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Reconciling Electrochem Branch with main
#2598
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Commits on Jun 14, 2024
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Added increment_charge and decrement_charge to Rx
and Rx!H atom types
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added updated charge method and revised
update
Molecule methodthe update method now updates lone pairs before updating charge
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try to generate_resonance_structures, and return a deep copy of the m…
…olecule if it fails
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however, we still need better thermo
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added reaction tests for charge transfer reactions
port the new reaction tests to the new testing file and style by Jackson Burns <jwburns@mit.edu> Date: Thu Feb 01 2024 10:47:18 GMT-0500 (Eastern Standard Time) Co-authored-by: davidfarinajr <farina.d@northeastern.edu> Co-authored-by: Jackson Burns <jwburns@mit.edu>
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filter out resonance structures that try to put - charges on Li
fix resonance bug (squash)
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add handling ArrheniusChargeTransfer and fix handling SurfaceChargeTr…
…ansfer for rms output
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Revert "Remove charge transfer types from average_kinetics (to be rev…
…erted)" This reverts commit 2180175. I also tweaked it a little bit.
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1) Enable fitting of ArrheniusChargeTransferBM 2) if the BM fit is bad: E0 < 0, A > 1e30 or abs(n) > 5 just average the kinetics
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standardize ascend option in cross validate
ascend based on original uncertainties and compute errors at that node in cross validate
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add comment to averaged kinetics
(Commit updated by rwest during rebase: In the original commit the comment used to specify /why/ it was averaged, but it is added in the averaging method itself. The /why/, if needed, should be added elsewhere.)
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consistenty use dH298 do not estimate e0 = w0/10 when |dHrxn| > 0.4w0
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only use kinetics that have arrhenius forms for tree generation
the TS solute data is used only for rule fitting after tree is generated fix tab error
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Fix ArrheniusBM.get_activation_energy unit test.
The E0 had been changed, but the expected Ea not updated.
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modifed arrbm
fit_to_data
unit testTest now compares the fitted rate to the rate it was trained on to make sure they agree.
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Refactor some rate fitting in rule generation.
It was:: if n > 1: # big long block else: return None I inverted the check so we can return early, and outdent a huge block of code.
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checks that the first group_atom.atomtype is either an appropriate charged atomtype or is a general version of an appropriate charged atomtype
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allow
cat
of regression diff to fail, print a warning insteadthis will allow the regression test results to all be reported even if there is such a huge difference between the dynamic and baseline that the system utilities cannot print it see: #2316 (comment)
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add a missing kwarg to fragment's overloaded update function
note that it is ignored however
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TEMPORARY: set database branch to lithium
remove this commit before merging
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Fixed atomtype charge checking
Now includes checks for negative charges temporary fix to an exponent overflow problem
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Fixed A-factor correction for SurfaceChargeTransfer
Added solvent correction for SurfaceChargeTransfer
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