Merge branch 'main' into 'gmp'

Main merge to gmp

See merge request dam-elbextreme/oxypom!4

Author: platipodium

LICENSE.md

@@ -0,0 +1,216 @@
+<!--
+SPDX-FileCopyRightText: {datetime.date.today().year} Helmholtz-Zentrum hereon GmbH
+SPDX-LicenseRef: CC0-1.0
+SPDX-FileContributor: Carsten Lemmen <carsten.lemmen@hereon.de>
+
+This file was autogenerated by `{sys.argv[0]}`, please do not edit by hand.
+To produce this content, run `reuse spdx | python {sys.argv[0]}`
+-->
+
+# Licenses used
+
+While the OxyPOM software itself is distributed under the Apache-2.0 permissive
+license, several other licenses are used by this project, all of them open source,
+and most of them under open source licenses approved by the Open Software
+Initiative.
+
+You can find the full license text for each license used
+in the  [LICENSES](./LICENSES/) folder.
+
+<img src=https://149753425.v2.pressablecdn.com/wp-content/uploads/2009/06/OSIApproved_100X125.png width=10px height=12.5px> [Apache-2.0](./LICENSES/Apache-2.0.txt); <img src=https://149753425.v2.pressablecdn.com/wp-content/uploads/2009/06/OSIApproved_100X125.png width=10px height=12.5px> [CC-BY-3.0](./LICENSES/CC-BY-3.0.txt); <img src=https://149753425.v2.pressablecdn.com/wp-content/uploads/2009/06/OSIApproved_100X125.png width=10px height=12.5px> [CC-BY-4.0](./LICENSES/CC-BY-4.0.txt); <img src=https://149753425.v2.pressablecdn.com/wp-content/uploads/2009/06/OSIApproved_100X125.png width=10px height=12.5px> [CC-BY-SA-4.0](./LICENSES/CC-BY-SA-4.0.txt); <img src=https://149753425.v2.pressablecdn.com/wp-content/uploads/2009/06/OSIApproved_100X125.png width=10px height=12.5px> [CC0-1.0](./LICENSES/CC0-1.0.txt).
+
+## Copyright holders
+
+The following organizations and individuals own copyrights to (parts of) this project.
+
+* Helmholtz-Zentrum hereon GmbH
+* Organization for Ethical Source
+* Project Harmony
+* The Journal of Open Source Software
+
+## License and copyright manifest
+
+Each file carries a license attribution, please consult the following list to identify
+the license applicable to an individual file:
+
+* ./.docker/Dockerfile-fabm:
+License: CC0-1.0
+Copyright: 2024-2025 Helmholtz-Zentrum hereon GmbH
+* ./.docker/Makefile:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./.editorconfig:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./.github/dependabot.yaml:
+License: CC0-1.0
+Copyright: 2022-2025 Helmholtz-Zentrum hereon GmbH
+* ./.github/workflows/cmake-multi-platform.yaml:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./.github/workflows/fabm.yaml:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./.github/workflows/gotm.yaml:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./.gitignore:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./.gitlab-ci.yml:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./.gitlab/fabm.yaml:
+License: CC0-1.0
+Copyright: 2023-2025 Helmholtz-Zentrum hereon GmbH
+* ./.gitlab/joss.yaml:
+License: CC0-1.0
+Copyright: 2022-2025 Helmholtz-Zentrum hereon GmbH
+* ./.gitlab/license.yaml:
+License: CC0-1.0
+Copyright: 2022-2025 Helmholtz-Zentrum hereon GmbH
+* ./.gitlab/r.yaml:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./.gitlab/zenodo.yaml:
+License: CC0-1.0
+Copyright: 2023-2025 Helmholtz-Zentrum hereon GmbH
+* ./.mailmap:
+License: CC0-1.0
+Copyright: 2023-2025 Helmholtz-Zentrum hereon GmbH
+* ./.pre-commit-config.yaml:
+License: CC0-1.0
+Copyright: 2022-2025 Helmholtz-Zentrum hereon GmbH
+* ./.zenodo.json:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./CITATION.cff:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./ChangeLog.md:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./Makefile:
+License: CC0-1.0
+Copyright: 2023-2025 Helmholtz-Zentrum hereon GmbH
+* ./ReadMe.md:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./codemeta.json:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./doc/contributing/ReadMe.md:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./doc/contributing/code_of_conduct.md:
+License: CC-BY-4.0
+Copyright: 2014-2023 Organization for Ethical Source
+* ./doc/contributing/coding_standard.md:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./doc/contributing/contributing-license.md:
+License: CC-BY-3.0
+Copyright: 2011 Project Harmony
+* ./doc/joss/.gitignore:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./doc/joss/Makefile:
+License: CC0-1.0
+Copyright: 2023-2025 Helmholtz-Zentrum hereon GmbH
+* ./doc/joss/ReadMe.md:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./doc/joss/figure1.pdf:
+License: CC-BY-4.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./doc/joss/joss-template.tex:
+License: CC-BY-SA-4.0
+Copyright: 2018-2023 The Journal of Open Source Software
+* ./doc/joss/joss_banner_title.png:
+License: CC-BY-4.0
+Copyright: 2018-2025 The Journal of Open Source Software
+* ./doc/joss/paper.bib:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./doc/joss/paper.md:
+License: CC-BY-4.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./python/reuse2txt.py:
+License: Apache-2.0
+Copyright: 2023-2025 Helmholtz-Zentrum hereon GmbH
+* ./src/CMakeLists.txt:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./src/diamo/README.md:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./src/diamo/diamo.F90:
+License: Apache-2.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./src/light/light.F90:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./src/oxypom/README.md:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./src/oxypom/oxypom.F90:
+License: Apache-2.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./src/oxypom_model_library.F90:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/ReadMe.md:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/estuary/ReadMe.md:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/estuary/fabm.yaml:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/estuary/get_data.sh:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/estuary/gotm.yaml:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/estuary/output.yaml:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/estuary/plot_output.R:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/estuary/setup_data.R:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/fabm-installation.sh:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/gotm-installation.sh:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/light/README.md:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/light/fabm.new.yaml:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/light/fabm.ref.yaml:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/light/gotm.yaml:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/light/model_comparison.R:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/light/output.yaml:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/run-estuary-testcase.sh:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+* ./testcases/run-light-testcase.sh:
+License: CC0-1.0
+Copyright: 2025 Helmholtz-Zentrum hereon GmbH
+

Makefile

@@ -13,6 +13,11 @@ default:
 	@echo Valid Makefile targets are: '"version"'
 	@echo To build this package, follow the instructions in the Readme.md file.
 
+LICENSE.md: python/reuse2txt.py
+	reuse spdx | python python/reuse2txt.py > ./LICENSE.md
+
+license: LICENSE.md
+
 # This target updates all files that control the versioning
 # of the software package
 version:

ReadMe.md

@@ -39,10 +39,10 @@ Together with `OxyPOM` and `DiaMO`, this repository includes the model `oxypom/l
 
 - This model requires:
 
-    - `FABM` (v1 or above) available in [fabm github](https://github.com/fabm-model/fabm/).
-      It can be cloned using `git clone https://github.com/fabm-model/fabm.git fabm`.
+  - `FABM` (v1 or above) available in [fabm github](https://github.com/fabm-model/fabm/).
+    It can be cloned using `git clone https://github.com/fabm-model/fabm.git fabm`.
 
-- The physical driver:
+  - The physical driver:
     - `GOTM` (v6.0 latest stable release) available in [gotm github](https://github.com/orgs/gotm-model/repositories).
       It can be cloned using via `git clone --recursive https://github.com/gotm-model/code.git -b v6.0 gotm6`.
 

doc/joss/figure1.pdf

@@ -102,4 +102,46 @@ @article{Maerz2009
 url = {http://dx.doi.org/10.1016/j.ecss.2009.05.015},
 volume = {84},
 year = {2009}
+}
+
+@article{Raymond2001,
+author = {Raymond, Peter A. and Cole, Jonathan J.},
+journal = {Estuaries},
+number = {2},
+pages = {312--317},
+title = {{Gas exchange in rivers and estuaries: Choosing a gas
+transfer velocity}},
+volume = {24},
+year = {2001},
+doi = {10.2307/1352954},
+issn = {01608347},
+}
+
+
+@article{Scharfe2009,
+author = {Scharfe, Mirco and Callies, Ulrich and
+Bl{\"{o}}cker, Gerd and Petersen, Wilhelm and
+Schroeder, Friedhelm},
+journal = {Ecol. Modell.},
+number = {18},
+pages = {2173--2186},
+title = {{A simple Lagrangian model to simulate temporal
+variability of algae in the Elbe River}},
+volume = {220},
+year = {2009},
+doi = {10.1016/j.ecolmodel.2009.04.048},
+issn = {03043800},
+}
+
+@article{Wirtz2019,
+author = {Wirtz, Kai W.},
+journal = {PLoS One},
+number = {2},
+title = {{Physics or biology? Persistent chlorophyll
+accumulation in a shallow coastal sea explained by
+pathogens and carnivorous grazing}},
+volume = {14},
+year = {2019},
+doi = {10.1371/journal.pone.0212143},
+issn = {19326203},
 }

doc/joss/paper.bib

@@ -13,11 +13,15 @@ tags:
 authors:
     - name: Ovidio García-Oliva
       orcid: 0000-0001-6060-2001
+      affiliation: 1
     - name: Carsten Lemmen
       orcid: 0000-0003-3483-6036
+      affiliation: 1
 affiliations:
     - name: Helmholtz-Zentrum Hereon, Institute of Coastal Systems - Modeling and Analysis, Germany, ovidio.garcia@hereon.de
-date: 21 March 2025
+      index: 1
+      ror: 03qjp1d79
+date: 22 August 2025
 year: 2025
 bibliography: paper.bib
 SPDX-FileCopyrightText: 2025 Helmholtz-Zentrum hereon GmbH
@@ -38,7 +42,9 @@ OxyPOM and DiaMO remove  much of this complexity and focus on the key processes
 
 A predecessor 1D long-channel version of OxyPOM was initially implemented by @Holzwarth2018 specifically for the closed-source UnTRIM-DELWAQ hydrodynamic and water quality system. 
 This implementation lacked portability, and was neither findable, nor accessible, interoperable or reusable (FAIR).  The reimplementation with the FABM API ensures FAIR principles, foremost the interoperability with (1) many hydrodynamic models, (2) other aquatic process models, and (3) reusability in different topological domains.
-For vertically resolved applications, we added formulations for re-aeration, primary production, and light attenuation.
+When porting OxyPOM to FABM, we introduced new features:
+For vertically resolved applications, we added vertically-explicit formulations for re-aeration in rivers and estuaries [@Raymond2001], primary production, and light attenuation.  We included additional mortality terms related to micro-algae viral infections [@Wirtz2019], and a step-wise temperature-sensitive micro-algae loss rate [@Scharfe2009].
+
 Where a complete representation of bio-geochemical dynamics is not needed, DiaMO is an even more simplified model for quick assessments of DO dynamics.
 
 ## OxyPOM: Oxygen and Particulate Organic Matter