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openforcefield / open-forcefield-tools

Tools for open forcefield development
MIT License
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Initial API outline proposal #3

Closed jchodera closed 8 years ago

jchodera commented 8 years ago

This PR begins the process of documenting the API proposed in https://github.com/open-forcefield-group/open-forcefield-tools/issues/1

See the README.md for the proposed API.

mrshirts commented 8 years ago

Wanted to point out that if the experimental data is being carried along, there will necessarily be a mismatch between the experimental mole fractions and the simulation mole fractions, and there should be some way to tag that so it's clear there are two different things.

I guess if it keeps track of number explicitly and separately, we just have to make it clear (examples, code enforcement) that when looking at the computation that it is the number that matters in calculating properties, not the mole fraction that was entered.

davidlmobley commented 8 years ago

I guess if it keeps track of number explicitly and separately, we just have to make it clear (examples, code enforcement) that when looking at the computation that it is the number that matters in calculating properties, not the mole fraction that was entered.

The code will end up setting up a simulation with a specific number of molecules of each type in some specified volume, so when we know what information we want to report back about that (and how) it can be reported back by the computedProperty object which computeProperties would return (see https://github.com/open-forcefield-group/open-forcefield-tools/pull/3#issuecomment-224485302 above).

davidlmobley commented 8 years ago

I think this should be good to merge once @jchodera merges https://github.com/jchodera/open-forcefield-tools/issues/1 .