Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

WIP: RMG-Electrocat #2000

Closed
wants to merge 36 commits into from
Closed

WIP: RMG-Electrocat #2000

wants to merge 36 commits into from

Commits on Jul 29, 2021

  1. added Faraday's Constant F

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    f2e644d View commit details
    Browse the repository at this point in the history

  2. added Potential as V quantity

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    c108446 View commit details
    Browse the repository at this point in the history

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

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    dc56485 View commit details
    Browse the repository at this point in the history

  4. added atomtype unit tests

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    14eebc8 View commit details
    Browse the repository at this point in the history

  5. added gain_charge and lose_charge actions

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    2e5b3a6 View commit details
    Browse the repository at this point in the history

  6. added is_proton and is_electron group methods

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    a8eb291 View commit details
    Browse the repository at this point in the history

  7. added group unit tests

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    50fd05c View commit details
    Browse the repository at this point in the history

  8. added is_electron and is_proton methods to Atom and Mol

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    f4e40e8 View commit details
    Browse the repository at this point in the history

  9. added GAIN and LOSE CHARGE actions to Atoms

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    3feb806 View commit details
    Browse the repository at this point in the history

  10. added updated charge method and revised update Molecule method 

    the update method now updates lone pairs before updating charge
    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    b055183 View commit details
    Browse the repository at this point in the history

  11. do not raise charge exception by default when creating molecule from … 

    …adj list
    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    c56a711 View commit details
    Browse the repository at this point in the history

  12. H -> H0 in find_h_bonds Molecule method

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    67856dd View commit details
    Browse the repository at this point in the history

  13. try to generate_resonance_structures, and return a deep copy of the m… 

    …olecule if it fails
    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    91b4f5c View commit details
    Browse the repository at this point in the history

  14. added molecule.pxd declarations

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    6da1615 View commit details
    Browse the repository at this point in the history

  15. added Species is_electron and is_proton methods

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    81958fe View commit details
    Browse the repository at this point in the history

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

    …dj list
    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    b64c0c4 View commit details
    Browse the repository at this point in the history

  17. added get_net_charge method for Species

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    018889a View commit details
    Browse the repository at this point in the history

  18. do not forbid ions 

    however, we still need better thermo
    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    178b34e View commit details
    Browse the repository at this point in the history

  19. added SurfaceChargeTransfer and SurfaceChargeTransferBEP kinetic … 

    …models
    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    8a7426e View commit details
    Browse the repository at this point in the history

  20. added unit tests for SurfaceChargeTranser kinetic model

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    090ec07 View commit details
    Browse the repository at this point in the history

  21. added Molecule unit tests

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    c587c21 View commit details
    Browse the repository at this point in the history

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

    …fer reactions
    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    04362cc View commit details
    Browse the repository at this point in the history

  23. added reaction tests for charge transfer reactions

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    3d4bdaa View commit details
    Browse the repository at this point in the history

  24. adding charged species and electrons to family.py

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    d41ac9b View commit details
    Browse the repository at this point in the history

  25. added family test for Surface_Proton_Electron_Reduction_Alpha family

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    01c5f22 View commit details
    Browse the repository at this point in the history

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

    …atabase
    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    78e7959 View commit details
    Browse the repository at this point in the history

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

    …e_pairs` method
    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    1d059b8 View commit details
    Browse the repository at this point in the history

  28. making rules for SurfaceChargeTransfer training reactions

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    657def1 View commit details
    Browse the repository at this point in the history

  29. added SurfaceChargeTransfer kinetics import

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    c0603f8 View commit details
    Browse the repository at this point in the history

  30. added H+ and e to translator

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    d6c079c View commit details
    Browse the repository at this point in the history

  31. update_atomtypes -> update in translator.py

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    bae3eab View commit details
    Browse the repository at this point in the history

  32. added SurfaceChargeTransfer to yml

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    00f7073 View commit details
    Browse the repository at this point in the history

  33. added ElectrodeReactor

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    3117b33 View commit details
    Browse the repository at this point in the history

  34. added ElectrodeReactor to input.py

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    ad16c47 View commit details
    Browse the repository at this point in the history

  35. adding potential and ElectrodeReactor to main.py and model.py

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    5decbb6 View commit details
    Browse the repository at this point in the history

  36. used electrocat DB branch for testing

    @davidfarinajr
    davidfarinajr committed Jul 29, 2021
    Configuration menu
    Copy the full SHA
    091fe9b View commit details
    Browse the repository at this point in the history