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uncertainty quantification in energy corrections #1558

Merged
merged 222 commits into from
Aug 14, 2020
Merged

uncertainty quantification in energy corrections #1558

merged 222 commits into from
Aug 14, 2020

Commits on Aug 21, 2019

  1. added correction error to compatibility module with tests

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    awvio committed Aug 21, 2019
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Commits on Aug 29, 2019

  1. merge Amanda's correction work into new branch

    @rkingsbury
    rkingsbury committed Aug 29, 2019
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Commits on Aug 30, 2019

  1. Reformat .yaml keys to match correction classes

    @rkingsbury
    rkingsbury committed Aug 30, 2019
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  2. added CorrectionCalculator class, the json files of calc/exp entries,… 

    … new MPCompatibility and Errors yaml
    @awvio
    awvio committed Aug 30, 2019
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  3. 'merged

    @awvio
    awvio committed Aug 30, 2019
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  4. merged format changes to yaml and made corresponding changes to Anion… 

    …Correction class; moved CorrectionCalculator to separate file
    @awvio
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Commits on Sep 5, 2019

  1. added docstrings and type hints to CorrectionCalculator

    @awvio
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  2. fixed defaultdict import, switched to plotly

    @awvio
    awvio committed Sep 5, 2019
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Commits on Sep 6, 2019

  1. ran style checker

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  2. manually fixed other style errors

    @awvio
    awvio committed Sep 6, 2019
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Commits on Sep 7, 2019

  1. changed json files containing exp/calc entries to gzip, removed no lo… 

    …nger needed files
    @awvio
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  2. fixed new style errors

    @awvio
    awvio committed Sep 7, 2019
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  3. changed input filename back to MPCompatibility.yaml, changed tests ac… 

    …cording to smaller number of sigfigs for corrections
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    awvio committed Sep 7, 2019
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Commits on Sep 10, 2019

  1. Remove polysulfide logic from sulfide_type()

    @rkingsbury
    rkingsbury committed Sep 10, 2019
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  2. Remove polysulfide logic from sulfide_type() 

    Remove polysulfide logic from sulfide_type()
    @rkingsbury
    rkingsbury committed Sep 10, 2019
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Commits on Sep 19, 2019

  1. fixed merge conflicts

    @awvio
    awvio committed Sep 19, 2019
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Commits on Sep 20, 2019

  1. added plotly to requirements, added in type hints

    @awvio
    awvio committed Sep 20, 2019
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  2. fixed style error

    @awvio
    awvio committed Sep 20, 2019
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  3. fixed imports from typing

    @awvio
    awvio committed Sep 20, 2019
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  4. one more type annotation fix

    @awvio
    awvio committed Sep 20, 2019
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  5. deleted unused import and variable

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Commits on Oct 2, 2019

  1. Replace GasCorrection with AnionCorrection

    @rkingsbury
    rkingsbury committed Oct 2, 2019
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  2. added test for correction calculator

    @awvio
    awvio committed Oct 2, 2019
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  3. fixed style errors

    @awvio
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  4. Replace diatomic formulas with elements

    @rkingsbury
    rkingsbury committed Oct 2, 2019
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  5. Change corrections to account for new method

    @rkingsbury
    rkingsbury committed Oct 2, 2019
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  6. Recalculate the corrections

    @rkingsbury
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  7. Shift corrections to compounds rather than elements

    @rkingsbury
    rkingsbury committed Oct 2, 2019
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Commits on Oct 3, 2019

  1. fixed typos, added tests for mp aqueous compatibility, print compatib… 

    …ilityerror before returning none
    @awvio
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  2. attempt to fix mypy error

    @awvio
    awvio committed Oct 3, 2019
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  3. added error value to explanation dict

    @awvio
    awvio committed Oct 3, 2019
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Commits on Oct 19, 2019

  1. Fix H2 correction

    @rkingsbury
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Commits on Oct 21, 2019

  1. Flip the sign on the corrections

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Commits on Oct 23, 2019

  1. Merge Amanda's master branch

    @rkingsbury
    rkingsbury committed Oct 23, 2019
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  2. Add fitted H2 error

    @rkingsbury
    rkingsbury committed Oct 23, 2019
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  3. Add fitted H2 to AnionCorrection

    @rkingsbury
    rkingsbury committed Oct 23, 2019
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  4. Remove GasCorrection heading

    @rkingsbury
    rkingsbury committed Oct 23, 2019
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  5. Rename AnionCorrection to CompositionCorrection

    @rkingsbury
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  6. Deeper renaming and add H2 fit to make_yaml

    @rkingsbury
    rkingsbury committed Oct 23, 2019
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Commits on Oct 24, 2019

  1. rm GasCorrection from errors yaml

    @rkingsbury
    rkingsbury committed Oct 24, 2019
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  2. fix linting errors and remove unneeded lines

    @rkingsbury
    rkingsbury committed Oct 24, 2019
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  3. more renames

    @rkingsbury
    rkingsbury committed Oct 24, 2019
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  4. merged change to comp_corr, computedreaction now also calculates erro… 

    …r in reaction energy
    @awvio
    awvio committed Oct 24, 2019
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Commits on Nov 7, 2019

  1. updated tests for hydrides

    @awvio
    awvio committed Nov 7, 2019
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  2. Rename 'errors' to 'uncertainties'

    @rkingsbury
    rkingsbury committed Nov 7, 2019
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  3. Scale correction_uncertainty via normalize()

    @rkingsbury
    rkingsbury committed Nov 7, 2019
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  4. fix for renaming error to uncertainty

    @rkingsbury
    rkingsbury committed Nov 7, 2019
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  5. resolved conflict with upstream

    @awvio
    awvio committed Nov 7, 2019
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  6. fixed style errors

    @awvio
    awvio committed Nov 7, 2019
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  7. fixed more style errors

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    awvio committed Nov 7, 2019
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Commits on Nov 8, 2019

  1. even more style errors

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  2. more style errors

    @awvio
    awvio committed Nov 8, 2019
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  3. change correction/error to initialize to 0.0 for mypy type checking

    @awvio
    awvio committed Nov 8, 2019
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  4. remove unused variable, change error to uncertainty

    @awvio
    awvio committed Nov 8, 2019
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Commits on Nov 20, 2019

  1. changed error to uncertainty in tests

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  2. resolve upstream conflict with searchindex.js

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    awvio committed Nov 20, 2019
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Commits on Nov 21, 2019

  1. added test for no uncertainties, added docstrings

    @awvio
    awvio committed Nov 21, 2019
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  2. fixed style errors in docstrings

    @awvio
    awvio committed Nov 21, 2019
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  3. moved docstring for pydocstyle

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Commits on Dec 4, 2019

  1. renamed new classes with 2020 suffix, added deprecation warnings to o… 

    …ld classes
    @awvio
    awvio committed Dec 4, 2019
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Commits on Dec 5, 2019

  1. added correction error to compatibility module with tests

    @awvio
    awvio committed Dec 5, 2019
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  2. merge Amanda's correction work into new branch

    @rkingsbury @awvio
    rkingsbury authored and awvio committed Dec 5, 2019
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  3. Reformat .yaml keys to match correction classes

    @rkingsbury @awvio
    rkingsbury authored and awvio committed Dec 5, 2019
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  4. added CorrectionCalculator class, the json files of calc/exp entries,… 

    … new MPCompatibility and Errors yaml
    @awvio
    awvio committed Dec 5, 2019
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  5. added docstrings and type hints to CorrectionCalculator

    @awvio
    awvio committed Dec 5, 2019
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  6. fixed defaultdict import, switched to plotly

    @awvio
    awvio committed Dec 5, 2019
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  7. ran style checker

    @awvio
    awvio committed Dec 5, 2019
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  8. manually fixed other style errors

    @awvio
    awvio committed Dec 5, 2019
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  9. changed json files containing exp/calc entries to gzip, removed no lo… 

    …nger needed files
    @awvio
    awvio committed Dec 5, 2019
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  10. fixed new style errors

    @awvio
    awvio committed Dec 5, 2019
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  11. changed input filename back to MPCompatibility.yaml, changed tests ac… 

    …cording to smaller number of sigfigs for corrections
    @awvio
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  12. Remove polysulfide logic from sulfide_type()

    @rkingsbury @awvio
    rkingsbury authored and awvio committed Dec 5, 2019
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  13. added plotly to requirements, added in type hints

    @awvio
    awvio committed Dec 5, 2019
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  14. fixed style error

    @awvio
    awvio committed Dec 5, 2019
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  15. fixed imports from typing

    @awvio
    awvio committed Dec 5, 2019
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  16. one more type annotation fix

    @awvio
    awvio committed Dec 5, 2019
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  17. deleted unused import and variable

    @awvio
    awvio committed Dec 5, 2019
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  18. Replace GasCorrection with AnionCorrection

    @rkingsbury @awvio
    rkingsbury authored and awvio committed Dec 5, 2019
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  19. added test for correction calculator

    @awvio
    awvio committed Dec 5, 2019
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  20. fixed style errors

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  21. Replace diatomic formulas with elements

    @rkingsbury @awvio
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  22. Change corrections to account for new method

    @rkingsbury @awvio
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  23. Recalculate the corrections

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  24. Shift corrections to compounds rather than elements

    @rkingsbury @awvio
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  25. fixed typos, added tests for mp aqueous compatibility, print compatib… 

    …ilityerror before returning none
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    awvio committed Dec 5, 2019
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  26. attempt to fix mypy error

    @awvio
    awvio committed Dec 5, 2019
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  27. added error value to explanation dict

    @awvio
    awvio committed Dec 5, 2019
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  28. Fix H2 correction

    @rkingsbury @awvio
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  29. Flip the sign on the corrections

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  30. Add fitted H2 error

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  31. Add fitted H2 to AnionCorrection

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  32. Rename AnionCorrection to CompositionCorrection

    @rkingsbury @awvio
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  33. Deeper renaming and add H2 fit to make_yaml

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  34. fix linting errors and remove unneeded lines

    @rkingsbury @awvio
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  35. more renames

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  36. merged change to comp_corr, computedreaction now also calculates erro… 

    …r in reaction energy
    @awvio
    awvio committed Dec 5, 2019
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  37. updated tests for hydrides

    @awvio
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  38. Rename 'errors' to 'uncertainties'

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  39. Scale correction_uncertainty via normalize()

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  40. fix for renaming error to uncertainty

    @rkingsbury @awvio
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  41. fixed style errors

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  42. fixed more style errors

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  43. even more style errors

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  44. more style errors

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  45. remove unused variable, change error to uncertainty

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  46. changed error to uncertainty in tests

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  47. added test for no uncertainties, added docstrings

    @awvio
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  48. fixed style errors in docstrings

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  49. moved docstring for pydocstyle

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  50. renamed new classes with 2020 suffix, added deprecation warnings to o… 

    …ld classes
    @awvio
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  51. rebased on upstream master

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  52. removed unused imports

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  53. removed mitcompatibility2020 classes, yamls, and tests

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Commits on Dec 23, 2019

  1. removed copper correction and added tungsten correction/compounds

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  2. Merge branch 'master' into master

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  3. Merge branch 'master' of git://github.com/materialsproject/pymatgen i… 

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Commits on Jan 7, 2020

  1. Merge branch 'master' into master

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Commits on Jan 23, 2020

  1. fixed signs of hydrides experimental energy

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Commits on Jan 24, 2020

  1. Merge branch 'master' of https://github.com/awvio/pymatgen

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Commits on Feb 14, 2020

  1. updated magnetic orderings, removed MnSiO3 and WOF4

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  2. updated tests for new corrections

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Commits on Feb 19, 2020

  1. changed no correction uncertainty value from float(nan) to np.nan

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  1. Merge branch 'master' into master

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Commits on Mar 4, 2020

  1. Merge branch 'master' into master

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Commits on Mar 6, 2020

  1. mostly finished with ufloats, need to add one more test

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  2. fixed calc_compounds.gz to updated version

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Commits on Mar 7, 2020

  1. fixed calc_compounds.gz to lowest energy entries, updated corrections

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  2. update Aqueous corrections for MP2020

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  3. Merge pull request #2 from rkingsbury/newcorrections 

    update Aqueous corrections for MP2020
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Commits on Mar 8, 2020

  1. fix H2O energy and update tests for refitted corrections

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  2. remove old aqueous corrections

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  3. Merge pull request #4 from rkingsbury/corrections-mp2020 

    fix H2O energy and update tests for refitted corrections
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Commits on Mar 9, 2020

  1. added test for nan rxn energy uncertainty

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  2. merged with upstream master

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  3. Merge branch 'uncertainties'

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  4. added correction_uncertainty back to explanation_dict

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  5. minor adjustments to when uncertainty is set to nan

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  6. fixed style errors

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  7. added uncertainties package to requirements.txt

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  8. added uncertainties to list of imported modules for mypy to ignore in… 

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  9. removed unused imports

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  10. moved module level docstring for pydocstyle

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Commits on Mar 10, 2020

  1. update Pourbaix and AqueousCorrections for MP2020

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Commits on Apr 7, 2020

  1. update O2 energy for Aqueous fit

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  2. Merge branch 'master' into master

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  3. update test

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  4. Merge branch 'master' of https://github.com/awvio/pymatgen into corre… 

    …ctions
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Commits on Apr 14, 2020

  1. Merge branch 'master' of git://github.com/materialsproject/pymatgen i… 

    …nto corrections
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  2. changed S to sulfide, crosschecked compounds with Hautier paper and c… 

    …hanged tests accordingly
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  3. fixed style

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  4. Merge branch 'master' of https://github.com/awvio/pymatgen

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  5. Merge branch 'master' of https://github.com/awvio/pymatgen into corre… 

    …ctions
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  6. update Aqueous for refitted mp2020

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  7. add warning for Pourbaix+Aqueous2020

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  8. fix mypy + pytest complaining

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Commits on Apr 28, 2020

  1. Merge branch 'master' of git://github.com/materialsproject/pymatgen i… 

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Commits on Apr 29, 2020

  1. merge with abstract compat

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Commits on Apr 30, 2020

  1. Merge branch 'abstractcompat' into corrections

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  2. remove aqueous corr from yaml

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Commits on May 5, 2020

  1. Merge branch 'master' of git://github.com/materialsproject/pymatgen i… 

    …nto corrections
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  2. integrate changes from materialsproject#1826

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  3. fix mypy errors

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Commits on Jun 8, 2020

  1. search calc dict by Composition(formula).reduced_formula for consiste… 

    …nt elem ordering
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  2. merged with upstream master

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  3. removed extra whitespace

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Commits on Jun 9, 2020

  1. remove any corrections in calc_compounds

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  2. changed calc_compounds dicts keys to be consistent with Composition(f… 

    …ormula).reduced_formula
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Commits on Jun 16, 2020

  1. add oxidation state check for anion corrections

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  2. Merge branch 'master' of git://github.com/materialsproject/pymatgen i… 

    …nto corrections
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Commits on Jun 17, 2020

  1. refactor name for consistency w/other classes

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Commits on Jun 20, 2020

  1. db release changes

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Commits on Jun 22, 2020

  1. performance-related oxi_state_guesses changes

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  2. updated how reaction_calculator accesses entry's correction_uncertainty

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Commits on Jun 29, 2020

  1. different approach to oxi state detection

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  2. Merge branch 'master' of git://github.com/materialsproject/pymatgen i… 

    …nto corrections
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  3. fix ComputedReaction test

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  4. linting

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Commits on Jul 9, 2020

  1. revert change to sulfide_type

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  2. remove deprecation warnings from MIT classes

    @rkingsbury
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  3. remove deprecation tests for MIT

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Commits on Jul 14, 2020

  1. make fitting helper func private

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Commits on Jul 15, 2020

  1. added magnetic ordering to entry.data dict

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  2. Merge branch 'master' of https://github.com/awvio/pymatgen

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Commits on Jul 20, 2020

  1. reformatted correctioncalculator to pass permissions to init and entr… 

    …y data to calculate
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  2. style fixes

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  3. raise error with message to compute corrections first if other calcul… 

    …ator methods called without corrections calculated
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  4. Merge branch 'master' of https://github.com/materialsproject/pymatgen

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Commits on Jul 21, 2020

  1. clarified CorrectionCalculator filters

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  2. reformatted comments to meet max character/line count

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  3. Merge branch 'master' of git://github.com/materialsproject/pymatgen i… 

    …nto corrections
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Commits on Jul 22, 2020

  1. pylint fixes part 1

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  2. pylint fixes part 2

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  3. pycodestyle fixes

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  4. pylint fix, CorrectionCalculator graph function returns fig

    @awvio
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  5. test fixes; make uncertainty kwarg always

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  6. remove pylint C0330 directive

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  7. Merge branch 'master' of git://github.com/materialsproject/pymatgen i… 

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  8. add @staticmethod to explain

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Commits on Jul 24, 2020

  1. allow user to input species list

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  2. pycodestyle fix, clarify .json.gz file in compute_from_files docstring

    @awvio
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Commits on Jul 25, 2020

  1. allow_unstable can be bool or float, polyanions filtered based on use… 

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Commits on Jul 30, 2020

  1. Merge branch 'master' of git://github.com/materialsproject/pymatgen i… 

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  2. missing import

    @rkingsbury
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Commits on Jul 31, 2020

  1. change unknown uncertainties to np.nan instead of 0

    @awvio
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  2. pycodestyle split line with too many characters

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  3. pycodestyle indent

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  4. pylint trailing whitespace

    @awvio
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Commits on Aug 3, 2020

  1. fix merge problem

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  2. Fix typo

    @mkhorton
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  3. revert sulfide_type docstring change

    @rkingsbury
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  4. make kwargs more verbose

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  5. label corrections kwarg in tests

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  6. lint docstring

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  7. Merge branch 'master' of https://github.com/awvio/pymatgen into corre… 

    …ctions
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  8. whitespace

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  9. Merge branch 'master' of https://github.com/awvio/pymatgen; branch 'm… 

    …aster' of git://github.com/materialsproject/pymatgen into corrections
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Commits on Aug 4, 2020

  1. replace .gz with .json.gz extension

    @rkingsbury
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  2. update file extension in test file

    @rkingsbury
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Commits on Aug 7, 2020

  1. changed sulfide back to S

    @awvio
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  2. Merge branch 'master' of git://github.com/materialsproject/pymatgen i… 

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Commits on Aug 14, 2020

  1. Merge branch 'master' of https://github.com/awvio/pymatgen; branch 'm… 

    …aster' of git://github.com/materialsproject/pymatgen into corrections
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  2. rename corrections_calc.py

    @rkingsbury
    rkingsbury committed Aug 14, 2020
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