (#485) (d0c9859)
6.11.0 (2024-09-04)
- ci: always mark draft PRs as not green (#473) (bb8ce10)
- ci: we don't actually need the fail-if-draft action (b953130)
6.10.3 (2024-08-20)
6.10.2 (2024-08-19)
- pin griffe version for quartodoc (d4b84ef)
6.10.1 (2024-08-19)
- ci: build docs on release (ca8fdc2)
6.10.0 (2024-08-16)
- ci: fix release tests (1cf898b)
- copy user supplied input data to setup dir (4b2d96f)
- simplify ci (765ed7b)
6.9.1 (2024-08-09)
- bug in output file discovery (9336a91)
- drop dill requirement (ff3a2c2)
- more stable slow growth parameters (aedffe0)
- prevent log spam (2b51a0e)
- prevent log spam (38cbf07)
- proper pairs in slow-growth (#465) (56db2ce)
- remove unreachable code (af0f11d)
- update task names for restarting changed in #422 (d31bc2e)
6.9.0 (2024-07-11)
- add xtc option to config (95160df)
- always setup tasks on init of RunManager (95160df)
- configure logger from init of Config (95160df)
- link nrexcl of reactive moleculetype to toplevel topology (#451) (b100117)
- close task logger handler after taks has run. fixes #452 (451f3fd)
- polymer_test (7485011)
- properly compare to empty dicts (95160df)
- recip parsing without eval (#448) (0a5a213)
- resolve all non-relative paths in config relative to config.cwd (95160df)
- update quarto version (95160df)
6.8.1 (2024-06-17)
6.8.3 (2024-06-25)
6.8.1 (2024-06-17)
- check for residuetypes.rtp existence (c4e831c)
- fix #440 (c4e831c)
- onlye require xtc or trr, not both (#439) (c4e831c)
- use nrexcl from first reactive molecultetype (c4e831c)
- make docs of kimmdy.yml much more readable (c4e831c)
6.8.0 (2024-06-11)
6.7.0 (2024-05-20)
6.6.1 (2024-05-07)
- generate matching gro for xtc in trjconv (800de0a)
6.6.0 (2024-04-25)
- add explicit includes and excludes for modify_top (#427) (c1318c3)
- Expose grappa model and charge type (#430) (57af388)
- modify top tut (#428) (823b7ff)
6.5.0 (2024-03-25)
- import get_task_directories from utils (8d4ba4d)
6.4.1 (2024-03-21)
- allow reactions with no chosen recipe (171c7e1)
- colormap normalization (#415) (1238397)
- energy labels sorted correctly (855272f)
- expose arrhenius equation in morse function and fix wrong default value (#417) (58c47b3)
- plot_energy now handles numbers in terms correctly. (c16888b)
- remove pd warning (abc4afe)
- runmanager now handles empty kmcresults correctly. (c94bd2a)
- fix docstring (9572791)
6.4.0 (2024-03-07)
6.3.0 (2024-03-07)
- allow customizing trjconv output group (#396) (97b5588)
- analysis radical migration tool (#388) (ba4cb0f)
6.2.5 (2024-02-27)
6.2.4 (2024-02-27)
6.2.3 (2024-02-27)
6.2.2 (2024-02-23)
- release-please config (b9a3622)
6.2.1 (2024-02-22)
- merge regression (9f9b162)
6.2.0 (2024-02-16)
6.1.0 (2024-02-14)
6.0.1 (2024-01-03)
- minor improvement (111112e)
6.0.0 (2024-01-03)
- Partial charge treatment (#353)
- don't truncate if there is no trajectory. (4e6e011)
- don't try to truncate to time 0 (52099e5)
- hotfix for aggregate_reactions hangs #355 (b5bc285)
5.3.2 (2023-12-19)
5.3.1 (2023-12-15)
- don't write top section headers for empty sections (#351) (1632f6f)
- update scheme url in examples and docs (#348) (2a72b90)
5.3.0 (2023-12-12)
5.2.3 (2023-12-08)
- fix an issue where merging multiples of a moleculetype incremented the residuenumbers too fast (#344) (7e78665)
5.2.2 (2023-12-08)
- escape file paths for shell commands (914550a)
- make ff dir optional in config (02c5d9f)
- replace spaces in name and out in config (304de69)
5.2.1 (2023-12-07)
- add title to scheme (#341) (a1b1ae5)
- kimmdy run bugs (#336) (ce558e7)
- make forcefield directory optional, only warn (#332) (eac4131)
- renumber atomnrs (#331) (e88f8cc)
5.2.0 (2023-11-14)
- add config for exclude and include in reactive moleculetype (44121e4)
- merge react-able molecules and make multiples explicit (#327) (ae8d45e)
- parse settles and exclusions (44121e4)
- use parsed exclusions for top merge (44121e4)
- declare kimmdy as being a typed library (44121e4)
- expected length of output folders including the new setup task (8fd2b44)
- make molecules section a list instead of dict because order is important (44121e4)
- start iteration at -1 such that setup task has index 0 (44121e4)
- tasklist test after integrating setup task (44121e4)
- improve dark theme (44121e4)
- more detailed ML installation instructions for upcoming plugins (c128069)
- use freeze to only re-render changed qmd docs (44121e4)
5.1.12 (2023-11-13)
- remove show schema path option (2285246)
5.1.11 (2023-11-08)
5.1.10 (2023-11-08)
- discover plugins for building docs (22018e4)
5.1.9 (2023-11-08)
5.1.8 (2023-11-07)
5.1.7 (2023-11-06)
- always write system and molecules top sections last (c49aa9c)
5.1.6 (2023-10-27)
- ci: set markdown content type for description (6dc116c)
5.1.5 (2023-10-27)
- ci: set markdown content type for description (ca9963e)
5.1.4 (2023-10-27)
- ci: markdown in readme (8a41e39)
5.1.3 (2023-10-27)
5.1.2 (2023-10-27)
- ci: unify release workflow (488779f)
5.1.1 (2023-10-27)
- ci: only build package on tag push 'stable' (3a839a3)
5.1.0 (2023-10-27)
- adjust resnum of a moving hydrogen (#312) (481cd84)
- Checkpoints optional (#311) (5e93913)
- ci: publish to PyPi (e513fb6)
- dev: visualize call graph with Pycallgraph (#303) (ab6ffe5)
- show gmx errors in log. fixes #260 (#313) (489eb2d)
- id in scheme (a597bba)
5.0.0 (2023-10-25)
- choose highest rate as reaction start time
- Allow having single optional file for mdrun (#151) (6b61a8c)
- choose highest rate as reaction start time (fc822b3)
- display residue name for radical population (77a8d72)
- extrande KMC algorithm (d1671db)
- only plot radical occupied atoms (#308) (77a8d72)
- Runtime analysis tool (#283) (e302be3)
- trr without edr can now be used. (6b61a8c)
- #261 improve error message if ff is not found in cwd (#307) (ab03cbe)
- after truncating place doesn't need a time (233d83c)
- catch edge cases in extrande algorithm (01d4df9)
- closes #286 don't modify task mapping inplace (c40f360)
- consistent naming for remove hydrogen cli (e615370)
- coordinates and runmanager (#271) (695026c)
- correct error message (facda23)
- correct truncated gro (2c49c80)
- duplicate key in yaml (6204e1e)
- error handling (d0dc8e7)
- execute
placeat first time in recipe (7234d72) - gmx trjconv --trunc not working with xtc (ba0b922)
- improved rate plotting (d0f6d19)
- improved reliability of rate plotting (6a355d4)
- make plugins and plugin schemas discoverable by pip install (73da927)
- only use mpme and ntmpi in test config. fixes #302 (#304) (764b083)
- parametrize before slow growth (ff14694)
- rate plot with less than 9 recipes (eb557d4)
- remove double log message (#290) (0182d20)
- rename idx to ix for moleculetype for consistency (e615370)
- runtime analysis double counting (14a875a)
- set needs_parametrization (e7a2996)
- truncate bug (bfc175c)
- type issue in log message formatting (fdee768)
- write backups of truncated trajectories to the correct directory (e615370)
- wrong type of top when parametrizing (fb2eb08)
4.4.1 (2023-09-13)
- test: increase hypothesis deadline (f7d8867)
4.4.0 (2023-09-13)
- dummy: this is not a feature, just a release trigger (6aa1190)
- analysis: remove y axis label for steps panel in plot_energy (a2bc88a)
- test: increase hypothesis deadline (4b9823d)
- test: increase hypothesis deadline (9810e84)
4.3.0 (2023-09-08)
- closes #265 , cleanup with flake8 (d79adbc)
- jobscript and logging (cbd4d5d)
- place_atom (0e0dc1d)
- properly merge mds general '.*' section and general options with defaults (cbd4d5d)
- set defaults on non-existent sections. fixes #264 (cbd4d5d)
4.2.1 (2023-09-07)
4.2.0 (2023-09-04)
- analysis: open-plot and open-vmd options (d306e66)
- plot multiple energy terms (d306e66)
- review analysis (#245) (d306e66)
- #236 rm concat cmd option (#240) (675ded5)
- missing test file (1e805c1)
- no grappa in tox tests (feaff46)
- Recipe aggregation broken, closes #252 (#253) (a6177e3)
4.1.0 (2023-08-28)
- --debug for post-mortem debugging (#214) (91360d1)
- add remove_hydrogen tool (#213) (b7f7e78)
- Automatic Radical Parameterization (#144) (4b4641b)
- automatically stop and restart KIMMDY for joblength-restricted HPC clusters (#162) (602d864)
- cleanup cmd.py (#228) (f77b6dc)
- config: use_plumed in md section (#234) (22dfacb)
- multimolecule topology (#211) (153af8c)
- single reaction tasks in config (#215) (1c07689)
- workflow for local testing (092b89e)
- 212 (016aa56)
- allow reading topology with an empty forcefield (#238) (a0824c3)
- also fix #200 (f2b2be2)
- catch plugin loading exception (268f77f)
- ci: render docs (a62f351)
- consolidate cmd interface with previous changes by @ehhartmann (f77b6dc)
- docs: getting started molstar resources (f77b6dc)
- don't increment logfile if starting from a checkpoint (f77b6dc)
- don't run tasks twice (c756793)
- examples use new plumed field (9493a45)
- fix docstring references after #229 (7c4ba75)
- install order and tox rquirements (e7d5957)
- logger instead of logging (272dd41)
- missing import (0ac234f)
- morse transition rate homolysis tests fails on ci but not locally #197 (#201) (f2b2be2)
- new build example (4c6b93e)
- plugins use task-logger (#207) (d5c419d)
- proper usage of str and repr for topology (#210) (6fd070f)
- removed need for strict bind break order (#231) (a7859ec)
- requirements typo (2f998d2)
- runmng logger getting overwritten (27baee9)
- show plugins (dcb92c8)
4.0.1 (2023-08-11)
- ci: add docs build workflow (#190) (#198) (5fdec0b)
- dev: add information for developers about conventional commits (5fdec0b)
4.0.0 (2023-08-11)
- ci: does this work?
- ci: update encode to support unicode (d9f16ad)
- ci: what if this doesn't have a body? (d9f16ad)
- this is a release-please test (d9f16ad)
3.6.0 (2023-08-11)
- #185 find gromacs data dir in docker container (#191) (7c0b90c)
- ci: use correct event context variable (33003a9)
- don't run tests on pr twice (7957269)
- fix #187 (587c426)
- merge issues (5880dbb)
- plumed_mod updating (3f815a2)
- register pytest mark properly (6c56ed9)
- remove unused tests (8632f8b)
- test releases in separate workflow to get easy link for a badge (0a3e11c)
- tests compatible with local gh act (71d8204)
- trigger workflow (e86dccd)
3.5.1 (2023-08-08)
3.5.0 (2023-08-08)
- ci: first try! (f2c686f)
3.4.0 (2023-08-08)
- add gmx_mdrun_flags option. fixes #145 (#161) (e780402)
- config: validation, completion and defaults for kimmdy.yml (#153) (de7c78f)
- example from tests (#175) (a096a45)
- consistent use of
edisin homolysis config (#170) (e847707) - don't allow
Movew/o ix/id_to_move (10c9231) - inconsistent inheritance (#154) (2bec671)
- load plugins only once in init (#171) (88b55ee)
- merge dihedrals (#174) (37f6be3)
- scheme keys not plugin names but entrypoints (b878b69)
- test input files now compatible (eda027a)
- test_merge_prm_top (9d333bc)
- update scheme paths after building examples (5076ca4)
- improve config option descriptions, names and error reporting (#163) (3318bdc)
- types: add custom renderer (3318bdc)
3.3.1 (2023-07-12)
3.3.0 (2023-07-05)
- linked ixs and ids for RecipSteps (#137) (8238df9)
- topology: enable multiple dihedrals (unique by their periodicity) for proper dihedrals (8238df9)
- add default funct for Bonds and BondTypes (8238df9)
- add more nestable sections in topology parsing (8238df9)
- match X as wildcards for atomic types (8238df9)
3.2.0 (2023-07-03)
3.1.0 (2023-06-30)
3.0.1 (2023-06-28)
- dihedraltypes sections in ff/topology (affa546)
3.0.0 (2023-06-26)
- put restrictions on the way top files are accepted
- deprecate generate_top_from_atom_list
- handle else macros (bcb6121)
- handle multiple moleculetype sections (bcb6121)
- parse top files with includes (#124) (bcb6121)
- resolve includes in gromacs data dir (located relative to gmx executable) if not in cwd (bcb6121)
- stop if no ff found, warn if multiple found (bcb6121)
- topology dictionary helpers to get and set sections (bcb6121)
- udpate top dict with parsed ff parameters (bcb6121)
- deprecate generate_top_from_atom_list (bcb6121)
- put restrictions on the way top files are accepted (bcb6121)
- use hat_naive instead of hat_reaction (bcb6121)
- use logging.warning instead of depcrecated warn (bcb6121)
- add tutorial section (with markdown support) (bcb6121)
- move qmd to preview topology to docs (bcb6121)
2.4.0 (2023-06-22)
- homolysis module and homolysis tests (3267642)
- KMC module testing (ebb771f)
- Move coordinates include time (10bb3a7)
- Use proper HAT plugin (6a4b0eb)
- allow restarting from checkpoint from python (2163173)
- correct assignment of charge and mass in ff (c5f92a6)
- homolysis test (178590d)
- initialize radical list (3196747)
- initialize Topology.radicals (5e0f335)
- remove deprecated imports in tests (d078109)
- rename variables in test_kmc (4df479d)
- test_integration_move_top (e0f71b6)
2.3.0 (2023-05-11)
- add MOVE conversion for HAT (0dbe4b1)
- make periodicity part of the id for dihedrals (0710086)
- parse dihedral and position restraints (1209714)
- test for radicals based on bondorder in top initialization (a446a70)
2.2.0 (2023-03-07)
- add --version command (bf3e183)
2.1.0 (2023-02-27)
- add kimmdy checkpoint files (b468378)
- test CI (d3dff98)
- write task file history to separate file (bdefba1)
- #84 (1bef009)
- 23 (a6eb2b7)
- abort kimmdy if gromacs fails (080ecc0), closes #83
- allow existing directories of starting from checkpoint (8370713)
- correctly apply atomtype and residue to jumping H (dbdd21e), closes #84
- don't create empty task files if no files are changed (615d11c)
- don't create logfile christmas trees. (fca231f), closes #82
- make plumed really optional (beb09cd)
- minimization path to mdp (971453b)
- use output file dir for histfile name (a069c3c)