Anisotropic polarizabilities #34
Open
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
o With/without PME o With/without neighborlist o Finite difference tests pass o No OPTn implementation yet
|
I should also add that I have not been able to extensively test the implicit solvation code, so that will need some scrutiny. The performance of the two-body terms in the approximate preconditioner seems to have degraded, so perhaps the averaging of the polarizabilities in that term is not the best choice. |
…n eprecip and eprecip1
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Outdated suggestions cannot be applied.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.
This PR adds anisotropic polarizabilities that @JoshRackers and I worked on during his visit. Note that it also contains the fix described in #33, so that I could test the changes. I have not addressed OPT yet, because this is already quite a large patch. Once merged (or ignored if you don't want this feature) I can address OPT and fix the long-standing virial bug. The current implementation assumes that the permanent multipole axes also define the anisotropy orientations. Implicit to this is the fact that the permanent moment axes are chosen as the natural axes (i.e. those that diagonalize the polarizability tensor) because we only receive xx, yy and zz components from the user. Generalization to arbitrary tensors would be very trivial. The input mechanism currently looks like:
For example, the water oxygen (with fictitious parameters) would look something like: