Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Support for AMBER proper and improper dihedrals in write_lammpsdata #896

Merged
merged 32 commits into from
Jul 8, 2021
Merged

Support for AMBER proper and improper dihedrals in write_lammpsdata #896

merged 32 commits into from
Jul 8, 2021

Commits on Apr 29, 2021

  1. Add support for AMBER-style improper torsions.

    @rwsmith7531
    rwsmith7531 committed Apr 29, 2021
    Configuration menu
    Copy the full SHA
    cc4eb10 View commit details
    Browse the repository at this point in the history

  2. Apply zero 1-4 weighting parameter in CHARMM-style dihedrals in non-C… 

    …HARMM forcefields.
    @rwsmith7531
    rwsmith7531 committed Apr 29, 2021
    Configuration menu
    Copy the full SHA
    9d1ba81 View commit details
    Browse the repository at this point in the history

  3. Make dihedral weighting parameters not default to zero, to restore ba… 

    …ckwards compatibility.
    @rwsmith7531
    rwsmith7531 committed Apr 29, 2021
    Configuration menu
    Copy the full SHA
    c6ced69 View commit details
    Browse the repository at this point in the history

Commits on May 4, 2021

  1. Add/improve unit tests and fix bugs found by them.

    @rwsmith7531
    rwsmith7531 committed May 4, 2021
    Configuration menu
    Copy the full SHA
    e61d99c View commit details
    Browse the repository at this point in the history

Commits on May 5, 2021

  1. Update syntax to maintain code style consistency.

    @rwsmith7531
    rwsmith7531 committed May 5, 2021
    Configuration menu
    Copy the full SHA
    8d44cee View commit details
    Browse the repository at this point in the history

  2. Merge master to resolve merge conflict.

    @rwsmith7531
    rwsmith7531 committed May 5, 2021
    Configuration menu
    Copy the full SHA
    9748085 View commit details
    Browse the repository at this point in the history

  3. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed May 5, 2021
    Configuration menu
    Copy the full SHA
    91445a5 View commit details
    Browse the repository at this point in the history

  4. Correct mistake in merge conflict correction.

    @rwsmith7531
    rwsmith7531 committed May 5, 2021
    Configuration menu
    Copy the full SHA
    f2c2b9c View commit details
    Browse the repository at this point in the history

  5. Merge branch 'lammpsdata_improper' of github.com:rwsmith7531/mbuild i… 

    …nto lammpsdata_improper
    @rwsmith7531
    rwsmith7531 committed May 5, 2021
    Configuration menu
    Copy the full SHA
    01996d9 View commit details
    Browse the repository at this point in the history

  6. Move imports to tops of functions in unit tests.

    @rwsmith7531
    rwsmith7531 committed May 5, 2021
    Configuration menu
    Copy the full SHA
    a70a002 View commit details
    Browse the repository at this point in the history

  7. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed May 5, 2021
    Configuration menu
    Copy the full SHA
    cf75b40 View commit details
    Browse the repository at this point in the history

  8. Sort non-central atoms in improper dihedral by atom type.

    @rwsmith7531
    rwsmith7531 committed May 5, 2021
    Configuration menu
    Copy the full SHA
    a5360ef View commit details
    Browse the repository at this point in the history

  9. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed May 5, 2021
    Configuration menu
    Copy the full SHA
    3aa7706 View commit details
    Browse the repository at this point in the history

Commits on May 6, 2021

  1. Fix bug in atom type sorting.

    @rwsmith7531
    rwsmith7531 committed May 6, 2021
    Configuration menu
    Copy the full SHA
    0dd1404 View commit details
    Browse the repository at this point in the history

  2. Integrate pre-commit.ci bot edits and resolve resulting merge conflict.

    @rwsmith7531
    rwsmith7531 committed May 6, 2021
    Configuration menu
    Copy the full SHA
    16771b0 View commit details
    Browse the repository at this point in the history

  3. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed May 6, 2021
    Configuration menu
    Copy the full SHA
    b0019b5 View commit details
    Browse the repository at this point in the history

Commits on May 13, 2021

  1. Write central-atom third for AMBER-style impropers.

    @rwsmith7531
    rwsmith7531 committed May 13, 2021
    Configuration menu
    Copy the full SHA
    1d4a35e View commit details
    Browse the repository at this point in the history

  2. Add comments explaining multiple reorderings of atoms in improper dih… 

    …edrals.
    @rwsmith7531
    rwsmith7531 committed May 13, 2021
    Configuration menu
    Copy the full SHA
    1965faf View commit details
    Browse the repository at this point in the history

  3. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed May 13, 2021
    Configuration menu
    Copy the full SHA
    c41cddd View commit details
    Browse the repository at this point in the history

Commits on May 14, 2021

  1. Rename borrowed_charmm flag and add additional comment.

    @rwsmith7531
    rwsmith7531 committed May 14, 2021
    Configuration menu
    Copy the full SHA
    ef2f803 View commit details
    Browse the repository at this point in the history

  2. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed May 14, 2021
    Configuration menu
    Copy the full SHA
    b102a50 View commit details
    Browse the repository at this point in the history

  3. Remove atom sorting in improper dihedrals.

    @rwsmith7531
    rwsmith7531 committed May 14, 2021
    Configuration menu
    Copy the full SHA
    bb9c162 View commit details
    Browse the repository at this point in the history

  4. Merge branch 'lammpsdata_improper' of github.com:rwsmith7531/mbuild i… 

    …nto lammpsdata_improper
    @rwsmith7531
    rwsmith7531 committed May 14, 2021
    Configuration menu
    Copy the full SHA
    d2cdadf View commit details
    Browse the repository at this point in the history

  5. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed May 14, 2021
    Configuration menu
    Copy the full SHA
    726f5b0 View commit details
    Browse the repository at this point in the history

Commits on Jul 1, 2021

  1. Check for the correct dihedral weighting factor in CHARMM dihedral.

    @rwsmith7531
    rwsmith7531 committed Jul 1, 2021
    Configuration menu
    Copy the full SHA
    03156bf View commit details
    Browse the repository at this point in the history

  2. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Jul 1, 2021
    Configuration menu
    Copy the full SHA
    11c62b3 View commit details
    Browse the repository at this point in the history

  3. Revert "Check for the correct dihedral weighting factor in CHARMM dih… 

    …edral."

This reverts commit 03156bf.
    @rwsmith7531
    rwsmith7531 committed Jul 1, 2021
    Configuration menu
    Copy the full SHA
    ab2e66c View commit details
    Browse the repository at this point in the history

  4. Add a unit test for the weighting parameter of a CHARMM dihedral.

    @rwsmith7531
    rwsmith7531 committed Jul 1, 2021
    Configuration menu
    Copy the full SHA
    3142394 View commit details
    Browse the repository at this point in the history

  5. Merge formatting changes

    @rwsmith7531
    rwsmith7531 committed Jul 1, 2021
    Configuration menu
    Copy the full SHA
    aabf6a3 View commit details
    Browse the repository at this point in the history

  6. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Jul 1, 2021
    Configuration menu
    Copy the full SHA
    b8eb9b5 View commit details
    Browse the repository at this point in the history

  7. Merge branch 'master' into lammpsdata_improper

    @rwsmith7531
    rwsmith7531 committed Jul 1, 2021
    Configuration menu
    Copy the full SHA
    a28094d View commit details
    Browse the repository at this point in the history

  8. Use get_boundingbox instead of boundingbox.

    @rwsmith7531
    rwsmith7531 committed Jul 1, 2021
    Configuration menu
    Copy the full SHA
    b1f96bc View commit details
    Browse the repository at this point in the history