[REVIEW]: The MOOSE geochemistry module

[whedon]

Submitting author: @WilkAndy (Andy Wilkins) Repository: https://github.com/idaholab/moose Version: Snapshop 21-November-14 Editor: @jedbrown Reviewers: @smolins, @volpatto Archive: 10.5281/zenodo.5701422

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/7f7aecfea203be112f86c0f45c1ae130/status.svg)](https://joss.theoj.org/papers/7f7aecfea203be112f86c0f45c1ae130)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@smolins, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @jedbrown know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @smolins

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@WilkAndy) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @volpatto

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@WilkAndy) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @smolins it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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For a list of things I can do to help you, just type:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/s11004-020-09898-7 is OK
- 10.2138/gselements.15.2.117 is OK
- 10.1007/s10596-015-9475-x is OK
- 10.3133/wri954227 is OK
- 10.3133/wri994259 is OK
- 10.3133/tm6A35 is OK
- 10.2172/834237 is OK
- 10.1007/978-3-642-27177-9 is OK
- 10.1007/s11242-019-01310-1 is OK
- 10.21105/joss.02176 is OK
- 10.1002/nme.5284 is OK
- 10.1002/nme.6215 is OK
- 10.1016/j.softx.2020.100430 is OK
- 10.1007/s00366-006-0049-3 is OK
- 10.1007/978-1-4612-1986-6_8 is OK
- 10.1016/j.engfracmech.2019.106713 is OK
- 10.1007/s00466-018-1544-2 is OK
- 10.1017/CBO9780511619670 is OK
- 10.2172/138894 is OK
- 10.1016/0016-7037(88)90334-1 is OK
- 10.15121/1638710 is OK
- 10.2172/1524048 is OK

MISSING DOIs

- 10.3133/ofr20041068 may be a valid DOI for title: A compilation of rate parameters of water-mineral interaction kinetics for application to geochemical modeling

INVALID DOIs

- None

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[jedbrown]

@smolins :wave: Welcome to JOSS and thanks for agreeing to review!

The comments from @whedon above outline the review process, which takes place in this thread (possibly with issues filed in the rsudp repository). I'll be watching this thread if you have any questions.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/3314 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within a month or so. Please let me know if you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@jedbrown) if you have any questions/concerns.

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=27.11 s (607.7 files/s, 70852.6 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
SWIG                           5516          63399              0         653686
C++                            3327          70406          64201         393813
C/C++ Header                   3309          50046         107754         142083
Markdown                       2816          33548             78          79588
Python                          919          16006          21498          69883
JSON                             71              1              0          36401
C                                25           4845           6605          27204
TeX                              71           3432            680          26156
SVG                              29              2             80          13518
CSS                              20            986            372           6146
Bourne Shell                     44            821            696           5149
JavaScript                       27           1314           1622           3461
YAML                             94            290             52           3031
make                             72            702           1403           2237
HTML                             56            215             28           1683
XML                              25              5              7           1202
Fortran 77                       11             59            507            574
Cython                            2             82             33            387
Bourne Again Shell               23             60             36            324
m4                                3             30              0            298
Fortran 90                        2            107            303            282
MATLAB                            2             35             20            109
Jupyter Notebook                  5              0            962             94
Dockerfile                        1             18             41             66
Specman e                         3              0              1             57
DOS Batch                         1              9              0             22
GLSL                              1              0             18             19
--------------------------------------------------------------------------------
SUM:                          16475         246418         206997        1467473
--------------------------------------------------------------------------------

Statistical information for the repository '7faef66e0276b2cd8fafa827' was
gathered on 2021/05/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Aaron Butterfield                8           230              1            0.01
Adam Cahill                      3             6              3            0.00
Adam X. Zabriskie                3           306             68            0.02
Akshay Dandekar                  5           140            113            0.01
Al Casagranda                   14           358            234            0.03
Alain B. Giorla                 28          1373            472            0.10
Alex Lindsay                   791         40407          36948            4.37
Alex McCaskey                    6        143931         140652           16.09
Alexandra Gertman                6            60             10            0.00
Andrea Alfonsi                   4             6              1            0.00
Andrea Jokisaari                30           843             60            0.05
Andrea Rovinelli                66          2212            679            0.16
Andrew E. Slaughter           1760        260161         126463           21.86
Andrew Parnell                   1            37              0            0.00
Andy Wilkins                   455         55746          12370            3.85
Antonio Cervone                  1             1              1            0.00
Antonio Recuero                 91          3920           1557            0.31
April Novak                     28          1601            210            0.10
Avery Bingham                   10           481             19            0.03
Axel Seoane                      2           198              4            0.01
Benjamin Spencer               318         11545           9425            1.19
Bertrand Lagree                  3           329              1            0.02
Bob Kinoshita                    2            19              6            0.00
Bradley Fromm                   10           203             43            0.01
Brandon Langley                  2           102             19            0.01
Brian Alger                    219         18022           5175            1.31
Brycen Wendt                    20          2850           1120            0.22
Casey Icenhour                  66          2277           1184            0.20
Casper Versteeg                  1             2              0            0.00
Chandana Jayasundara             4           250             82            0.02
Chandrakanth Boliset             2            80              0            0.00
Chandu Bolisetti                19           506            112            0.03
Chris Green                    267         17498           8406            1.46
Chris Newman                     1            31              0            0.00
Christopher Walton               4           175             22            0.01
Christopher Wong                 2             8              8            0.00
Chuan Lu                         1            31              0            0.00
CiCi Pham                        1           124              0            0.01
Cody Permann                  1839        118256          67489           10.50
Congjian Wang                    4           632             16            0.04
Cormac Garvey                    2             2              2            0.00
Cristian Rabiti                  1             6              6            0.00
Daniel Ruprecht                  2           100              0            0.01
Daniel Schwen                  898         34584          23813            3.30
Daniel VanWasshenova            18           916            674            0.09
Daniel Vogler                    1            67              0            0.00
Danielle Perez                   1             2              0            0.00
David Andrs                    862         57978          48115            6.00
Dehao Liu                        1           147              0            0.01
Derek Gaston                  1004         72644          15430            4.98
Derek Stucki                     2             3              3            0.00
Dewen Yushu                      2           165            362            0.03
Dmitry Karpeev                  28           959            254            0.07
Dylan McDowell                   5           122              2            0.01
Fande Kong                     298          7468           3163            0.60
Floyd Hilty                      3            78             15            0.01
Frederick Gleicher               2            43              0            0.00
Gary Hu                         41          2556            775            0.19
Gavin Ridley                     7           120              9            0.01
Giovanni Pastore                 1             9              1            0.00
Guillaume Giudicelli            67          1783            472            0.13
Hai Huang                        1            99              0            0.01
Hailong Chen                    55          5959           1882            0.44
Hao Wang                         3           109              0            0.01
Heather Sheldon                 11           635             41            0.04
Ian                              4            30             20            0.00
Ian Greenquist                   7           384             11            0.02
Ian Halvic                      49          2028           1378            0.19
Jacob Bair                       6           113             11            0.01
Jacob Hirschhorn                 1           120              0            0.01
Jacob L. Bair                    2            62             16            0.00
Jacob Peterson                   1            18              5            0.00
James B. Tompkins                7           487            272            0.04
Jarin French                     3            80             19            0.01
Jaron Senecal                    1            14              0            0.00
Jason                           15           129             71            0.01
Jason D. Hales                 347          7820           3932            0.66
Jason M. Miller                467         43764          22458            3.74
Jed Brown                        8           595             78            0.04
Jesse Carter                    21           398             28            0.02
Jieun Lee                        5            55             40            0.01
John Hutchins                   13           335            153            0.03
John Mangeri                     5           262             26            0.02
John W. Peterson               439         14894          11171            1.47
John-Michael Bradley             4            94              6            0.01
Joshua E. Hansel                95          4259           2178            0.36
Joshua J. Cogliati               2             2              2            0.00
Ju-Yuan Yeh                      3           101              1            0.01
Justin Coleman                   1           136              0            0.01
Karim Ahmed                      5           271             10            0.02
Karthikeyan Chockali            22           710             38            0.04
Katherine Smith                  7           108             82            0.01
Kevin Dugan                      2             8              0            0.00
Kevin J. Dugan                   1             1              0            0.00
Kyle Gamble                     14           323             57            0.02
Kyoungdoc Kim                    1            49              0            0.00
Larry Aagesen                   63          1593            271            0.11
Lauren Winterholler              2           362              0            0.02
Lei Zhao                         1             5              1            0.00
Leo Borrel                       1            79              0            0.00
Leora Chapuis                   19          2744            384            0.18
Liangzhe Zhang                   1            42              0            0.00
Ling Liu                         3           265              7            0.02
Ling Zou                         1             3              0            0.00
Logan Harbour                  116         11659           3235            0.84
Luanjing Guo                     4           803              6            0.05
Luke Robinson                    2             2              1            0.00
Lynn Munday                     11           526            164            0.04
MOOSEBUILD                       1             9             21            0.00
Malachi Tolman                   9           255            105            0.02
Marie Backman                   26           950             54            0.06
Mark C. Messner                  1             9             18            0.00
Mark L. Baird                    1             1              1            0.00
Martin Lesueur                   1             2              0            0.00
Martin Luethi                    2           454            454            0.05
Mathias Winkel                   2            75             51            0.01
Matt Ellis                       1             3              1            0.00
Matthias                         1             5              3            0.00
Matthias Kunick                 16          1135            420            0.09
Micah Johnson                    4             7              5            0.00
Michael Pernice                  2            28              0            0.00
Michael Short                    3            94              0            0.01
Michael Tonks                  173          6081           1470            0.43
Moosetest                        1             1              1            0.00
Nathaniel Peat                   2             8          20299            1.15
Nicolo Grilli                    1           143              0            0.01
Paul Millet                      1             2              2            0.00
Paul Talbot                      8           401             11            0.02
Peter German                    52          1358            464            0.10
Philip Jagielski                76         10135            830            0.62
Philipp Schaedle                 1            43              0            0.00
Pritam Chakraborty              36          2987            483            0.20
Richard Williamson              10           286             17            0.02
Robert A. Kinoshita              2             7              1            0.00
Robert Carlsen                 344         59292          12250            4.05
Robert Nourgaliev                2            71              0            0.00
Robert Podgorney                 1             4              4            0.00
Roger Pawlowski                  1             1            304            0.02
Roy H. Stogner                  81           848            448            0.07
Roy Stogner                      9           126             28            0.01
Ryan Norman                      7            43             21            0.00
Ryosuke Park                    36           642            177            0.05
Samet Kadioglu                   1            48              0            0.00
Samuel K. Tew                   12           530            119            0.04
Scott A. Schoen                 17           547             92            0.04
Sebastian Schunert              93          3053            552            0.20
Shane Stafford                  20           259            192            0.03
Shiyuan Gu                       3           113              0            0.01
Shrey Satpathy                   1           149              0            0.01
Shuaifang Zhang                  1             4              7            0.00
Som Dhulipala                    1             1              1            0.00
Som L. Dhulipala                 5           267             27            0.02
Srivatsan Hulikal                1            27              5            0.00
Stephanie Pitts                 50          2722            750            0.20
Stephen Novascone               26           763             72            0.05
Stephen Thomas                   1            47              0            0.00
Sterling Harper                 32           749            464            0.07
Steve Prescott                   2           170             48            0.01
Steven Wacker                    1             5              0            0.00
Sudipta Biswas                  82          2893            827            0.21
Swetha Veeraraghavan            36          3657            657            0.24
Tami Grimmett                    1             1              1            0.00
Thomas Poulet                    1             2              0            0.00
Tianchen Hu                      2           456            102            0.03
Topher Matthews                156          4917           1953            0.39
Toptan, Aysenur                  1            41              0            0.00
Vanessa Gertman                  7           215            543            0.04
Vincent Laboure                 11           161             20            0.01
Vishal Patel                     7            80             34            0.01
Wen Jiang                       63          4369           1678            0.34
Wenfeng Liu                      4            49              4            0.00
William Hoffman                  2             9              1            0.00
William Taitano                  1             8              0            0.00
Yang Xia                         1           196              0            0.01
Yaqi Wang                      260          8267           3133            0.64
Yeh, Ju-Yuan                     1            35              0            0.00
Yeon Sang Jung                   2           272              4            0.02
Yidong Xia                       6          2665              1            0.15
Yinbin Miao                      1             2              1            0.00
Yingjie Liu                      1           139             11            0.01
Yipeng Gao                       1            40              0            0.00
Zachary M. Prince               73          3862            886            0.27
Ziyu Zhang                      38          2606           1047            0.21
balep                            1            10              7            0.00
crswong888                      38          2628            327            0.17
daniel.vanwasshenova             3            51             31            0.00
dewenyushu                      14           928            738            0.09
helen-brooks                     1             2              1            0.00
jbtompkins                       1             0              1            0.00
jmeziere                         2             0              2            0.00
killerpenguin12                  1            34              0            0.00
knw7x9                           1             3              0            0.00
moose                            4            36              5            0.00
moose-maintenance                6         30938          28909            3.38
moosetest                        4            30             14            0.00
rayaprolu143                     2            16              4            0.00
schuseba                        14          1005             32            0.06
wesleyzzz                        1            10              3            0.00
wuxueyang                        1           121              0            0.01

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Aaron Butterfield           101           43.9         11.1               69.31
Adam Cahill                   5           83.3         50.4               40.00
Adam X. Zabriskie           299           97.7         20.7               18.06
Akshay Dandekar              27           19.3         13.7               18.52
Al Casagranda               202           56.4         37.4               49.01
Alain B. Giorla             722           52.6         43.2               62.05
Alex Lindsay              23522           58.2         21.1               53.71
Alex McCaskey                13            0.0         65.8                0.00
Andrea Alfonsi                5           83.3         34.1                0.00
Andrea Jokisaari            151           17.9          4.5               47.02
Andrea Rovinelli           1189           53.8         20.9               74.18
Andrew E. Slaughter      119825           46.1         24.8               25.17
Andy Wilkins              35607           63.9         42.4               35.95
Antonio                    1667          100.0          7.5               60.89
Antonio Recuero             191            4.9         14.1               79.06
April Novak                1351           84.4         23.2               70.24
Axel Seoane                 145           73.2         58.0               48.28
Benjamin Spencer           5746           49.8         45.2               68.45
Bob Kinoshita                 4           21.1         77.6               50.00
Bradley Fromm                42           20.7         44.6               40.48
Brandon Langley              57           55.9         45.4               61.40
Brian Alger               11772           65.3         49.3               12.30
Brycen Wendt               1474           51.7         41.0               68.59
Casey Icenhour             1988           87.3         18.8               32.80
Casper Versteeg               2          100.0          6.4                0.00
Chandana Jayasundara          3            1.2         81.9               33.33
Chandrakanth Boliset         13           16.2         42.9               69.23
Chandu Bolisetti            285           56.3         17.7               61.40
Chris Green               10093           57.7         33.2               53.07
CiCi Pham                   108           87.1         46.2               75.93
Cody Permann              60968           51.6          9.4               34.21
Congjian Wang               230           36.4         50.1               72.61
Daniel Ruprecht              17           17.0         70.1               76.47
Daniel Schwen             17604           50.9         42.2               58.20
Danielle Perez                1           50.0         83.6                0.00
David Andrs               17186           29.6          8.7               59.89
Dehao Liu                   121           82.3         34.6               71.90
Derek Gaston              15011           20.7         24.1               57.77
Derek Stucki                  1           33.3         38.9                0.00
Dmitry Karpeev              162           16.9          0.0               67.90
Dylan McDowell              121           99.2         11.9               19.01
Fande Kong                 4561           61.1         28.7               52.75
Floyd Hilty                  36           46.2         59.1               16.67
Frederick Gleicher           22           51.2         67.9               50.00
Gary Hu                    1873           73.3         16.7               73.14
Gavin Ridley                114           95.0          7.5               86.84
Giovanni Pastore              4           44.4         61.9               75.00
Guillaume Giudicelli       1268           71.1          3.1               80.13
Hai Huang                    24           24.2         67.1               25.00
Hailong Chen               3556           59.7         34.0               78.04
Hao Wang                     64           58.7         59.4               43.75
Heather Sheldon             270           42.5         49.4               52.96
Ian                         630         2100.0         10.3              111.11
Ian Greenquist              268           69.8         41.2               63.06
Jacob Bair                   50           44.2         66.1               58.00
Jacob Hirschhorn             87           72.5         18.2               93.10
Jacob L. Bair                20           32.3         67.0               40.00
Jacob Peterson               11           61.1         83.7               72.73
James B. Tompkins           225           46.2         40.3               91.11
Jarin French                 34           42.5         58.9               44.12
Jaron Senecal                 1            7.1         48.3                0.00
Jason                        26           20.2         19.2              126.92
Jason D. Hales              975           12.5         20.1               68.21
Jason M. Miller           14800           33.8         24.4               20.15
Jed Brown                    10            1.7          0.0               50.00
Jesse Carter                247           62.1         47.1               52.23
Jieun Lee                    25           45.5         32.5               44.00
John Hutchins                68           20.3          0.0               54.41
John Mangeri                136           51.9         52.4               53.68
John W. Peterson           7654           51.4         42.0               62.07
John-Michael Bradley         46           48.9         65.5               63.04
Joshua E. Hansel           2641           62.0         29.7               70.58
Ju-Yuan Yeh                  61           60.4         44.6               59.02
Justin Coleman               46           33.8          0.0               71.74
Karim Ahmed                 164           60.5         58.7               42.68
Katherine Smith              17           15.7          0.0               64.71
Kevin J. Dugan                9          900.0         38.0               44.44
Kyle Gamble                 249           77.1         33.1               77.91
Kyoungdoc Kim                41           83.7         39.4               73.17
Larry Aagesen               983           61.7         52.7               51.68
Lei Zhao                      1           20.0         78.5                0.00
Leora Chapuis              1885           68.7         31.6               84.19
Ling Liu                    211           79.6         41.2               49.29
Ling Zou                      2           66.7         21.6               50.00
Logan Harbour             10805           92.7          6.4               60.98
Luanjing Guo                147           18.3          0.0               59.86
Luke Robinson                 1           50.0          0.4                0.00
Lynn Munday                 321           61.0          8.8               74.14
MOOSEBUILD                    3           33.3          8.6                0.00
Malachi Tolman                2            0.8         52.0                0.00
Marie Backman               285           30.0         61.1               52.28
Mark C. Messner               9          100.0         47.4               88.89
Mark L. Baird                 1          100.0         39.4                0.00
Martin Lesueur                1           50.0         62.4                0.00
Mathias Winkel                1            1.3         77.5                0.00
Matt Ellis                    3          100.0         78.2               33.33
Matthias                      5          100.0          4.0               20.00
Matthias Kunick             856           75.4         29.3               68.11
Michael Pernice              11           39.3          0.0               54.55
Michael Short                19           20.2          0.0               47.37
Michael Tonks              1478           24.3         38.6               59.61
Moosetest                     1          100.0         35.0                0.00
Paul Talbot                  88           21.9          0.0               82.95
Peter German                893           65.8         10.8               94.29
Philip Jagielski             48            0.5          0.0               58.33
Philipp Schaedle             39           90.7         38.1               82.05
Pritam Chakraborty         1240           41.5         66.0               44.35
Richard Williamson           15            5.2          0.0               26.67
Robert Carlsen            41574           70.1         45.3               29.42
Roy H. Stogner              604           71.2         49.7               84.60
Roy Stogner                 101           80.2          2.0               61.39
Samuel K. Tew               234           44.2         23.7               68.38
Sebastian Schunert         2824           92.5         25.9               66.68
Shane Stafford              169           65.3         75.7               28.40
Shiyuan Gu                   13           11.5          0.0              107.69
Shrey Satpathy               49           32.9         45.0               75.51
Som L. Dhulipala            240           89.9         10.4               87.08
Srivatsan Hulikal            15           55.6         59.1               26.67
Stephanie Pitts             867           31.9         47.0               67.24
Stephen Novascone           133           17.4         12.0               53.38
Sterling Harper             605           80.8         25.3               52.73
Steven Wacker                 1           20.0         41.4              100.00
Sudipta Biswas             1492           51.6         54.4               64.21
Swetha Veeraraghavan       2153           58.9         37.8               73.76
Tami Grimmett                 1          100.0         72.7              100.00
Topher Matthews            2893           58.8         19.1               72.62
Toptan, Aysenur              41          100.0         12.3                2.44
Vincent Laboure             146           90.7         14.7               69.18
Vishal Patel                 14           17.5         39.8               35.71
Wen Jiang                  2693           61.6         43.8               60.19
William Hoffman               7           77.8         55.2               28.57
Yang Xia                     71           36.2         68.8               39.44
Yaqi Wang                  5605           67.8         25.6               70.31
Yeh, Ju-Yuan                 26           74.3         28.2               88.46
Yeon Sang Jung              272          100.0          0.7               83.46
Yidong Xia                  748           28.1         55.0               60.96
Yingjie Liu                  17           12.2         45.3                0.00
Yipeng Gao                   26           65.0         48.3               61.54
Zachary M. Prince          3136           81.2          9.4               57.49
Ziyu Zhang                  127            4.9         76.0               78.74
balep                        10          100.0         14.5               30.00
crswong888                 2236           85.1          8.2               26.48
daniel.vanwasshenova        398          780.4         12.9               88.44
dewenyushu                  900           97.0          5.5               61.11
helen-brooks                  2          100.0          2.7              100.00
killerpenguin12              31           91.2         14.4              122.58
knw7x9                        3          100.0          3.6                0.00
moose                        29           80.6         24.5               62.07
moosetest                 25843        86143.3         42.0              136.20
rayaprolu143                 14           87.5         21.4               42.86
wesleyzzz                     9           90.0         24.6              177.78
wuxueyang                   103           85.1         17.7               82.52

[WilkAndy]

Hi @jedbrown ,

In case you're stumped for reviewers, a couple of suggestions are

• Allan Leal https://github.com/reaktoro/reaktoro
• Most people who contribute to OpenGeoSys https://github.com/ufz , probably contributors to https://github.com/ufz/iphreeqc or https://github.com/ufz/userguide might be the best

[jedbrown]

Hah, I'm waiting for a reply from Allan after he returns (per auto responder).

[whedon]

:wave: @smolins, please update us on how your review is going (this is an automated reminder).

[jedbrown]

@whedon add @volpatto as reviewer

[whedon]

OK, @volpatto is now a reviewer

[jedbrown]

@volpatto :wave: Welcome to JOSS and thanks for agreeing to review!

The comments from @whedon up top :point_up: outline the review process, which takes place in this thread (possibly with issues filed in the rsudp repository). I'll be watching this thread if you have any questions.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/3314 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within a month or so. Please let me know if you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@jedbrown) if you have any questions/concerns.

[WilkAndy]

Hey @jedbrown . I'm just wondering whether we could speed up this review somehow?

[jedbrown]

@smolins @volpatto :wave: Could you please let us know how your reviews are going and if you need anything from us? It's usually helpful to start the dialog early and incrementally, rather than waiting to complete your review in one shot.

[volpatto]

Hi, @jedbrown. Yes, I have begun my review and I will make some comments below.

[volpatto]

Firstly, I would like to say that MOOSE's geochemistry module is quite interesting and provides an easy way to simulate coupled phenomena with geochemical reactions. For the authors, my congratulations.

Following the JOSS Reviewer's guideline, I will draw some comments below:

General checks

Repository: Is the source code for this software available at the repository URL?

Not clear to me if it should be the MOOSE's URL, despite it makes sense since the piece of software in this submission is a MOOSE's module. Very minor suggestion, but I think it would be more appropriate to point to the geochemistry module's URL, where the paper.md is hosted.

Software paper

Well written and clear.

References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

~The .bib file is there, but references are not rendered in paper.md (only hyperlinks), and the bibliography file is not configured in the References (at least in thenext branch). After fixing that, I think it would be OK after generating the PDF file with pandoc. @jedbrown, I am not sure if this point should be marked as "checked" or not.~

Apologies, I have checked the paper's proof (I haven't noticed it before). Looks good to me.

[jedbrown]

Thanks, @volpatto. The repository URL is meant to be clonable, which a sub-tree is not. We understand that some projects take a monorepo approach while others use separate repositories, and JOSS is okay working with both so long as the scope of the module meant for review is clear.

And regarding references, those are automatically picked up by Whedon, as you saw in the proof.

[WilkAndy]

Many thanks for your positive review, @volpatto :-)

[smolins]

I started with the software paper. There are minor and major issues noted below (I refer to the lines in the pdf) :

line 13: flow --> transport

line 17: it is not clear just by the abstract how chemistry deforms the subsurface. It is a confusing sentence overall

line 35: complicated --> complex?

Section Existing software: This list is missing probably the most active open-source RT code around, PFLOTRAN Also, I would strongly suggest using this reference for CrunchFlow: (Steefel et al 2015) https://link.springer.com/article/10.1007/s10596-014-9443-x That's what Carl Steefel is using. Generally, this section should make a distinction between codes with their own geochemical capabilities (like MOOSE) and the ones that tap into external geochemical capabilities (unlike MOOSE). This is the theme of this paper so it must be there. Please read the intro to section "4 Code descriptions" of the reference above (Steefel et al 2015) to see what I mean. MOOSE is not the first to offer native geochemical capabilities. Also, there are RT codes that were born out of geochemical codes, while there are RT codes that were first Flow and Transport codes and then added geochemical capabilities. So lots to discuss here.

line 68: beautifully-designed --> this is a subjective statement. Remove, replace

lines 79-82: This is a very general statement that is not justified. It goes with my comment for the "Existing software" section. There are many codes around and comparisons are hard to make without going into detail. It is in unfair to make such general statements without discussion or appropriate references.

line 87: it's ---> its

line 104: so mineral equilibrium is enforced, and the precipitation/dissolution rate calculated after that from mass balance? Is this is a time-dependent calculation?

Section "Reactive Transport": In this section it is not clear whether one can or cannot use a global implicit approach to solve reactive transport with MOOSE. It is recommended to use operator splitting but what if I want to use global implicit. This is actually important. OS uses a linear transport solver while GI requires a non-linear solver for reactive transport. It appears that only the non-linear Newton solution approach for the geochemical problem is described in the Mathematical solution strategy section, not the global implicit. It is also not clear whether the canonical approach, where the number of species to be transported is reduced using the equilibrium assumption (see Steefel et al 2015), is part of MOOSE or not. Does transport solve for primary aqueous species concentration or does it solve for total component concentrations Or is it flexible?

line 201: a rudimentary

line 211: is only the finite-element-method supported?

Figure 1: Is that obtained with an operator splitting approach? What are the time step contraints here?

[smolins]

Could you please help me to find the instructions to build the code to run the examples in the geochemical module included in the paper? What MOOSE component do I need? One is a batch calculation and the other is a reactive transport run, so I am assuming different modules from MOOSE are needed but I can't find the description anywhere.

[jedbrown]

Thanks, @smolins.

@WilkAndy Please advise on the question about running and revise/respond to the other review points. In case the project documentation is unclear about how new users (who may not be experienced MOOSE users) can start running demos, it would be appropriate to revise that documentation so that it benefits other users, not just @smolins here. Thanks.

[WilkAndy]

Thanks @smolins . I need to check that the following instructions actually work before including them in the paper, but here's something to get you started

To build geochemistry and run the examples:

1. Download and install the entire MOOSE package. Instructions are at https://mooseframework.inl.gov/getting_started/installation/index.html . Even if you're interested only in geochemistry (without transport, solid mechanics, etc), MOOSE comes as a complete package, so needs to be installed in its entirety. Depending on your computer setup, this can be straightfoward (on a personal Mac computer) or complicated (on an administered supercomputer).
2. During the installation of MOOSE in part 1, only the "framework" will have been compiled. To compile all the physics modules, including the geochemistry module, use the following instructions run from the command line:

   cd ~/projects/moose/modules
   make -j 4
   cd ~/projects/moose/modules/geochemistry
   make -j 4

3. Check that the geochemistry module is correctly compiled using the following instructions:

   cd ~/projects/moose/modules/geochemistry
   ./run_tests

   Virtually all the tests should run and pass. Some may be "skipped" due to your computer setup (for instance, not enough threads).

4. Now you're ready to use the geochemistry module. For example, to run the Weber-Tensleep GeoTES example from the command line:

   cd ~/projects/moose/modules/combined/examples/geochem-porous_flow/geotes_weber_tensleep
   ../../../combined-opt -i exchanger.i

[WilkAndy]

Just confirming that the above instructions work. I will add them to the paper, but that will take a little time to merge through to the master branch.

[jedbrown]

You can use the syntax @whedon generate pdf from branch joss-paper-edits to get an updated draft for review before the branch merges.

[smolins]

Both examples in the manuscript seem to run. There are 2 issues

1.When I plot the results of the reactive transport example, the mesh (and resolution) seems to be different from the figure in the manuscript. Is that expected?

2. Why were these two examples highlighted in the manuscript? The code has many documented examples (https://mooseframework.inl.gov/modules/geochemistry/tests_and_examples/index.html). Are these specially interesting?

Overall, the main issue with the examples is the reliance almost exclusively on 1 source (Bethke 2007) and comparison to a single proprietary code, GWB. The examples are generally described sufficiently in the documentation but I feel that I would have benefited from having the book and GWB to fully follow everything.

[WilkAndy]

Thank you @smolins . I have addressed your comments immediately above in https://github.com/idaholab/moose/pull/18689 . I have not yet addressed your comments of 14 days ago, but will do soon. If you like, inspect the diffs at that PullRequest. Or, you can generate a new PDF by going to https://whedon.theoj.org/ and using repo https://github.com/WilkAndy/moose and branch joss_geochem_18610. Or, you can wait for a while until the PullRequest makes it through to the main branch of MOOSE.

1. You are correct that the mesh resolution is different from the figure. I'm going to add the following remark:

These results are derived using a higher resolution than the example included in the test suite, since the latter must be small enough to rapidly pass MOOSE's automatic regression testing.

2. You are correct that there are other examples I could have included. To explain, I'm going to add:

Tests and examples

The geochemistry module's code coverage currently exceeds 96%. Many of the more complicated benchmark tests and examples are comprehensively documented and the sections below present one benchmark study and one example by way of illustration.

3. Yes, we did a lot of comparisons against GWB. I'm not sure whether it's appropriate to explain this in the paper, but the reason we did a lot of GWB comparisons is that it's considered a "gold standard", and it has excellent documentation in the form of Bethke's book, and we believe that many potential users would be familiar with GWB, so hopefully they'd find the transition to MOOSE easier. I totally agree that not having Bethke's book makes reading the current paper and the documentation more difficult, but I'm also aware that we don't want to reproduce a lot of theory and explanation in this hopefully-brief paper.

[WilkAndy]

Hi @smolins . I believe that i've addressed all your concerns - the software ones from 3 days ago, and the article ones from 14 days ago. The changes may be seen at https://github.com/idaholab/moose/pull/18689/files and a new PDF may be made by going to https://whedon.theoj.org/ and using repo https://github.com/WilkAndy/moose and branch joss_geochem_18610 .

[smolins]

Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest

Review checklist for @smolins

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@WilkAndy) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [ ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• [ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

As noted above the submission meets most of the criteria above. My outstanding issues are

1. relating to the "Substantial scholarly effort". From manuscript:

33 In the past, researchers have typically answered such questions using separate models for 34 subsets of the physical processes, or loosely-coupled models solved using multiple software 35 packages. The MOOSE geochemistry module introduced here allows researchers to perform 36 stand-alone geochemical modelling, but also to draw upon the power of other MOOSE modules 37 to solve complicated coupled transport, geomechanical and geochemical models using a single 38 code

While I see that integrating all these capabilities in the Moose framework is new. It is not new in the reactive transport community. This needs to be explicitly stated. Plus, the example presented shows some of these coupled capabilities for the resulting code but it is not clear whether these are unique to moose, or which ones are unique to moose.

2. I think you should state as well that why you chose to use GWB in the manuscript. It is clearly at odds with the open source angle of this journal and the open source licence for moose. Also, there are community benchmarking efforts for reactive transport that offer solutions that have been obtained and compared by a range of reactive transport codes each

Computational Geosciences Volume 19, issue 3 https://link.springer.com/journal/10596/volumes-and-issues/19-3

Computational Geosciences Volume 25, issue 4, https://link.springer.com/journal/10596/volumes-and-issues/25-4

3. It is not clear what "nevertheless" means here.

215: Nevertheless, a rudimentary transport capability has been included in the geochemistry module, 216 which models advective-diffusive transport of the mobile concentrations, with hydrodynamic 217 dispersion

I believe that the test problems use this simple transport solver rather that PorousFlow, so you should mention this too.

4. "Reactive transport" section, lines 192, 195: what does the word "usually" mean here? Is it needed? It is not clear what other unusual options are there...

[jedbrown]

Thanks @smolins. To clarify regarding "substantial scholarly effort", this verbiage exists mainly to screen "small" products that shouldn't be "counted" as paper-like units. JOSS does not have a "novelty" criteria like some journals -- quality software that fills a research need is in-scope even if for each specific problem instance that can be solved with the new software, there is existing software that can also solve it similarly well. It still needs an honest statement of need that does justice to alternatives. For instance, a new package might be preferred because of how it facilitates some type of integration for which there is a research need. That could be reaching a different language/library community, though the software should be well integrated in that environment.

JOSS papers should not claim novel methods or new scientific results -- there are existing venues for that sort of work. (JOSS software, and any sufficiently mature software for that matter, often contains some unpublished work of that sort, it just isn't the scholarship that JOSS intends to evaluate.)

I'll leave it to @WilkAndy to revise and reply to specific points.

[smolins]

Thanks @jedbrown for the clarification. I would say then that the paragraph (lines 33-38)

33 In the past, researchers have typically answered such questions using separate models for 34 subsets of the physical processes, or loosely-coupled models solved using multiple software 35 packages. The MOOSE geochemistry module introduced here allows researchers to perform 36 stand-alone geochemical modelling, but also to draw upon the power of other MOOSE modules 37 to solve complicated coupled transport, geomechanical and geochemical models using a single 38 code.

should be more specific to moose. In other words, there are other codes that implement coupled models with their own capabilities. It is moose that did not have geochemistry and that was the need.

[WilkAndy]

Thanks for more suggestions on how to improve the manuscript, @smolins . I believe i have addressed all your points. The changes may be seen at https://github.com/idaholab/moose/pull/18689/files and a new PDF may be made by going to https://whedon.theoj.org/ and using repo https://github.com/WilkAndy/moose and branch joss_geochem_18610 .

• Regarding use of geochemistry's inbuilt transport capability, or PorousFlow's version: about half the tests/examples use the former and half use the latter. PorousFlow is always preferred in real-life situations so is used in the more complicated models.
• Regarding benchmarking against GWB (which I've highlighted in the new manuscript): the reason we benchmarked against GWB was to try to attract the attention of people who tend to dismiss open-source/research codes as impractical/buggy/idealised/unreliable. Those people may also treat Bethke's (excellent) book as a bible, so we provided references to it throughout the online documentation. Perhaps you and others wouldn't have taken this approach!

[smolins]

I think I can check all items now. My criticism with the approach did not seek to cast doubts about the tests or test results (i.e. that the code does solve the problems correctly.) I am mostly concerned in comparing mostly with a proprietary software when other open-source codes and results are also available. I find the use of a json formatted database as an interesting development, which I have also considered. One of the main obstacles to compare results between codes is to feed the same geochemical data. The disparity in database formats definitely hinders these efforts. A read format that is flexible to implement in different codes would facilitate that. But this is not the topic here.

Review checklist for @smolins

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@WilkAndy) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• [ x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[WilkAndy]

Thanks @smolins . Can you confirm that no further revisions are required? Then I can get the MOOSE PullRequest merged. This current issue currently has "10 of 40 tasks" complete, so perhaps you or I have to check some boxes in one of the comments above.

[smolins]

Yes, I am ok with this. The task lists are in the very first comment in this Issue/Review. I can't edit that comment, so somebody else will have to do it.

[volpatto]

@smolins for me, I have clicked on the check-boxes in the first comment. Then the progress status was automatically updated.

@WilkAndy I will continue my review in the next few days. I think @smolins addressed a lot of relevant things already.

[jedbrown]

@whedon re-invite @smolins as reviewer

[whedon]

The reviewer already has a pending invite.

@smolins please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[jedbrown]

Thanks @volpatto.

@smolins If you accept the invitation, you should be able to click in the top comment. Thanks for your thoughtful review and discussion.

[smolins]

I accepted and it still does not work.

On Sun, Sep 5, 2021 at 8:41 PM Jed Brown @.***> wrote:

Thanks @volpatto https://github.com/volpatto.

@smolins https://github.com/smolins If you accept the invitation, you should be able to click in the top comment. Thanks for your thoughtful review and discussion.

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[jedbrown]

Weird, I have not encountered that before and will investigate/report. In the meantime, I've updated the checklist based on your comment. Thanks again for your review.

[volpatto]

Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

2 and 3 are properly addressed on MOOSE website. However, I did not find that 1 is clear enough. I looked in MOOSE's README.md and found a link that is not working. Thus I opened an Issue in the MOOSE repo. By the way, this is a minor issue, easy to solve.

[volpatto]

Functionality

Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

The authors performed (strong) scaling analyses and space complexity estimation. Results (in the paper and in the MOOSE website) are interesting, nearly optimal for scaling. However, I should remark that there are no instructions on reproducibility (I mean, related to profiling). Moreover, the case "Reactive-transport using multiple processors" is only possible in HPC environments or in a good workstation.

AFAIK, this is not a terrible problem, it is quite common to be unable to reproduce performance analyses, but I have to state that I can't confirm the results by running them.

[WilkAndy]

@volpatto - you'll see that the "README.md" issue you mentioned above has now been fixed. I'm not sure whether you need me to address your "Functionality - Performance" issue above. Could you please confirm one way or the other?

[volpatto]

@volpatto - you'll see that the "README.md" issue you mentioned above has now been fixed.

Great, thanks.

I'm not sure whether you need me to address your "Functionality - Performance" issue above. Could you please confirm one way or the other?

Sure, sorry for not being clear. I think there is no need for changes, it was just a comment/feedback. Since measurements are provided, I understand that this is enough.

[volpatto]

Okay, I think I almost finished my review. I will draw some comments.

Minor/side comments

• Installations: Following the instructions to install MOOSE and everything would be fine. MOOSE uses conda to manage dependencies, which is great, IMO.

• I have compiled MOOSE in WSL2 (using Ubuntu 20.04), it worked fine. Compilation may take some time (around 10 min on my PC).

Comments

Automated tests

I executed the MOOSE test set and it runs properly on my PC. However, as I am not an experienced user/dev of MOOSE (and MOOSE is huge, the tutorial is huge too, naturally), it was not immediately clear to me how to test the geochemistry module alone. It turns out to be very simple, and the geochemistry module has 126 tests when running run_tests in the geochemistry module's root dir. This is not the number of tests the manuscript claims to be implemented (350 tests), please see the first paragraph here. I understand that this claimed number of tests probably included some benchmarks, but they are not formally implemented in the test set. Or the geochemistry module has another test script?

Example cases

I tried to reproduce the cooling with feldspars example. Unfortunately, I had to look in the tests and examples page to find the example. The listed name is "Progressively changing the temperature", which is provided here. I would like to suggest adding this link and the example name to the manuscript.

In the aforementioned example docs, I found no direct instructions on how to run the case. I have check other examples, and I didn't find instructions as well. I know that this is a very basic MOOSE usage, but for some user that just has found MOOSE's geochemistry module and wants to give it a try (as standalone), it can discourage the user to try the software. In MOOSE's examples and tutorial, sometimes a "Running the Problem" section is provided. I think it would be convenient to have something like that in the geochemistry module example, as it offers standalone capabilities. Moreover, the example has a Python script to plot the results.

Mathematical solution strategy

The geochemistry module online docs are great. Why the Theory page is not mentioned in this section?

Coupling

The authors may face some queries about the coupling strategy (with transport solver) when presenting the geochemistry module to the community. In the manuscript, it is recommended the usage of a Sequential Non-Iterative Approach (SNIA). Although great for implementation ease and computational performance, this approach has limitations. Remarkably, the time-step size can affect/violate the chemical species' mass conservation due to the delay in the spatial operator discretization. The manuscript briefly mentions that different types of coupling are available. I would like to suggest mentioning these couplings in terms of Steefel and co-workers' (see references below) nomenclatures (GIA, SIA, and SNIA). I understand that every approach is possible using MOOSE, is that correct?

1. C. Steefel and K. MacQuarrie, “Approaches to modeling of reactive transport in porous media, ”Reviews in Mineralogy and Geochemistry, vol. 34, pp. 85–129, 1996.
2. C. Steefel, C. Appelo, B. Arora, D. Jacques, T. Kalbacher, O. Kolditz, V. Lagneau, P. Lichtner, K. U. Mayer, J. Meeussen, et al., “Reactive transport codes for subsurface environmental simulation, ”Computational Geosciences, vol. 19, no. 3, pp. 445–478, 2015.

[volpatto]

Since the geochemistry module has "standalone" capabilities, I think it would be interesting for new users the instructions cited below. Maybe it could be documented in the online documentations?

Thanks @smolins . I need to check that the following instructions actually work before including them in the paper, but here's something to get you started

To build geochemistry and run the examples:

1. Download and install the entire MOOSE package.  Instructions are at https://mooseframework.inl.gov/getting_started/installation/index.html .  Even if you're interested only in geochemistry (without transport, solid mechanics, etc), MOOSE comes as a complete package, so needs to be installed in its entirety.  Depending on your computer setup, this can be straightfoward (on a personal Mac computer) or complicated (on an administered supercomputer).

2. During the installation of MOOSE in part 1, only the "framework" will have been compiled.  To compile all the physics modules, including the `geochemistry` module, use the following instructions run from the command line:

cd ~/projects/moose/modules
make -j 4
cd ~/projects/moose/modules/geochemistry
make -j 4

1. Check that the geochemistry module is correctly compiled using the following instructions:

cd ~/projects/moose/modules/geochemistry
./run_tests

Virtually all the tests should run and pass. Some may be "skipped" due to your computer setup (for instance, not enough threads).

4. Now you're ready to use the geochemistry module. For example, to run the Weber-Tensleep GeoTES example from the command line:

cd ~/projects/moose/modules/combined/examples/geochem-porous_flow/geotes_weber_tensleep
../../../combined-opt -i exchanger.i

[WilkAndy]

Hi @volpatto , The revised article may be seen by going to https://whedon.theoj.org/ and using repo https://github.com/WilkAndy/moose and branch joss_volpatto_18610 . The revisions will take a while to merge into MOOSE: the PR is at https://github.com/idaholab/moose/pull/19030 . To answer all your points above:

1. _"... the geochemistry module has 126 tests when running runtests in the geochemistry module's root dir. This is not the number of tests the manuscript claims to be implemented (350 tests)..." I apologize. There are also 252 unit tests. These may be run using

   cd ~/projects/moose/modules/geochemistry/unit
   make
   ./run_tests

   I have added those instructions to the JOSS article.

2. "...I would like to suggest adding this link and the example name to the manuscript..." (cooling feldspars example) I've added the appropriate link.

3. "... I found no direct instructions on how to run the case..." The JOSS article does contain the paragraph: The geochemistry executable is called geochemistry-opt and is found at ~/projects/moose/modules/geochemistry. This may be used to run pure geochemistry simulations. For coupled reactive-transport simulations using the PorousFlow module, the combined-opt executable must be used. For example, to run the Weber-Tensleep GeoTES example from the command line:

   cd ~/projects/moose/modules/combined/examples/geochem-porous_flow/geotes_weber_tensleep
   ../../../combined-opt -i exchanger.i

   But I agree that the "standalone" capabilities of the module mean it should have standalone instructions. I have expanded the instructions in the article, and also added to the online MOOSE documentation.

4. _"...Why the Theory page is not mentioned in this section?..." I've added the link to the article.

5. Coupling strategies: I've now mentioned SIA and SNIA explicitly, and that users have to be careful with timestep sizes, and i've cited the Steefel2015 article.

[WilkAndy]

@jedbrown - i believe the review process is completed. What is the next step?

[WilkAndy]

Pinging @jedbrown again - i believe the review process is completed. What is the next step?

[kyleniemeyer]

@whedon generate pdf

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left: