mosdef-hub / mbuild

A hierarchical, component based molecule builder
https://mbuild.mosdef.org
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Add more notes about unit conversions to the hoomd functions #1062

Closed chrisjonesBSU closed 1 year ago

chrisjonesBSU commented 1 year ago

PR Summary:

This PR addresses #1057. It provides further explanation about the behind-the-scenes conversion of units, and an example of how to use the reference value parameters to convert to another unit system (mosdef units in this case).

Let me know if anything looks incorrect, or isn't clear.

PR Checklist


codecov[bot] commented 1 year ago

Codecov Report

Base: 90.49% // Head: 78.21% // Decreases project coverage by -12.28% :warning:

Coverage data is based on head (c12c9f2) compared to base (4df37e7). Patch has no changes to coverable lines.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #1062 +/- ## =========================================== - Coverage 90.49% 78.21% -12.29% =========================================== Files 61 57 -4 Lines 6157 5513 -644 =========================================== - Hits 5572 4312 -1260 - Misses 585 1201 +616 ``` | [Impacted Files](https://codecov.io/gh/mosdef-hub/mbuild/pull/1062?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=mosdef-hub) | Coverage Δ | | |---|---|---| | [mbuild/formats/hoomd\_forcefield.py](https://codecov.io/gh/mosdef-hub/mbuild/pull/1062/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=mosdef-hub#diff-bWJ1aWxkL2Zvcm1hdHMvaG9vbWRfZm9yY2VmaWVsZC5weQ==) | `0.00% <ø> (-78.46%)` | :arrow_down: | | [mbuild/formats/hoomd\_snapshot.py](https://codecov.io/gh/mosdef-hub/mbuild/pull/1062/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=mosdef-hub#diff-bWJ1aWxkL2Zvcm1hdHMvaG9vbWRfc25hcHNob3QucHk=) | `0.00% <ø> (-79.02%)` | :arrow_down: | | [mbuild/formats/hoomd\_simulation.py](https://codecov.io/gh/mosdef-hub/mbuild/pull/1062/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=mosdef-hub#diff-bWJ1aWxkL2Zvcm1hdHMvaG9vbWRfc2ltdWxhdGlvbi5weQ==) | `0.00% <0.00%> (-78.72%)` | :arrow_down: | | [mbuild/compound.py](https://codecov.io/gh/mosdef-hub/mbuild/pull/1062/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=mosdef-hub#diff-bWJ1aWxkL2NvbXBvdW5kLnB5) | `83.00% <0.00%> (-13.86%)` | :arrow_down: | | [mbuild/utils/decorators.py](https://codecov.io/gh/mosdef-hub/mbuild/pull/1062/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=mosdef-hub#diff-bWJ1aWxkL3V0aWxzL2RlY29yYXRvcnMucHk=) | `88.88% <0.00%> (-11.12%)` | :arrow_down: | | [mbuild/utils/io.py](https://codecov.io/gh/mosdef-hub/mbuild/pull/1062/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=mosdef-hub#diff-bWJ1aWxkL3V0aWxzL2lvLnB5) | `80.17% <0.00%> (-3.45%)` | :arrow_down: | | [mbuild/conversion.py](https://codecov.io/gh/mosdef-hub/mbuild/pull/1062/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=mosdef-hub#diff-bWJ1aWxkL2NvbnZlcnNpb24ucHk=) | | | | [mbuild/\_\_init\_\_.py](https://codecov.io/gh/mosdef-hub/mbuild/pull/1062/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=mosdef-hub#diff-bWJ1aWxkL19faW5pdF9fLnB5) | | | | ... and [2 more](https://codecov.io/gh/mosdef-hub/mbuild/pull/1062/diff?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=mosdef-hub) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=mosdef-hub). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=mosdef-hub)

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