Change Reaction Methods interface #4305
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
Change the name of the variable temperature to kT, for consistency with the rest of the code and its physical meaning.
All product and reactant coefficients must equal one in the constant pH method.
jngrad
force-pushed
the
refactoring_reaction_ensamble_2
branch
from
4c28b51
to
996e529
Compare
jngrad
changed the title
jngrad
approved these changes
Jul 20, 2021
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fixes minor issues in #4251
Description of changes:
ReactionAlgorithm::generic_oneway_reaction(): changed the name of the accumulators toaccumulator_potential_energy_difference_exponentialfor claritytemperaturehas been replaced bykT. The related tests have been modified accordingly.reactant_coefficientsandproduct_coefficientsare now optional parameters for the constant pH ensemble, with default values of[1]resp.[1, 1]. If the user provides these parameters he gets either (i) an error message if values other than the default ones are supplied or (ii) a one-time warning stating that these arguments are only kept as input for backward compatibility and are deprecated.