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Reconciling Electrochem Branch with main #2598

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Commits on May 14, 2024

  1. Add reaction library to test example for liquidSurfaceReactor

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  2. added Faraday's Constant F

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  3. added Potential as V quantity

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  4. added H+ and e atomtypes, increment/decrement charge attributes

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  5. Added increment_charge and decrement_charge to Rx 

    and Rx!H atom types
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  6. H -> H0 in find_h_bonds Molecule method

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  7. added gain_charge and lose_charge actions

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  8. added is_proton and is_electron group methods

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  9. added group unit tests

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  10. added is_electron and is_proton methods to Atom and Mol

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  11. added GAIN and LOSE CHARGE actions to Atoms

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  12. added updated charge method and revised update Molecule method 

    the update method now updates lone pairs before updating charge
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  13. do not raise charge exception by default when creating molecule from … 

    …adj list
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  14. try to generate_resonance_structures, and return a deep copy of the m… 

    …olecule if it fails
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  15. added molecule.pxd declarations

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  16. added Species is_electron and is_proton methods

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  17. do not raise charge exception by default when creating species from a… 

    …dj list
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  18. added get_net_charge method for Species

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  19. do not forbid ions 

    however, we still need better thermo
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  20. added SurfaceChargeTransfer and SurfaceChargeTransferBEP kinetic … 

    …models
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  21. added Molecule unit tests

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  22. added electrons reaction attr and reaction methods for charge trans… 

    …fer reactions
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  23. 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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  24. adding charged species and electrons to family.py

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  25. added family test for Surface_Proton_Electron_Reduction_Alpha family

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  26. added support for loading SurfaceChargeTransfer kinetics from the d… 

    …atabase
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  27. update charge before updating lone pairs for solvation `transform_lon… 

    …e_pairs` method
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  28. making rules for SurfaceChargeTransfer training reactions

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  29. added SurfaceChargeTransfer kinetics import

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  30. added H+ and e to translator

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  31. update_atomtypes -> update in translator.py

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  32. added SurfaceChargeTransfer to yml

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  33. added adsorption_groups attr to thermoDB

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  34. added fluorine to thermo correct_binding_energy method

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  35. add LiH and LiF to atom energy corrections fitting species list

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  36. add Li atom spin

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  37. don't check Li partial charges in adjlists

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  38. add Li atomtype

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  39. add atom information for Li

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  40. add Li to R and R!H lists

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  41. add Li0 and Li+ atomtypes

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  42. add Li McGowan volume

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  43. add additional Li BDEs

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  44. add Li to bond dictionaries in thermo

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  45. handle Lithium electron calculations

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  46. add is_lithium for GroupAtom

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  47. handle SurfaceChargeTransfer in to_rms

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  48. filter out resonance structures that try to put - charges on Li 

    fix resonance bug (squash)
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  49. ensure atomtypes get updated on loading in thermo entries

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  50. add solute data to KineticsModel and Arrhenius

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  51. add ArrheniusChargeTransfer kinetics type

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  52. create ArrheniusChargeTransferBM type

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  53. add ChargeTransfer types to kinetics/__init__.py

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  54. avoid issue with auto decay reactions

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  55. handle ChargeTransfer kinetics with in reaction.py

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  56. add handling ArrheniusChargeTransfer and fix handling SurfaceChargeTr… 

    …ansfer for rms output
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  57. 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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  58. enable access to SoluteData object in kinetics database

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  59. update rule fitting 

    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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  60. enable use of non-surface charge transfer families

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  61. add charge transfer types to database context

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  62. enable surface and bulk potentials to be specified separately

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  63. Allow approximating a solvent not in the database with another solvent

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  64. standardize ascend option in cross validate 

    ascend based on original uncertainties and compute errors at that node in cross validate
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  65. Average kinetics when n=1 or E0<0

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  66. 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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  67. fix BM fitting 

    consistenty use dH298
do not estimate e0 = w0/10 when  |dHrxn| > 0.4w0
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  68. add functions for solvent correcting kinetics

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  69. add functionality for site specific solvent corrections

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  70. apply_solvent_correction in fix_barrier_height

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  71. enable solvent parameters to be directly specified in input file

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  72. adapt fix_barrier_height calls

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  73. handle ArrheniusChargeTransfer => Arrheniusq

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  74. add index of refraction to SolventData objects

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  75. fix KineticsModel outputs

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  76. add SoluteTSData object

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  77. add SoluteTSDIffData object

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  78. add function to convert SoluteData and SoluteTSDiffData to SoluteTSData

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  79. Enable database to understand new objects

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  80. Enable LibraryReaction to handle SoluteTSData

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  81. Enable TemplateReaction to handle new TS solvent corrections

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  82. 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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  83. enable solute data to be pulled from further up the tree as necessary

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  84. enable fitting of TS solute rules

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  85. allow training reaction notebook to handle reactions without gas phas… 

    …e kinetics
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  86. fix arrhenius test

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  87. Fix ArrheniusBM.get_activation_energy unit test. 

    The E0 had been changed, but the expected Ea not updated.
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  88. modifed arrbm fit_to_data unit test 

    Test now compares the fitted rate to the rate it was trained on to make sure they agree.
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  89. port arrheniusTest changes to pytest

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  90. add is_lithium to fragment

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  91. handle charge properly in fragment smiles hack

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  92. skip nodes that are empty when pulling solute data

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  93. update product template after generation

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  94. add Li adsorption to test data

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  95. add adsorptionLi.py to testing database

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  96. don't check collision limit for reactions without kinetics

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  97. fix charge handling in make sample molecule

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  98. 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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  99. Minor refactor.

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  100. Consistently use T=298. K for fitting and evaluating Blowers-Masel ra… 

    …tes.

Closes #1748
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  101. Fixes and tweaks to Blowers Masel classes' fit_to_reactions methods.

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  102. fix atomtype charge checking 

    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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  103. allow cat of regression diff to fail, print a warning instead 

    this 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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  104. combine the messy Cython declarations (and remove dupes) in reaction.py

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  105. include changes to corrTest - lost in rebase somehow

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  106. change from unittest assert style to pytest

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  107. port new test for kinetics families

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  108. skip a test in solvation 

    see this commit from matt (64bb21a) for why: 64bb21a
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  109. port surface test to new file and style

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  110. port atom type test to new style and file

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  111. change moleculeTest to pytest style

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  112. port groupTest to pytest

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  113. move database test files, port tests and update style

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  114. pytest.skip -> pytest.mark.skip

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  115. add a missing kwarg to fragment's overloaded update function 

    note that it is ignored however
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  116. remove deprecated check for nose test

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  117. bad automated conversion of assert equal

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  118. missed some unittest-style assert + copied some tests into wrong class

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  119. add missing kwarg to fragment update method

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  120. TEMPORARY: set database branch to lithium 

    remove this commit before merging
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  121. enable fitting of TS solute rules

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  122. set database branch to lithium

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  123. fix charge handling in make sample molecule

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  124. allow inclusion of refractive index in Solvent object

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  125. change TS solvation handling to new system

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  126. add Marcus kinetics

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  127. handle Marcus kinetics in the RMS reactors

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  128. fix bug with species initialization

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  129. allow direct specification of viscosity and electrode distance for th… 

    …e RMS reactor
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  130. properly handle electronchange when constructing RMS reaction objects

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  131. add epsilon_0 to constants

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  132. handle Marcus in RMS yaml constructionn

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  133. specify electronchange in RMS yaml construction

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  134. handle Marcus kinetics in fix_barrier_height

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  135. handle solvation for Marcus kinetics for library reactions

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  136. allow Marcus kinetics to be loaded

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  137. alllow Marcus kinetics in families

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  138. handle solvation for Marcus kinetics in families

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  139. handle kinetics averaging for Marcus

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  140. squash

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  141. handle Marcus kinetics within tree generation and rule generation

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  142. add ethylene carbonate example

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  143. add acetonitrile SEI chemistry example

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  144. Fixed a typo in test lose charge

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  145. Fixed syntax problems with SEI examples

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  146. Add set_reference_potential for SurfaceChargeTransfer 

    in to_rms
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  147. temporary fix to an exponent overflow problem

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  148. Fixed atomtype charge checking 

    Now includes checks for negative charges
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