* MRS comments

Some notes from MRS

* Update joss_paper/paper.md

Co-authored-by: Zhiyi Wu <[email protected]>

---------

Co-authored-by: Zhiyi Wu <[email protected]>

…s, standard data forms

…angement of paper metadata items

- infinite linesbreak at periods
- hard line break at periods so that diffs are limited to sentences

No text changes.

- move DD up in design
- added OB to writing

Manual condastats were about 30k, condastats gace 5k, pypistats 25k for 2023-10-27 - 2024-04-24,
so I am not sure how best to measure and in any case, these numbers will not age well in
a paper so I am going to remove them. We can write in our cover letter that we have sizable
downloads.

- create Author Contributions section
- add funding to Ack section

Some additional rephrasings and clarifications.  Also adding another reference in (will do in another commit)

added Mey et al. on best practices.

- major rewrite: added sub headings
- added more citations (scikit-learn, pandas, MDPOW) as well as Mey 2020
- added design principles from https://alchemlyb.readthedocs.io/en/latest/api_principles.html
- added full caption for figure
- added license (BSD-3)

… 71-joss-paper

- combined @MrShirt's revisions with @orbeckst's rewrite
  (we both added Mey2020...)
- fixed small omissions on my part

TODO: @davidlmobley please check

Added MRS and DM to project design.

See https://pandoc.org/MANUAL.html#citation-syntax

source: AUTHORS file

Changed "maintain" to "maintained" to more accurately capture
present AND past contributions by ZW, DD, OB.

State that funds were not involved, per guidelines/policies
https://joss.readthedocs.io/en/latest/submitting.html#policies

…there

- use canonical reference for Amber (and write software name
  as "Amber" instead of "AMBER" as in the paper/website)
- use more recent GROMACS reference
- use software / JOSS citation for BioSimSpace (instead of
  tutorial reference)
- use proper GOMC reference (note that the 2021 is the one containing
  free energy calculations)
- added DOIs to references
- fixed treatment of "Jr"

- attach all URLs to anchors
- add URLs for software packages

)

* Add T. Joseph to authors and grant to acknowledgements

* Remove TTJ from Acknowledgements, add to Author Contributions

- add @schlaicha to authors
- edits throughout, in particular emphasis on general simulation packages (not just MD)

Co-authored-by: Alexander Schlaich <[email protected]>

- add LAMMPS to list of packages
- add more references (LAMMPS, paper for free energy in materials)
- only talk about MD later, keep it initially general

* Add mention of SAFEP

* Add JH to author list, first SAFEP reference

also reorder middle authors alphabetically.

---------

Co-authored-by: Tom Joseph <[email protected]>

* Add HL to author list with affiliation

* update

* update

* Added Ian M. Kenney to author list

* Added I.M.K. to author contributions

- state that we follow NEP29 (transition to SPEC0, which is basically the same for us)
- state that we use SemVer
- minor text fixes throughout and adding of citations where needed

Changed with #369

REMOVE BEFORE SUBMISSION

… 71-joss-paper

- add department
- add grant information

Co-authored-by: Ian Kenney <[email protected]>

Co-authored-by: Pascal Merz <[email protected]>

* Add affiliation

* change the order

---------

Co-authored-by: Zhiyi Wu <[email protected]>

Co-authored-by: Zhiyi Wu <[email protected]>

* Update paper.md for authorship

* revert the deleted names

* fix the format

---------

Co-authored-by: Zhiyi Wu <[email protected]>

- re-ordered affiliations to increase numerically in first occurrence in
  author order
- updated date to today

- new section on background
- move Implementation right before Core design principles

Follows #328 (comment)

#328 (comment)

- highlight contributors that are not authors on the paper:
  Travis Jensen (@trje3733) and Dominik Wille (@harlor)
- acknowledge contributors for small fixes @helmutcarter @wehs7661
- acknowledge @VOD555 s initial contribution of code for fractional equilibration time