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Use NetworkX to identify bonds, angles, dihedral, impropers #140

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Use NetworkX to identify bonds, angles, dihedral, impropers #140

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Commits on Feb 18, 2020

  1. Merge branch 'master' into iss239

    @mattwthompson
    mattwthompson committed Feb 18, 2020
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  2. Merge pull request #240 from uppittu11/iss239 

    Ensure correct subtop/site behavior when converting from mBuild
    @mattwthompson
    mattwthompson committed Feb 18, 2020
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  3. add ethane xml snippet

    @daico007
    daico007 committed Feb 18, 2020
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  4. Fix merge conflict in test_reference_xmls

    @rmatsum836
    rmatsum836 committed Feb 18, 2020
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  5. Fix mixup between spce and tip3p from merge conflict

    @rmatsum836
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  6. Merge pull request #241 from rmatsum836/add_water_xmls 

    Merging, the PRs this depended on have been merged.
    @rmatsum836
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  7. Merge branch 'master' of https://github.com/mattwthompson/topology in… 

    …to update_top
    @rmatsum836
    rmatsum836 committed Feb 18, 2020
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  8. Add unit parsing function for units and physical constants

    @uppittu11
    uppittu11 committed Feb 18, 2020
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  9. Add mol2 file for tip3p and misc. updates

    @rmatsum836
    rmatsum836 committed Feb 18, 2020
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  10. Remove debug tracer

    @rmatsum836
    rmatsum836 committed Feb 18, 2020
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  11. Make all unit readers (defaults and params) use the string parser

    @uppittu11
    uppittu11 committed Feb 18, 2020
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Commits on Feb 19, 2020

  1. Handle radian and degree units in sympy expressions

    @uppittu11
    uppittu11 committed Feb 19, 2020
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  2. Convert u.elementary_charge to a u.Unit object for test

    @uppittu11
    uppittu11 committed Feb 19, 2020
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  3. Modify test for unit with physical constant

    @uppittu11
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  4. my ethane is an ehylene in disguise

    @daico007
    daico007 committed Feb 19, 2020
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  5. Merge branch 'master' of https://github.com/mattwthompson/topology in… 

    …to sample_ethane_xml
    @daico007
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  6. WIP: Adding temporary tests

    @rsdefever
    rsdefever committed Feb 19, 2020
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  7. Merge pull request #244 from justinGilmer/lammps_units 

    Correct energy unit conversion for epsilon
    @mattwthompson
    mattwthompson committed Feb 19, 2020
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  8. Fix issues with pytest

    @rsdefever
    rsdefever committed Feb 19, 2020
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  9. Add note about phi=0 convention to docstring

    @rsdefever
    rsdefever committed Feb 19, 2020
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  10. Change test FF energy units 

    K/Kb to K*kb
    @uppittu11
    uppittu11 committed Feb 19, 2020
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  11. add test for ethylene xml

    @daico007
    daico007 committed Feb 19, 2020
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  12. Update the units in assertion to match FF. 

    See mosdef-hub/gmso@9a1a077
    @uppittu11
    uppittu11 committed Feb 19, 2020
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Commits on Feb 20, 2020

  1. Create XML for Mie noble gases

    @rsdefever
    rsdefever committed Feb 20, 2020
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  2. Clean up and add 0.5 in k0 OPLS for consistency

    @rsdefever
    rsdefever committed Feb 20, 2020
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  3. Merge pull request #260 from uppittu11/unyt_parsing 

    Add XML unit parsing function for units and physical constants
    @uppittu11
    uppittu11 committed Feb 20, 2020
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  4. Accept and return DihedralType

    @rsdefever
    rsdefever committed Feb 20, 2020
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  5. Update unit tests to use sympy subs. Add test to convert 1->2->1

    @rsdefever
    rsdefever committed Feb 20, 2020
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  6. Remove temporary test code

    @rsdefever
    rsdefever committed Feb 20, 2020
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  7. change filename from ethylene_snippet.xml to ethylene.xml"

    @daico007
    daico007 committed Feb 20, 2020
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Commits on Feb 21, 2020

  1. Merge branch 'master' of https://github.com/mattwthompson/topology in… 

    …to box_from_mbuild
    @daico007
    daico007 committed Feb 21, 2020
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  2. Merge pull request #219 from daico007/box_from_mbuild 

    convert BoxArray into np array before passing to topology
    @daico007
    daico007 committed Feb 21, 2020
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  3. Merge branch 'master' of https://github.com/mattwthompson/topology in… 

    …to element.__repr__
    @daico007
    daico007 committed Feb 21, 2020
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  4. change xml filename in test files"

    @daico007
    daico007 committed Feb 21, 2020
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  5. Merge pull request #259 from daico007/sample_ethane_xml 

    Add ethylene xml
    @daico007
    daico007 committed Feb 21, 2020
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  6. Merge pull request #220 from daico007/element.__repr__ 

    change element.__str__ to element.__repr__
    @daico007
    daico007 committed Feb 21, 2020
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  7. Style improvements

    @rsdefever
    rsdefever committed Feb 21, 2020
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  8. Merge branch 'master' into add-mie-xml. 

    Fix conflict in test_reference_xmls.py
    @rsdefever
    rsdefever committed Feb 21, 2020
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  9. Move noble_mie.xml to test dir

    @rsdefever
    rsdefever committed Feb 21, 2020
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  10. Fix typo in noble_mie.xml

    @rsdefever
    rsdefever committed Feb 21, 2020
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  11. Fix parameter values in Mie XML test

    @rsdefever
    rsdefever committed Feb 21, 2020
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  12. Merge remote-tracking branch 'parashara/iss239_p1' into argon-example

    @mattwthompson
    mattwthompson committed Feb 21, 2020
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  13. Add comparison of Mie potential expression

    @rsdefever
    rsdefever committed Feb 21, 2020
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  14. Add argon example

    @mattwthompson
    mattwthompson committed Feb 21, 2020
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Commits on Feb 24, 2020

  1. Merge pull request #263 from rsdefever/add-mie-xml 

    Create XML for Mie noble gases
    @mattwthompson
    mattwthompson committed Feb 24, 2020
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  2. Merge pull request #242 from rsdefever/rb-opls-conversions 

    Add OPLS and Ryckaert-Bellemans dihedral conversions
    @mattwthompson
    mattwthompson committed Feb 24, 2020
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  3. Merge pull request #258 from uppittu11/iss239_p1 

    Better treatment of mBuild hierarchy conversion
    @rmatsum836
    rmatsum836 committed Feb 24, 2020
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  4. Merge branch 'master' of https://github.com/mattwthompson/topology in… 

    …to update_top
    @rmatsum836
    rmatsum836 committed Feb 24, 2020
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  5. Add potential templates for checking compatibility

    @rmatsum836
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  6. Add angle template for compatibility check

    @rmatsum836
    rmatsum836 committed Feb 24, 2020
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  7. Add todo about writing out molecules

    @rmatsum836
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  8. Merge branch 'master' into argon-example

    @mattwthompson
    mattwthompson committed Feb 24, 2020
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  9. A minimal sphinx configuration complete

    @umesh-timalsina
    umesh-timalsina committed Feb 24, 2020
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  10. Revert subtop structure after #258

    @mattwthompson
    mattwthompson committed Feb 24, 2020
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  11. Revert to README.md in root repo

    @umesh-timalsina
    umesh-timalsina committed Feb 24, 2020
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  12. Merge remote-tracking branch 'rmatsum836/update_top' into argon-example

    @mattwthompson
    mattwthompson committed Feb 24, 2020
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  13. Add argon example for lammps

    @rmatsum836
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  14. Add argon lammps data file

    @rmatsum836
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  15. Add test to read in argon top file

    @rmatsum836
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  16. Add input file for argon

    @rmatsum836
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  17. Minor update to notebook

    @rmatsum836
    rmatsum836 committed Feb 24, 2020
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  18. Update lammps input file and fix bug in lammps writer

    @rmatsum836
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  19. Change system to a liquid density with reasonable force field parameters 

    From 10.1021/acs.jctc.5b00784
    @mattwthompson
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  20. Merge pull request #273 from umesh-timalsina/256-sphinx-conf 

    A minimal sphinx configuration(closes #268)
    @mattwthompson
    mattwthompson committed Feb 24, 2020
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  21. Test TOP writer against parmed and move some functions around

    @mattwthompson
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  22. Make changes to notebook and input file

    @rmatsum836
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  23. Remove data file

    @rmatsum836
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Commits on Feb 25, 2020

  1. Add initial xml with opls charmm and water params

    @rmatsum836
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  2. Add angles and bonds for water

    @rmatsum836
    rmatsum836 committed Feb 25, 2020
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  3. Add some doc pages

    @mattwthompson
    mattwthompson committed Feb 25, 2020
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  4. Merge pull request #280 from mattwthompson/docs 

    Add some more documentation pages
    @umesh-timalsina
    umesh-timalsina committed Feb 25, 2020
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  5. Merge pull request #252 from rmatsum836/update_top 

    Update GROMACS TOP writer
    @mattwthompson
    mattwthompson committed Feb 25, 2020
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  6. Merge pull request #266 from mattwthompson/argon-example 

    Add argon example
    @mattwthompson
    mattwthompson committed Feb 25, 2020
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  7. Merge branch 'master' into add_lammps_argon

    @mattwthompson
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  8. Rename executable and clear output

    @rmatsum836
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  9. Merge branch 'master' of https://github.com/mattwthompson/topology in… 

    …to add_lammps_argon
    @rmatsum836
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  10. Update minor issues with docstrings 

    There were some inconsistent spacings and a small typo present in the
current documentation. This PR fixes these.
    @justinGilmer
    justinGilmer committed Feb 25, 2020
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  11. Rename gromacs example

    @rmatsum836
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  12. Remove old gromacs example

    @rmatsum836
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  13. fix one additional spacing issue

    @justinGilmer
    justinGilmer committed Feb 25, 2020
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  14. Move ForceField class into core submodule

    @mattwthompson
    mattwthompson committed Feb 25, 2020
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  15. follow numpydocs styleguide

    @justinGilmer
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  16. Merge pull request #281 from justinGilmer/doc_edits 

    Doc edits
    @mattwthompson
    mattwthompson committed Feb 25, 2020
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  17. Add initial Site docstring

    @rmatsum836
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  18. Add initial docstrings

    @rmatsum836
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Commits on Feb 26, 2020

  1. remove topology-charmm.xml and include the trimmed atomtypes and dihe… 

    …draltypes tested in trimmed_charmm.xml
    @umesh-timalsina
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  2. Fix errors in xml

    @rmatsum836
    rmatsum836 committed Feb 26, 2020
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  3. Change name of package from topology to gmso

    @mattwthompson
    mattwthompson committed Feb 26, 2020
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  4. Update reference to schema filename

    @mattwthompson
    mattwthompson committed Feb 26, 2020
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  5. Add docstring for Connection and its subclasses

    @daico007
    daico007 committed Feb 26, 2020
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  6. add docstring for element.py

    @daico007
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  7. Fix typo

    @mattwthompson
    mattwthompson committed Feb 26, 2020
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  8. Rename types to be more verbose and add wildcard

    @rmatsum836
    rmatsum836 committed Feb 26, 2020
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  9. fix sentences

    @daico007
    daico007 committed Feb 26, 2020
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  10. add sanity checks for connection_members, edit docs

    @daico007
    daico007 committed Feb 26, 2020
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  11. add docs for from_parmed and xyz.py

    @daico007
    daico007 committed Feb 26, 2020
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  12. Remove a stray file

    @mattwthompson
    mattwthompson committed Feb 26, 2020
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  13. fix sentences

    @daico007
    daico007 committed Feb 26, 2020
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  14. Typo

    @daico007
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  15. Merge pull request #287 from mattwthompson/rename-to-gmso 

    Change name of package from Topology to GMSO
    @mattwthompson
    mattwthompson committed Feb 26, 2020
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  16. Merge branch 'master' of https://github.com/mattwthompson/topology in… 

    …to element_docstring
    @daico007
    daico007 committed Feb 26, 2020
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  17. Fix name change conflicts

    @daico007
    daico007 committed Feb 26, 2020
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  18. Add properly formatted docstrings for Box 

    Currently, the docstrings for the `Box` class located in `core/box.py`
are lacking.

This pr better defines the important methods, as well as more fully
flushed out docstrings for the class itself.
    @justinGilmer
    justinGilmer committed Feb 26, 2020
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  19. Add docstrings for Potential and subclasses

    @mattwthompson
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  20. incorporate suggested revisions

    @justinGilmer
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  21. Add back function that was accidentally dropped

    @mattwthompson
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  22. Update .gitignore with simulation files

    @mattwthompson
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  23. Merge pull request #288 from daico007/connection_docs 

    Add docstring for Connection and its subclasses
    @mattwthompson
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  24. Merge pull request #289 from daico007/element_docstring 

    Add docstring for element.py, xyz.py, and convert_parmed.py
    @mattwthompson
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  25. Merge branch master with changed package name

    @umesh-timalsina
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  26. Remove checkout xml from the merge

    @umesh-timalsina
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  27. Merge pull request #290 from justinGilmer/box_docstrings 

    Add properly formatted docstrings for `Box`
    @mattwthompson
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  28. Address matt's comments

    @rmatsum836
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  29. Add Docstring for forcefield class and move forcefield inside datastr… 

    …uctures
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  30. Merge branch 'master' into move-ff

    @mattwthompson
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  31. Add schema back

    @mattwthompson
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  32. Provide docstrings for the gro file reader/writer 

    Previously, the documentation for both the gro file reader and writer
were lacking.

Both the reader and writer are now documented and additional notes have
been included to document the current limitations of each reader and
writer. These can be removed as the updates are implemented.
    @justinGilmer
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  33. Add/Update docstrings for from_mbuild, to_mbuild, and from_mbuild_box

    @uppittu11
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Commits on Feb 27, 2020

  1. Fix some typos and add clarify error messages

    @uppittu11
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  2. Provide addtional information in gsd writer docs 

    While the docstrings for `write_gsd` were quite detailed already,
additional information and warnings have also been added to the
necessary functions.
    @justinGilmer
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  3. Address changes from code review 

    mosdef-hub/gmso#294 (review)
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  4. Merge remote-tracking branch 'upstream/master' into add_group_xml

    @umesh-timalsina
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  5. Add the deleted XML file from the PR

    @umesh-timalsina
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  6. Add atom_class test for opls_charmm_buck.xml by checking out files fr… 

    …om #276, modify atom_class parsing in forcefield.py
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  7. Add Missing XML file (tests should pass)

    @umesh-timalsina
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  8. Remove path topology from the repo by deleting the cached file [skip-ci]

    @umesh-timalsina
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  9. Merge pull request #279 from rmatsum836/add_group_xml 

    Add group xml file
    @umesh-timalsina
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  10. Merge branch 'master' into 256-trim-charmm-xml

    @mattwthompson
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  11. Change regex match logic when consolidating periodic parameters(Close… 

    …s #275) (#276)

* use expression's free symbols to consolidate params when reading in XML file

* Add Periodic dihedral test lines

* Remove ignoreCase in regex match, checkout opls_charmm_buck.xml from #279
    @umesh-timalsina
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  12. Fix newline at end of docstrings

    @mattwthompson
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  13. Delete file from #276

    @umesh-timalsina
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  14. Merge pull request #296 from umesh-timalsina/delete-vestiges-from-squ… 

    …ash-merge

Delete file from #276
    @mattwthompson
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  15. Copy mBuild's CONTRIBUTING.md to contributing.rst

    @umesh-timalsina
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  16. Modify links to black, capitalize GMSO [skip-ci]

    @umesh-timalsina
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  17. Merge pull request #297 from umesh-timalsina/293-add-contributing 

    Add contributing.rst
    @mattwthompson
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  18. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
    @rmatsum836 @justinGilmer
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  19. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  20. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  21. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  22. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  23. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  24. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  25. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  26. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  27. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  28. Update topology/formats/lammpsdata.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
    @rmatsum836 @justinGilmer
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  29. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  30. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  31. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  32. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  33. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  34. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  35. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  36. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  37. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  38. Update topology/external/convert_openmm.py 

    Co-Authored-By: Justin Gilmer <justin.b.gilmer@gmail.com>
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  39. Update docstrings

    @mattwthompson
    mattwthompson committed Feb 27, 2020
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  40. Wrap docstring lines to <80 characters

    @uppittu11
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  41. Merge pull request #294 from uppittu11/mbuild_docs 

    Docathon: convert_mbuild docs
    @mattwthompson
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  42. Merge pull request #291 from mattwthompson/docs-1 

    Improve docstrings for Potential and subclasses
    @mattwthompson
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  43. Merge branch '256-trim-charmm-xml' of https://github.com/umesh-timals… 

    …ina/topology into 256-trim-charmm-xml
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  44. Fix grabbing XML paths

    @mattwthompson
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  45. Merge branch 'master' into ray_documentation

    @mattwthompson
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  46. Merge pull request #286 from umesh-timalsina/256-trim-charmm-xml 

    Trim topology-charmm.xml file used in tests
    @mattwthompson
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  47. Format to 80 column length

    @justinGilmer
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  48. Merge pull request #285 from rmatsum836/ray_documentation 

    Add site, openmm, and lammps documentation
    @mattwthompson
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  49. Merge pull request #295 from justinGilmer/formats_docstrings_gro_gsd 

    Formats docstrings for gro  and gsd io
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  50. Merge branch 'master' into move-ff

    @mattwthompson
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  51. Merge branch 'master' into add_lammps_argon

    @mattwthompson
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  52. Merge branch 'add_lammps_argon' of https://github.com/rmatsum836/topo… 

    …logy into add_lammps_argon
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  53. Update to gmso

    @mattwthompson
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  54. Merge pull request #274 from rmatsum836/add_lammps_argon 

    Add argon example for lammps
    @mattwthompson
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  55. Update __init__ for the formats module

    @daico007
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  56. update __init__ for the external module

    @daico007
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  57. add SubTopology to __init__

    @daico007
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  58. typo

    @daico007
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  59. Merge pull request #301 from daico007/update_formats_init 

    Update __init__ for the formats and external module
    @mattwthompson
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  60. Complete Barebone Formats and External documentation

    @umesh-timalsina
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  61. Merge remote-tracking branch 'upstream/master' into 284-docstrings

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  62. Add Incomplete documentation for topology

    @umesh-timalsina
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Commits on Feb 28, 2020

  1. Handle docstring specific changes to conf.py topology.py forcefield.py

    @umesh-timalsina
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  2. Complete documentation for topology, subtopology and forcefield along… 

    … with minor config changes
    @umesh-timalsina
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  3. Add Forgotten subtopology.py

    @umesh-timalsina
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  4. Incorporate PR change requests 

    1. Change subpackage word to submodule
2. Capitalize LAMMPS
3. Remove Empty Lines (Leaving the last blank line)
    @umesh-timalsina
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  5. Merge pull request #282 from mattwthompson/move-ff 

    Move ForceField class into core submodule
    @mattwthompson
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  6. Merge pull request #302 from umesh-timalsina/298-format-external-docs 

    Formats and External documentation (Closes #298)
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  7. Merge upstream/master and incorporate PR change suggestions

    @umesh-timalsina
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  8. Add into bit to landing page

    @mattwthompson
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  9. Merge pull request #305 from mattwthompson/docs-2 

    Add intro to landing page
    @mattwthompson
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  10. Add Spacing between colon and variable types

    @umesh-timalsina
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  11. Merge pull request #299 from umesh-timalsina/284-docstrings 

    Docathon Assignments
    @justinGilmer
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Commits on Mar 2, 2020

  1. Hotfix to get the top writer working. 

    This will work as per ParmEd's combine=all style top file
    @uppittu11
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  2. Dummy commit

    @mattwthompson
    mattwthompson committed Mar 2, 2020
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Commits on Mar 3, 2020

  1. Add codecov command to AZP config

    @mattwthompson
    mattwthompson committed Mar 3, 2020
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  2. Add codecov to testing framework

    @mattwthompson
    mattwthompson committed Mar 3, 2020
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  3. Run coverage during tests

    @mattwthompson
    mattwthompson committed Mar 3, 2020
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  4. Change arg

    @mattwthompson
    mattwthompson committed Mar 3, 2020
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  5. Build testing matrix

    @mattwthompson
    mattwthompson committed Mar 3, 2020
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  6. Try Python 3.8

    @mattwthompson
    mattwthompson committed Mar 3, 2020
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  7. Update url for pull requests, cloning url, and directory name for ins… 

    …tallation of gmso to reflect change from 'topology' to 'gmso'
    @rwsmith7531
    rwsmith7531 committed Mar 3, 2020
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  8. Merge pull request #316 from mattwthompson/foo-bar 

    Update status checks
    @mattwthompson
    mattwthompson committed Mar 3, 2020
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  9. Merge branch 'master' of https://github.com/mosdef-hub/gmso into top_… 

    …writer
    @uppittu11
    uppittu11 committed Mar 3, 2020
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  10. Merge branch 'master' into docs_topology_to_gmso_namechange

    @mattwthompson
    mattwthompson committed Mar 3, 2020
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  11. Merge pull request #322 from rwsmith7531/docs_topology_to_gmso_namech… 

    …ange

Update URL in README
    @mattwthompson
    mattwthompson committed Mar 3, 2020
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  12. Remove Foyer for top.py

    @umesh-timalsina
    umesh-timalsina committed Mar 3, 2020
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  13. Remove foyer from top.py (Closes #325)(#327)

    @umesh-timalsina
    umesh-timalsina committed Mar 3, 2020
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  14. rtd-initial commit

    @umesh-timalsina
    umesh-timalsina committed Mar 3, 2020
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  15. Add unyts to requirements

    @umesh-timalsina
    umesh-timalsina committed Mar 3, 2020
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  16. Add pytest(reluctantly) to docs requirements

    @umesh-timalsina
    umesh-timalsina committed Mar 3, 2020
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  17. Remove pytest from requirements.txt and add it to docs/requirements.txt

    @umesh-timalsina
    umesh-timalsina committed Mar 3, 2020
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  18. Update setup.py to include requirements, fix urls.

    @bdice
    bdice committed Mar 3, 2020
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  19. Add typed water system as fixture and in parmed loop

    @mattwthompson
    mattwthompson committed Mar 3, 2020
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  20. Update packages for conda-forge compatibility.

    @bdice
    bdice committed Mar 3, 2020
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Commits on Mar 4, 2020

  1. Update setup.py 

    Co-Authored-By: Matt Thompson <matt.thompson@vanderbilt.edu>
    @bdice @mattwthompson
    bdice and mattwthompson committed Mar 4, 2020
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  2. Store bond.bond_type in bond.connection_type

    @mattwthompson
    mattwthompson committed Mar 4, 2020
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  3. Merge pull request #306 from uppittu11/top_writer 

    Update GROMACS Topology writer to use correct moleculename
    @mattwthompson
    mattwthompson committed Mar 4, 2020
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Commits on Mar 5, 2020

  1. Properly iterate over fixtures in parmed round-trip

    @mattwthompson
    mattwthompson committed Mar 5, 2020
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  2. Start adding bonds and angles

    @rmatsum836
    rmatsum836 committed Mar 5, 2020
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Commits on Mar 6, 2020

  1. Add improper and impropertype

    @rsdefever
    rsdefever committed Mar 6, 2020
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  2. Add edits to topology object

    @rsdefever
    rsdefever committed Mar 6, 2020
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  3. Cleanup typos in docstrings

    @rsdefever
    rsdefever committed Mar 6, 2020
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  4. Write out all bonds and angles

    @rmatsum836
    rmatsum836 committed Mar 6, 2020
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  5. Rearrange and reformat variables

    @rmatsum836
    rmatsum836 committed Mar 6, 2020
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  6. Add water test to check bonds and angles

    @rmatsum836
    rmatsum836 committed Mar 6, 2020
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  7. Fix bug related to writing out angles

    @rmatsum836
    rmatsum836 committed Mar 6, 2020
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Commits on Mar 9, 2020

  1. Add descriptions of dihedral and improper connectivity

    @rsdefever
    rsdefever committed Mar 9, 2020
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  2. Merge pull request #330 from mattwthompson/top_writer 

    Add more tests for GROMACS topology writer
    @mattwthompson
    mattwthompson committed Mar 9, 2020
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  3. Write out dihedrals

    @rmatsum836
    rmatsum836 committed Mar 9, 2020
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  4. Get atom indices by indexed set

    @rmatsum836
    rmatsum836 committed Mar 9, 2020
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  5. Use indexed_set to write out site indices

    @rmatsum836
    rmatsum836 committed Mar 9, 2020
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  6. Remove parameter lists and dictionaries

    @rmatsum836
    rmatsum836 committed Mar 9, 2020
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  7. Remove natural_sort

    @rmatsum836
    rmatsum836 committed Mar 9, 2020
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  8. Merge pull request #343 from rmatsum836/update_top_indices 

    Get site indices by indexed set
    @justinGilmer
    justinGilmer committed Mar 9, 2020
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  9. Check if topology is typed through is_typed

    @rmatsum836
    rmatsum836 committed Mar 9, 2020
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  10. Merge pull request #328 from mosdef-hub/319-rtd-build 

    Read the docs build for gmso (Closes #319)
    @justinGilmer
    justinGilmer committed Mar 9, 2020
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Commits on Mar 10, 2020

  1. Make changes based on Matt's comments

    @rmatsum836
    rmatsum836 committed Mar 10, 2020
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  2. Move mass code and fix bonds and angles

    @rmatsum836
    rmatsum836 committed Mar 10, 2020
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  3. Add conversion from rb to opls dihedrals

    @rmatsum836
    rmatsum836 committed Mar 10, 2020
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Commits on Mar 11, 2020

  1. Add Improper and ImproperType to init

    @rsdefever
    rsdefever committed Mar 11, 2020
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  2. Write out parameters only if they exist

    @rmatsum836
    rmatsum836 committed Mar 11, 2020
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  3. Add number of bonds, angles, and dihedrals

    @rmatsum836
    rmatsum836 committed Mar 11, 2020
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Commits on Mar 12, 2020

  1. Merge pull request #329 from bdice/fix/setup 

    Update setup.py to fix packages, requirements, urls
    @mattwthompson
    mattwthompson committed Mar 12, 2020
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  2. Merge branch 'master' of https://github.com/mosdef-hub/gmso into lamm… 

    …ps_bonds_angles
    @rmatsum836
    rmatsum836 committed Mar 12, 2020
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  3. Use typed_water_system in lammps test

    @rmatsum836
    rmatsum836 committed Mar 12, 2020
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  4. Correct formatting, grammar, typos, and a command in installation doc. 

    Previously, the command provided for the pip installation of the
dependencies from requirements.txt used --file, which is an option in
conda but not in pip, which uses -r instead, so --file was replaced with
-r.
    @rwsmith7531
    rwsmith7531 committed Mar 12, 2020
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  5. Merge pull request #338 from rsdefever/add/impropers 

    Add improper and impropertype
    @mattwthompson
    mattwthompson committed Mar 12, 2020
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  6. Merge pull request #353 from rwsmith7531/install_doc_fix 

    Fix some issues in installation docs
    @mattwthompson
    mattwthompson committed Mar 12, 2020
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  7. Write out angle k in radians

    @rmatsum836
    rmatsum836 committed Mar 12, 2020
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  8. Merge pull request #339 from rmatsum836/lammps_bonds_angles 

    Write out bonds, angles, and dihedrals to LAMMPS data file
    @mattwthompson
    mattwthompson committed Mar 12, 2020
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Commits on Mar 16, 2020

  1. Merge master into ahy3nz:lt_site

    @uppittu11
    uppittu11 committed Mar 16, 2020
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