search

cdsgroup / resp

A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4
BSD 3-Clause "New" or "Revised" License
27 stars 8 forks source link

update multi-conformation fit and stage-two atoms #14

Closed alenaizan closed 5 years ago

alenaizan commented 5 years ago

Addresses this issue: https://github.com/cdsgroup/resp/issues/12 Also, I update the multi-conformation fit. Instead of creating a block diagonal A matrix, now we add the A matrices for each conformer and add the B vectors for each element. This turned out to be mathematically equivalent but simpler to implement. Now the user does not need to specify inter-molecular constraints or specify options for each conformer. This makes specifying the options easier. This is also the way Chris Bayly implemented it.

For the second-stage atoms, now we refit any sp3 carbon that has one or more hydrogen.

codecov-io commented 5 years ago

Codecov Report

Merging #14 into master will increase coverage by 2.66%. The diff coverage is 94.04%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #14      +/-   ##
==========================================
+ Coverage   86.35%   89.01%   +2.66%     
==========================================
  Files           6        6              
  Lines         601      428     -173     
==========================================
- Hits          519      381     -138     
+ Misses         82       47      -35
Impacted Files Coverage Δ
resp/tests/test_resp.py 100% <100%> (ø) :arrow_up:
resp/stage2_helper.py 86.84% <82.35%> (+3.79%) :arrow_up:
resp/espfit.py 85% <88.23%> (+2.34%) :arrow_up:
resp/driver.py 85.98% <96.66%> (+2.1%) :arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 6f58025...41c58f4. Read the comment docs.