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Overhaul forcefield parameters for ions #15

Merged
merged 68 commits into from
Dec 14, 2021
Merged

Overhaul forcefield parameters for ions #15

merged 68 commits into from
Dec 14, 2021

Commits on Jun 22, 2021

  1. add minimal support for merz and TIP4PFB water model

    @rkingsbury
    rkingsbury committed Jun 22, 2021
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Commits on Jun 23, 2021

  1. add stiff bonds to water models for energy min

    @rkingsbury
    rkingsbury committed Jun 23, 2021
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Commits on Jun 25, 2021

  1. fix typo in tip4p_fb water charge

    @rkingsbury
    rkingsbury committed Jun 25, 2021
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Commits on Jun 29, 2021

  1. Merge branch 'main' of https://github.com/htz1992213/mdgo into ions_l… 

    …atest
    @rkingsbury
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Commits on Jul 1, 2021

  1. Merge branch 'main' of https://github.com/htz1992213/mdgo into ions_l… 

    …atest
    @rkingsbury
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Commits on Jul 3, 2021

  1. Merge branch 'main' of https://github.com/htz1992213/mdgo into ions_l… 

    …atest
    @rkingsbury
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Commits on Jul 16, 2021

  1. Merge branch 'main' of https://github.com/htz1992213/mdgo into ions_l… 

    …atest
    @rkingsbury
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  2. fix ion conversion mistake; add Na+

    @rkingsbury
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Commits on Jul 19, 2021

  1. Merge branch 'main' of https://github.com/htz1992213/mdgo into ions_l… 

    …atest
    @rkingsbury
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  2. Merge branch 'main' of https://github.com/htz1992213/mdgo into ions_l… 

    …atest
    @rkingsbury
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  3. Merge branch 'main' of https://github.com/htz1992213/mdgo into ions_l… 

    …atest
    @rkingsbury
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Commits on Jul 21, 2021

  1. Merge remote-tracking branch 'tz/main' into ions_latest

    @rkingsbury
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  2. correct units of epsilon in tip4pfb; add tip3pfb 

    reported as kJ/mol; need to convert to kcal/mol
    @rkingsbury
    rkingsbury committed Jul 21, 2021
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Commits on Jul 22, 2021

  1. overhaul ion parameter sets 

    -Went back to original papers
-checked and converted all values
-cross-checked previous data entry
-moved ion parameters into an .xlsx file instead of text files
-reworked call signature of get_ion

In the future it would be preferable to store the ion data as a .json instead of .xlsx.
However pandas read_json does not support MultiIndex very well.
    @rkingsbury
    rkingsbury committed Jul 22, 2021
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  2. organize imports

    @rkingsbury
    rkingsbury committed Jul 22, 2021
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  3. bugfixes

    @rkingsbury
    rkingsbury committed Jul 22, 2021
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Commits on Jul 29, 2021

  1. add minimal support for merz and TIP4PFB water model

    @rkingsbury
    rkingsbury committed Jul 29, 2021
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  2. add stiff bonds to water models for energy min

    @rkingsbury
    rkingsbury committed Jul 29, 2021
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  3. fix typo in tip4p_fb water charge

    @rkingsbury
    rkingsbury committed Jul 29, 2021
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  4. fix ion conversion mistake; add Na+

    @rkingsbury
    rkingsbury committed Jul 29, 2021
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  5. correct units of epsilon in tip4pfb; add tip3pfb 

    reported as kJ/mol; need to convert to kcal/mol
    @rkingsbury
    rkingsbury committed Jul 29, 2021
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  6. overhaul ion parameter sets 

    -Went back to original papers
-checked and converted all values
-cross-checked previous data entry
-moved ion parameters into an .xlsx file instead of text files
-reworked call signature of get_ion

In the future it would be preferable to store the ion data as a .json instead of .xlsx.
However pandas read_json does not support MultiIndex very well.
    @rkingsbury
    rkingsbury committed Jul 29, 2021
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  7. organize imports

    @rkingsbury
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Commits on Sep 18, 2021

  1. Merge branch 'main' of https://github.com/htz1992213/mdgo into ions_l… 

    …atest
    @rkingsbury
    rkingsbury committed Sep 18, 2021
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Commits on Sep 19, 2021

  1. Merge branch 'ions_latest' of https://github.com/rkingsbury/mdgo into… 

    … ions_latest
    @rkingsbury
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Commits on Oct 13, 2021

  1. linting

    @rkingsbury
    rkingsbury committed Oct 13, 2021
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  2. Packmol: overhaul and add tests

    @rkingsbury
    rkingsbury committed Oct 13, 2021
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  3. add'l tests and fix for spaces in path name

    @rkingsbury
    rkingsbury committed Oct 13, 2021
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  4. add info message if packmol not installed

    @rkingsbury
    rkingsbury committed Oct 13, 2021
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Commits on Oct 27, 2021

  1. Merge branch 'ions_latest' of https://github.com/rkingsbury/mdgo into… 

    … ions_latest
    @rkingsbury
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  2. add OPC and OPC3 water models

    @rkingsbury
    rkingsbury committed Oct 27, 2021
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  3. change ion param storage; add tests

    @rkingsbury
    rkingsbury committed Oct 27, 2021
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  4. restore FFCrawlerTest

    @rkingsbury
    rkingsbury committed Oct 27, 2021
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  5. rm text files for ion parameters

    @rkingsbury
    rkingsbury committed Oct 27, 2021
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Commits on Nov 11, 2021

  1. add packmol

    @htz1992213
    htz1992213 committed Nov 11, 2021
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  2. change actions working directory

    @htz1992213
    htz1992213 committed Nov 11, 2021
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  3. fortran compile error

    @htz1992213
    htz1992213 committed Nov 11, 2021
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  4. made executable

    @htz1992213
    htz1992213 committed Nov 11, 2021
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  5. test actions

    @htz1992213
    htz1992213 committed Nov 11, 2021
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  6. test actions 2

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  7. test actions 3

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  8. test actions 4

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  9. test actions 5

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  10. test actions 6

    @htz1992213
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  11. test actions 7

    @htz1992213
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  12. identified test_random_seed

    @htz1992213
    htz1992213 committed Nov 11, 2021
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  13. bump up python (3.8); fix typo

    @htz1992213
    htz1992213 committed Nov 11, 2021
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  14. Update lint.yml

    @htz1992213
    htz1992213 committed Nov 11, 2021
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  15. Revert "Update lint.yml" 

    This reverts commit d469e30.
    @htz1992213
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  16. Revert "bump up python (3.8); fix typo" 

    This reverts commit 8569dcf.
    @htz1992213
    htz1992213 committed Nov 11, 2021
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  17. fix typo

    @htz1992213
    htz1992213 committed Nov 11, 2021
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  18. using Literal with typing-extensions

    @htz1992213
    htz1992213 committed Nov 11, 2021
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Commits on Nov 16, 2021

  1. Update tests/test_mdgopackmol.py 

    Co-authored-by: Tingzheng Hou <thou@berkeley.edu>
    @rkingsbury @htz1992213
    rkingsbury and htz1992213 authored Nov 16, 2021
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  2. Update tests/test_mdgopackmol.py 

    Co-authored-by: Tingzheng Hou <thou@berkeley.edu>
    @rkingsbury @htz1992213
    rkingsbury and htz1992213 authored Nov 16, 2021
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  3. Update tests/test_mdgopackmol.py 

    Co-authored-by: Tingzheng Hou <thou@berkeley.edu>
    @rkingsbury @htz1992213
    rkingsbury and htz1992213 authored Nov 16, 2021
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  4. Update tests/test_mdgopackmol.py 

    Co-authored-by: Tingzheng Hou <thou@berkeley.edu>
    @rkingsbury @htz1992213
    rkingsbury and htz1992213 authored Nov 16, 2021
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  5. Packmol: test file case error, rm spurious quotes

    @rkingsbury
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  6. Merge branch 'ions_latest' of https://github.com/rkingsbury/mdgo into… 

    … ions_latest
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  7. Merge branch 'packmol' into ions_latest

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Commits on Nov 22, 2021

  1. Add mixing_rule kwarg 

    Co-authored-by: Tingzheng Hou <thou@berkeley.edu>
    @rkingsbury @htz1992213
    rkingsbury and htz1992213 authored Nov 22, 2021
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  2. add mixing_rule logic 

    Co-authored-by: Tingzheng Hou <thou@berkeley.edu>
    @rkingsbury @htz1992213
    rkingsbury and htz1992213 authored Nov 22, 2021
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  3. add WATER_SIGMA to support mixing rules 

    Co-authored-by: Tingzheng Hou <thou@berkeley.edu>
    @rkingsbury @htz1992213
    rkingsbury and htz1992213 authored Nov 22, 2021
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  4. Ions: update .json with formula bugfix 

    See pymatgen #2287
materialsproject/pymatgen#2287

The data file is now keyed by
Ion.reduced_formula, meaning all
ions have charges appended in
brackets, with explicit magnitudes
e.g. `Li[+1]`
    @rkingsbury
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Commits on Nov 23, 2021

  1. rearrange Aqueous.get_ion kwargs

    @rkingsbury
    rkingsbury committed Nov 23, 2021
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  2. black

    @rkingsbury
    rkingsbury committed Nov 23, 2021
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Commits on Nov 30, 2021

  1. modify get_ion signature; add tests for mixing rule

    @htz1992213
    htz1992213 committed Nov 30, 2021
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  2. lint

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    htz1992213 committed Nov 30, 2021
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Commits on Dec 14, 2021

  1. bump up pymatgen

    @htz1992213
    htz1992213 committed Dec 14, 2021
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