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DOC: JOSS submission and updated documentation #160

Merged
merged 108 commits into from
Jul 10, 2023
Merged

DOC: JOSS submission and updated documentation #160

merged 108 commits into from
Jul 10, 2023

Commits on Oct 14, 2022

  1. added initial structure of the paper files

    @pgrigorev
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  2. added github workflow for draft pdf

    @pgrigorev
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  3. added James orcid and a bit more text

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  4. fixed identation

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Commits on Oct 17, 2022

  1. added more text and proposed structure

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Commits on Oct 19, 2022

  1. Merge pull request #111 from pgrigorev/108-JOSS-submission 

    108 joss submission
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Commits on Oct 27, 2022

  1. Text suggestion for pressurecoupling module

    @threich
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  2. fixed typos

    @threich
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Commits on Oct 28, 2022

  1. Merge pull request #113 from threich/108-JOSS-submission 

    108 joss submission, pressure coupling module
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Commits on Dec 6, 2022

  1. JOSS: drafted short paragraph on elastic constants

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Commits on Dec 8, 2022

  1. Update paper.bib

    @griessej
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  2. Update paper.md

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Commits on Dec 9, 2022

  1. Added fracture paragraph and start of general section

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  2. Update paper.bib

    @jameskermode
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  3. Update paper.bib

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  4. add funder info

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  5. add some more section heading to general tools

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Commits on Dec 13, 2022

  1. Update paper.md

    @griessej
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  2. Update paper.md

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  3. Update paper.md

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  4. Update paper.md

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  5. Update paper.md

    @griessej
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  6. Update paper.bib

    @griessej
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  7. Update paper.bib

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  8. Update paper.md

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  9. Update paper.md

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  10. fixed references

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  11. Merge branch '108-JOSS-submission-freiburg' of github.com:libAtoms/ma… 

    …tscipy into 108-JOSS-submission-freiburg
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  12. Update paper.md

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Commits on Jan 31, 2023

  1. Merge branch '108-JOSS-submission' into 108-JOSS-submission-freiburg

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Commits on Feb 9, 2023

  1. ENH: Author

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  2. Merge branch '108-JOSS-submission-freiburg' of https://github.com/lib… 

    …Atoms/matscipy into 108-JOSS-submission-freiburg
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  3. WIP: Abstract draft for electrochemistry

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  4. DOC: revisiting electrochemistry README

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Commits on Feb 10, 2023

  1. DOC: restructured electrochemistry paragraph, inserted references

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  2. DOC: electrochemistry references appended at bottom of bib file#

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  3. MAINT: continuous2discrete code and spelling cleanup

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  4. MAINT: Poisson-Boltzmann code and spelling cleanup

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  5. MAINT: Poisson-Nernst-Planck code and spelling cleanup

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  6. Merge pull request #140 from jotelha/108-JOSS-submission-freiburg-ele… 

    …ctrochemistry

joss: electrochemistry description
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Commits on Feb 13, 2023

  1. Added text about OPLS module.

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  2. fixed typos

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Commits on Feb 17, 2023

  1. joss: added neighbour list time comparison

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  2. Merge branch '108-JOSS-submission' into 108-JOSS-submission-freiburg

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Commits on Jun 23, 2023

  1. Merge pull request #144 from libAtoms/108-JOSS-submission-freiburg 

    Contributions from Freiburg
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Commits on Jun 29, 2023

  1. DOC: Added compile.sh, sorted authors alphabetically (except for Petr… 

    … first, James last)
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  2. DOC: Updated paper with more information

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  3. Further changes on paper

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  4. DOC: Updated AUTHORS file

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Commits on Jul 2, 2023

  1. Add MCFM, committee models and one more acknowledgement

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  2. fix typo in bib entry

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  3. respond to some comments

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Commits on Jul 3, 2023

  1. answered comment about kinks

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  2. added reference to 2023 paper

    @pgrigorev
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  3. Merge pull request #159 from pgrigorev/108-JOSS-submission 

    108 joss submission
    @pastewka
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Commits on Jul 4, 2023

  1. Updated author list

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  2. MAINT: Updated AUTHORS

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  3. DOC: Restructured paper and added references

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  4. Merge branch 'master' into 108-JOSS-submission

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  5. DOC: More updates to paper

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  6. DOC: fixed citation

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  7. proof read, small changes

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  8. fix affiliation

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  9. DOC: Updated documentation to use MYST_nb

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  10. DOC: Added main index to TOC and moved calculators

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  11. Gian comments

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  12. Merge branch '108-JOSS-submission' of github.com:libAtoms/matscipy in… 

    …to 108-JOSS-submission
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  13. DOC: Updated order of affiliations

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  14. DOC: Added ring analysis example

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  15. DOC: Removed unused rst files

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  16. DOC: Added manybody example

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  17. add Lakshmi ORCID

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  18. Merge branch '108-JOSS-submission' of github.com:libAtoms/matscipy in… 

    …to 108-JOSS-submission
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  19. DOC: Fixed math display

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  20. Merge remote-tracking branch 'origin/108-JOSS-submission' into 108-JO… 

    …SS-submission
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  21. DOC: Fixed typo

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  22. DOC: setup elastic constants documentation as a notebook

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Commits on Jul 5, 2023

  1. WIP on frature tutorial

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  2. Merge branch '108-JOSS-submission' of github.com:libAtoms/matscipy in… 

    …to 108-JOSS-submission
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  3. Thomas/Lars corrections to topology

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  4. DOC: Added atomsk to paper

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  5. DOC: elasticity tutorial

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Commits on Jul 6, 2023

  1. add Fraser orcid, flip last two authors

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  2. Small fixes

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  3. MAINT: added born_constants as Manybody property

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  4. DOC: added visualization to manybody

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  5. Added EAM reference

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Commits on Jul 7, 2023

  1. DOC: Minor updates to paper

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  2. Merge pull request #164 from wgnoehring/patch-1-eam-reference 

    Patch 1 eam reference
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  3. DOC: Minor fixes to paper

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  4. WIP on fracture tutorial

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  5. Merge branch '108-JOSS-submission' of github.com:libAtoms/matscipy in… 

    …to 108-JOSS-submission
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  6. fix: display of neighbour_list docstring

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  7. DOC: populating API documentation page

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  8. DOC: added module-level docstrings for autosummary

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Commits on Jul 9, 2023

  1. DOC: add tribology pressurecoupling doc example

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  2. DOC: removed pressure coupling from examples directory

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  3. DOC: fixed documentation in pressureocoupling.py

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  4. Merge pull request #165 from threich/108-JOSS-submission 

    DOC joss submission -  example for pressurecoupling
    @pastewka
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  5. DOC: Final changes to paper

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  6. Merge branch '108-JOSS-submission' of github.com:libAtoms/matscipy in… 

    …to 108-JOSS-submission
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Commits on Jul 10, 2023

  1. Merge branch 'master' into 108-JOSS-submission

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  2. DOC: Removed comments from paper

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  3. DOC: collected small changes to manuscript

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  4. Merge branch '108-JOSS-submission' of github.com:libAtoms/matscipy in… 

    …to 108-JOSS-submission
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  5. MAINT: cleanup generated files

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    prs513rosewood committed Jul 10, 2023
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  6. MAINT: added gitignores

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    prs513rosewood committed Jul 10, 2023
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  7. DOC: UK english

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    prs513rosewood committed Jul 10, 2023
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