diff --git a/LICENSES/GPL-2.0-only.txt b/LICENSES/GPL-2.0-only.txt
deleted file mode 100644
index 9efa6fbc962836e243e20f7f23db062e2c077d28..0000000000000000000000000000000000000000
--- a/LICENSES/GPL-2.0-only.txt
+++ /dev/null
@@ -1,338 +0,0 @@
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diff --git a/ReadMe.md b/ReadMe.md
index 1ac5fd2f5ac20e5ed5500fae3393454e2763401b..cb9c99fe45117846aa8b1e268fd94b926460c7fc 100644
--- a/ReadMe.md
+++ b/ReadMe.md
@@ -2,6 +2,7 @@
SPDX-FileCopyrightText: 2025 Helmholtz-Zentrum hereon GmbH
SPDX-License-Identifier: CC0-1.0
SPDX-FileContributor Ovidio Garcia-Oliva <ovidio.garcia@hereon.de>
+SPDX-FileContributor Carsten Lemmen <carsten.lemmen@hereon.de>
-->
[](https://www.repostatus.org/#active)
@@ -19,7 +20,6 @@ SPDX-FileContributor Ovidio Garcia-Oliva <ovidio.garcia@hereon.de>
[](LINK HERE)
-->
-
# OxyPOM and DiaMO: simple models for dissolved oxygen and biogeochemistry
`OxyPOM` (**Oxygen and Particulate Organic Matter**) and `DiaMO` (**Diagnostic Model for Oxygen**) are two models that resolve dissolved oxygen dynamics implemented in FABM.
@@ -32,7 +32,7 @@ SPDX-FileContributor Ovidio Garcia-Oliva <ovidio.garcia@hereon.de>
The code of these models is located in the directory `./src` (e.g., `./src/oxypom` and `./src/diamo`), and future code developed as part of this model should be here included.
-Together with `OxyPOM` and `DiaMO`, this repository includes the model `oxypom/light`: a second order correction for the calculation of photosynthetically active radiation depth profiles.
+Together with `OxyPOM` and `DiaMO`, this repository includes the model `oxypom/light`: a second-order correction for the calculation of photosynthetically active radiation depth profiles.
## Requirements
@@ -112,7 +112,6 @@ The entire procedure is included in `./testcases/run-light-testcase.sh`.
## License
Apache-2.0 (OxyPOM and DiaMo)
-GPL-2.0-only (light)
## Project status
@@ -121,15 +120,14 @@ This is part of the `DAM-ElbeXtreme` project.
## Contributing and reporting
We recommend to use latest git commit an branch main version of the model.
-We appreciate your feedback, bug reports and improvement suggestions on our [issue tracker](https://codebase.helmholtz.cloud/dam-elbextreme/oxypom/-/issues).
-We also welcome your contributions, subject to our Contributor Covenant [code of conduct](https://codebase.helmholtz.cloud/dam-elbextreme/oxypom/-/blob/main/doc/contributing/code_of_conduct.md) and our [contributor license agreement](https://codebase.helmholtz.cloud/dam-elbextreme/oxypom/-/blob/main/doc/contributing/contributing-license.md).
+We appreciate your feedback, bug reports and improvement suggestions on our GitLab [issue tracker](https://codebase.helmholtz.cloud/dam-elbextreme/oxypom/-/issues).
+We also welcome your contributions, subject to our Contributor Covenant [code of conduct](https://codebase.helmholtz.cloud/dam-elbextreme/oxypom/-/blob/main/doc/contributing/code_of_conduct.md) and our [Contributor License Agreement](https://codebase.helmholtz.cloud/dam-elbextreme/oxypom/-/blob/main/doc/contributing/contributing-license.md).
The best way to contribute is by (1) creating a fork off our repository, (2) committing your changes on your fork and then (3) creating a pull request ("PR") to push your changes back to us.
-To file an issue or to contribute, you are asked to (1) authenticate with an existing identity and (2) to register on the HIFIS GitLab instance and sign in.
+To file an issue or to contribute, you are asked to (1) authenticate with an existing identity and (2) to register on the HIFIS GitLab instance and sign in.
When asked, click "Sign in with Helmholtz AAI".
On the following page "Login to Helmholtz AAI OAuth2 Authorization Server", search for one of your existing authentication providers (this may be your university, company, ORCID, GitHub, or many others) and provide their login credentials for authorization.
-If you are not already registered on the HIFIS GitLab instance, a confirmation email will be sent to the primary email address registered with your authentication provider.
-After clicking the confirmation link, you will also be asked to provide a name on this Gitlab instance; this will be your nickname.
+If you are not already registered on the HIFIS GitLab instance, a confirmation email will be sent to the primary email address registered with your authentication provider.
+After clicking the confirmation link, you will also be asked to provide a name on this GitLab instance; this will be your nickname.
Help on this one-time registration process is available from [https://hifis.net/tutorial/2021/06/23/how-to-helmholtz-aai.html](https://hifis.net/tutorial/2021/06/23/how-to-helmholtz-aai.html).
-
diff --git a/doc/joss/paper.md b/doc/joss/paper.md
index e37bb1fd760b54cac76a78b85e2d45acda52b400..bbe1cdb327fcc4b09a4659143cddcd7a63895c9a 100644
--- a/doc/joss/paper.md
+++ b/doc/joss/paper.md
@@ -1,21 +1,21 @@
---
title: "FABM OxyPOM and DiaMO: simple models for dissolved oxygen and biogeochemistry"
tags:
- - FABM
- - Biogeochemistry
- - Oxygen
- - ElbeXtreme
- - OxyPOM
- - DiaMO
- - Fortran
- - Water quality
+ - FABM
+ - Biogeochemistry
+ - Oxygen
+ - ElbeXtreme
+ - OxyPOM
+ - DiaMO
+ - Fortran
+ - Water quality
authors:
- - name: Ovidio GarcÃa-Oliva
- orcid: 0000-0001-6060-2001
- - name: Carsten Lemmen
- orcid: 0000-0003-3483-6036
+ - name: Ovidio GarcÃa-Oliva
+ orcid: 0000-0001-6060-2001
+ - name: Carsten Lemmen
+ orcid: 0000-0003-3483-6036
affiliations:
- - name: Helmholtz-Zentrum Hereon, Institute of Coastal Systems - Modeling and Analysis, Germany, ovidio.garcia@hereon.de
+ - name: Helmholtz-Zentrum Hereon, Institute of Coastal Systems - Modeling and Analysis, Germany, ovidio.garcia@hereon.de
date: 19 March 2025
year: 2025
bibliography: paper.bib
@@ -54,8 +54,8 @@ and two micro-algae classes (ALGi).
DO dynamics is based on a mass balance equation accounting for re-aeration and photosynthesis as oxygen sources, and respiration, mineralization and nitrification as sinks:
\begin{equation}
- \frac{d \textrm{DO}}{dt} = \textrm{re-aeration} + (\textrm{photosynthesis} - \textrm{respiration}) - \textrm{mineralization} + \textrm{nitrification}.
- \label{eq:do}
+\frac{d \textrm{DO}}{dt} = \textrm{re-aeration} + (\textrm{photosynthesis} - \textrm{respiration}) - \textrm{mineralization} + \textrm{nitrification}.
+\label{eq:do}
\end{equation}
This equation is applied to each water volume considered by the physical driver.
@@ -67,7 +67,7 @@ Nitrification is the oxygen consumed to oxidize ammonia into nitrate.
Temperature-dependent rates limit these processes.
In OxyPOM, POM and DOM have an explicit elemental composition (carbon, nitrogen and phosphorus).
-POM is present in two qualities, fresh and refractory, which transition in the sequence fresh $\rightarrow$ refractory $\rightarrow$ dissolved.
+POM is present in two qualities, fresh and refractory, which transition in the sequence fresh $\rightarrow$ refractory $\rightarrow$ dissolved.
POM and DOM mineralize to inorganic dissolved inorganic nutrients: nitrogen and ortho-phosphate.
Dissolved inorganic nitrogen is further subdivided into ammonium and nitrate.
Ammonia transitions to nitrate--nitrification-- as a function of DO.
@@ -78,12 +78,12 @@ Microalgae uptake dissolved inorganic nutrients and release dissolved nutrients
While the full description of the processes in OxyPOM is available in @Holzwarth2018, some changes were required for a vertically explicit implementation within FABM:
- 1. Re-aeration is calculated as surface oxygen transference using saturation concentration as a function of temperature, salinity and wind speed [@Weiss1970].
- This approach is commonly used in other models, such as ERSEM [@Butenschon2016].
+1. Re-aeration is calculated as surface oxygen transference using saturation concentration as a function of temperature, salinity and wind speed [@Weiss1970].
+ This approach is commonly used in other models, such as ERSEM [@Butenschon2016].
- 2. Light limitation for photosynthesis is calculated with an exponential saturation [@Platt1980].
+2. Light limitation for photosynthesis is calculated with an exponential saturation [@Platt1980].
- 3. Settling velocities are set constant, and vertical redistribution of matter is carried out by the physical driver.
+3. Settling velocities are set constant, and vertical redistribution of matter is carried out by the physical driver.
We validate both models in the Cuxhaven station in the Elbe estuary, where OxyPOM shows high skill by reproducing surface DO.
@@ -97,16 +97,18 @@ DO is solved with the mass balance equation of OxyPOM (\autoref{eq:do}), setting
The complete system is represented as
\begin{eqnarray}
- \frac{d \textrm{Phy}}{dt} &=& \textrm{photosynthesis} - \textrm{respiration} - \textrm{aggregation} \\
- \frac{d \textrm{Det}}{dt} &=& \textrm{aggregation} - \textrm{mineralization} \\
- \frac{d \textrm{DO}}{dt} &=& \textrm{re-aeration} + (\textrm{photosynthesis} - \textrm{respiration}) - \textrm{mineralization}.
+\frac{d \textrm{Phy}}{dt} &=& \textrm{photosynthesis} - \textrm{respiration} - \textrm{aggregation} \\
+\frac{d \textrm{Det}}{dt} &=& \textrm{aggregation} - \textrm{mineralization} \\
+\frac{d \textrm{DO}}{dt} &=& \textrm{re-aeration} + (\textrm{photosynthesis} - \textrm{respiration}) - \textrm{mineralization}.
\end{eqnarray}
In DiaMO, aggregation rate is a mortality term for phytoplankton [@Maerz2009].
As in OxyPOM, all rates in DiaMO are temperature-dependent.
## Light in OxyPOM and DiaMO
+
<!-- this paragraph needs rewriting as light is its own model -->
+
Together with OxyPOM and DiaMO, this repository includes the model oxypom/light as an alternative model to the FABM implementation of the light model used by GOTM [@Burchard2002].
While the default light model assumes that the photosynthetically active radiation (PAR) in a vertical layer $z$ of thickness $\Delta z$ is in the centre of the layer, oxypom/light calculates PAR in the representative depth $\bar{z}$, which satisfies the mean value theorem.
PAR evaluated at $\bar{z}$ is thus the mean PAR intensity on the layer.
@@ -114,8 +116,8 @@ Since this calculation can be computationally expensive to evaluate, first- and
The first-order solution is equal to the centre of the layer $z + \frac{1}{2} \Delta z$, and the second-order approximation is
\begin{equation}
- \bar{z} = z + \frac{1}{2} \Delta z - \frac{\alpha}{3} \Delta z ^ 2,
- \label{eq:secondorder}
+\bar{z} = z + \frac{1}{2} \Delta z - \frac{\alpha}{3} \Delta z ^ 2,
+\label{eq:secondorder}
\end{equation}
where $\alpha$ is the light extinction coefficient for the layer, accounting for physical and biological light absorption, assuming an exponential light decay.
@@ -124,11 +126,10 @@ where $\alpha$ is the light extinction coefficient for the layer, accounting for
The models are documented in short form in the `ReadMe.md` section of the repository and a complete description of the science behind OxyPOM is in @Holzwarth2018.
Open access data from third parties are not included with the model, scripts for their download are however included.
-Our own models, scripts and documentations are are released under open source licenses, mostly Apache 2.0, CC0-1.0, and CC-BY-SA-4.0, and where required upstream GPL-2.0-only. A comprehensive documentation of all licenses is provided via REUSE Software.
+Our own models, scripts and documentations are are released under open source licenses, mostly Apache 2.0, CC0-1.0, and CC-BY-SA-4.0; a comprehensive documentation of all licenses is provided via REUSE Software.
# Acknowledgements
-The development of this model was made possible by the grant no. 03F0954D of the BMBF as part of the DAM mission ‘mareXtreme’, project ElbeXtreme.
-<!-- We are grateful for the open source community that facilitated this research, amongst them the developers of and contributors to FABM, GOTM, Python, R, pandoc, and LaTeX. -->
+The development of this model was made possible by the grant no. 03F0954D of the BMBF as part of the DAM mission ‘mareXtreme’, project ElbeXtreme. We are grateful for the open source community that facilitated this research, amongst them the developers of and contributors to FABM, GOTM, R, pandoc, and LaTeX.
-# References
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+# References