Code

MT-REXEE development #58

Code

Merged

wehs7661 merged 76 commits intomasterwehs7661/ensemble_md:masterfrom pr-57wehs7661/ensemble_md:pr-57Copy head branch name to clipboardOct 17, 2024

+57,786-10

Commits

Commits on Sep 4, 2024

• Add deafult swapping function

  ajfriedman22

  committed
  2d33a51

Commits on Sep 5, 2024

• Update replica_exchange_EE.py

  ajfriedman22

  authored
  ee7cc45

Commits on Sep 9, 2024

• Fix Errors

  ajfriedman22

  committed
  a9f46a2

Commits on Sep 10, 2024

• Fix minor error

  ajfriedman22

  committed
  90976c5

• Fix comment typo

  ajfriedman22

  committed
  5532d43

• Remove unnessary prints

  ajfriedman22

  committed
  12d6959

• Tweaked README.md and fixed linting errors for run_REXEE.py and replica_exchange_EE.py

  wehs7661

  committed
  71e3d8f

Commits on Sep 11, 2024

• Some work on tweaking the docstrings in coordinate_swap.py

  wehs7661

  committed
  f85d914

• Finished tweaking the docstrings in coordinate_swap.py

  wehs7661

  committed
  42c6a0d

• Fixed some linting errors

  wehs7661

  committed
  9179c62

• Fixed all the linting errors! Modified lint.yaml

  wehs7661

  committed
  7f2e09b

• Added simple unit tests for get_dimensions and compute_angle in coordinate_swap

  wehs7661

  committed
  e70770c

• Tweaked the docstrings of the new functions in replica_exchange_EE.py

  wehs7661

  committed
  c5cbd33

• Fill in missing docstring for add_or_swap function

  ajfriedman22

  authored
  2ea895b

• Merge branch 'pr-57' of https://github.com/wehs7661/ensemble_md into test_MTREXEE

  wehs7661

  committed
  dbd487a

• Fix error in compute_angle function

  ajfriedman22

  authored
  f3fdbfa

• Merge branch 'pr-57' of https://github.com/wehs7661/ensemble_md into test_MTREXEE

  wehs7661

  committed
  5f8080f

• Fill in docstring for get_miss_coord

  ajfriedman22

  authored
  878121b

• Fixed linting errors

  wehs7661

  committed
  710db92

• Merge branch 'pr-57' of https://github.com/wehs7661/ensemble_md into test_MTREXEE

  wehs7661

  committed
  b77ab14

• Fixed the unit test for compute_angle

  wehs7661

  committed
  b6d5fe1

Commits on Sep 18, 2024

• Fix minor error for large systems(>10,000 atoms)

  ajfriedman22

  committed
  d366422

• add test

  ajfriedman22

  committed
  59f477d

• fix error in coordinate_swap find_common function

  ajfriedman22

  committed
  0aa3ef9

Commits on Sep 19, 2024

• Resolved conflicts of merging into pr-57

  wehs7661

  committed
  90edc32

• Merge pull request #59 from wehs7661/test_MTREXEE

  Show description for c789ec2
  wehs7661

  authored
  c789ec2

• Fix error in pbc shift function in coordinate_swap

  ajfriedman22

  committed
  046d236

• add tests

  ajfriedman22

  committed
  b221831

• Update tests

  ajfriedman22

  committed
  0451c84

• Add more tests

  ajfriedman22

  committed
  5a9587c

• Add more tests

  ajfriedman22

  committed
  3594fbe

• Fix linting error

  ajfriedman22

  committed
  23144c8

Commits on Sep 20, 2024

• Add more tests for coordinate_swap

  ajfriedman22

  committed
  25ee50f

• Fix linting errors

  ajfriedman22

  committed
  1ae3b38

• Fix linting errors

  ajfriedman22

  committed
  44d8801

Commits on Sep 23, 2024

• Add more tests

  ajfriedman22

  committed
  12d784f

• Fix linting errors

  ajfriedman22

  committed
  4c7d8ec

• Add more tests

  ajfriedman22

  committed
  d210b89

• fix linting errors

  ajfriedman22

  committed
  978ea06

• Add tests for built-in MT-REXEE functions

  ajfriedman22

  committed
  b2392d7

• Fix linting errors

  ajfriedman22

  committed
  db64e8b

• Fix linting errors

  ajfriedman22

  committed
  7d67f25

• Fix file paths

  ajfriedman22

  committed
  5c77dfa

• Fix test error

  ajfriedman22

  committed
  991cef5

• Fix read_top when top files are in a different dir

  ajfriedman22

  committed
  87dc95b

Commits on Sep 24, 2024

• Fix test errors

  ajfriedman22

  committed
  3b58267

Commits on Sep 26, 2024

• Fix test errors

  ajfriedman22

  committed
  262ef80

Commits on Sep 27, 2024

• Fix test file paths

  ajfriedman22

  committed
  65b487f

Commits on Sep 30, 2024

• Fix file path issue in test

  ajfriedman22

  committed
  47710ce

• Fix lint error

  ajfriedman22

  committed
  1a73e7e

Commits on Oct 4, 2024

• Fix test file path

  ajfriedman22

  committed
  8ccb59d

Commits on Oct 7, 2024

• Fix tests

  ajfriedman22

  committed
  c39916c

• Move read_top function

  ajfriedman22

  committed
  3addd41

• Make compute angle an internal function

  ajfriedman22

  committed
  c21bd0d

• Combine perform shift functions

  ajfriedman22

  committed
  15c1fd2

• Fix linting errors

  ajfriedman22

  committed
  b7abcdb

• Fix linting errors

  ajfriedman22

  committed
  f17660a

• Fix test errors

  ajfriedman22

  committed
  01c4de3

• Merge branch 'master' into pr-57

  ajfriedman22

  authored
  0ef16ce

Commits on Oct 9, 2024

• Improve test coverage for gmx_parser

  ajfriedman22

  committed
  e7f6919

• Increase test coverage for set_params

  ajfriedman22

  committed
  db3d682

• Improve test coverage and remove redundant code

  ajfriedman22

  committed
  b726199

• Merge branch 'pr-57' of github.com:wehs7661/ensemble_md into pr-57

  ajfriedman22

  committed
  8b25cd6

• Fix linting

  ajfriedman22

  committed
  6546093

• Fix linting

  ajfriedman22

  committed
  713a7b0

• Fix linting

  ajfriedman22

  committed
  18042b5

Commits on Oct 10, 2024

• Revise the GRO file writting step for coordinate modification

  ajfriedman22

  committed
  2fcee10

• Fix minor error with topology reading

  ajfriedman22

  committed
  cf8b95f

• Fix linting error

  ajfriedman22

  committed
  296c181

Commits on Oct 11, 2024

• Fix tests

  ajfriedman22

  committed
  7024610

• Fix tests

  ajfriedman22

  committed
  424fec2

• Generalize file writting and update test

  ajfriedman22

  committed
  867ae17

• Clean-up files and move to internal functions

  ajfriedman22

  committed
  69f307d

• Improve test coverage

  ajfriedman22

  committed
  d635f9d

• Fix linting

  ajfriedman22

  committed
  41edb07

• Fix small error

  ajfriedman22

  committed
  98af948