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Packing fixes #385

Merged
merged 27 commits into from
Nov 13, 2017
Merged

Packing fixes #385

merged 27 commits into from
Nov 13, 2017

Commits on Sep 7, 2017

  1. Add edge buffer in packing functions

    @mattwthompson
    mattwthompson committed Sep 7, 2017
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  2. Support aspect ratio for generated boxes

    @mattwthompson
    mattwthompson committed Sep 7, 2017
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  3. Start working with compound_ratio

    @mattwthompson
    mattwthompson committed Sep 7, 2017
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  4. Support compound_ratio and add test

    @mattwthompson
    mattwthompson committed Sep 7, 2017
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  5. Cleanup

    @mattwthompson
    mattwthompson committed Sep 7, 2017
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Commits on Sep 9, 2017

  1. Actually build n_compounds and test it

    @mattwthompson
    mattwthompson committed Sep 9, 2017
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Commits on Sep 10, 2017

  1. Ensure n_compounds contains ints if list

    @mattwthompson
    mattwthompson committed Sep 10, 2017
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Commits on Sep 21, 2017

  1. Add docstrings for packing functions

    @mattwthompson
    mattwthompson committed Sep 21, 2017
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  2. Merge branch 'pack-fixes' of https://github.com/mattwthompson/mbuild … 

    …into pack-fixes
    @mattwthompson
    mattwthompson committed Sep 21, 2017
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Commits on Oct 14, 2017

  1. Test for bad combinations of input parameters

    @mattwthompson
    mattwthompson committed Oct 14, 2017
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  2. Raise an error if compound and n_compounds are of different len

    @mattwthompson
    mattwthompson committed Oct 14, 2017
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Commits on Oct 19, 2017

  1. Add optional flag for writing packmol output

    @mattwthompson
    mattwthompson committed Oct 19, 2017
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  2. Copy packmol PDB directly; don't write from mbuild compound

    @mattwthompson
    mattwthompson committed Oct 19, 2017
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  3. First attempt at handling packmol errors

    @mattwthompson
    mattwthompson committed Oct 19, 2017
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  4. Merge branch 'pack-fixes-2' of https://github.com/mattwthompson/mbuild … 

    …into pack-fixes-2
    @mattwthompson
    mattwthompson committed Oct 19, 2017
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  5. Merge branch 'pack-tempfile' into pack-fixes-2

    @mattwthompson
    mattwthompson committed Oct 19, 2017
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Commits on Oct 20, 2017

  1. Reorder arguments to match previous versions

    @mattwthompson
    mattwthompson committed Oct 20, 2017
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  2. Force ruby 2.3 for homebrew (mosdef-hub#392)

    @mattwthompson
    mattwthompson committed Oct 20, 2017
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  3. Test packmol error and warning

    @mattwthompson
    mattwthompson committed Oct 20, 2017
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Commits on Nov 9, 2017

  1. Merge branch 'master' into pack-fixes

    @mattwthompson
    mattwthompson committed Nov 9, 2017
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Commits on Nov 11, 2017

  1. Small requested fixes

    @mattwthompson
    mattwthompson committed Nov 11, 2017
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  2. Add _run_packmol helper function and rework tempfile

    @mattwthompson
    mattwthompson committed Nov 11, 2017
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  3. Add new arguments to some docstrings

    @mattwthompson
    mattwthompson committed Nov 11, 2017
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  4. Add _check_packmol helper function

    @mattwthompson
    mattwthompson committed Nov 11, 2017
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  5. Test temp_file behavior in each packing function

    @mattwthompson
    mattwthompson committed Nov 11, 2017
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  6. Cleanup some docstrings

    @mattwthompson
    mattwthompson committed Nov 11, 2017
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  7. Cleanup in fill_region: applying edge buffer & docstrings

    @mattwthompson
    mattwthompson committed Nov 11, 2017
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