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https://github.com/oceanmodeling/fabm-oxypom

FABM OxyPOM and DiaMO: simple models for dissolved oxygen and biogeochemistry
https://github.com/oceanmodeling/fabm-oxypom

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FABM OxyPOM and DiaMO: simple models for dissolved oxygen and biogeochemistry

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# 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.



## Description



-   `OxyPOM` simulates oxygen consumption and production in river based on [Holzwarth and Wirtz, 2018](https://doi.org/10.1016/j.ecss.2018.01.020), including key biogeochemical processes as photosynthesis, respiration, mineralization, and nitrification.



-   `DiaMO` is a simplification of `OxyPOM` and calculates oxygen consumption and production using a statistical inspired model.



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.



## Requirements



-   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`.



-   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`.



The following is not required to build and run the model but it is for running the test case:



-   The script for downloading forcing and validation data requires the following shell commands:



    -   `wget`

    -   `unzip`

    -   `sed`



-   The scripts for generating forcing files setup and plotting routines for model validation require: -`R` (v4.3 or above) available in [r home](https://www.r-project.org/) with the library `ncdf4` installed.



## Testcases



We provide the model with a testcase in the directory `./testcases`.

New testcases for **OxyPOM** and **DiaMO** should be included in a single directory within `./testcases`.

Currently, we include the testcase "Estuary".



### Testcase Estuary



This setup uses the physical driver `GOTM` to simulate the water column dynamics in the Elbe estuary in 2005-2024.



1. To run the testcase go to the directory `.\testcases`.



The model is build with the script `gotm-installation.sh`, in where these variables must be defined: - `GOTM_DIR` base directory of GOTM source code - `FABM_DIR` base directory of FABM source code - `OXYPOM_DIR` base directory of OxyPOM source code



By default they are:



    ``` bash

    export GOTM_DIR=$HOME/tools/gotm6

    export FABM_DIR=$HOME/tools/fabm/fabm

    export OXYPOM_DIR=$HOME/tools/oxypom/src

    ```



2. The script `gotm-installation.sh` creates the directory `.\build` with the building files, and a copy of `gotm` executable in the `.\estuary` directory.

   Now move to the directory `.\estuary`.



3. The script `get_data.sh` download and unzip the forcing and validation data from [kuestendaten.de](https://www.kuestendaten.de) in a newly created directory `.\data`.

   The downloaded files are used under license [DL-DE->Zero-2.0](https://www.govdata.de/dl-de/zero-2-0).



4. The script `setup_data.R` formatted the data to be read by `GOTM`. It generates the file `meteofile.csv`.



5. Run the model with `./gotm`. It generates the files `output.nc` and `restart.nc`.



6. The script `plot_output.R` analyses the model output.



If everything is correct, the figure `estuary_validation.png` should be produced.

It displays a comparison of simulation and data for temperature and dissolved oxygen values.



The entire procedure is included in `./testcases/run-estuary-testcase.sh`.



### Testcase light



This setup uses the physical driver `GOTM` to simulate the water column dynamics in the Elbe estuary in 2005-2024 and compares the default light implementation with the provided by `oxypom/light`.



Follow steps 1-2 of the estuary testcase.



Now move to the directory `.\light`.



-   The script `model_comparison.R` analyses the model output.



If everything is correct, the figure `light_validation.png` should be produced.

It displays a comparison of simulations using the default light implementation with the provided by `oxypom/light`.



The entire procedure is included in `./testcases/run-light-testcase.sh`.



## License



Apache-2.0 (OxyPOM and DiaMo)



## Project status



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 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.

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.

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).