Code

fix: restarting#504

Code

Merged

jmbuhr merged 47 commits intomaingraeter-group/kimmdy:mainfrom fix/restartinggraeter-group/kimmdy:fix/restartingCopy head branch name to clipboardFeb 4, 2025

+879-598

Commits

Commits on Dec 19, 2024

• feat: pass restart flag via config for cli

  jmbuhr

  committed
  d0013a5

  Copy full SHA for d0013a5

• wip

  jmbuhr

  committed
  79046b2

  Copy full SHA for 79046b2

Commits on Jan 13, 2025

• fix index error

  jmbuhr

  committed
  49c4025

  Copy full SHA for 49c4025

• autofildict should return an optional on missing

  jmbuhr

  committed
  6347f40

  Copy full SHA for 6347f40

• wip

  jmbuhr

  committed
  49d84f0

  Copy full SHA for 49d84f0

Commits on Jan 15, 2025

• merge restart flag with config

  jmbuhr

  committed
  6e586a7

  Copy full SHA for 6e586a7

• simplify get_task_directories

  jmbuhr

  committed
  610eb1a

  Copy full SHA for 610eb1a

• wip on analysis tool

  jmbuhr

  committed
  8ba728d

  Copy full SHA for 8ba728d

• adapte analys tool

  jmbuhr

  committed
  ddc7ddd

  Copy full SHA for ddc7ddd

• fix jobscript

  jmbuhr

  committed
  c93a2ce

  Copy full SHA for c93a2ce

• minor cleanup

  jmbuhr

  committed
  2f2604d

  Copy full SHA for 2f2604d

• cleanup old truncation function

  jmbuhr

  committed
  164f59c

  Copy full SHA for 164f59c

• exit early if run already finished

  jmbuhr

  committed
  2841525

  Copy full SHA for 2841525

Commits on Jan 16, 2025

• wip

  jmbuhr

  committed
  5055696

  Copy full SHA for 5055696

• fix everything

  jmbuhr

  committed
  2360ddf

  Copy full SHA for 2360ddf

• handle more edgecases

  jmbuhr

  committed
  bd9494e

  Copy full SHA for bd9494e

• adjust expected number of output files in tests due to new

  Show description for 18a7582
  jmbuhr

  committed
  18a7582

  Copy full SHA for 18a7582

Commits on Jan 17, 2025

• add grappa to dev requirements

  jmbuhr

  committed
  57d199c

  Copy full SHA for 57d199c

• check kimmdy finished marker files in integration tests

  jmbuhr

  committed
  bd26af1

  Copy full SHA for bd26af1

• add config.slurm.runcmd to replace sbatch in jobscript for local testing

  jmbuhr

  committed
  a89261a

  Copy full SHA for a89261a

• account for different output index group in compressed xtc

  jmbuhr

  committed
  4a2d196

  Copy full SHA for 4a2d196

• fix indentation

  jmbuhr

  committed
  706896d

  Copy full SHA for 706896d

• Merge branch 'fix/restarting' of github.com:hits-mbm-dev/kimmdy into fix/restarting

  jmbuhr

  committed
  e42c081

  Copy full SHA for e42c081

• feat: get dir from kimmdy.yml input file if not specified in analysis

  jmbuhr

  committed
  d38d9c5

  Copy full SHA for d38d9c5

• write time markers also retroactively next to trajectory in the task it

  Show description for afb70d7
  jmbuhr

  committed
  afb70d7

  Copy full SHA for afb70d7

• adjust analysis tools accordingly

  jmbuhr

  committed
  58e2017

  Copy full SHA for 58e2017

• cleanup linter warnings

  jmbuhr

  committed
  f53dd64

  Copy full SHA for f53dd64

• format

  jmbuhr

  committed
  34bb2c2

  Copy full SHA for 34bb2c2

Commits on Jan 23, 2025

• cleanup logging

  jmbuhr

  committed
  e020ff2

  Copy full SHA for e020ff2

• feat: dummy_first kmc method that ignores rates and always chooses the first recipe for debugging

  jmbuhr

  committed
  e18ca9e

  Copy full SHA for e18ca9e

• format

  jmbuhr

  committed
  387e4c5

  Copy full SHA for 387e4c5

• chore: fix gh ci (publish workflow is not allowed to be re-usable workflow)

  jmbuhr

  committed
  63f8eee

  Copy full SHA for 63f8eee

• fix: trigger release

  jmbuhr

  committed
  5c77737

  Copy full SHA for 5c77737

Commits on Jan 29, 2025

• fully specify --nodes for slurm

  jmbuhr

  committed
  beaa8b9

  Copy full SHA for beaa8b9

• don't use debug dummy kmc in example

  jmbuhr

  committed
  e3f0914

  Copy full SHA for e3f0914

• add markers to marker list

  jmbuhr

  committed
  b022b82

  Copy full SHA for b022b82

Commits on Jan 30, 2025

• silently ignore directories in the kimmdy output folder that don't match

  Show description for 6c89e7e
  jmbuhr

  committed
  6c89e7e

  Copy full SHA for 6c89e7e

• clean up cli arguments

  jmbuhr

  committed
  35fec76

  Copy full SHA for 35fec76

• format

  jmbuhr

  committed
  df83556

  Copy full SHA for df83556

• add trr_reaction file writing, temporary solution

  

  Eric Hartmann

  committed
  e00796b

  Copy full SHA for e00796b

Commits on Jan 31, 2025

• fix: handle latest files in intermediate tasks like relax and place

  Show description for 1861df5
  jmbuhr

  committed
  1861df5

  Copy full SHA for 1861df5

• format

  jmbuhr

  committed
  d94456e

  Copy full SHA for d94456e

• update expected number out output files now that a kimmdy.history file

  Show description for 71dce22
  jmbuhr

  committed
  71dce22

  Copy full SHA for 71dce22

Commits on Feb 4, 2025

• Merge branch 'main' into fix/restarting

  jmbuhr

  authored
  224bab0

  Copy full SHA for 224bab0

• add counter for each individual MD task for restart

  

  Eric Hartmann

  committed
  7cdf93a

  Copy full SHA for 7cdf93a

• Merge branch 'fix/restarting' of /~https://github.com/hits-mbm-dev/kimmdy into fix/restarting

  

  Eric Hartmann

  committed
  5e7874a

  Copy full SHA for 5e7874a

• do not run grompp for checkpoint restarts

  

  Eric Hartmann

  committed
  a1d3eae

  Copy full SHA for a1d3eae