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

Polymer class revamp #851

Merged
merged 72 commits into from
May 20, 2021
Merged

Polymer class revamp #851

merged 72 commits into from
May 20, 2021

Commits on Feb 3, 2021

  1. added a couple new functions, moved existing code into build function

    @chrisjonesBSU
    chrisjonesBSU committed Feb 3, 2021
    Configuration menu
    Copy the full SHA
    0668608 View commit details
    Browse the repository at this point in the history

  2. added some doc strings

    chrisjonesBSU committed Feb 3, 2021
    Configuration menu
    Copy the full SHA
    3edbabb View commit details
    Browse the repository at this point in the history

  3. added a default value to the port labels

    @chrisjonesBSU
    chrisjonesBSU committed Feb 3, 2021
    Configuration menu
    Copy the full SHA
    7463549 View commit details
    Browse the repository at this point in the history

Commits on Feb 5, 2021

  1. reworked the _add_port function

    chrisjonesBSU committed Feb 5, 2021
    Configuration menu
    Copy the full SHA
    8b80df7 View commit details
    Browse the repository at this point in the history

  2. saving my progress with the add_end_groups function

    chrisjonesBSU committed Feb 5, 2021
    Configuration menu
    Copy the full SHA
    25161ef View commit details
    Browse the repository at this point in the history

Commits on Feb 6, 2021

  1. made progress with end group funcitonality

    chrisjonesBSU committed Feb 6, 2021
    Configuration menu
    Copy the full SHA
    e0f5224 View commit details
    Browse the repository at this point in the history

  2. removing a couple print statements

    chrisjonesBSU committed Feb 6, 2021
    Configuration menu
    Copy the full SHA
    02b3f44 View commit details
    Browse the repository at this point in the history

Commits on Feb 11, 2021

  1. added 2 new attributes to port class

    @chrisjonesBSU
    chrisjonesBSU committed Feb 11, 2021
    Configuration menu
    Copy the full SHA
    17819ae View commit details
    Browse the repository at this point in the history

  2. removed changes from port.py, commented out orientation and separatio… 

    …n lines
    @chrisjonesBSU
    chrisjonesBSU committed Feb 11, 2021
    Configuration menu
    Copy the full SHA
    c1b1575 View commit details
    Browse the repository at this point in the history

Commits on Feb 18, 2021

  1. changed method of removing hydrogens, added n_monomers var for findin… 

    …g last monomer
    chrisjonesBSU committed Feb 18, 2021
    Configuration menu
    Copy the full SHA
    658e1f8 View commit details
    Browse the repository at this point in the history

Commits on Feb 19, 2021

  1. Merge branch 'master' of github.com:mosdef-hub/mbuild into feat/polymer

    chrisjonesBSU committed Feb 19, 2021
    Configuration menu
    Copy the full SHA
    57f4513 View commit details
    Browse the repository at this point in the history

Commits on Feb 22, 2021

  1. adding to the doc strings

    @chrisjonesBSU
    chrisjonesBSU committed Feb 22, 2021
    Configuration menu
    Copy the full SHA
    7c2c178 View commit details
    Browse the repository at this point in the history

Commits on Feb 24, 2021

  1. Merge branch 'feat/polymer' of github.com:chrisjonesBSU/mbuild into f… 

    …eat/polymer
    chrisjonesBSU committed Feb 24, 2021
    Configuration menu
    Copy the full SHA
    b433079 View commit details
    Browse the repository at this point in the history

  2. added update_separation function

    chrisjonesBSU committed Feb 24, 2021
    Configuration menu
    Copy the full SHA
    7b6ccc0 View commit details
    Browse the repository at this point in the history

  3. update orientation func; separation property func

    chrisjonesBSU committed Feb 24, 2021
    Configuration menu
    Copy the full SHA
    650d899 View commit details
    Browse the repository at this point in the history

Commits on Feb 25, 2021

  1. added the up subports to the rotations

    chrisjonesBSU committed Feb 25, 2021
    Configuration menu
    Copy the full SHA
    9b4d93b View commit details
    Browse the repository at this point in the history

  2. fixed the change_orientation function

    chrisjonesBSU committed Feb 25, 2021
    Configuration menu
    Copy the full SHA
    67b6f28 View commit details
    Browse the repository at this point in the history

  3. fix handling when their is no anchor particle

    chrisjonesBSU committed Feb 25, 2021
    Configuration menu
    Copy the full SHA
    ccd312f View commit details
    Browse the repository at this point in the history

Commits on Mar 4, 2021

  1. fix typo

    @jennyfothergill
    jennyfothergill committed Mar 4, 2021
    Configuration menu
    Copy the full SHA
    80a54b8 View commit details
    Browse the repository at this point in the history

  2. docstring: separation is None when port has no anchor

    @jennyfothergill
    jennyfothergill committed Mar 4, 2021
    Configuration menu
    Copy the full SHA
    41aec95 View commit details
    Browse the repository at this point in the history

Commits on Mar 15, 2021

  1. added 3 unit tests

    chrisjonesBSU committed Mar 15, 2021
    Configuration menu
    Copy the full SHA
    33b7eca View commit details
    Browse the repository at this point in the history

  2. remove the port updating stuff I was trying to use

    chrisjonesBSU committed Mar 15, 2021
    Configuration menu
    Copy the full SHA
    a8fb3b9 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'feat/port' into feat/polymer

    @chrisjonesBSU
    chrisjonesBSU committed Mar 15, 2021
    Configuration menu
    Copy the full SHA
    c0b3a6c View commit details
    Browse the repository at this point in the history

  4. updating port separations for end groups

    @chrisjonesBSU
    chrisjonesBSU committed Mar 15, 2021
    Configuration menu
    Copy the full SHA
    c4c894f View commit details
    Browse the repository at this point in the history

  5. fix the way clone is being called

    chrisjonesBSU committed Mar 15, 2021
    Configuration menu
    Copy the full SHA
    a111ebf View commit details
    Browse the repository at this point in the history

Commits on Mar 16, 2021

  1. added some doc strings and comments

    chrisjonesBSU committed Mar 16, 2021
    Configuration menu
    Copy the full SHA
    df35343 View commit details
    Browse the repository at this point in the history

Commits on Mar 22, 2021

  1. updated doc strings

    chrisjonesBSU committed Mar 22, 2021
    Configuration menu
    Copy the full SHA
    e71fc53 View commit details
    Browse the repository at this point in the history

  2. including jupyter notebook example and walk through

    chrisjonesBSU committed Mar 22, 2021
    Configuration menu
    Copy the full SHA
    90b5eed View commit details
    Browse the repository at this point in the history

  3. Merge branch 'master' of github.com:mosdef-hub/mbuild into feat/polymer

    chrisjonesBSU committed Mar 22, 2021
    Configuration menu
    Copy the full SHA
    77adbbb View commit details
    Browse the repository at this point in the history

  4. example notebook ready

    chrisjonesBSU committed Mar 22, 2021
    Configuration menu
    Copy the full SHA
    07c016c View commit details
    Browse the repository at this point in the history

  5. added to recipe examples

    chrisjonesBSU committed Mar 22, 2021
    Configuration menu
    Copy the full SHA
    8588666 View commit details
    Browse the repository at this point in the history

Commits on Mar 29, 2021

  1. expanded end_group options

    @chrisjonesBSU
    chrisjonesBSU committed Mar 29, 2021
    Configuration menu
    Copy the full SHA
    1120d5f View commit details
    Browse the repository at this point in the history

  2. update alkane recipe to make tests pass

    @jennyfothergill
    jennyfothergill committed Mar 29, 2021
    Configuration menu
    Copy the full SHA
    031d5eb View commit details
    Browse the repository at this point in the history

Commits on Mar 30, 2021

  1. cleaned up if statements when updating head/tail ports

    @chrisjonesBSU
    chrisjonesBSU committed Mar 30, 2021
    Configuration menu
    Copy the full SHA
    96c675b View commit details
    Browse the repository at this point in the history

Commits on Apr 1, 2021

  1. Merge branch 'master' of github.com:mosdef-hub/mbuild into feat/polymer

    @jennyfothergill
    jennyfothergill committed Apr 1, 2021
    Configuration menu
    Copy the full SHA
    417c58b View commit details
    Browse the repository at this point in the history

  2. remove trailing whitespace

    @jennyfothergill
    jennyfothergill committed Apr 1, 2021
    Configuration menu
    Copy the full SHA
    11a082c View commit details
    Browse the repository at this point in the history

Commits on Apr 5, 2021

  1. allow use of compound with existing ports to be specified in init 

    whitespace/formatting
    @jennyfothergill
    jennyfothergill committed Apr 5, 2021
    Configuration menu
    Copy the full SHA
    a1b6654 View commit details
    Browse the repository at this point in the history

Commits on Apr 6, 2021

  1. Merge branch 'master' of github.com:mosdef-hub/mbuild into feat/polymer

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
    Configuration menu
    Copy the full SHA
    5d5340f View commit details
    Browse the repository at this point in the history

  2. update alkane to new schema

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
    Configuration menu
    Copy the full SHA
    db0d723 View commit details
    Browse the repository at this point in the history

  3. update tests

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
    Configuration menu
    Copy the full SHA
    a169da9 View commit details
    Browse the repository at this point in the history

  4. blacked, changed how head/tail port work

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
    Configuration menu
    Copy the full SHA
    5208f66 View commit details
    Browse the repository at this point in the history

  5. remove debug print

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
    Configuration menu
    Copy the full SHA
    cfdfbcf View commit details
    Browse the repository at this point in the history

  6. update notebook

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
    Configuration menu
    Copy the full SHA
    31a9bd9 View commit details
    Browse the repository at this point in the history

  7. Merge branch 'master' of github.com:mosdef-hub/mbuild into feat/polymer

    @chrisjonesBSU
    chrisjonesBSU committed Apr 6, 2021
    Configuration menu
    Copy the full SHA
    0a44c85 View commit details
    Browse the repository at this point in the history

  8. Merge branch 'feat/polymer' of github.com:chrisjonesBSU/mbuild into f… 

    …eat/polymer
    @chrisjonesBSU
    chrisjonesBSU committed Apr 6, 2021
    Configuration menu
    Copy the full SHA
    c98bfb5 View commit details
    Browse the repository at this point in the history

  9. update notebook

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
    Configuration menu
    Copy the full SHA
    54064ec View commit details
    Browse the repository at this point in the history

  10. clear nb

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
    Configuration menu
    Copy the full SHA
    2265a00 View commit details
    Browse the repository at this point in the history

  11. add back add_hydrogens

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
    Configuration menu
    Copy the full SHA
    95e10b4 View commit details
    Browse the repository at this point in the history

  12. add add_hydrogens=False

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
    Configuration menu
    Copy the full SHA
    9975ec2 View commit details
    Browse the repository at this point in the history

  13. add_hydrogens=False, all tests pass

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
    Configuration menu
    Copy the full SHA
    3e937de View commit details
    Browse the repository at this point in the history

  14. Merge branch 'feat/polymer' of github.com:chrisjonesBSU/mbuild into f… 

    …eat/polymer
    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
    Configuration menu
    Copy the full SHA
    9a5b39a View commit details
    Browse the repository at this point in the history

  15. Merge pull request #1 from jennyfothergill/feat/polymer 

    polymer changes
    @chrisjonesBSU
    chrisjonesBSU committed Apr 6, 2021
    Configuration menu
    Copy the full SHA
    bda023c View commit details
    Browse the repository at this point in the history

  16. changed orientation of down port to face opposite direction of up port

    @chrisjonesBSU
    chrisjonesBSU committed Apr 6, 2021
    Configuration menu
    Copy the full SHA
    aea0dde View commit details
    Browse the repository at this point in the history

  17. Few more examples added to show new functionality

    @chrisjonesBSU
    chrisjonesBSU committed Apr 6, 2021
    Configuration menu
    Copy the full SHA
    01965ef View commit details
    Browse the repository at this point in the history

Commits on Apr 14, 2021

  1. merge upstream

    @chrisjonesBSU
    chrisjonesBSU committed Apr 14, 2021
    Configuration menu
    Copy the full SHA
    1e111fc View commit details
    Browse the repository at this point in the history

  2. adding a few unit tests

    @chrisjonesBSU
    chrisjonesBSU committed Apr 14, 2021
    Configuration menu
    Copy the full SHA
    deca5b2 View commit details
    Browse the repository at this point in the history

  3. removing the example notebook from the PR

    @chrisjonesBSU
    chrisjonesBSU committed Apr 14, 2021
    Configuration menu
    Copy the full SHA
    56575f0 View commit details
    Browse the repository at this point in the history

  4. test for errors, and manually passing in end group compounds

    @chrisjonesBSU
    chrisjonesBSU committed Apr 14, 2021
    Configuration menu
    Copy the full SHA
    7b7e14a View commit details
    Browse the repository at this point in the history

  5. expanded doc strings with more detailed explanations, and some examples

    @chrisjonesBSU
    chrisjonesBSU committed Apr 14, 2021
    Configuration menu
    Copy the full SHA
    3eab819 View commit details
    Browse the repository at this point in the history

  6. fix a conflict that was sticking around in the port doc strings

    @chrisjonesBSU
    chrisjonesBSU committed Apr 14, 2021
    Configuration menu
    Copy the full SHA
    15d14b4 View commit details
    Browse the repository at this point in the history

  7. fix formatting in the doc strings

    @chrisjonesBSU
    chrisjonesBSU committed Apr 14, 2021
    Configuration menu
    Copy the full SHA
    19cb631 View commit details
    Browse the repository at this point in the history

Commits on Apr 15, 2021

  1. Doc strings to explain implementation of sequence in the build function

    @chrisjonesBSU
    chrisjonesBSU committed Apr 15, 2021
    Configuration menu
    Copy the full SHA
    4bbeec1 View commit details
    Browse the repository at this point in the history

Commits on Apr 23, 2021

  1. Merge branch 'master' of github.com:mosdef-hub/mbuild into feat/polymer

    chrisjonesBSU committed Apr 23, 2021
    Configuration menu
    Copy the full SHA
    707418b View commit details
    Browse the repository at this point in the history

  2. Merge branch 'master' of github.com:mosdef-hub/mbuild into feat/polymer

    @chrisjonesBSU
    chrisjonesBSU committed Apr 23, 2021
    Configuration menu
    Copy the full SHA
    926a570 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'feat/polymer' of github.com:chrisjonesBSU/mbuild into f… 

    …eat/polymer
    @chrisjonesBSU
    chrisjonesBSU committed Apr 23, 2021
    Configuration menu
    Copy the full SHA
    a06bc72 View commit details
    Browse the repository at this point in the history

Commits on Apr 27, 2021

  1. Merge branch 'master' of github.com:mosdef-hub/mbuild into feat/polymer

    @chrisjonesBSU
    chrisjonesBSU committed Apr 27, 2021
    Configuration menu
    Copy the full SHA
    04138b9 View commit details
    Browse the repository at this point in the history

Commits on Apr 28, 2021

  1. add unit test for value of n < 1

    @chrisjonesBSU
    chrisjonesBSU committed Apr 28, 2021
    Configuration menu
    Copy the full SHA
    4bf8660 View commit details
    Browse the repository at this point in the history

  2. 2 new tests to test for errors

    @chrisjonesBSU
    chrisjonesBSU committed Apr 28, 2021
    Configuration menu
    Copy the full SHA
    cdfd80d View commit details
    Browse the repository at this point in the history

Commits on May 13, 2021

  1. Merge branch 'master' of github.com:mosdef-hub/mbuild into feat/polymer

    @jennyfothergill
    jennyfothergill committed May 13, 2021
    Configuration menu
    Copy the full SHA
    0e36cd0 View commit details
    Browse the repository at this point in the history

  2. remove unused imports

    @jennyfothergill
    jennyfothergill committed May 13, 2021
    Configuration menu
    Copy the full SHA
    883f25f View commit details
    Browse the repository at this point in the history

  3. oops, typo

    @jennyfothergill
    jennyfothergill committed May 13, 2021
    Configuration menu
    Copy the full SHA
    ed10425 View commit details
    Browse the repository at this point in the history

Commits on May 18, 2021

  1. Merge branch 'master' of github.com:mosdef-hub/mbuild into feat/polymer

    @chrisjonesBSU
    chrisjonesBSU committed May 18, 2021
    Configuration menu
    Copy the full SHA
    2608b9d View commit details
    Browse the repository at this point in the history