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Typing abstraction #9

Merged
merged 44 commits into from
Jun 9, 2020
Merged

Typing abstraction #9

merged 44 commits into from
Jun 9, 2020

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mattwthompson
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Description

Working on abstracting typing into a separate layer

Todos

Notable points that this PR has either accomplished or will accomplish.

  • Make interface more clear and instances more defined
  • Docs
  • Examples

Questions

  • Is defining a mapping between slots and potentials sufficient?
  • Suggestions for a simple typing engine I can use (just for testing purposes)?

Status

  • Ready to go

mattwthompson and others added 30 commits May 12, 2020 10:51
@mattwthompson
Add Potential class
8332c40
@mattwthompson
Update Potential class
f691154
@mattwthompson
Make barebones system class
b6bfc77
@mattwthompson
Merge branch 'master' into potential-1
414453e
@mattwthompson
Merge branch 'master' into potential-1
c88302a
@mattwthompson
Update conda env
f70fb5e
@mattwthompson
Update test structure
9cee3db
@mattwthompson
Make separate classes for parametrized and un-parametrized potentials
e9acbb6
@mattwthompson
Store expressions as strings
09554cd
@mattwthompson
Validate parameters with sympy and update tests
b875977
@mattwthompson
Let independent_variables be a string
9c8ae08
@mattwthompson
Copy evaluator simtk->pint function from evaluator
2531561
@mattwthompson
Merge branch 'potential-1' into system-1
c92003e
@mattwthompson
Add some templates for a class API
157b366
@mattwthompson
Merge remote-tracking branch 'origin/potential-1' into system-1
4cf3013
@mattwthompson
Add some basic classes
480e3d5
@mattwthompson
Add a prototype with example
e575f28
@mattwthompson
Merge branch 'master' into system-1
4b3fcee
@mattwthompson
More clearly distinguish between toolkit and system objects and add t…
30667ea 
…ests
@mattwthompson
Add toolkit dependency
1ed5b1e
@mattwthompson
Test constructing directly from toolkit objects
a12b9ff
@mattwthompson
Don't assume toolkit >0.7.0
69c9260
@mattwthompson
Directly use toolit atom
d45af88
@mattwthompson
Add SMIRKS attribute
cd7f2f2
@mattwthompson
Move System ForceField to PotentialCollection
78710aa
@mattwthompson
Merge branch 'master' into potential-1
b31fce0
@mattwthompson
Switch to directly using toolkit topology
4af5cda
@mattwthompson
Update gitignore
f38542d
@mattwthompson
Rebrand System.forcefield to System.potential_collection
9a9148d
@mattwthompson
Start typing module
1732ce4
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codecov-commenter commented Jun 4, 2020 •
edited
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Codecov Report

Merging #9 into master will increase coverage by 6.83%.
The diff coverage is 82.35%.

@mattwthompson mattwthompson merged commit 7d1563c into openforcefield:master Jun 9, 2020
@mattwthompson mattwthompson mentioned this pull request Jun 9, 2020
Merged
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