Fluctuated leading term water force field #31
Merged
Conversation
This file contains hidden or 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
…d xml (input:pdb,xml output: multipoles/polarizabilities/tholes...) use forcefield.xml instead of other xmls, add read_admp_xml in parser in order to read the new form of xml file change line 795 in pme.py and add distribute_matrix in pairwise.py in order to wrap a jit outside my admp_calculator
KuangYu
requested changes
Jun 11, 2022
| c0="-1.0614" | ||
| dX="0.0" dY="0.0" dZ="-0.023671684" | ||
| qXX="0.000150963" qXY="0.0" qYY="0.00008707" qXZ="0.0" qYZ="0.0" qZZ="-0.000238034" | ||
| oXXX="0.0" oXXY="0.0" oXYY="0.0" oYYY="0.0" oXXZ="0.0000" oXYZ="0.0" oYYZ="0.00000" oXZZ="0.0" oYZZ="0.0" oZZZ="-0.0000" |
Collaborator
There was a problem hiding this comment.
Remove the octupole lines to avoid confusion, we do not support octupoles now
| c0="0.5307" | ||
| dX="0.0" dY="0.0" dZ="0.0" | ||
| qXX="0.0" qXY="0.0" qYY="0.0" qXZ="0.0" qYZ="0.0" qZZ="0.0" | ||
| oXXX="0.0" oXXY="0.0" oXYY="0.0" oYYY="0.0" oXXZ="0.0" oXYZ="0.0" oYYZ="0.0" oXZZ="0.0" oYZZ="0.0" oZZZ="0.0" |
| @@ -0,0 +1,485 @@ | |||
| Traced<ConcreteArray([-0.7778535 0.38892674 0.38892674 -0.7754795 0.38773975 0.38773975], dtype=float32)>with<JVPTrace(level=2/0)> with | |||
Collaborator
There was a problem hiding this comment.
Remove all the tmp file, keep it clean
| return c0, c6_list | ||
|
|
||
| #compute energy with fluctuated leading terms | ||
| def admp_calculator(positions, Q_local, axis_type, axis_indices, box, covalent_map, pol, tholes, c_list, q_list, a_list, b_list, pairs, rc): |
Collaborator
There was a problem hiding this comment.
Use standard api to obtain potential functions.
Member
|
@humourist Plz remove |
…d params into fluctuated one amf jit
KuangYu
approved these changes
Jun 14, 2022
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
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.
modifications:
1.add read_input_info function in dmff.admp.parse.py to deal with info in pdb and xml files (input:pdb,xml output: multipoles/polarizabilities/tholes... and other atomic parameters)
2.use forcefield.xml instead of other xmls, add read_admp_xml in parser in order to read the new form of xml file
3.change line 795 in pme.py and add distribute_matrix in pairwise.py in order to wrap a jit outside my admp_calculator