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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
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  2. added some doc strings

    chrisjonesBSU committed Feb 3, 2021
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  3. added a default value to the port labels

    @chrisjonesBSU
    chrisjonesBSU committed Feb 3, 2021
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Commits on Feb 5, 2021

  1. reworked the _add_port function

    chrisjonesBSU committed Feb 5, 2021
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  2. saving my progress with the add_end_groups function

    chrisjonesBSU committed Feb 5, 2021
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Commits on Feb 6, 2021

  1. made progress with end group funcitonality

    chrisjonesBSU committed Feb 6, 2021
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  2. removing a couple print statements

    chrisjonesBSU committed Feb 6, 2021
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Commits on Feb 11, 2021

  1. added 2 new attributes to port class

    @chrisjonesBSU
    chrisjonesBSU committed Feb 11, 2021
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  2. removed changes from port.py, commented out orientation and separatio… 

    …n lines
    @chrisjonesBSU
    chrisjonesBSU committed Feb 11, 2021
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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
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Commits on Feb 19, 2021

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

    chrisjonesBSU committed Feb 19, 2021
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Commits on Feb 22, 2021

  1. adding to the doc strings

    @chrisjonesBSU
    chrisjonesBSU committed Feb 22, 2021
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Commits on Feb 24, 2021

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

    …eat/polymer
    chrisjonesBSU committed Feb 24, 2021
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  2. added update_separation function

    chrisjonesBSU committed Feb 24, 2021
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  3. update orientation func; separation property func

    chrisjonesBSU committed Feb 24, 2021
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Commits on Feb 25, 2021

  1. added the up subports to the rotations

    chrisjonesBSU committed Feb 25, 2021
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  2. fixed the change_orientation function

    chrisjonesBSU committed Feb 25, 2021
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  3. fix handling when their is no anchor particle

    chrisjonesBSU committed Feb 25, 2021
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Commits on Mar 4, 2021

  1. fix typo

    @jennyfothergill
    jennyfothergill authored Mar 4, 2021
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  2. docstring: separation is None when port has no anchor

    @jennyfothergill
    jennyfothergill authored Mar 4, 2021
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Commits on Mar 15, 2021

  1. added 3 unit tests

    chrisjonesBSU committed Mar 15, 2021
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  2. remove the port updating stuff I was trying to use

    chrisjonesBSU committed Mar 15, 2021
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  3. Merge branch 'feat/port' into feat/polymer

    @chrisjonesBSU
    chrisjonesBSU committed Mar 15, 2021
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  4. updating port separations for end groups

    @chrisjonesBSU
    chrisjonesBSU committed Mar 15, 2021
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  5. fix the way clone is being called

    chrisjonesBSU committed Mar 15, 2021
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Commits on Mar 16, 2021

  1. added some doc strings and comments

    chrisjonesBSU committed Mar 16, 2021
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Commits on Mar 22, 2021

  1. updated doc strings

    chrisjonesBSU committed Mar 22, 2021
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  2. including jupyter notebook example and walk through

    chrisjonesBSU committed Mar 22, 2021
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  3. Merge branch 'master' of github.com:mosdef-hub/mbuild into feat/polymer

    chrisjonesBSU committed Mar 22, 2021
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  4. example notebook ready

    chrisjonesBSU committed Mar 22, 2021
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  5. added to recipe examples

    chrisjonesBSU committed Mar 22, 2021
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Commits on Mar 29, 2021

  1. expanded end_group options

    @chrisjonesBSU
    chrisjonesBSU committed Mar 29, 2021
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  2. update alkane recipe to make tests pass

    @jennyfothergill
    jennyfothergill committed Mar 29, 2021
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Commits on Mar 30, 2021

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

    @chrisjonesBSU
    chrisjonesBSU committed Mar 30, 2021
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Commits on Apr 1, 2021

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

    @jennyfothergill
    jennyfothergill committed Apr 1, 2021
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  2. remove trailing whitespace

    @jennyfothergill
    jennyfothergill committed Apr 1, 2021
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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
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Commits on Apr 6, 2021

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

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
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  2. update alkane to new schema

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
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  3. update tests

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
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  4. blacked, changed how head/tail port work

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
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  5. remove debug print

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
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  6. update notebook

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
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  7. Merge branch 'master' of github.com:mosdef-hub/mbuild into feat/polymer

    @chrisjonesBSU
    chrisjonesBSU committed Apr 6, 2021
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  8. Merge branch 'feat/polymer' of github.com:chrisjonesBSU/mbuild into f… 

    …eat/polymer
    @chrisjonesBSU
    chrisjonesBSU committed Apr 6, 2021
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  9. update notebook

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
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  10. clear nb

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
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  11. add back add_hydrogens

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
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  12. add add_hydrogens=False

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
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  13. add_hydrogens=False, all tests pass

    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
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  14. Merge branch 'feat/polymer' of github.com:chrisjonesBSU/mbuild into f… 

    …eat/polymer
    @jennyfothergill
    jennyfothergill committed Apr 6, 2021
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  15. Merge pull request #1 from jennyfothergill/feat/polymer 

    polymer changes
    @chrisjonesBSU
    chrisjonesBSU authored Apr 6, 2021
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  16. changed orientation of down port to face opposite direction of up port

    @chrisjonesBSU
    chrisjonesBSU committed Apr 6, 2021
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  17. Few more examples added to show new functionality

    @chrisjonesBSU
    chrisjonesBSU committed Apr 6, 2021
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Commits on Apr 14, 2021

  1. merge upstream

    @chrisjonesBSU
    chrisjonesBSU committed Apr 14, 2021
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  2. adding a few unit tests

    @chrisjonesBSU
    chrisjonesBSU committed Apr 14, 2021
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  3. removing the example notebook from the PR

    @chrisjonesBSU
    chrisjonesBSU committed Apr 14, 2021
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  4. test for errors, and manually passing in end group compounds

    @chrisjonesBSU
    chrisjonesBSU committed Apr 14, 2021
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  5. expanded doc strings with more detailed explanations, and some examples

    @chrisjonesBSU
    chrisjonesBSU committed Apr 14, 2021
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  6. fix a conflict that was sticking around in the port doc strings

    @chrisjonesBSU
    chrisjonesBSU committed Apr 14, 2021
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  7. fix formatting in the doc strings

    @chrisjonesBSU
    chrisjonesBSU committed Apr 14, 2021
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Commits on Apr 15, 2021

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

    @chrisjonesBSU
    chrisjonesBSU committed Apr 15, 2021
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Commits on Apr 23, 2021

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

    chrisjonesBSU committed Apr 23, 2021
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  2. Merge branch 'master' of github.com:mosdef-hub/mbuild into feat/polymer

    @chrisjonesBSU
    chrisjonesBSU committed Apr 23, 2021
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  3. Merge branch 'feat/polymer' of github.com:chrisjonesBSU/mbuild into f… 

    …eat/polymer
    @chrisjonesBSU
    chrisjonesBSU committed Apr 23, 2021
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Commits on Apr 27, 2021

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

    @chrisjonesBSU
    chrisjonesBSU committed Apr 27, 2021
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Commits on Apr 28, 2021

  1. add unit test for value of n < 1

    @chrisjonesBSU
    chrisjonesBSU committed Apr 28, 2021
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  2. 2 new tests to test for errors

    @chrisjonesBSU
    chrisjonesBSU committed Apr 28, 2021
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Commits on May 13, 2021

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

    @jennyfothergill
    jennyfothergill committed May 13, 2021
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  2. remove unused imports

    @jennyfothergill
    jennyfothergill committed May 13, 2021
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  3. oops, typo

    @jennyfothergill
    jennyfothergill committed May 13, 2021
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Commits on May 18, 2021

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

    @chrisjonesBSU
    chrisjonesBSU committed May 18, 2021
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